ReporterKey Affx ID Name Chromosome Position Sequence SNPType ProbeCount Tile Replicates DesignNumber Rank Strand SetBack taxonomy_key organism cust_id cust_chr cust_pos cust_ref cust_alt cust_cn_region tiling_order cust_type notes pconvert recommendation Error chip Category Gene reference Parentage/haplogroups/causal/… Comment Discovery breeds 468272553 Affx-1111832849 AX-519546269 1 18960 TGGAGCTGTGGCCACGCAGGCGGAATATGAAACGC[A/G]TTTTGGAGGCATAGGAGATCTGGGGCAAGGACCAA R 2 1 2 1 202000 f 74 goat 1_18960_AF-PAKI 1 18960 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402380 Affx-122959030 AX-123272733 1 21647 TCTCCTCCCGCATCCAGTTAGGTACCACTTCCTAG[A/C]TCGATCAGCCCTGATAGAAATCTCAGGAGCAGATT M 2 1 2 1 202000 f 74 goat snp14078-scaffold1560-21647 1 41022348 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423358 Affx-122943149 AX-123293704 1 51801 TAATCTCCCTGGATTTTCCCTGCCCGACCTTGAAA[C/T]GATGCTAGAGAGCGCAGAGATCCAGCAGGATCCAG Y 2 1 2 1 101000 f 74 goat snp14079-scaffold1560-51801 1 41053350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789107 Affx-122955870 AX-385276120 1 100946 CAAAATACCACTTGGTAGTTAGAAAGACTGAAAAG[C/T]AGCTTTTCTGTTGCCCTACATCAAGATTCGGCTTT Y 2 1 2 1 101000 r 74 goat snp14080-scaffold1560-100946 1 41102828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444637 Affx-122926927 AX-123314974 1 185575 TGCAGTAGTTACGAGGGTGGACTCCAGAGTCAAGT[C/T]GGTCTGCACTGTGAGACCTTGGTCAAGGACGTTAT Y 2 1 2 1 101000 f 74 goat snp14082-scaffold1560-185575 1 41188297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777036 Affx-122958650 AX-385264158 1 228319 CTCTGTCAGTAACTGGGCTGAAGTTTTCCATTTCA[G/T]AGTTGATTTAAAATTAATCCGAACGGCTGGTTACC K 2 1 2 1 101000 f 74 goat snp14083-scaffold1560-228319 1 41231606 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772775 Affx-122969248 AX-385259920 1 297224 CACATCTGAAATTCTCACTCTCGTGACTCACCAAA[C/T]GTTACATGGCAATCAGGTAGATGGATTTTATTCTC Y 2 1 2 1 101000 f 74 goat snp14084-scaffold1560-297224 1 41300818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440829 Affx-122929273 AX-123311166 1 330454 ACAGACCCTCTGCCTGGAGGCTTGAACTGGCCTGC[A/G]TTCCCTCTTCTAAGACTTTTGCAGAAGATCTGGGA R 2 1 2 1 101000 r 74 goat snp14085-scaffold1560-330454 1 41333934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389185 Affx-122969082 AX-123259543 1 378997 CATGAAATGTTTTCCCAAATTATTTGTCCAAAACA[C/T]GCCTTAATTTTCATCCAAGGTGAGGAATGGGAAGA Y 2 1 2 1 101000 r 74 goat snp14086-scaffold1560-378997 1 41383727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391766 Affx-122967468 AX-123262123 1 412202 CCTGGGGGCAGTCCATTAGCCTCTCCAAGCGAAAG[C/T]GTTACCATTTTAAAAATCCAAAGAACAGCGCTGCA Y 2 1 2 1 201000 f 74 goat snp14087-scaffold1560-412202 1 41421847 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382849 Affx-122973534 AX-123253207 1 452762 ACACAAGTGTTCTTCACTGAGTTCTGAAGAGGAAG[C/T]GGGTGGCCGTGGTGAGGAGCAGGAGGAAGAGAAGC Y 2 1 2 1 101000 f 74 goat snp14088-scaffold1560-452762 1 41461484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419761 Affx-122945874 AX-123290109 1 488156 AAAGTAAATGACTTGGAAAGTAAGATGGTGGCAAG[C/T]GGAGCGTGAGGATAGGGTTTTGAGAAGAAATTTCT Y 2 1 2 1 101000 f 74 goat snp14089-scaffold1560-488156 1 41496881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392992 Affx-122965661 AX-123263349 1 516844 ATGCAGGGTGTACTCGGTCACCAATTGAGCGTCAC[A/G]TGAGGGAGGAACAAACTTGCAGTGTGTCAAGTGAC R 2 1 2 1 201000 r 74 goat snp14090-scaffold1560-516844 1 41525458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449111 Affx-122923581 AX-123319446 1 581464 GGCCATCGCCATGGCCAGGGTGTACCTTTTATGGC[A/G]TTTCTTGCAGCTGGGGGCAACATTTATGTCCAGAC R 2 1 2 1 202000 f 74 goat snp14091-scaffold1560-581464 1 41590174 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409983 Affx-122953281 AX-123280333 1 614162 AGTTTTAAAAATAAAACATAAAACGTAAGAACACT[A/G]AAGCCAAAATGGAAGATGAGGGAAGTCTTGCTTTT R 2 1 2 1 101000 r 74 goat snp14092-scaffold1560-614162 1 41622945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404556 Affx-122957381 AX-123274908 1 666974 CGGCAAGCTGCAGCCAATGGGGTCCCAAAGAGTCA[G/T]AAACGACTTAGTGACTAAACACATAGGGAAGGGAA K 2 1 2 1 303000 f 74 goat snp14093-scaffold1560-666974 1 41772385 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381223 Affx-122974512 AX-123251581 1 721048 TCTCACAGTGAAATGAGAAGGTTTTGATTGTATGT[A/G]TTTACACCGTGACAGCCACGTGCACCTAGACTAAC R 2 1 2 1 101000 r 74 goat snp14094-scaffold1560-721048 1 41731107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437153 Affx-122932140 AX-123307491 1 755958 GTTAGTAAATTTTCTGCTGTGTGCTCAGTCGCTTT[A/G]CTGTGTCTGACTCTTTGCAACCTCATAGACTGTAG R 2 1 2 1 103000 f 74 goat snp14095-scaffold1560-755958 1 41765765 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400762 Affx-122959882 AX-123271117 1 786871 ATGGCAGTGCCAAAGCACAGAAGGACCCAATTTCC[C/T]AGAGCCCTCACATAGCAAAGTTGCTTGGTCCAGTG Y 2 1 2 1 101000 f 74 goat snp14096-scaffold1560-786871 1 41797117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400763 Affx-122959882 AX-123271118 1 786871 ATGGCAGTGCCAAAGCACAGAAGGACCCAATTTCC[C/T]AGAGCCCTCACATAGCAAAGTTGCTTGGTCCAGTG Y 2 1 2 1 600000 r 74 goat snp14096-scaffold1560-786871 1 786871 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437763 Affx-122931711 AX-123308101 1 830197 ACTGAGATCCAGGATGGATCCAGCCCCCTGATATT[A/G]TACGAGACTCCCCTTGGCCCCAAGGGGTCCCAAAC R 2 1 2 1 202000 r 74 goat snp14097-scaffold1560-830197 1 41840238 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388556 Affx-122969180 AX-123258914 1 872326 ACCTCGAATCCAGGATGGACTCAGTCTAGCTTGGC[A/G]TCATCTTCAGGTTTACTTGCATTAACTGACACTCA R 2 1 2 1 101000 r 74 goat snp14098-scaffold1560-872326 1 41882235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424904 Affx-122941307 AX-123295250 1 920888 TCATAACATGCCCTATCCATGTCCCTACCAAGATA[C/T]GAAGGCTTCCTGACACTGTTTTCACAGTCAACATG Y 2 1 2 1 101000 f 74 goat snp14099-scaffold1560-920888 1 47271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398577 Affx-122961502 AX-123268932 1 986550 TCTATGTACTGCTTAGGATGAGACAGACAGACATA[C/T]ATTCATTCACTCACTTAACTTCTCGGAACACCATG Y 2 1 2 1 201000 f 74 goat snp14100-scaffold1560-986550 1 113316 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380553 Affx-122975286 AX-123250911 1 1032913 GTGGAATCACCAGTTTATCACCAGGCCCAGCCTTA[C/T]GCCCCAAGCAGCTATGGGTCTGGTAAATGGCTACA Y 2 1 2 1 201000 f 74 goat snp14101-scaffold1560-1032913 1 159328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400831 Affx-122959794 AX-123271186 1 1087568 TCTGCATACCATCCTAAAAGGTGATCAGTTTTGGA[C/T]ACCATGACTTTAATTTCAGCTTCTTTTTCTCAGCC Y 2 1 2 1 101000 f 74 goat snp2819-scaffold1082-727669 1 212193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778772 Affx-122975827 AX-385265882 1 1156554 TACAAAGGGATCTGATCAGGCCTGTTAAAGTTACC[A/G]TATAGATGACATGATTCCAAACTTCCTGTGCTTGA R 2 1 2 1 101000 f 74 goat snp2817-scaffold1082-658683 1 281100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430886 Affx-122936876 AX-123301227 1 1200204 TGGGAGATTAAAGAAATAACATGTTTTTTCTTACT[A/G]TCAAAACGGTACATGTTTATTGAAGACAGCTCTGA R 2 1 2 1 101000 r 74 goat snp2816-scaffold1082-615033 1 324817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790867 Affx-122954109 AX-385277865 1 1257683 GTAGTGAGTGTCTGTTGAATATTTTATTTGAGGGC[A/G]TGGATTAAGATTCTTATAGAGGGAGTAGTTGTTTT R 2 1 2 1 101000 f 74 goat snp2815-scaffold1082-557554 1 382409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386182 Affx-122971373 AX-123256540 1 1290542 TCCATTGCCAATGACAAGTACTCGGGCTGCCATTG[C/T]GCTATCTGCAAAGCAGGAATTCAGCAGGAAGATGA Y 2 1 2 1 201000 f 74 goat snp2814-scaffold1082-524695 1 415331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395962 Affx-122963563 AX-123266317 1 1332065 TCTCATCTGCCAAAGGTGCAAATGAGCACAAAATT[A/C]TGACATCTTGTAGTTGCTTATTAAAGGGTTCCTAA M 2 1 2 1 101000 f 74 goat snp2813-scaffold1082-483172 1 456935 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779591 Affx-122926656 AX-385266694 1 1376667 CTAACACTCGGCTTACATGCTCCTTAACATTTCAC[A/G]TTCTCTATGGACCATATAATTGAAACATGCAATGA R 2 1 2 1 101000 f 74 goat snp2812-scaffold1082-438570 1 496137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395176 Affx-122964105 AX-123265531 1 1413162 TGGACATTGTTGCCTGGGCTGGGTGGTCAGGAGAC[A/G]GGGTCTTCTCCTTGGTTCTGGCAAGGACCTCGGGC R 2 1 2 1 201000 r 74 goat snp2811-scaffold1082-402075 1 533477 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795503 Affx-122933273 AX-385282458 1 1466572 TGCTGAGGAATTAACAGGTAAATCGATTCCTTTCT[A/G]TGGAAACTTGAGTAAGTCAACACTTCAGGGTTAGT R 2 1 2 1 101000 r 74 goat snp2810-scaffold1082-348665 1 586692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393594 Affx-122965377 AX-123263950 1 1502774 TGGACCGTTTTTCCAAAAGACTGGATTTAGGCCTT[A/G]AATGTATCATAAGATAGCAACGTGCCTTTTTGTGT R 2 1 2 1 201000 r 74 goat snp2809-scaffold1082-312463 1 623097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421402 Affx-122943980 AX-123291749 1 1542077 AATTCACTCTCCACCCTGCTGCCAGAATGTTTCTA[C/T]GTGGAAAGTTGGAGCAAGTTATTTCTCCTTTTGAC Y 2 1 2 1 101000 r 74 goat snp2808-scaffold1082-273160 1 662449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409759 Affx-122953003 AX-123280110 1 1572127 CAAGTGACATTAACTGAATAAAAAAGCAGAAACCC[A/G]CATGAACAATAGTGGAAGAAGAGCAAAGAGAGCCA R 2 1 2 1 101000 r 74 goat snp2807-scaffold1082-243110 1 693185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796884 Affx-122964778 AX-385283826 1 1623890 TCTGGTCACATTCTTGACCTCAGCTTCTCAGGTCT[G/T]CAAAATGGGCATATAACCCATTTCATTAATAAAGT K 2 1 2 1 102000 f 74 goat snp2806-scaffold1082-191347 1 745961 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380077 Affx-122975551 AX-123250435 1 1679696 CATGTTCTAGATGAGCGAGTTGTCTCAAATTCCCC[A/G]CTTTCTTTTTTCTTTCCTTTCCAGCCTTGGTGGCT R 2 1 2 1 303000 f 74 goat snp2805-scaffold1082-135541 1 801872 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414741 Affx-122949723 AX-123285090 1 1718229 CTTGGGCCCCGCCAGGAAAAGGAACTTGGACCATC[A/G]TTCTGAGACCTACTTCTCTGATTCTCTGTTCCCCA R 2 1 2 1 101000 r 74 goat snp2804-scaffold1082-97008 1 840087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419533 Affx-122945431 AX-123289881 1 1764272 ACACTGCAGAGAGCTAGATGTTAAATCTTTATACC[G/T]CACACCACTGGCTGAAAGGAGCTTTTATCTTGGAG K 2 1 2 1 101000 f 74 goat snp2803-scaffold1082-50965 1 886848 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790091 Affx-122952440 AX-385277097 1 1804136 ACAATACTGTCATCACTCATAGATAATTCAGATGT[A/G]TCAATTATAATAAGTTCACAGCAGCAGCAAGCTCA R 2 1 2 1 101000 f 74 goat snp2802-scaffold1082-11101 1 926757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436603 Affx-122932515 AX-123306941 1 1837193 ACCTGTGTATGTCCCACTGAAAGGCCGGACACCAG[A/G]CAGCCTCCCATTTCTCCTTTTGGACTTCCTCCTGG R 2 1 2 1 101000 f 74 goat snp59371-scaffold979-21857 1 959556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438452 Affx-122931251 AX-123308790 1 1897292 TGAGAAGATGAAAGGGTTGCACTTAGCTTTTAAGT[A/G]TCTTCACTGATGAAACAAACAAACCAAATAACAAT R 2 1 2 1 101000 f 74 goat snp59372-scaffold979-81956 1 1019948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433954 Affx-122934275 AX-123304295 1 1941533 GGCAAACGTCAATCCCACTGCTCAGGAATAAGTTA[A/G]CCAGACGACAGGGGTGGGCAGATAAAAGTCCCCTG R 2 1 2 1 101000 f 74 goat snp59373-scaffold979-126197 1 1064316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449556 Affx-122923244 AX-123319891 1 1975096 AGGACCAACCTCAGCACTGAGACAAAAAGCTGGAC[A/G]GCTGTGTTCCCAGCCTCACTCACCAAGCCCCGCAT R 2 1 2 1 101000 f 74 goat snp59374-scaffold979-159760 1 1098176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447218 Affx-122924979 AX-123317554 1 2013278 GTCTTAACTTTATCAAGCGATCGTCTCTGTATGTA[C/T]GTATCTATCAGCCATCTGTTTACCATCTGTCTACT Y 2 1 2 1 101000 f 74 goat snp59375-scaffold979-197942 1 1137176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430400 Affx-122937761 AX-123300741 1 2048005 GAGAGAGGAGGCAAAATTGTCCTGCCGTGGATCAG[C/T]GAGAGCAGAACACGGACACGAGGAGCTGGTCCATT Y 2 1 2 1 101000 f 74 goat snp59376-scaffold979-232669 1 1172623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432149 Affx-122936425 AX-123302490 1 2077428 TGCTCTACTCGTATCCAGCCACCCTTTCAGCCCCA[C/T]GTCAAGCACTTTTCCACAGACATTTCTCCAGTCTT Y 2 1 2 1 101000 r 74 goat snp59377-scaffold979-262092 1 1201782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446335 Affx-122925621 AX-123316671 1 2129907 TAAAGAAATTGTCATGGTGCACTCTTGTAATAAAT[C/T]ATAAATCAGTATTGTTAAGAAACATGAAAGAGAGG Y 2 1 2 1 101000 f 74 goat snp59378-scaffold979-314571 1 1253548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406328 Affx-122955451 AX-123276680 1 2185994 TTTCCCCTGGTTTGTGGTGGAAAACACATCTGTTT[C/T]ATACTCAGAACATCTCAGCTTGAGCCTATCTGCCA Y 2 1 2 1 101000 r 74 goat snp59379-scaffold979-370658 1 1310088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433687 Affx-122934547 AX-123304028 1 2237428 AAACCCAAAAGATCTCGTTGTAAGAGTCCCTGTCC[A/G]TGCTGACGTCTACAGCATGAAGCCCTGAAACAGTG R 2 1 2 1 101000 f 74 goat snp59380-scaffold979-422092 1 1361517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277454 Affx-1111835919 AX-519550958 1 2262262 TGAAGGTAAGGTCAGGTGTGTCTGTGCACTTAGAG[A/G]ATTGTATCATTTTTTGTACATGATATGTTTGGAAT R 2 1 2 1 101000 f 74 goat Random2.2K-2 1 2262262 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448886 Affx-122923262 AX-123319221 1 2281335 ATGGATACATTTTTAGGAAAATAAAATGTACCCAA[A/C]TAGAGATAGAATATGTATACAGACAACTTCGATAG M 2 1 2 1 103000 r 74 goat snp59381-scaffold979-465999 1 1405809 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416184 Affx-122948254 AX-123286533 1 2317613 GGAGGCTCAGATCTCAGCGGCTGCTACGTTTCATG[C/T]CTAGTCAAGAAATCCAGCCCCTGTGATCTGACAGG Y 2 1 2 1 201000 f 74 goat snp59382-scaffold979-502277 1 1440938 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450777 Affx-122921832 AX-123321111 1 2348977 CATTTATTAGCATATTTATGAAAAATTGTTAACAG[A/G]AGCATCATTTTAAAGAGTTGTATAGTTTCTCACTT R 2 1 2 1 101000 r 74 goat snp59383-scaffold979-533641 1 1472858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393892 Affx-122965116 AX-123264247 1 2406784 TGCAAGGAGCATTTGGGAAAATGAGTAATGTCTCT[A/G]TGTCTACATTTTCAAATGTGTACTGATAAAAAAGA R 2 1 2 1 101000 f 74 goat snp59384-scaffold979-591448 1 1529499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405299 Affx-122956845 AX-123275651 1 2448454 TGTCCCAGGTACAGACGTATATTGAGTTGTCTGTT[A/G]TTTTCTGCTTCCAAAGGGGTTCAGAATTTGAGGTG R 2 1 2 1 101000 f 74 goat snp59385-scaffold979-633118 1 1570176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447102 Affx-122924483 AX-123317438 1 2497256 GACAAGTTGACATGTCCTAAGTGTGAGAGATCGCT[A/G]CAGAGCCAACTGTCATAAACTGCTGAATTGGAGAG R 2 1 2 1 101000 f 74 goat snp59386-scaffold979-681920 1 1618998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272477 Affx-1111832852 AX-519546199 1 2546794 CCTGTGTTAAAAACTGAGCTGTGAGCTCAGAGATA[A/C]AGAACAAAGGAAACCAAACAGAGGTAAAGACTACG M 2 1 2 1 201000 f 74 goat 1_2546794_AF-PAKI 1 2546794 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38411193 Affx-122952372 AX-123281543 1 2568316 TATTGAGTGCTTGGAAAATCTTAGAGGTGTTTCCA[C/T]CTACTGTGTGGTTGAATCTTCTTTGAAAACTAATG Y 2 1 2 1 101000 r 74 goat snp59388-scaffold979-752980 1 1690477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420924 Affx-122944590 AX-123291271 1 2614938 GATTCTGGCCAGAACCGAATGTGTGACTGCTACAT[A/G]CTTTATTCTCTGCCCTAAGCTTGAAACAGTAAGGA R 2 1 2 1 101000 f 74 goat snp59389-scaffold979-799602 1 1737743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772138 Affx-122970016 AX-385259293 1 2659398 AGCCAGCAAGCCCAATCTGTGATGAGGGATAAGTC[A/G]CCATATTGAATTTTATGTATATTGACTTGGAAGCA R 2 1 2 1 101000 f 74 goat snp59390-scaffold979-844062 1 1781860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422942 Affx-122943026 AX-123293288 1 2695262 TAAACCCCAGTGGACCTTCTGCAGTTTAATTTAGA[C/T]GGGAGTTTCTAAGCTGCTTTCTGAAATGGCAAGGC Y 2 1 2 1 201000 f 74 goat snp59391-scaffold979-879926 1 1836750 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784245 Affx-122954932 AX-385271296 1 2750518 ACCCCCACCCTCAATTTCATAAGCCCTAAAGATTC[A/G]TCTTTGGGCAATGAATAAATCTTCAGAATCATTCC R 2 1 2 1 201000 r 74 goat snp59392-scaffold979-935182 1 1892194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385339 Affx-122971656 AX-123255697 1 2788491 GTGCAGAACTTCCACGAGCAAAGAAAGGCTGAAAC[A/G]CAAGAATTTGCTGGGATGCTGTAGCAGGTTGAATT R 2 1 2 1 101000 f 74 goat snp59393-scaffold979-973155 1 1930088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439465 Affx-122930170 AX-123309802 1 2853843 GTTTTCTCAATCAACAAAAGCATGCATGAAAACGG[C/T]GCCCGGATCAAGAAACAGAACCCAGCCAACACCCA Y 2 1 2 1 101000 f 74 goat snp59394-scaffold979-1038507 1 1994962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767409 Affx-122949119 AX-385254682 1 2889741 TTGACTAAGGAACACACAATAGCAATGTGATGATC[A/G]ACCTTCTTTTTTCTGAGTCAACATTATAATATGGT R 2 1 2 1 101000 f 74 goat snp59395-scaffold979-1074405 1 2030934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411017 Affx-122951979 AX-123281367 1 2921448 TCAAATGAGCCTCTCGGCAGAATTGGCATTCTTGA[G/T]GATGGATGGTAAGGTCGACGCTTTTTGTATGATAG K 2 1 2 1 101000 f 74 goat snp59396-scaffold979-1106112 1 2062608 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403149 Affx-122958098 AX-123273502 1 2957058 GCTTGCACAGAGCTCTGGCGAAAAGTAAGTCACGA[C/T]GAAGAGAGGAGCTTCCTGGAAGAAGAATGTCTGAG Y 2 1 2 1 201000 f 74 goat snp59397-scaffold979-1141722 1 2098231 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786164 Affx-122978286 AX-385273200 1 2985785 TGAGCAGATATGGATTTTACAGGTTATCTCCCTGA[C/T]ACAGTTGAAGTAGGTGGCCATCGCACTGGCTCACT Y 2 1 2 1 202000 r 74 goat snp59398-scaffold979-1170449 1 2127162 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603156 Affx-1002479372 AX-413837345 1 3004051 CCTGTTTACATTTTGCTTAGATTTCCTTGGGATTT[A/C]ATTTTGATGTGTGAGTTCTAGTGTGTGTTCCCTCT M 2 1 2 1 101000 r 74 goat 1_3004051_RH-map 1 3004051 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38433022 Affx-122935778 AX-123303363 1 3017024 TCTCAATCTTCAGTGAAGTTTCTTGGGCCCTCCTC[A/G]ACATCAAATAATCCTGCTCTCCAAGAAAGGAGGAC R 2 1 2 1 101000 r 74 goat snp59399-scaffold979-1201688 1 2158850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436451 Affx-122932993 AX-123306789 1 3060222 AGACTGGGAGATCCGAAGGGCTTCCTTGAGCAGAC[A/G]CCATTTAAGTTGAGAATCGGGTGCATCAGGAGATG R 2 1 2 1 101000 r 74 goat snp59400-scaffold979-1244886 1 2202325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603586 Affx-1002479373 AX-413837738 1 3061337 GAAGATGCCCTGGAGGAGGGCATGGAAACCCATTC[G/T]AGTATTCTGCCCTGGAGAATCCTCATGGAAAGAGG K 2 1 2 1 303000 f 74 goat 1_3061337_RH-map 1 3061337 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320787478 Affx-122936280 AX-385274503 1 3100759 AGTCCCAGGGGAAATTGTTCTGTATAAACTGTTCT[A/G]TATTTTACCTCTTGATTACTGCTATGATTATCTTC R 2 1 2 1 101000 f 74 goat snp59401-scaffold979-1285423 1 2242567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274670 Affx-1111834432 AX-519548256 1 3119769 GGAAACATGTCAAGGGTAATGTAATCTTTGCAGAG[A/G]GGTGGAGGCCTG R 2 1 2 1 101000 f 74 goat GoatD01.035509 1 3119769 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414452 Affx-122949574 AX-123284801 1 3161753 AGGTTGTGCTTGTGCGTGGCTAAGTATATATGCAC[A/G]TATCAAACTTGTGAACCCAACTGTTTGCACGTCAT R 2 1 2 1 101000 f 74 goat snp59402-scaffold979-1346417 1 2303447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603060 Affx-1002479374 AX-413837271 1 3191804 GGGAGCAGAAGTGAGCTGCTGCATATTAAAATACA[A/G]CTGGTATTATATAATAGCTCATGGTATCAAAGCTT R 2 1 2 1 101000 f 74 goat 1_3191804_RH-map 1 3191804 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38383771 Affx-122972427 AX-123254129 1 3200827 TTGAATTTTCCCAATTGTCCTTAAAAAACCACTTT[A/G]TTACAGTTGATTTGAGTTCATGTAGAACAATTCCA R 2 1 2 1 101000 f 74 goat snp59403-scaffold979-1385491 1 2342189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403021 Affx-122958557 AX-123273374 1 3242012 AATACGCAAGACCATTCAGCACCTTAAAGCCACCC[A/G]TTGTCCCTCATTTACTTCCTCTTATCCTCCCACAA R 2 1 2 1 201000 r 74 goat snp23394-scaffold2342-28469 1 2386949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603063 Affx-1002479375 AX-413837272 1 3277507 AAAATCTCTGTTAAAGACATTCAATAAAGTACTCG[A/C]TCACCACTTATTCCTTTGTTGTTGAAATTCAAGTA M 2 1 2 1 101000 f 74 goat 1_3277507_RH-map 1 3277507 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603162 Affx-1002479376 AX-413837351 1 3308297 TAATATATATCTTATATTAAAAATGTGAGAAGCAA[C/T]GTAGAAAAACTTTGCCCCTTTTCTCTCTCTTCTTT Y 2 1 2 1 101000 r 74 goat 1_3308297_RH-map 1 3308297 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401312 Affx-122959847 AX-123271665 1 3331723 CCTTTTTACAGCTTTGAGTCTGTACCAGGCATATT[A/G]TACTTTATAAATATTGACTGATTTGATTTTCATAA R 2 1 2 1 101000 f 74 goat snp23396-scaffold2342-118180 1 2475759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603067 Affx-1002479377 AX-413837274 1 3341708 CTTCTTTCAATGTCATGTCTTTTTGCTCTTCTATA[C/G]TGTTTATGGGGTTCCCAAGGCAATAATACTGAAGT S 4 1 2 1 201000 f 74 goat 1_3341708_RH-map 1 3341708 C G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320802169 Affx-122971953 AX-385289073 1 3367820 CTTCTCTTTTTCTTAAGATCTTTAGCAAAGACTTC[C/T]ACCTTTTTTTCTTCTTGCTGTTGAATACTTGCTTT Y 2 1 2 1 101000 r 74 goat snp23397-scaffold2342-154277 1 2511898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603069 Affx-1002479378 AX-413837276 1 3368511 TCAGATTGATTATATTCTATGCAGCCAAAGATGGA[G/T]AAGGTCTATACAGTCAGTAAAAACAAGACCAGGAG K 2 1 2 1 303000 f 74 goat 1_3368511_RH-map 1 3368511 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38430211 Affx-122937337 AX-123300552 1 3396797 AGGGTGCAAGGTCATTGGGGTACCATCTAAAATAC[A/G]TTGGTCAGGACTTGTTTGATGAGAAGGGGCTTTTG R 2 1 2 1 101000 f 74 goat snp23398-scaffold2342-183254 1 2541134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430240 Affx-122937315 AX-123300581 1 3456156 ACTCGGTGTGATGTGAAACTATGGAGCTGATCACT[C/T]ACCCCATGTCACTGACAAAGAAAAACAGAAACAGA Y 2 1 2 1 101000 f 74 goat snp55868-scaffold868-1126684 1 2601371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603071 Affx-1002479379 AX-413837277 1 3485949 CACAAACATACACATACATAATGAAGAAAAATAAA[C/G]TCAAGCACAATACATTAATATATTCAAAGATATAG S 4 1 2 1 103000 f 74 goat 1_3485949_RH-map 1 3485949 C G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38382853 Affx-122973532 AX-123253211 1 3486635 AGGAACAGCACAGAGGGGCACAGAGCTTAAAGACC[A/G]GGACATCCCTTTTCTACTTCTAGGTCGGTCAGTTA R 2 1 2 1 101000 r 74 goat snp55867-scaffold868-1096205 1 2632391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603646 Affx-1002479380 AX-413837785 1 3507304 GAATTTATTATATTAAAAAAGTAAATAAACATGTG[A/G]AAATAGTTTGAGTCTTATGGACCCTTGACAGGGTC R 2 1 2 1 101000 r 74 goat 1_3507304_RH-map 1 3507304 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38396966 Affx-122963168 AX-123267321 1 3546452 CTGACCCAGGCTTCCACAGAGCAAATGCTAAGCCT[A/G]CTGACTGTCAGTTCTTGTTGGGGCTTGTGCAGTGT R 2 1 2 1 202000 f 74 goat snp55866-scaffold868-1036388 1 2691960 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603073 Affx-1002479381 AX-413837278 1 3570452 CATCTTCTCAATCCTTGTCTCTAGGCTATTTATCT[G/T]TGATTCCATTTTGATTTCAAGATTTTGGATCATTT K 2 1 2 1 103000 f 74 goat 1_3570452_RH-map 1 3570452 G T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603171 Affx-1002479382 AX-413837359 1 3592225 ATCAAATGTTTGTTCTTTGTTATGCTACATAAAGT[A/G]CCCCTTTCTAAACATCGAAGATGTGAACAGTTGCT R 2 1 2 1 101000 r 74 goat 1_3592225_RH-map 1 3592225 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409168 Affx-122953200 AX-123279519 1 3601450 ACATCAGAACGAACTTCTCAGCCAAGCCAATCACA[C/T]TGTCCTGCATGAGGCCCAAACAGGCGCTGTGCCCT Y 2 1 2 1 101000 f 74 goat snp55865-scaffold868-981390 1 2744278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603077 Affx-1002479383 AX-166869927 1 3624775 TCCTCGTGCTGCAATTCATGGGGTCACAAAGAGTC[A/G]GACACGACTGAGCGACTGAACTGAACTGAACTGAT R 2 1 2 1 303000 f 74 goat 1_3624775_RH-map 1 3624775 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320783778 Affx-122966365 AX-385270834 1 3634900 AAACCACATTATAGCCTTCATGTCCTATGTTTAGG[C/T]GAAAGAGGAATAAGAGTTGTATTTCCTCAATCATG Y 2 1 2 1 101000 f 74 goat snp55864-scaffold868-947940 1 2777812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603175 Affx-1002479384 AX-413837362 1 3652751 GGTCACAAAAGAATCAGACATGACTCAGAAACTAA[A/G]TAACAATATGTTTGATTAGTTGAAGAATCATTACA R 2 1 2 1 201000 r 74 goat 1_3652751_RH-map 1 3652751 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603081 Affx-1002479385 AX-413837282 1 3668994 TTGTAGCTCACTGTCCCAAATCTTTTTGTTTCAGT[A/G]TCCTTCTTGTATAATTTATCAATAAATGCAGGAGC R 2 1 2 1 101000 f 74 goat 1_3668994_RH-map 1 3668994 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603179 Affx-1002479386 AX-413837366 1 3685336 GCTTCAATCATGAGAGGGGCTATGATCCTCTGCTT[C/T]ATGTTTGACTTCAGTTCTCTCTTCTTATCCTTCTA Y 2 1 2 1 201000 r 74 goat 1_3685336_RH-map 1 3685336 T C 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603086 Affx-1002479387 AX-413837285 1 3748182 TCAGACTGTGAAAGGGTTTTCACTGTTATGAAAGT[A/G]AATTTCTTCCCTTGGAAAGATCCATGCTACTTCTG R 2 1 2 1 101000 f 74 goat 1_3748182_RH-map 1 3748182 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790314 Affx-122977412 AX-385277317 1 3750176 GGTAGAGTAGGGACATTTCCTAGAGGAAAGGCATT[A/G]CTGTTTACTTACTTATGAAAACAAGATCCAAGGCA R 2 1 2 1 101000 f 74 goat snp55862-scaffold868-832664 1 2893055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416763 Affx-122948181 AX-123287111 1 3824291 CAAAATGAGGATTGTAGCCTGTAAGGAGAAAATTC[A/G]TCATGAAGGACTCCAAGTCTGTGAAAGTTTTCTCA R 2 1 2 1 101000 f 74 goat snp55860-scaffold868-758549 1 2969339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798944 Affx-122936555 AX-385285874 1 3899785 GAGCCAGGAAAAGTTGACTGAGAGAGTATTTGTAA[C/T]GGAGGAAGAATATAGGAATAATGGTGATGATGATA Y 2 1 2 1 201000 r 74 goat snp55858-scaffold868-683055 1 3043796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411813 Affx-122951250 AX-123282163 1 3935209 AGAGTGAGGGAATATTTCCACCTGTCCCAAAACTC[A/G]CTCAACCTGACCACAGCAATAAACAGACTAAATTT R 2 1 2 1 101000 f 74 goat snp55857-scaffold868-647631 1 3079285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785264 Affx-122938764 AX-385272309 1 3974165 TTTTCATTTAAGCTAAGACCCAATTTAAATAATTC[A/G]TTAGAACAATGACTGTTCATCGCAAATCTGCTCTA R 2 1 2 1 101000 r 74 goat snp55856-scaffold868-608675 1 3118658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603088 Affx-1002479388 AX-413837286 1 3986406 TCACTGCGTCCATTGTTTTGCCATCTATTTGGCAT[A/G]AAGTGATGGGACCAGATGCCATGATCTTAGTTTTT R 2 1 2 1 103000 f 74 goat 1_3986406_RH-map 1 3986406 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320801626 Affx-122966463 AX-385288534 1 4013831 GGCAGAAGAAATCCCAAGATGGAGTTTCTGGGGAG[A/G]ATGAATTTCAAGAATCCCAGGGCAAAAGAAAAAGA R 2 1 2 1 101000 f 74 goat snp55855-scaffold868-569009 1 3157592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438924 Affx-122930424 AX-123309261 1 4063802 CCATCATATCAAAAGAGCCTGTCAGAGAGGTCAGT[A/G]CAGAGGAAAGAGGAGCCAAATGATGGAGAGACTTG R 2 1 2 1 101000 f 74 goat snp55854-scaffold868-519038 1 3207812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438099 Affx-122931509 AX-123308437 1 4294906 TTGTTGACAGGGAAAAGAGTCCTATACTAGGTTCT[C/T]GGGATTGCTATAGCAAAGTACCATGAATTAGATGG Y 2 1 2 1 101000 f 74 goat snp55849-scaffold868-287934 1 3441506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476138 Affx-1251763640 AX-586011571 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 4 1 4 1 20000 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 539476394 Affx-1251763640 AX-423606319 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 4 1 4 1 20000 r 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165069 Affx-1251763640 AX-606940481 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165280 Affx-1251763640 AX-606940691 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 r 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165727 Affx-1251763640 AX-606941136 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562166518 Affx-1251763640 AX-606941926 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562166568 Affx-1251763640 AX-606941976 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 320801896 Affx-122970905 AX-385288803 1 4383048 TCCATGTACTGTGTGTCTTTTGGCAGAGTAGTAGC[A/G]TAGTGAGATTTATTTTCAACTCCAGTGTTTTTCCC R 2 1 2 1 101000 f 74 goat snp55847-scaffold868-199792 1 3530748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789237 Affx-122977316 AX-385276248 1 4567031 CGCTGTCACAGAGTTACCCATGACTGGCAGAATTG[C/T]GATGCTTGCTCTTAAATACCTTAGAATTCATTCAT Y 2 1 2 1 101000 f 74 goat snp55842-scaffold868-15809 1 3714739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438373 Affx-122931314 AX-123308711 1 4587459 AATGTTGAAACCAATGACAATATTGCTCCACCAAG[C/T]GAAAGAACTCACTCAATCAACGAGTCAAGGCCTTA Y 2 1 2 1 103000 r 74 goat snp14436-scaffold1577-4520 1 3738974 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396301 Affx-122963089 AX-123266656 1 4619099 TGGTCAAGGTTACAAACTTCCAATTACAAATTAGA[C/T]GTCATGGGATACTGTATTGTACATCTGAAAGTTAT Y 2 1 2 1 101000 f 74 goat snp14437-scaffold1577-36160 1 3772200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450366 Affx-122922097 AX-123320701 1 4668101 AAAAAAGCAAATGTACAGTTAGTATCAACAGCAGC[A/G]TGCGATGCTGGTGAAAAAAGGAATCAACAGCAATT R 2 1 2 1 101000 r 74 goat snp14438-scaffold1577-85162 1 3822282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778734 Affx-122957109 AX-385265845 1 4703639 TTTTCTCAATTTAAAAGGTAAAATTGTTCAGTGTC[A/G]TTTAGGTTTGGAAGAAATTATTTCATCCTTTCATG R 2 1 2 1 202000 f 74 goat snp14439-scaffold1577-120700 1 3858000 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771488 Affx-122975364 AX-385258646 1 4737308 CAAAAGATTTCCATCTCTGATAACCACTGTGTTCA[G/T]AATTAGAAGTTAGCATTTGGATTTTGGGGTCAAAT K 2 1 2 1 202000 r 74 goat snp14440-scaffold1577-154369 1 3892026 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448849 Affx-122923290 AX-123319185 1 4771512 GTGTCCACTTGGCTAGGATATGGTGTCCAGTTGTT[C/T]GCCAAACACCAACCCAGATGTTTCTGTATAATGTA Y 2 1 2 1 201000 r 74 goat snp14441-scaffold1577-188573 1 3926226 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387111 Affx-122970668 AX-123257469 1 4811546 TTTCACTGATTTTACTTATTTACCTTTCAGGTAGG[C/T]ATGGTTATTATTATCTCTTTTTTATAACCTCTGTG Y 2 1 2 1 101000 r 74 goat snp14442-scaffold1577-228607 1 3966599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402334 Affx-122959068 AX-123272687 1 4875518 TGCCATGAGTGAATAAGATAAAACATAAAAGCCAA[C/T]GAGACAAGCTGGGCTAACTGCCTTTGCAAACTGCA Y 2 1 2 1 101000 r 74 goat snp14443-scaffold1577-292579 1 4030858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772586 Affx-122922371 AX-385259735 1 4922650 CTAAAAAGTAAATTAAAGTGAATTCTCATTTTTCC[A/G]TAGTCATGAGGAAGCCCACACCTAGAGTTTCATTA R 2 1 2 1 101000 r 74 goat snp14444-scaffold1577-339711 1 4078341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378223 Affx-122976918 AX-123248582 1 5019966 CAAATTTCATACCACAAACCCCAATGTGGAAGAAA[C/T]GCATCTTCAGTTTCTAAAATCTGATTTAAATTCAA Y 2 1 2 1 201000 r 74 goat snp14446-scaffold1577-437027 1 4176907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791888 Affx-122927329 AX-385278878 1 5049184 TGGAAATTGCTTCTCCCCTACTCTGCTTTATTTAC[C/T]ACCAAAGTATTTATCAAAGGCTAACATATCGGGCT Y 2 1 2 1 102000 f 74 goat snp14447-scaffold1577-466245 1 4206140 A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399834 Affx-122960257 AX-123270189 1 5059043 ATTTTAGCTCTTCTCCATCTCATCTTGAATTGCCT[A/G]TCCTTTCTTTACAAAGTGGTATTTTTTTCACCATG R 2 1 2 1 201000 r 74 goat snp19294-scaffold1944-916977 1 4215228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780119 Affx-122958939 AX-385267216 1 5092811 CTTTCTGAAAGGATAATGTGTGGCACAGAGAAATA[G/T]ATTTAGTTATCACAATATTCCATGAAAGGGAGTAA K 2 1 2 1 101000 f 74 goat snp19293-scaffold1944-883209 1 4248285 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384509 Affx-122973051 AX-123254867 1 5123880 AAAACAAGTCATTAGATCAGCCTGAGGCAGGGGAG[A/C]TACATTCCACCTCTTAAAGGGAGGCATGGCAAAAG M 2 1 2 1 201000 r 74 goat snp19292-scaffold1944-852140 1 4280087 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408269 Affx-122953805 AX-123278620 1 5154584 AGAGAATTGGGCTATTTCAGATCTGTCACTGTCCA[C/T]GATGACAGATTAAGAATTGTCATCTTCCTTTGAGA Y 2 1 2 1 102000 f 74 goat snp19291-scaffold1944-821436 1 4311226 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271830 Affx-1111832861 AX-498625149 1 5207791 AAAGAAATACATTTAGAGCTTAAACTGTACTTGCA[A/G]CAGTCCAAGAGACAACGAAGCAGGCAAAGTTGGTG R 2 1 2 1 201000 f 74 goat 1_5207791_AF-PAKI 1 5207791 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409573 Affx-122953583 AX-123279924 1 5211110 ACAATATTTATCCAATTCCTACTGAAAGTATCTTT[A/G]CGATTAATCAAATATTTTGTTTGTTTCGGACACCT R 2 1 2 1 103000 f 74 goat snp19290-scaffold1944-764910 1 4368265 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765028 Affx-122924958 AX-385252599 1 5240284 CATCTTCAGGAAGATGCACTGAAATGGAGGTAAGA[C/T]GAATCTACAGGCTTGTCATCATGCTCTAAGATCAA Y 2 1 2 1 101000 f 74 goat snp19289-scaffold1944-735736 1 4398046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437946 Affx-122931624 AX-123308284 1 5298941 CTGCTCAGTTTCCTCATGGTCCTTATCAATTCTTT[A/G]CATATCTGTTTACTTTATTAGAGACTCAGAGATGG R 2 1 2 1 101000 f 74 goat snp19288-scaffold1944-677079 1 4458236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446876 Affx-122925237 AX-123317212 1 5345369 GTTTCCATTCATGGATTAAAGAGCAAGTTAAATTA[C/T]ACTGTCCTCTCCCAGATTTACTAAGGATGAGAAGG Y 2 1 2 1 101000 r 74 goat snp19287-scaffold1944-630651 1 4504251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278315 Affx-1111836280 AX-519551801 1 5354789 TAAAATATATGAGGTCCAGTCAAATCTTAGTGTTA[A/T]TCAGCAACAAGTTTTAGTGGTGGTGTTGTTCAGTT W 4 1 2 1 101000 r 74 goat Random2.2K-5 1 5354789 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434338 Affx-122934730 AX-123304679 1 5389920 GCCAATGTTCCCACTCTTATTTCTCTCTTTTATTC[A/G]TTTACTCTGTTTTTTCAACATGTACATACTGAAGC R 2 1 2 1 201000 r 74 goat snp19286-scaffold1944-586100 1 4548618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416718 Affx-122947553 AX-123287066 1 5433767 TTCATGGCAGCAGGCACACTTGTTTGAAGAATGCT[A/G]TACCAGAGGCTGATCCCCTTGAAAACAATAGCATG R 2 1 2 1 101000 r 74 goat snp19285-scaffold1944-542253 1 4593203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385368 Affx-122971635 AX-123255726 1 5470121 ACTGTACTTTTGTTTAAGGAACTGAGAAAAATGCA[C/T]AGTATAAGTAAAAGCAGAATAATTATGATTAGCAT Y 2 1 2 1 101000 r 74 goat snp19284-scaffold1944-505899 1 4630009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278276 Affx-1111836339 AX-519551763 1 5498712 TTTTAGAGGGAATCAGCTTATTACCAAATGCTCCA[A/G]CAGCAACTCACATAAGTATGAAGTTGATTAAGAGC R 2 1 2 1 101000 f 74 goat Random2.2K-6 1 5498712 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777180 Affx-122954436 AX-385264303 1 5564182 GGTGAGTGAAGGTAGATAAAAGTTAACAAAACTCA[C/T]ACCTGATATTTTCCACTTTCTCTTCAAATTAAGAG Y 2 1 2 1 201000 r 74 goat snp19282-scaffold1944-411838 1 4724100 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419625 Affx-122945976 AX-123289973 1 5619488 GGGGCCACTCTCAGACTGCAGAAATTCACAAAGAC[A/G]GTTTGTTCACACGAGAGCTCTGCTCCTCCGTAGCC R 2 1 2 1 101000 f 74 goat snp19281-scaffold1944-356532 1 4779498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790393 Affx-122968758 AX-385277396 1 5684406 CTCCAGGAGACTTGCTGAATTTACTCTTTTCTTGA[C/T]AAACATACCACTTTCTTACCCACCGAGCAAGTAAA Y 2 1 2 1 101000 f 74 goat snp19280-scaffold1944-291614 1 4844324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399139 Affx-122960658 AX-123269494 1 5758725 TAAACTCTCAAGGTCTTGTGTGGATGTAAACCTAC[C/T]ATGTTCAATATGTTCTGGACCTAGAGTCCAGAAGT Y 2 1 2 1 201000 r 74 goat snp19278-scaffold1944-217295 1 4918536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278558 Affx-1111836399 AX-185819423 1 5802008 TCTGCCTACTGGACACATGCCTTACCTCAGGGGAC[A/G]TGAATAGCATTTGCTCCATTACCTTCATCCTTACG R 2 1 2 1 101000 r 74 goat Random2.2K-7 1 5802008 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398228 Affx-122962210 AX-123268583 1 5834059 CTGGAGTCCCAACTAGTACATACAATTGTCTTAAC[A/G]TTTCCTTAGGAGGTTTCCAGGCAAACAAAAGTTAA R 2 1 2 1 101000 f 74 goat snp19277-scaffold1944-141961 1 4993671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390704 Affx-122967939 AX-123261061 1 5884182 CTTTCTTCTTTTCTCTCAGTTGTAGGTTTACCATC[A/G]TGTTTTATTTTCTTGGGCTCCTAACTCACTGTGAA R 2 1 2 1 201000 f 74 goat snp19276-scaffold1944-91838 1 5044740 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772554 Affx-122978398 AX-385259704 1 5980393 AATCTGATGAAATAAGAGGCTGTGGACATGGGAAT[A/C]GTATTTGGGAGAGAAGAAACAATAGTTGTCCATGG M 2 1 2 1 101000 r 74 goat snp20593-scaffold2027-972600 1 5137732 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449181 Affx-122923527 AX-123319516 1 6026788 GCCAAATTAAAATCCCTGTTTTATAAGTATCACAA[A/G]GAGGTTTTCATCTTGCCACCCTGCTGCTTCTCTCG R 2 1 2 1 201000 f 74 goat snp20592-scaffold2027-926205 1 5184119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791712 Affx-122974990 AX-385278703 1 6099517 ACACCCATGGTGTGTATGTGCTACAAATATTGTTC[A/G]TTACATTTAGTATTTGTGGTTCATTATTTCTGTGT R 2 1 2 1 101000 f 74 goat snp20591-scaffold2027-853476 1 5256876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417049 Affx-122947523 AX-123287397 1 6158762 CTAGCAGAATGTGTGTAATGCTTGTAGAATGTTTA[C/T]GGTATACCAAAATAAAGAATTTTGGTAGAGGAACC Y 2 1 2 1 101000 f 74 goat snp20590-scaffold2027-794231 1 5316996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788795 Affx-122972268 AX-385275810 1 6233916 GATTCATGAGCGCCAGTGTTTTAAATGTCACCTGA[C/T]GTAAGCCTACTAGTAGCTCCATTTTAAAATTGGAA Y 2 1 2 1 101000 f 74 goat snp20588-scaffold2027-719077 1 5392991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452033 Affx-122920899 AX-123322366 1 6273074 GACCAAAGAGCTTTGGGAATACCAAAGGTAGAATG[A/C]TTATGCAGAGGAGGTGACAGCAGAGATAGCCTTGA M 2 1 2 1 101000 f 74 goat snp20587-scaffold2027-679919 1 5432216 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438248 Affx-122931426 AX-123308586 1 6303282 TTCATTAAGACAATTAGAATAAATACACAGAGACC[C/T]GCAAAACAGTTAAAGTGATACCACTCAATGGTGTC Y 2 1 2 1 101000 r 74 goat snp20586-scaffold2027-649711 1 5460626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417304 Affx-122947230 AX-123287652 1 6347937 GTCTATGCCGTTGACCATCCTGAAGATAATGAATG[C/T]GAAGTTGAAATGTCACTTCAGGGAGAAGCAGATAT Y 2 1 2 1 101000 f 74 goat snp20585-scaffold2027-605056 1 5503616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771562 Affx-122941172 AX-385258720 1 6392033 TAACTGACCAGTACACATATAAAAAGTTATTAACT[C/T]ACACTAAAAGTCAAATGAGGTGAAGAGCTAAGTCG Y 2 1 2 1 101000 r 74 goat snp20584-scaffold2027-560960 1 5547756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405465 Affx-122956033 AX-123275817 1 6426565 AGTTAGGAAAATAGGCGGATTGTCTAATTCTTCAT[A/G]CCACTGCAATGAATAGAGCAGTTCTGCAGCTAACA R 2 1 2 1 201000 f 74 goat "GoatD01.001540;snp20583-scaffold2027-526428" 1 5581623 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774275 Affx-122954909 AX-385261411 1 6481255 TTCCTTTCTGCCATATTCCTACTACTAAGCTATGC[A/G]TGTAATTATACAGATAATTGAGTGTGGGCAATGTC R 2 1 2 1 101000 f 74 goat snp20582-scaffold2027-471738 1 5636419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778762 Affx-122956008 AX-385265871 1 6513600 TACTTGACCCTTTTGCCCAATACTAGTTCTGCTCT[A/G]TCACTTCCCTGTAGGAAATCCTCTAGGTTTTACAT R 2 1 2 1 101000 f 74 goat snp20581-scaffold2027-439393 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433261 Affx-122935232 AX-123303602 1 6544523 GTCCATGGCTGTCAGTATGCAATGTCATTTTCACT[A/C]TCTGTGCACAAGTTAGTGGAAAACAAACCAAAAAA M 2 1 2 1 101000 f 74 goat snp20580-scaffold2027-408470 1 5700987 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764483 Affx-986698945 AX-385252163 1 6553494 AACCCGGACCCAGATTTGGCCTTGTACACCAATGG[C/T]ACCAGCCTGGTGAAACAAGGACAATGACTGTTGGA Y 2 1 2 1 600010 f 74 goat 1_6553494 1 6553494 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38429139 Affx-122937997 AX-123299481 1 6588867 AAGTGAGATCTGAGCTCCCAAACCCACCGAGGGGC[A/G]TGGAAGGCACAGCAAGGAATTCCACAGTCACTGTG R 2 1 2 1 201000 r 74 goat snp20579-scaffold2027-364126 1 5744993 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437357 Affx-122931935 AX-123307695 1 6651364 ACAAGAGTCCCAGTGAACACAAAACTAAGACAAAA[C/T]GAAGTGTTTAGGAAGGAAAAAAGATTTTCTGTCCT Y 2 1 2 1 101000 f 74 goat snp20578-scaffold2027-301629 1 5807697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376923 Affx-122977789 AX-123247282 1 6714298 CAAGAGACAATACAGAAAAATATACAAAACAAATG[C/T]ATAAGGTAAAAACACCTGTGCAGGCAGAATTCTAA Y 2 1 2 1 103000 r 74 goat snp20577-scaffold2027-238695 1 5871428 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429649 Affx-122937673 AX-123299990 1 6749957 CCTCTGGCAGGTTACTTATTCTCTCTGGGACTGAA[A/G]TTCTCATCTGTATGATCCGGATAAATATTATCTAG R 2 1 2 1 201000 r 74 goat snp20576-scaffold2027-203036 1 5907279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778164 Affx-122962656 AX-385265279 1 6785383 AACTACGATTCCCACAAACCATAATCTGAGATAAA[C/T]GCCATATGACTCAGTAAATCTAAGGAAATGTCTCT Y 2 1 2 1 101000 r 74 goat snp20575-scaffold2027-167610 1 5942841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797791 Affx-122932259 AX-385284730 1 6829201 TGTAAGTGTTTATGCCATCACCCCTCAATCTGCTG[C/T]ATATATACATTGATCCTATGGTAATTCACAAGTTT Y 2 1 2 1 102000 f 74 goat snp20574-scaffold2027-123792 1 5987184 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454214 Affx-122919281 AX-123324547 1 6864011 TTGCCTTCTACTGACCTTTTATAGATTTTTCTCCT[A/G]TTCTACTAAGAAGCCAGGGTTGGATATTGTCAAGA R 2 1 2 1 101000 r 74 goat snp20573-scaffold2027-88982 1 6022027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770800 Affx-122940105 AX-385257964 1 6917248 TATCTACTACTTGCCAGGTGCTTTGGAAGCCTTAC[C/T]GATTCTTTCAACCATGCTCATTTACCAAGTGTTAT Y 2 1 2 1 101000 f 74 goat snp20572-scaffold2027-35745 1 6076169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787321 Affx-122936999 AX-385274346 1 6947617 AGTTGTCCTTGCTCTGGCCCTTAGGGAACAGGTTA[C/T]GAATCACTCTGTACCCTGAGTGCTTATTTCTGTTG Y 2 1 2 1 201000 f 74 goat snp20571-scaffold2027-5376 1 6107244 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383166 Affx-122973229 AX-123253524 1 6953991 TGTCCTTGGGACATCTTTAGTTCATTCTTAGCATA[C/T]GCTTTTCTTTATTGTCTAAGTTTTTACGCTCATCC Y 2 1 2 1 101000 f 74 goat snp44228-scaffold601-899 1 6113419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439043 Affx-122930334 AX-123309380 1 6984781 TGAGGGAGCCAGAGAAAGTGATGCAGAGTCAGTTA[C/T]AGGCTCTGTTCACATTCTATATCCAGCAAACAATG Y 2 1 2 1 101000 f 74 goat snp44229-scaffold601-31689 1 6144487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278789 Affx-1111836513 AX-519552262 1 7026543 AAAGATTTTAAATTATATGTGAAAACTATTTATGA[A/C]TTACATTTCTGTTTCATCAAAGATCAAAGGAAAAC M 2 1 2 1 101000 r 74 goat Random2.2K-9 1 7026543 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777823 Affx-122960093 AX-385264940 1 7044141 AAATAAGTTTATTTCAACTAAGGAATTATCTTACA[C/T]ATGCAAATATGTTCTCTGTTTTCTTTAAGCATTAT Y 2 1 2 1 101000 r 74 goat snp44230-scaffold601-91049 1 6203682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272492 Affx-1111835350 AX-519546214 1 7059443 GACTGGAAAATGTCAGCTTTCATTCCAATCCCAAA[A/G]AAAGGCAGTGCAAAGACGGTTAAATCATCATACAA R 2 1 2 1 101000 r 74 goat Random2.2K-10 1 7059443 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448735 Affx-122923833 AX-123319071 1 7077342 GTTAGCGACTGAGCAACAGCAAAGGTGCTTTGGAT[A/G]CACAAGAAGTTTATTCTGAGGCAGAAAGGAACTGA R 2 1 2 1 101000 r 74 goat snp44231-scaffold601-124250 1 6237063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426968 Affx-122940401 AX-123297313 1 7135412 ATCACTGAGCGTCATGGTAAACCAACCTCGGCTAG[C/T]ACTGGGAAGTGTGCACATTTCAAGAGGTGTTTATG Y 2 1 2 1 101000 r 74 goat snp44232-scaffold601-182320 1 6295772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396585 Affx-122962910 AX-123266940 1 7184932 AAAGAGATTACAAGCAGAGATGAAAGGAAACAGAC[C/T]AACGGACTTAGAAAACACACTTATGGTTACCAAAG Y 2 1 2 1 101000 r 74 goat snp44233-scaffold601-231840 1 6344651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423484 Affx-122942572 AX-123293830 1 7248445 TGGAAATAGTAACTATGCCAGGGTAAGCTCTGGCA[C/T]GTCTACTTTTCTTTTCACAGAAACTTACAAAATAA Y 2 1 2 1 101000 r 74 goat snp44234-scaffold601-295353 1 6407914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407378 Affx-122955264 AX-123277729 1 7302950 ACTGAGATTCTCTCACTGATATTCTTAATATTCAT[A/G]TAACTAACGACAGTTTTATCCATTGTATCTCCCAC R 2 1 2 1 101000 r 74 goat snp44235-scaffold601-349858 1 6462452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385261 Affx-122972080 AX-123255619 1 7379068 AGTTAAAAAATGACCAAATATTTAAAATGACTCAA[A/G]CTGAATAAGATCTTGTTTAGCTCAGGTCTGTTAAA R 2 1 2 1 101000 r 74 goat snp44237-scaffold601-425976 1 6539441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411078 Affx-122951934 AX-123281428 1 7423604 TTTCATTTGCTGACCCTTGTTCCAGACAGATAACA[C/T]GGGGGGAAACAGTACATAAATACAAAATAGGTCAG Y 2 1 2 1 101000 f 74 goat snp44238-scaffold601-470512 1 6584302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423286 Affx-122942649 AX-123293632 1 7460334 CAAAAATGCCTTTAAACTGTTTTAAAATTCCAGTG[A/C]TGTACCTCCATGCAACACTCTTAATTGCCTTACAA M 2 1 2 1 101000 r 74 goat snp44239-scaffold601-507242 1 6621557 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784873 Affx-122963051 AX-385271920 1 7510327 AATTAAAAAAATAATATAAGCAGCAGTAGGGGAAC[A/G]TTCATTATGATCAAATGTCTCTATTCTACGAATTG R 2 1 2 1 101000 f 74 goat snp44240-scaffold601-557235 1 6671447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404633 Affx-122957320 AX-123274985 1 7580264 ACACTGGTATAACGCATGGGGCATAATACACAGTA[A/C]CTCTTGTGATCATTATATCCAATTTACAGATGAAA M 2 1 2 1 101000 f 74 goat snp44242-scaffold601-627172 1 6741956 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777366 Affx-122933698 AX-385264488 1 7634710 CTGTATCCCTGTCATAAGTAAGCTGTATCCCTGTC[A/G]TAGATTGGGCAATTGCATCAGCATCTCTTTCCATC R 2 1 2 1 101000 f 74 goat snp44243-scaffold601-681618 1 6793862 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385787 Affx-122971047 AX-123256145 1 7706584 CAACTTTGGTAGTAGTTTCACCATCTGCAGCAAAA[C/T]GTAAAATGTTTTCCTATTTTTATTAACAGCTACTG Y 2 1 2 1 103000 f 74 goat snp44244-scaffold601-753492 1 6864331 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446563 Affx-122924839 AX-123316899 1 7792228 CTCTCCCACACTTCTGAACACCAGAAAGTGCAAGC[A/G]TAGTACCACCCATAACCTTGGCCAGTGGGAAATGA R 2 1 2 1 201000 r 74 goat snp44245-scaffold601-839136 1 6946516 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379414 Affx-122976116 AX-123249772 1 7822598 AGTTGGGAAGGATTCTCTCCTGTGCAATCATCTTC[G/T]GATGCCTATTTGGGATGGTAACTGCTCTACTCAGT K 2 1 2 1 201000 r 74 goat snp44246-scaffold601-869506 1 6975496 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272561 Affx-1111832870 AX-519546277 1 7855338 GTGCTAAGTCACTTCAATCATGTCTCACTCTTTGC[A/G]ACCCCATGGACTGTAGCCCGCCAGGCTCCTCTGTC R 2 1 2 1 103000 f 74 goat 1_7855338_AF-PAKI 1 7855338 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435608 Affx-122933789 AX-123305948 1 7856190 AGGTGGCAGCTAAAAAGACTCTGAGGACAGCAAAG[C/T]AGTCATGTGACAATCAGGGACAGCATATTTCAGGA Y 2 1 2 1 101000 r 74 goat snp44247-scaffold601-903098 1 7011562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385067 Affx-122971818 AX-123255425 1 7911745 AACAAGACTATAAACCACAAAGATAATTATTAATG[C/T]ACATAAATATTAAAAATACCGGTCAGCATATGGAG Y 2 1 2 1 303000 f 74 goat snp44248-scaffold601-958653 1 7066484 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381793 Affx-122974288 AX-123252151 1 8008953 AATCATCTTACTATGACCACCCTATTCAAACCACC[A/G]TCATCCTCACCTGGAGACTTCCATTAGCTCTCTAA R 2 1 2 1 201000 r 74 goat snp44250-scaffold601-1055861 1 7160352 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392131 Affx-122966336 AX-123262488 1 8078447 CAAAGGGGCTTTGCTTCACAGCAAGTATCTAAGAA[C/T]GTTATTTTCAGTTTATGTCAGTGTTACATCAAGGG Y 2 1 2 1 101000 f 74 goat snp44251-scaffold601-1125355 1 7228763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276510 Affx-1111835453 AX-519550021 1 8129604 TCCCAGAATCATCAAGCCAAGTTTAACTTAGTTGG[A/G]TAGAGACATGAAAACTTGGCGCAGCTAAATTTTGC R 2 1 2 1 101000 f 74 goat Random2.2K-12 1 8129604 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797502 Affx-122926687 AX-385284441 1 8140152 TGAAAAAGTTTTGTCATCATTTCTGTTGTTACTGT[C/T]CATTTCAAATGCAGGTTATTATTAAAACAATTATC Y 2 1 2 1 102000 f 74 goat snp44252-scaffold601-1187060 1 7290562 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378232 Affx-122976912 AX-123248591 1 8188321 GTTTATGCTTTTCTTTCATTTTCCACCTCCTATAT[A/G]AGACTATTCCTTTAGCTTACCCTCTCCAGAAGTGT R 2 1 2 1 101000 r 74 goat snp44253-scaffold601-1235229 1 7345434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769739 Affx-122961897 AX-385256909 1 8270691 AGTTAAAAGAAAAAAGATCATACTAGATCCAGGAT[A/G]CATTCTACTACACAGACCTGTGTAACAGGTCTAAG R 2 1 2 1 201000 r 74 goat snp44254-scaffold601-1317599 1 7429034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798810 Affx-122957286 AX-385285741 1 8295574 TAGGACACTGACTCATATTTTTCATCCGAGTGAAT[A/G]TGATTTATTCAGTGATCCTATATAAATGTATTATG R 2 1 2 1 101000 f 74 goat snp17081-scaffold1783-272495 1 7454440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780180 Affx-122972127 AX-385267276 1 8326207 TTTCACGATTCCATTACCTCTCACTCTTTTTTGCA[G/T]GTATGGATCTTGTGGATGATTCAAAGAACTATTGT K 2 1 2 1 101000 f 74 goat snp17080-scaffold1783-241862 1 7485263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787022 Affx-122967395 AX-385274050 1 8361416 AACAATTAGTCAATCTAAGAAAGATTTATTGGAAA[C/T]AATTGAAGATTATTACCTGGGAAAAGCCACTTTGA Y 2 1 2 1 201000 f 74 goat snp17079-scaffold1783-206653 1 7520301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797694 Affx-122939431 AX-385284633 1 8405670 CCACTCAGATTGTCATGCTGAACTACTGCATTGTC[A/G]GTTTTCTTTTACCATGATGATTTCTCTTGCACTTT R 2 1 2 1 101000 f 74 goat snp17078-scaffold1783-162399 1 7563723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783298 Affx-122929666 AX-385270363 1 8447700 TGCTTGTCTCCCAATATCTGAATTACAGATACAGA[A/G]GTAGATATAGATATATTTACTATGAAACATAAATT R 2 1 2 1 201000 r 74 goat snp17077-scaffold1783-120369 1 7605812 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412033 Affx-122951730 AX-123282383 1 8508813 GTAGGAAAAGGAATAAAAAAATAAAGTAATGAAAT[A/G]CATTTTTTAAGACATGCGTTTCCTCCCAAAGTATG R 2 1 2 1 101000 r 74 goat snp17076-scaffold1783-59256 1 7666912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795236 Affx-122935464 AX-385282194 1 8586569 CTCCTATTTAATGTTCTCTCTTATTATTTCCTCAT[A/G]CTACCCACAATGAAAATAATCTTGCAAAGCTCTAC R 2 1 2 1 101000 r 74 goat snp48423-scaffold688-18401 1 7745595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771822 Affx-122957453 AX-385258979 1 8620938 CTGATCTAAGATTGGGAAATGGCATGGTCATAAGA[C/T]AGAACTATGTTAGTAACTATTTAAGAAACCAACCA Y 2 1 2 1 101000 f 74 goat snp48424-scaffold688-52770 1 7779742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379399 Affx-122976129 AX-123249757 1 8684730 AACTAACTAGCTGAGTAAATGCTATTGAAGTAAAT[A/G]ACTGTATAAATAGCATCAAAATGCAAAGCTTAGAA R 2 1 2 1 101000 f 74 goat snp48425-scaffold688-116562 1 7844147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399350 Affx-122961353 AX-123269705 1 8716725 CTGTAAAATTAAACATTGGTTTTGTGGTTTCAGTG[A/G]GCATAATAAATGTAAACTGTAAAATAGGTTAAAGT R 2 1 2 1 101000 f 74 goat snp48426-scaffold688-148557 1 7875834 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441635 Affx-122928635 AX-123311972 1 8754110 CAGAGGCAGTAGGAAATCTGTTCCAAAACCAGCTG[C/T]ACCACATCTGTTTTCCAGGGCATCAGTAGCAATGG Y 2 1 2 1 101000 r 74 goat snp48427-scaffold688-185942 1 7915964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403661 Affx-122957514 AX-123274013 1 8817404 ATTATATATATTAAATTCATATATCAGCACATTCA[A/G]TTTCAAAGTAGGACAACTTTGCTTCTGGATACATT R 2 1 2 1 101000 r 74 goat snp48429-scaffold688-249236 1 7980410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276813 Affx-1111835534 AX-519550322 1 8842614 GCAGACAAAACAGTCCTTTTATTATTTATTTATTT[A/T]TGGATGTGGACCTTTTATTAAGATCCCTATTAAAT W 4 1 2 1 202000 r 74 goat Random2.2K-13 1 8842614 T A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782151 Affx-122930536 AX-385269229 1 8873761 AACTTTATGTTTTCTCCTGTAATAACAAGTACATC[A/C]TAAGTCATTTATTGTTCATTTGTTGTAGCAAAGCC M 2 1 2 1 201000 r 74 goat snp48430-scaffold688-305593 1 8037219 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798008 Affx-122945215 AX-385284944 1 8948806 TTATCATTTTAGCTAGTCCTAAGTCATTGCAAAGC[A/G]TCAACAGAGTTTACAAAGAGAACATTAAATTAATT R 2 1 2 1 101000 r 74 goat snp48432-scaffold688-380638 1 8112978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790213 Affx-122970653 AX-385277217 1 8999891 TCTTAGAAATATAAGCAGAAATAGGCTTAAGGATC[A/G]GATAACTTTACACTCATCCAGGTAATCTGCTAACA R 2 1 2 1 101000 r 74 goat snp48433-scaffold688-431723 1 8164861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795807 Affx-122952839 AX-385282760 1 9028982 GAGCAGGTCTGAACGAGGCATCTAGAATGGATTAA[C/T]GTTCTGCTTCAGGACCTGAATCATGTTTACTTTAG Y 2 1 2 1 101000 r 74 goat snp48434-scaffold688-460814 1 8194401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789859 Affx-122962433 AX-385276866 1 9068842 TTCAACTAATTTCATTTAAGCTTGACTGTGGATAC[A/G]TGGTCACTATAATATTCCTCATATTTTCTATAATG R 2 1 2 1 101000 f 74 goat snp48435-scaffold688-500674 1 8234362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384436 Affx-122973106 AX-123254794 1 9106826 ATTGGACCAAGAGATGAAGTTTCTCAAAAACCAGG[A/G]ATTAAATGTTTGGATTTTAACTTAAAGGCAACAGG R 2 1 2 1 201000 r 74 goat snp48436-scaffold688-538658 1 8271780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794700 Affx-122977703 AX-385281660 1 9142763 GGCAGGCTTTCTCAACTATGTTCATACATTTAAAA[A/G]AATTCATTAAGGTTTTTAAAAGAATGATCCTGGCT R 2 1 2 1 202000 r 74 goat snp48437-scaffold688-574595 1 8307924 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408711 Affx-122953429 AX-123279062 1 9179141 GTCATCTGATGTTTTAAGACCACAGTCCCCAACCT[A/G]TCTGGCATCAGGGACTGCTTTCATGGACTACAGTT R 2 1 2 1 201000 r 74 goat snp48438-scaffold688-610973 1 8344502 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799572 Affx-122921823 AX-385286502 1 9243355 GATTCTATTATGAGCAAGCTGACAAAGCTTTTGTT[A/G]CCTTCTCAGTTGGAGTAAGTTTTACATTGTAAGTT R 2 1 2 1 201000 r 74 goat snp48440-scaffold688-675187 1 8408276 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415169 Affx-122949011 AX-123285518 1 9301018 CAGGCTGAGCCAGCAGAATTACTGGCTTCTCCAAT[A/G]CAATTGTCAGAACAGGAATGACGGAATCAAGAGGT R 2 1 2 1 101000 f 74 goat snp48441-scaffold688-732850 1 8465295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447467 Affx-122924356 AX-123317803 1 9391925 CCTCCACTGCCAGGCTTTAGCCTGACACCTGGTCA[C/T]GTCTCAAGGTGTCTCCCTCTCAGATTTAATTAGCA Y 2 1 2 1 101000 r 74 goat snp48443-scaffold688-823757 1 8557176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786628 Affx-122936003 AX-385273660 1 9438142 AAGGTTGCAAAAAGTCTTACTCAACTAACAGGGTT[C/T]GGAATTTAACATGGCAAAACCTAGACCCTCAATAT Y 2 1 2 1 101000 f 74 goat snp48444-scaffold688-869974 1 8603434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764706 Affx-122948825 AX-185846846 1 9472085 GTCAAGGAACGATGGAAGGAAAGTAGAATTCCTCA[A/G]TCTCTTTCTATTGAGCTGAATGATCTTCCAACTGA R 2 1 2 1 101000 f 74 goat snp48445-scaffold688-903917 1 8637284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393055 Affx-122965619 AX-123263412 1 9510059 GGTTTTGATGTCTTCATTTCTGCTGTCAGCCTCTG[C/T]AGGGTTCTGTCATTCCCAGCAGGGAGGGGGTCCTG Y 2 1 2 1 101000 f 74 goat snp48446-scaffold688-941891 1 8675129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434918 Affx-122934316 AX-123305258 1 9541542 CCAGATCTGGTCTACTGCCTGTTTTATGAAGAAAA[C/T]GTTCCTATGAAGCAGCCACACCCATGGTGTCTGCG Y 2 1 2 1 101000 f 74 goat snp48447-scaffold688-973374 1 8706726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418942 Affx-122946499 AX-123289290 1 9575706 CACTTTCCCAGGCCGGGTATAGTATCTGGTGTTAA[C/T]TTAGCACATCACAACACCTCTTCTTGACTACTCGT Y 2 1 2 1 101000 r 74 goat snp48448-scaffold688-1007538 1 8740743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766746 Affx-122967861 AX-385254082 1 9652058 CAGTTACAAGGGAATTTTAATCAGCTTTATTGAAG[C/T]GTACCTATTAGACTTTTAAATTAACTGGAGGCCCT Y 2 1 2 1 303000 f 74 goat snp48449-scaffold688-1083890 NW_017195430.1 7321 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415124 Affx-122949430 AX-123285473 1 9706965 TGTCATATTTTGCTCTAGCAAAGGTTGCATGTGCT[A/G]TGCCATGCTAAGTCTCTTCAGTCGTGTCCGACTCT R 2 1 2 1 101000 f 74 goat snp48450-scaffold688-1138797 1 8869620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418015 Affx-122946654 AX-123288363 1 9740316 GGAAACTTACTTGAAATTCACATTCTCTGGTCCCA[C/T]CCCTGACCTCCTGATTCAGCATTGCTGGGCTGAGG Y 2 1 2 1 101000 f 74 goat snp48451-scaffold688-1172148 1 8903202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771542 Affx-122919842 AX-385258700 1 9805947 AACTTGAATCAACTTAGACTGAAAACACCCAAAGC[A/G]TGAAGTTAGGAATAAGCAATCGATGAAGAACGATG R 2 1 2 1 101000 f 74 goat snp48453-scaffold688-1237779 1 8968647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774671 Affx-122974221 AX-385261805 1 9835323 AAAGAGGGGGAGAGCACTGGGTTAGATCTAATTAC[A/G]TGGTATACCTTGGGATGATGCCCAAAAGGGCAACT R 2 1 2 1 201000 r 74 goat snp48454-scaffold688-1267155 1 8997440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418841 Affx-122946142 AX-123289189 1 9875634 AAAGAACTTGGGTACTTTTAAAATAAGGAGATCTG[C/T]GCATGTTGTGTGCATGCATGTGAGTCTAAATATAT Y 2 1 2 1 101000 f 74 goat snp48455-scaffold688-1307466 1 9038325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388115 Affx-122969487 AX-123258473 1 9917052 AAGATATTCATGTAGGCCACGGGGCTGTTACTTTT[A/G]TAAACAAAACAATTCCAAAGCAGAGCTCCTCTGTA R 2 1 2 1 201000 r 74 goat snp48456-scaffold688-1348884 1 9080472 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393077 Affx-122965605 AX-123263434 1 9945578 TGAAATCTCCCTGTTTAGCTTAGCAAAAGTGACCC[C/T]TCACCTCTAGTAGCTTTTTGTTAAACTGTGCCTTT Y 2 1 2 1 101000 f 74 goat snp48457-scaffold688-1377410 1 9108778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402247 Affx-122959136 AX-123272600 1 9977903 TGTTCTCACTGGTGAATAAAAGGGTCTGGGGTACA[C/T]GGTGCCCTCTTTCTCTCACCTCATTGAGTCCCCAA Y 2 1 2 1 101000 f 74 goat snp48458-scaffold688-1409735 1 9141331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409037 Affx-122953861 AX-123279388 1 10011026 AGTGACATGTCTCACCCTCTTTCCACTAGCCTAAC[A/G]GACATTTTTAGTTGACTATTTTCTTCCCTCCTGAA R 2 1 2 1 201000 r 74 goat snp48459-scaffold688-1442858 1 9175161 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448961 Affx-122923132 AX-123319296 1 10043939 GGAGTCTCAAGCACTGGACAGCTGGGGAAGTCTCC[A/G]TTTTTCTCCGATTTTTAACCTTCCTCCTTCTCTCC R 2 1 2 1 101000 r 74 goat snp55833-scaffold867-19405 1 9207636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801904 Affx-122940749 AX-385288809 1 10149214 GAATATATGCTTTTAGGTCAGCATAGTACGTAAAA[G/T]CATAGACTCTGGGGACAGAATGCTAATTTCAAGCT K 2 1 2 1 102000 r 74 goat snp55836-scaffold867-124680 1 9313941 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399569 Affx-122961122 AX-123269924 1 10182767 GTGCTCTGCATTGAACCCCTGAGGTCTGTTTGTGA[C/T]GAAAGTCACAATGAGGCAAAAGTCCTTGTTCCTGG Y 2 1 2 1 102000 f 74 goat snp55837-scaffold867-158233 1 9347664 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439863 Affx-122930054 AX-123310200 1 10216707 CAGGTTCTTTGGTTAAATTAGCAGTCCCTTTTCAC[A/G]TCAGGCTTCTCTTCATTCGGCTACACAGATTTTTT R 2 1 2 1 101000 f 74 goat snp55838-scaffold867-192173 1 9382099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376128 Affx-122978868 AX-123246487 1 10247386 AAGGGACTGAAACTGATTGTGAACTGAAAAATTAC[G/T]ATGAGCTTTTGATTTAAGCAATGCCTACCAAAATA K 2 1 2 1 101000 f 74 goat snp55839-scaffold867-222852 1 9413786 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382236 Affx-122973962 AX-123252594 1 10330619 AGTTTCTCAACACTTTTAAAAAGGCATCAACAGAG[G/T]TTGTATCAATTACAATGCCTCCAGGAACTGTTACA K 2 1 2 1 101000 f 74 goat snp55841-scaffold867-306085 1 9498306 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400952 Affx-122959700 AX-123271305 1 10353936 GAGCAAAGAATATTTGGGGGAGAAAGAGTTCACAA[C/T]GCACAATGTGCCCCTAATGCTCTTCTGTTGCTTGA Y 2 1 2 1 201000 f 74 goat snp8479-scaffold1307-528093 1 9521685 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771436 Affx-122974379 AX-385258594 1 10388131 CTGAAGTAATTGATTGAATGTTCTACAGTACTGCA[C/T]AGAACAAAAGCCCAGATATCAAGTCAATATTCATG Y 2 1 2 1 101000 r 74 goat snp8478-scaffold1307-493898 1 9556496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272457 Affx-1111836714 AX-519546182 1 10408764 ACAAAAACTTGTTTGCACCAGGACTCAGGAGAAAG[A/G]AGCAGTGATCCCACAAGAGACTGACCCAGACTTGT R 2 1 2 1 103000 f 74 goat 1_10408764_AF-PAKI 1 10408764 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798378 Affx-122973987 AX-385285312 1 10438434 TGTTTATTTCACAAGCACTTTCTCATTTTAAACTC[A/G]CAAGACTTATGACAAATTTCCACTTCACTCTTGAG R 2 1 2 1 101000 f 74 goat snp8477-scaffold1307-443595 1 9606365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454319 Affx-122919244 AX-123324652 1 10493516 TTTTGTGATACTACTGAAAAGGCAAAATCTAGTTA[C/T]GTTTTTCCTTTGACCGAATAAAACTCCTGCAATTT Y 2 1 2 1 101000 f 74 goat snp8476-scaffold1307-388513 1 9662286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439011 Affx-122930358 AX-123309348 1 10546669 CTAACACTAGACTTCTAACCATGGACTGCAATTTC[A/G]TTGGCTGGGCCAAGACACCTTGCCTATTTTTCATT R 2 1 2 1 101000 f 74 goat snp8475-scaffold1307-335360 1 9714340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407580 Affx-122954664 AX-123277931 1 10579347 AGTTCTTCTCTTTTTCTCTATTAGTTAAAAGATAA[C/T]GAACCATTGTATATGCTTTTTCTGAGTTGCTTAAA Y 2 1 2 1 201000 f 74 goat snp8474-scaffold1307-302682 1 9747544 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765119 Affx-122966742 AX-385252679 1 10660683 CCAGTATAAGGCTTTGCCTCTTTGGTATGAAATAG[C/T]TTCATTAAATAACCACCCACTGCTCTCTCTAATCC Y 2 1 2 1 101000 f 74 goat snp8472-scaffold1307-221346 1 9830796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792594 Affx-122968253 AX-385279574 1 10706551 ACATCACATATCAAATTTACTAATTTTAGTTAGTG[C/T]AAGACTCCATAGCATCCTATCCTGTCCAATGAAGC Y 2 1 2 1 101000 r 74 goat snp8471-scaffold1307-175478 1 9876800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405779 Affx-122955918 AX-123276131 1 10737123 TAAAGTAAGAACCTAGTTTTCCTCAAGTATAGATA[G/T]AGTGTAGCTTCTGAATTCATCCATGTGGCAACTTA K 2 1 2 1 201000 f 74 goat snp8470-scaffold1307-144906 1 9907995 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794450 Affx-122954449 AX-385281413 1 10766409 AAGAAGTGAACAAAAGTCTAAGAGTTACTAGTAAA[C/T]AATGATCATGAAAATAGAGTGAATATAATAAATGC Y 2 1 2 1 202000 r 74 goat snp8469-scaffold1307-115620 1 9938053 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780646 Affx-122949957 AX-385267736 1 10849927 ATTCTTGAACTTTGTTCAGCTTTACCAAATATGTC[C/T]GATTAACATTCCTGGAAGTTCACAAGTAGAGTGCA Y 2 1 2 1 101000 r 74 goat snp8467-scaffold1307-32102 1 10020932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397852 Affx-122962458 AX-123268207 1 10896602 ATGGATTAACTAGCAGTCATATTTTCAGTGACCAC[A/G]TCTAACAGGAGGGAAACAAATTCTAAGTGAAGTCC R 2 1 2 1 101000 f 74 goat snp42339-scaffold559-14474 1 10121414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419872 Affx-122945361 AX-123290220 1 10928535 AGATAAATATTTTTTCTTTCTACTTTAGTTTTCAT[C/T]GATTTTAAGAAACGCATTCATCACTCTTAGAAGTT Y 2 1 2 1 101000 r 74 goat snp42340-scaffold559-46407 1 10152332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385122 Affx-122971776 AX-123255480 1 10976246 GGTATTATTTTCCAAAATATTCAGAATCCCTAGGA[C/T]GGGAAGAATACTACTTATCACAGACTTCCATCCCT Y 2 1 2 1 101000 r 74 goat snp42341-scaffold559-94118 1 10200055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409911 Affx-122952887 AX-123280262 1 11040773 GGAACATAGGTTTCTATGATATGTATCTAGGAGAT[A/G]CTAACAAAATAAAGTCTTATCTTTTTATGCTTCAA R 2 1 2 1 101000 f 74 goat snp42342-scaffold559-158645 1 10264446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792036 Affx-122956490 AX-385279024 1 11079155 AACTGATTCTAGTACCTGTGTGTTTCTGCTTAGAG[A/G]TGCTTAATGATTACACCCTTGATAGAACAAATCTT R 2 1 2 1 101000 f 74 goat snp42343-scaffold559-197027 1 10303410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772555 Affx-122973668 AX-385259705 1 11117868 ACACATTTTAATCATGTTTGTTTGAAAAGGCTGAC[A/G]TATAATATGTAATGACATCTGGTTGTCAGAAGTAC R 2 1 2 1 201000 f 74 goat snp42344-scaffold559-235740 1 10342341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402864 Affx-122958238 AX-123273217 1 11150557 GTGTGAACACTCAATCATTCACTCAACAAATACTT[A/G]TCGGTAATATTTATTTGCCTGGTATTGTGTCAAAT R 2 1 2 1 201000 r 74 goat snp42345-scaffold559-268429 1 10374718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799397 Affx-122927273 AX-385286327 1 11193184 TGAGCAATTTTACATATGCCTTAGATATATCAAAT[A/G]CAATGCTGGAGATCTCTGTATACTTAATGACTGCT R 2 1 2 1 101000 r 74 goat snp42346-scaffold559-311056 1 10418692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419032 Affx-122946032 AX-123289380 1 11222860 AAGTATATTGTACATTAGTGCAGTTCAGTTCAATC[A/G]CTCAGTTGTGTCTGACTGAATATTTAATGCAATGT R 2 1 2 1 303000 f 74 goat snp42347-scaffold559-340732 1 10448945 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798921 Affx-122964344 AX-385285851 1 11254849 TCTCCAGAAGATATGGGAAAAGTTTCAAGGCAAGG[C/T]AAAACTTTATTTGATCATCTTCAGAGACAGAGGGA Y 2 1 2 1 101000 f 74 goat snp42348-scaffold559-372721 1 10480653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398823 Affx-122961395 AX-123269178 1 11303237 GGGAGAGCAGGATAATTTTAGATTGTGTAAAAAGA[G/T]AAATATATATCTAGGAAAATGCAATGAAGCATACT K 2 1 2 1 101000 f 74 goat snp42349-scaffold559-421109 1 10529911 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388953 Affx-122968809 AX-123259311 1 11334926 TGGCTGTGCTGAGCCTCCAACAATTCATCAATTTC[A/G]CTTTCATCCCCCACCACAGTAGTTCCTGACCCAAC R 2 1 2 1 101000 f 74 goat snp42350-scaffold559-452798 1 10562733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277139 Affx-1111835699 AX-519550645 1 11381248 ATAATAACAAATACTTATATGCTCTTCATTGGGTA[A/G]CTGTCTCAAAAATGCTTGGATTAAATAAGTCCCAA R 2 1 2 1 101000 r 74 goat Random2.2K-16 1 11381248 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430925 Affx-122936847 AX-123301266 1 11402862 CATAAAGCTATATCAGCCTGCTCTGAGCTATTTAA[C/T]AAAGAGATGTGAATTCTATCGCCTTCATTTAGCAA Y 2 1 2 1 101000 f 74 goat snp42351-scaffold559-520734 1 10632303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780333 Affx-122958872 AX-385267428 1 11443598 GGTGCTTTCCAAGACCTGGAAGAAAGAGGAATATG[A/C]GGTGTTGTTGTTCAATACCTATAAAATTTCTGTAA M 2 1 2 1 101000 f 74 goat snp42352-scaffold559-561470 1 10673301 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442218 Affx-122928779 AX-123312555 1 11503151 TTCTACTTGGCTGGTCCATTGCCACGCAGGTATAA[C/T]ACAGTCAAAACTGAACTTGTTATTGTTGAATCAAC Y 2 1 2 1 101000 f 74 goat snp42354-scaffold559-621023 1 10733021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403249 Affx-122957881 AX-123273602 1 11543370 CAAGTTCCTCCTCCATGTTTCACCTCTTACTATTT[A/G]CAATGATCACCATATCGGTACTCCTCTCATAAAGC R 2 1 2 1 101000 r 74 goat snp42355-scaffold559-661242 1 10763058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430767 Affx-122937489 AX-123301108 1 11582672 ACTAGATTAACAGTGATCCAGGGAAGCCAGACTTG[C/T]GGTTTGCACTGGAATCTGGTAGCTGAGAATGAGAA Y 2 1 2 1 201000 r 74 goat snp42356-scaffold559-700544 1 10802319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783501 Affx-122944746 AX-385270564 1 11621828 ATTAAAAAGATAATTTGTGCAAAGCACCTAGCACA[C/T]GGCATAGCAAATAATAAAGTTCAATAGATATAACT Y 2 1 2 1 101000 f 74 goat snp42357-scaffold559-739700 1 10841517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788183 Affx-122966352 AX-385275202 1 11676341 AACCAACTCCATAATGTAATATGCTCAGTGTATTT[A/G]TTTGTCTGACATAAAATTATGTACATGGATATGCC R 2 1 2 1 102000 r 74 goat snp42358-scaffold559-794213 1 10886462 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769061 Affx-122938869 AX-385256236 1 11724563 TAGCACTAGAATAAACGTTGAATCTGTTAGAAGAT[A/G]CTTACATAAGGTCTCAATGGAATCAGGCAGCTTCC R 2 1 2 1 101000 r 74 goat snp42359-scaffold559-842435 1 10935158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768924 Affx-122938067 AX-385256100 1 11772216 TGTCATGGATAAGGCAAAACTGAAGTCTGCATAAA[G/T]AGTAAAGCTTTACCTTAAAGGGCACATTAAAGAAT K 2 1 2 1 101000 f 74 goat snp42360-scaffold559-890088 1 10982749 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390812 Affx-122967856 AX-123261169 1 11808128 GTACCACTTTTTCCTAGAAAGGACACATATTTGAT[C/T]GATTTAATCAGGACCACATCCTTGAAGGTCAGGCT Y 2 1 2 1 101000 f 74 goat snp42361-scaffold559-926000 1 11018785 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393233 Affx-122965481 AX-123263590 1 11850250 ATAAGTTTCACTGGGCCTAAGAGAAGCAATGCATG[C/T]ATTAGTAAGAATAAAGAAGAATCATTTATGTCTTA Y 2 1 2 1 101000 f 74 goat snp42362-scaffold559-968122 1 11061548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783017 Affx-122977261 AX-385270085 1 11892475 AGAGAACTATGTGGCCTATTTTATCATTAATCGGT[A/G]GACTGATTAACTGCTCAATATTTATTGATAATTTT R 2 1 2 1 101000 f 74 goat snp42363-scaffold559-1010347 1 11103709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802202 Affx-122937038 AX-385289106 1 12020360 TTTGATGGCTGGAAAGAAATTTAATTAAGCAATCA[C/T]AACCACAACTACACCAATGCCCAAAATATGATTTT Y 2 1 2 1 101000 f 74 goat snp15927-scaffold1670-150085 1 11230406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388600 Affx-122969150 AX-123258958 1 12070904 TCCTGTCATGTCTGTAAATTATTTTCCAACCCATG[C/T]ATGGACCATGACAAAAGATACAGATTCTAAAAGAA Y 2 1 2 1 201000 r 74 goat snp15926-scaffold1670-99541 1 11281018 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437490 Affx-122932360 AX-123307828 1 12116460 CTAAACTTACTGATGAACAGAACACAAAGGTTTCT[A/C]TGGTGGCTCAGTGGTAAAGAATCTGTCTGCAGTGC M 2 1 2 1 201000 f 74 goat snp15925-scaffold1670-53985 1 11325992 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795363 Affx-122943886 AX-385282319 1 12158309 TCAATGGAATGGAAGTAATGGATGTGAGAATAGAG[G/T]GTCTGTATTTTAAGATAAACTGATTATCAGTCTTA K 2 1 2 1 101000 f 74 goat snp15924-scaffold1670-12136 1 11367857 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399060 Affx-122960900 AX-123269415 1 12179283 TGCAAGTGGGAATCTCATAAGGCAATGAAGTAACC[G/T]CTACTAAGGCACTGTAAGATGAATAAAGCCCAGTA K 2 1 2 1 101000 f 74 goat snp16300-scaffold1716-229833 1 11631316 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434905 Affx-122934328 AX-123305245 1 12223615 GAGAGGATTGGTGAAGTTTATTGTATGATTATGTT[A/C]TTTGCTGTTCAACTTCAGCTTCTTCAGCATTACTG M 2 1 2 1 201000 f 74 goat snp16299-scaffold1716-185501 1 11676250 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412763 Affx-122950512 AX-123283112 1 12256522 TTTACTTGTTCACACTGGGTATCATTTTTCCTAAG[C/T]GACAGTTGGTATTTGGATATTACAATATCTGACCT Y 2 1 2 1 101000 f 74 goat snp16298-scaffold1716-152594 1 11709415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775351 Affx-122936988 AX-385262482 1 12288852 AATTGAAGGAATTCGGAAAGGCAAGCAAGATTTCT[A/G]CCTCAATACAAATTCTTATCTAATAAGCGTTTATA R 2 1 2 1 101000 r 74 goat snp16297-scaffold1716-120264 1 11742753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786193 Affx-122937316 AX-385273228 1 12320002 CAGTGAAATATTAGTCTATTTTGCTCCTGCATATT[G/T]ATAACTTTAATTTCACTTTAATACTATATTATTAA K 2 1 2 1 202000 r 74 goat snp16296-scaffold1716-89114 1 11774022 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793008 Affx-122973331 AX-385279986 1 12350681 TCAGGTTTATCATGGATATTCTATATAATGATATG[C/T]TGGCTGGTCATTTCATAAGACCTGGGTCATTGTTG Y 2 1 2 1 101000 r 74 goat snp16295-scaffold1716-58435 1 11804316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770012 Affx-122941738 AX-385257179 1 12423536 CCTGCAGGCTAGGAGCAAAACAAAATTCTCTGTTG[C/T]ACAGCTGAATAATTAATTAAACATTGGTAAGTCTG Y 2 1 2 1 101000 f 74 goat snp2867-scaffold1084-438967 1 11996501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385923 Affx-122971567 AX-123256281 1 12458647 TTAGGAAACCATATTCTATTTTTGACATTTTAAAA[C/T]GAAATCAATTTGGCAATTCTGATATCAGTGTTAAG Y 2 1 2 1 103000 r 74 goat snp2866-scaffold1084-403856 1 12032537 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379234 Affx-122976270 AX-123249593 1 12492663 AATTTCTCACAAGGGAAGAATGAATTGTTACAGAC[A/C]TTTTCCTTCTCTTCTGCTAAACACTAAGGATCTCA M 2 1 2 1 101000 r 74 goat snp2865-scaffold1084-369840 1 12066863 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375704 Affx-122978646 AX-123246063 1 12527932 ATTATCAGCATCAGGCACTTCAGAAATATAATTGG[C/T]ACTCAAAAAATAATGTAAATAAGTGAATGAATGAA Y 2 1 2 1 101000 f 74 goat snp2864-scaffold1084-334571 1 12101917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428007 Affx-122939159 AX-123298350 1 12582082 ATTAATTTTCTTCTTATTTATGTTCTCATACAATT[A/C]GATTATTCAGCTTGAGAATTTCATATTGCAATCAG M 2 1 2 1 101000 r 74 goat snp2863-scaffold1084-280421 1 12165235 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794588 Affx-122950686 AX-385281550 1 12615744 TTTTATCAGAACATATTATTATTAATCTAGCAATT[A/C]TTTTAGGGAATAAATTATATTCTACTGGAGTAGGA M 2 1 2 1 202000 f 74 goat snp2862-scaffold1084-246759 1 12199316 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770643 Affx-122933602 AX-385257807 1 12648302 TGAAAGAGAAGGACTCAAAAATTTCTATTAACTTC[A/G]TCAAATCATAAAAATGACAGCACCAAAAAACTGAT R 2 1 2 1 201000 f 74 goat snp2861-scaffold1084-214201 1 12231940 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450532 Affx-122922488 AX-123320866 1 12727265 CACATTCACTTGGCTCATTTCAAAACTGTATTCTT[A/G]TTATAACAATCAGTGGCATTCCTGAGTAAAGTGAC R 2 1 2 1 201000 r 74 goat snp2859-scaffold1084-135238 1 12311515 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774243 Affx-122969079 AX-385261379 1 12771377 CAGTGATGTCCTTGAAGACACATTGTGACGGTTTT[A/G]CCTGTGGAGATCAGGATGCTTGACCATGACCATTC R 2 1 2 1 101000 r 74 goat snp2858-scaffold1084-91126 1 12354656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406312 Affx-122955463 AX-123276664 1 12810601 TTTCTCATTATTCTCTATGGTGCATATTCTTTCTT[A/G]CAGTGTTCTACTATACCCAACTTTGAATATAGGTT R 2 1 2 1 101000 r 74 goat snp2857-scaffold1084-51902 1 12394378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793947 Affx-122955356 AX-385280916 1 12861853 TGCTCACACCCACACCTTCTTCCATAGAAGCGCCC[G/T]ACATCTAATTACTGTTTGACATGTGGTTATAAAGG K 2 1 2 1 102000 f 74 goat snp2856-scaffold1084-650 1 12446791 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788564 Affx-122939488 AX-385275581 1 12863672 AAGAAGTGGGAAGGCTATGGGCTCTGCATTCTTAT[A/C]TTCAAGATCTGATTCTTGCCATAGTACTAAGAATC M 2 1 2 1 101000 f 74 goat snp1254-scaffold10319-713 1 12464500 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426662 Affx-122939928 AX-123297008 1 12902821 GATTTTCTTAGTACAAATATTTTTATGGTTATTTT[A/G]CTCTATTTTAGCTATTGGTCTCTGATTTTAACAAA R 2 1 2 1 101000 r 74 goat snp31515-scaffold35-27797 1 12501694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271814 Affx-1111832836 AX-519545601 1 12912774 TCAGGGTCTTCCAATGAGTCAGCTCTTTGCATTAA[A/G]TGGCTAGAGTATTGGAGTTTCAGCTTCAACATCAT R 2 1 2 1 103000 f 74 goat 1_12912774_AF-PAKI 1 12912774 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764492 Affx-986698949 AX-385252169 1 12919858 ATGGAGATGCTTTGAGATTTAAATGTTATAAAGTT[C/T]ATGTAAATAGATGCTAAATGTGTATATTTTAATTT Y 2 1 2 1 600010 f 74 goat 1_12919858 1 12919858 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320799308 Affx-122944706 AX-385286238 1 12962407 TGTTTTCCCACTTGTTGATATAATTTAATAGTATA[G/T]CAGCAGACATCCATGGGAAAACAAATGAAAGAAGG K 2 1 2 1 101000 r 74 goat snp31516-scaffold35-87383 1 12561327 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417151 Affx-122947349 AX-123287499 1 12993640 TGTTCAAGCCCTAGATAACATGATTCTGTGCAAAA[C/T]AGGGAATCAGTTCAGTTCAGTCTCTCAGTTGTGTC Y 2 1 2 1 201000 f 74 goat snp31517-scaffold35-118616 1 12595927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431227 Affx-122937146 AX-123301568 1 13028816 TGAAAAAGAATAATATTTTCTGTTACCACAGAAGG[C/T]AGAATTTTAGAAAAAGATTACTAAGCAATCCAAAG Y 2 1 2 1 103000 r 74 goat snp31518-scaffold35-153792 1 12631964 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448083 Affx-122924330 AX-123318419 1 13067345 AAGATAAAATTCTCATGAAAAAGAGGAACAATTTT[A/G]TTAACCACCTGCCAAAGCCATTAAAATGTAGACAC R 2 1 2 1 103000 r 74 goat snp31519-scaffold35-192321 1 12670183 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792015 Affx-122962376 AX-385279003 1 13093640 ATACTGTCACCTTTGTAAAAACAAGGGAATCATTA[A/C]ATTAGCAGTAATACTTTCTTGTTTTCTTGAACCTC M 2 1 2 1 201000 r 74 goat snp15439-scaffold1636-419017 1 12706212 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405553 Affx-122955964 AX-123275905 1 13125917 AAGCATCCACACAGTATCCTGTTTGATGTTTTGTT[G/T]TAGATAAAACATTGTCTGGCATGATTTTACCAAAC K 2 1 2 1 201000 r 74 goat snp15438-scaffold1636-386740 1 12738048 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277373 Affx-1111835816 AX-519550877 1 13142090 CATGTAAATTATAATATGAAAATGTGCACTATCCA[A/C]AAGGAAGAAACTTTATTACTGCCCTGCAACTATTA M 2 1 2 1 101000 r 74 goat Random2.2K-18 1 13142090 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799095 Affx-122966915 AX-385286025 1 13159806 TGGTGTGTTTTCACCTGTCACACATTCGTATTCCA[C/T]GATCTATTGTTACAGGTACTCTTTATGAGAAAATA Y 2 1 2 1 101000 f 74 goat snp15437-scaffold1636-352851 1 12772721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405970 Affx-122955534 AX-123276322 1 13214828 TTACTCTTTTCTATTGAGAGGAGGACATGAGAGAA[C/T]GGGGCTTAATGTTTCATCCATTTGCATTCTAGTCA Y 2 1 2 1 101000 f 74 goat snp15436-scaffold1636-297829 1 12830355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778558 Affx-122965520 AX-385265670 1 13245172 CATGTTTGTTATCCATGTCATTTTTGTGGCAACTT[A/G]TATCTTCAACTCTTTATCCCACTTTTTAAACTGAG R 2 1 2 1 101000 f 74 goat snp15435-scaffold1636-267485 1 12860739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778121 Affx-122977053 AX-385265235 1 13282213 GTATGTGGTGCGATTAGACAGAACTGATCTCATAT[A/G]TACTGACATTACACATGCAACATTTTGTTTGGTCG R 2 1 2 1 101000 r 74 goat snp15434-scaffold1636-230444 1 12898699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395763 Affx-122963678 AX-123266118 1 13311234 ACAAGCTATTTGAGGATAACTTCTTTACACAGAAA[C/T]GAAGAGTGAAGAACATATGTTACCTTAACATTTAT Y 2 1 2 1 101000 f 74 goat snp15433-scaffold1636-201423 1 12928354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417496 Affx-122947160 AX-123287844 1 13351528 TTCTTGTCTATAAAATGGAAATAAATTAAGACAGA[A/G]CATAAGATTGTCTAGGATTTATTTCCAGTTGGACT R 2 1 2 1 103000 r 74 goat snp15432-scaffold1636-161129 1 12969108 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796998 Affx-122931555 AX-385283939 1 13390072 TGTCAGTGAATAAATGATTATATGTAAAAAAGGCA[C/T]GTAGGGCTAATGTTTACCTCGAGTCTGCTCTTCAT Y 2 1 2 1 101000 r 74 goat snp15431-scaffold1636-122585 1 13008167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779671 Affx-122936358 AX-385266772 1 13427553 GTTTAAGAATGCTTTCTTTAAGAAAATGTGTTATC[A/G]CTTTTCTAGGAATCAAAAACATATGTCTTAGAATG R 2 1 2 1 101000 f 74 goat snp15430-scaffold1636-85104 1 13045365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418133 Affx-122947114 AX-123288481 1 13459847 TTGAGAGTTTAAATATCAAATATAATAAAATGAAA[C/T]GCTAGAAGCCTTTTGCAGGTAGATATCATTATCTT Y 2 1 2 1 103000 r 74 goat snp15429-scaffold1636-52810 1 13077639 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453263 Affx-122920399 AX-123323596 1 13493406 AAAAGGGCTATTAAGACAAATACTTGGATTTTTGG[C/T]TTGAGGTAATGGGTTTGATGCAGGTATCAATTGCT Y 2 1 2 1 201000 r 74 goat snp15428-scaffold1636-19251 1 13110947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800947 Affx-122959396 AX-385287862 1 13524719 CTTTATCCTGATAAAAATTCTAGACCTTAAAGTTA[C/T]TATGCTTAGATTCCTTACAAAAAGAAAAGAAACAT Y 2 1 2 1 101000 r 74 goat snp23407-scaffold235-11963 1 13147714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786271 Affx-122978627 AX-385273306 1 13553311 GACTGGTTTGGAGGATGGATTAAGACCTGAGTTTA[A/G]CAGTGCTAAATTTCAGGTGGTGTGAGATGCCCTTA R 2 1 2 1 101000 r 74 goat snp23408-scaffold235-40555 1 13177292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430273 Affx-122937295 AX-123300614 1 13622642 TTGTGCAAAATGCAGCAATTTTTAACTAGAAAAAA[A/C]TGAATAAAAGTCACAAATATATTAGCTGGACCCAT M 2 1 2 1 201000 f 74 goat snp23410-scaffold235-109886 1 13248265 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778157 Affx-122936603 AX-385265271 1 13655885 AGAGAGTAGGACCATTCAGGAAAATTAAGCTAGTT[A/C]TATTTAAGCATGGAGACTTAAAGAGTATATAGTGG M 2 1 2 1 101000 f 74 goat snp23411-scaffold235-143129 1 13282538 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428658 Affx-122938654 AX-123299000 1 13687769 TCTCTTCTTTAAACACCAAGTTAATTATGACTTGT[C/T]GGGGCCTCTGATGGTATCTGATGACCTTTGAGACA Y 2 1 2 1 201000 f 74 goat snp23412-scaffold235-175013 1 13314796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407352 Affx-122955280 AX-123277703 1 13719969 AGCTTATAAAGCCATTTAAAAGGCAATTACATTTG[C/T]GTCAAGACAAAAAAAGTCCCACGAATGTCACCTGT Y 2 1 2 1 201000 f 74 goat snp23413-scaffold235-207213 1 13347253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786059 Affx-122934327 AX-385273095 1 13752505 TTCTTATCACTGTCAAACTGTGGGTTTAGTAATCT[A/G]TTCATGCAAGTTGAATTTGATCTTGAGCAAAAGTC R 2 1 2 1 101000 f 74 goat snp23414-scaffold235-239749 1 13380150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777774 Affx-122924020 AX-385264892 1 13795356 GTAAGCATGAATGATTGTAAACCATTAACAAACAC[A/G]TGGAGTTTTCTCTACCAGGTAAATATGTCAAAATG R 2 1 2 1 101000 r 74 goat snp23415-scaffold235-282600 1 13423424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378662 Affx-122977089 AX-123249021 1 13833009 GGGGCAGTGACACATGGACTGTTTTCTTCTTATGA[C/T]AGAGGGGAGAGGCTCAAGAGACAATGGCAAACCAT Y 2 1 2 1 101000 f 74 goat snp23416-scaffold235-320253 1 13461890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778543 Affx-122942885 AX-385265655 1 13861982 ATTCTCTGTTAACTGTTGCATTAACTCTTCTGTCT[A/G]CGTTCAAAATGTTTCCAATTATAATATACCCCTGA R 2 1 2 1 101000 f 74 goat snp23417-scaffold235-349226 1 13491289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793152 Affx-122956230 AX-385280130 1 13892976 CATGTAAAGACGAAATGCACTCGTATAGTTATGTC[A/G]TCTTTCTGTCTTTCTACCTATTTATCTAAAAGTTA R 2 1 2 1 201000 r 74 goat snp23418-scaffold235-380220 1 13523428 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273563 Affx-1111833673 AX-519547176 1 13946393 AGAGACTGAAAGTCCAAAGAAAAATAAAAGGAAGA[A/G]AAGAGCTCCCTGATGACAGTGTTCTGCAGAAAAGT R 2 1 2 1 202000 r 74 goat GoatD01.001135 1 13946393 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441909 Affx-122928606 AX-123312246 1 13951768 TTAGGCAGAAGGGGAAGCTGAACTGAGATGTAGGT[A/G]CCACAGTAACCACCAGAAATTTTATAAGATATTTG R 2 1 2 1 201000 r 74 goat snp23419-scaffold235-439012 1 13583197 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476142 Affx-1251763644 AX-586011575 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20000 f 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 560378493 Affx-1251763644 AX-605230908 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20000 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562165159 Affx-1251763644 AX-606940571 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562165220 Affx-1251763644 AX-606940632 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 f 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562166389 Affx-1251763644 AX-606941797 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 38406347 Affx-122955437 AX-123276699 1 13994031 AAGACTGTTATTTCAGGGCTAAAAGTTGGGTATAC[A/G]TCAACTTAATGTTTCATTCCACATCTTCAAATGAG R 2 1 2 1 101000 r 74 goat snp23420-scaffold235-481275 1 13624612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394272 Affx-122964717 AX-123264627 1 14020087 GGATCAAACCCAGGTCTCCCACACTGCAGGCAGAT[A/G]CTTTACTAGCTGAGCCACAGAGGTCTATAACACTT R 2 1 2 1 103000 r 74 goat snp16371-scaffold1727-15166 1 13751034 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403289 Affx-122957850 AX-123273642 1 14077671 CTATGTTCCATTGTCAATTTATTCATCATTTAAAT[A/G]CAGTATCTGGACAGTTGCTGGAGGCATATGCAATA R 2 1 2 1 303000 f 74 goat snp16372-scaffold1727-72750 1 13807104 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451200 Affx-122921325 AX-123321534 1 14141421 TTTCCTGATATGTACTAAAAGAGATTAAAACTAAC[A/G]TAAGTCTTTAGGCTTAACATACATTGATTGAAGTT R 2 1 2 1 101000 f 74 goat snp16373-scaffold1727-136500 1 13871108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389377 Affx-122968398 AX-123259735 1 14169936 TCCCCTAGGCATCAAAATCTCATTTATGCATTTGT[A/G]GAGTGCCTGATTTACAGAATTTAAACGCCTAGGGA R 2 1 2 1 101000 f 74 goat snp16374-scaffold1727-165015 1 13899660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770450 Affx-122975358 AX-385257616 1 14203008 TAGAGAGATGGTTTTTGCAGTCAGCTTCTCTTATG[A/C]CTTTCACCACTGAAATATAGCCATTTAGAAATGAT M 2 1 2 1 201000 r 74 goat snp16375-scaffold1727-198087 1 13933570 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776905 Affx-122939812 AX-385264029 1 14231667 TTCTCAAAAACTACACACCAAATTTACTGGATATT[A/G]TCAGTAAATTTAACCCAATGGTTCAGTTAAAATGA R 2 1 2 1 201000 r 74 goat snp16376-scaffold1727-226746 1 13963234 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421568 Affx-122943849 AX-123291915 1 14272734 ACTCCTTAGCCTGATATTGATGGACTTCCATATGG[C/T]ATTATCTTTCTGTTTAAGGACACCTTACAATTTGG Y 2 1 2 1 101000 r 74 goat snp16377-scaffold1727-267813 1 14010404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419568 Affx-122945403 AX-123289916 1 14352381 ATTTAGCTAAAGCACAGGTTACCCAGACTGAATGA[C/T]TAGGGAAGGTAGCTAATGATCAGCTTCCTATAGGA Y 2 1 2 1 101000 r 74 goat snp16378-scaffold1727-347460 1 14089551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773611 Affx-122941871 AX-385260751 1 14384893 TAATAGTTCAGTGCTGATTCCAAATTTCCCAAACC[A/G]GCAATCTTACTTGTGTCAAATCCTATAGCATTTGC R 2 1 2 1 101000 f 74 goat snp16379-scaffold1727-379972 1 14122278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421235 Affx-122944120 AX-123291582 1 14421890 GATTATGAGCAACACTGTTGCATACCATTTTCTCC[C/T]TCAAACGCATTTTCTGCCTCTTAAAATATTTCTGC Y 2 1 2 1 101000 f 74 goat snp16380-scaffold1727-416969 1 14160137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439962 Affx-122929817 AX-123310299 1 14463980 GATTAAATTTCAGTCAATGTTTTGATTGAATTACT[A/G]TTCCCACCAGTTGACCCTTGCTGAACACTTTTGGA R 2 1 2 1 201000 f 74 goat snp16381-scaffold1727-459059 1 14202454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802492 Affx-122925854 AX-385289396 1 14503982 CTCATTTATACAATAAAGGAGTTACACTAGATAAA[C/T]GCTAATATTTTATTGGGTCCAACACTGTATAATCT Y 2 1 2 1 101000 r 74 goat snp16382-scaffold1727-499061 1 14242917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792970 Affx-122945814 AX-385279948 1 14544545 GGATAAACTCTCAAATTACACCTATAAAGAAGTCC[A/G]TGGCGAATAAACATGGCAGTGTAGTAAATGCACAC R 2 1 2 1 101000 r 74 goat snp16383-scaffold1727-539624 1 14283599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376968 Affx-122977756 AX-123247327 1 14589393 CAAGATTGCTTAACTGTAAAGCACAAGATATGCCC[G/T]AGGTCATTATGTGAAAGAAAAATGCTACCACTCTT K 2 1 2 1 101000 f 74 goat snp16384-scaffold1727-584472 1 14329021 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781886 Affx-122967570 AX-385268967 1 14633153 ACTCTCTACTCAACACACTGCCTCCTTTTACATGA[C/T]AAACTATCTCTGATAATAGAAAGAAATCAGCCTCA Y 2 1 2 1 101000 f 74 goat snp16385-scaffold1727-628232 1 14370655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413538 Affx-122950612 AX-123283887 1 14697913 AAGAATCCATTTAGTACCCAACCATTCAGCCAGAA[C/T]GCTTCAACAACCAATAACGTGATGTGAATTCTGAA Y 2 1 2 1 101000 r 74 goat snp16386-scaffold1727-692992 1 14435997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437449 Affx-122932393 AX-123307787 1 14732095 TTCTTGCAACATTTTGGGTAATTTTCTGAAGTGTT[A/C]GTGAGCCAAATTACTGATCTTCATGAAGATGAGTA M 2 1 2 1 101000 r 74 goat snp16387-scaffold1727-727174 1 14470321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401317 Affx-122959843 AX-123271670 1 14779903 AAGATAAAGTTTAAATTATTTCTTCATCTTCATAT[A/C]GAAGTCAACTGCCAATGAAGTTTCATCCTATTTAA M 2 1 2 1 101000 r 74 goat snp16388-scaffold1727-774982 1 14517944 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790403 Affx-122941182 AX-385277406 1 14814983 TCACAAGTTACAGATTGGTAAAAGGAAAATGCTAC[A/G]GAAAATAACAATTTTTGATGAAGCAATCAAAATCG R 2 1 2 1 101000 f 74 goat snp16389-scaffold1727-810062 1 14553692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795177 Affx-122963974 AX-385282135 1 14869528 TGGAATGTGAATTTCACTACAACTCTGATTAAAGC[C/T]TTCTCTTTTAAGTCCTTAATAGTTGTTTGTCTCAT Y 2 1 2 1 101000 f 74 goat snp22899-scaffold2280-49319 1 14608347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409299 Affx-122953102 AX-123279650 1 14883481 CAGGGATACAAAAATAGCCTCTCTGTAGTAAAAGC[C/T]TCACAAAAAGTCTGGCATGGTTGCTCCATATTATT Y 2 1 2 1 101000 f 74 goat snp18406-scaffold1864-4910 1 14630040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777847 Affx-122926417 AX-385264964 1 14920942 CTTTCCAGATTTTGAGTAGTGAGAATAGAGTTCTC[A/G]AAAAACAGACATTGTTCAGAGGGTGAGAAATAGAA R 2 1 2 1 102000 f 74 goat snp18407-scaffold1864-42371 1 14668052 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802027 Affx-122930862 AX-385288931 1 14960526 TTCTTGTCTTCAAGCAATCATGAGTTTCAAGAATC[A/G]TGAACATGCCTTCTCTTGTCACAACTAAAATATGA R 2 1 2 1 101000 r 74 goat snp18408-scaffold1864-81955 1 14707743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426792 Affx-122940542 AX-123297138 1 15040338 GACTGAATGATGATTACTAAGATGCTTAAAGACCA[C/T]GCAACTTTATTTAAGGCAGGACTCACAAATATCTC Y 2 1 2 1 101000 f 74 goat snp18410-scaffold1864-161767 1 14788828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443674 Affx-122927182 AX-123314011 1 15093499 GTGTGGGACTCTTACGACCCCACACAGAGTAGCCT[A/G]CAGGGCTCCTCTGACCATAGGAATTGTCAGGCAAA R 2 1 2 1 303000 r 74 goat snp18411-scaffold1864-214928 1 14841795 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397641 Affx-122962616 AX-123267996 1 15125512 GTTCATTTGAATTTGGGGTTAATATTACCAGTAAC[A/G]GAATACAAGGTGAATATTAAATATGATATTATATT R 2 1 2 1 101000 f 74 goat snp18412-scaffold1864-246941 1 14874511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794023 Affx-122946782 AX-385280992 1 15180968 TCAAATAGTCAATTTATCATTTCATGGAAGTACTC[A/G]TTGCCATTGTTTCCACATTTCTAATCTAAAACATC R 2 1 2 1 303000 r 74 goat snp18413-scaffold1864-302397 1 14929867 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384190 Affx-122972406 AX-123254548 1 15248695 CAGAGTCCTGGAATCAGTCATTTCTCTAAGGAGCC[A/G]TGGTTCCCTCTATTGGAGAGTTATATTACAAACTA R 2 1 2 1 201000 r 74 goat snp18415-scaffold1864-370124 1 14998569 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410729 Affx-122952711 AX-123281079 1 15315349 CAAATCTTTTGTCCCACCTGATTACTGCAACCATG[A/G]GTTTACCCCATTTTTCCTGCCCAAATCATTAGGGA R 2 1 2 1 101000 r 74 goat snp18417-scaffold1864-436778 1 15067323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389367 Affx-122968456 AX-123259725 1 15380937 TAAACAAGTTTTTCTTTGTTGCATTTCAAAACACC[A/G]CTAAAATGACAAGAGTCATATAGGTCCCCAAGAAC R 2 1 2 1 101000 r 74 goat snp18418-scaffold1864-502366 1 15133883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775400 Affx-122923272 AX-385262531 1 15417113 TCCATGGGGTCTTGAGTTGGACACAAACGTGCAAA[G/T]AATTAGTGATTAGTTAGTCATAATATTTGGTACAA K 2 1 2 1 101000 f 74 goat snp18419-scaffold1864-538542 1 15169302 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786197 Affx-122951076 AX-385273232 1 15458548 ATATGGATGCTATTCCAAATGCAGTGTTCTGAAAT[A/G]CAGGTAACACTGAAGAATGGGTATTTTCCATTTGG R 2 1 2 1 102000 r 74 goat snp18420-scaffold1864-579977 1 15211781 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419955 Affx-122945207 AX-123290303 1 15490697 CTAACACATAGCTTATATGTTATATATTTTTAGCT[A/G]CATAGTCTTAGATCCTTTTTTTATTTCATACAGAC R 2 1 2 1 101000 r 74 goat snp18421-scaffold1864-612126 1 15243638 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451209 Affx-122921972 AX-123321543 1 15528492 AGAGTATAAGATCTCATTTGCAGATAAATAGCTCA[C/T]AGGATTTTGAAGCATAGATTTGTGGTATCTTTGCT Y 2 1 2 1 101000 r 74 goat snp18422-scaffold1864-649921 1 15281751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409565 Affx-122953589 AX-123279916 1 15580030 TTCATACCATAAACATTTTAGCATCTTCTTCATAA[C/T]GACAGGCAGATAGCATTATATATACCTGTAACACG Y 2 1 2 1 201000 f 74 goat snp18423-scaffold1864-701459 1 15333412 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272600 Affx-1111832847 AX-519546313 1 15607879 AAACGCATGAGCCAGACAGCACTAGCCAAGAAAGC[A/C]TTCAGTTTCCTGACCCCACATAACATGACCCTAAA M 2 1 2 1 101000 r 74 goat 1_15607879_AF-PAKI 1 15607879 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798617 Affx-122941262 AX-385285550 1 15625874 GAATCATTTCATGTAGTTTCCCTCATAGAACTATG[C/T]AGACATTTTCTAAATGTATCAGTCTAATTTTTTCT Y 2 1 2 1 101000 f 74 goat snp18424-scaffold1864-747303 1 15377225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451838 Affx-122921462 AX-123322171 1 15675078 TGTCTGTGTATGCTTAGATACAATGACTATTCTCA[C/T]GTTTATGGTCATCCTTGTCATTCATGAAAATAGGG Y 2 1 2 1 101000 r 74 goat snp18425-scaffold1864-796507 1 15423607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385137 Affx-122971766 AX-123255495 1 15713247 CACACTAGAACTACTTAACAGAATTAAGTTTCAAA[C/T]AGGTCTGAGGAAAAACAACAACAAAACAAACAAAC Y 2 1 2 1 201000 f 74 goat snp18426-scaffold1864-834676 1 15461775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388076 Affx-122969516 AX-123258434 1 15750262 GATTTATTATTACTTTCCCAATCACCATTGCTTTG[C/T]ACTTCTACAAATACTAACAGACTCTTTGTTACTTT Y 2 1 2 1 101000 f 74 goat snp19490-scaffold197-29113 1 15499271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388467 Affx-122969244 AX-123258825 1 15809457 TAGATACTTAAAACAATGTCACTCTACTCAGTGGG[C/T]ATTTCTACACAAATACATAATAGGTTCGTTTTAAA Y 2 1 2 1 201000 r 74 goat snp19491-scaffold197-88308 1 15558791 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412411 Affx-122951437 AX-123282760 1 15865002 AGGTGAAGCAGTTTCTGCAGACCACAGGCTGCAGC[A/G]AAATTGTTCAAAAACGTCTGCTAAATGTTGCACAG R 2 1 2 1 101000 r 74 goat snp19492-scaffold197-143853 1 15607985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789768 Affx-122976768 AX-385276776 1 15898241 TAAAACTCCTTAATGAAGAGATGGTTTATAAAAGT[A/G]TATGCCGGAATGATGAAGAGCCACTAATAAAAATA R 2 1 2 1 101000 r 74 goat snp19493-scaffold197-177092 1 15641529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386367 Affx-122970852 AX-123256725 1 15930305 CATAAACATCAAGCTCAGATTTTTCATTTTAAGTT[A/G]CAGGACACTATGAATTTCCTTTCACTGGTTGACAA R 2 1 2 1 201000 f 74 goat snp19494-scaffold197-209156 1 15673363 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801207 Affx-122951951 AX-385288120 1 15961397 TTCTTACATATTAGAGGGAGCAAAACAGACCCTAC[A/G]TTAAATCACACTATTAGGACCCTATTATTTGGTGA R 2 1 2 1 101000 f 74 goat snp19495-scaffold197-240248 1 15704998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423204 Affx-122942714 AX-123293550 1 15992368 CTTGAATTTTTTCTGAAATTTGTCAAATCCAAGTA[C/T]ATCACCAGGTGTTTTGGAACATCTGTCAGCTGCAA Y 2 1 2 1 101000 r 74 goat snp19496-scaffold197-271219 1 15735873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408205 Affx-122953854 AX-123278556 1 16050629 TGGTTCACAGGAAGACAAAATATGCAATTTTAAAA[C/T]GGTTGTGATTTTGAGGGGCTCTCTATTTGTTCTAG Y 2 1 2 1 303000 f 74 goat snp19497-scaffold197-329480 1 15795171 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418510 Affx-122946428 AX-123288858 1 16095004 TACAAATCCTGTTCAGATTCACTAGTTTTTCCATG[C/T]GCATTTTTTGGGTGTTAGTGTTATGTAATTTTATC Y 2 1 2 1 103000 f 74 goat snp19498-scaffold197-373855 1 15839481 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386024 Affx-122971491 AX-123256382 1 16141683 AAGATCCTAGAGGCTACCTTAAGCTCCTTAGCATG[C/T]AGTCCTTCTCCATCTTCTTTACTAGCAATGAAGTT Y 2 1 2 1 101000 f 74 goat snp19499-scaffold197-420534 1 15884859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453840 Affx-122919543 AX-123324173 1 16194476 TTTACTTCTTTCTTCTTTCCATATGGCAAAGTTTC[A/G]TGCTTAGTCAATGAGGTGTGTGAAAGTATGATGAA R 2 1 2 1 101000 f 74 goat snp19500-scaffold197-473327 1 15938301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797487 Affx-122959478 AX-385284426 1 16247710 AGTAGTTTTGAAAGGCAAGGACTTTTCAAATTATT[A/G]CTCTCTGTTGCTTTCTCAATTGGCTAGCGCCCAAA R 2 1 2 1 101000 r 74 goat snp19501-scaffold197-526561 1 15996266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768684 Affx-122921870 AX-385255862 1 16336958 ATTGATAAACTGCTTTAGGTTGAGAATAAAACTTC[A/G]TGATTATTGGGCCAGATTTTACAAATGCTTGTTAT R 2 1 2 1 101000 r 74 goat snp19503-scaffold197-615809 1 16086430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773072 Affx-122945495 AX-385260215 1 16385627 AGATAAAGGACAAGAAAGAGATGGCAGATTAACTG[C/T]TCAATCCTCCTTTACTGTCTTTCACAATCATTGAA Y 2 1 2 1 101000 f 74 goat snp19504-scaffold197-664478 1 16135116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770863 Affx-122976015 AX-385258027 1 16417387 TCTACTGGTAAAATTTTAGATTCTTTAGAGAAGGT[A/G]CCCTAGATGCTATCTAAAATAATGTAGAATAAATA R 2 1 2 1 101000 f 74 goat snp19505-scaffold197-696238 1 16167120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439099 Affx-122931116 AX-123309436 1 16492927 CAAGAATTCAAATCCAAGACTCTCTCTCCAAGGCC[A/G]TTGTTTTACCAGGGTACCATAGAATTTGTAAGAAA R 2 1 2 1 201000 r 74 goat snp19507-scaffold197-771778 1 16243259 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397952 Affx-122961913 AX-123268307 1 16532941 CACACAATTAAGGAATTTAGCTCTTCAGAACTTCC[A/G]CATGGTAGTTTATGTAACCATTGATGTTCAACAAT R 2 1 2 1 201000 r 74 goat snp19508-scaffold197-811792 1 16283586 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413887 Affx-122949843 AX-123284236 1 16597410 CTTTACAAATTGTGTTCTTTCTTTCTTTGGAATAT[A/G]ACATTTAAGAGATGTTCTTTTGGCATCATTTGCTG R 2 1 2 1 103000 r 74 goat snp19509-scaffold197-876261 1 16347912 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432973 Affx-122935272 AX-123303314 1 16640472 CAAGAGAGATTTAGCCGGGATGAGTCTCCCAGCAC[G/T]CTCCCCAATGGAAAACACATAGAACTTCACAGTTA K 2 1 2 1 201000 r 74 goat snp19510-scaffold197-919323 1 16390838 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385300 Affx-122971684 AX-123255658 1 16713835 AATTATAGAAGCAAAAAATAAAACCCTGAAAAAAT[A/G]TGGCTCATTAATAGCAATTCTTGCTGACAAAATAG R 2 1 2 1 103000 r 74 goat snp19512-scaffold197-992686 1 16462542 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777485 Affx-122954100 AX-385264605 1 16805343 TGACTTCCCCAGTATCATACAGCTGACCTGAGCTA[C/T]AGCTGAACTGTAAGTTTCAGATCAAATCTCTTCTC Y 2 1 2 1 102000 f 74 goat snp19514-scaffold197-1084194 1 16555901 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415318 Affx-122948806 AX-123285667 1 16859866 AATCCACCCAAAAAAAACACATTATTTCAAAAATT[A/G]CATCAGGTTGGAAGTAGGTTCCTTCCCCATCAGAG R 2 1 2 1 101000 r 74 goat snp19515-scaffold197-1138717 1 16607936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788330 Affx-122962306 AX-385275348 1 16916269 TTCTGTGGCAATTTCCAATTTGAGACAATCTAAAG[C/T]ATGTTAGGAATACAAGTCTGGAGGTATATTTCTTA Y 2 1 2 1 101000 f 74 goat snp19516-scaffold197-1195120 1 16665610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772068 Affx-122974700 AX-385259223 1 16949442 GTTTCTGTACCCTCTTGTCTCTTGTGAGTTGTCCA[G/T]AATTATATACAGGTTAAATATTACTTTATATTTAG K 2 1 2 1 202000 r 74 goat snp19517-scaffold197-1228293 1 16700132 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422974 Affx-122943004 AX-123293320 1 17045845 GATGTCAGGACATTAATCTCTCAGGGGCAAAAAGA[G/T]TCATCAACATACTGTTTGTCTCCTTAGGTCACAGA K 2 1 2 1 101000 f 74 goat snp19519-scaffold197-1324696 1 16797730 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430986 Affx-122936693 AX-123301327 1 17079512 GTGAGCCTGGGGAGATAGATCAGCCCTTTCTCTCT[A/G]CATATTCCTACCAACAAGCATGGACTTTCTTCCTA R 2 1 2 1 101000 r 74 goat snp19520-scaffold197-1358363 1 16830539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769234 Affx-122969762 AX-385256407 1 17112156 GAATTTTAGTCTTTCCATGTATTCTTAATTATTCA[C/T]GGTAATCTGACTAAGGATTCATAAGCCACTTGCTA Y 2 1 2 1 101000 r 74 goat snp19521-scaffold197-1391007 1 16863396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422698 Affx-122943655 AX-123293044 1 17180168 AAATCCACTTGGCCATCTCCCAGTCTGTCTCATAC[A/G]CAGAATATTTTTGGTTCTTTCCCCTCCCATTTGTT R 2 1 2 1 201000 r 74 goat snp19522-scaffold197-1459019 1 16931963 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770833 Affx-122938466 AX-385257997 1 17290035 ATTAAACTTCAGGTAAAACTGTCCCTTAACTAAAG[C/T]GCAAGCAGGGTTAAGTGAAATCAAAGTAAAAGCTG Y 2 1 2 1 101000 r 74 goat snp19524-scaffold197-1568886 1 17037791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794956 Affx-122963618 AX-385281916 1 17343621 CTTAGAAATAATTGATGAAGCAGATAAAAAATATG[C/T]AAAACTCTCAATGAAAACTTAAAGATTCCAGAAAG Y 2 1 2 1 101000 r 74 goat snp19525-scaffold197-1622472 1 17091020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777541 Affx-122932081 AX-385264660 1 17373796 AAGCACCACACAAGTGTAAAGCAATATTTATAGTT[A/G]TTACTTAACCACTTTTATACCTTTTAGCTTACCAC R 2 1 2 1 101000 f 74 goat snp19526-scaffold197-1652647 1 17121500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387263 Affx-122970553 AX-123257621 1 17404086 AGCTTGGCTACAGAAAGTGCTCACAGGTGAATATA[C/T]ACACTTCAGTCTCCAGAATCCTGCCAGCATTTTAT Y 2 1 2 1 201000 f 74 goat snp19527-scaffold197-1682937 1 17151965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377056 Affx-122978295 AX-123247415 1 17462381 AATTCATTGTGCTTTAAAAGCTCCAAGTACAAATA[C/T]AATAATGAGTATACATAAAACAGATGAACTCATGG Y 2 1 2 1 101000 f 74 goat snp19528-scaffold197-1741232 1 17210716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397671 Affx-122962592 AX-123268026 1 17546289 ATTTCAGCAAAGATTAGAGTAAAAAGTATTGGCCC[A/G]TGATAAATGGGTAACAGTGGTACTGAATGCATTGC R 2 1 2 1 101000 f 74 goat snp29443-scaffold3180-212691 1 17334849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797283 Affx-122970022 AX-385284222 1 17580079 TTGAGATTCTCCTATGACAGTATCATATTTTAAAA[C/T]ATTTGTCTTCAAAGGGAAATTGCTAATTATCCTGC Y 2 1 2 1 202000 f 74 goat snp29442-scaffold3180-178901 1 17370077 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779419 Affx-122929951 AX-385266522 1 17625673 ATTGGGAAAAATCAAGTTAGAATTCTTATCGTTTA[G/T]AAAAGCACACTTTGAGGAATTAAAAAAGACTTTAA K 2 1 2 1 201000 r 74 goat snp29441-scaffold3180-133307 1 17415537 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799183 Affx-122956427 AX-385286113 1 17754620 CATATCCTTTCTTTGATTGGTACTTGAGGATGTGC[G/T]TAAGTAAAGTGAGGGAGTAAATTAAGAAATAATGC K 2 1 2 1 101000 f 74 goat snp29439-scaffold3180-4360 1 17545808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403912 Affx-122957480 AX-123274264 1 17759900 TACCAATTGAGGAACAGCTTTTATGAGTAGACTTC[A/G]TGGAAAAGATTGATGCTTGTACCCATTAATAATAT R 2 1 2 1 101000 f 74 goat snp2705-scaffold1077-1700112 1 17569339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764610 Affx-122931537 AX-385252252 1 17808446 GGTTGGGATTTATGCTTCCCTAATGTCAGGGGCAT[A/G]CTAAATAATTATCCTTTGTGCAAACACATTGAAAA R 2 1 2 1 101000 f 74 goat snp2704-scaffold1077-1651566 1 17617912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397101 Affx-122962701 AX-123267456 1 17843940 GCTTCTTAATAATAGGACTGGAATGAAAACTTCCT[A/G]GTACTGAATCTCCATCTCACTGCTTTTGGTGTGTG R 2 1 2 1 101000 r 74 goat snp2703-scaffold1077-1616072 1 17653273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779271 Affx-122968770 AX-385266375 1 17908915 CCTCTCATTATTTCCTCAATCAAGATGTAGAATAA[C/T]TTTGCCAACTTTTTACTTACTATGACATTTCTCAT Y 2 1 2 1 202000 f 74 goat snp2702-scaffold1077-1551097 1 17719089 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420469 Affx-122944877 AX-123290816 1 17945287 TTTAATTTATGGAATATCCTCAGCTTCCCAGGTGG[C/T]GCCTGATTCTTGGCATCACTGATGGTTCTTGCTGG Y 2 1 2 1 201000 r 74 goat snp2701-scaffold1077-1514725 1 17755756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476145 Affx-1251763647 AX-586011578 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 4 1 4 1 20000 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 539476400 Affx-1251763647 AX-586011804 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20000 r 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165135 Affx-1251763647 AX-606940547 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165389 Affx-1251763647 AX-606940800 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165414 Affx-1251763647 AX-606940825 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 r 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165459 Affx-1251763647 AX-606940870 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165550 Affx-1251763647 AX-606940961 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165997 Affx-1251763647 AX-606941407 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 38375649 Affx-122978689 AX-123246008 1 17997133 CAGTTCCCATCCCCTGTCACATGTTTAAGGACCAC[A/G]CATCAGCAGTTGGCTTCTCTCTTCTGTAAAATCAT R 2 1 2 1 101000 r 74 goat snp2700-scaffold1077-1462879 1 17808217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775878 Affx-122939225 AX-385263009 1 18053497 GTGTAACTATAATATACAGAGCCATTCAAATACAC[A/G]TTATAAAGAGAATGAAAAGGTACCTAAAATAGCAT R 2 1 2 1 201000 r 74 goat snp2699-scaffold1077-1406515 1 17864847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450879 Affx-122922215 AX-123321213 1 18110254 CTCTGTATTTGGATGGCTAGAATTCTGTCCAGATT[A/C]TGCCTGTTTCATGAAGCGTTTCCTGAGTTCACTCC M 2 1 2 1 101000 f 74 goat snp2698-scaffold1077-1349758 1 17920803 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272602 Affx-1111832848 AX-519546315 1 18125748 AGACATGGTTTGATTTCTCTATATAGCTAATCTAG[A/G]GAGCACAGGATTGTTATTTTATCTAAAAGGGCTAT R 2 1 2 1 101000 r 74 goat 1_18125748_AF-PAKI 1 18125748 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445131 Affx-122926176 AX-123315468 1 18149506 AAATAATTATAGATTCACAGGAAATTGCAAAAATC[A/G]TACATGGAGGCTCCTTGTTCCATTCATCCAGCATG R 2 1 2 1 201000 f 74 goat snp2697-scaffold1077-1310506 1 17960341 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378282 Affx-122976870 AX-123248641 1 18198617 GAAATGGAGGTTTTCTAATTCCGGAATTTGGACTG[A/G]GATAAGAGTAAGGGGAAGGCATTCTGAGAGCTGGA R 2 1 2 1 201000 f 74 goat snp2696-scaffold1077-1261395 1 18014442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408302 Affx-122953778 AX-123278653 1 18253882 AAAACACTACAGTGTTCTAGAAATCACCTAGTTCC[A/G]TGTAATTCATAAGCCTTGGTTATGAAATGATTTCT R 2 1 2 1 101000 f 74 goat snp2695-scaffold1077-1206130 1 18069593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442467 Affx-122927942 AX-123312804 1 18307237 TCAATGTGCATGGAGACATTTAGCCCCAACTGAGG[A/G]CAGAGTTTTGAATAAAGAAGGAGAATTAAACACAT R 2 1 2 1 201000 r 74 goat snp2694-scaffold1077-1152775 1 18122998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392544 Affx-122966096 AX-123262901 1 18340697 CCAGAAGGAAAATAGCAGTAGTAGTGAGTCTCCAA[A/G]AAGACCTTTGACAATCCCCATCTCCTGGTCTTCAC R 2 1 2 1 101000 f 74 goat snp2693-scaffold1077-1119315 1 18156026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393881 Affx-122965126 AX-123264236 1 18376008 AAATAGGTATTTTTAATCTGATAGGCCACCTCATG[C/T]GAAGAGTTGACTCATTGGAAAAGACTCTGATGCTG Y 2 1 2 1 303000 f 74 goat snp2692-scaffold1077-1084004 1 18190341 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419179 Affx-122945722 AX-123289527 1 18436490 CCCTGAGAAAGCTGACTATAGGCTTATGCTACATC[A/G]TGCAAGACAGGGAAGAAGTCTCCTGGGGAAACCGT R 2 1 2 1 101000 f 74 goat snp2691-scaffold1077-1023522 1 18252605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430529 Affx-122937205 AX-123300870 1 18467996 TTCCTGCTTCCCTGCACATGTACACCCACACATAC[A/C]AATATGACTATGGCCACAGAAAACTTCTATGTCTT M 2 1 2 1 201000 r 74 goat snp2690-scaffold1077-992016 1 18284228 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768719 Affx-122960103 AX-385255897 1 18516828 TTGAGACACATGGAGCTCCTTCCTAGGAAAGGAAG[C/T]TATCTTAAACCAATGTATGTAAGATCATGTTTTCA Y 2 1 2 1 102000 f 74 goat snp2689-scaffold1077-943184 1 18333202 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776918 Affx-122954159 AX-385264042 1 18560891 TATTAGGGAGAGCCACTTGGTAAAGCTGTATATGC[A/C]TGTTAGGGTGCTTGTCAATATATTTGCTCTGATAT M 2 1 2 1 101000 f 74 goat snp2688-scaffold1077-899121 1 18377589 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782722 Affx-122976367 AX-385269794 1 18602527 ACAAACCTAAAGATTAAAAGATTTAAGGTACATAG[C/T]AATGCATCTCCACAAGTACAACATGTAGATCTTGT Y 2 1 2 1 101000 r 74 goat snp2687-scaffold1077-857485 1 18419764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382901 Affx-122973407 AX-123253259 1 18648980 AGTAGAGACAACCGTACTCCTGGTAGCTTCCAGGG[C/T]GATAGCTGTATTTTCTCTTTTACTACATTAGCTCA Y 2 1 2 1 101000 r 74 goat snp2686-scaffold1077-811032 1 18466695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386664 Affx-122970197 AX-123257022 1 18703429 ATCACAGAAACTTTGTAATTTGCCCAAGCTCACAC[A/G]TCTAGCAAATGGTGGAGCTGGAATTTAAGCACAGC R 2 1 2 1 202000 f 74 goat snp2685-scaffold1077-756583 1 18521280 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446519 Affx-122925027 AX-123316855 1 18734999 CTGAGCTACCAGGAGAGAAGAAATAAAGAATAAAT[A/G]TATCTTAATGTGCTACAGGAAACCAATGGATGAAT R 2 1 2 1 201000 r 74 goat snp2684-scaffold1077-725013 1 18553207 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432369 Affx-122935865 AX-123302710 1 18767669 ATCGACCCTTTAAAGTCATGAATTTTTCTGGGTCT[A/G]TCATTGTAGATTGGAGTCCAGATCATGGGCAATTC R 2 1 2 1 103000 f 74 goat snp2683-scaffold1077-692343 1 10051755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446110 Affx-122925792 AX-123316447 1 18800966 TATGTGGGCTGAGCTCAGTCATGCCCAATTCTTTG[C/T]AACCCCATGGATTCTCTATGACTATTGAGGAGCTT Y 2 1 2 1 202000 r 74 goat snp2682-scaffold1077-659046 1 18619442 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802762 Affx-122933466 AX-385289661 1 18834475 ACTTGGGGAAAAGAAATACAGATATTCATAGATTG[C/T]GGTAGCTCAGTATCTACTGAGTTAAAATTGGGGCC Y 2 1 2 1 201000 f 74 goat snp2681-scaffold1077-625537 1 18653095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430946 Affx-122936832 AX-123301287 1 18876050 TTTCATATAGCTGGAATGTCTGACAACTGCCAAAA[C/T]GAATAAGGCAGCACGGCAAGAGAGCCATAAAAGTT Y 2 1 2 1 102000 r 74 goat snp2680-scaffold1077-583962 1 18694091 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444059 Affx-122926856 AX-123314396 1 18905445 GTCACAAGCAAGTGCTGTGTTACAACTGTCCCACA[C/T]GAAGTATTTCTGTCTTTAGTAGACCACACTAATGT Y 2 1 2 1 201000 r 74 goat snp2679-scaffold1077-554567 1 18723440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445972 Affx-122925890 AX-123316309 1 18946938 TGTGGTGCTATGAGCATTTATTTCTATTGTATTTA[G/T]AACTCTTTTATTTCTCTTAAGTGTATACCGAGGAC K 2 1 2 1 101000 f 74 goat snp2678-scaffold1077-513074 1 18765410 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778145 Affx-122954334 AX-385265261 1 18987098 CATAATATTGATTCTTGATGGAGGAACATCATTCT[A/G]TATAAGGAACTACACTTCCTCCTGCCTACTCCCAC R 2 1 2 1 101000 r 74 goat snp2677-scaffold1077-472914 1 18805752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422853 Affx-122943095 AX-123293199 1 19019081 TCAGACTACTGAAGGGTGAAAGGTGGATTTAAGGT[A/G]AGGTATTTGCAGTTAGAAAGCCACTAGGTTGCTGC R 2 1 2 1 101000 f 74 goat snp2676-scaffold1077-440931 1 18837735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393521 Affx-122965799 AX-123263877 1 19067346 TCAAATGGAAAACCTCTAACTTAAAAACACAATCA[A/G]TGCAAACCACAGCTCTTTCATACAATCTTCAAGAA R 2 1 2 1 101000 r 74 goat snp2675-scaffold1077-392666 1 18887414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800846 Affx-122969247 AX-385287761 1 19098932 AGCCAAGTATGGCTCTTGGGGAGTGAGAATGAAAG[C/T]GGTAGATGATGAGGATTATTGCCAAAGGGACAGAC Y 2 1 2 1 101000 f 74 goat snp2674-scaffold1077-361080 1 18918879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417996 Affx-122946669 AX-123288344 1 19136201 TTGGCCATTGCTTTATATAACACACAGGAGTCTAT[A/G]TTTGGAATTCGTTAGTCTTCTCTCACCTGTACATC R 2 1 2 1 101000 r 74 goat snp2673-scaffold1077-323811 1 18956296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425636 Affx-122940894 AX-123295982 1 19199769 AGTCTATATAAAGGCTCACCCATGATAGTTTTAAA[C/T]GGCTTGCTTAGTAAAATCACTTTCCCTGTCATTTA Y 2 1 2 1 201000 f 74 goat snp2671-scaffold1077-260243 1 19019546 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384292 Affx-122972292 AX-123254650 1 19229782 AGAGTTTGGGATAAACTACTCCATCTGCCTGGAAG[C/T]GAATATCTGCCACATCTTCTGTGTTTGTTCTTCAG Y 2 1 2 1 101000 f 74 goat snp2670-scaffold1077-230230 1 19049735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379954 Affx-122975641 AX-123250312 1 19264942 ATGTCTAAGAAGGCCTTTTCACTAATTCTGTAGTC[A/G]GAATCCAGGCTCCAAATTAGACTGATAGCATATTT R 2 1 2 1 101000 f 74 goat snp2669-scaffold1077-195070 1 19085024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277694 Affx-1111835977 AX-519551193 1 19290545 TATTCTATTCTTTTATAAAGATGAAAATAAAATAT[A/G]AACTAAACATCATAGTATTTAAATCATTCTGCTTA R 2 1 2 1 101000 r 74 goat Random2.2K-21 1 19290545 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790946 Affx-122975990 AX-385277943 1 19299651 CAAGTATGCCAATTTTGTCACATAATCATTAATGA[A/G]TAAACATGGGTTCAGTGGACTCTGGTTCGTTTTAC R 2 1 2 1 101000 r 74 goat snp2668-scaffold1077-160361 1 19119513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429240 Affx-122937913 AX-123299582 1 19354423 AGCAGCATACAGAGTATTATGCTAAACCGTTATAG[C/T]GCCTCTGTTAAACACCTTTTAACTAATGTAGTAAA Y 2 1 2 1 101000 f 74 goat snp2667-scaffold1077-105589 1 19174073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435943 Affx-122933540 AX-123306282 1 19397167 TGTGGAACAGTAGGAAACTTTTTAAAAAATGATAG[C/T]ACTATGCATGTTCTGACTTGAGAATTTTCCATAAT Y 2 1 2 1 103000 r 74 goat snp2666-scaffold1077-62845 1 19217337 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438312 Affx-122931358 AX-123308650 1 19457159 ATTTAGTTCATATACTTAAGTATGCAGGCAGCAAA[C/T]GGAGGAGCTAGGGGGCAAAGTCCAGCCCTGCTGTC Y 2 1 2 1 201000 f 74 goat snp2665-scaffold1077-2853 1 19277280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435233 Affx-122934083 AX-123305573 1 19509817 AAGGAAAACAGAAAAATGCAAACTCCTATAGAATC[C/T]GGTCTACATCATGACTCCTTTGCATCTTATCGAGT Y 2 1 2 1 101000 r 74 goat snp56449-scaffold889-49706 1 19330053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443239 Affx-122927558 AX-123313576 1 19542010 CTCATAAGGAAAGAATTGGAATGAAAAGATGTAAA[C/T]AATAGTTCTAAGTTAAAAGAGAATGCAATCTCTGT Y 2 1 2 1 201000 r 74 goat snp56450-scaffold889-81899 1 19362028 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778988 Affx-122957579 AX-385266095 1 19577894 GTATGCCAAATATCATCACAATCAACTTTCATCAT[A/G]TATTCCTGAGTAGTTTTCAATCTCAGGTGTTTCTA R 2 1 2 1 101000 r 74 goat snp56451-scaffold889-117783 1 19397799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417692 Affx-122947461 AX-123288040 1 19609811 CTCATTGTCATTTACCTCTCAGGCTCCACCTCCCA[C/T]GGATTCGGGGATTATCTGCTTTGTTCACTTTTACA Y 2 1 2 1 101000 f 74 goat snp56452-scaffold889-149700 1 19429813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448736 Affx-122923832 AX-123319072 1 19651658 ATGCTCTTTCCTCAAAGGATCATTTCATAGCAGCT[A/C]TATGACAGGCTAAAAATCAGAACATGTTGTTCCTT M 2 1 2 1 201000 r 74 goat snp56453-scaffold889-191547 1 19471380 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777163 Affx-122922551 AX-385264286 1 19683465 GCTACTGTTGCTATATGATGGCACAGTTGAATAAA[C/T]GTGCCACAAAGCCCAAAACATTCATTGATCTTTTT Y 2 1 2 1 202000 r 74 goat snp56454-scaffold889-223354 1 19503096 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397862 Affx-122962451 AX-123268217 1 19712959 TATTAAACACTGGCAACTCCAGGATATGATCTATT[A/G]TAACTTTGATTTTCTCATTTGTATAATACCAACTA R 2 1 2 1 201000 r 74 goat snp56455-scaffold889-252848 1 19533214 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431072 Affx-122936632 AX-123301413 1 19757651 AAAGTAACATTTTTTTTCTTTAATTAAGATGTTCC[A/G]CATTTACTCAATCACTCTACATGCTGTTAAACATC R 2 1 2 1 101000 r 74 goat snp56456-scaffold889-297540 1 19577868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454302 Affx-122919259 AX-123324635 1 19795515 TTTTAGTAGGCAAATTAAAATATTTAGCCTCAATT[A/G]TATTTCAAATGTACAATTTAAAGTCAGTGACATAA R 2 1 2 1 303000 r 74 goat snp56457-scaffold889-335404 1 19616232 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796985 Affx-122966832 AX-385283926 1 19856019 GAACTATGTTTAGCTTCACAGTATATATACATTTG[C/T]ATTATGGAAATATGGAAAGGAAAACTAACTGGGTC Y 2 1 2 1 101000 r 74 goat snp56459-scaffold889-395908 1 19677244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390870 Affx-122967812 AX-123261227 1 19890667 TTTCTAGAAGAGTTGGATCGGGGGCAGATCCTCTC[A/C]TGTCATCTTCCTGTCCTCACATAGATTCACTCACT M 2 1 2 1 101000 r 74 goat snp56460-scaffold889-430556 1 19711896 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782738 Affx-122961124 AX-385269810 1 19944890 TTTTACTGTAATCCTATTTTATAGTGGAGGAACTT[A/G]GGCACAGAGGAGTTGAAGAGTTCACTCAAGACCAA R 2 1 2 1 101000 r 74 goat snp56461-scaffold889-484779 1 19766969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384484 Affx-122973069 AX-123254842 1 20006375 TTCTTCCCTAAATGCTACTTCCCTAGTGTCAAAAG[C/T]ATCTTAGTTTTCACTTTTCTGACTGGAATCTTATA Y 2 1 2 1 101000 f 74 goat snp56462-scaffold889-546264 1 19828718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377290 Affx-122978117 AX-123247649 1 20061685 GGAGGCACTACAACCACCCCACATCTGTGAGTATG[C/T]GATATGGTAGATCCATGAACACGGGAAACAGTAAT Y 2 1 2 1 201000 r 74 goat snp56463-scaffold889-601574 1 19883705 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422036 Affx-122943619 AX-123292383 1 20093407 AATCTCTTAAACTAATAGAGCAAAATTAGCATGCT[C/T]TAAGTAGAACTTTCCAACTAGAATACCACATAACT Y 2 1 2 1 101000 r 74 goat snp56464-scaffold889-633296 1 19915406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418916 Affx-122946087 AX-123289264 1 20123791 ACTCTTTATGTCTCTCAGGTAACATGTATCACTAC[A/G]GTGATCCTTTGAGAAATTGAGGTGGAAACAAATTG R 2 1 2 1 101000 f 74 goat snp56465-scaffold889-663680 1 19946048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384639 Affx-122972155 AX-123254997 1 20161733 AAGTCTGCTTCTTGTAGGACTAAGAGATGTAATCC[A/G]CTGTTTCACTGGAGCCCTGTTGGTGTGGTAGTAAG R 2 1 2 1 101000 f 74 goat snp56466-scaffold889-701622 1 19985203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776762 Affx-122971179 AX-385263886 1 20198281 ATCATGTTATTGAGTCAGTTGCATGTAGTAACAGC[A/G]TTATCTATATCTTGAGATGTGTAATGTGTTTAACT R 2 1 2 1 101000 f 74 goat snp56467-scaffold889-738170 1 20022442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448211 Affx-122924229 AX-123318547 1 20226840 GTGGTATCAGTGCTAAGCTAGGATTGCATAGATTC[G/T]AAAAGTCACAATGGAGAGTAGGTATTTCTTGTACT K 2 1 2 1 101000 f 74 goat snp56468-scaffold889-766729 1 20051363 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454123 Affx-122919346 AX-123324456 1 20344598 TCAGTTTAGAGATAAATATCTTTGAACTCCTGATA[A/G]AGAAGAGCTATAGAAATAACATGTGCCATCTCAAG R 2 1 2 1 201000 f 74 goat snp56470-scaffold889-884487 1 20166884 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764892 Affx-122938902 AX-385252486 1 20385517 AGACATGAATGAAATTTGCTAGATTTTGTCACCTT[C/T]AGATGTTTTGTGAGGGTCTCTTTTCTGATTAATAA Y 2 1 2 1 101000 f 74 goat snp56471-scaffold889-925406 1 20208352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384496 Affx-122973059 AX-123254854 1 20415076 TCTAAATAATGCTTCTTACACCTTTATTCCAAATA[C/T]AGCTTTTAAGCATGTATCTTTGGCTTCAACCTGGC Y 2 1 2 1 101000 r 74 goat snp29894-scaffold325-4846 1 20238472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390554 Affx-122967215 AX-123260911 1 20524193 AGAGGCTCCTGCTGTCTCAAACTGTCTCCTTCACG[A/C]GATGACCATGAACTGGGCTCAGAAATGATTTGAAC M 2 1 2 1 201000 r 74 goat snp29897-scaffold325-113963 1 20348412 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419079 Affx-122945796 AX-123289427 1 20556486 GCCGAGGATATTTACCAGACATTATAAAATGCGAA[C/T]AACATAAAGAAGTTCTATTTGAACATACATGTCCT Y 2 1 2 1 101000 f 74 goat snp29898-scaffold325-146256 1 20380745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772526 Affx-122955048 AX-385259677 1 20609912 GAGACAGGTGAGCAGTTCATAAGAGCCATTCTTTC[A/G]TTTGAAAAATCAAGCACAGTCATCTGCCAGGGTTT R 2 1 2 1 101000 r 74 goat snp29899-scaffold325-199682 1 20435641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402171 Affx-122959190 AX-123272524 1 20646880 AAATTGTCAGTCAGTACTTAGACAATCAACATCAC[G/T]ATGGACATGCTGATCTAAAAATGGCTTTAGAGGAG K 2 1 2 1 101000 r 74 goat snp29900-scaffold325-236650 1 20472127 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272555 Affx-1111832850 AX-519546271 1 20660990 GTGAAATAGCTTTGGCTGACAGTATCATTTATGGT[A/G]AGCACTATGGCATTTTTTTTTATTACTAGTTAATC R 2 1 2 1 101000 f 74 goat 1_20660990_AF-PAKI 1 20660990 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440371 Affx-122929642 AX-123310708 1 20703081 AGAAGGGTTGCGTTCTATTTCAGACGTGTTGAGTC[G/T]AAGGTGACTTCAGGACAATCCAGGGAAGATGTTCC K 2 1 2 1 101000 f 74 goat snp29901-scaffold325-292851 1 20528559 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423480 Affx-122942574 AX-123293826 1 20738138 GTAGCTATTCCTGTGACTCATAACATTCATGAAAC[A/G]TTAAAAGTACTGTCTTTTTTAGAGTAGGGCCTCTT R 2 1 2 1 101000 f 74 goat snp29902-scaffold325-327908 1 20563688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800359 Affx-122930837 AX-385287281 1 20853430 CCTGAATAATAAGTCTACTTAGATGCTTGCTGGCT[A/G]CTTATTCAACATTCCAATATTTATACCCAAATTTG R 2 1 2 1 101000 f 74 goat snp29905-scaffold325-443200 1 20679854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382149 Affx-122974043 AX-123252507 1 20888598 AATGGAGTTATAAACCTCTCCACCTCTTTTTACTT[A/G]CCTCATTTAAAATTTATGGAATTTTGAACCCAAAA R 2 1 2 1 101000 f 74 goat snp29906-scaffold325-478368 1 20714937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790791 Affx-122948194 AX-385277791 1 20939595 GAAATTAATTAAATTTCCAAGTGATTGTCTGGACA[A/G]CTTGCAAGATTATAAGCGTTTGTTAAACAACAAAT R 2 1 2 1 202000 r 74 goat snp29907-scaffold325-529365 1 20765979 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770400 Affx-122920168 AX-385257566 1 20979083 TGTCTGAGATTGTGCTTTTCCCTAGCTAACTGATA[C/T]GAAACGGTCATTTAGGATAAAACTGAGATGTTGGG Y 2 1 2 1 101000 f 74 goat snp29908-scaffold325-568853 1 20805849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413771 Affx-122949929 AX-123284120 1 21033345 GTCATGCCAGTCATTACTCTCTTTGACTTACCTTG[C/T]GTTCTCAAGTCAATATGTTCCAGATTAATGAGGCA Y 2 1 2 1 201000 r 74 goat snp29909-scaffold325-623115 1 20860946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403339 Affx-122957813 AX-123273692 1 21071169 GATGGGCTTGAATAATAGTATAAAAGCTAATGAAT[A/G]GCCATGTAATGTGACATTTTAAAAGAGTATTATGT R 2 1 2 1 101000 f 74 goat snp29910-scaffold325-660939 1 20898678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800104 Affx-122974126 AX-385287027 1 21104239 TAATAGGTTGGACAGAGGTTGAGTATGACTATTAC[A/G]CCTAAGTGACTGTTTCATGGAGCTTCTAGCTGGAC R 2 1 2 1 101000 r 74 goat snp29911-scaffold325-694009 1 20931282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422495 Affx-122943308 AX-123292841 1 21164412 TGCACAGTTTAGGACTCCTCACCTCTCTTTTGTGA[A/G]CAAAAGAAGAATTGGCTAAAACTGGGATCATTTCC R 2 1 2 1 101000 f 74 goat snp29912-scaffold325-754182 1 20990291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405677 Affx-122956559 AX-123276029 1 21228213 ATCATCAATCAGTTACACAAAGTCTGAGCCCCACA[A/G]TATATTAGACTATTTGAGCACTGTTGAGTATGTTA R 2 1 2 1 201000 r 74 goat snp29913-scaffold325-817983 1 21054055 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278021 Affx-1111836134 AX-519551513 1 21345248 CCTGGCGCTTTCAAGTGTAAAAACTGCCTCATATC[A/G]GTGACAGATTCCATCCATTGTATTCATACCGGATC R 2 1 2 1 101000 r 74 goat Random2.2K-25 1 21345248 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797917 Affx-122977143 AX-385284855 1 21393278 CACCTTGCCTGGGTTAAGACCATTAAGGTAATGTG[C/T]GAAAACAAAGCACCAAGACTTTGCTCTTTTGCAAT Y 2 1 2 1 201000 r 74 goat snp29917-scaffold325-983048 1 21220232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415170 Affx-122949010 AX-123285519 1 21423543 ACATTTTACAAACCATGAACACCTTAAAATGTAGC[G/T]TAAGAAAAGCTTCCTATAAGCTTATTGACATCATC K 2 1 2 1 101000 f 74 goat snp29918-scaffold325-1013313 1 21250505 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380349 Affx-122975361 AX-123250707 1 21452884 CATTTAAAAGCAGGAGAAATGTAGACAAGATAAAG[C/T]GTGGATTACTTGAGTCAACTGAGGAAAATTACACC Y 2 1 2 1 101000 r 74 goat snp29919-scaffold325-1042654 1 21279864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446733 Affx-122924712 AX-123317069 1 21484685 AGAGCTTCAGAGGTTGATTGAGAAAAAATATTCAG[G/T]ATGAAAGCAGTAAAAAATGTGCTGCAGATAACATA K 2 1 2 1 101000 f 74 goat snp29920-scaffold325-1074455 1 21311623 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406363 Affx-122955421 AX-123276715 1 21515485 AAAATTTTAGAAGTTTAAGTGAGCTGCAACATCTG[C/T]AATTTCCAAAATTTTTAATGAAATCATAAATAACA Y 2 1 2 1 101000 f 74 goat snp29921-scaffold325-1105255 1 21342785 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404154 Affx-122957080 AX-123274506 1 21546410 AACATGAAAACCTATTTGAGAAAATTAAAAACTGT[A/G]CCACTGGACATAGAAGTCCTTATTAAAAACAGAAA R 2 1 2 1 101000 r 74 goat snp29922-scaffold325-1136180 1 21374409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429675 Affx-122937651 AX-123300016 1 21577560 ATTTATTCAGATATTTCATTACCAATTTACATTTT[A/G]TTTCTTTAATCTGCTATCATTCTCTGCTTCGATTT R 2 1 2 1 102000 r 74 goat snp29923-scaffold325-1167330 1 21405756 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770711 Affx-122924078 AX-385257875 1 21612084 AAACTCAATCCGTCTTTTCAGTGTCGCCTTGAATG[A/C]CAACTATGTCTTGGGAATTATCTGAATCTCTCAAT M 2 1 2 1 101000 f 74 goat snp29924-scaffold325-1201854 1 21440366 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782121 Affx-122947279 AX-385269199 1 21670755 TTGTCATTGTTACTGAACAATCTGAATTGATTGAC[C/T]CCGGAATGGATTTAAATCCCGTGGTAACCAGTCTC Y 2 1 2 1 101000 f 74 goat snp29925-scaffold325-1260525 1 21499298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379879 Affx-122975782 AX-123250237 1 21705211 CTGAGCAGAGATAGCCACTCTCAATTAATGTTGAG[A/C]TGGTTGGATGGTATCACCAACTCAATGAATATGAA M 2 1 2 1 303000 f 74 goat snp29926-scaffold325-1294981 1 21533826 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769862 Affx-122936774 AX-186027589 1 21774903 AAGTGAAAGTATCAACTAATTCAAATTGATTCAGA[C/T]AAGAAGGGAAATGTATTAGCTCACAAAATAGGAAG Y 2 1 2 1 101000 r 74 goat snp14115-scaffold1564-24142 1 24066270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442183 Affx-122928802 AX-123312520 1 21834677 AGTATCAAGAAAACTCAAGGAAAAACCATAATTTG[C/T]AATATCTATTTAAAAACCCTTTTTTCTTTTTTTAT Y 2 1 2 1 103000 f 74 goat snp14116-scaffold1564-83916 1 24005696 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798520 Affx-122952317 AX-385285453 1 21889667 CAGAATTGAAGGTACTGTAAGCCTTTGTAGGCAGC[A/G]TAATTAAAGTAGAGTGATTACCTCAATGCCAATAA R 2 1 2 1 201000 r 74 goat snp14117-scaffold1564-138906 1 23951761 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400054 Affx-122960770 AX-123270409 1 21921333 AGTCACTCAGTCGTGTCCAACTCTTTGCAACCCGA[C/T]GGACTATACATATTATATATCTCTTCATTCCTCTA Y 2 1 2 1 201000 r 74 goat snp14118-scaffold1564-170572 1 23919379 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776740 Affx-122968845 AX-385263865 1 21963656 TGAATAGAATAAAACATAATGAAGAACACATGCTT[A/G]CTTGGTGCTAATGACATAACGTTTTGCAGTTTTAT R 2 1 2 1 101000 r 74 goat snp14119-scaffold1564-212895 1 23864512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768406 Affx-122969435 AX-385255586 1 22005219 AGATCCCTCTTCTTGCCTGGTAAGAGCTCAGCTAA[C/T]GAGACTATCACAATTCAGCCAATAGAAAGCCTTTA Y 2 1 2 1 101000 f 74 goat snp14120-scaffold1564-254458 1 23823245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424853 Affx-122941346 AX-123295199 1 22042592 TTCTTTGCCAGCACTGTCCCTAATTCATTGGAAAA[C/T]GGGTCTCTGTTCTTTGAGGAACAGCAGAGTCAGGT Y 2 1 2 1 102000 f 74 goat snp14121-scaffold1564-291831 1 23785929 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384414 Affx-122972195 AX-123254772 1 22075707 TTGCTTCACTGATACTAAGAGTGCTCACAATAGCA[C/T]ACCCTGCCCTCCTGGCTCCATCTTTAACAAAAATA Y 2 1 2 1 201000 f 74 goat snp14122-scaffold1564-324946 1 23752414 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786244 Affx-122955039 AX-385273279 1 22165524 TTAAGTGTAGCAGAGAAAGATAGAGTTTTGATTCT[A/G]TTTGCCAAAAGCATGGATATGCACTTTTTCCTTTC R 2 1 2 1 201000 f 74 goat snp14124-scaffold1564-414763 1 23662115 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774983 Affx-122977826 AX-385262115 1 22219198 TTTATGTTGCCCAAGGTGTATTACTGTTTCTTGTA[C/T]AGCTAGTACTTCTGAAACAATGTTGTCAGTTGAAC Y 2 1 2 1 101000 r 74 goat snp14125-scaffold1564-468437 1 23610448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443068 Affx-122928129 AX-123313405 1 22275513 CTACATTCAGCCCAAGCTGGCTTCAATCAAAGTCA[C/T]GCTACAGTTCTGTTATGCTAATGCCTGCTGCTGTG Y 2 1 2 1 101000 r 74 goat snp14126-scaffold1564-524752 1 23554202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802744 Affx-122951007 AX-385289643 1 22320255 AGTGACAGGCAGTCCTTAAATGAAAATTCCCTCTG[C/T]GGATAGTGATATGCCTTTTCATTCTAGTATTGAAT Y 2 1 2 1 101000 f 74 goat snp14127-scaffold1564-569494 1 23509169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768204 Affx-986698955 AX-385255391 1 22327472 GTATTTGTTCTGGACAAGAGACATGGATTTGTTAT[A/G]GGTTCTCTTGGGGCCACGACAGTTGTGTTCTTCAA R 2 1 2 1 600010 r 74 goat 1_22327472 1 22327472 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38435002 Affx-122933818 AX-123305342 1 22355127 CCAAGAAAAGAAAATCTGTCTTCCTGTGATACCCT[A/G]GAGTCAGTCTTGGTCAGCCACAGAGTATATGCTCA R 2 1 2 1 201000 r 74 goat snp14128-scaffold1564-604366 1 23474379 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398940 Affx-122960991 AX-123269295 1 22393749 GGGTTGGCCTGATGGGACAAAAATGTCATGAAACA[C/T]AAGAGATGTATTAAATAATATGCCATTAAATTTTG Y 2 1 2 1 101000 f 74 goat snp14129-scaffold1564-642988 1 23435701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439928 Affx-122930008 AX-123310265 1 22449341 TTAAAGAAGAGCATGTTTGCTATTATTTTAATGCT[A/G]TAATTTAGAACGTCTTAATTTTAGTGGTGTTTTTT R 2 1 2 1 103000 r 74 goat snp14130-scaffold1564-698580 1 23380011 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396093 Affx-122963427 AX-123266448 1 22494076 AAAGAATAATTCATTAAGACATTTTTCTCAGAAAA[C/T]AGTCATATTACTAATTCTATTGCTAATAAATCACC Y 2 1 2 1 103000 r 74 goat snp14131-scaffold1564-743315 1 23335041 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433153 Affx-122935674 AX-123303494 1 22541129 TTTGCTCCTTCTGACCTTCATAATTATGTGTCTTC[A/G]TGCCAATGTGCTTTCTATTCCACGGTCTGCTTTTC R 2 1 2 1 101000 r 74 goat snp14132-scaffold1564-790368 1 23287987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786607 Affx-122936972 AX-385273639 1 22594761 ATAGCATAAGCTAAGTGTCTACTTTTCCACTAAAT[A/G]CCTTCCTACACCTTAGATTTAAGGTGCTTTATCAT R 2 1 2 1 101000 r 74 goat snp14133-scaffold1564-844000 1 23233959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405577 Affx-122955944 AX-123275929 1 22634173 TACCACAAGGACATGAAAGCCCAGAATGGAATCCT[A/G]CAAGAGATTATAAAATATTCTCCCCAAAGAGGCCA R 2 1 2 1 101000 r 74 goat snp14134-scaffold1564-883412 1 23194909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273960 Affx-1111833920 AX-519547565 1 22656188 CCTAGGAACCCCACACACTCTACCTGCAGATGCTA[A/C]TAAAAGCAAGTATACCAGGTCCTGTCACTCTGCAG M 2 1 2 1 101000 r 74 goat GoatD01.010459 1 22656188 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802093 Affx-122957822 AX-385288997 1 22683694 AAGGATGTCTAGCCTTATCACTTCCACTGAACACC[A/G]TACTGGAGGTTGTAGCCTGATCAATTAGGTAAGAA R 2 1 2 1 101000 f 74 goat snp14135-scaffold1564-932933 1 23146087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395995 Affx-122963500 AX-123266350 1 22715731 GAACTGACACACAAGGATTCAAAAATCCCCTCTGA[C/T]GAGCTGTATAGCTTTGGGCAAAGATTTTGTCTAAT Y 2 1 2 1 101000 r 74 goat snp14136-scaffold1564-964970 1 23114054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388320 Affx-122969369 AX-123258678 1 22773994 TATATGAATATAATTTTTAAATTGTGGATAATGCC[A/G]TAAAGAAGGATGTAGCAAAAAGAACTAGTTTGGAT R 2 1 2 1 101000 r 74 goat snp14137-scaffold1564-1023233 1 23055089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789754 Affx-122952153 AX-385276762 1 22804183 GCATAAAGCTTTACAGGACAGTAAAAGAAAACTGA[C/T]GTCAAGGTCCCAACTGGGTATGTCCCAAGTTAAAA Y 2 1 2 1 101000 r 74 goat snp14138-scaffold1564-1053422 1 23024932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438423 Affx-122931273 AX-123308761 1 22842438 TATACTTGAGCTTGGCCAACATGGGTAGTTGCAAG[C/T]GATTTTAAAGCAGAAAGAGGTGTACTTGGGAATTT Y 2 1 2 1 101000 f 74 goat snp38013-scaffold472-1246997 1 22986453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782994 Affx-122948945 AX-385270062 1 22873332 GCAAAGTCAGATTCATTACCTGCACTTAGCTTACA[A/G]TTCTTCAAGGATCCAACCACAGGAATATCTGTATT R 2 1 2 1 201000 r 74 goat snp38012-scaffold472-1216103 1 22955455 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783301 Affx-122937693 AX-385270366 1 22903275 TTACAATGAAGTGAGAGAGAAATCAGTGACTTGAC[A/G]TTTACAAGTCCCAACTGATTCGTTTATTTATTCAA R 2 1 2 1 102000 f 74 goat snp38011-scaffold472-1186160 1 22925465 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438408 Affx-122931285 AX-123308746 1 22965603 CAAGCAATTTTTTGAGCACCTGCTGAGTATGAGAC[A/G]TATTTCATGGTGAGTTTCTTAAACAAAACCCTCAC R 2 1 2 1 201000 r 74 goat snp38010-scaffold472-1123832 1 22863125 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781409 Affx-122958665 AX-385268494 1 23001312 ACCAACTTGATTCAGTTCAGAGAATTCCACCATTA[C/T]GATTCATGGAACACTATATACATTCCCTTATTTTG Y 2 1 2 1 101000 f 74 goat snp38009-scaffold472-1088123 1 22827028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769302 Affx-122945759 AX-385256473 1 23043409 ATACCGTAGTTAATATATCATTTTTCCAAAAACCT[A/G]CAGAAAAATCCTACTTGTGCTTTGTTGCAGTATGA R 2 1 2 1 201000 f 74 goat snp38008-scaffold472-1046026 1 22784752 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382323 Affx-122973898 AX-123252681 1 23137537 TATTTCAATATGCTTCCTCTCTGCTCCAAACGATG[C/T]GTAACTTTATGCAGTTTTGACTACTTTGAAATATT Y 2 1 2 1 201000 r 74 goat snp38006-scaffold472-951898 1 22690672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770017 Affx-122968595 AX-385257183 1 23188544 TTGGGCACAGAGAAAGAGAAGGTCCTTTTCCATCT[A/G]CTAAATGATTAGAAACCCAGGTCCAGATTAGTAAA R 2 1 2 1 101000 f 74 goat snp38005-scaffold472-900891 1 22639513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404354 Affx-122956820 AX-123274706 1 23239362 GATCTGTTGATTAGAAGTTCACAAACGACATCTGA[C/T]AAAGCCATTTTTGTGTGCTTATGGGAGCCAAAGCA Y 2 1 2 1 101000 f 74 goat snp38004-scaffold472-850073 1 22588910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773249 Affx-122953233 AX-385260392 1 23280550 CTGAATTCAGGAGGATGTTGGAAAGAGTGTTTTAA[C/T]GAAAGAAGGGAATCCGTCCTGTGCATAGATTTGGA Y 2 1 2 1 101000 r 74 goat snp38003-scaffold472-808885 1 22548057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443099 Affx-122928105 AX-123313436 1 23387334 TGTTTCTAGGTCTCTCCTCACCTCCAGCAGTTGGT[A/C]TGTGCCCAGGGTATGTAAAATCATTTCAATATTGG M 2 1 2 1 101000 r 74 goat snp38000-scaffold472-702101 1 22442246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448747 Affx-122923323 AX-123319083 1 23421051 TTTTCCAGCACCATTTATTGAAGAAATTGTCTCTC[A/G]TCCATTGTACTGTCTTACCTCCTTTGGAGCTCTAG R 2 1 2 1 201000 r 74 goat snp37999-scaffold472-668384 1 22408502 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453064 Affx-122920061 AX-123323397 1 23461199 AACTTCTAGGATATATTCACAAAAATCCTTCCAAA[C/T]GGAAAGACAAACTTATTGTGGGTAAATGTAAAGAA Y 2 1 2 1 101000 r 74 goat snp37998-scaffold472-628236 1 22368850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278036 Affx-1111836141 AX-519551528 1 23478169 ATCAAATGATCTTTCTCAAGGTGGTAACAAAGGGA[A/G]ACATCAGATTATTTCAAGCTAAAATACTGTCTCCG R 2 1 2 1 101000 r 74 goat Random2.2K-26 1 23478169 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468271818 Affx-1111832851 AX-519545605 1 23480415 AAATGCACTGTCTTCTAAATCCTACCAACAAAAGT[A/G]TTCTTCAGAAATGACATTTTGAAATCAAATTAAGA R 2 1 2 1 101000 f 74 goat 1_23480415_AF-PAKI 1 23480415 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800997 Affx-122937257 AX-385287911 1 23540244 TAGTTAAAAATCAAACCAGAAAGCCTACTGTCAAG[C/T]ACAATGTTATGTTATGTTTCTAGTCCAGAAATATT Y 2 1 2 1 101000 f 74 goat snp37997-scaffold472-549191 1 22295743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388429 Affx-122969273 AX-123258787 1 23574489 ACTGGAAAGAGCTGAGTTCAGTCCTACAGTAGCGC[A/C]CAGAGATCTGTGCTCAACATTATTGTGGCAGGCTG M 2 1 2 1 201000 r 74 goat snp37996-scaffold472-514946 1 22261615 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380501 Affx-122975701 AX-123250859 1 23620253 AGATTTATTTCCAGAAAGAGAATGTGTTTTATAGA[C/T]GGCTAGGAAGAAGAGGTTTTCTTCTTTTTTTCCTC Y 2 1 2 1 201000 f 74 goat snp37995-scaffold472-469182 1 22215833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389776 Affx-122968229 AX-123260133 1 23650027 GGGTCCTTCCCAGGCAGGCTTGGCTTTCATGAGCC[A/G]TAGGGATGTAACTTTTTCCTGGGTGACCCTCTGAA R 2 1 2 1 101000 r 74 goat snp37994-scaffold472-439408 1 22186054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395942 Affx-122963578 AX-123266297 1 23746879 GCTCGTGACTGGCAGATACAGAATTTTCCTCTATA[C/T]GACTCACTTCCAAGCAATTTTAAAGCAAGGATGTT Y 2 1 2 1 101000 f 74 goat snp37992-scaffold472-342556 1 22086368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378501 Affx-122976653 AX-123248860 1 23780868 TTGTAATATTATTAAGCCAAACAATATAAGACAAT[A/G]TTAAAAAAACTTAGAGGCCTGCATAAGACATTGGG R 2 1 2 1 101000 r 74 goat snp37991-scaffold472-308567 1 22052438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772213 Affx-122972170 AX-385259368 1 23831943 TGATGGCATGTTTCTTGGTTAAAGGAAATAGCTGT[A/G]CATAAAAACATTTGAGAGATCCCAAAGCATGGGTG R 2 1 2 1 101000 f 74 goat snp37990-scaffold472-257492 1 22001329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420042 Affx-122945139 AX-123290390 1 23868174 CATAGAGTCAACAGAAAAGAAATGAACAAAACCCA[A/G]ACTGCTTTCCTTCTGCAATCCTGCAAGTCTAGGCA R 2 1 2 1 101000 r 74 goat snp37989-scaffold472-221261 1 21965584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768206 Affx-986698956 AX-385255393 1 23877003 TCACTCATCGCATACTCTTCCGTCAGTCATATAGC[A/G]CTTGTTATCGTCGCCATCCTCATCCAAACACCCTG R 2 1 2 1 600010 r 74 goat 1_23877003 1 23877003 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38375423 Affx-122979190 AX-123245782 1 23899049 AATACCAGTTCCTAGTAAAACGTTCAACATAATAC[A/G]CAAATCAAAAACTCAATTTACTCCTTTAAAAACAA R 2 1 2 1 101000 f 74 goat snp37988-scaffold472-190386 1 21934836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394442 Affx-122965087 AX-123264797 1 23963947 TTCTAGAGTTTGGAGCTGTTTAGAAAAGATAAGAC[C/T]CTCTAGAGTCCCAAATTATTAGGTGGAACCTGTAA Y 2 1 2 1 101000 f 74 goat snp37987-scaffold472-125488 1 21870138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439207 Affx-122931034 AX-123309544 1 24023895 AAATGTAGTATGCGTACAGTCAGTGGTGCTTCTAG[C/T]GGAGACAAGTTAGCCTAGGTGAGCTTTGAGCTTCA Y 2 1 2 1 102000 r 74 goat snp37986-scaffold472-65540 1 21810725 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795202 Affx-122939135 AX-385282160 1 24058553 TTTCAGTTTCAGTACTATGGCACATCTATTAATCA[C/T]CATTAAGGCTGTCTGTGAAATATTTGGCAATATAG Y 2 1 2 1 101000 r 74 goat snp37985-scaffold472-30882 1 21776055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390672 Affx-122967123 AX-123261029 1 24091022 ACTTTGGGCAGTGAAAATTTGTCTAAGTCACATTA[A/C]ATAAGGCCTTCCTTAATATTCACCATGTGGAATTT M 2 1 2 1 101000 f 74 goat snp8055-scaffold1292-1488 1 21737122 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780016 Affx-122928258 AX-385267115 1 24141291 ACTGTCTCCTAAGCTTGACCAAGCATTTCTGCTGA[C/T]GCTCAACACTGTTTTCCATTAAGCCCACATCCCAA Y 2 1 2 1 101000 r 74 goat snp8056-scaffold1292-51757 1 21685764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273799 Affx-1111833850 AX-519547410 1 24161518 CACCTTCAGGCTTCCCTGCAAGGCAATTGATTAAA[A/G]TAAGGCTGCTGGCAGAAGGAGGCAGGGATACAGAA R 2 1 2 1 101000 f 74 goat GoatD01.007254 1 24161518 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402314 Affx-122959084 AX-123272667 1 24171311 AATCTTACCCTGACATATATTGACCACTACTCCAT[A/C]GCTCCAGCAGTAGCTGACACCAATGGCCAGTGTCC M 2 1 2 1 101000 f 74 goat snp8057-scaffold1292-81777 1 21655724 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431405 Affx-122936537 AX-123301746 1 24203790 AAATAATATTGAGAGGCACTCATTTGGTACACAAG[C/T]AATAGATTTTCCCTCTTGTTAAATTTTCACTAGTC Y 2 1 2 1 101000 f 74 goat snp8058-scaffold1292-114256 1 21622678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440339 Affx-122929668 AX-123310676 1 24245331 GGTATAAAAAATGACAAGGAGAGTTTATTCAAATG[C/T]GGTTTCTTGAGCCATGCCCAGAGATTCTGATTTGG Y 2 1 2 1 201000 f 74 goat snp8059-scaffold1292-155797 1 21580683 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439250 Affx-122931003 AX-123309587 1 24321451 AAAATCAGATGCATTTTAAAAGTTTCAGTTATTGT[A/G]ATCTTCAACTCTGATTGCTTCTTTTTTATACAGTC R 2 1 2 1 101000 r 74 goat snp46388-scaffold640-654371 1 24166036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784809 Affx-122939636 AX-385271856 1 24355230 CTCCCATACTCAGATTATTAGTAAAATTGGTGACT[C/T]GGGAAAATCACAAATGAATATGTCATAGATTCTAG Y 2 1 2 1 101000 r 74 goat snp46387-scaffold640-620592 1 24199807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788872 Affx-122926170 AX-385275887 1 24384319 AACTATATACTGAAGAGATACATTCCTATCATAAG[C/T]GACTCTTAGAACTTTTCTCACAGTGTTTCTAGAGT Y 2 1 2 1 101000 r 74 goat snp46386-scaffold640-591503 1 24228795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385358 Affx-122971643 AX-123255716 1 24414306 ATGTGAATGGATGAGAATAAAGTCTACAGATAAAC[A/G]CATAGCCCTATGTCTTAAGAAGCTCAACTGAGCAT R 2 1 2 1 101000 f 74 goat snp46385-scaffold640-561516 1 24258799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411744 Affx-122951510 AX-123282094 1 24443294 TTCAACAAATTCAGTTTTGGACATATTGATGCCTG[A/G]ATACCAGAAATCTTTCCCATCATCTAACAGAAAGC R 2 1 2 1 101000 f 74 goat snp46384-scaffold640-532528 1 24288110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431837 Affx-122936091 AX-123302178 1 24487411 CAGCAGGAGCATTCTACTTCAGAGACTGTGGAAGC[A/G]TTTACCCAGGGTCTTTGGAATGCCCTACATCTTTC R 2 1 2 1 101000 r 74 goat snp46383-scaffold640-488411 1 24332905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426596 Affx-122939981 AX-123296942 1 24518167 GCAGGATTAGAAGTTAGAAGGAAGGAAGTCATAGA[C/T]GGAGAATCTTAGAGAACTGACAACAACCCCATGGC Y 2 1 2 1 101000 r 74 goat snp46382-scaffold640-457655 1 24363513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787585 Affx-122940352 AX-385274609 1 24551095 AAATTTGTAGTTTCAGGAAATTAGATGATTTTATG[C/T]AGCTTCAAATGACCTGTTCTTTCCTAACTTTTTGT Y 2 1 2 1 101000 r 74 goat snp46381-scaffold640-424727 1 24397173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774918 Affx-122954485 AX-385262051 1 24589984 GATGAATGCAGTAATGGGTCATGTGCAGAGAGCTA[C/T]GGACACGCAAATCTCAGCTGAATCCAACTGCCAAC Y 2 1 2 1 101000 r 74 goat snp46380-scaffold640-385838 1 24436611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771598 Affx-122972464 AX-385258756 1 24653709 TTGACCATGTTCATGTGGTACCTGCACATCACTTG[C/T]ATGCTGAGTCTTTATTAATCCTAGTCAGGTGCAAG Y 2 1 2 1 101000 f 74 goat snp46379-scaffold640-322113 1 24501137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768005 Affx-122926136 AX-385255219 1 24682757 CATGCAAGAAATTAAGTTGTCTGTAACCTTTGGTG[C/T]GTGCATCATTTCCACATGAATAATCTCAATTCTAT Y 2 1 2 1 101000 f 74 goat snp46378-scaffold640-293065 1 24530658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397759 Affx-122962525 AX-123268114 1 24716986 AAATGTTTCCCCAAAAAACACTTTGATAAGGAGTA[C/T]ATCATTGCCATCAGTGACACGGTGTGAAGATATCA Y 2 1 2 1 101000 r 74 goat snp46377-scaffold640-258836 1 24565049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420395 Affx-122944929 AX-123290742 1 24782455 TAAAAGAGCAAGATTTATGGGTACCTAGTTTATAG[A/C]GTGATACTGCAGTTATTAAAAGTATCTGACACTTA M 2 1 2 1 101000 f 74 goat snp46376-scaffold640-193367 1 24631520 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782871 Affx-122935125 AX-385269941 1 24811984 TCTAATATTGTAATCTTGAAGACAATAGTGCAGAA[G/T]AATTCATGGAACTAACTCAAGGAGTGGATGTGAGG K 2 1 2 1 101000 r 74 goat snp46375-scaffold640-163838 1 24660944 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452775 Affx-122920250 AX-123323108 1 24867569 TAGAGACATTGAAATGTTTTGTCACTAGCCTTAGA[C/T]TGCAAAATAAGTCCAAGTCAGAATTAGGTACACCC Y 2 1 2 1 101000 r 74 goat snp46374-scaffold640-108253 1 24717248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277904 Affx-1111836151 AX-519551400 1 24875022 TGATTTTGTAAAATACATCCTCAGCTGTAAATGGG[A/G]AGTTGTTAATGCTTTATCTGTTAACTTGTTTTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-28 1 24875022 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793883 Affx-122968511 AX-385280852 1 24905413 GAGTATCTGTTGATTTAATTGTAACAAGTGACACA[C/T]GAGAAACATTGCATTTTGTGGCAGACACTGAGGCT Y 2 1 2 1 101000 r 74 goat snp46373-scaffold640-70409 1 24755419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800284 Affx-122953410 AX-385287207 1 24956218 ATAGGATATTTGTATAACAAATAGGTTGTTAGGGA[A/G]TAAGAACTATTGATCTAGATAATTATAATTCATAG R 2 1 2 1 201000 r 74 goat snp46372-scaffold640-19604 1 24806876 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416727 Affx-122947545 AX-123287075 1 24990211 CCTCCACTTACTTGTCTTGTCTTGGAATGGCTGTG[C/T]GTGTACTGAGGAGCTGACTGTACTCACAGCCTTTG Y 2 1 2 1 101000 f 74 goat snp23367-scaffold234-14290 1 24840552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778504 Affx-122935190 AX-385265618 1 25026568 TTACCTTGTGTTTTCACTGGGTCTGATATCTGGCT[A/G]GGATCACTAATTCCATATGCATTGGCAGCCCTCAC R 2 1 2 1 101000 f 74 goat snp23368-scaffold234-50647 1 24876581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386519 Affx-122970742 AX-123256877 1 25080657 GCCCAGTGAATTTTAGGACTTGGCTGAATTCCATA[C/T]TGAAGGTGCCAGGCATTCTAGAAACTAATATTTGG Y 2 1 2 1 101000 f 74 goat snp23369-scaffold234-104736 1 24929758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800555 Affx-122939874 AX-385287474 1 25110294 TAAAGTCCTAACTCTGTGATTTCAATTGTATGAAC[A/G]CACACTTTACGTGTTGTTCCACTCTACCTAACAAG R 2 1 2 1 201000 f 74 goat snp23370-scaffold234-134373 1 24959442 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419205 Affx-122945701 AX-123289553 1 25143112 TTATATCAATGAAAGCAAACTAAAACCAGCATTAA[C/T]AGTCTCTAACATGCGTTAAGTTTATAACATTTGCT Y 2 1 2 1 101000 r 74 goat snp23371-scaffold234-167191 1 24991713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773076 Affx-122967307 AX-385260219 1 25199226 CAAATAGGTACTAGGTAAACATGTCGCAGAGAAAG[C/T]ATCTTTCAGTAATAGCTAATTTCTCCAAAATTATT Y 2 1 2 1 101000 f 74 goat snp23372-scaffold234-223305 1 25048419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401836 Affx-122959440 AX-123272189 1 25260500 TGCACACAAGCCATTGTTCCATTCCCGAAGAATTA[C/T]ATTAATCAATGCTCACAGGCTGCACCTCTGGAACA Y 2 1 2 1 101000 f 74 goat snp23374-scaffold234-284579 1 25110090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800915 Affx-122919514 AX-385287830 1 25323675 ATTTCTACATACTGTTTGCACAATTAAAGGTAAAT[A/G]CCCCTGATTCCTGTTATTTTCCACCAACATGCTTT R 2 1 2 1 101000 r 74 goat snp23376-scaffold234-347754 1 25172950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390306 Affx-122967718 AX-123260663 1 25362618 CATGTTTCCCCGAAACCAAACTCAGGGTCACTCCG[C/T]CTTTCCTCTTCGTATCAGCATGTGCCCAATTTTAG Y 2 1 2 1 101000 r 74 goat snp23377-scaffold234-386697 1 25211936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400330 Affx-122960051 AX-123270685 1 25400408 TTGTGTTTTTACCAAGAACCAAGCCCCACGGAAGA[C/T]GGGTCTCCTGACTCTCTTCCACTAACACCTCTTGC Y 2 1 2 1 101000 r 74 goat snp23378-scaffold234-424487 1 25250180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395598 Affx-122963824 AX-123265953 1 25431902 TCTCAGACACCACCCCCACCTCATACTGAGGACGT[A/G]TCTTGTATCATAGAGTTCCCCTCGGTTTTCTATTG R 2 1 2 1 101000 r 74 goat snp23379-scaffold234-455981 1 25281125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278066 Affx-1111836156 AX-519551556 1 25462691 ATAACTGCTCTCATTAATCAAATTCCTCCCAGGAG[A/G]TAGGTCAATATGAAATAAGATTAGAGCGGGGTTGT R 2 1 2 1 101000 r 74 goat Random2.2K-29 1 25462691 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776210 Affx-122962430 AX-385263338 1 25470047 GAAGAGGGTTTTGCTGCCACACTTTTCCCTCAAAC[A/G]TTACGCTAGAAAATTCCTATGATTTTCATCTTGAA R 2 1 2 1 101000 f 74 goat snp23380-scaffold234-494126 1 25319810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437098 Affx-122932182 AX-123307436 1 25508908 CTTTTGTGTCTGGTCCTGTGTGTATGGATTCTCTT[C/T]AAGTGAAATTTGTTCTACTATAGATGGGTAATAAA Y 2 1 2 1 201000 r 74 goat snp23381-scaffold234-532987 1 25358890 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422130 Affx-122943550 AX-123292477 1 25556137 GATATATTAGTCACTGTGCTAAGCAATATAGTAAA[C/T]AAGACTTGAATAAAATAGGGTCCCAAATATTTAGG Y 2 1 2 1 201000 f 74 goat snp23382-scaffold234-580216 1 25405673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799957 Affx-122968261 AX-385286883 1 25594447 GGAGCAGGGCTGAGTTAATGGGAAGGGGTTTTATG[C/T]AGAGCTGTTGTTTTCAGGAAAAGTTTCCTTCAGGT Y 2 1 2 1 101000 r 74 goat snp23383-scaffold234-618526 1 25443446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778851 Affx-122923003 AX-385265959 1 25623224 ATTTCTTGGCACCCTAATTTCCTAACTCTTGTAAC[A/G]GAAGTCTAGATGCACTAGACGATGTGGGAAATGAT R 2 1 2 1 201000 f 74 goat snp23384-scaffold234-647303 1 25473051 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382535 Affx-122973791 AX-123252893 1 25659580 TTTTCCTCCAAGCTCCCTGGCAATTTAATCATCCC[G/T]CACTAGATCCCTTAATGTGGGAATTACTCAAGGCT K 2 1 2 1 101000 r 74 goat snp23385-scaffold234-683659 1 25509749 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381470 Affx-122974973 AX-123251828 1 25722417 TCTATGTAAACTCTGTGCCATGTGGCAATAAGTTC[C/T]AGGATCATTCTAAACAATTTTAAATACCCAATTAA Y 2 1 2 1 101000 f 74 goat snp23386-scaffold234-746496 1 25572742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414914 Affx-122949110 AX-123285263 1 25747521 CATTTCTCTGGGCCTGAGAGCTAGTGTTGTAAATC[G/T]ACTTAGCATACCAAGCTATTCCAGGTAAGTATGTA K 2 1 2 1 101000 f 74 goat snp45807-scaffold629-1505 1 25597721 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802134 Affx-122924137 AX-385289038 1 25801803 TTCATTCGGGTAATATATCTGACACTGTAGTTCTG[C/T]AAGAAGGCTCTTGATTCAACACCCCCCAACTTTTT Y 2 1 2 1 101000 r 74 goat snp45808-scaffold629-55787 1 25652832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408243 Affx-122953823 AX-123278594 1 25856512 CCCATTCCATTTAGATTAACATCTCGAACCCTTAC[A/G]TTGGTTTACAATGATCCACATGATCTGTCCCCACT R 2 1 2 1 101000 f 74 goat snp45809-scaffold629-110496 1 25707994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277925 Affx-1111836162 AX-519551420 1 25867206 TTATCCTAAAATGAAAGAGGTATTGAAGAATGTCT[C/G]CATAATATCTAATAATTTTTAAAACTTGCAAAACA S 4 1 2 1 101000 f 74 goat Random2.2K-30 1 25867206 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389959 Affx-122968077 AX-123260316 1 25904425 GTTGTTAATTTAGACTGAATTGAGCAAAATAATTT[A/G]AGTGGAAGAATGCAGACAAGACAATGTATCAAGAA R 2 1 2 1 101000 r 74 goat snp45810-scaffold629-158409 1 25755690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772485 Affx-122974463 AX-385259636 1 25949389 TTTGAAGACTTGAGCTTGGAAATCACTTGCCAAGG[C/T]TCTTTCTCGTATCCCACATCTAGTTGGTTATCTGA Y 2 1 2 1 101000 f 74 goat snp45811-scaffold629-203373 1 25800392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770835 Affx-122932941 AX-385257999 1 26001420 AGGTGTGATTTTATCAAAATATTGCACATTCAACT[A/G]TTGAAATGGTTTGGTTATTACAACAAAGCAGCTAA R 2 1 2 1 101000 r 74 goat snp45812-scaffold629-255404 1 25852649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796361 Affx-122919795 AX-385283311 1 26053184 CCTTTTTTGTTTTGTTCAGGTAGTTATGTAAAATC[A/G]TTTCTCATAAGCTTTGTTGTTACATGACTTGGCTT R 2 1 2 1 201000 r 74 goat snp45813-scaffold629-307168 1 25904072 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274363 Affx-1111834212 AX-519547958 1 26082022 GGCAGACGGGATGCTAAAACATGTCAGCCCAGCCC[A/G]GGGTTTGAGCTGCAGGCGCTAACCGTAGGGTGACC R 2 1 2 1 102000 f 74 goat GoatD01.025749 1 26082022 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320799273 Affx-122935174 AX-385286202 1 26085274 CCATGCTAGCATGACTTTTAGATTAGATATTTTAA[C/T]ATAGTTTGTTCCAAGAATTCATATATGTGTTTCAA Y 2 1 2 1 201000 r 74 goat snp45814-scaffold629-339258 1 25936370 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402765 Affx-122958316 AX-123273118 1 26120674 TGTATCAGAATTACTTACATGACCAGTTAACCCAT[G/T]GTAAAAATTTACCTTCTTGTCACATTATTTCAGAT K 2 1 2 1 101000 f 74 goat snp45815-scaffold629-374658 1 25970965 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792404 Affx-122934367 AX-385279385 1 26158811 ACTCAATTTATCATGTAATGCACTGATAGGGTAAT[A/G]TTAAAGTCATTGTTTGAATTTCAATTTGTGTTTCT R 2 1 2 1 201000 r 74 goat snp45816-scaffold629-412795 1 26009370 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437959 Affx-122931613 AX-123308297 1 26230231 CATTGTGCTTCAATTCTTCAGATTATACAACAAGA[C/T]GCATAAAGCAAAAGATACATGGAGAAAGGTTAAAG Y 2 1 2 1 101000 f 74 goat snp45817-scaffold629-484215 1 26080828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376846 Affx-122977906 AX-123247205 1 26258890 CTTGTTTGATGTATTAACATTCTTCTATTCATTGC[A/G]TCTTCACTGCCTAAGTTCTCTTTAACCTGGTTTAC R 2 1 2 1 101000 r 74 goat snp45818-scaffold629-512874 1 26109305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793767 Affx-122935944 AX-385280739 1 26304035 CTGGAATAACTGGGTATTCCTCTTTATGCACCATC[A/G]TTTGTTTAGCCTAAGTGTAACATTTCATCCAGCAA R 2 1 2 1 101000 f 74 goat snp45819-scaffold629-558019 1 26155113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777406 Affx-122943459 AX-385264527 1 26359672 AGAGAGTATGCACTGATTGTCATAAATTTCTTAAC[G/T]GAATCCTGCGATGAAGTTAATCAGGAAATGGGGAC K 2 1 2 1 101000 r 74 goat snp45820-scaffold629-613656 1 26211106 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463632162 Affx-1110079937 AX-515113302 1 26383901 ACTGTCTATGGGGTTCTCTGGTGCTTCCCTGATGG[C/T]TCAGCTGTAAAGCATCCACCTTCAGTCAGGAGCCA Y 2 1 2 1 303000 r 74 goat 1_26383901_AF-PAKI 1 26383901 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783836 Affx-122920702 AX-385270892 1 26388372 TGTTCTATCAGTGGATTTTACATTCCATTTAACAT[C/T]TCAGGAACTTGCAACAGGAACGTGAGGATCTTTGC Y 2 1 2 1 101000 r 74 goat snp45821-scaffold629-642356 1 26240146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769062 Affx-122952464 AX-385256237 1 26448728 TAAATCCCAAGAGTTTTCCTTGGAAATTATAAACC[C/T]TAAAATGTCTTTGTCTTTAGTTGTGACATATTTTA Y 2 1 2 1 202000 r 74 goat snp45822-scaffold629-702712 1 26300828 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387588 Affx-122970262 AX-123257946 1 26469618 TTCAGCCTGTCAATATTCAGAAAAAATATATTTAC[C/T]CAATATCCTGAAGAAAATCTATTTATCTGAGTAAA Y 2 1 2 1 303000 r 74 goat snp11780-scaffold1437-813 1 26324795 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449623 Affx-122923195 AX-123319958 1 26510216 TTGGCTGGAGCACAAGCTTCAGGATTTCTTGAAGA[C/T]ATCTTTTCAAGAAACTTAGAGATACCAAAGGAACA Y 2 1 2 1 103000 f 74 goat snp11781-scaffold1437-41411 1 26363652 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797051 Affx-122933538 AX-313468630 1 26583668 TTTTTAACTCCCAAACATTCTTAGAATCTGATTAA[C/T]GGAGGGCATCCAAGAAAGTGTTTATTGAAATGTTT Y 2 1 2 1 102000 r 74 goat snp11782-scaffold1437-114863 1 26438566 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442446 Affx-122927958 AX-123312783 1 26643752 GTTTCTTGCTCCATGTCATTCCTTGCTGTTCTGTC[A/G]CTCAGTCATGTCTGACTCTTTGCGACCCTATGGAC R 2 1 2 1 102000 f 74 goat snp11784-scaffold1437-174947 1 26495698 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793051 Affx-122971404 AX-385280029 1 26687203 TTGATGCCACATTGTTGAAATAAACCAACATTTAA[C/T]GTTCTGTGTACTCTATTTGTAAATTCCTGCTTTAC Y 2 1 2 1 201000 f 74 goat snp11785-scaffold1437-218398 1 26539816 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417088 Affx-122947492 AX-123287436 1 26717714 ATTATAATAGTCATAAGCAAATAATTTTTGCATTT[A/G]CTTGTACTACCCAAGACTTGCTTCCACATGCTTAC R 2 1 2 1 101000 r 74 goat snp11786-scaffold1437-248909 1 26573034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793959 Affx-122933853 AX-385280928 1 26777073 AAATTAAGGATAGAGAAAAACAGTGCTTTCCTTTG[A/G]TAAACATTTAGATGCTTTGGCACCAAAATAGAGTC R 2 1 2 1 101000 f 74 goat snp11787-scaffold1437-308268 1 26634080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409763 Affx-122952995 AX-123280114 1 26834535 ATGGATGCAACAAGAATTTGCTTGTTAAATAGTAG[C/T]AAAGTAGAAGTGATTGTTATGCCGTGTCCGAGCTT Y 2 1 2 1 101000 r 74 goat snp11788-scaffold1437-365730 1 26692538 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436015 Affx-122932743 AX-123306354 1 26882646 TGTCTTACATTATAGCTCTCCTCATAGGCAGCTTC[A/C]TTCTTCAAGACCAGCTAGAGGATCCCTTCCTCCAT M 2 1 2 1 101000 f 74 goat snp11789-scaffold1437-413841 1 26739201 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411925 Affx-122951162 AX-123282275 1 26920343 TTCCCATATTTTGATATTGTTATGCTATTAATCAA[G/T]ATTTTGATCCCAAACTTATCATCCTCATAAAGACC K 2 1 2 1 101000 r 74 goat snp11790-scaffold1437-451538 1 26776199 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800653 Affx-122956140 AX-385287572 1 26965515 GCCGCTGGTGAAAGGGAGCAAGTTAGACAATTTCC[A/G]CTTTATTAATACCACTGTGACTCTATTGTGCCATC R 2 1 2 1 101000 f 74 goat snp11791-scaffold1437-496710 1 26820994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780289 Affx-122959358 AX-385267384 1 26996467 CACTTTCCATATTACTGGAACTACTAGGCCTCAAT[A/G]TGAAACTCTTATGAAAGTGAGTGCAAATTGGAAAA R 2 1 2 1 101000 f 74 goat snp11792-scaffold1437-527662 1 26852491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767026 Affx-122938822 AX-385254318 1 27025932 GTTAGCCAAGGGAGTTTTAAGGTGACTAAGTTATT[A/G]CTGAAACATATATGGCTTTCTATTTTTTCACCTGG R 2 1 2 1 101000 f 74 goat snp11793-scaffold1437-557127 1 26882251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424368 Affx-122941844 AX-123294714 1 27066775 GTGATTTGTTTTCCTGCCTTTTAAATCATCATCTA[C/T]ACTGAAAACTTTATATTTATTTAAGGGAAATCTCT Y 2 1 2 1 101000 f 74 goat snp11794-scaffold1437-597970 1 26923861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440763 Affx-122929858 AX-123311100 1 27102919 TTTACAACTTTCTCTTTTGTCCTTCTCTCCCCATC[G/T]CTGTCTATGTCTCTGTCACTTTTTGCCTCTCTCTC K 2 1 2 1 101000 r 74 goat snp11795-scaffold1437-634114 1 26959531 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392644 Affx-122966450 AX-123263001 1 27118415 CTGTAAGCCTATAATATTTTTTTCTTAAGTAAGCA[C/T]ATTTAAAATCCACTGAAGCCTTTTCCTTTGTTGTT Y 2 1 2 1 103000 r 74 goat snp51940-scaffold763-313236 1 26989032 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786379 Affx-122966869 AX-385273413 1 27147074 ATATGTAAACACCTATTTGTTATCTATCTAGCTAT[C/T]TTGCTGTCATCTTTCTACCATCAATAATTTGTCTA Y 2 1 2 1 101000 r 74 goat snp51939-scaffold763-284577 1 27018059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380985 Affx-122974680 AX-123251343 1 27194805 ATTGCTGAGGGATTGAACCTATTTCTTGGCTCATT[A/G]CTATGCATATGATAGACTGAAAGAATGACCTAGCA R 2 1 2 1 101000 r 74 goat snp51938-scaffold763-236846 1 27063464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796763 Affx-122953413 AX-385283707 1 27245777 ATAATTTAGTTATTATAATAATTAATCATTAGATT[A/G]CAGTAAAGTAATTTATTAGGAGAAACAGATATTTG R 2 1 2 1 202000 f 74 goat snp51937-scaffold763-185874 1 27114353 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769883 Affx-122936262 AX-385257052 1 27289997 TCACATAGCAATGGAAAAGAATTGATAAACAAAAG[C/T]AAAATTAGCAGTCTATGTCCAATCACATGAAACAA Y 2 1 2 1 101000 f 74 goat snp51936-scaffold763-141654 1 27158433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792049 Affx-122955733 AX-385279037 1 27328970 GAAACTGAGATTGCTAAGTGAAATCATCTTTCTAT[A/G]TCTTACAATAAATGAGAGAAGCAGAATTTGAATGC R 2 1 2 1 101000 r 74 goat snp51935-scaffold763-102681 1 27197572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799614 Affx-122943842 AX-385286544 1 27380542 GTGGAGATGTAAGTTACTTCTATGGACTAGATAAA[G/T]AGGGGAGGAGCAATATAGGTGTAGGGAAATAAGAG K 2 1 2 1 103000 r 74 goat snp51934-scaffold763-51109 1 27249676 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778317 Affx-122960269 AX-385265432 1 27414767 GCAGAACTGAGTAGGACAATTAGCAAATTAGTGGC[G/T]TATTAGCACAATAGTAGTGTTTCTAATGACTTTTC K 2 1 2 1 101000 f 74 goat snp51933-scaffold763-16884 1 27284044 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411737 Affx-122951515 AX-123282087 1 27454715 ACAGTTCAATATTACCTTGAGTCTTTAAGATACAG[C/T]ATAGCCTTAGACTATATTAAGAACTATGTTGCATT Y 2 1 2 1 101000 f 74 goat snp15734-scaffold1652-1168377 1 27338324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773457 Affx-122936135 AX-385260599 1 27496126 CTGCTTTCTCCACCTTGTTTCAGGAGTAAGAAAAT[A/G]TGTGTGTAGTCTTCATGGGCAGGTCTATACTTAAA R 2 1 2 1 101000 f 74 goat snp15733-scaffold1652-1126966 1 27379911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439086 Affx-122931127 AX-123309423 1 27546768 TATTGATAAAGATAAGACCATGAAGAAATCAGCCA[C/T]GGGGTCTTGGTAAGCCATGTTAGGAATTTAGATCT Y 2 1 2 1 201000 f 74 goat snp15732-scaffold1652-1076324 1 27430949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278096 Affx-1111836170 AX-519551586 1 27550186 CTTAGCAAGAAAAATTTGGTCTCTGTTACTCTCCT[A/G]TCTCCAATCTGTATTGAAAGCAACTAATCAAAATA R 2 1 2 1 201000 r 74 goat Random2.2K-31 1 27550186 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765709 Affx-122971154 AX-385253171 1 27613258 TGTTCAGACTGAAACAGTCAGCTCTATAGTCAATT[C/T]GTAATTGATTATTGATCATAAGCATCCTGTTATAC Y 2 1 2 1 101000 f 74 goat snp15731-scaffold1652-1009834 1 27497574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417460 Affx-122947190 AX-123287808 1 27643134 TGTATGTGATGAGAATAGAAATGGCTGAGCACAAA[C/T]ATTTAAAGGCAAGGAAAAAAGGAGCAGAAGTCTTC Y 2 1 2 1 201000 f 74 goat snp15730-scaffold1652-979958 1 27527204 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786418 Affx-122945228 AX-385273452 1 27747045 TTGAAGGGACTTTAGAAGTTCACAGCTAATAGCAG[C/T]ACTCCTGTTCACTGTAAAGGAATGTTAATTTTGTC Y 2 1 2 1 101000 f 74 goat snp15728-scaffold1652-876047 1 27632005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786537 Affx-122939601 AX-385273570 1 27782288 CCATTACAAGCTATAAGTTATGCTTCATCTTGGCC[A/G]TTACTACAATCATTTTACACTTTATGAATTCTCAA R 2 1 2 1 101000 f 74 goat snp15727-scaffold1652-840804 1 27667084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768432 Affx-122930636 AX-385255612 1 27831294 TCAAAATTAGATGCAATGGGTAATTATTTTGGTAG[A/G]GAATATAAATTCAGGCTTTGATTCCTTTCATAGAT R 2 1 2 1 101000 r 74 goat snp15726-scaffold1652-791798 1 27716205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395876 Affx-122963998 AX-123266231 1 27862464 TATATACATTGCCATATACTTTCGGTAGGGCCCTT[G/T]CACTCGAACCCTTGAACTCCGCATTTGGCCAACGG K 2 1 2 1 101000 f 74 goat snp15725-scaffold1652-760628 1 27747113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412681 Affx-122950767 AX-123283030 1 27908549 GCCTCCCTCCCCTTTCCACTCCAGGCAACACAGTC[A/G]CCCTGGGCCCCTTCAGTATTTCAGGTGTTACTCTA R 2 1 2 1 101000 r 74 goat snp15724-scaffold1652-714543 1 27793333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397714 Affx-122962557 AX-123268069 1 27937789 TGACATGTGTAATTTGCTTTAATTTCAAAGTAGAG[C/T]AATAGTTTGATTTCCTGACAGTGAAGCCAGCTGAT Y 2 1 2 1 201000 f 74 goat snp15723-scaffold1652-685303 1 27823343 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775291 Affx-122921768 AX-385262422 1 27981560 TTACATTAGTGATCATAATCGTAATTTAATGAGCA[G/T]AAAGAGCATGCTTTGATGGTTAGTGCCTGGTTACT K 2 1 2 1 101000 r 74 goat snp15722-scaffold1652-641532 1 27867105 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397998 Affx-122961796 AX-123268353 1 28016846 GTGTCAAGTATATAACAATATGAAAATTAAAATAC[A/G]TTTTAAGCTTCTAGCCCATTGTAGCACATTTGGGT R 2 1 2 1 102000 r 74 goat snp15721-scaffold1652-606246 1 27902505 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768837 Affx-122973230 AX-385256014 1 28074128 CACCTGATATACAGTGTCTCCTCCAATCTTTTGCC[A/G]TTTCCTATCTTCTGTCCCTGCCTCATTTTTCTCTG R 2 1 2 1 101000 f 74 goat snp15720-scaffold1652-548964 1 27959936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391598 Affx-122966600 AX-123261955 1 28123734 TTATATCCAGTGTTGCTGATAAAATGCTGATAAAT[C/T]TGATTTTTATTCCTTTGTGTGTAATCAGCCTTTTC Y 2 1 2 1 101000 f 74 goat snp15719-scaffold1652-499358 1 28014323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423310 Affx-122942630 AX-123293656 1 28161414 GAAAGAAGAACACATTCTTCCTGGAAAGAATCAGG[C/T]AGGCTCGTCAGTTACAGGGGAGGTTAGAGAACAAT Y 2 1 2 1 201000 f 74 goat snp15718-scaffold1652-461678 1 28051500 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786431 Affx-122926381 AX-385273465 1 28202350 ACCAAATGTCACTTCAATTTATTCAGTATGAATTT[A/G]TCTTCCAAAAGAAGCTTAAAAATATACTGCTTGTT R 2 1 2 1 101000 r 74 goat snp15717-scaffold1652-420742 1 28092577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376043 Affx-122978937 AX-123246402 1 28239774 GCAGCTGGGATGTCTGCAAACTATTCTATAAGGGA[C/T]ACCAAAATATCACTAGAATAACTTGAATAGATCGT Y 2 1 2 1 201000 r 74 goat snp15716-scaffold1652-383318 1 28130282 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772197 Affx-122924570 AX-385259352 1 28292037 TATTCTGAAAGAAATCACTGTCTACCCTTCCATGA[A/G]AGATCCAAATTTCAGTACCTTAATTCAAATTTTAG R 2 1 2 1 101000 f 74 goat snp15715-scaffold1652-331055 1 28183186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423273 Affx-122942660 AX-123293619 1 28324950 TTATCTAATGAACATATAGTTTCCACAGAAGCAGT[G/T]AAATATGCAAATATTTACACATATACACACAAACA K 2 1 2 1 101000 f 74 goat snp15714-scaffold1652-298142 1 28216763 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785539 Affx-122972230 AX-385272583 1 28363292 AATAGCAGGACAAACAAAATTCCTGAAGATTAATC[C/T]ATGACAGAGAACCTGGAAAGTTGGCACAGCCCTGA Y 2 1 2 1 101000 r 74 goat snp15713-scaffold1652-259800 1 28251788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793257 Affx-122950577 AX-385280235 1 28400001 AAGTATCCTATATAGCTTAGCAATAAATACAATTT[A/C]GCTAATCAAAATAATGTAAACATGATACAGTAATC M 2 1 2 1 101000 r 74 goat snp15712-scaffold1652-223091 1 28288909 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380997 Affx-122974670 AX-123251355 1 28446823 CTGCATGTCTTGTTGTACCAGTGACATCCCAGTTC[A/C]GTGCAAGCACATTAGCTGATTTTACAAGATACGTG M 2 1 2 1 101000 r 74 goat snp15711-scaffold1652-176269 1 28336136 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376949 Affx-122977769 AX-123247308 1 28515440 TACTAATGACTAACATTTATTATAGAGACAGTAAA[G/T]ATCACAGCCAGATCAGAAAGAGAAAATGACATCTG K 2 1 2 1 303000 f 74 goat snp15709-scaffold1652-107652 1 28404607 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422060 Affx-122943605 AX-123292407 1 28562872 TCAATTCAAACCCACAAAGTCAACCCACAGAGTCC[A/G]TGTTCTCAACTGCTACATGAGATAGCCTTCTGACT R 2 1 2 1 101000 r 74 goat snp15708-scaffold1652-60220 1 28451286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424187 Affx-122942517 AX-123294533 1 28601982 TTCATGAAAACTGACCCATCACTTGTTGTTAGCAA[C/T]ACATCTTTCTAAAAATTTAATTTTTAATAAATTCA Y 2 1 2 1 101000 f 74 goat snp15707-scaffold1652-21110 1 28490337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403043 Affx-122958540 AX-123273396 1 28722307 CCCAGGATTGCTCACTAATTCTAGGATCTGAAACA[G/T]TGCCAAAGCTTTCAGGTAGGGTTGGAGGCCCTGAT K 2 1 2 1 101000 f 74 goat snp52909-scaffold794-813793 1 28610260 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387249 Affx-122970564 AX-123257607 1 28753361 GACAAATACTTGTAATACATGGCTTATTACATACT[A/G]CTCACAGTTGTTTTCTTTTTGTCTGGATAGAATGC R 2 1 2 1 101000 f 74 goat snp52908-scaffold794-782739 1 28641342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769031 Affx-122945443 AX-385256206 1 28824214 TACTTTCAACTGTTGGATAAAACCTTTAGAGAGAG[A/G]CTACAGTTGAGGTAAAATATTTGGATTTGTAAGAA R 2 1 2 1 101000 r 74 goat snp52907-scaffold794-711886 1 28712948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788021 Affx-122969126 AX-385275042 1 28865894 ACTTATTCTACAACTGCATTTTTGTCTAATAGTTC[A/G]GCTGAACAATGTCCATTTTCCAGGGCTATTGATGA R 2 1 2 1 101000 r 74 goat snp52906-scaffold794-670206 1 28755163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411037 Affx-122951965 AX-123281387 1 28908572 TAGTCTATTGTTATTTGGATGAATATACTAGCACA[C/T]GAACATCCCTAGATAGACTGATAAAAATTAATATC Y 2 1 2 1 101000 f 74 goat snp52905-scaffold794-627528 1 28796310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389309 Affx-122968503 AX-123259667 1 28976732 TTAGTAGTACAATCATGAGCGGGGTTTTCAGCATT[A/G]TGATTTCATTATTTTGCTTTGCAACCTTTTAAAGC R 2 1 2 1 101000 f 74 goat snp52904-scaffold794-559368 1 28865198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787761 Affx-122921354 AX-385274784 1 29006364 TCATACGTTGTAAAATTGCGGTTGTTTCTAGCACT[A/G]CATTCTATTTGCTAAAGCTCTGCTAAAATTATTTA R 2 1 2 1 101000 f 74 goat snp52903-scaffold794-529736 1 28895337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447970 Affx-122923761 AX-123318306 1 29044980 AACTCTGCATACAAATTATCATGAGACAGATTAAA[C/T]GAGTAAAAACACTAGGAAAATTATTTACCACGCTT Y 2 1 2 1 201000 f 74 goat snp52902-scaffold794-491120 1 28933522 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408916 Affx-122953957 AX-123279267 1 29115476 TTTCTGGATGACATATTCTGGTTTCCTTCAGTAGG[A/G]AGGCAAGAACATGAATAAGAAGTGAATCAGTTAGA R 2 1 2 1 201000 r 74 goat snp52900-scaffold794-420624 1 29004543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785972 Affx-122950890 AX-385273008 1 29190865 CTGAATGTATCTGGTTGCAAAGGAATAAAGGCATA[C/T]ATTCACATAGTTTCTATAACATAAAATCATCCATC Y 2 1 2 1 101000 f 74 goat snp52899-scaffold794-345235 1 29077702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777850 Affx-122970585 AX-385264967 1 29220763 TGTCCTGACCCTCTTATTTATCTCCTTTAAAAATG[C/T]AGTAAATCACAACTGCAGTTCCTTCCATCTCACCA Y 2 1 2 1 201000 f 74 goat snp52898-scaffold794-315337 1 29107970 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431528 Affx-122936223 AX-123301869 1 29264107 AGGGTGACAAATTCCATCACCTTTCAACCCATACC[A/G]CAACATATTCACAGGTCCCAGTGATAGTGGACATT R 2 1 2 1 101000 f 74 goat snp52897-scaffold794-271993 1 29151218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794805 Affx-122960958 AX-385281765 1 29296737 ACATGTTGGAAAAGAGTTGAAAATCACTCTAGAAA[C/T]GGCCAAGATTGTTGTAAAGGGATTTTTAAAAGCAA Y 2 1 2 1 101000 r 74 goat snp52896-scaffold794-239363 1 29182861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778578 Affx-122944052 AX-385265690 1 29329957 GGGAGTGTGAAGGTAGTTTCATGGCCATAAAAGGG[C/T]ATCATTAATCATAATGATATGGTTACAGGATGAGT Y 2 1 2 1 202000 r 74 goat snp52895-scaffold794-206143 1 29215809 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444215 Affx-122927246 AX-123314552 1 29376251 CCAACACCTATTTATAATAAAAACTCTTAGTAAAC[G/T]AGAAATAGAGAGGAACTTTTGCAACTTGTTAAAGA K 2 1 2 1 103000 r 74 goat snp52894-scaffold794-159849 1 29262181 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776801 Affx-122924633 AX-385263925 1 29419176 ATGGATCACCTTCATTTATCCACTTAATTGTGGAT[A/G]TTCTTGGCCTTGAGCTTGACTGGGGCATTGCTATT R 2 1 2 1 102000 r 74 goat snp52893-scaffold794-116924 1 29306575 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405869 Affx-122955847 AX-123276221 1 29481587 CAATTTTATATCTTTCTTTTTACTCTCTACCTCTT[A/C]TTTATTTTGCATTAAGTGAAGGGTGCTGAAGTATT M 2 1 2 1 103000 r 74 goat snp52892-scaffold794-54513 1 29369334 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420793 Affx-122944691 AX-123291140 1 29513063 CCATATGACCCTCTCTACACCATGGGAATTAGATT[A/C]TTCAAGGAAAACAGCAGAACTCTGCTTCTGTTCCT M 2 1 2 1 101000 f 74 goat snp52891-scaffold794-23037 1 29400936 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272479 Affx-1111832853 AX-519546201 1 29530756 CACCTGGGACATTTGTCTTACAGCAGCAGAGAACT[A/G]TATTATGCCAACAACCTAAACAAGACTGAAAGTGA R 2 1 2 1 101000 f 74 goat 1_29530756_AF-PAKI 1 29530756 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445293 Affx-122925451 AX-123315630 1 29559298 GAGAAATGTTTGCTCCCAGAATTTCCCACAGTGGA[A/G]TGGCATAGGAGCAGGAGAATATGCATAGCTAAGAG R 2 1 2 1 101000 r 74 goat snp52334-scaffold778-553965 1 29447533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432750 Affx-122935447 AX-123303091 1 29621257 GCCTTTTCCTAAATCAGCACCTGGGGTTAACGATT[A/G]CAATTCATGGGGGTTTAGTCACGAAGTCCCGTTCA R 2 1 2 1 201000 f 74 goat snp52333-scaffold778-492006 1 29510924 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447627 Affx-122923985 AX-123317963 1 29653611 AGCAGCAGGCAACCAGGGAAAGCACTTGTCATGGA[A/G]ATGGCAGAGGCAGAAGAGAAGGAGCAAAACATGAA R 2 1 2 1 201000 f 74 goat snp52332-scaffold778-459652 1 29543192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443844 Affx-122927529 AX-123314181 1 29699022 AAGCAAATAGGCTTGTTTCACATAAAAATGAAAGG[C/T]GTATCAGTCTCCTATTTGTGAAATGACTTTGCATG Y 2 1 2 1 101000 r 74 goat snp52331-scaffold778-414241 1 29589044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432894 Affx-122935332 AX-123303235 1 29751706 AATCAACGTAGAAACATTTTTCTTCCTCAGGCAAG[C/T]TGAATCTGACAGCAGTATAAAGCTTTTACAAAGGA Y 2 1 2 1 201000 r 74 goat snp52330-scaffold778-361557 1 29641780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785610 Affx-122944572 AX-385272653 1 29810851 CACTTAATCCAAACCCTTATCTAAAATATAGTGGA[C/T]GATTATTTCACTAATAAAATCATTCAGTTATCTTG Y 2 1 2 1 201000 r 74 goat snp52329-scaffold778-302412 1 29701218 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800636 Affx-122941575 AX-385287555 1 29949507 TAATTTTGATATTCAAAGTTCCCCAACTGTTAATA[G/T]AATTATAATCGATGGGAAAAGATAATAAAAAGAAA K 2 1 2 1 102000 f 74 goat snp52326-scaffold778-163756 1 29842616 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417141 Affx-122947356 AX-123287489 1 29979019 GAAGACAGCTTGGTTTTCATCCAAGTGTTATTTTT[A/G]CAATGTTTGTTTACTTCTTAAAGCACAGCAGACTG R 2 1 2 1 101000 r 74 goat snp52325-scaffold778-134244 1 29872322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799987 Affx-122923417 AX-385286911 1 30032311 TCCTTTTAATCAAAGTATGCTCAAAGCATATATCC[A/G]TTAAAAGAGAACAGGAAAAACTCTCTGGTATAAAT R 2 1 2 1 103000 r 74 goat snp52324-scaffold778-80952 1 29917051 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788401 Affx-122951495 AX-385275419 1 30061645 TTAGAAATCTCTTATAATCAATTCTACATCTGTCT[A/G]TTAGAAGCAACAACCATCATCCTTTGAACTGTTTA R 2 1 2 1 101000 r 74 goat snp52323-scaffold778-51618 1 29946801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402651 Affx-122958381 AX-123273004 1 30106429 AATCTTCTGCATGCCTTTAGAAAGAGAATTAAAGG[C/T]TACCTAACTCACACCATTTTTACCAATGACATAAT Y 2 1 2 1 101000 r 74 goat snp52322-scaffold778-6834 1 29992398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783409 Affx-122924894 AX-385270472 1 30127029 TCCTCAAATGCTTTGATTTGTTAGAATGATAGCAG[A/C]TGTTCTGTTGAGAAAATCCCTGCAGTTTTGTTTCT M 2 1 2 1 101000 r 74 goat snp43727-scaffold586-1168057 1 30017075 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427363 Affx-122940100 AX-123297706 1 30172903 AAAAGTAGGAACCAGATGCCAAAGTCTGAATGTGC[A/G]TTCTATTCAAAGCATTGGGGCCCGTGGCTAACTCC R 2 1 2 1 201000 f 74 goat snp43726-scaffold586-1122183 1 30063468 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437564 Affx-122931887 AX-123307902 1 30206773 GTATCCTAATGATGCAAGCTTGTGCTCCCTAGAAA[C/T]GCAGAATGGAAGGTAAAATTTGATTATAAAATGAG Y 2 1 2 1 101000 f 74 goat snp43725-scaffold586-1088313 1 30097186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770510 Affx-122965263 AX-385257675 1 30259548 AACCTCAAACTTCTTTCTCTCTTCTACACATAGTA[C/T]GACTATATATTTTTCTCCAAGCTAAAACATTTTAA Y 2 1 2 1 101000 f 74 goat snp43724-scaffold586-1035538 1 30150036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768515 Affx-122964753 AX-385255695 1 30293371 TCAGCAGAGCTAAAGTCTTAAATGAGAATCCCAGT[C/T]ATTTTATTTGGTTCATAGAGACCTGATGATGACCT Y 2 1 2 1 101000 f 74 goat snp43723-scaffold586-1001715 1 30183991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419458 Affx-122945488 AX-123289806 1 30347541 TGCTATATCCCTTCATTCTTTAACATTTATGGATT[A/G]ACTTATCCTTCTCACTAGTTAGATTTTAGTAATAT R 2 1 2 1 201000 r 74 goat snp43722-scaffold586-947545 1 30238201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794264 Affx-122943945 AX-385281229 1 30381955 CATGCCACTGAATGTTGTTCAAAAGTGGGTTCCTG[C/T]GGATCTTTCAATTGCTCAGTACAAAAGAACATGTT Y 2 1 2 1 101000 f 74 goat snp43721-scaffold586-913131 1 30272666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424444 Affx-122941789 AX-123294790 1 30433216 TTAAAGTAAAGCTAACAATGTTAAAAATGAGAATG[A/C]TCTTCCTAACCTGTACTGAAGAATAAATGAAATAT M 2 1 2 1 101000 r 74 goat snp43720-scaffold586-861870 1 30325096 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792026 Affx-122919704 AX-385279014 1 30471395 CCAGTGTGAATTTGTAGCACAAATGGAAACAAACT[A/G]TAATTGTTTTAAGCTCTATAGCTATGAAGCTATTT R 2 1 2 1 101000 f 74 goat snp43719-scaffold586-823691 1 30364149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394478 Affx-122964566 AX-123264833 1 30524748 ATACCGTTTCCTTGACTTCACATACATGCAGAAAA[G/T]ATAAATATATCAGAAAAAAACGAGAGAATAGAAGC K 2 1 2 1 303000 r 74 goat snp43718-scaffold586-770338 1 30418441 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424448 Affx-122941786 AX-123294794 1 30554005 GGTTGTAGTTTTTCCCTTCAGTACTTTTTAAACAT[A/G]TCCTGTCTTTCTCCTCTGGCCTGCAGAGTTTCTGC R 2 1 2 1 201000 f 74 goat snp43717-scaffold586-741081 1 30447867 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410018 Affx-122953257 AX-123280368 1 30584876 CAGGTGGACCTATATAAATCCAAAAAGGTTAATAG[C/T]ATAAATAAACACTATGTGTTTTATAGGCTGTTACA Y 2 1 2 1 101000 f 74 goat snp43716-scaffold586-710210 1 30478942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802852 Affx-122925542 AX-385289750 1 30624582 TTACTCTGATGTAGACATCTTCTAAGAGCTTATGA[C/T]AATGAAGTCTCAGTTCTTATGAATTTTCCATTTTA Y 2 1 2 1 101000 f 74 goat snp43715-scaffold586-670504 1 30518648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786972 Affx-122922120 AX-385274001 1 30653276 GACTCTGAGAAACATTAGGAGGAGACATTTGGCAA[A/C]ATTTGCCATCAGGAAGACAAGGTAGAAAATAAATG M 2 1 2 1 101000 f 74 goat snp43714-scaffold586-641810 1 30547331 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790818 Affx-122921409 AX-385277818 1 30690969 GCTTGTGAAAACAAGTAATACTTTAAGAATCAAGG[A/C]GTGTTCTGTAAATATCTTTTTTCCTCCATCCACCA M 2 1 2 1 101000 r 74 goat snp43713-scaffold586-604117 1 30582775 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782941 Affx-122970302 AX-385270011 1 30762335 TGCTGGTCATATTTTTTGCAGATAAATGCAATAAT[A/C]TTTTCCAAGAATTGGGCAGTAAATAAAAGAGGTTC M 2 1 2 1 102000 f 74 goat snp43712-scaffold586-532751 1 30654781 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414502 Affx-122949535 AX-123284851 1 30796428 TGTGGATGCATTTGTGTGTGGAACATTCAAAGGGG[C/T]GCGAGGAAACTCTCTGATGTGATGGAGTTGTTTTA Y 2 1 2 1 101000 f 74 goat snp43711-scaffold586-498658 1 30689303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431357 Affx-122937044 AX-123301698 1 30825755 TTCTACTTCCAGGCCATCTTCCCTGGTGCCTCAGA[C/T]GGTTAAAAATCTGCCTGCAATGAAAGAGACACAGG Y 2 1 2 1 103000 f 74 goat snp43710-scaffold586-469331 1 30719350 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427903 Affx-122939682 AX-123298246 1 30901588 TCACTAGCCAGCACGCTGAGCGCAGGTGGCTGCGA[A/G]CCAGCACGCTGAGCATGCCTGAGAGGAGATACCCC R 2 1 2 1 303000 r 74 goat snp43709-scaffold586-393498 1 30795267 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275399 Affx-1111834774 AX-519548972 1 30939116 GCCAACCTGCTTTTTAAAATTGACTGTTGGTATGA[A/G]TAATCTTTCACCTCATCAGATATTTTGGTCACTGC R 2 1 2 1 201000 r 74 goat GoatD01.052322 1 30939116 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453543 Affx-122919787 AX-123323876 1 30958182 CAAACTCAATATTACCATTTTGTACTGACTTTCTC[G/T]CCATCTCTGTTTTCTTCCTTTTCACTGCATCTCTG K 2 1 2 1 201000 f 74 goat snp43708-scaffold586-336904 1 30852766 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419737 Affx-122945891 AX-123290085 1 31009965 TCACGTCTGAGGATCTTATCTAAACTGTTGAGAAG[A/G]TTCTTGTCTGCCGGTCCTAGGTATCAGTTCTCTTG R 2 1 2 1 101000 f 74 goat snp43707-scaffold586-285121 1 30904697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436179 Affx-122932611 AX-123306518 1 31045734 TTCACTATCTCCCTGAGTTTGCTCACATTCATGTC[G/T]GTTGAATCTGTGATCCCGTTCAGTCTTCTCATCCT K 2 1 2 1 201000 r 74 goat snp43706-scaffold586-249352 1 30941455 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777559 Affx-122951796 AX-385264678 1 31076048 AATTTCTATTCTATATCCATATTTCAAAGGGGAGG[A/C]TAATCCAAACTATATAATGTTAATTCATCTTCTTT M 2 1 2 1 101000 f 74 goat snp43705-scaffold586-219038 1 30971355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435144 Affx-122933675 AX-123305484 1 31142700 TGAGTTCAGACACATGAACAATCCAAGAGGTCTCA[A/G]AATTATCTTGCTTTCACAAAGCTATGGCCTTGGAA R 2 1 2 1 101000 r 74 goat snp43704-scaffold586-152386 1 31039453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383338 Affx-122972680 AX-123253696 1 31207931 TCATAGACATACTTTTCAAAGAAGTCAGCAACAGG[C/T]AAGGGAAGAAAACTGTAGAGGTTTAATATTTTGGG Y 2 1 2 1 202000 f 74 goat snp43703-scaffold586-87155 1 31104168 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393407 Affx-122965887 AX-123263763 1 31246803 AAGGTACTATAAACTTCAAGGTAAAAAGGAAGAAA[G/T]AGAGCTTATGCAAGAAGTAGGGGCACCAAAACTTC K 2 1 2 1 201000 f 74 goat snp43702-scaffold586-48283 NW_017216825.1 5106 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400479 Affx-122961296 AX-123270834 1 31290981 AAACTCTTGGTAATTTGGTAGAGGGCTCAGTTTGT[C/T]AATCATAATTCAATTAGAAATTTTTTAGAAGATAC Y 2 1 2 1 101000 f 74 goat snp43701-scaffold586-4105 1 31190808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399771 Affx-122960306 AX-123270126 1 31300494 CTTGGAATGCTGTTGCTTCCCTTGGACTATCTATC[A/G]CAGGATATCGGCATGACTCATTTCTCCACCACCTT R 2 1 2 1 101000 r 74 goat snp39621-scaffold504-1771923 1 31200246 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452440 Affx-122920573 AX-123322773 1 31372611 ATTTACTCCAAAACATATCAAAATTACAAGTACAT[A/G]TAAAGCAACTCTTGCTGAGAATGACCTGAAGGCTA R 2 1 2 1 101000 r 74 goat snp39623-scaffold504-1844040 1 31273379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437575 Affx-122931878 AX-123307913 1 31406776 ATAAAATGAAGGGCCCCATGACTTGGCCTTGCTTG[C/T]AATGCCAAACTCAGAGCCTATGTCACATCTCTCTG Y 2 1 2 1 201000 r 74 goat snp39624-scaffold504-1878205 1 31308155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392118 Affx-122966346 AX-123262475 1 31438929 ACATCATTGGGTGTAAAAGTAGTGGTAGATGACAT[A/G]GGTGTTTTTAAATGACTTTTTACTTTTTATATAAA R 2 1 2 1 101000 f 74 goat snp39625-scaffold504-1910358 1 31340588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770969 Affx-122976126 AX-385258132 1 31468932 GTAGGATACAGTAAAAATGGCAGTTGAAGGCAACT[A/C]AGAATTGGCCAGAGATGATCATGTAGGCTCAGTGT M 2 1 2 1 101000 r 74 goat snp39626-scaffold504-1940361 1 31370413 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439638 Affx-122930615 AX-123309975 1 31505181 AGCAGCAAAAATATGGAATCTCACAGATCTCCATC[A/G]TCCCTTCTCCTATTGCATGAATATCTCCCCCTAAG R 2 1 2 1 101000 f 74 goat snp39627-scaffold504-1976610 1 31407403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787354 Affx-122959444 AX-385274379 1 31572944 AAACCAGAATGCAATGGGCATTACAGGGAATTCAC[G/T]AAGAATTTGTAAATGCAGAAAGAAACCTCACTCCC K 2 1 2 1 201000 r 74 goat snp39628-scaffold504-2044373 1 31475731 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443046 Affx-122928146 AX-123313383 1 31650404 GAGAATTTCCTGCAAGTTGTAGGGACTTCTTACAA[C/T]GGTAATGGAGTTGGTGATAAGAATTGAGTATTTAA Y 2 1 2 1 101000 r 74 goat snp39629-scaffold504-2121833 1 31554758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787942 Affx-122977847 AX-385274963 1 31686810 TTGCCTATCATGGACTCTGTGTACATGGAACAAGG[C/T]ATATTTTGTAGTAATAATTTTGTGTCTCTCTTTTC Y 2 1 2 1 101000 f 74 goat snp39630-scaffold504-2158239 1 31591091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378367 Affx-122976820 AX-123248726 1 31735067 TTTTCCTTCACAGCAACCTTGATAGATTGACCTTA[G/T]GCCAAATTCTAGCCATTGCTCACCAGTATTATTTT K 2 1 2 1 101000 f 74 goat snp39631-scaffold504-2206496 1 31639443 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320791658 Affx-122942323 AX-385278649 1 31792497 TTAAATCTGCCTTATATTTCATCTTTTTGCATGCT[A/C]TTTAATCTCTAAATTTTTATCAGGGTGTAATTTTA M 2 1 2 1 102000 f 74 goat snp39632-scaffold504-2263926 1 31695876 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446053 Affx-122925834 AX-123316390 1 31844300 CAGTGGTTGCATGTTGACTAGTGTCTTAAAAAATG[C/T]ATATACATAGAAGAAAGGAGAGTTTTTCTATATTC Y 2 1 2 1 101000 f 74 goat snp39633-scaffold504-2315729 1 31747777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782581 Affx-122960165 AX-385269655 1 31877341 ATCTCTAAGCCAAACTAGGATTTATCTTTTTGAGC[A/G]TGGTAAATTTGAAAGTCAATGAATAAGCTAAATAT R 2 1 2 1 101000 f 74 goat snp39634-scaffold504-2348770 1 31780687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422103 Affx-122943572 AX-123292450 1 31989669 TGGTAAGACTGTAACAAAAGGATAGCAATACTGGT[A/G]GTATTACTTAGATAAGACTTGCCATAAGGAACCTA R 2 1 2 1 101000 r 74 goat snp39636-scaffold504-2461098 1 31891409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378873 Affx-122976510 AX-123249232 1 32029005 TGTTCAAACAAAATGAAAATAATTTTCTTCTGTTG[C/T]ACACTGAACAGTTGTCTTCTGAATTTTCTCTCATG Y 2 1 2 1 103000 r 74 goat snp39637-scaffold504-2500434 1 31930942 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272481 Affx-1111832854 AX-519546203 1 32052342 TGGTAATCTTATCCAAATCAGCCTTACAAAAATAC[A/C]AGAATAATATTTGACCAGATATTTGGGCATTACAT M 2 1 2 1 201000 f 74 goat 1_32052342_AF-PAKI 1 32052342 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378404 Affx-122976791 AX-123248763 1 32105813 AATCTTAGTTTTCTGAATGTTGAGCAGAAAGCTCA[G/T]CATTCAGATACTTGGTATTTTTCACATGACACAAA K 2 1 2 1 201000 r 74 goat snp39638-scaffold504-2577242 1 32007183 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793173 Affx-122977795 AX-385280151 1 32168715 TTTTCAACAAACGTACTTGAATAGAAGAGAACTAT[A/G]CTTCAGGCAAAATATCATAGCAATCAAAATCTTTG R 2 1 2 1 101000 f 74 goat snp39639-scaffold504-2640144 1 32070418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414976 Affx-122949060 AX-123285325 1 32203281 TTCAGCCTTTTCTGAGTGACCTCTGTGATCCTGTT[A/G]GTTCCACTCACAGCACACAGAATTCTGCAAGTATC R 2 1 2 1 102000 f 74 goat snp39640-scaffold504-2674710 1 32104190 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453570 Affx-122919767 AX-123323903 1 32247874 CCCTAGCCTGACAATGTTTTCTCCTTGTTGATGAT[A/C]GGTAAATAACTTGGCTTCCCTGGTGACTCAGATGG M 2 1 2 1 101000 f 74 goat snp39641-scaffold504-2719303 1 32149008 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375375 Affx-122979225 AX-123245734 1 32284750 TTATCATAGTTGATTTAAGGATAATCTAATCCCCC[A/G]CCCTCATTTTCTTTCCTAGTTACATTTTTGGTGTC R 2 1 2 1 101000 r 74 goat snp39642-scaffold504-2756179 1 32185936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788909 Affx-122954246 AX-385275924 1 32317187 TCCCAGGTCAGGAGCTCTTCAGTCATCTTTAAACA[G/T]CATGGCAAAAGTATTCTGAGTATCCCATTTAAGAT K 2 1 2 1 101000 f 74 goat snp39643-scaffold504-2788616 1 32218548 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768585 Affx-122969662 AX-385255765 1 32371900 ATATCATAAATCAGTTTGGATTGGAAATATTTACA[C/T]GTCTCTATTTTCATGTCTGTCTTATAATATGTAAC Y 2 1 2 1 101000 r 74 goat snp39644-scaffold504-2843329 1 32273239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398866 Affx-122961047 AX-123269221 1 32400762 ATGCATTCATTGTTTAGCATAATTCTAAATCGTTG[C/T]AGAATTTTAATAATCACTAGTTTTCTTATTAATTT Y 2 1 2 1 101000 f 74 goat snp39645-scaffold504-2872191 1 32302098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781136 Affx-122935655 AX-385268221 1 32441442 TAATATGTTACTAGAAATGTAAAATAATAGAGATC[A/G]TAGAATACCACAAGTTATTCTGTGATTAGGGAGAT R 2 1 2 1 201000 f 74 goat snp39646-scaffold504-2912871 1 32341875 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448971 Affx-122923123 AX-123319306 1 32478836 ACTTTTAAGTAATAGCTAATTAATTAGAGTTGATC[A/G]TGTGAAGTTATGAAGGCAACGCCAAAGAAAGCTCA R 2 1 2 1 201000 f 74 goat snp39647-scaffold504-2950265 1 32380002 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427258 Affx-122939550 AX-123297601 1 32571782 TACTGCCCAGTTACACATGAAACCCAGTTACAAGA[A/G]GCCTTATTCCCTGGTGGCTCAGCAGTAAAATACCT R 2 1 2 1 101000 f 74 goat snp39649-scaffold504-3043211 1 32474058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787598 Affx-122964789 AX-385274622 1 32607163 TATATTAAGAAGCTCCACTTTGCAATCTGAATTGC[A/G]TAGATCAAATCCTGGTTTTTCAACTTACCTGATTT R 2 1 2 1 201000 f 74 goat snp39650-scaffold504-3078592 1 32510721 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419758 Affx-122945876 AX-123290106 1 32648201 GAAATTTTTCCCAGCTGTGTCCTTAAAAGATGCCT[A/G]CTTCTTCTCTTCCTTCTTTTTTAATTCATTTTATC R 2 1 2 1 103000 f 74 goat snp39651-scaffold504-3119630 1 32551520 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396927 Affx-122963197 AX-123267282 1 32701218 TATATAATGTGGTCACGAACTTCTGTGCTTGTGTC[A/G]TTTAGGTCTGGAAAGAAATTTTCCCCTTCAGGCTC R 2 1 2 1 101000 r 74 goat snp39652-scaffold504-3172647 1 32605549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441542 Affx-122928704 AX-123311879 1 32745517 ACCAGGGAACCCCCTGAAGGTGTTTTAAGTTCAGG[C/T]ATACCATCAAGAGCATTAAGGATGACTGAATCTAT Y 2 1 2 1 101000 r 74 goat snp39653-scaffold504-3216946 1 32649975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377442 Affx-122977532 AX-123247801 1 32795978 ATTAAATTAGTTAGTGAATTAGTCAGCTTCTCCTA[A/G]TTTCTTACCATTTTATTTGTGTTTTAGATAAATAT R 2 1 2 1 101000 f 74 goat snp39654-scaffold504-3267407 1 32700396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772166 Affx-122942405 AX-385259321 1 32854399 ACAAAAACCCAATTATTTTGAGGGATTATGTAAAT[A/G]TTCAGTGGAAAACTCCAACACCAAAGAATCCTCTC R 2 1 2 1 101000 r 74 goat snp39655-scaffold504-3325828 1 32759036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798863 Affx-122961313 AX-385285793 1 32904812 CATGTTTGGCCATTAAATATAATCCTATTAAGTGT[A/G]TTCCCAAAATATTGCTGCTTGAAAGATCTCCCTTT R 2 1 2 1 101000 r 74 goat snp39656-scaffold504-3376241 1 32809892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802266 Affx-122972284 AX-385289170 1 32949446 CAACAAAATATGTAAAAACTTTCCGAAGTTTGTAC[A/G]CATGTTTCAGATTGTTCTTTGGATTTGTTGTTCGG R 2 1 2 1 101000 r 74 goat snp39657-scaffold504-3420875 1 32854543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415223 Affx-122948968 AX-123285572 1 32992808 AACATACTGATAAACTTTAATTAATAATTGTATGG[C/T]AGTTTTCCGCTTTGAGAGGGATTTTCATAATGTGA Y 2 1 2 1 101000 r 74 goat snp39658-scaffold504-3464237 1 32898402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771161 Affx-122972674 AX-385258321 1 33047065 TTTCTGGACACTGAGCATAACCTTCTTGCTTTCAA[A/G]CAAGAGTTTTCTCAGCAGCAAGTGCTCTGTGCTTA R 2 1 2 1 102000 r 74 goat snp39659-scaffold504-3518494 1 32953856 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405500 Affx-122956005 AX-123275852 1 33138232 CTTTGTAAACTCTACAATAAGAAGTCACTTCATCA[C/T]ATTACCTTTCAAATTTCTCTTCAAAGCAGGTGAAA Y 2 1 2 1 201000 f 74 goat snp39661-scaffold504-3609661 1 33046832 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777111 Affx-122968383 AX-385264234 1 33170352 TATTAATACAGTGTTGAACTCTTGCCAAGTTCTTC[A/G]TTCATTTTAAATATCACTAGAGTTGTTTTTAGTCA R 2 1 2 1 101000 f 74 goat snp39662-scaffold504-3641781 1 33078697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449881 Affx-122922351 AX-123320216 1 33214499 TGATTTTTCTAAGTTAGATTTTTTTCCTCTCCTGA[G/T]CTCTTCTAGCCCTGCACATGTCTATATTTTAGCAC K 2 1 2 1 101000 r 74 goat snp33078-scaffold385-4043804 1 33122610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796122 Affx-122973958 AX-385283073 1 33244710 GTAGTTCTGCAAATTCAAATTGTCAATACTTAGCG[A/C]GACTGCTGAGCATAGCATCTTTCACCCTATATATA M 2 1 2 1 101000 r 74 goat snp33077-scaffold385-4013593 1 33152870 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404933 Affx-122956435 AX-123275285 1 33277508 AGTGTGCAGCACTGAATAACAAACAATGACTGTTA[C/T]GGGAATTATAGTCTGAACCTTTATTAAGCATTCTT Y 2 1 2 1 101000 r 74 goat snp33076-scaffold385-3980795 1 33186052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785477 Affx-122975112 AX-385272522 1 33323047 ACACAGAATATAGAGTGGGATAAAATTAATGATTC[C/T]AAAGGAAAATGTTTTACTTTCCAGAATGTAAATGA Y 2 1 2 1 101000 r 74 goat snp33075-scaffold385-3935256 1 33232874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775475 Affx-122941155 AX-385262606 1 33367693 GTCTCCCACCTTTTACCCTTCCAACGATTTCTTCA[C/T]GGACTTCCCAAATTCTGCACTCTCTCTTTTCCTTC Y 2 1 2 1 101000 f 74 goat snp33074-scaffold385-3890610 1 33279852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408471 Affx-122954427 AX-123278822 1 33411509 TCCAATCTTTTTATTTAAATGCCTAGTTTATTCCT[A/G]TGTAGAAGTCAGAGGACTTCTTATTCCATAAATTG R 2 1 2 1 101000 r 74 goat snp33073-scaffold385-3846794 1 33323465 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445465 Affx-122925216 AX-123315802 1 33441438 CTTTCACTTAGCTCTTATATTTATCATATAAATTC[A/G]TAAATTATCATTCTGCTCTTTACCTGTCATCTCTG R 2 1 2 1 102000 r 74 goat snp33072-scaffold385-3816865 1 33353498 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444213 Affx-122927247 AX-123314550 1 33496096 CTCTCTTCCATTTATGAGCTTGAAACCTTAGTCAA[C/T]AGTTGTAGACAGACTTCCCAGTTAAATTGTTCCAC Y 2 1 2 1 101000 f 74 goat snp33071-scaffold385-3762207 1 33409174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781335 Affx-122925732 AX-385268420 1 33556765 GGGAAGCCTCTTTGTGTAGTATGCAGTGCTTGAGG[C/T]CTATTTCCATTCTGTGGCATGATTTTGGCTAAGGT Y 2 1 2 1 201000 f 74 goat snp33070-scaffold385-3701538 1 33470260 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428955 Affx-122938881 AX-123299297 1 33652553 ATTAACAGCTCTGCCATGTCTGGCTCTGGCACTTG[A/C]TCTGCCTCTTCAAATTGTGTTTATTACTTTTTTCA M 2 1 2 1 101000 f 74 goat snp33068-scaffold385-3605750 1 33568531 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786446 Affx-122924677 AX-385273480 1 33683921 TTTTGTAAAAGTAATTCTCTCATAGAATACTTTGG[A/C]GTGCTAATGCTAGAGAGAAAACACAGCGACCAGCA M 2 1 2 1 201000 r 74 goat snp33067-scaffold385-3574382 1 33600278 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453877 Affx-122919516 AX-123324210 1 33743729 CATACCTTGGACTTCTGCGGCTCCTCCCCAGGGGT[A/G]CAAAGCAATGATGTGAGAAATTGAGTTGAGGGAGT R 2 1 2 1 101000 r 74 goat snp33066-scaffold385-3514574 1 33660195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440511 Affx-122929351 AX-123310848 1 33779278 TCATAAGTAGCAAGTTAGAGTGCACCTCTTTGAAG[C/T]AGATATTTTATCAGTTCAGTTCAGTTCAGAAGCTC Y 2 1 2 1 101000 f 74 goat snp33065-scaffold385-3479025 1 33695905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797438 Affx-122949131 AX-385284377 1 33822290 GTTAAGTAGAAAGAAAAATATAGGTGGATGTATTC[A/G]CTTTGAAACTTGATGTTTTTTATCTGACTTGCATG R 2 1 2 1 201000 f 74 goat snp33064-scaffold385-3436013 1 33739319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768632 Affx-122946982 AX-385255811 1 33867309 GTTTGGGGTTCCTTTGCCCTATCTTAATTATGGCT[A/G]TTTTATATTTGTCCACATCCCTAAAATAGATGAAT R 2 1 2 1 101000 f 74 goat snp33063-scaffold385-3390994 1 33784322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392479 Affx-122966147 AX-123262836 1 33920665 GGCCCAATGTAGTCACAAGGGTCTTTATAAGAGGA[C/T]GATGGAGACATCAGAGTCAGAGAAAGTGATGATGG Y 2 1 2 1 202000 r 74 goat snp33062-scaffold385-3337638 1 33838037 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439175 Affx-122931057 AX-123309512 1 33972323 AATATTGCTGGTGAAATAAGCATCGTTGTCACATA[A/G]GATAAACAGTGGTGTATGTATGTACATCTGAAGTA R 2 1 2 1 102000 f 74 goat snp33061-scaffold385-3285980 1 33890095 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389891 Affx-122968128 AX-123260248 1 34010730 ACACTTGAATCTCATTCTCATAGGCCCTATTTCCA[G/T]CTGGCTTTAGAAAGAAATCTCAAAACTGATAAATC K 2 1 2 1 101000 f 74 goat snp33060-scaffold385-3247573 1 33928646 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770941 Affx-122944838 AX-385258104 1 34086621 ATCCCCAGAGATGTTTTTTACCCATCCTTTTAGCT[A/G]TTTCAGAGGATTAAAGGAGCTAAACTTTTATTCAG R 2 1 2 1 101000 f 74 goat snp33058-scaffold385-3171682 1 34004534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415393 Affx-122948748 AX-123285742 1 34120799 ACCTATTATATATACATGCATGTATGATTATAAAC[C/T]ACATGCTGTGTGGGAGTGGTGTGTACAGAAATAAC Y 2 1 2 1 303000 f 74 goat snp33057-scaffold385-3137504 1 34039039 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408321 Affx-122953764 AX-123278672 1 34165403 TTTTCCATCCCCTTCCAAGAACAGAGCCCAGGGGG[G/T]GCTTCAAAGATGTGCAGCTTTCCTCCCACTTTCAA K 2 1 2 1 101000 r 74 goat snp33056-scaffold385-3092900 1 34083982 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793704 Affx-122969553 AX-385280676 1 34223245 GCAGAGGTTGAGATCATGGTTATATAAACCATGTG[C/T]GAGACTATTCCATTGCATAGTAAAGCAAAATTTGC Y 2 1 2 1 201000 r 74 goat snp33055-scaffold385-3035058 1 34138097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799808 Affx-122920212 AX-385286734 1 34277586 AATGTGTATGGCTGCACATCATTGGTTTTATAGTC[A/G]CAAAGTGTTCTTGTGTTATTTGGAATATGTAACAG R 2 1 2 1 101000 f 74 goat snp33054-scaffold385-2980717 1 34193175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435157 Affx-122933665 AX-123305497 1 34328839 ACATTTACATAGGAAAACAGTCTACTTTGGAGGCC[A/G]TCTCTTCATTCTTGTCTTTTTTCTCTTTCCTTTTT R 2 1 2 1 101000 f 74 goat snp33053-scaffold385-2929464 1 34244474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384704 Affx-122972109 AX-123255062 1 34394851 TAACTCCTCTCTCTTTTTATATGAATTTTAATATC[A/G]TCCACACTTTATTGATTTTTGCAGCAATGGCTTTG R 2 1 2 1 101000 r 74 goat snp33052-scaffold385-2863452 1 34310491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789302 Affx-122920767 AX-385276313 1 34428777 GCCAAGGTGTACCAATGCAAACATAAAAGGGAAAG[C/T]AGCAATACAAGTTGAGAATGGGTGATTCTGGTAAG Y 2 1 2 1 101000 f 74 goat snp33051-scaffold385-2829526 1 34344499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778171 Affx-122959189 AX-385265286 1 34470009 CTTCTTTTTCACCAGTATCTGTTTATCTCCTGATG[C/T]GAACTTTTCCCTTAGAGTTCTATTTTATTGTTGTC Y 2 1 2 1 101000 f 74 goat snp33050-scaffold385-2788294 1 34383535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377661 Affx-122977852 AX-123248020 1 34542502 AAATGATAGGATTGTTTCAAGAGTCTCAACAAAAA[C/T]TAACAGGAATTTGGTGAGTTAATAGCACACATTAT Y 2 1 2 1 201000 f 74 goat snp33049-scaffold385-2715801 1 34456345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272483 Affx-1111832855 AX-519546205 1 34568359 CAATGCAGGAGACACAGGTTTGATCTCAGGGTCAG[A/G]AAGATCCCCTGGAGGAAATGATAATCCATTCCAGT R 2 1 2 1 303000 f 74 goat 1_34568359_AF-PAKI 1 34568359 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776955 Affx-122929705 AX-385264079 1 34574697 AAGAAAAAAAATCGAGGCAAATTTGATGCAGTCAA[C/T]GAAATCAGACTATGGGCAATTTCAAAGGGCATATT Y 2 1 2 1 101000 r 74 goat snp33048-scaffold385-2683606 1 34488831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379405 Affx-122976124 AX-123249763 1 34604390 AGGCCAACCAAGAGTGCATATTATAAACATTGACA[C/T]ATAAATACTTGAAATCAATGAAAATGACTGTAGAG Y 2 1 2 1 101000 f 74 goat snp33047-scaffold385-2653913 1 34519393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769578 Affx-122969229 AX-385256748 1 34661964 ATGACAATTTTAGATATCCTGCATTTGAGATAATG[A/G]GGAGTCAAATGGAAAAAGCAGAACAGAATATTTAG R 2 1 2 1 101000 r 74 goat snp33046-scaffold385-2596339 1 34577468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432904 Affx-122935323 AX-123303245 1 34700536 AAAGATGGGTGTGCATCGCTGAGATGGTCTGGGAA[A/G]CCAGTGGGTGGCCAGATAGATCCTGGAGAGCCCAG R 2 1 2 1 101000 f 74 goat snp33045-scaffold385-2557767 1 34616605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399325 Affx-122961372 AX-123269680 1 34733894 CCAGTCTTGCTGCTGGGTGCATGATGCCTCTATAA[C/T]ACGCTCTGCAAAACAAACGCTGAAATGTTTGCACA Y 2 1 2 1 201000 f 74 goat snp33044-scaffold385-2524409 1 34649810 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790135 Affx-122960685 AX-385277140 1 34765898 TTTGACACAATGAAGTATTGTCAAGGTTGCAAATC[A/G]TTTGATCAATATCTTGTCAACACATACAAGCTAAA R 2 1 2 1 201000 r 74 goat snp33043-scaffold385-2492405 1 34681855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768233 Affx-122920824 AX-385255414 1 34854285 ACCTACTGGTGCTAATGTTCAATATTTTCAAGTTG[C/T]ATTTCTTTGCTTCTTACTCAAATACTATGAAGACG Y 2 1 2 1 101000 f 74 goat snp33041-scaffold385-2404018 1 34771056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423387 Affx-122943130 AX-123293733 1 34922766 GCCCTAATACAGACAATTTGAATGCAGTATAACTA[C/T]GATTGACTAAAATACATCAAATAAGATTAAATCCA Y 2 1 2 1 101000 f 74 goat snp33040-scaffold385-2335537 1 34839863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379121 Affx-122976745 AX-123249480 1 34968008 ACTGAAGAAATGCTGGAGAGCGGAAGACACTAATG[A/C]CTAAACACAATGCGAGATCAGAAACAATATCCTGA M 2 1 2 1 101000 f 74 goat snp33039-scaffold385-2290295 1 34885351 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442480 Affx-122927932 AX-123312817 1 35013622 TAGGGAATTACCAGAGATAGTTTTACCTAATCTTG[C/T]GTCAAATCACTCTTGGGCTGGGTTAATATAGCAAA Y 2 1 2 1 101000 r 74 goat snp33038-scaffold385-2244681 1 34931170 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427352 Affx-122940108 AX-123297695 1 35102649 CTCTGCTTGCCTGGCGTTTCTTTTAAGACTATTTT[A/C]AATAACACCAGCATCTTAAAACAATTTTAAAAATT M 2 1 2 1 102000 f 74 goat snp33037-scaffold385-2155654 1 35020771 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398464 Affx-122961589 AX-123268819 1 35142195 CTGTGTATAAGAAAATATATATAATCATTCATTTG[A/G]TTGGAAACACCATGAAAATGTTTCCCATGGGTACT R 2 1 2 1 103000 r 74 goat snp33036-scaffold385-2116108 1 35059688 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764520 Affx-986698961 AX-385252190 1 35175132 TCGAGGGGTTCTTCCTTAATCAGGGGTCTAACTGC[A/G]TCTACTACATTGCACGTGGGTTCTTTACTGACTGA R 2 1 2 1 600010 f 74 goat 1_35175132 1 35175132 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38431369 Affx-122937034 AX-123301710 1 35179576 GAGCCATGGTGGGTGACTATCTTTAAGTCTTCTCT[A/G]CTATCTTCAGAAGAGTATCAAGCATCATTTCTGTC R 2 1 2 1 101000 r 74 goat snp33035-scaffold385-2078727 1 35097123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419350 Affx-122945641 AX-123289698 1 35236784 GAAGTGACTGTCCATTGTAAGGCTATTAAACAGTA[C/T]AAGCATATGCTTAACTCAACTATAGGGAAACAACA Y 2 1 2 1 101000 f 74 goat snp33034-scaffold385-2021519 1 35154404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378090 Affx-122977161 AX-123248449 1 35280244 TAAACATAAAAGGTACCTGAAAACTGAAACAGAGA[A/C]TATAACTCAAAGAGCTAGATCCTGAAGCTAGTGAA M 2 1 2 1 101000 r 74 goat snp33033-scaffold385-1978059 1 35198354 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409749 Affx-122953011 AX-123280100 1 35310183 CTAGCTTTTCTAGGTCCAGCTCAGATAAAAATATT[A/G]CTTTGATGTCTCAATTATTCCAATTTAAGTGGATT R 2 1 2 1 101000 r 74 goat snp33032-scaffold385-1948120 1 35228638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791754 Affx-122964808 AX-385278745 1 35369088 ACTAATAATAATAACTGAGAGCATTTACATTATTC[A/G]TCTTTCCTTTTTACAGTAACTTTTTAATGCTCTCC R 2 1 2 1 101000 r 74 goat snp33031-scaffold385-1889215 1 35288988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775430 Affx-122924492 AX-385262561 1 35427159 TCTCTTAGGATACTTCTCTATTCATTTCTTTATTC[A/G]TTTAGCTATTTATGTGTAAATGAAAATCTAGTATG R 2 1 2 1 202000 f 74 goat snp33030-scaffold385-1831144 1 35347269 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442535 Affx-122928536 AX-123312872 1 35484937 AAAACAGCTCAACTGAAATGAACAAGATCAGGACT[A/G]CTATAAGAGGATGGTACCCAGCTCCCTGGGCACAC R 2 1 2 1 101000 f 74 goat snp33029-scaffold385-1773366 1 35405378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384146 Affx-122972805 AX-123254504 1 35528794 TATGGTGAGTGAAGAAGCAAAAACATTTAGAGAAG[G/T]GTCACCCCGGTTCATTTTCTAGTAGCTGGTTGATA K 2 1 2 1 101000 r 74 goat snp33028-scaffold385-1729509 1 35449368 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774895 Affx-122974207 AX-385262029 1 35560005 AATCCTTTCAACACTTACGGATTGAGAACCTACTA[C/T]GAGTCAGGTACTTCCCTAAGTGCTAGGGATGTGTA Y 2 1 2 1 101000 r 74 goat snp33027-scaffold385-1698298 1 35480656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408476 Affx-122954423 AX-123278827 1 35620318 CATTTTTTCAGTAAATAGTTTGGAGCAACACACCA[G/T]GTGATCTTTCAGTTTAGAGGGATTATCTCAACCTG K 2 1 2 1 101000 r 74 goat snp33026-scaffold385-1637985 1 35542059 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796692 Affx-122933036 AX-385283637 1 35665220 TGAAGTCAAGGATTTTTTGGTCTATTTAGGTTCAC[A/G]ATTTGCACAGAGGGCTGTATCTTTTCCCACGTCAC R 2 1 2 1 101000 r 74 goat snp33025-scaffold385-1593083 1 35586673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768221 Affx-986698964 AX-385255406 1 35668607 CTGACCTGCATATAGGTTTCTCAAGAGGCAGGCAG[A/G]TCTTTTATAATGAGCATCTAATGAGACAGTAGCCA R 2 1 2 1 600010 r 74 goat 1_35668607 1 35668607 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 38394014 Affx-122965015 AX-123264369 1 35725684 CTACATTGTACAGTGATTTCTAAATTAAAATAAGC[A/G]TAGATTGATGTCTGCCCCTTGCCATTTAGTGTTGA R 2 1 2 1 101000 r 74 goat snp33024-scaffold385-1532619 1 35647014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447640 Affx-122923976 AX-123317976 1 35758508 TATACATACAACTACGGAAGTTTCTGGAGCTGGTT[A/C]TAAAATATTGTGTTAGACTTTATAAAGTATGCAGT M 2 1 2 1 102000 f 74 goat snp33023-scaffold385-1499795 1 35679903 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429161 Affx-122937979 AX-123299503 1 35787611 AGAGACATAAGGAAATGTGTCACTTTGTTAAATGA[C/T]GAATGACTATTATTGTGGCATTTTATTAATATTTA Y 2 1 2 1 101000 f 74 goat snp33022-scaffold385-1470692 1 35708926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798742 Affx-122930341 AX-385285673 1 35824319 AACATAGTGATTAGGAATAATATCCACCTTATTCT[A/G]CTCAGTTCAAATTCTAGGTGGACTCCATGCTGCTT R 2 1 2 1 101000 r 74 goat snp33021-scaffold385-1433984 1 35745570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426966 Affx-122940402 AX-123297311 1 35872468 ATCCTGCAGAAAGCTAAGGCTTTTCAACATATTTG[C/T]GGCTTCATTGCAGGAAGCAGACTGTTATTTGTTGA Y 2 1 2 1 101000 f 74 goat snp33020-scaffold385-1385835 1 35793670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788074 Affx-122941272 AX-385275094 1 35908486 TGTGTCCAGGAAAATGACTCTAGAGAACTAGCACC[A/G]TGTCAGCCAAGTGTATGCTAAAGGTCTCTTTCATA R 2 1 2 1 101000 f 74 goat snp33019-scaffold385-1349817 1 35829812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770808 Affx-122944956 AX-385257972 1 35938663 AGTAGAAAAGAATCAAGGATTGTTTGTTTCACTCA[G/T]ATTTTGCAAATAACAGTCAAATTGTTATTGATCAA K 2 1 2 1 101000 f 74 goat snp33018-scaffold385-1319640 1 35860363 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770686 Affx-122972459 AX-385257850 1 35974730 CCCTAAGGGAAAATGGATTTGGGTGCTGAAGAAGA[C/T]GGAGATGACTAAGACATTTGCAAGACTGTATTCCC Y 2 1 2 1 101000 f 74 goat snp33017-scaffold385-1283573 1 35892630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377725 Affx-122977390 AX-123248084 1 36010079 GAACATCACTAGCAAAAAACAAACAAAACTGATGG[C/T]AATCAGTGAGCTACGAAGTTTGCAGAAATACTTGA Y 2 1 2 1 103000 r 74 goat snp33016-scaffold385-1248224 1 35928096 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411471 Affx-122951801 AX-123281821 1 36058743 AAGATTGAATGACTAGGACAAGAATAAAGAGCTAG[C/T]GGATAAAAGATATCTCCAGGTCAAGTTCATTAACT Y 2 1 2 1 101000 r 74 goat snp33015-scaffold385-1199560 1 35975222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415406 Affx-122948737 AX-123285755 1 36100519 GTGTCTGGAAACATAGCCAAATTCTTCACTGTAAA[C/T]GGGCACTTTTTGAAGTACACTCTCACAGACACTAA Y 2 1 2 1 101000 f 74 goat snp33014-scaffold385-1157784 1 36016892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802467 Affx-122925705 AX-385289371 1 36159580 TTTCTAATTCTGCTTAGAAAATCTGATTTCTGTTC[A/G]TCCAGTTTGTTTCTAAACTTTGCAAACTTTTTTAT R 2 1 2 1 201000 f 74 goat snp33013-scaffold385-1098723 1 36075408 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454262 Affx-122919645 AX-123324595 1 36196279 TTCCTGAATACAATTATTGCCATTTATACCTGTAA[C/T]ATTTCTCCTGTCTTCTTTTTTATTATAATTATCAA Y 2 1 2 1 101000 f 74 goat snp33012-scaffold385-1062024 1 36112237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434227 Affx-122934840 AX-123304568 1 36243448 AATCATTTTTTGTTAATATTATAAATGGCTATGTA[C/T]ATGATACGTAAAGAAAAGACAAGACAGTCATCTAA Y 2 1 2 1 101000 r 74 goat snp33011-scaffold385-1014855 1 36159321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416396 Affx-122947859 AX-123286745 1 36281052 TCTGATCTGTTGAAACTTGCTTTCCTGTTCTTTGA[C/T]GACATTGCTAAAATATCTCATAGCTTCTTGTTCAC Y 2 1 2 1 201000 r 74 goat snp33010-scaffold385-977251 1 36196783 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395788 Affx-122963661 AX-123266143 1 36339852 GTGTACATTTTTTTCCCTTTCTGCAAGAATTTGTG[C/T]AAGACTAGAATTACTCAGTTGTGAAACAAGTGTAC Y 2 1 2 1 303000 r 74 goat snp33009-scaffold385-918451 1 36255924 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415479 Affx-122948707 AX-123285828 1 36383616 GGACCAGCCCAGCTTTAGGACTCTTGTTTCAACAA[A/G]TAGTTGGACTGAGTCTTCTTCTGCAGTCCAATGCT R 2 1 2 1 101000 r 74 goat snp33008-scaffold385-874687 1 36299605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425381 Affx-122941564 AX-123295727 1 36419846 AAATTCCCCAGAGGCTTCTAGTGAATCACCAAACC[C/T]GAGGATGAGAATCACCAAACCTGTGTAAGGGAGCC Y 2 1 2 1 202000 r 74 goat snp33007-scaffold385-838457 1 36335724 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415966 Affx-122948421 AX-123286315 1 36451947 CTAGAAATCTCTAATTTTATGATAATTCAGATGTC[A/G]TTATGCATTTGTTCCAGACCCAAAAGGTACTTTAA R 2 1 2 1 101000 r 74 goat snp33006-scaffold385-806356 1 36367854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393212 Affx-122965497 AX-123263569 1 36486943 AAGCTCTAAATGGTCTGGAGTAATATTAGCATAAA[C/T]AGATGGCAATTTCAAAAACACCTACTCTTAACAAT Y 2 1 2 1 101000 f 74 goat snp33005-scaffold385-771360 1 36402633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426252 Affx-122940335 AX-123296598 1 36517028 TTATAGTTCGCAATGTTTTATCATATATTTTGTTA[C/T]ACAGTCCTCATAAGAATGCTATGCTATAGGGACAG Y 2 1 2 1 101000 r 74 goat snp33004-scaffold385-741275 1 36434010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776315 Affx-122967986 AX-385263443 1 36567970 ATTAGTTAATATCTTGTTAACAAGGTATTTCTTTG[A/C]GCTGAAGGGATAAAATGAGTTTTATTTCCTTCAAG M 2 1 2 1 101000 r 74 goat snp33003-scaffold385-690333 1 36485405 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405293 Affx-122956849 AX-123275645 1 36600695 GAAGTGTAAATGTGAGAAGGCTTCCTTAGTAGCAG[A/G]TAAAGAAGTCCTTTGTTTCTTGCATGAACTTAAAG R 2 1 2 1 101000 f 74 goat snp33002-scaffold385-657608 1 36518594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443233 Affx-122927562 AX-123313570 1 36648141 ATCGTAACTTAAGAAAATGAAAGGATTACCATTCT[A/G]TTCCCAGAAGAAAATATATTAAAATAAGTAAATGT R 2 1 2 1 101000 f 74 goat snp33001-scaffold385-610162 1 36565845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787823 Affx-122939435 AX-385274846 1 36733745 AATATTATATTGCTTTCAAGTTTGACTGGACAACT[A/G]TTGCACAAACCTTCTCATATTTAGCATTCATTTGT R 2 1 2 1 101000 f 74 goat snp33000-scaffold385-524558 1 36651757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791085 Affx-122927991 AX-385278080 1 36785168 CTTATTTAAAAAGCATACTGAAACAGGAAAAAATA[C/T]ACCATATGGCTTATATCAGTAAATTACTAAATCAC Y 2 1 2 1 201000 f 74 goat snp32999-scaffold385-473135 1 36703248 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436109 Affx-122932663 AX-123306448 1 36827094 CTACCTGAAACTATATTTATGATGATTTTGTGAGG[A/G]AGAATTTAAATTTATTTTCCTAAGGTTAATTTTCA R 2 1 2 1 101000 f 74 goat snp32998-scaffold385-431209 1 36745589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435756 Affx-122932884 AX-123306095 1 36888070 TGACACTATCTGTTTCAGGTTGAGGGACTCCTTGA[C/T]TCAGAGCTATAGCCATGTTGACTTTTGGCCAGAAT Y 2 1 2 1 101000 f 74 goat snp32997-scaffold385-370233 1 36806837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422994 Affx-122942988 AX-123293340 1 36923275 CTGTTTGTATTCTTTTCTTAACTTCTCTCCTTCAT[G/T]TTATATTTAAGGATTGCCAGTCAGGGGAACAGCCC K 2 1 2 1 202000 f 74 goat snp32996-scaffold385-335028 1 36842054 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425272 Affx-122940974 AX-123295618 1 36967672 GAATAGTGAACAAGTCACTATGGGATGGAATAAAA[C/T]GGTTTAGCCTGATGTTTTCTGCCACTTGTAGTATG Y 2 1 2 1 201000 f 74 goat snp32995-scaffold385-290631 1 36886485 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441992 Affx-122928432 AX-123312329 1 37009256 GGGTGATTGTGTTTCCTCTCTGGATGAATTAGAGT[A/G]GTATATTTGAGATTATATTTCATTAGTTTTATTGC R 2 1 2 1 101000 f 74 goat snp32994-scaffold385-249047 1 36928989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410120 Affx-122952819 AX-123280470 1 37047090 CAGCAGGCACTGGTGTTATGCTGGCCTTGGTTTCC[A/G]GTAACACAGTGCCCTTTGCCTTGTCCTTGGTGGAT R 2 1 2 1 202000 r 74 goat snp32993-scaffold385-211213 1 36966695 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381351 Affx-122974413 AX-123251709 1 37083740 GTACTCTTATTGTGTAGGAAGCAAATACACAAATA[C/T]ACATATACATAAATGTATCTTTTTATTATGGAAAT Y 2 1 2 1 101000 f 74 goat snp32992-scaffold385-174563 1 37003110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412878 Affx-122950429 AX-123283227 1 37124395 TGTGATCTCTGGCTGAATGCTGAATGACTGAGCTT[C/T]ACCAGGAAATGGGAAGAAATGGAATAAACAGAATT Y 2 1 2 1 101000 f 74 goat snp32991-scaffold385-133908 1 37043827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463637633 Affx-1110082673 AX-515118707 1 37207420 TCCTGGCCTCTAATATTCTGTTATAATTTTCTTTT[C/T]CTGTCCTGTTATATATTTCTTTGTCTCCTTTGGAC Y 2 1 2 1 201000 r 74 goat 1_37207420_AF-PAKI 1 37207420 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789618 Affx-122974987 AX-385276627 1 37218918 TGGTGTCTTTCTGAAGGCATTCTGTGAGGAGTTCT[A/G]CTAAGGTAACATTTCATTGATTGAGGATAGTAGGG R 2 1 2 1 101000 f 74 goat snp32990-scaffold385-39385 1 37138655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781011 Affx-122945462 AX-385268098 1 37286107 CACCTAAGAGTGATGTTTGAATGACACCTTTAGTC[A/G]TTCAGCCCACAGAGTCCTGCAACCCACTTAGTACA R 2 1 2 1 101000 f 74 goat snp3220-scaffold1097-27705 1 37206100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277967 Affx-1111836183 AX-519551461 1 37291883 CACAAGCTCATAAGTATTTCCCATAGATATCTTTT[A/T]AAAAGAATTGAAGAAGATAAATGGATAGGGGTATT W 4 1 2 1 103000 f 74 goat Random2.2K-34 1 37291883 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779215 Affx-122934523 AX-385266319 1 37340764 AAGAAAATCAATCATTTGATGGATTTTGTTGAGTG[C/T]AATGCTAACATCCTTCATCAGGATTTACAGTAAAA Y 2 1 2 1 101000 r 74 goat snp3221-scaffold1097-82362 1 37262202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278845 Affx-1111836633 AX-519552316 1 37373686 AATTACTTGCTCAACCATTTACAACTGTTTTCTCA[A/G]GAGGTGGCCTTTTTGTCTCTCAAGGAAATGACAAA R 2 1 2 1 201000 f 74 goat Random2.2K_MT-180 1 37373686 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382810 Affx-122973563 AX-123253168 1 37382051 GCCAAATTACTATGTGGAACAGAGCCCTTCCCTCC[A/G]TCCTATTTCTAATTGAACTTAACATAGGTGAGAAG R 2 1 2 1 201000 r 74 goat snp3222-scaffold1097-123649 1 37303405 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773686 Affx-122935480 AX-385260826 1 37421025 TTTTTTGAATAATGTAGATGATAGGCCTCTGTCCT[C/T]CTTGGAAGTACCTGGGACACATTGAAATGTGATTT Y 2 1 2 1 101000 f 74 goat snp3223-scaffold1097-162623 1 37341709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397268 Affx-122962346 AX-123267623 1 37449902 AGGACACCTCTTAGGTAGGAATATTTGCAAGAGCA[A/G]AATCTCCTCAAGCCATGCCAACAGTGCTTCTATGG R 2 1 2 1 201000 f 74 goat snp3224-scaffold1097-191500 1 37369256 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789034 Affx-122919458 AX-385276047 1 37506683 TTCATCTATAAACCATCAGAATTATTTTTAGGAAT[A/G]CATTTTATTTATAAGCCATTGGAACCATTTAAAAC R 2 1 2 1 101000 f 74 goat snp3225-scaffold1097-248281 1 37410487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800064 Affx-122957697 AX-385286987 1 37537584 AGGTGCCTGTGTCATGCATGGTCAGGTCCGATAAC[A/G]ATATATTTCCTTGGTACTTAAAGAAACCAAATTCC R 2 1 2 1 101000 f 74 goat snp3226-scaffold1097-279182 1 37441520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379377 Affx-122976145 AX-123249736 1 37596237 ATTTCTGTAATATCACAAGTTACTTCCTCTCCATA[C/T]GCCAATTTCTTACCTCAATTCTAATCACAGTAGAT Y 2 1 2 1 101000 f 74 goat snp3227-scaffold1097-337835 1 37500953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400406 Affx-122959993 AX-123270761 1 37628188 ATGAAGTGATGCCCTTGGGTCTTATCCAAGTTGCT[A/G]TTTACTTCTGTGATGGAAGGAATGGTGACCTATAG R 2 1 2 1 201000 r 74 goat snp3228-scaffold1097-369786 1 37532726 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794407 Affx-122946840 AX-385281370 1 37664341 TCAGATTCTGACTTAGCAGCTCTATCAAGACTGTG[C/T]GTTTGTTTCTTTGCAGCTCTACCAACTCACAATAA Y 2 1 2 1 101000 f 74 goat snp3229-scaffold1097-405939 1 37569352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442142 Affx-122928326 AX-123312479 1 37706073 AATCTAGTTGAAGATTAAGCAATCATTATTCACAT[A/G]TTTAAGGGAAATGGGAGCTCACAACTTAGTGAAGT R 2 1 2 1 101000 r 74 goat snp3230-scaffold1097-447671 1 37611484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800414 Affx-122940884 AX-385287335 1 37741603 TTACTCTGTGTCTCTCTGGGAGGAAATGTAAATAT[C/T]TGATGTGAAAACACTCAACTGATAGATAAAATATG Y 2 1 2 1 101000 f 74 goat snp3231-scaffold1097-483201 1 37647463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393037 Affx-122965633 AX-123263394 1 37803036 CTCTTCCAAGAAATGATAAATATTTATGTTACCTT[A/G]TTGACAATTTTTTAGAACTTTCTTTTTTTAATCTG R 2 1 2 1 201000 r 74 goat snp3232-scaffold1097-544634 1 37710199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792929 Affx-122978819 AX-385279907 1 37818983 TATCCTTCCACTCAGTCTAATCTAGATTTCACATC[A/G]CTACTTCCCAATCTCCTTAAGAGGCCTCTCACTAA R 2 1 2 1 101000 r 74 goat snp50712-scaffold731-186 1 37725969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390220 Affx-122967782 AX-123260577 1 37849595 TTTCTACTTGTCTTTTTTTAAGAAAGATATCTTGA[A/G]ACTCTTACCATTATGGTTGACTTTAGAATAATTCC R 2 1 2 1 101000 r 74 goat snp50713-scaffold731-30798 1 37757044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782847 Affx-122933809 AX-385269918 1 37878921 GAAAAATGAGCCAAACTTATGTGAAATTCTCATGG[C/T]AACTCTTTCCCATAACCAACTCATATTCACATAAA Y 2 1 2 1 101000 f 74 goat snp50714-scaffold731-60124 1 37786349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449404 Affx-122922700 AX-123319739 1 37921830 CTCACTGGAATTTCACTGTTGGAGTGTGAAAGAAG[A/C]GATATCAGGAAGGAGTAATGCTTATTTCATTCTAA M 2 1 2 1 101000 f 74 goat snp50715-scaffold731-103033 1 37827402 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786498 Affx-122928750 AX-385273532 1 37975749 GACTATTTATTTCTGTTAAACTCACATAAAACATG[C/T]ATTGAAATTGAGTTAAATACTCCCATTCTATAAAC Y 2 1 2 1 101000 f 74 goat snp50716-scaffold731-156952 1 37881615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387584 Affx-122970265 AX-123257942 1 38005141 AAAGTTATATTGTCAAGTGTATTTCCCATTATAAA[C/T]AAGCAAAATACAAAATGTTCTGATAACTTGCAAAT Y 2 1 2 1 101000 f 74 goat snp50717-scaffold731-186344 1 37911682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410758 Affx-122952690 AX-123281108 1 38078729 TTAAAGTTCCAAGAGTAAGCAACAGAACATAGTAC[A/G]TTAATAACCTCTAGGATCCTTTCCTCTCAAGGCTG R 2 1 2 1 101000 r 74 goat snp50718-scaffold731-259932 1 37974563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788581 Affx-122921182 AX-385275598 1 38117143 AGGAAGCTGCATCCTGGGATAAGAAGAATAAAAGT[A/G]CTAGGTGATATTATCAGAGGCCAGAATTTAATACC R 2 1 2 1 101000 f 74 goat snp50719-scaffold731-298346 1 38013596 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386779 Affx-122970109 AX-123257137 1 38157991 GATTCATTCTAGCATGCTTTATAGCAGTTGCTGCC[A/G]TTTGATAAGTAACTCCATATGGACTGATGCTGAAG R 2 1 2 1 101000 r 74 goat snp50720-scaffold731-339194 1 38056256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436090 Affx-122932683 AX-123306429 1 38200476 TACCTTTCTTTGAAAGACACTTTCTAATTTGTTAG[C/T]GGGTGTTGAAGGAAACTGCTATTGCCACTGAAGGA Y 2 1 2 1 201000 f 74 goat snp50721-scaffold731-381679 1 38098862 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768873 Affx-122957803 AX-385256050 1 38251382 GTAAATTTCACACCTGTATATTTTCTCAGTGAGTT[A/G]TTAATATGTAAGGGAATGCTGGGATTTAGAACTAT R 2 1 2 1 101000 f 74 goat snp50722-scaffold731-432585 1 38152280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779168 Affx-122931979 AX-385266272 1 38282037 AAAACATCATGAGCTAATTGACACTTTTGAGAGAT[A/G]TTTTTTGCTCTAAAGCCTTTTCCCAGATTAATCAA R 2 1 2 1 101000 r 74 goat snp50723-scaffold731-463240 1 38183892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404165 Affx-122957072 AX-123274517 1 38314030 TTTCCTCTGAAATGCTAGCATTCTTCAAAGGGAAC[A/G]TATCTCTAGCTTTTAAAAATATCTGTGGAATATTT R 2 1 2 1 101000 f 74 goat snp50724-scaffold731-495233 1 38216497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277997 Affx-1111836198 AX-519551489 1 38364804 CGATTAAGAGAATATGAGCAAGCAAGCAGGCATAC[A/G]TATATGGTTTTATGAAGTCCAATCGCAATTCTGGT R 2 1 2 1 101000 f 74 goat Random2.2K-36 1 38364804 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786405 Affx-122919406 AX-385273439 1 38380679 CAAATATGAGAAAAAGAGAATATGAGTTTATACTT[A/G]TCTATGTTTTGTTATAATAAAACATAGCCATTGTC R 2 1 2 1 201000 f 74 goat snp50725-scaffold731-561882 1 38282655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773401 Affx-122975521 AX-385260543 1 38441496 TGTTTGCTCTAAGAAGATAGTCTCTTAATATTCTT[A/G]TTAAGTATATTTTATTAGGTTGATAAGCCAAAATG R 2 1 2 1 102000 f 74 goat snp50726-scaffold731-622699 1 38343797 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408117 Affx-122954251 AX-123278468 1 38497738 GTCTGTTCTAGGTCCTTCAATAAAGCCAGTATCTA[A/C]AGTATATCTCAATATGTATTTTTCTATAGAGGTAT M 2 1 2 1 101000 f 74 goat snp50727-scaffold731-678941 1 38400618 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788196 Affx-122941044 AX-385275215 1 38544627 ATCACTCTAAATGATGAGGTTTTATTGGTGCTAAT[A/G]ATTCAGAAGATTAAATGACAGGAAGCATCTTAAAG R 2 1 2 1 101000 r 74 goat snp50728-scaffold731-725830 1 38447218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797967 Affx-122922044 AX-385284903 1 38570266 ACATAATTTCCATTTCTAGTTATCTTTATTCCTTT[A/G]TGAAGCTGAATATTTCCATCTGGTATTTGTTTTTC R 2 1 2 1 101000 r 74 goat snp54661-scaffold835-1131537 1 38472544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802159 Affx-122955166 AX-385289063 1 38600702 TTTTCCCTCTAATAACTCCTGCTTATTATACTACT[A/G]TATATTCAGTGATTCCCTTTTCAAAATACTAAAAT R 2 1 2 1 201000 r 74 goat snp54660-scaffold835-1101101 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797027 Affx-122926338 AX-385283968 1 38646884 CAAAAAATGACCTGTTACTAGCCTCATGGCCGTCA[G/T]ATTATGTTACAGGCTAGACTGAATTCCTGCAGCTC K 2 1 2 1 201000 r 74 goat snp54659-scaffold835-1054919 1 38552209 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802265 Affx-122932565 AX-385289169 1 38682659 GTCTATAACTGAATACTATAAATCAATGAAAAAAG[C/T]ATAATCAATCTATGGGGAAAGTTCTATGAATATAA Y 2 1 2 1 101000 f 74 goat snp54658-scaffold835-1019144 1 38588810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776499 Affx-122953386 AX-385263626 1 38727175 AAAAGTTCGTATCTGTGTGATGTTATGTTACAAAG[C/T]ATGAGAATACGGAACAATTGCTTGTGATTGTTTAT Y 2 1 2 1 101000 r 74 goat snp54657-scaffold835-974628 1 38633539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386284 Affx-122970936 AX-123256642 1 38758902 CACTGAACTACCTATGCAATCTTCTTCCTGAGCAG[C/T]AGTTATTTTCCTAGGCCTTAAGGGATGTCTCAAAC Y 2 1 2 1 101000 r 74 goat snp54656-scaffold835-942901 1 38665588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432016 Affx-122935922 AX-123302357 1 38835121 TAGTCAGTATTACCTAAATTGTTTTTTAGGTCCAC[A/G]TTTAAATTGTATTCTGTGTTTTTGAGTCACAGTTA R 2 1 2 1 201000 r 74 goat snp54655-scaffold835-866682 1 38742639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405229 Affx-122956891 AX-123275581 1 38891952 TCCATCTAGGAATCTGTCAAAGAAATAAAGCAGTC[A/G]TTAATTAAATCCAGTGATACTGAAGCAGATTTTAC R 2 1 2 1 202000 r 74 goat snp54654-scaffold835-809851 1 38797156 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785850 Affx-122938348 AX-385272887 1 38925927 GGAATCAACCTTCTTATGCTTAGTGATTTTCAATG[C/T]AAAATATTAACCTTTTGAACACATAATAGGAAGAT Y 2 1 2 1 101000 f 74 goat snp54653-scaffold835-775876 1 38831680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799080 Affx-122939634 AX-385286010 1 38996315 TATTCTTTTTTGTTGTTTGGAGGCATATATTTGAA[C/T]ATAATGGTATATTTCAGTCTTAAATGTTCACTTCT Y 2 1 2 1 201000 r 74 goat snp54652-scaffold835-705488 1 38900381 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378495 Affx-122976657 AX-123248854 1 39101424 AGTAGTCTCTGACAGTCAGTAGCTGGTTTTACACT[A/G]TCATCAAGTCTTTGCTGTTCATAAGAACTTGTACA R 2 1 2 1 101000 r 74 goat snp54650-scaffold835-600379 1 39006247 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430929 Affx-122936845 AX-123301270 1 39131429 TTTACTTAATTCCATAGCTGTGTTTAGAATTTATG[C/T]AAGTTTGTCGGTTACTACTGGTTTTATTTTCTGAA Y 2 1 2 1 101000 f 74 goat snp54649-scaffold835-570374 1 39036266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440980 Affx-122928980 AX-123311317 1 39199482 TGCTGTATATTTTGTAATGACATGTCATTTGTTGT[A/G]TCATGGTTTTCCTCTTATTCTATATACTCCCTTAG R 2 1 2 1 201000 f 74 goat snp54648-scaffold835-502321 1 39106870 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771944 Affx-122956642 AX-385259100 1 39272991 CAATTCTTTGTTACAATAACATACAATGCCCTGCT[A/G]CATTTTTCTCTACCTATTTAAAGAACTTTGCCCCT R 2 1 2 1 201000 r 74 goat snp54647-scaffold835-428812 1 39180904 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768420 Affx-122952063 AX-385255600 1 39326464 CCTTCCATTCTGATCATATCAAGAGTTGTTCTCTC[A/G]TGCATAGACATATATTCTGAGTATGGGTTTGCCTT R 2 1 2 1 101000 r 74 goat snp54646-scaffold835-375339 NW_017212145.1 4338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414091 Affx-122949746 AX-123284440 1 39374544 AACTCTGACTTGCTTCTGTGTGAAAGAATGCAAAA[C/T]AACTCTCTTTACAGTAATTTATTTTATTTTTGTCT Y 2 1 2 1 103000 f 74 goat snp54645-scaffold835-327259 1 39285531 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779046 Affx-122932364 AX-385266152 1 39408423 GAAATAAAAACATATTAGTCTAGAATGCTTTGCAT[A/G]CATTAAAAATGTCAATTCTAGAGTCTCTTCAAAAT R 2 1 2 1 101000 r 74 goat snp54644-scaffold835-293380 1 39319428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382523 Affx-122973799 AX-123252881 1 39467151 ATTAACATCACTGTGACGTGATGGTTAATTTTATG[C/T]GTCAACTTGACTAGGCTAGAGAGTACCCAGATTTG Y 2 1 2 1 202000 r 74 goat snp54642-scaffold835-234652 1 39376585 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776057 Affx-122964844 AX-385263187 1 39498397 ATAATAAATTCATAATTCATTCACTTAGGAAGCTA[G/T]AAAGAATGCACTAAGGAAAACTGCAACAATTATTG K 2 1 2 1 101000 r 74 goat snp54641-scaffold835-203406 1 39408080 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791439 Affx-122963688 AX-385278430 1 39564609 TTTTTAAGTTAAATGGAATAGAAACATTATGAAAA[C/T]GAGCTGATTCAGTTCCTATATTTAAAAGTCTGTTT Y 2 1 2 1 101000 r 74 goat snp54639-scaffold835-137194 1 39474944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793628 Affx-122963992 AX-385280602 1 39598218 TTTTATAGCATATTTTAGCATTTGAGTTAAATGTA[C/T]GTTCCAAGATTTGTCTTATAATTTTCCTTTTTTGA Y 2 1 2 1 101000 r 74 goat snp54638-scaffold835-103585 1 39510206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790482 Affx-122954458 AX-385277485 1 39630830 GCAAGTGACTGATTTTAACATAACTACATATTCAC[A/C]TTTAAGTAATTATGTATGAAATATACTTTTATAAC M 2 1 2 1 202000 r 74 goat snp54637-scaffold835-70973 1 39543168 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400620 Affx-122960378 AX-123270975 1 39679410 TTTATAAACATGGAATCGTGCCTATCTAAAAGGAC[A/G]CTGGAAAGATTAAATGAGATGTCTGCAAGTGTCCT R 2 1 2 1 101000 f 74 goat snp54636-scaffold835-22393 1 39591951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448559 Affx-122923422 AX-123318895 1 39725029 TCTTGTGTTTATGGCAAAGATGAAGAAAGAAAACT[A/G]TTCTGATGTATGCCCAGAGTGTCCTTCATAAGAAA R 2 1 2 1 102000 r 74 goat snp45624-scaffold627-23127 1 39649784 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447100 Affx-122924484 AX-123317436 1 39765979 TCATGGGGCCAATCCATTCTAAATCGCTCCTAAAC[A/G]CCAGCTTTACCATAATTTTTCTATATCTTTAGACT R 2 1 2 1 101000 f 74 goat snp45625-scaffold627-64077 1 39691067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476146 Affx-1251763649 AX-586011579 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 4 1 4 1 20000 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 539476402 Affx-1251763649 AX-586011806 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 4 1 4 1 20000 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562165094 Affx-1251763649 AX-606940506 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166073 Affx-1251763649 AX-606941482 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166132 Affx-1251763649 AX-606941540 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166217 Affx-1251763649 AX-606941625 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166273 Affx-1251763649 AX-606941681 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166356 Affx-1251763649 AX-606941764 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166358 Affx-1251763649 AX-606941766 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 320793759 Affx-122929684 AX-385280731 1 39818492 TTGACAATATTATGCCTCCAAATGTCAAAATAAGG[C/T]AGAGTTACACCTTTAAAGAGTTCTTTTTAAAACAA Y 2 1 2 1 101000 f 74 goat snp45626-scaffold627-116590 1 39744620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789868 Affx-122924402 AX-385276875 1 39861782 TTCCACAACAGATTCTAAGCTGGATTCTACAACAG[C/T]GATTATCATACGGTCTCTATTCTTTAGAAAATCAA Y 2 1 2 1 101000 f 74 goat snp45627-scaffold627-159880 1 39794053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396808 Affx-122963289 AX-123267163 1 39891664 CCTGCAAATTATACTCTACTCCCTAACCTGTAATT[A/G]TTTATTTAGCACTTATAACAGGATTAGAGTATTAT R 2 1 2 1 201000 r 74 goat snp45628-scaffold627-189762 1 39823947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771970 Affx-122928209 AX-385259126 1 39937203 GAAAAATTGGTTGTAGGAAGTAACATATCAGTAAC[A/G]TATCAGCCCTTTCTTATACATTGAAGGAATCATAG R 2 1 2 1 101000 r 74 goat snp45629-scaffold627-235301 1 39870443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775363 Affx-122977884 AX-385262494 1 39974998 TATCAAAGGATGAAATATATTAACTGGAAAGAAAA[G/T]AAGAGGGAATCTTCTTGTTTCCTGGGACAATGGAG K 2 1 2 1 102000 r 74 goat snp45630-scaffold627-273096 1 39908671 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786216 Affx-122921120 AX-385273251 1 40008925 ACTTCATTTATGGAAATATAACATCCTCATATCTA[A/G]CCTCTGATGTTCTTTGTTTTATGTTCTTTATTTTA R 2 1 2 1 101000 r 74 goat snp45631-scaffold627-307023 1 39943149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784532 Affx-122959662 AX-385271581 1 40064962 CTTAAACAGTTGCCTGGGTTCAGCGAAAAGCATCA[C/T]GGGCTGATGACTCAAGGTCTAAAAAAGCTTAGAAA Y 2 1 2 1 101000 f 74 goat snp45632-scaffold627-363060 1 40000300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401681 Affx-122959559 AX-123272034 1 40098906 CTCGGATGTCCTCTTGGAATTGAAGAATTTAGGCA[C/T]GCTCACCTCTTGTGGCCTTCAATGTAATTTTCAGA Y 2 1 2 1 101000 f 74 goat snp45633-scaffold627-397004 1 40034873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772103 Affx-122963762 AX-385259258 1 40152526 ACTTATAAGAATGGATGGCCTTGCATGTAACACCT[A/G]TAAAGTAAAAATATTCATGAAAACTTACTCTTATC R 2 1 2 1 201000 r 74 goat snp45634-scaffold627-450624 1 40080187 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413167 Affx-122950345 AX-123283516 1 40242625 GTGAGGACACAAGACAATTCTGAAAAGAACAGTAT[A/G]CAATAGCCAAATCTATACTTACAGTAGATGCTATC R 2 1 2 1 101000 r 74 goat snp45635-scaffold627-540723 1 40170770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790996 Affx-122975835 AX-385277993 1 40351474 AGCAACATCTGGCATATTTATATTTAAGCATTCTT[A/G]CGTTGTTTTGACATCTTAAGAAATGACTTGAGTAA R 2 1 2 1 101000 f 74 goat snp45637-scaffold627-649572 NW_017213414.1 11436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271729 Affx-1111832856 AX-519545525 1 40382233 ATTTCTTATGAGTTTTGTATCACTTGAACTTGAAT[A/G]CTAAATAATTATGAGACAAAATATAAGACACTGGT R 2 1 2 1 101000 r 74 goat 1_40382233_AF-PAKI 1 40382233 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793260 Affx-122978213 AX-385280238 1 40392392 TCATTTTATTGTTTTATGAGCATGATATTTTTATA[C/T]ACAGTGAGTACACCTTAAAGGACACATTAGATGAT Y 2 1 2 1 101000 r 74 goat snp45638-scaffold627-690490 1 40320736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407273 Affx-122955341 AX-123277624 1 40448394 TTCTGGTAAGTAACATAGAAAAAAGAGAACACTGA[C/T]ATTGTATATTAAATAAGAAAAATCTATAGGATCAG Y 2 1 2 1 101000 f 74 goat snp45639-scaffold627-746492 1 40376869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278041 Affx-1111836221 AX-519551532 1 40493433 CTACTACTCATATTTTAGGCAAATTTTGGGATATA[C/G]TGGACGACAGGGAGGCCTGATATGCTGTAGTTCGT S 4 1 2 1 201000 f 74 goat Random2.2K-40 1 40493433 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391266 Affx-122967364 AX-123261623 1 40536709 TACCACTGTATCCCCAGTATGTCTCAGTGCCTGCC[A/G]TATAATAGGTGCTCAGTAATATAGAGTCTACTAGC R 2 1 2 1 102000 r 74 goat snp45640-scaffold627-834807 1 40465437 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772135 Affx-122976298 AX-385259291 1 40646208 CCTACTGAATATAAATATAGGTAAGACCACTGGAC[A/G]TAACCCATATTTGGGGAAAATGTAATATTAATTTA R 2 1 2 1 202000 r 74 goat snp45642-scaffold627-944306 1 40576012 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443985 Affx-122926919 AX-123314322 1 40692485 CAGGTATATTATTGTACAGAAGCTCTCTAGAGTTT[A/C]TTCATCTTGCTTAAATAGCCCTTTATGCCCATTGA M 2 1 2 1 101000 r 74 goat snp45643-scaffold627-990583 1 40622392 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383012 Affx-122973321 AX-123253370 1 40737264 CTTGCTAATGCTTCATAACACACTCAGGCAAGAAT[A/G]GTTGCAATGTACTTCTTTTCAGCAGTTCATTTTTA R 2 1 2 1 101000 f 74 goat snp45644-scaffold627-1035362 1 40666859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794490 Affx-122968171 AX-385281453 1 40778205 CCTCAGCAAATAATCATTAAATTCCTATTATAATC[A/G]TAGCACCACACTAAATACTGTAAAGTAGATTACAA R 2 1 2 1 101000 f 74 goat snp45645-scaffold627-1076303 1 40707648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415050 Affx-122949486 AX-123285399 1 40825652 AAACTAACATGAATAATTATTTTTTAGATAATTAT[A/G]CTCAACTCTGTGGGTCATATTGTTACTTTATTCTA R 2 1 2 1 101000 r 74 goat snp45646-scaffold627-1123750 1 40754893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430535 Affx-122937200 AX-123300876 1 40877770 ATAGAAGAGGGTACTGACTGTTTCCTTTGTTTCTG[C/T]AATCTCCAAATCTAGTTTATAAGCATCCTTTCGTA Y 2 1 2 1 201000 r 74 goat snp45647-scaffold627-1175868 1 40807132 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797961 Affx-122974596 AX-385284897 1 40906966 TCTGTGTGTTCCTAACGTTTTCATCATTTGATTTG[A/G]AAAGCTCACCAATGTTTTTAACAAGAATCCCTTTG R 2 1 2 1 101000 r 74 goat snp45648-scaffold627-1205064 1 41912588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441850 Affx-122929042 AX-123312187 1 40985539 TTCTTTAAATATTGAGCCTCTGTTTCATTTTATAC[A/G]TGATTCTAGCTCAGAAAAAGCAACTTGAATATTTT R 2 1 2 1 101000 r 74 goat snp45650-scaffold627-1283637 1 41991755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438590 Affx-122930947 AX-123308927 1 41023263 CATGCATTCTGGGTTGGAACAAACCTCTGTTTCAT[G/T]TCCCATCATGTGTGTGTCTCTCCTATTCTGTAAGG K 2 1 2 1 101000 f 74 goat snp45651-scaffold627-1321361 1 42029469 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764475 Affx-986698941 AX-385252160 1 41040072 TACATTTGTGTGTCTCCACCTGCGTGGCCTCTGCA[A/G]GTGCTGCAGGTGACCTGGGTACTGCTGCTGGTGTT R 2 1 2 1 600010 f 74 goat 1_41040072 1 41040072 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320768117 Affx-986698907 AX-385255319 1 41040084 TCTCCACCTGCGTGGCCTCTGCAAGTGCTGCAGGT[A/G]ACCTGGGTACTGCTGCTGGTGTTACTGGGATGTGC R 2 1 2 1 600010 r 74 goat 1_41040084 1 41040084 Ancestral_priority_1043 ancestry 0.452 neutral IMAGE 10K 10K ancestral 38416588 Affx-122947649 AX-123286936 1 41086564 AATGGGAGGCTTGTTTGGACTCAAGACTAGCCACA[C/T]GTGCTTTGCAGACAGCAGCTGCTCAATAAATGCTC Y 2 1 2 1 101000 f 74 goat snp45652-scaffold627-1384662 1 42092506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394540 Affx-122964518 AX-123264895 1 41119103 GAAATATCTGGCAGGTCATATACCTCCTCACCACC[A/G]CTTAGTCATATCAGGGTGCCCTATGTGCCCCCCTC R 2 1 2 1 201000 r 74 goat snp45653-scaffold627-1417201 1 42124959 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796841 Affx-122925584 AX-385283784 1 41175942 CATTCAGTTTTAAGATATTTATGAATGACAAGTTA[C/T]GGACTAAGTTAACTGGTGTTTATAGCCTCCTCCAT Y 2 1 2 1 101000 r 74 goat snp45654-scaffold627-1474040 1 42183311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408997 Affx-122953892 AX-123279348 1 41205379 TGGAAGTGAGTCAGATCCGCTTTAAGATATCAGGA[C/T]AGAAACCACTATATTCTTCTGAAAGAGAAAGATGG Y 2 1 2 1 101000 f 74 goat snp45655-scaffold627-1503477 1 42213350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377639 Affx-122977870 AX-123247998 1 41240203 TAAAATAAAATTTAAAATTGAAGTCTCCTTTTCAT[A/G]CACAAAGTCTATAGGAAAATAAACTGAATAAATAA R 2 1 2 1 101000 r 74 goat snp45656-scaffold627-1538301 1 42248227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765422 Affx-122922880 AX-385252926 1 41291547 CATCTGCCCAGTCACTTAGTTAGTCTCTCTCCTTT[A/G]CTAATCACTCCTTCACATCTTACATGTCACCAAGT R 2 1 2 1 101000 f 74 goat snp45657-scaffold627-1589645 1 42300836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425314 Affx-122940943 AX-123295660 1 41321332 CACTGTTCAGTAGCCTTTTCTGGTCTTTTCTTTTC[A/G]CTCCTTGTGTGAGCCAATGTTCCTGGTTGCAACAT R 2 1 2 1 201000 r 74 goat snp45658-scaffold627-1619430 1 42330682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802850 Affx-122978572 AX-385289748 1 41351022 CAGCTTTATGACTTAATAATTACCCACACACTGAG[A/C]TGAACATTTTGATTATTTAGTTTTAGGACTGCATA M 2 1 2 1 101000 f 74 goat snp45659-scaffold627-1649120 1 42360248 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423898 Affx-122942287 AX-123294244 1 41393212 CCACAAAGTAGCCCAAAAATCTGAATTCTCAAATT[A/C]AATTTGTGATGACCATCTATCCAACTGTCTCCTTT M 2 1 2 1 101000 r 74 goat snp45660-scaffold627-1691310 1 42402942 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775371 Affx-122928590 AX-385262502 1 41424091 ATTAAAATCATCACATGGTTGTAAAGATTAGATGT[A/G]TCTCTGTTTTGGTTACTATTCCAATCTTCTTGTGT R 2 1 2 1 101000 r 74 goat snp45661-scaffold627-1722189 1 42432156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389014 Affx-122968640 AX-123259372 1 41467809 CTATTGCATAGCTCTGTGCTAGAGCAAAGGCTGCT[A/G]TGGCTGACAGGAAAACTCAGTTGTGAGAGATGGAG R 2 1 2 1 101000 f 74 goat snp45662-scaffold627-1765907 1 42476634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802003 Affx-122922758 AX-385288907 1 41515686 AAGAACTATCCTGTAAAGGAGGAGGTGTTCGTGGA[A/G]ATTCAAGCCAACAGGAGAGGTCTAGCTATCTAGCA R 2 1 2 1 101000 r 74 goat snp45663-scaffold627-1813784 1 42527294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407689 Affx-122954582 AX-123278040 1 41575735 TACTACCAATTTTCCTCACAAATTTGTGCCAAGAC[C/T]CTACCCATTTTTTTCTGTCTGGACTCTGAACCTAG Y 2 1 2 1 101000 f 74 goat snp45664-scaffold627-1873833 1 42587747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395912 Affx-122963603 AX-123266267 1 41619883 AACATGCCTGCCCTCTTCTGCTATTCCAAATACCT[C/T]CTCTCTATACATAATTATGCAGAATCTTACCTTAA Y 2 1 2 1 201000 r 74 goat snp45665-scaffold627-1917981 1 42631758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440548 Affx-122929319 AX-123310885 1 41684337 CTTCCTCATGAAGCTTATAAACTAATAAGGGAAAC[A/G]TGCACAAAGAACAGAATATAGAGAATAATAGATGC R 2 1 2 1 101000 f 74 goat snp45667-scaffold627-1982435 1 42696022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386993 Affx-122969949 AX-123257351 1 41720467 ATCCCTTGTGTTAGTATCTCCCTGGAAAATGAGCA[G/T]CAGGAGAGCTCCATAAGGAAAGAAAGGGACAATAA K 2 1 2 1 101000 f 74 goat snp45668-scaffold627-2018565 1 42733630 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427472 Affx-122940019 AX-123297815 1 41751899 CCAGACAAAGTCCTACTAATCCTCTGAGACCTAGT[C/T]CAAACTCTCTTTCAAAAACAAAAATTCTTTTAAGA Y 2 1 2 1 101000 f 74 goat snp45669-scaffold627-2049997 1 42765831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274919 Affx-1111834493 AX-519548501 1 41775891 TGCTCTCACCTCACCCCGGAAGCCTGGCCCCTCTA[A/C]GATCCCTGCAGATGCTGTCTGATCCATCTGCAACC M 2 1 2 1 202000 r 74 goat GoatD01.038250 1 41775891 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444462 Affx-122926541 AX-123314799 1 41826427 GGCAGTAAATGAGTTAAAGAGAACTGAGGCCTTTC[C/T]ACCCATCACTACAGAGTCCTGTGTGTCTCCTTTAA Y 2 1 2 1 201000 f 74 goat snp45670-scaffold627-2124525 1 42840961 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414867 Affx-122949146 AX-123285216 1 41866739 ACACTTGTGTGATTTCTGTAGGAAAGACACCTGGA[A/G]GTGGATTTCCGAAGTCAAAAAAGCATAAATATTAA R 2 1 2 1 101000 r 74 goat snp45671-scaffold627-2164837 1 42881260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773601 Affx-122969083 AX-385260741 1 41927914 GAAAATATTTAGCTTCTCTTTTAGAGATCTACCCA[C/T]AAATTCCTTCATCCCCCCAAAAGTTCATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp45672-scaffold627-2226012 1 42943225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411514 Affx-122951674 AX-123281864 1 41963997 AGCACCTACAAAATAATATCCCCAACAGAGAGCCA[C/T]GCAATGTGTATATAATTCAATTAAAATTCTCTACA Y 2 1 2 1 101000 f 74 goat snp45673-scaffold627-2262095 1 42979321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439777 Affx-122930509 AX-123310114 1 42005589 TGTGGTTCCTTCAGAAGTAGCCAACTACAACTTCA[A/G]TGCTACCAAATCATTCCTTGTTTCCTCTTTAGCTA R 2 1 2 1 101000 f 74 goat snp45674-scaffold627-2303687 1 43021857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403296 Affx-122957845 AX-123273649 1 42056149 TTAACTAGGCTAGGAAAAGCTATATGGCTTCTGCT[C/T]ACTGCTTCTGAGATGCTGGCTCAGCTCTCTGGAAG Y 2 1 2 1 101000 f 74 goat snp45675-scaffold627-2354247 1 43072890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787531 Affx-122963317 AX-385274555 1 42169072 GAGTTATATAAAAATTAAGCTATTAAATCAATAGA[C/T]GAATGAATTTTCTTAGGTCTAGTTGGAAAGTCAAA Y 2 1 2 1 202000 f 74 goat snp45677-scaffold627-2467170 1 43186110 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768405 Affx-122952801 AX-385255585 1 42204788 CTTAAATTACAAGGTAATGAGTTTTTAATATCACT[A/G]TAAAGCAAAAAAACCAAGTTGTTGAAGTAGCTCTC R 2 1 2 1 101000 r 74 goat snp45678-scaffold627-2502886 1 43222479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393764 Affx-122965206 AX-123264119 1 42246346 TATCCAAAAGCGTATTTCTTTTGGAGAAAACTGAT[A/G]CAAATGTGCTAAACTATGTTTGAGTTAGAAGCAGG R 2 1 2 1 101000 f 74 goat snp45679-scaffold627-2544444 1 43264436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432821 Affx-122935391 AX-123303162 1 42283895 TCAGGGAAAGAGTTATTAAACCCAGTCTGGGATAA[A/C]ATGTTGAGATGGAATTGAATTTGGAGCCCTCTTCT M 2 1 2 1 101000 f 74 goat snp45680-scaffold627-2581993 1 43301912 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380698 Affx-122975165 AX-123251056 1 42315461 AAGAGAACCTCTTCGAAGTATAAGACATGAGTAGA[A/G]TATGGTACATGACTCATGGTTGAAAAATGTTTTAG R 2 1 2 1 101000 r 74 goat snp45681-scaffold627-2613559 1 43333599 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442021 Affx-122928410 AX-123312358 1 42476050 CAACCTGACATAACTCAGGAAAGAAACAATGATCA[C/T]GAAGAAGAGTCAATAAATATTACCCAAAGCAAAGC Y 2 1 2 1 101000 r 74 goat snp45684-scaffold627-2774148 1 43495461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790224 Affx-122923839 AX-385277228 1 42506261 AGCTACCAGTAAATGGTAACCAATAAAACGTTCAA[C/T]GTGGTAATTCACAAATTCATAAACTGAGAGCAAAC Y 2 1 2 1 101000 f 74 goat snp45685-scaffold627-2804359 1 43522281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388995 Affx-122968653 AX-123259353 1 42675968 AGATTTTTCCTAATTAAAGAAATAAAGAGGTGGAG[C/T]ACTTGGGAAAGGGAAGAATTCATAGTGGGAAAAGA Y 2 1 2 1 201000 f 74 goat snp45689-scaffold627-2974066 1 43695904 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780973 Affx-122964132 AX-385268060 1 42719188 GTTTTAAGAGGAGTAAGTATTCAATTATCTAAATC[A/G]TCTCTCCCAAATCTGCTACAAAAGAAAAAAGCAGG R 2 1 2 1 101000 r 74 goat snp45690-scaffold627-3017286 1 43739121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429441 Affx-122938502 AX-123299783 1 42764315 GGTAAACATGGAAGTGAACAAAACAGAAAACCTAT[A/G]CTCTCTGGAAAAAAAACAAAGTTATACTTTGGAAT R 2 1 2 1 201000 r 74 goat snp45691-scaffold627-3062413 1 43783780 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440573 Affx-122929301 AX-123310910 1 42842609 CTTCAGAACTAGGAGAGAAATGTGGTAAGAACCTG[C/T]GGTGTTAAAAAAGAAAATCATATGCAACTAGATGC Y 2 1 2 1 101000 f 74 goat snp45693-scaffold627-3140707 1 43862317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271730 Affx-1111832857 AX-519545526 1 42912608 TAGAAAACCAGTGTCTCTGTCGCTTACTCTTTTTC[A/G]TTTTATTGACAACTTTTTAACCATGTAAAAACCAT R 2 1 2 1 201000 r 74 goat 1_42912608_AF-PAKI 1 42912608 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801543 Affx-122975885 AX-385288452 1 42924341 TCAAAGTACAGGTGAACAGGTTTTTTAGTTGAAAC[G/T]CATTGTAGCAGTTCAGGATGTTACTAGAATAGTTG K 2 1 2 1 101000 f 74 goat snp45695-scaffold627-3222439 1 43943543 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405123 Affx-122956970 AX-123275475 1 42987386 ACAGAGACGTATGAAAATATAATGAGTCACTACAT[A/G]CTACCACACAGATTTGTAAAATCTCCATTTATTAT R 2 1 2 1 101000 f 74 goat snp45697-scaffold627-3285484 1 44006897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403820 Affx-122957957 AX-123274172 1 43019891 TGTAACAGTTTACAGTGTAGCCCCTGGAGTCACTC[C/T]GGAGTGTGCACAGCCCAAATGACGTAACCTTGGAA Y 2 1 2 1 101000 r 74 goat snp45698-scaffold627-3317989 1 44039576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416709 Affx-122947560 AX-123287057 1 43085413 TACTCATTAATTTATCAAATATATAATTTTAAAAC[C/T]TCAGAATGCAAGGGCAGAGTTTAGTTACTAACTTT Y 2 1 2 1 102000 r 74 goat snp45699-scaffold627-3383511 1 44105754 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435947 Affx-122933537 AX-123306286 1 43126836 ACCCTAGCATATGTCACACACTCACCCCTGTGTGT[A/G]CACAGCAAAACACTATTCTAGACATTGTGTTTGAT R 2 1 2 1 101000 r 74 goat snp45700-scaffold627-3424934 1 44147063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396240 Affx-122963333 AX-123266595 1 43213913 TCTGTTTGTTTTATGTATAATGTTCAGGGGTTTTC[A/G]CTGTAACTTAATAGGAGGAATAGGGGAAAATATGA R 2 1 2 1 202000 f 74 goat snp45701-scaffold627-3512011 1 44234714 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409169 Affx-122953199 AX-123279520 1 43287950 AAGTCTCGGGTATTTATTTGAAGCCCTTGTGCCTG[A/C]AAACAGGTGAATGCCTGGGAGGGTAGCATCACCAG M 2 1 2 1 102000 f 74 goat snp45702-scaffold627-3586048 1 44307169 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411946 Affx-122951147 AX-123282296 1 43350764 GAAATAAATGGTGGTGAATCTAGGATAGCATCGTG[A/C]TTGTCTCTGTTTGGGAAAAAAAACAGTTGTCTCTG M 2 1 2 1 201000 f 74 goat snp45703-scaffold627-3648862 1 44370048 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429395 Affx-122938535 AX-123299737 1 43421226 TTCTATAGAACATAAGGCTGTCCAGGTTTTCATTG[G/T]AATTGTATTGAATCTATGGAAAGTTAACATCTTAC K 2 1 2 1 101000 f 74 goat snp45704-scaffold627-3719324 1 44440450 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404430 Affx-122956762 AX-123274782 1 43455370 AACCCCTATAATTTCAAAACAACTTCAAAAAGTGT[A/G]TTAGACATATTTGAGGGGCATTAGCTAAAACATTA R 2 1 2 1 201000 f 74 goat snp45705-scaffold627-3753468 1 44475064 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381717 Affx-122974701 AX-123252075 1 43523812 AAAACTTGGCTTTTGCCATACTATTTTTGAGAGTA[A/G]ACTCTCTTAATTTAGATTGCATCCTCCTCCACTTT R 2 1 2 1 101000 r 74 goat snp45706-scaffold627-3821910 1 44543678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451924 Affx-122921018 AX-123322257 1 43559892 TCATTACCACAGTGGTAAATAAACGCTCTGACTAC[A/G]TGCAAAGCTTCACCTCCTTCACATGTGCTGACAAC R 2 1 2 1 201000 f 74 goat snp45707-scaffold627-3857990 1 44580536 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440988 Affx-122928974 AX-123311325 1 43606522 TAATGTTTCTTGGCTAAAACTCATGTCTATTTGCT[A/G]TAAATTCTGGATTCGTCTTTCACCTGGAGCTGGGT R 2 1 2 1 101000 r 74 goat snp45708-scaffold627-3904620 1 44627650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423251 Affx-122942676 AX-123293597 1 43641800 TGTTTAATGTAGTGGGAGTGGCCTTTGGAGTAAGA[C/T]GGTCTGGATTCAAATCTTAGCATTGTTTTTTAGTA Y 2 1 2 1 101000 f 74 goat snp45709-scaffold627-3939898 1 44663553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782627 Affx-122947481 AX-385269700 1 43679308 CCACATAATGATTTGAGGTGTGAAATTCTTGTTTT[A/G]TTCTTTCATCTACAAGCTCAGGCTTGGACTGATGC R 2 1 2 1 101000 r 74 goat snp45710-scaffold627-3977406 1 44700317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774788 Affx-122940393 AX-385261922 1 43722397 CTTTTATAAGTGGCTTAGAACTACAGTTTCTACAG[C/T]ATCTTCAACAAAGAGCAATAACTGTGGAAAGAAAT Y 2 1 2 1 101000 r 74 goat snp45711-scaffold627-4020495 1 44743752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410533 Affx-122952162 AX-123280883 1 43760353 ACCACAGTGCAGAGAGAATCAAGGAAAGAGGAGGA[C/T]ACACCTGGGAGGGATTTGATTTTGGAAACTCCAAA Y 2 1 2 1 201000 f 74 goat snp45712-scaffold627-4058451 1 44783106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783054 Affx-122941389 AX-385270121 1 43810013 TATAGGGCTGTTATGAGGATTAGTTAATACATTTA[C/T]AAGTTAAAGATGATATCTAGTACACTGTAGGCACT Y 2 1 2 1 101000 f 74 goat snp45713-scaffold627-4108111 1 44833935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787602 Affx-122961545 AX-385274625 1 43849860 CTATTCACCCAGTGACCACCATTATTACCTCTCCA[C/T]ATGTCTAAGAGTACATACTCATATGGAACATACTT Y 2 1 2 1 102000 f 74 goat snp45714-scaffold627-4147958 1 44874041 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274222 Affx-1111834075 AX-519547822 1 43860293 CCATGACACTCTATTTTGTTAAGTCCTTTAATAAG[A/G]TATGAGAACAAAGCTTTCTGTGTGGTTTTAGATCT R 2 1 2 1 101000 r 74 goat GoatD01.017256 1 43860293 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782253 Affx-122971705 AX-385269331 1 43903364 AGGTTCTCATGAATACCTGACCTGTCAGCTTCCAA[C/T]GGTATGCCTAATACGGTGCTAGTAACTTTTGGGAT Y 2 1 2 1 101000 f 74 goat snp45715-scaffold627-4201462 1 44928327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411504 Affx-122951683 AX-123281854 1 43940061 CAGAGAAGATACAGTGGTAAGGAACCTTGCCTTTA[C/T]AATGTAAGACAGTATGAAAACAGTTTGTAACAAAA Y 2 1 2 1 201000 r 74 goat snp45716-scaffold627-4238159 1 44965062 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412800 Affx-122950488 AX-123283149 1 43971635 CCCTGAGGGGGATCCCAGTAGAGAAACATGAGAAC[A/G]TAGAACGTGTGCAACACGCTTTGACTGGGGACGTT R 2 1 2 1 201000 f 74 goat snp45717-scaffold627-4269733 1 44996660 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446767 Affx-122925319 AX-123317103 1 44019493 TTGTTATTGATGATACTTTGGGGAAAAAGCTGATA[C/T]ATAAAATGAAGGTAATAATTCAGATAGTCAAGATA Y 2 1 2 1 101000 f 74 goat snp45718-scaffold627-4317591 1 45044651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423418 Affx-122942618 AX-123293764 1 44051428 GTGACTTAACCGTATCGTGTGAGGCATGCTCATAA[C/T]GGAGGGTACATTGGGCAGCTGATAGCTTTCATGGA Y 2 1 2 1 101000 f 74 goat snp45719-scaffold627-4349526 1 45076527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410376 Affx-122952442 AX-123280726 1 44104991 ACTACTTTTTTTTTAAATACGCAGGACCCCAAACA[C/T]ACATTTCTGTTGATTAACTCTCCTGAGCCTTATCA Y 2 1 2 1 101000 r 74 goat snp45720-scaffold627-4403089 1 45127830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385438 Affx-122971318 AX-123255796 1 44141261 ATTTGACCTAGGTTACCTTCTTCTCACAGATGGTG[A/C]CTGCAGCCATGAAATTAAAAGACGCTTACTCCTTG M 2 1 2 1 101000 f 74 goat snp45721-scaffold627-4439359 1 45164326 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424701 Affx-122941692 AX-123295047 1 44204071 TCAAGCCCTGTCTTCCCACCTCAATGCTTTGCATA[G/T]ACATGGAATACAGTTTGTTACTTGAACAAATAAAC K 2 1 2 1 201000 r 74 goat snp45722-scaffold627-4502169 1 45227493 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444945 Affx-122926689 AX-123315282 1 44246286 GAACATCATGGTTAGTAACAGTTGATCTTAGAACA[C/T]AGAAAATTTTAAAACTACATTAAAAGAAATCATTT Y 2 1 2 1 101000 f 74 goat snp45723-scaffold627-4544384 1 45270236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278057 Affx-1111836229 AX-519551547 1 44276563 GGGTGGGGAGAAAAGAACAAATGAGGCCAGAAAAA[A/G]AAAGCAACCAAAGGAATAAAAAATCCTTTTAATAA R 2 1 2 1 103000 f 74 goat Random2.2K-41 1 44276563 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406149 Affx-122956180 AX-123276501 1 44282338 TAGTAAAGTTAAATCAATATGCTTTCAGCTGAGCT[A/C]CCTGCCACTTACAGTTATCCTCTGATCCTTAAATT M 2 1 2 1 101000 r 74 goat snp45724-scaffold627-4580436 1 45306556 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386592 Affx-122970689 AX-123256950 1 44322066 CTATATAAGTATGCTAAAACTGCACTTTCAATCAA[A/G]ATGTCCCTATAGTTTTCACTTGCCCAGAGTGGGAG R 2 1 2 1 101000 r 74 goat snp45725-scaffold627-4620164 1 45346020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418349 Affx-122946592 AX-123288697 1 44354500 TTTCAGGCTTCAGCCCATAATATCACACTCCAGAG[C/T]GCCAGACTCTAATTTCCAACTGCCTGATGGCTATT Y 2 1 2 1 201000 r 74 goat snp45726-scaffold627-4652598 1 45379239 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778808 Affx-122962163 AX-385265916 1 44441627 ATTACCATATTAAGTGCAGGCCTTTGTTAGAAATT[A/C]TTCTGTAAGCAAAACCATCCACTCACCTTTGCAAG M 2 1 2 1 101000 f 74 goat snp45728-scaffold627-4739725 1 45469437 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452024 Affx-122920905 AX-123322357 1 44484946 CTTCATTTAACCACTGCAGAAGGCTTAAATTATCC[A/G]CTCATGGTTGGGTCCATGAGTTGACAAATATGAAT R 2 1 2 1 101000 f 74 goat snp45729-scaffold627-4783044 1 45512858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787628 Affx-122973468 AX-385274651 1 44542856 GCAAGATACCAGTGAGACCTGTTGAAAAAGAAATA[C/T]AATCTTAACACAAAATCTAAGCAATACAGAAGAAT Y 2 1 2 1 101000 f 74 goat snp45730-scaffold627-4840954 1 45570681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436096 Affx-122932678 AX-123306435 1 44576529 AACATTATTTGGTCACAGTCAATTCATTTTTATCA[C/T]AGGACAAATTATTTCATATGACATCTAAATGCCTC Y 2 1 2 1 101000 r 74 goat snp45731-scaffold627-4874627 1 45604530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433696 Affx-122934539 AX-123304037 1 44642395 AAAATGCAATCTACAAAAAAAACCTGGCATCTTTA[A/G]CTGGTGGAGAAACAAAAACCCACTAAATAATAGAA R 2 1 2 1 101000 f 74 goat snp45732-scaffold627-4940493 1 45672113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409532 Affx-122953615 AX-123279883 1 44713787 TTTAAAATGTAAGTCACATTGCTAAGATTTTTCAC[A/G]TTACTAATCTGTGACCATTCAAAATTTTGTTTTCC R 2 1 2 1 101000 r 74 goat snp45733-scaffold627-5011885 1 45743895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404201 Affx-122957673 AX-123274553 1 44752854 ATCAGTAGCTAGAAATCTTGCCCAAAAGTCTACTA[C/T]AGGCCCAGTCAATTTGAGCCATCATTCTAACAAAT Y 2 1 2 1 101000 r 74 goat snp45734-scaffold627-5050952 1 45783017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411566 Affx-122951634 AX-123281916 1 44798907 GTATCTAGTGCTGAGATTGGAATATAGATGCAGCA[G/T]AGCAGTAAATGTTGGATGAAGTGCATGCCTTATGG K 2 1 2 1 201000 f 74 goat snp45735-scaffold627-5097005 1 45829266 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431121 Affx-122936594 AX-123301462 1 44978248 CTGTATTAGTAAGAGGGTGGTATTCGGTGACTCTG[C/T]GGCTTCCAGGGCCCTGAAGGGGCCTGTGCACCAGG Y 2 1 2 1 101000 f 74 goat snp45738-scaffold627-5276346 1 46009213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787755 Affx-122939991 AX-385274778 1 45017243 GTTTAACAAATGCTGGTTTTCTACCCACATTCCTT[A/C]GTTTCTCCATGGTAAAGTTGTGAGGTTATTTTCAA M 2 1 2 1 101000 f 74 goat snp45739-scaffold627-5315341 1 46047812 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396680 Affx-122962836 AX-123267035 1 45078234 TCACACTGCAGGCGGATTCTTTACCAGCTGAGCCA[C/T]GAGGGAAGCCCAAACTTATTTAGGTTGTACCCTAA Y 2 1 2 1 103000 r 74 goat snp45740-scaffold627-5376332 1 46108279 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476149 Affx-1251763652 AX-586011582 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 4 1 4 1 20000 f 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 539476405 Affx-1251763652 AX-586011809 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20000 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562165893 Affx-1251763652 AX-606941302 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562166286 Affx-1251763652 AX-606941694 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 f 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562166534 Affx-1251763652 AX-606941942 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 320781734 Affx-122958763 AX-385268816 1 45120445 ACCATGTTTTAAGATATGGCTTATTATGTTACCTT[A/G]CTGAGATCTCTTTAGAGCTAATTGTCAACAACCCT R 2 1 2 1 101000 r 74 goat snp45741-scaffold627-5418543 1 46151442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787546 Affx-122933049 AX-385274570 1 45162409 AAGTTATAAAGTGATCACAATTGACTTCTATTTCA[C/T]CCTTTGACGTCAAGACCATTTATAGTTTGGTGTTT Y 2 1 2 1 101000 f 74 goat snp45742-scaffold627-5460507 1 46193883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794721 Affx-122965569 AX-385281681 1 45191764 TGATTATCCATAGTGCTGATAAAGGCTCTGCTACT[A/G]TCTTTGGATTTGCAGCTGTTATTTTCACTCACCTT R 2 1 2 1 101000 f 74 goat snp45743-scaffold627-5489862 1 46223584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395272 Affx-122964085 AX-123265627 1 45240392 TTCCCATAATTGCCTCTGCCCCTGGGGTTAAGCAG[C/T]GGCTATATAAAGAGAAACAAGCAATGGGATTCCTT Y 2 1 2 1 101000 r 74 goat snp45744-scaffold627-5538490 1 46272440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431922 Affx-122935992 AX-123302263 1 45287136 ACATAAGAAGAGTACTTATATCCACTGTCAGAGAG[C/T]ACAGGCTAATTCTAATGAATAGCGTTTGGAAAAAG Y 2 1 2 1 101000 f 74 goat snp45745-scaffold627-5585234 1 46324507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379111 Affx-122976752 AX-123249470 1 45318610 CAACTCCTGAACTTCTATTGGACCTTTTGGAACTC[A/C]TGAGACATCATAGTGAAAATTTAAAGGCATCAGCT M 2 1 2 1 101000 f 74 goat snp45746-scaffold627-5616708 1 46348481 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416049 Affx-122948352 AX-123286398 1 45352002 AAATTCCCTTTATCACCCTGTACTTCCACACAAAG[C/T]AGTGTTAGAAGCCAAATAAGATTCAGGGGCCAACT Y 2 1 2 1 101000 f 74 goat snp45747-scaffold627-5650100 1 46381671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776619 Affx-122967135 AX-385263746 1 45366965 AATTCAGAGAAGGAAAATTTAAAGGGGTTCTTGAG[C/T]GATCTCAGAAAAGCTGCCCAGGGAATGTTGAATAG Y 2 1 2 1 101000 r 74 goat snp12636-scaffold1480-1163799 1 46411147 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386655 Affx-122970204 AX-123257013 1 45417195 TAACCAAGAACTCAGTCAATTCTGCAAACTACTAA[C/T]GGAAGAAAAGCCAAGTAGATTTGGTAGGGGAAAAC Y 2 1 2 1 101000 f 74 goat snp12635-scaffold1480-1113569 1 46461277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423731 Affx-122942867 AX-123294077 1 45460504 CACTCTTAAAAATATATCAAACTATACTGTCTCCA[G/T]CACCCTCTATAGTTAACCACCTCTATAGCTACACA K 2 1 2 1 101000 r 74 goat snp12634-scaffold1480-1070260 1 46504863 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447842 Affx-122923901 AX-123318178 1 45512664 AAATAGGACGTGTAAAATTATTCATCTTTTTTTTC[C/T]CAAGATGCCTGGCAACTTTTGTACTTGTTGGAATA Y 2 1 2 1 103000 r 74 goat snp12633-scaffold1480-1018100 1 46557154 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428362 Affx-122938974 AX-123298705 1 45546537 ATTTTTGGGACCTAATTCATTTCCATCAGGTCATG[C/T]ATTTGCATTGCAAGGAAGGAAGAATAATTTTTCTA Y 2 1 2 1 101000 f 74 goat snp12632-scaffold1480-984227 1 46591721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398576 Affx-122961503 AX-123268931 1 45581766 TGGCTGAATGATTCTTTTGGAGGCTTAACTCTGTG[C/T]GTAACACTATCTGCCCAGATTTACCTCATATGCAG Y 2 1 2 1 101000 r 74 goat snp12631-scaffold1480-948998 1 46625453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271731 Affx-1111832858 AX-519545527 1 45587785 ATCTTGGTTGATAGTACTGACCAAAATAGGATTAT[A/G]TAATTTTCTTAGTTACACTGTGCTTAGTTTACTGC R 2 1 2 1 101000 r 74 goat 1_45587785_AF-PAKI 1 45587785 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772990 Affx-122928551 AX-385260134 1 45614919 ATCACTCTTTACAGATACAGTTAGAGAAAAGATTG[A/G]TTTCAGACTTACCAGGAAATCTACTGTGGAGATTG R 2 1 2 1 101000 r 74 goat snp12630-scaffold1480-915845 1 46658757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424906 Affx-122941306 AX-123295252 1 45646028 AAAAATGCATGCCATGGAATTCCTGTGCTAGATAA[C/T]GTGGTGAGGACTTAGAGAAGGGTGTCTTAGGGCTT Y 2 1 2 1 201000 f 74 goat snp12629-scaffold1480-884736 1 46689802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417048 Affx-122947524 AX-123287396 1 45679436 GACCTAAGATTTGCCTGAATCCAAAGCTGTCAACC[A/G]CTTTAGCTTGTAGTACCTTCTACAATACCAGTCAG R 2 1 2 1 101000 r 74 goat snp12628-scaffold1480-851328 1 46723221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381368 Affx-122974400 AX-123251726 1 45720761 GCGAGTCAGCGCTGAGGTGTCTTTTGAAAGAGTAT[A/G]CATTAGTGCAAGGTAACTCTACTACCATTTGCATC R 2 1 2 1 101000 r 74 goat snp12627-scaffold1480-810003 1 46765249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416631 Affx-122947619 AX-123286979 1 45768638 GTTTAAAGCAGAATTAAAAGATAAAGTTCACAGCA[C/T]GCTACGTTGGAGATGGAAAGAAGAAACCAGCGTTG Y 2 1 2 1 101000 r 74 goat snp12626-scaffold1480-762126 1 46813492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411053 Affx-122951953 AX-123281403 1 45816172 TATAATGACTTTATGAATAGTAAAATAAAAGGAAA[C/T]GTATGTACTAAAATATTAGAGCAGAATAGGAAAAG Y 2 1 2 1 101000 r 74 goat snp12625-scaffold1480-714592 1 46861271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440852 Affx-122929257 AX-123311189 1 45846091 TGGTTTCAAGGGAACAGAATAAAAAATTCAATCAA[C/T]GTAGGAATTCAACAGAGAAAAATGAGGGTAGTAAC Y 2 1 2 1 101000 r 74 goat snp12624-scaffold1480-684673 1 46889973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380823 Affx-122975076 AX-123251181 1 45883122 AAAAGGCTGAAGGGAGTCTTAGTCCATAGTCAATT[A/G]TCCATTTAATCAACATCGTTTACTGAATCTCTAGC R 2 1 2 1 101000 r 74 goat snp12623-scaffold1480-647642 1 46929949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797811 Affx-122946354 AX-385284750 1 46002412 CATATGAAATAACATGTACACATGGCATCATATGA[G/T]CAGGACCATCTGGAAAGAAGTGTCCAGAATCATCT K 2 1 2 1 101000 r 74 goat snp12621-scaffold1480-528352 1 47051236 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798792 Affx-122944785 AX-385285723 1 46035328 GCAATGATTCTGAGCCAGCAGGACTGGGTTCAGCC[A/G]CTGGATGTGCTAATTACTTGTTACTGAAACTTACA R 2 1 2 1 102000 f 74 goat snp12620-scaffold1480-495436 1 47084055 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417041 Affx-122947528 AX-123287389 1 46064190 CATGTTTCAACAGGAAGAAAATTAAAATCAAACAC[A/G]TTGTGGTTAAGAATGTAACAAACACATGGGAACTA R 2 1 2 1 101000 r 74 goat snp12619-scaffold1480-466574 1 47113193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772831 Affx-122934344 AX-385259976 1 46094171 AAGAAAGAACAAAGAAAGCCAAAGAATGAAGGAGA[G/T]AAATGAAGACAAGTATTTAAGAAACTAGAAAATAA K 2 1 2 1 102000 f 74 goat snp12618-scaffold1480-436593 1 47143705 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388212 Affx-122969414 AX-123258570 1 46128996 TACCGATTCTTTAATTCTGAATGTAAGGGTAAACA[G/T]TTACAAACTGGAGAGGCCAGGTGCTCAGTGTAGCT K 2 1 2 1 201000 f 74 goat snp12617-scaffold1480-401768 1 47178831 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790770 Affx-122939064 AX-385277771 1 46188164 TACATAGGAAAAATGCATGTTACAGTGGAAAACTA[C/T]GAATTGTGGAGATCTTGGAGGACCCACTTCAGAAC Y 2 1 2 1 101000 r 74 goat snp12616-scaffold1480-342600 1 47238651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779793 Affx-122961879 AX-385266893 1 46216784 CCTCATCACAGAATAAACTTTTTCCATATCCAGGA[C/T]GCCAGGACCCAAAATTCACCTATTTTCCATATTAA Y 2 1 2 1 101000 r 74 goat snp12615-scaffold1480-313980 1 47267647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440830 Affx-122929272 AX-123311167 1 46250999 AAGTGCTAAGGAGAAAATATAAACCAGTAGTAAAT[A/G]TTAAGCCCTAAGGAGGAATCTATTATTTTCAAGAG R 2 1 2 1 101000 r 74 goat snp12614-scaffold1480-279765 1 47302011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782676 Affx-122955411 AX-385269749 1 46280585 AGGTTCAACTGAATTTATCTGTGCAATCCCAAATC[A/G]TAATCCCAGTGCTTGCTTCGGTAGCACATATACCA R 2 1 2 1 101000 r 74 goat snp12613-scaffold1480-250179 1 47332650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800608 Affx-122930274 AX-385287527 1 46311470 CTTTACCAAGTAAGTAATCAATAGCTTCCAGCTTC[A/C]GAAGGCTTTGCTTCATACAGTGTTTGGTTTGTCTC M 2 1 2 1 101000 r 74 goat snp12612-scaffold1480-219294 1 47363420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392409 Affx-122966207 AX-123262766 1 46346553 TATTCTTTCTCTGCTCAGATTAATATTGTAAGACC[A/G]TGACTGCTATTACTAAAATTTTTACATACTTATTG R 2 1 2 1 101000 f 74 goat snp12611-scaffold1480-184211 1 47399390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431805 Affx-122936115 AX-123302146 1 46383081 ATATTACTGAAAAAAAAATGTGGTATAGATGCTCA[C/T]GGTAGTTGTTTACAGATCTGTGAAACAAAAGCAGA Y 2 1 2 1 103000 r 74 goat snp12610-scaffold1480-147683 1 47436104 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476150 Affx-1251763653 AX-586011583 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 4 1 4 1 20000 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 539476406 Affx-1251763653 AX-586011810 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 4 1 4 1 20000 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562165051 Affx-1251763653 AX-606940463 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562165361 Affx-1251763653 AX-606940772 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166094 Affx-1251763653 AX-606941503 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166175 Affx-1251763653 AX-606941583 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166295 Affx-1251763653 AX-606941703 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166411 Affx-1251763653 AX-606941819 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 320788404 Affx-122933378 AX-385275422 1 46421838 CAAAAGAAAATTAAAAATCAACTTGGACAAAGGAG[C/T]GGTCAAGAGAATTATAACCATTTGCTACAATTCAA Y 2 1 2 1 101000 f 74 goat snp12609-scaffold1480-108926 1 47474944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398683 Affx-122961869 AX-123269038 1 46478263 TTTAACAATCAATTTAACTAATTCCTCCCTCCATC[A/G]CCTTTTAATACTCAAGCAATAAGCCTAATGGGCTT R 2 1 2 1 101000 r 74 goat snp12608-scaffold1480-52501 1 47531942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421063 Affx-122944246 AX-123291410 1 46514933 GCAGAGTCACCACAGAATAGCCTGGTGGGGACATG[G/T]GAGGGTATTCTCTTGTCCTGGTTCAGTCTCAGGTT K 2 1 2 1 101000 r 74 goat snp12607-scaffold1480-15831 1 47569160 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421999 Affx-122943783 AX-123292346 1 46534808 CCATATATGTAATGTAAGGACTCTTGTTCATGTGC[A/G]TGAGAATATCTGTAGAATAATTATTTTAGCAGCAT R 2 1 2 1 101000 f 74 goat snp48341-scaffold686-887750 1 47619106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376258 Affx-122978768 AX-123246617 1 46617720 CAAGAATACACAAAACCAGGTGTATAATGGCATTT[C/T]ATGGAGTTCTCTGTGGGGTTAGAACAGGATTAGTT Y 2 1 2 1 201000 f 74 goat snp48340-scaffold686-804838 1 47704739 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413662 Affx-122950115 AX-123284011 1 46671915 TGGCATCTCTTTTAGACTTAATTCCAGAAGAAAAA[C/T]CCAATCAGTTTTCAGGTCTGATTCCAAAGTTTTAC Y 2 1 2 1 202000 f 74 goat snp48339-scaffold686-750643 1 47759699 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785880 Affx-122934266 AX-385272916 1 46719634 CAAATATCAGTGCATATTACGTGAGCTGAAATAAA[A/G]TGTGATTTTATTGCACCAGGGATCCATTAAGCAGA R 2 1 2 1 101000 r 74 goat snp48338-scaffold686-702924 1 47807864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801578 Affx-122945423 AX-385288487 1 46774224 GAGTCTATATTTATTTATAATGTTCTTGATTTTAT[C/T]CATAAATCAGATTCACAGTGTAGCATATCTTAAAA Y 2 1 2 1 202000 f 74 goat snp48337-scaffold686-648334 1 47862256 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411410 Affx-122951843 AX-123281760 1 46820258 TTTGAGATTTATTTCTGTAACTCCCTAGATTTGTC[A/G]TCAACATTAGGACTAGTTTTGATCTACAGAATGTG R 2 1 2 1 101000 r 74 goat snp48336-scaffold686-602300 1 47909392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795559 Affx-122925467 AX-385282514 1 46866236 CAAATATTTCTGGTACCAAAGTCTGGAAATAGAAC[A/G]CCATGTTTTAGCTGCCAACTCAACATCAGTTTAAT R 2 1 2 1 101000 f 74 goat snp48335-scaffold686-556322 1 47955872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401733 Affx-122959519 AX-123272086 1 46960088 CATATATTGTCTTGAAATTAAAATTATGATGAAAA[C/T]AAATAGAGTAGAAAAACCTGAGATTTAAAGAAAGG Y 2 1 2 1 303000 f 74 goat snp48334-scaffold686-462470 1 48051444 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793657 Affx-122963263 AX-385280630 1 46994973 GACATATTCTGGTGAAACAAGAAGTTAAGTTATCT[A/G]AAATGGCTACAGTCTTTTTGAATGAATACTGTCTT R 2 1 2 1 101000 r 74 goat snp48333-scaffold686-427585 1 48085411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768860 Affx-122929651 AX-385256037 1 47025267 TGAGGTTGTTTGTCATCACATTTGAAAAGGTTACT[G/T]CATGACCACTCAAATGAAGTGTGAAGCACTTAAAC K 2 1 2 1 101000 r 74 goat snp48332-scaffold686-397291 1 48115624 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278072 Affx-1111836237 AX-519551562 1 47051032 AGCAAATGCAAAGAGAAGCACTTGGAAAGACTGCT[A/G]GAGGATGGGAAGGCAAATGAAGATGCCACTGGAAT R 2 1 2 1 201000 f 74 goat Random2.2K-43 1 47051032 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444202 Affx-122927256 AX-123314539 1 47056527 TCTGAGGAACTGTAACTTTTTATTTTAACAGTAAA[C/T]GAGTAATCTTGAAATATAAGAAAATACATGAGTTT Y 2 1 2 1 103000 f 74 goat snp48331-scaffold686-366031 1 48147084 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776200 Affx-122945756 AX-385263328 1 47134189 TTTTAACTGAGATGTTAAAACCTATTTCAGGAATT[A/C]TTTTTGTCCATTTAATTATGCTTATACTTAATTAA M 2 1 2 1 102000 f 74 goat snp48329-scaffold686-288369 1 48225349 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406966 Affx-122955055 AX-123277317 1 47228711 GGCCACGACATCACTTATGCCTTCCCTCCTCTTTC[A/G]TGATACGCTTGGTGTACCCATTCATTGAGTTGTTG R 2 1 2 1 101000 r 74 goat snp48327-scaffold686-193847 1 48321647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434793 Affx-122933876 AX-123305134 1 47274139 GTGGTCTCTTTGGTAGGTTAGCTGTATGCAATGCC[A/G]TAAGGAGGGATTCTAGACAGCAGGTAACTGAGTAA R 2 1 2 1 101000 f 74 goat snp48326-scaffold686-148419 1 48368391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767638 Affx-122920428 AX-385254882 1 47303473 AGTACACAGAAGCCAAAATGCCTTTTTATACATAT[A/C]TCAAACAACAATATCACTCTAAACACTATAACTTT M 2 1 2 1 101000 f 74 goat snp48325-scaffold686-119085 1 48397835 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793018 Affx-122945410 AX-385279996 1 47369912 ATTTATGAGGTAAATATATGTGTCAAGTACCATGG[C/T]AGGCTCTAAAAATGTGTTTGTGAGCATCACTTACT Y 2 1 2 1 101000 r 74 goat snp48324-scaffold686-52646 1 48464620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405845 Affx-122955865 AX-123276197 1 47451274 GAAACAAACATTGTGCGGTGGATCACTAGGGGTAA[G/T]AGTGAATAGAGACACTCCCATTTTCAAGCTTTTAT K 2 1 2 1 101000 f 74 goat snp7889-scaffold1284-28617 1 48564591 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403999 Affx-122957199 AX-123274351 1 47541704 GTGCCATATCTGAATCTAAGTGTTCAGAAGCCTCA[C/T]ATGGTTCTGTGTGTTCCTCTGTACTCTTACAAGTG Y 2 1 2 1 101000 f 74 goat snp7890-scaffold1284-119047 1 48656524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436785 Affx-122932261 AX-123307123 1 47578594 CATCCTTTCCTCTGAAGTCAAATTTCATCATCATT[A/G]TTCCTTGTTGAGTTAATATTTTTCAGCACTTTAAA R 2 1 2 1 201000 r 74 goat snp7891-scaffold1284-155937 1 48693640 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796009 Affx-122950724 AX-385282961 1 47609798 CAGTTTCTACATTTCTTATGCTTTGATCTGGAAAT[G/T]TAAAATATGTGATGTAATGAAATCTGATAGTAGGT K 2 1 2 1 102000 r 74 goat snp7892-scaffold1284-187141 1 48725503 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446661 Affx-122924766 AX-123316997 1 47673747 TGTTCTGACATTTCATAGGAAGCCTTGCCCTGGAC[C/T]GTGATGGGGAAGGGCAGAATTGTTCTCATTCTACA Y 2 1 2 1 101000 f 74 goat snp7893-scaffold1284-251090 1 48790110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768096 Affx-122970894 AX-385255298 1 47724253 TTAATCACAACTATTTCAAAACCCCTTCCTAATCG[G/T]TCTACCATCTGGGTCACTTCTGAATGTAATTTCTT K 2 1 2 1 202000 f 74 goat snp7894-scaffold1284-301596 1 48840674 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440399 Affx-122929618 AX-123310736 1 47793999 AATAATACTTAATAAATATATTTTTGTCATGTTTG[A/G]GCTGCATATCTTATTTAATTACTGAAACAGATAAT R 2 1 2 1 101000 r 74 goat snp55677-scaffold863-1765843 1 48911689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450936 Affx-122921769 AX-123321270 1 47867208 GCTAAAGGTAGAACGTACATCATGTACCTAGAAGG[C/T]GAATTAAATAAGGCTTAAGAGAGTCTCCTGGGAAA Y 2 1 2 1 101000 f 74 goat snp55676-scaffold863-1692634 1 48987492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441945 Affx-122928576 AX-123312282 1 47955633 GGTGATTTAGATAATCAAGAACTATACTTTAGAAC[A/G]TTTTGCAAAATATTGTCCTTATATTTAGACTTTAT R 2 1 2 1 101000 f 74 goat snp55675-scaffold863-1604209 1 49076511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408628 Affx-122953489 AX-123278979 1 48018399 TGTGTCTCTTTTGCTGTCTCGCATACCGGGTCATC[A/G]TTGCCTGATGCTTTAGTTTAATTGTGCATCCCACT R 2 1 2 1 101000 r 74 goat snp55674-scaffold863-1541443 1 49140292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797649 Affx-122932347 AX-385284589 1 48048986 TAACAGGACAATAAAAGATATCATCCAGATGTGCA[A/C]AGTTGACAGAAGATGGAACAATAAATTAGGATTAT M 2 1 2 1 101000 f 74 goat snp55673-scaffold863-1510856 1 49171800 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780350 Affx-122972303 AX-385267445 1 48089317 AGCGCAAAGTGGATAGTATATACAAAAGTGTCACA[A/G]GAGTTTAGGGAGAGATTGGTCTCTTAAGATTTCAG R 2 1 2 1 101000 r 74 goat snp55672-scaffold863-1470525 1 49212772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771356 Affx-122961756 AX-385258514 1 48156301 AGAGTCACATAGTGGGATCAATTAAAGAAACAGTT[A/G]TAAAATATCATATTCCCTCTTTTTTATGCTTGTGT R 2 1 2 1 201000 r 74 goat snp55670-scaffold863-1403541 1 49280854 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785154 Affx-122925756 AX-385272200 1 48191227 CAGTTGATTAACATCAATATTGATAAATGTTAAAA[C/T]ATGTACACACAACTGCAGTTAAACATGAAACACCA Y 2 1 2 1 102000 r 74 goat snp55669-scaffold863-1368615 1 49316567 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403066 Affx-122958521 AX-123273419 1 48242578 TGGCCAAACAAACACCTCTGTGGTAATAGATGAGC[A/G]ATAGAGAGATCTGCTTGGTCTATGGAGAGGAAATA R 2 1 2 1 101000 f 74 goat snp55668-scaffold863-1317264 1 49367861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430134 Affx-122937397 AX-123300475 1 48277781 CTTTTGCCTTGATAGCATGCACAGAAGACTATGGG[A/G]AGCTCAATGTGGCCAGTGGTTATGTAACATTCCAT R 2 1 2 1 101000 f 74 goat snp55667-scaffold863-1282061 1 49402905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777837 Affx-122971797 AX-385264954 1 48351877 ACCTTCAACAATACCTCAAACTACAATCACTCCTG[A/C]GCTTGCTGACTTAATTACAAATACTAACAAATATC M 2 1 2 1 101000 f 74 goat snp55665-scaffold863-1207965 1 49476342 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399952 Affx-122960842 AX-123270307 1 48433286 TTTCTGTCTTAATTCCACTTCATCTGATATTAGCT[A/G]TGTTGCACTCAGTTTCTTTTGACTGGCATTGATCT R 2 1 2 1 101000 r 74 goat snp55663-scaffold863-1126556 1 49558720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271826 Affx-1111832859 AX-185407711 1 48439248 AGTTGGTGATGGACAGGGAGGCTTGGCGTGCTGCA[A/G]TTTATGGGGTCGCAAAGAGTCGGACATGAATGAGC R 2 1 2 1 303000 f 74 goat 1_48439248_AF-PAKI 1 48439248 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320769230 Affx-122949714 AX-186298626 1 48473913 GCTTAGAGTCAAAAGCATTGTATAGAATTTACTGA[C/T]GCTTGTGTCTGGAAGGAGTATTTTTCAGTCAAATC Y 2 1 2 1 101000 r 74 goat snp55662-scaffold863-1085929 1 49599249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414353 Affx-122950019 AX-123284702 1 48505482 AGTGGCCTTGTGGAGGAATGTTCTGTAGCACTAAC[G/T]AGTAACAGCTTTTTCTCTGAACTCCAAGCCCTCTC K 2 1 2 1 101000 f 74 goat snp55661-scaffold863-1054360 1 49630739 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792314 Affx-122949685 AX-385279296 1 48550525 TAAACTGAACAGTACACATGGGAGTTTCCTTACAG[C/T]ACTTTTTTGGATGAGACCACCTTTTGAAGAACTTT Y 2 1 2 1 101000 r 74 goat snp55660-scaffold863-1009317 1 49676483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407406 Affx-122955244 AX-123277757 1 48637775 CTTATTGGTATATCAGAGATCAATTTTTCTGGTTC[C/T]TAATTTTAAACACCAAGACCAGGAGAAACAAGAAG Y 2 1 2 1 101000 r 74 goat snp55659-scaffold863-922067 1 49764661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278112 Affx-1111836258 AX-519551602 1 48656984 TAAGTAGGCCACATGAAGGAGTACATCAAGGCTGC[A/G]TATTGTCATGCTGTTTATTTAACTTCTATGTAGAG R 2 1 2 1 103000 f 74 goat Random2.2K-46 1 48656984 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401676 Affx-122959563 AX-123272029 1 48677242 TAAATGGTTCTCAATACAGGAGCACATTGATATAA[C/T]ATGAAGCATATAATTTCATTCATCCCGTCTCTGAA Y 2 1 2 1 101000 f 74 goat snp55658-scaffold863-882600 1 49804540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392617 Affx-122966042 AX-123262974 1 48766106 CATTTTGCATTTGAAGCAAATAGTAATTCTGCATT[A/G]TCCAGACCTTTAGGCTTCCCAGATGGCTCAATGGT R 2 1 2 1 201000 f 74 goat snp55656-scaffold863-793736 1 49895211 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791630 Affx-122970331 AX-385278621 1 48820405 ATAAGAAAGTATTTGCTGACCTTTTAATAGCACAA[C/T]AGTCAAGCTTTCACAGCCAAGATGTTCTTAGAAAA Y 2 1 2 1 101000 r 74 goat snp55655-scaffold863-739437 1 49949644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414898 Affx-122949122 AX-123285247 1 48859203 AGTCTTAAGAGGTTTGGTGTTGCTTCAAGGACAGT[G/T]AAGTATAGAGAATGGTACCCACTGTAGCTTGTCTA K 2 1 2 1 101000 f 74 goat snp55654-scaffold863-700639 1 49988259 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426126 Affx-122940623 AX-123296472 1 48932670 TTCAACTATCCTGAGGATAATGATTTTCTTGAGGA[C/T]GGGGAGTCCTTTGAAATTCCATTCTTCTGAGAATA Y 2 1 2 1 202000 f 74 goat snp55652-scaffold863-627172 1 50064347 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796867 Affx-122961340 AX-385283810 1 48968913 TCCAGCTCTCTTGACTCTGGATTTCACCAACACTT[A/C]TCTTCTCAGGTCTTGCTATTAATATAGTCTTTCCC M 2 1 2 1 101000 f 74 goat snp55651-scaffold863-590929 1 50100577 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795207 Affx-122938688 AX-385282165 1 49036135 CATAAAAATCCCTCTGTAGTTTCATAAGTTTTCAT[A/G]CTTGAATATAACTCGGAAAATTTTACTAACTTTTT R 2 1 2 1 101000 f 74 goat snp55649-scaffold863-523707 1 50167374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278299 Affx-1111836272 AX-519551784 1 49065262 TGACATTTACATGTAGCTCCTTTTCTTGACCAAGA[A/G]AATCTGTAGACCTAGGACCTTGTTTGGTTTAAAGT R 2 1 2 1 101000 r 74 goat Random2.2K-49 1 49065262 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425144 Affx-122941202 AX-123295490 1 49177314 CATCATCCAATGTAGCAGAACAAAAGGAGTTCTGA[A/G]GAGTTGTTCAGAAGGAAGGACTTCTACAGGCAGGC R 2 1 2 1 101000 f 74 goat snp55646-scaffold863-382528 1 50305997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414639 Affx-122949328 AX-123284988 1 49210968 TCAATTTTATTGATATTCTCCATTATTCGTATTCC[A/G]TTCTCTGGTCTATTGAATGTCTTCAGGCTTCTTTC R 2 1 2 1 101000 r 74 goat snp55645-scaffold863-348874 1 50339728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380012 Affx-122975601 AX-123250370 1 49271004 TAACTTATTCCCATATGGGGAGAGCTTGCTTACGA[G/T]TAGGACCAACACAGTGGGTGTTTGAGCACCTGGAA K 2 1 2 1 101000 f 74 goat snp55644-scaffold863-288838 1 50399829 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787470 Affx-122957175 AX-385274495 1 49309311 TTAGTGGATTTCCCTAGAGAACTATCTGTTTTAAG[C/T]CTCTTTACCTTTGTTGTTGACTATATTACTGGTCT Y 2 1 2 1 101000 r 74 goat snp55643-scaffold863-250531 1 50438031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398664 Affx-122961884 AX-123269019 1 49351443 TACAAGAGATAGTCATAAGAAGCTTCTGGCCAAGA[C/T]AGAGTCACAAGGGCTGGATTTACTGTTCCACCTGA Y 2 1 2 1 101000 r 74 goat snp55642-scaffold863-208399 1 50481152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428987 Affx-122938856 AX-123299329 1 49394331 CATCTAAGAACATTCATGTAAAATCTGTATGAGGA[C/T]ATATGTTTTATTTCTCTTTGCTAAATAGCAAAGAA Y 2 1 2 1 101000 f 74 goat snp55641-scaffold863-165511 1 50524009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767776 Affx-122960106 AX-385255003 1 49449653 GCAATCAAAGGTACAAATCACTCCTACTCATTCTC[A/G]CATTTTAATGCAAGGGCTTTTAGGAATCATACTGA R 2 1 2 1 101000 f 74 goat snp55640-scaffold863-110189 1 50579371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379062 Affx-122976334 AX-123249421 1 49529228 ACAAAATGTCTATGAATCCCTGATTATAGTAAAGC[A/G]CCTCCAACTTTAATTCATTTCAATATTTCCGTTGG R 2 1 2 1 101000 f 74 goat snp55638-scaffold863-30614 1 50659866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449699 Affx-122922544 AX-123320034 1 49590738 GGATTAAAGTAGATTAAAGGGATAATATAAGTAAA[C/T]GAAAAAGATGACAACAAACCAGAAAAATTTTTCTT Y 2 1 2 1 101000 f 74 goat snp27909-scaffold2996-56754 1 50722301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414449 Affx-122949946 AX-123284798 1 49620784 GGCAGAATTTCCCAGTTTCTCCAGCTTAGTTGTAG[C/T]AGTACTAGTAGTTGTAGTAGGAGTAGCATCAGCAG Y 2 1 2 1 201000 r 74 goat snp27908-scaffold2996-26708 1 50752322 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796747 Affx-122953903 AX-385283691 1 49652947 ATTTTGTCATGTAGTTTATTAATGCTTCTCTTAGC[A/G]TTAGTATTAAACTATTATTGGCCAATATTATTTTC R 2 1 2 1 101000 f 74 goat snp14230-scaffold1568-1787801 1 50789391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441029 Affx-122928942 AX-123311366 1 49698034 CCTAACGTGCCTCTGCCCCTCAGTCAGGAAGCAGT[A/G]TACATGCCACAGTTAGGTGTTTGGGAAGAGCTACT R 2 1 2 1 101000 r 74 goat snp14229-scaffold1568-1742714 1 50834538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414872 Affx-122949142 AX-123285221 1 49747435 TCAAGAGAATCTATTTTTTTTCTAATAGGGATTGA[C/T]GAAGGGATAGTAAGAGAGAAGTGACTGAAAAGGAA Y 2 1 2 1 101000 r 74 goat snp14228-scaffold1568-1693313 1 50884075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769925 Affx-122971899 AX-385257094 1 49799773 AAAAATATTGCTCCTTTTTATAGAGAACCAAATCA[C/T]AGCTATACCCAACCTTTGTGACATTAATGACAGAG Y 2 1 2 1 101000 r 74 goat snp14227-scaffold1568-1640975 1 50938524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454076 Affx-122919380 AX-123324409 1 49861012 AATATTTTGTTTTTCTATATTGAAGAAATATCCTC[A/G]TTTGTTATTCTTGCAATACTTTCCACCACAGAAGT R 2 1 2 1 101000 r 74 goat snp14225-scaffold1568-1579736 1 50999753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449571 Affx-122923233 AX-123319906 1 49890372 ACAGGAGTGCTGTGAGGTCAACAGGGAGGACACTG[C/T]AGTTAGAAACAGATGTTAGTGAACACGAAGCTTTG Y 2 1 2 1 101000 r 74 goat snp14224-scaffold1568-1550376 1 51029010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769122 Affx-122976695 AX-385256297 1 49938352 CTGAGATGCTTTACTCCTTTTTGTATTCTATTCCA[C/T]TGGCAGAGTAAATCACATAGTGGTAGTTTTTGGCT Y 2 1 2 1 101000 f 74 goat snp14223-scaffold1568-1502396 1 51077800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419791 Affx-122945851 AX-123290139 1 49969607 TGACCCCTGCAGTCACAGTAGTGAGAGCTGCAAAG[A/G]CTTTTATTGGAAGAATATAAAGAAGCTGCAGTCTG R 2 1 2 1 201000 r 74 goat snp14222-scaffold1568-1471141 1 51109331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800576 Affx-122951148 AX-385287495 1 50004337 GGGTAAAAGGAAGTCAAGCCACAGAAGAGGACCAA[C/T]ATTTCAGTTTGGAATATGTCAGCAAAACAGACAAG Y 2 1 2 1 101000 f 74 goat snp14221-scaffold1568-1436411 1 51144639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399339 Affx-122961361 AX-123269694 1 50038931 TCTACACAACAACCCTTGAGGCATTCCTAAAACAC[A/G]TGCACACATACAAACACCTACATACACAAGAAACA R 2 1 2 1 101000 f 74 goat snp14220-scaffold1568-1401817 1 51177975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440032 Affx-122929764 AX-123310369 1 50096433 ATTGATTAAATACATGGGGAGAAAGAGACCTTTAG[A/G]ATTTTGAAAGTGTAGATTTCTCCAAAGGGAATATA R 2 1 2 1 101000 r 74 goat snp14219-scaffold1568-1344315 1 51235629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432580 Affx-122935520 AX-123302921 1 50142331 TTGGCAAAAGGTAGGAGCATAGCCAGCATAATTTA[C/T]ACTGAAATTTTTAAGAAAACATAAATTTGAAAAGT Y 2 1 2 1 101000 f 74 goat snp14218-scaffold1568-1298417 1 51282663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775019 Affx-122971224 AX-385262151 1 50177184 TATATTTACACACATAAACAAAGCAACATTTGGCA[A/G]TTTAGGATTTGTCAGGATAAAAGACATTTAATAAA R 2 1 2 1 101000 f 74 goat snp14217-scaffold1568-1263564 1 51317480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403238 Affx-122957890 AX-123273591 1 50214589 TTTATAGATTGATGGCAGTTTAAGTATCTTGGACC[A/G]TAGGTATTTCCATTTGGCATGATGCTGCTCTATAC R 2 1 2 1 101000 f 74 goat snp14216-scaffold1568-1226159 1 51353428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803440 Affx-122945858 AX-385290270 1 50249719 TTGAAATTTCACACAAATGACACATCTCAAATATA[G/T]CCTGTCTCAAACTGGAATCATTTTTGTATCATCAA K 2 1 2 1 101000 r 74 goat snp14215-scaffold1568-1191029 1 51389058 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410243 Affx-122952543 AX-123280593 1 50294704 ACAAAGAGTTGGAAATGACTGAGGGACTGAACTGA[A/G]CTGAACTGATAGCATTAGCATTAGGGTCACCTGCT R 2 1 2 1 103000 r 74 goat snp14214-scaffold1568-1146044 1 51434143 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399242 Affx-122960579 AX-123269597 1 50342858 CCACAGAGGTCCTATATTAACTATATTAAAAATTC[C/T]AAATAATTGCTTTTGTTTGTGATTTTTGGGGAGGA Y 2 1 2 1 103000 r 74 goat snp14213-scaffold1568-1097890 1 51482441 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278360 Affx-1111836302 AX-519551846 1 50363538 ACTGCCAAAACTTGGAAGCAACCAAGATCGCCTTC[A/G]ATAGATGAGTGGGTTAAACAAATTGTACTACATCC R 2 1 2 1 201000 r 74 goat Random2.2K-54 1 50363538 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794891 Affx-122955514 AX-385281851 1 50415423 GCTTTACAGTATTGCGCTGGTTCCAGCTAAACATC[A/C]ACATTCCTGCCTCTTTTCTTAACTGCTCTCTCTGT M 2 1 2 1 101000 r 74 goat snp14211-scaffold1568-1025325 1 51555055 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409600 Affx-122953559 AX-123279951 1 50451247 ATTCATTCACTTATTATTTTAATGTTAAGTTTAGC[C/T]GTTTAGATGTCTTAGAATAGATAAAATCTTGGGTG Y 2 1 2 1 101000 r 74 goat snp14210-scaffold1568-989501 1 51590929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769259 Affx-122953807 AX-385256432 1 50509093 AAAATGCCACCCATTTAAGACCAACTAAAAAAGGT[G/T]AACATTCATAAATAATAATGGCTAATATGTTGTGA K 2 1 2 1 201000 r 74 goat snp14209-scaffold1568-931655 1 51649274 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278219 Affx-1111836309 AX-519551707 1 50615387 GCCTAGGTTCAATTTTGATTTCAATTCAGTCACTC[A/C]GTCGTGTCTGACTCTTTGCAACCCCATGAACTGCA M 2 1 2 1 103000 f 74 goat Random2.2K-55 1 50615387 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413094 Affx-122950949 AX-123283443 1 50633096 GAAACATAGAGGCTTAACCACTGGATGTATAGGGA[C/T]GTCCCAAGAGGGTTCTCACCATTTACCTTTCTCTG Y 2 1 2 1 101000 r 74 goat snp14207-scaffold1568-807652 1 51773659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398251 Affx-122962190 AX-123268606 1 50665494 ATATTTTACTTGAAGGCTAGATACATCTTTTTGAA[C/T]TACTTGCTGATCCAATGCAGTGCTTTCCTAGTAGT Y 2 1 2 1 101000 r 74 goat snp14206-scaffold1568-775254 1 51806247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788918 Affx-122971913 AX-385275932 1 50701532 ATGATATTTACAAAAATTACATTACAATGGCAACC[A/G]CCTATTATGTCCAGGAATGAAGTCCACCCTGGATG R 2 1 2 1 101000 r 74 goat snp14205-scaffold1568-739216 1 51842984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776549 Affx-122951215 AX-385263676 1 50743524 TCATTTGTATTGACAGAGTATTTATACCCTTTTTA[A/G]TTTTCCTGTAGAAGGCTATCTGATGATTTAACTTT R 2 1 2 1 202000 f 74 goat snp14204-scaffold1568-697224 1 51885580 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388173 Affx-122969441 AX-123258531 1 50821403 TACTACTCATCTCAGTGTTACCTGACCAGGTATAA[C/T]AGAGGAAGGCAGTGGTTCCCAAAGTATATGATGCA Y 2 1 2 1 101000 f 74 goat snp14202-scaffold1568-619345 1 51964163 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446530 Affx-122925019 AX-123316866 1 50872296 CAAATATGCTTACTCTTATTGCTCACTCCCACCCC[G/T]ACCTATTTTTATATAGTTTTTACATTTTTGTAATG K 2 1 2 1 303000 r 74 goat snp14201-scaffold1568-568452 1 52015571 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789301 Affx-122939194 AX-385276312 1 50936371 ATCTATGTGCACATCCATAACAGACACACCTAAGA[C/T]AAAATGACACATGAAATGTTAAAAGTCAGGGATAT Y 2 1 2 1 101000 r 74 goat snp14199-scaffold1568-504377 1 52080052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446901 Affx-122924706 AX-123317237 1 50996098 GGTGTGATCTGTTGTTGGGATCTGCTGATCCTGAA[A/G]TGCCCTCTCCTTACAGCACCCTACACCCTGCCTGT R 2 1 2 1 101000 f 74 goat snp14198-scaffold1568-444650 1 52140450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388400 Affx-122969295 AX-123258758 1 51033291 AGGGGGAATATTTCAAACATATATAAATACTTTCT[G/T]CCTTGACTACTCTGCAAAAACTGCTTCTCCAAATT K 2 1 2 1 101000 r 74 goat snp14197-scaffold1568-407457 1 52178031 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271827 Affx-1111832860 AX-519545613 1 51039466 CCCATCTATTCACCATGAAGTGATGGGACTGGATG[A/C]CATGATCTTAGTTTTCTGAATGTTGTTTTAAGACA M 2 1 2 1 103000 f 74 goat 1_51039466_AF-PAKI 1 51039466 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320765468 Affx-122938362 AX-385252965 1 51105459 GGGTTCATGTAACCCAGTCTGTTACTTTCAAGGCA[C/T]AATACCATGCACATAGAAACCTTAATGAAAATTAA Y 2 1 2 1 101000 f 74 goat snp14196-scaffold1568-335289 1 52250097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429672 Affx-122937654 AX-123300013 1 51134136 ACAACTGGAGAACAGGTTCCTAGAGGACAGGAGGT[A/G]TATACTGTAATTTCCTATAGTCCTCACAGTATCTC R 2 1 2 1 201000 r 74 goat snp14195-scaffold1568-306612 1 52278719 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434523 Affx-122934160 AX-123304864 1 51178523 TAGAAAATCTTTGGAAAGAGTAGTAATGTTCACAA[C/T]AACTAGGTTCTCTGCATAAAAATCAATTTAAGGGC Y 2 1 2 1 101000 f 74 goat snp14194-scaffold1568-262225 1 52323147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802610 Affx-122944743 AX-385289512 1 51234683 CAATTCCATTAAGTTAAAAGGATTAGCTTCCAAGG[C/T]ATTGTTGTCCTCTGATCCTATTTCATGTTAATTAC Y 2 1 2 1 101000 r 74 goat snp14193-scaffold1568-206065 1 52378620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378834 Affx-122976541 AX-123249193 1 51285370 TGTTGATCAAATAACTTTCAGAAATTTACAAGGGA[G/T]AAAACTTTCTGCTTAACCAGAAGCTGTCAGGCATT K 2 1 2 1 101000 r 74 goat snp14192-scaffold1568-155378 1 52429959 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278391 Affx-1111836317 AX-519551876 1 51314247 GAATTCTCCAGGCAAGAATACTGGAAAAAAATGAA[A/C]TCCTAGTAAATTGTTCATGGGAATGTGGGTTGAGG M 2 1 2 1 101000 r 74 goat Random2.2K-57 1 51314247 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386002 Affx-122971508 AX-123256360 1 51352595 CACTCTGCTTTATTCAGAAAGACAGTCTCTCCAAG[G/T]GTTCTCCTTGTGGTGAACACTCTTCCTACAATCTA K 2 1 2 1 201000 f 74 goat snp14191-scaffold1568-88153 1 52497288 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783013 Affx-122958246 AX-385270081 1 51408978 AGCAAAGCTAGCAGTGAAATTCAGGTCTAGGTGAG[C/T]GGCAGAAATAATTAGCATAGAGAGGAAAATAAATT Y 2 1 2 1 101000 f 74 goat snp14190-scaffold1568-31770 1 52553074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441307 Affx-122929450 AX-123311644 1 51438357 TAGTCATTATCCCACCTGTGTTCTCACTGCTTCCC[A/G]TCTTCTCGACCAAGCAGCCTGGCTCCAAGAGGATA R 2 1 2 1 202000 r 74 goat snp14189-scaffold1568-2391 1 52582919 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410210 Affx-122952568 AX-123280560 1 51448183 CATGAACATATGCATATTGTAAGGCTGTAAGCTGG[C/T]CAGCTCCTCCCATCCTCTCCTGGTGTCACCCTCAC Y 2 1 2 1 101000 f 74 goat snp44268-scaffold602-533448 1 52592722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791852 Affx-122949851 AX-385278842 1 51478600 AAAGTCTATGCCCTATAAGAAGGCAGGGATATGAC[C/T]GAGTCATAGTCACATAAGTTCCAACGCTGGATAGA Y 2 1 2 1 101000 f 74 goat snp44267-scaffold602-503031 1 52623696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412958 Affx-122951046 AX-123283307 1 51512389 TAAGTAACTTGCCTAAGCTTAAACACCTAGCAAGC[A/G]CTAAGTGTTGAGCCAAGTGTGTGCCCTTACCTGTA R 2 1 2 1 101000 f 74 goat snp44266-scaffold602-469242 1 52657481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407615 Affx-122954638 AX-123277966 1 51550081 TAGAAACTGAAAGCAACATGTTCAAGGCAACATTA[G/T]CTTTAACAGGAAAAAAATCTGTGAAAATGCTGAAC K 2 1 2 1 103000 f 74 goat snp44265-scaffold602-431550 1 52695498 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442639 Affx-122928453 AX-123312976 1 51603103 ACTCATTCCAGCAGAAGGAAAGACAGTCATGGGAG[C/T]GTGTTATGATATGAAGGGATCAGATGGTCCAGAGG Y 2 1 2 1 201000 r 74 goat snp44264-scaffold602-378528 1 52749255 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772279 Affx-122972722 AX-385259434 1 51631794 GAACCCAGTACCCAACCTGAAAGAGAACTGGATCA[C/T]TACAATACCCTGGAAGTTGTCCATGTGCTGCCCTG Y 2 1 2 1 201000 r 74 goat snp44263-scaffold602-349837 1 52778800 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449676 Affx-122922560 AX-123320011 1 51701247 GTAAATGGGCAATTATAACACAAGTGAAGTGTGTT[A/C]TGATGAACATAAATCCAGGAAGCTAGCAATGGCAA M 2 1 2 1 101000 r 74 goat snp44262-scaffold602-280384 1 52848242 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782962 Affx-122970360 AX-385270031 1 51738392 AAGCAAAGGAAGAGCAAGCCTCTACTACTCAAAAT[G/T]TAAAAGTAACCCTCTGAAGGGACATTTAGCAGGCT K 2 1 2 1 101000 f 74 goat snp44261-scaffold602-243239 1 52885658 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409132 Affx-122953300 AX-123279483 1 51785827 TCAATGTGACAAACACAGGAGCATTTACAATTCTC[A/G]TTTGTAACCTGGGTGGAAGATTCAAAGGTTTTTTT R 2 1 2 1 101000 f 74 goat snp44260-scaffold602-195804 1 52932798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375767 Affx-122978595 AX-123246126 1 51814695 TTAACCATTCAGTTTCCAGGCACACGTTGCTCAGT[C/T]GGTGCTACCTGTTCACATCACTGCAGCCTTTTCAG Y 2 1 2 1 101000 f 74 goat snp44259-scaffold602-166936 1 52962642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381599 Affx-122974792 AX-123251957 1 51845923 GCTTTTTTCTTTTTATTTTCCTATGGGTTATTCTT[A/G]CAGTTTTCTTCTGTAAACAGGTTCATTATACAACA R 2 1 2 1 101000 r 74 goat snp44258-scaffold602-135708 1 52994341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397515 Affx-122962053 AX-123267870 1 51885706 GTGACAGCGCAGAAGACAAAGCTACGGAGTGAGAA[C/T]GGTAAGGAAACTTTCAGTGTTGCTTCACTCACAAG Y 2 1 2 1 101000 f 74 goat snp44257-scaffold602-95925 1 53033952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426563 Affx-122940170 AX-123296909 1 51942640 AATGCTCACTGTGGATGCTGTGCTGTGTGCTTTGT[A/G]TGCACGGTTCATTCAATCAAACAGCAAGTCTGCAA R 2 1 2 1 201000 r 74 goat snp44256-scaffold602-38991 1 53091421 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799455 Affx-122953780 AX-385286385 1 51972184 GCTCTTCCTAAGCAATGATGATGCCAGCTCATGTA[G/T]CTGTTGGCTTTAGTCATCCCCAGAAAAATAATAGG K 2 1 2 1 101000 f 74 goat snp44255-scaffold602-9447 1 53120951 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406408 Affx-122955219 AX-123276760 1 52025244 TTAAAAAAAAAGGCTGAAAACTACATGAAGTCTCT[A/G]CCTACACAGGTTTTTAAGAATAGGCAAATTGAGTG R 2 1 2 1 101000 r 74 goat snp29278-scaffold3155-43514 1 53173473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397730 Affx-122962546 AX-123268085 1 52071174 TAAAAAATTGTCTTATCTTTAGGCAAAATGCATGC[A/G]TAAGTATTAGAGTAGAAATGCTGTGGCTATATATA R 2 1 2 1 101000 r 74 goat snp4116-scaffold113-5653 1 53217077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386594 Affx-122970688 AX-123256952 1 52102759 TTTTTCTCCTATTAAAACATTTGCTAAGTCCTGTT[A/G]TACTTTCTTGGCTTTCTTTTCCATTTGACTATAGT R 2 1 2 1 101000 r 74 goat snp4117-scaffold113-37238 1 53248874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426682 Affx-122939912 AX-123297028 1 52199142 TATTTTGGATAAAGCAAAATGAGTCCCACTCCTAA[C/T]AGCAGTTATGTGAAGGTTCCTGTTTCCTTACACAA Y 2 1 2 1 101000 r 74 goat snp4119-scaffold113-133621 1 53347371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769294 Affx-122953995 AX-385256466 1 52230009 GAGGAATAGGAGAAAGAGAGTCATGAAAGATCAAG[A/C]TTATGTTCTGAACAGCTTGTTGAAGAGCGATACCT M 2 1 2 1 101000 f 74 goat snp4120-scaffold113-164488 1 53379210 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401174 Affx-122959354 AX-123271527 1 52294093 TTGGACAATCTTGTTCTATCTCCTGAGTATGTAAG[G/T]CTATGACTTGGGGAACATTGTAATGCAGGTCATTT K 2 1 2 1 101000 f 74 goat snp4121-scaffold113-228572 1 53434276 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384971 Affx-122971902 AX-123255329 1 52350335 CTGTTTTATACTACTCAGAATAATCTTAGAGATCA[C/T]AGAAAAGCCACATTTTAGGAAGAAAAATGCATATT Y 2 1 2 1 101000 f 74 goat snp4122-scaffold113-284814 1 53490004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397254 Affx-122962358 AX-123267609 1 52384163 TGCAGAATTTGTTTTAATGGGGAGAGGCCAAGAAA[C/T]GAAATAACCAAGGAGATAGTAGGTTAGAAGATAAA Y 2 1 2 1 101000 f 74 goat snp4123-scaffold113-318642 1 53524300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387531 Affx-122970307 AX-123257889 1 52412843 CTGGCTTCCCCCAGGGATATTCTCCCTCCAGGAGC[A/G]CCAATGAGATGAATCAGTACACACACTAGTTCTCT R 2 1 2 1 101000 r 74 goat snp4124-scaffold113-347322 1 53551600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777728 Affx-122952374 AX-385264846 1 52442747 AACAAACATCCCTAAGTACACTGAATTCTGTTTAA[C/T]AGTCACTGACTACTTCCTAAATTCAAGGCACTGAA Y 2 1 2 1 101000 r 74 goat snp4125-scaffold113-377226 1 53581776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415715 Affx-122948519 AX-123286064 1 52497803 CTCACCTTTCAGAGGTCCTCTATTCAGTAATTACC[A/G]TATCTTATAATGATTTATACAGTTTTTAAAAGACA R 2 1 2 1 101000 f 74 goat snp4126-scaffold113-432282 1 53636096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404046 Affx-122957163 AX-123274398 1 52554930 GCTAATCTTATCTTTCTAGCACAATCTCAGACTCA[C/T]GGAAGGTTTTGATAAATGTTTAGTAAATAAATGAA Y 2 1 2 1 101000 f 74 goat snp4127-scaffold113-489409 1 53693006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400735 Affx-122959905 AX-123271090 1 52587178 AACTTCAAAACATACATACCTCTAAGAAAAAGGCA[C/T]GCTCCCAGGGAAAGGAAAAGACAGAAATGGCTCTC Y 2 1 2 1 201000 f 74 goat snp4128-scaffold113-521657 1 53720624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393941 Affx-122965069 AX-123264296 1 52615821 CTTTAAAGCTACTCCTTTCCTAAAGAATCCATCTC[A/G]TTGTTTTTATACAGTAAACTGAAGCACATGCACGT R 2 1 2 1 101000 f 74 goat snp4129-scaffold113-550300 1 53749013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422438 Affx-122943354 AX-123292784 1 52651878 TTTACTTCGTCCTCCAGCCCCTGGTAACCATTTTT[A/C]TGCTCTCTGTTTTTATGTGTGATTTTTGTTTTAGA M 2 1 2 1 303000 r 74 goat snp4130-scaffold113-586357 1 53785296 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451165 Affx-122921351 AX-123321499 1 52687812 AATTGTCTGAATGTAAAACATGCAGGCTCAAAACC[A/G]TCTACCTCTGCACTGTGGGATGGCATCAGTATTCC R 2 1 2 1 101000 f 74 goat snp4131-scaffold113-622291 1 53821310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442526 Affx-122928542 AX-123312863 1 52774571 CAAAAAGATCTTTGTTTAAAAGTCTAAGAAACAAT[C/T]TAACTGGGGAGATGGGATATTTGAGAGACAACAGA Y 2 1 2 1 101000 r 74 goat snp4132-scaffold113-709050 1 53907979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418634 Affx-122946344 AX-123288982 1 52807778 GCTGGAGGCTCTTCCCCCCACCACCTGAGGCTTCA[A/G]TTTTCCAACTGCCCTAGACCTCTGGCATTCAGTCA R 2 1 2 1 101000 r 74 goat snp4133-scaffold113-742257 1 53933969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422636 Affx-122943704 AX-123292982 1 52861695 AACCTACCAATCCAGAGTGGACTGCCTCTTTCTTC[A/G]TTCTTTCCTTGCCCGCCGTGTTTGGGGCCCAGTTT R 2 1 2 1 101000 f 74 goat snp4134-scaffold113-796174 1 53988594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423427 Affx-122942611 AX-123293773 1 52904268 GAGTAAAAGGGCATGTAATAAAAGTCTTCCTTTCT[A/G]CCCTTTCTTAACATCCACCTGGTTCCCCTCCTAAG R 2 1 2 1 201000 f 74 goat snp4135-scaffold113-838747 1 54031246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391025 Affx-122966876 AX-123261382 1 52937739 TCATCTCATAAAACATGATCTGGTTTTGTGATTGT[A/G]ATGGCAGATGCTACAGTTATCTGATTTCTTTCTAA R 2 1 2 1 101000 r 74 goat snp4136-scaffold113-872218 1 54065775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278412 Affx-1111836327 AX-519551897 1 52944895 CAAACAGTAGAGGACAGGGAAGCCTGGCATGCTGC[A/G]ATCCACAGGGTCACAGGACTAAACAACAACATGCC R 2 1 2 1 102000 r 74 goat Random2.2K-58 1 52944895 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275245 Affx-1111834790 AX-123246127 1 52962642 CTGAAAAGGCTGCAGTGATGTGAACAGGTAGCACC[A/G]ACTGAGCAAC R 2 1 2 1 103000 f 74 goat GoatD01.052991 1 52962642 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38449754 Affx-122922453 AX-123320089 1 52971262 AGTCTATCCATTAGCATAAAGGTGTGCAGAGTTAA[C/T]GATGAGTAAACAATATGCATTTTATGTGTTTTACA Y 2 1 2 1 101000 f 74 goat snp4137-scaffold113-905741 1 54099509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399346 Affx-122961357 AX-123269701 1 53006233 GACCTGACCACTGGATGAAGCAGTCTTCATTCACA[A/G]GTTATTAACTATATGATTTGGACAGGCCTCAGCAC R 2 1 2 1 101000 r 74 goat snp4138-scaffold113-940712 1 54134166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794636 Affx-122922834 AX-385281597 1 53039735 TTGACAACATCCTCGTCAGTTCTGTCTAAATTTTG[C/T]GAGATATGCACTTGCTAATTTTATATATTATATAT Y 2 1 2 1 101000 f 74 goat snp4139-scaffold113-974214 1 54167880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419502 Affx-122945456 AX-123289850 1 53068437 GCTGAAGAAAAGGGAAATGTTATCTTGTAAGCAAC[C/T]GCTCTCCACCAGCAGCTGGGTAATAAAATTGCACA Y 2 1 2 1 201000 f 74 goat snp4140-scaffold113-1002916 1 54199056 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399412 Affx-122961238 AX-123269767 1 53106714 ATAAGCCTTTATTCTTTCTTTAAGAGCAACAATTG[C/T]GTCATCTATGTCCTACATATCACATGTTCAGTGTT Y 2 1 2 1 101000 r 74 goat snp4141-scaffold113-1041193 1 54238179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789809 Affx-122965156 AX-385276816 1 53148518 TATTAAGCTGTGAAGTGACAGGCTAGACTAGAACT[A/G]TGTTCAAACTCTGCTCCTATCCATCTTGGAACTCT R 2 1 2 1 101000 f 74 goat snp4142-scaffold113-1082997 1 54279781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407855 Affx-122954517 AX-123278206 1 53178256 TTTGGAAACACAGCTTCTCTAAGGCTGCTGTCCCT[C/T]GAGCCTGAGCAGTCAGTGGACCATGCTGCAAAGCT Y 2 1 2 1 101000 f 74 goat snp4143-scaffold113-1112735 1 54309548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396135 Affx-122963398 AX-123266490 1 53213033 CAAATAAAAGAAAATTTGTTACCAACTGATTTATA[C/T]GGAAGCTGGAACTTCTGAAGAAAAATGGCCTGTGA Y 2 1 2 1 201000 f 74 goat snp4144-scaffold113-1147512 1 54344380 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380835 Affx-122975066 AX-123251193 1 53263948 ACAGCATCTAAGACTTACTTATTGTAGGTACTCAA[C/T]AGAGACCTCTTTGAAGAAAGAGGAAGAGGAGGGAG Y 2 1 2 1 201000 f 74 goat snp4145-scaffold113-1198427 1 54393770 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783652 Affx-122939691 AX-385270711 1 53325463 TGAAACTTCTTTAAAGTAGGAGGATAGTCTATTGT[A/G]TTCTGTTTGGACCCTGTCTCCATTATTTGTGCTTT R 2 1 2 1 101000 f 74 goat snp4147-scaffold113-1259942 1 54456423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796632 Affx-122932063 AX-385283578 1 53371392 GTCTGGGTTAAACAATCACCAGTGGTATGAGAAGA[C/T]AGTTCACTTTTAGGCATCTCAGCATGTCTTAGTTA Y 2 1 2 1 101000 f 74 goat snp4148-scaffold113-1305871 1 54502712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783108 Affx-122956769 AX-385270175 1 53401600 CTGAATATTTCTACAGTTTGATAGTTGCTACTTAA[C/T]GTTCCTTAAATTCAATCATATATGTAAGAAGTTTA Y 2 1 2 1 101000 f 74 goat snp4149-scaffold113-1336079 1 54532857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437721 Affx-122931741 AX-123308059 1 53453785 TCACTTATGTGTGTGTTCCATATGCACTGACATGC[A/G]TTAGCTTCAGATGAAAGGAGAAACTTTGTGCTCAT R 2 1 2 1 101000 f 74 goat snp4150-scaffold113-1388264 1 54585286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788657 Affx-122962995 AX-385275673 1 53491417 GTTGAAATCTACCAATAAGAGAAATGTACAAGACC[C/T]TCTTAGCTGTATTAGAAAGAGTCAGTGCTCATTCA Y 2 1 2 1 101000 r 74 goat snp4151-scaffold113-1425896 1 54623217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415780 Affx-122948916 AX-123286129 1 53524854 TGCTGCTACAGGCAAAGCAGATGTTGCTTCAGAAA[C/T]GTTTCTTCCCAAAGGGAAATCCATATGCAATTGAA Y 2 1 2 1 101000 f 74 goat snp4152-scaffold113-1459333 1 54655618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775029 Affx-122973436 AX-385262161 1 53569285 TAAAACATTATTTATTATGTAGGCATGATTTATTT[A/G]CTCTGTGAAAAGAAAGATTTTTTATTCACATACTT R 2 1 2 1 101000 r 74 goat snp4153-scaffold113-1503764 1 54703884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772852 Affx-122954220 AX-385259997 1 53603860 AAGAATACTTAAAATCCAGTGATCTGCACTCAAGA[C/T]GCCATATTTCTGTCCCCCTTTCAGCTTAATTCTCT Y 2 1 2 1 101000 r 74 goat snp4154-scaffold113-1538339 1 54738946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463646165 Affx-1110086955 AX-515127116 1 53633334 AGCTAGAGAGAAGCCCACATGCCACAAATAAGACA[C/T]GACCCAGTCAAATATATGGAGAAGGCGAGGGCACC Y 2 1 2 1 202000 r 74 goat 1_53633334_AF-PAKI 1 53633334 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435034 Affx-122933757 AX-123305374 1 53641334 AACAGAAAGAGAAAGTGTCTGAGACAGTCATGAGA[A/C]TGTACTGTTCACATCTTCTTTGATGAGAGAACTTT M 2 1 2 1 101000 f 74 goat snp4155-scaffold113-1575813 1 54776633 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420351 Affx-122944963 AX-123290698 1 53679140 GAAACACTGAGAGTGAAAGAAAGGGAGAAAGATGT[C/T]ATCTAATTTAATCTTTGCAACTCTGTGAGATACTA Y 2 1 2 1 102000 f 74 goat snp4156-scaffold113-1613619 1 54814006 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436928 Affx-122933192 AX-123307266 1 53708705 TGTTCTGTGAATGGAACATTTGAGTAAGTAGAGAA[C/T]GATGTGGCAAAACTTCTTTCTTTGATTTATTAATA Y 2 1 2 1 101000 f 74 goat snp4157-scaffold113-1643184 1 54843876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437422 Affx-122932413 AX-123307760 1 53764757 CTTGGCATTTCCTGGCTTCAAAACAGTCCCAGGTG[A/G]TTGAAACTTTAAGATAACTATATCAATATATATGA R 2 1 2 1 101000 f 74 goat snp4158-scaffold113-1699236 1 54901685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380809 Affx-122975086 AX-123251167 1 53817917 CTCTGTATAAGAGGGAATTTGAAAAAAGACACAAC[A/G]TTTGTTTAAAAATAGTAATGTAATCTTAAGTAACT R 2 1 2 1 101000 f 74 goat snp4159-scaffold113-1752396 1 54955529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386101 Affx-122971434 AX-123256459 1 53848818 GGTAATGTTCTATTTACAGTGAAAATGTGAAATGC[A/G]TACATTTTTTATTCCCCCCACCCCCAACGAAGTCA R 2 1 2 1 201000 f 74 goat snp4160-scaffold113-1783297 1 54986636 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427557 Affx-122939490 AX-123297900 1 53881996 ACCACATAACAGCTTGCCCCCTAGATCTAATGTAA[A/G]TGGGAAATATTTCTGAGTAAGGACTGCATAAAGCA R 2 1 2 1 201000 r 74 goat snp4161-scaffold113-1816475 1 55020236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446731 Affx-122924714 AX-123317067 1 53914625 CACAGATATGGAGGCTAGAAGTCTAAGATTAGAGC[A/G]CCAGCATGGTCCCATGAGAGCATTTTGAGGGGAGT R 2 1 2 1 101000 r 74 goat snp4162-scaffold113-1849104 1 55052910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803821 Affx-986696530 AX-385290561 1 53932591 ACTGGAAACAGCTTTGTCTCGGCCCAGTCATACTC[C/T]GCCCCCCTCTCCTGCAACAGCAGCCAGCCATACTC Y 2 1 2 1 600010 f 74 goat 1_53932591 1 53932591 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 320803826 Affx-986696533 AX-385290566 1 53932804 GCACTATAATGTATCATTTAATCCGGAACACTTAA[A/C]AAATTACACATAAAATACACATAAAATATAGACAT M 2 1 2 1 600010 f 74 goat 1_53932804 1 53932804 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320778684 Affx-122962718 AX-385265795 1 53953254 TGTAACAAATGTGAGAAAAGAATGGGGTATTCAAG[C/T]ATGGAGCTAGGCAGGGAGTATCAGTTAATTGGAGA Y 2 1 2 1 101000 r 74 goat snp4163-scaffold113-1887733 1 55091371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392017 Affx-122966482 AX-123262374 1 54016253 GAAATTTTAGCACTTCCACCTTCAAAGAACTAAGC[A/G]GCCCTTATTTAGACCAGGGGTGGGCAGAAAAATAA R 2 1 2 1 201000 f 74 goat snp4164-scaffold113-1950732 1 55154788 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435617 Affx-122933782 AX-123305957 1 54054344 TAAGAAATAAAAAACTGGAAATCTAAGAGTTACAT[A/G]CAAACTTAAGAGCTGTTACTCCCAACTCTGAAAAG R 2 1 2 1 201000 f 74 goat snp4165-scaffold113-1988823 1 55193988 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777081 Affx-122938685 AX-385264204 1 54096463 TTACTTAACATGTGAATGCTTAAATTTTAGAGTAA[C/T]GCATTGAGAGTAGAGGAAAAAATGGTCTCTCCTGT Y 2 1 2 1 101000 r 74 goat snp4166-scaffold113-2030942 1 55237486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410480 Affx-122952203 AX-123280830 1 54135473 AAAAGGGAGAGTGTTTGAAGGCAGAAGCTCAGAAC[C/T]GGACTCTCCCCATAACACTTACGAGATGTGCTACC Y 2 1 2 1 101000 f 74 goat snp4167-scaffold113-2069952 1 55277076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437589 Affx-122931868 AX-123307927 1 54165327 TGAAAGAGTATTCAAATAAGAGATCAGGAAGTGAA[C/T]AAATCTCTTACTAAGAAATGAATGGGATCTAATAT Y 2 1 2 1 101000 f 74 goat snp4168-scaffold113-2099806 1 55307142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383189 Affx-122973212 AX-123253547 1 54199048 AACAATCCAAGAAACAGAACTGCTAATTCACAGGA[C/T]ATGGATAGTTCTAAAGTTTTAATGTACATTCTAAT Y 2 1 2 1 201000 r 74 goat snp4169-scaffold113-2133527 1 55341198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396692 Affx-122962829 AX-123267047 1 54243164 TCCAAGCTCTGTCCCAACCTGTCTCTTGGTAGTTC[A/G]CAGAGATTTGCAGCAGGCAAAGAAGTACTAATGGT R 2 1 2 1 101000 r 74 goat snp4170-scaffold113-2177643 1 55386065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433510 Affx-122935019 AX-123303851 1 54271930 CAAGGAAGGCCTCTAAGCATTCCTTCAAGAACACA[C/T]GGTCCATCAACCATGAGACTTCCCTACCCAACAGC Y 2 1 2 1 201000 r 74 goat snp4171-scaffold113-2206409 1 55415843 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792525 Affx-122924853 AX-385279506 1 54329739 TTCATGCACTTAAGAGTTTCTAACTCACAACATTG[C/T]AATTGACCCTTCAATGATCCCCCTACTTGCAGCTC Y 2 1 2 1 201000 r 74 goat snp4172-scaffold113-2264218 1 55474455 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775137 Affx-122938506 AX-385262269 1 54367245 TTTCTGAATTTGAAAATTAAAGAATCTCTATTAAT[A/C]TTTTCCTTGCGCCTTCTCCTCCAGCAATAATACTT M 2 1 2 1 202000 f 74 goat snp4173-scaffold113-2301724 1 55511972 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437931 Affx-122931636 AX-123308269 1 54397760 TCAGCTAAACTCTAATCTGCCTTGAAGGAAAACTG[C/T]AGTCATTATTTATATTTCACCTGTGAGAGTTAAAT Y 2 1 2 1 101000 f 74 goat snp4174-scaffold113-2332239 1 55542668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442261 Affx-122928276 AX-123312598 1 54435814 AGCTTTCCTCCCACTGCTCTGCTACTAATTCATCC[C/T]TTTGCGCTGTGTGTGCTAAGTCGCTTCAGTCATGT Y 2 1 2 1 101000 f 74 goat snp4175-scaffold113-2370293 1 55581071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781202 Affx-122950269 AX-385268287 1 54483779 GTCATAGCTACAAGTTTTAAGATTTTTGGCCTTTA[C/T]AGAAACTTTCAGCGTTTCAATTTCAATCACAGCTT Y 2 1 2 1 101000 f 74 goat snp4176-scaffold113-2418258 1 55629430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767886 Affx-122968403 AX-385255106 1 54532428 TGCATCTATTCATTAGCTAAGTGCTGGGTATGTAT[A/G]TAGTAGTCAGCCGAATAGACTAGATTATAATGAAG R 2 1 2 1 101000 f 74 goat snp4177-scaffold113-2466907 1 55678216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422501 Affx-122943304 AX-123292847 1 54566794 GATTTTCTAGCTGAACCTTGAAGAAAGAGTTTTCC[A/G]TTTCTGAGGGAAGTCAGTAAAAAAGCATTCTAGGC R 2 1 2 1 101000 r 74 goat snp4178-scaffold113-2501273 1 55712735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790624 Affx-122935144 AX-385277626 1 54615101 AGAGTCATTTAATATTCCTGCTCTTCCTGTCATCA[A/G]TTGAGCAGCCAGATTAACCCTTTTAAAGGACATGC R 2 1 2 1 101000 r 74 goat snp4179-scaffold113-2549580 1 55761118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407262 Affx-122955349 AX-123277613 1 54649539 TATTAATTTTTTCCCACTTTATCACAGGCAGCAGT[A/G]CCTCTAAAGTTTATCCCACCGTGTAATAGGATCCC R 2 1 2 1 101000 r 74 goat snp4180-scaffold113-2584018 1 55795713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798563 Affx-122922813 AX-385285496 1 54717481 GCTAAGTGCAATTTAAGGAGTGAGGATGTGCAACC[G/T]GGAAAGTAAGCCATTAGCAATAAAGTTAGGCCATT K 2 1 2 1 101000 f 74 goat snp4182-scaffold113-2651960 1 55863809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446800 Affx-122925297 AX-123317136 1 54766318 AAGAAGGCTGGAGGCAAATTCAATACGTGGTGAAA[C/T]GAATGTGTAGTGGAAGTGGAGCTATGTGTTTTCAG Y 2 1 2 1 101000 f 74 goat snp4183-scaffold113-2700797 1 55912815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426696 Affx-122939901 AX-123297042 1 54821852 AGCACATCACTGGACTTGGCAGTGGTCTTGGCAAC[G/T]CATGATGTACCACCTTTCTGCCATCACTTAATAAC K 2 1 2 1 201000 r 74 goat snp4184-scaffold113-2756331 1 55967635 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417747 Affx-122947418 AX-123288095 1 54865591 ATAACAGAATTTGGGTTAGTGCAAAGGAAAGGTAC[A/G]TCTGGGCAGCTGGACACTCCCGTCTTAGGTGTTGC R 2 1 2 1 101000 f 74 goat snp4185-scaffold113-2800070 1 56011198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453105 Affx-122920029 AX-123323438 1 54926113 ACTCATAGTCCTGGTAACCTAAGCTATGTGGATGT[A/G]TAAATGAGCTCCCTTGACCTCTGGTCCAGCCAATG R 2 1 2 1 101000 f 74 goat snp4186-scaffold113-2860592 1 56072310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772280 Affx-122963953 AX-385259436 1 54964549 TCATCATCTCCATTGTCACAAAGAACAACTGGATT[A/G]CTCTGTGTGGAATGCCTAGTCCAGAGCTGGCACGA R 2 1 2 1 202000 r 74 goat snp4187-scaffold113-2899028 1 56110177 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410358 Affx-122952997 AX-123280708 1 55007519 TTGAATGTTGAAGAGGATTTGCCATGTTGTGAGTG[C/T]AAACATAACCTTGAAACAGAAAAGACAAAAAGCAA Y 2 1 2 1 101000 f 74 goat snp4188-scaffold113-2941998 1 56153035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445857 Affx-122925999 AX-123316194 1 55046263 ATCTGGGTAGTTTGGCTGATGCTTTAGATTGAACA[A/G]GTTTCTGGGTCAGTTTTAAAGTTTCTCTTTGGTGC R 2 1 2 1 101000 f 74 goat snp4189-scaffold113-2980742 1 56191399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391922 Affx-122966939 AX-123262279 1 55091550 TCCCTGGGTATCAGGGAATAGCCATTATCCAAGCA[C/T]GGAGAAGAGCAAATCCCTGCTGGTATTCTCTGGCT Y 2 1 2 1 101000 f 74 goat snp24547-scaffold2495-471333 1 56236441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408017 Affx-122954305 AX-123278368 1 55123598 CACCATATAAGACTTATCTTAAGAAATGAATCCTT[A/G]AAAACATCAGCCCAGCAATGACAGAAAAGAATTCT R 2 1 2 1 201000 f 74 goat snp24546-scaffold2495-439285 1 56269055 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278292 Affx-1111836347 AX-519551779 1 55130041 TTCTAAATGGGCACCAACATGCATCCTAGTAAAAT[A/T]ACTGGACTTCAAAGATAAAGAAGAGGTAAAAAATA W 4 1 2 1 101000 f 74 goat Random2.2K-61 1 55130041 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453495 Affx-122919825 AX-123323828 1 55153342 CAGACTAGTTCTCAGGGAGGAGGTAAGCCCTTTGA[C/T]GAAGAAAGCCACCTTGAATATTCTCTTGGGGGAAC Y 2 1 2 1 101000 f 74 goat snp24545-scaffold2495-409541 1 56299249 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452575 Affx-122920511 AX-123322908 1 55194426 TGTGATTTCCTTTGCTTGCCATTTTAGTTACTTGC[A/G]GTCACCAGATATTCCAGAAGTAAACAATGTGTAAG R 2 1 2 1 201000 r 74 goat snp24544-scaffold2495-368457 1 56339817 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379668 Affx-122975928 AX-123250026 1 55226295 GAGAACCTGAGAGCATCAATGATAAGCTAACACAA[A/G]CAATAAAATGAATGTACTCTTTTTTTAAATGCTAA R 2 1 2 1 101000 f 74 goat snp24543-scaffold2495-336588 1 56372525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415641 Affx-122948577 AX-123285990 1 55262534 TCCCGAAGGACAGGCTGGGGGGTTCCTGAGGCCTG[C/T]CTGAGGCTGTCCAAGTCTGCATCATCAAACTCGAC Y 2 1 2 1 101000 r 74 goat snp24542-scaffold2495-300349 1 56408820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382989 Affx-122973340 AX-123253347 1 55294084 AGCTTAAACGTCTAAATATATGGTACCTCAGCTGA[C/T]AGATCTTGAAGCAGGTCAGAAAGCATACACCAGTT Y 2 1 2 1 201000 f 74 goat snp24541-scaffold2495-268799 1 56440284 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421219 Affx-122944133 AX-123291566 1 55331509 CTCCTCCCTCCTGAGCAATTCCAAAAAAACAAGTG[A/G]TCCCTGAAATTACAAATAAGGGTACAGACCTCCCC R 2 1 2 1 101000 r 74 goat snp24540-scaffold2495-231374 1 56477612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447572 Affx-122924027 AX-123317908 1 55407095 TAGACACGTCAGAAGAGATGAATTATGTCATCCAA[C/T]ATTTAGTAGGTGCTCAGTAAGTATCTTTCAAGTGG Y 2 1 2 1 101000 f 74 goat snp24538-scaffold2495-155788 1 56552803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407882 Affx-122954497 AX-123278233 1 55477443 CTATGTTTCAGGCATTCTTCTGGGTGCTTGAGATG[C/T]GTCTGAAGAGATAGCTGAATAAAACAAACTCATTG Y 2 1 2 1 201000 r 74 goat snp24537-scaffold2495-85440 1 56625113 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397828 Affx-122962478 AX-123268183 1 55537727 GTTCAGTGGCTTGAAGAGTTATCTGTACTTTTCCC[A/G]TGGTTTCAGGAGAAGCTTTTGAAAAAGCCACTGCA R 2 1 2 1 201000 r 74 goat snp24536-scaffold2495-25156 1 56686399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427888 Affx-122939694 AX-123298231 1 55579623 CCTTTATTATAGCATAATTACAATTATTACCTTTA[C/T]ACCTCTCCCCCCTTCTATAATTTTTTCCTCATTAA Y 2 1 2 1 201000 f 74 goat snp12450-scaffold1474-602914 1 56725680 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278463 Affx-1111836351 AX-519551946 1 55632931 AAAAAAAAAAAAGAGGATAAATCCAAAAATTAAGA[A/C]TAGAATCCAGGAGTTAAGAATAGTACTGATTTTGG M 2 1 2 1 101000 r 74 goat Random2.2K-62 1 55632931 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409418 Affx-122954127 AX-123279769 1 55699285 CATGGAGGTTCAAGTAATCATTAAACACGCAGAAA[C/T]AGCCAAGGTAGAGGGGATCGGAGCAGCAGAGTAAA Y 2 1 2 1 101000 f 74 goat snp12448-scaffold1474-483252 1 56841317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775081 Affx-122948651 AX-385262213 1 55747622 AGTTTATAAATTTTCACTGCCAAGAAAATTTTGTG[A/C]TTGAGTTATTCTAAGTGACTCAAATGTTTACAACT M 2 1 2 1 202000 r 74 goat snp12447-scaffold1474-434915 1 56888761 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447254 Affx-122924952 AX-123317590 1 55805334 TTTCAGTTAAAAAATTAAAAAGAAAAATTAAAGTC[A/G]AAAGACTCTTGCTCTTCTAAGAAAGTTAAATGAAT R 2 1 2 1 103000 r 74 goat snp12446-scaffold1474-377203 1 56946078 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380812 Affx-122975084 AX-123251170 1 55833968 TCAGGGAAGTTGAGTGGAGAGTACAGAAAGTTCCC[A/G]TATGTCCCCTGCCCTCAAACAGGCACAGCCTCTTA R 2 1 2 1 201000 f 74 goat snp12445-scaffold1474-348569 1 56975517 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398591 Affx-122961494 AX-123268946 1 55868059 TGTCAGTAGGCTGCCCCATCCTCAGTGAGTGACTC[C/T]AGCTGAGAGGCCCTGGACCACTTGATGCTCAACTT Y 2 1 2 1 102000 r 74 goat snp12444-scaffold1474-314478 1 57009873 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778391 Affx-122949130 AX-385265506 1 55915586 TTACTCAGTTAATTTACTCAGGTAATTACTCTGAT[A/G]TCACCATTTTATGTAGCATAGGAGATTGACCAGTT R 2 1 2 1 101000 r 74 goat snp12443-scaffold1474-266951 1 57057795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778015 Affx-122978610 AX-385265131 1 55968340 AAACTGTGGAGAAAAAACCCATCACAGCTGTAACT[A/G]ATGTAAAATACAAGAGATAACTGAGGACTTTCACC R 2 1 2 1 101000 f 74 goat snp12442-scaffold1474-214197 1 57109888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452513 Affx-122920556 AX-123322846 1 56018601 TAGCCTACCACAACCAGATCTCAGAATTGGAGGTC[A/G]TAGTGGCCTTTCCCTGTGTAATGGCTGACCACAAT R 2 1 2 1 101000 f 74 goat snp12441-scaffold1474-163936 1 57157818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430368 Affx-122937785 AX-123300709 1 56064268 AGTGAAGAATGATCCAGCCCATGATGTTAATAATG[A/C]TGAGGTTAGAAAACCCTGCTTTAAGCTCTTATATT M 2 1 2 1 101000 f 74 goat snp12440-scaffold1474-118269 1 57203991 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788284 Affx-122952635 AX-385275302 1 56100920 TGTTCTTAAACCAAATGCGACCAACCAATTGAGCA[C/T]GTATGAGAACCAGAATAACTGGTCATGACAACAGC Y 2 1 2 1 101000 r 74 goat snp12439-scaffold1474-81617 1 57240702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419416 Affx-122945522 AX-123289764 1 56144191 TTCCATTAGAAGGTAGTAATTAGAGAAAACGAAAC[A/G]TACACTTAACAGTATTTGTTACTTTTAGAAACAGA R 2 1 2 1 101000 f 74 goat snp12438-scaffold1474-38346 1 57285055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773101 Affx-122937790 AX-385260244 1 56180368 CTTCTAGGGCCACTGTAAACTGGAACCTTATCTTC[A/G]TTGATATTTATGGTAAACTTGTATTAAAAAAGTAT R 2 1 2 1 101000 f 74 goat snp12437-scaffold1474-2169 1 57313168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271832 Affx-1111832862 AX-519545616 1 56198096 ATGAGGGGTAATAATAATAGAAGTGCATGTGGAGG[A/G]CAATTACATTTTGATGGGGGAAGGGCCAAGAGATG R 2 1 2 1 201000 f 74 goat 1_56198096_AF-PAKI 1 56198096 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780449 Affx-122952456 AX-385267540 1 56200120 TGCATATAGGTCTCAAAAACTATGAAACTGAGAAC[G/T]TGAACAAAGTAAAGACTGTTACCTCTCTCTCTGTA K 2 1 2 1 101000 r 74 goat snp609-scaffold1017-548943 1 57341585 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412283 Affx-122950879 AX-123282632 1 56245804 AACCCTAACTCTCCCACAGGAAAAATGTAGAACTC[C/T]GACCTCACTCTCCTTCCACCTCTGATCTACATTTG Y 2 1 2 1 101000 f 74 goat snp608-scaffold1017-503259 1 57387637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794138 Affx-122975813 AX-385281104 1 56277279 TGAGTTAAATGGTGCCTCCACCTCAAGATCTGTCC[A/G]CCAGGAACCTACAAATGTGGGTACATTTGGACAAA R 2 1 2 1 101000 f 74 goat snp607-scaffold1017-471784 1 57419570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401022 Affx-122959676 AX-123271375 1 56307896 GATTCTTTACCACTAGCTCCACCTGGGAAGCCCAG[C/T]GGTAGTAATAGCTTCTCTTTTTTTCCTCATCCTCT Y 2 1 2 1 101000 r 74 goat snp606-scaffold1017-441167 1 57450345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393930 Affx-122965077 AX-123264285 1 56365921 CAAAGCATTTCAATTTGGCAAGGTTATTTAAACAG[C/T]AAAAATAATATTAATTTTTCTAAGGGTAAATACTG Y 2 1 2 1 101000 f 74 goat snp605-scaffold1017-383142 1 57508982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431056 Affx-122936643 AX-123301397 1 56400985 TGCGACCTTGGGTTACACCTGAGCAGAACTGCAGA[C/T]GCCTACACAGGTGATGCATAATTCCTCTGTGACCA Y 2 1 2 1 101000 r 74 goat snp604-scaffold1017-348078 1 57544769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439858 Affx-122930448 AX-123310195 1 56453627 GAACCACTTGCCAAGAAGCCAGTGTTTCTGTCTTC[A/G]CTAGACTATAAGTTCCTGGAATGTATGCACCCTGT R 2 1 2 1 201000 r 74 goat snp603-scaffold1017-295436 1 57597486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799369 Affx-122940981 AX-385286299 1 56483905 AGTCATGGCCAATATACTATACTCCTAATACTATA[C/T]GTCTCCCAGGAAGTTTATACATTGTGACGATAATA Y 2 1 2 1 101000 r 74 goat snp602-scaffold1017-265158 1 57627853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776455 Affx-122977733 AX-385263582 1 56552928 CTTCTCCTGAGACATCTTTAGAAATAGCAAATTCA[A/G]TCATGCCATATCGATTCCTCTTTCCGACCTCACCA R 2 1 2 1 101000 f 74 goat snp600-scaffold1017-196135 1 57696147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430085 Affx-122937538 AX-123300426 1 56593759 TTGTCACGGCTTCCAAGCAATGAGGATCTCTGCTG[C/T]GCCACATCACTGCCCAGTGTACAGACTAAAAGCAT Y 2 1 2 1 101000 r 74 goat snp599-scaffold1017-155304 1 57737055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416248 Affx-122948206 AX-123286597 1 56645824 TAGACTGACTAGGCATGGTGGGGAGAGGGGCACAC[A/G]TTTACCTGTAACAAATGAGAGTAGCTCAGACAAAT R 2 1 2 1 101000 r 74 goat snp598-scaffold1017-103239 1 57786867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396848 Affx-122963259 AX-123267203 1 56675015 TCTTTTTCTTTTTTTTCCACTACAACATAGACAGT[A/G]TAGAGGCACTGTGGGGTTCCAGAGGAGAGGATATA R 2 1 2 1 201000 f 74 goat snp597-scaffold1017-74048 1 57816005 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445290 Affx-122925453 AX-123315627 1 56720318 TTCACAGGCTCTTACAAGTTTGTTATCTCATAATC[A/G]CACCAGGTTAACACTTCCAGAGATACCAGTGTATC R 2 1 2 1 101000 f 74 goat snp596-scaffold1017-28745 1 57862262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782144 Affx-122975175 AX-385269222 1 56762876 AACTGTCAAGATTTAGTCATATTTATTGAGCCCTC[A/G]CTGTATTAAAGAGAATGTATAGTAGTGATAGTATA R 2 1 2 1 101000 f 74 goat snp35158-scaffold4205-266708 1 57905519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446899 Affx-122924708 AX-123317235 1 56834009 ATTATGTACCTTGATGTAACATTCTTTGTGTTTCA[G/T]ATTTTGTTGAGTTTGGAAAGCAGGTTCATGGGTAA K 2 1 2 1 101000 r 74 goat snp35156-scaffold4205-195575 1 57976652 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424108 Affx-122942026 AX-123294454 1 56885348 CTCATTTTAGTCTCAGAAAAGCACTTGTAACTATG[C/T]GCATTTTGAAACAGTCTTGAATGTCTGGTTGCTGA Y 2 1 2 1 101000 r 74 goat snp35155-scaffold4205-144236 1 58027916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403508 Affx-122957632 AX-123273861 1 56940085 AGGCTTAGTCACTGACAATGCAGAACACTCCACTG[C/T]GGCCCGAGCTTTTGTGGCCAGGATGAAGATGTCCT Y 2 1 2 1 101000 f 74 goat snp35154-scaffold4205-89499 1 58083194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445328 Affx-122925424 AX-123315665 1 56969767 GCAGAGTACATAGATATTTTCCATTTTGTCCTTGC[A/G]TTTTGCATCAGGCCATAAGGATGATAGCCAGTTGT R 2 1 2 1 101000 r 74 goat snp35153-scaffold4205-59817 1 58112935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389865 Affx-122968149 AX-123260222 1 57013033 GAAATAAATTGTTCTGAAGTGTTTTGCCTAACCAA[A/G]GATTTGGAAGAAGATCAGAATTGAAATGTTAGCTG R 2 1 2 1 101000 f 74 goat snp35152-scaffold4205-16551 1 58156502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380459 Affx-122975735 AX-123250817 1 57036210 CAATATAACCTGTCTTATATTTAAAATAAATTACT[A/G]CACCCAGTTTGTAGTACAGTACTGAAGAGCAATAT R 2 1 2 1 101000 r 74 goat snp37452-scaffold456-5411884 1 58179430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387858 Affx-122969643 AX-123258216 1 57136000 GTACTCTTGCCTAGAAAATTCATAGACACAGAGAG[C/T]GGAATGGAAGTTTTAGGGAGAGAAGGCAAAATGGG Y 2 1 2 1 201000 r 74 goat snp37450-scaffold456-5312094 1 58280097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427143 Affx-122939641 AX-123297486 1 57165223 TCTCCAGGGAAATATGATGAGTGAAAACAGCCAAC[A/G]TAGAGTGTTACATAACTGTACTATCCCCTTTATAT R 2 1 2 1 101000 f 74 goat snp37449-scaffold456-5282871 1 58304411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440530 Affx-122929336 AX-123310867 1 57203069 TCTCAAAGATGACACTAACTTGATCAGTTAACCAC[G/T]ATTTGGAGAATGGCCTCAGCACTGTTGACTTCCTA K 2 1 2 1 101000 f 74 goat snp37448-scaffold456-5245025 1 58342168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452931 Affx-122920189 AX-123323264 1 57267821 GCACAGGTCGCACGCAGGTTCCCAGCATCTCCACC[A/G]TAAGCGCTTTGGCTGCTCAAGCCCTCGCTTCTCTA R 2 1 2 1 101000 r 74 goat snp37447-scaffold456-5180273 1 58407118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422239 Affx-122944012 AX-123292585 1 57305221 TCCCCTAGTCTTATTTCTGCCTCCTTAAAGACAGT[C/T]TCATTCCTGACATCTGTGGCACCCCCACTATTCTT Y 2 1 2 1 101000 f 74 goat snp37446-scaffold456-5142873 1 58445648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382697 Affx-122973636 AX-123253055 1 57342111 GAAGGGAAAAATAGCAACTTTACACTGGAAAAGCT[A/G]CCTTAACCAAGTGATGGGTCATATTCTCAGTAATA R 2 1 2 1 101000 r 74 goat snp37445-scaffold456-5105983 1 58482700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415351 Affx-122948782 AX-123285700 1 57389759 TGAACAGGAATATAAACATATGAACAAGTCCAGTC[C/T]AATATATTTCAAAACAAGAAGATTCTTGAGAATAG Y 2 1 2 1 101000 f 74 goat snp37444-scaffold456-5058335 1 58530099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391182 Affx-122967430 AX-123261539 1 57419893 GAAGACTCCCTGTGCCCACCTTTAGCTGCCAGGCC[A/G]CAGTGCTGCTGGCCAAGTCCTGCTCAGAACTATGG R 2 1 2 1 101000 r 74 goat snp37443-scaffold456-5028201 1 58560320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382706 Affx-122973629 AX-123253064 1 57452878 TTTTAGACTCCTATGACCTCCCACAGCTTCCTAAA[C/T]GGCCCTTCAACCACGCTCAGAATTATTTCCCCAGA Y 2 1 2 1 101000 r 74 goat snp37442-scaffold456-4995216 1 58593673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385730 Affx-122971094 AX-123256088 1 57504377 CTGCTGAGAAGGAACTGATGAGATGTGACATAGAA[C/T]GGGGAAGCAGGATGTCTTTGTTTTGAAATGACAGG Y 2 1 2 1 101000 f 74 goat snp37441-scaffold456-4943717 1 58645840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798938 Affx-122956520 AX-385285868 1 57560141 GTCCAGCTTTCAATTCTCTCACCACTGATTTAATT[A/C]AAGTGACAGGAATGCCAATGCTTTCGTACTAGTCC M 2 1 2 1 101000 r 74 goat snp37440-scaffold456-4887953 1 58701370 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433519 Affx-122935012 AX-123303860 1 57616660 GGGTGGCAATAGGTCAGGCTGTCCACGTGTGCCAC[A/G]TTTCAGACTGCTGCCTTCCTCCTGGCAACTGTCTG R 2 1 2 1 101000 r 74 goat snp37439-scaffold456-4831434 1 58757875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416228 Affx-122948220 AX-123286577 1 57657118 ATGTCTCCATTTAAGTATAATATGCACAATTTAAA[G/T]CAAATGTTAGACATATTTAAAATGTACACTTACGT K 2 1 2 1 202000 f 74 goat snp37438-scaffold456-4790976 1 58798085 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419551 Affx-122945416 AX-123289899 1 57702372 TCGGAATCTCACTAGTGCTCTCAATAGCCTCCCCC[A/G]CACCTGGCCTTCCTGACCAAAGTGAGCACACTGTC R 2 1 2 1 101000 r 74 goat snp37437-scaffold456-4745722 1 58843306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380765 Affx-122975117 AX-123251123 1 57742551 ACTTAGCACAATGCCTGGCAGATAGGAAAATATTC[A/G]TTAAATAAAATGTGAATAAATTTGCACTCCCATCA R 2 1 2 1 303000 r 74 goat snp37436-scaffold456-4705543 1 58883659 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772015 Affx-122943192 AX-385259171 1 57781932 TGTTAGAGCTCTCCCTGAGTCTGTCATGAGATTTA[C/T]ATTCTTAATCATATGGAGCCCATTTTGGCCATTTA Y 2 1 2 1 101000 f 74 goat snp37435-scaffold456-4666162 1 58923035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375390 Affx-122979214 AX-123245749 1 57831380 AGGAGAGGGATTCTGTCTCAGAATCTCCAGAAAGA[C/T]GCAATCCACTGACACCTTGATTTAAGGATTTCTGA Y 2 1 2 1 101000 f 74 goat snp37434-scaffold456-4616714 1 58972567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781355 Affx-122931444 AX-385268441 1 57860201 TTTATGCACAGTTTCCAAATAACAACAATTTAAGA[C/T]ATAGATATGACCATCCACTTCAGAAAAAAGATAGT Y 2 1 2 1 101000 f 74 goat snp37433-scaffold456-4587893 1 59001370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800730 Affx-122934506 AX-385287647 1 57933538 AACAGTGAAATATGAAAAGACCTATTCAGATTTAC[C/T]AAAAATCTCCCATGATACCATTATCCATTATATTT Y 2 1 2 1 201000 r 74 goat snp37432-scaffold456-4514556 1 59074768 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773909 Affx-122931037 AX-385261048 1 57965981 ACACTTTCTGTGGAATGTAATTTAGTAAGATGTCC[A/G]TCTAAGCTTTCCTCAACCATTCTTTAGGTCAGATT R 2 1 2 1 101000 f 74 goat snp37431-scaffold456-4482113 1 59107226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415163 Affx-122949399 AX-123285512 1 58019331 TGTTTGTGAAAGTGCTTTATACACTGTAAAACACT[A/G]TACAAATGCTATTTCTTTCTTCTTATGAGTGGATG R 2 1 2 1 303000 f 74 goat snp37430-scaffold456-4428763 1 59160216 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273493 Affx-1111833651 AX-519547109 1 58034921 GTTTTCAGTCTACAAAGTCCATCACGACATTCAGG[A/C]CTCTGGACTGGACTATTAGACTGTACTCTTTCTGC M 2 1 2 1 101000 f 74 goat GoatD01.000586 1 58034921 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431253 Affx-122937125 AX-123301594 1 58059569 AAAAATTATTTTTAAAATGAATATAAATAATTTTC[A/G]TTATTGTAGCTAAGGCATGAGCTGTGTCCTCAAAC R 2 1 2 1 103000 r 74 goat snp37429-scaffold456-4388525 1 59200339 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773033 Affx-122929414 AX-385260177 1 58115236 ACAGAGGGCTGCTGTTACATGCTAAAAACACGTTA[C/T]AGAGGGCTTCTGTTACTTGTGCCGAGGTTAGAGCA Y 2 1 2 1 101000 r 74 goat snp37428-scaffold456-4332858 1 59256309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413655 Affx-122950121 AX-123284004 1 58182399 TCTCCTTGGAGGTAAACTAATATTGAATATATAAA[C/T]GATGGACTTTGGAATCAGTTCTGAGTTTGAATCCT Y 2 1 2 1 201000 f 74 goat snp37426-scaffold456-4265695 1 59323418 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800912 Affx-122930391 AX-385287827 1 58237595 AAGAGGTCATATGACTGATACTCTGACTCTCTAAG[C/T]GTTTTCCTTTCCTCGATATTCAGCAAGTTTGGCTC Y 2 1 2 1 101000 f 74 goat snp37425-scaffold456-4210499 1 59378737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445392 Affx-122925395 AX-123315729 1 58268365 TATTCTATTCTTCAGCCTCTCATAAATTTACTTCT[A/G]CATATAAGCCAATTAAATTTTATTCATTAGTTGTA R 2 1 2 1 101000 f 74 goat snp37424-scaffold456-4179729 1 59409177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791859 Affx-122920229 AX-385278849 1 58305351 TTTCTAAAATTATGGAAGAACCTTGTGTCCTTTCT[A/G]TTCATTAATTATTGCCAGCAATATTTTGGGGGTGA R 2 1 2 1 201000 f 74 goat snp37423-scaffold456-4142743 1 59446198 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796912 Affx-122924579 AX-385283853 1 58357297 TAGCATCCCAGAAAATACCCATCTTTATTCTGAAA[C/T]ATGATATGCTTGGTATTCAGACTTCTCCCTAGTGA Y 2 1 2 1 101000 r 74 goat snp37422-scaffold456-4090797 1 59498389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432285 Affx-122936324 AX-123302626 1 58414215 AGGATACTCTGTATTTTGCCCCCGTCTGACCTAAA[C/T]GCATCCTGACAGTATCTTCCCCCTCAAATCTTAAT Y 2 1 2 1 201000 r 74 goat snp37421-scaffold456-4033879 1 59555493 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769737 Affx-122957244 AX-385256907 1 58446664 ATGATGAAAGGTAAATAAATGTTCAGCATAATGCT[C/T]AGGGACCTCCTTGAGCTCCAGATATAGTTGTGCTT Y 2 1 2 1 101000 r 74 goat snp37420-scaffold456-4001430 1 59587958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440505 Affx-122929355 AX-123310842 1 58481314 GCTTCCTGGCACTGTAAAATATACTTTAAAAAATA[C/T]AATAATCTTTTGTTCTTTTAGGAAAAAGATTTATA Y 2 1 2 1 103000 f 74 goat snp37419-scaffold456-3966780 1 59622861 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389324 Affx-122968490 AX-123259682 1 58517560 AAAGCTGTTCCAAACAGCAGGCTGTTAGTCCCAGG[A/C]CCTGCCTGATGTCCCAGTACCGCCTCCCCCAGAGT M 2 1 2 1 101000 f 74 goat snp37418-scaffold456-3930534 1 59658933 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786579 Affx-122970246 AX-385273611 1 58547244 CTCTTAATAGGTAAATATGCCCATGGGCTTTTTGT[A/G]CTCCATTTGTGAAGCTATAGTATAGGTTGTCCCAA R 2 1 2 1 101000 f 74 goat snp37417-scaffold456-3900850 1 59688632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440424 Affx-122929421 AX-123310761 1 58602389 CAATATCACCTTCAGGTTTTATACATATCTTCAAT[A/G]CAGCAGACTTTCGGGACCAGGCAGAGCCTGAGGAC R 2 1 2 1 201000 f 74 goat snp37416-scaffold456-3845705 1 59742488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450553 Affx-122922473 AX-123320887 1 58655432 GATGTAGACAAAAGAAAAACACATACACAAAATTC[A/G]CTAAATTAACTGATTAATTGAAATAAACATAGAAA R 2 1 2 1 201000 r 74 goat snp37415-scaffold456-3792662 1 59794887 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396878 Affx-122963237 AX-123267233 1 58684281 CATTCTTGTTACTTTTTTTTCTTTTCCAGAGTTTA[C/T]AGAATTGAAAGGAGAGAATCAGTTGGTAATTTCTC Y 2 1 2 1 101000 r 74 goat snp37414-scaffold456-3763813 1 59823879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398409 Affx-122961633 AX-123268764 1 58742561 TTTCCATCACCCTCCATACATGTCTTCCTGAGCCT[A/G]TCTCTAAACTGAATATTACATCTTTCTACTTCTTT R 2 1 2 1 201000 r 74 goat snp37413-scaffold456-3705533 1 59884268 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271833 Affx-1111832863 AX-519545617 1 58782018 AGGCTTGACAGTTGTCAGGAAAGGTTTTCCTGGGA[A/C]GAGCTCCGACGGCTCTCCTGCCTTGGTTCAGCCCG M 2 1 2 1 101000 f 74 goat 1_58782018_AF-PAKI 1 58782018 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454008 Affx-122919431 AX-123324341 1 58797469 GTGTTTTGAGGTAGGTAAGGGCATTTCCAGAGAAG[A/G]GGACATGGTTCTCCAAAAGTGAGTGGACGCCCAAA R 2 1 2 1 101000 f 74 goat snp37412-scaffold456-3650625 1 59939542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391420 Affx-122966763 AX-123261777 1 58844891 TTTGTGTAGGGCACTGAGAGATAAGAGCAGGAAAT[A/G]CTGGGAAAAAGAAGACACATTTCCAATCTCTAGGG R 2 1 2 1 101000 f 74 goat snp37411-scaffold456-3603203 1 59987517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775411 Affx-122949509 AX-385262542 1 58898384 AACACATTGATCCCTGCATCCAATAGCAAGTCCTC[A/G]GTATATATCCACCCAGTGCTTGTGTGTATATATCC R 2 1 2 1 101000 f 74 goat snp37410-scaffold456-3549710 1 60041106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765124 Affx-122973558 AX-385252683 1 58929231 TCTCTCGCCAGGGAAAGATGAATGATTGAATAATA[G/T]CTTTTTTAGGCCCCCTGCCTCAACAAGACAGTCAG K 2 1 2 1 101000 f 74 goat snp37409-scaffold456-3518863 1 60072299 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448913 Affx-122923170 AX-123319248 1 58994299 ATCCTTCCTGAGGAAGAAAGAGTGAACCACATTGC[A/G]TCTGTCACTTCGGTTGTTTTCTCACTTCACTGATA R 2 1 2 1 101000 r 74 goat snp37407-scaffold456-3453795 1 60137712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385333 Affx-122971659 AX-123255691 1 59026527 GGGGACCCTGCTTATAATAGCGGTGACTCAGCACC[A/G]CCTTGCAGATCTTTCCCTCTTTCAGCTCCTTACAG R 2 1 2 1 201000 f 74 goat snp37406-scaffold456-3421567 1 60170819 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414145 Affx-122949698 AX-123284494 1 59055126 GCTGATCTGAGTACCCCTTTCTTTTTCTTTCCCAA[C/T]GCCTAAGGGAAGAATCAAGGTGGTCTTTCTGGTGG Y 2 1 2 1 101000 r 74 goat snp37405-scaffold456-3392968 1 60199074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794614 Affx-122956980 AX-385281576 1 59090896 TTGACCTGGTGTGTTGACTCAAGATTCCCACTCCC[A/G]CTGCAGCTAAATTTTGCACTTTTCATGTCAAACAT R 2 1 2 1 101000 f 74 goat snp37404-scaffold456-3357198 1 60234782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278488 Affx-1111836362 AX-519551971 1 59096342 TTCCCTTTCTGGGAAGCACTCTAATATAACGGAAA[A/G]TTTTGAAATTTGAAATCTTGCTTTCTAGTTCTGCC R 2 1 2 1 101000 r 74 goat Random2.2K-64 1 59096342 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422927 Affx-122943038 AX-123293273 1 59140875 CAGTTTGCATAATCCACACCCTGTTGTGTCTTACT[A/G]TTCAAAGAGGGAGCATTTCTATAGCAGAGTAACCA R 2 1 2 1 101000 r 74 goat snp37403-scaffold456-3307219 1 60284002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447014 Affx-122924549 AX-123317350 1 59181352 TTTAGAGAGAAAATGGGGAAATGTGGAACTCTGAA[C/T]GACAAAAGGGATTTATACCAAAAGACACTGAGATA Y 2 1 2 1 101000 r 74 goat snp37402-scaffold456-3266742 1 60323049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433545 Affx-122934994 AX-123303886 1 59211823 TCTTATCCTAGATCTGTGCTGGTAATATCCCTACA[G/T]AAGAATCCACCAACAGACCTGGGGTCTTAATGGCA K 2 1 2 1 101000 f 74 goat snp37401-scaffold456-3236271 1 60353585 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423752 Affx-122942851 AX-123294098 1 59247772 CATTTATGGTAGCTCTGCTGGCACCAGAATTTTGC[G/T]AGCTAGAGCACTGAGCTAAGTTACCCAGTAAAGGA K 2 1 2 1 202000 r 74 goat snp37400-scaffold456-3200322 1 60389735 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416843 Affx-122948108 AX-123287191 1 59279202 CTACAATGTTAACAGGTTTGGAAAATGTATTTTGC[A/G]TCTTTAGAAAGTGGGAAAGATTGAGGACAAGAGGG R 2 1 2 1 201000 r 74 goat snp37399-scaffold456-3168892 1 60421729 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442819 Affx-122927708 AX-123313156 1 59355179 AGCAACTTAGCATGCAGGATGCATGCTGCTCAGGA[G/T]TCCTCAATACCGTTTATTTATGTATTCCACTTTAA K 2 1 2 1 201000 r 74 goat snp37397-scaffold456-3092915 1 60498241 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429087 Affx-122938273 AX-123299429 1 59383709 GAATTGAGTCTGAAATTGTTTCCAGAACCTAAAAC[A/G]TAAATCATATCTTAAATAATCTCATTTAATCCAAA R 2 1 2 1 101000 f 74 goat snp37396-scaffold456-3064385 1 60526698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278501 Affx-1111836369 AX-519551984 1 59397299 GTAAAATGTGAAGTGTAGATGTATAACAGATAAGA[A/C]AGGCAGCCATTTGTATAAGCTTTGACTATGTAATT M 2 1 2 1 101000 r 74 goat Random2.2K-66 1 59397299 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378229 Affx-122976914 AX-123248588 1 59414390 ATCACTAGCCTTCATTGTAGTGTCTCTGTCACAAA[C/T]GTGACTTATAATTCAAGGGCTTTGCTGGTGGCAAT Y 2 1 2 1 101000 f 74 goat snp37395-scaffold456-3033704 1 60557330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434235 Affx-122934835 AX-123304576 1 59451059 ACATGACTCCTCTTCCACTACACTATGATCTGGTT[A/C]GGGTGACAATTCCGTCTTCACTCTTGTGACCCCTC M 2 1 2 1 201000 r 74 goat snp37394-scaffold456-2997035 1 60592222 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433491 Affx-122935034 AX-123303832 1 59496193 AAGACAATAATGGAAAAGAGAAAGGTGGATGGGCA[A/G]TTTTGAAAGGAAGTTGATAGAGCTTGCATATGATG R 2 1 2 1 101000 r 74 goat snp37393-scaffold456-2951901 1 60637464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417107 Affx-122947475 AX-123287455 1 59554060 CAACTTGGGCACGTTCTCTGGCAACCAAAATGTCA[C/T]GATGAAGCACCCCTGCCATTTTGTAGTCAGCTCAA Y 2 1 2 1 101000 f 74 goat snp37392-scaffold456-2894034 1 60695589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397255 Affx-122962357 AX-123267610 1 59602657 TCAGTCACTGGAAGATAAGTAATCACTGCAGGTAA[C/T]AAGACCACATCATTGCACATCAGTACCAACCCCAC Y 2 1 2 1 101000 f 74 goat snp37391-scaffold456-2845437 1 60744409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787298 Affx-122972397 AX-385274323 1 59637232 TCCATTGTGAATATCTTTAAATAATGGTACAATGT[A/G]CAGTGATTTTCATTGTAGTTGACAATGCAAACCCC R 2 1 2 1 101000 r 74 goat snp37390-scaffold456-2810862 1 60778794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792183 Affx-122963159 AX-385279168 1 59666182 TCCTTAGTTAAATCAAAAGATAATTATTGAGCAAG[C/T]ACTACTAATATTACCTTTAGTAACTGCTGTTACTT Y 2 1 2 1 201000 f 74 goat snp37389-scaffold456-2781912 1 60807676 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425715 Affx-122940766 AX-123296061 1 59696656 ACTTTAAAGCATGCTCCTAATTGGGTGTACTTGTG[C/T]AGTATCACTTTTGGAGAGTCTAGATATGGGGGAAT Y 2 1 2 1 101000 f 74 goat snp37388-scaffold456-2751438 1 60837934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411120 Affx-122951904 AX-123281470 1 59772319 TAACATTCTAGATTTTCACCTCTGTCTGGATTCTT[C/T]TGCAAACACAGGTTTTCATCAATTCCTTACTTTTC Y 2 1 2 1 101000 f 74 goat snp37387-scaffold456-2675775 1 60913576 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389093 Affx-122968581 AX-123259451 1 59810654 GGAACAAAATTTGAAATTCAGTCTAAGATCACATG[C/T]AAGCAAAAATGTAATTTGTGTGTATATCTGTCTTA Y 2 1 2 1 101000 f 74 goat snp37386-scaffold456-2637440 1 60951762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434057 Affx-122934194 AX-123304398 1 59840914 AGGAATCAAAGCCGCCGCACGTAAAGTCGGATGCG[C/T]ACTCCCAAGGAGACAGAGAGGTCCCAGAAAAAAAA Y 2 1 2 1 201000 r 74 goat snp37385-scaffold456-2607180 1 60981960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779616 Affx-122948836 AX-385266718 1 59895630 TGATGTTCCATAGTTGAGTTACTGACATTATCAAT[C/T]TTGGACCCTAGCTTAGACTCTGTAAATGAAGATCA Y 2 1 2 1 101000 r 74 goat snp37384-scaffold456-2552464 1 61036720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418208 Affx-122947057 AX-123288556 1 59931711 CCAGTGACCTCCTTTCACCAGTGAACAGGATGATT[A/G]TTCTGAAAATGTATTCCACATGTCCAGGAAAGATG R 2 1 2 1 101000 f 74 goat snp37383-scaffold456-2516383 1 61073550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406885 Affx-122955637 AX-123277236 1 59986622 ACAAGCTTTCTATTTTAAAAAGATCACTGCTTCCT[A/G]TATTGACAATACACCATGACAAATGCAAGAAAGAA R 2 1 2 1 303000 r 74 goat snp37382-scaffold456-2461472 1 61128560 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435135 Affx-122933682 AX-123305475 1 60039077 TAGAAGGTGGCCATGCTAAGAAGTGGGAAAGCTGA[G/T]CAGGAATGGTGTTTTCAGTGTGTAGAATGGGAGTG K 2 1 2 1 101000 r 74 goat snp37381-scaffold456-2409017 1 61180801 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278349 Affx-1111836376 AX-519551835 1 60075044 TCAGAAGAGATCTCAACCATTGAGAATTACTTGCA[A/C]TTTGGTGCTATATTGTATGTCAAAAACCCTTTTTC M 2 1 2 1 101000 f 74 goat Random2.2K-67 1 60075044 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788225 Affx-122961431 AX-385275244 1 60082074 CATTTTAGTGGGGCGTGGAGAAAGTGGAAACTAAG[C/T]ATTAACTTTAAGGATACGATTTGGATTGATTAGTA Y 2 1 2 1 101000 f 74 goat snp37380-scaffold456-2366020 1 61224187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278363 Affx-1111836383 AX-519551849 1 60092245 TCTTCGCAGGTAGGAAAGCTTAGGACTTCCCTAGC[A/G]GTCCAGTGGTTAAGACCTCGTGCTTCCAATGCAAG R 2 1 2 1 202000 f 74 goat Random2.2K-68 1 60092245 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429781 Affx-122938239 AX-123300122 1 60129151 ATGAATTTAGGACTGATGACTGAATGTCACAAGTG[C/T]GTCGCCCTTTGGAGGCACAGAGCCTATTTCCACTG Y 2 1 2 1 101000 f 74 goat snp37379-scaffold456-2318943 1 61271085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781750 Affx-122948154 AX-385268832 1 60215694 AATGGAGTATTGAAAAGAAACAAAGCTGAAACGCT[A/G]TTTACATTTGAGGTGTTTTCTTAAAACAGTCTTTA R 2 1 2 1 101000 f 74 goat snp37377-scaffold456-2232400 1 61357198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426742 Affx-122939867 AX-123297088 1 60258228 AATTGTTATTTACACCTAGCTAGGAGTTCTGATGA[C/T]GAGACCAAAAGCAAAAACTTGGTATAATTCCAGTG Y 2 1 2 1 101000 f 74 goat snp37376-scaffold456-2189866 1 61400985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451446 Affx-122921159 AX-123321779 1 60307458 ACCAAGAAGGCAGAGATAGAAGCTGCTTCAGATGA[C/T]GTAGTGAAGGGGCCCAGGCTGCCGATTAGAAGAGC Y 2 1 2 1 101000 f 74 goat snp37375-scaffold456-2140636 1 61450126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426533 Affx-122940194 AX-123296879 1 60363839 CCATAAAGATGATTTTTATTATATTTTGTTACCAT[C/T]GAATTAGAAACACCATTCACAAAGTTAAAATACAA Y 2 1 2 1 101000 r 74 goat snp37374-scaffold456-2084255 1 61506587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410437 Affx-122952396 AX-123280787 1 60405511 AGACACTCTGAAGCTGCGGGACAGGAAATTTAAAT[A/G]AGTTCGGTTTATGAGAGAGTTGAACTGTGTTCGGG R 2 1 2 1 202000 f 74 goat snp37373-scaffold456-2042583 1 61548197 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783948 Affx-122963605 AX-385271002 1 60437049 TTTCAACTTCAATATACTGTCATTGCTTTCTAGCT[A/G]CCCAATAAGTGTTGCTATAATTATTTCCAGTAACC R 2 1 2 1 101000 r 74 goat snp37372-scaffold456-2011045 1 61579557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431211 Affx-122937158 AX-123301552 1 60483160 GAGATTATATAGGAAAGATAGAAGTCATGCTACAA[C/T]GGGTAAATCAGTATGTCTATTTTTTATGTTTTTGA Y 2 1 2 1 101000 f 74 goat snp37371-scaffold456-1964934 1 61626298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430183 Affx-122937357 AX-123300524 1 60555306 GTCGTGTGCCTAATAATGGAAATAACCTGTTCAGC[A/G]CTTTTCATATTTTTTAGAAAAGGTTGTCTGCATAC R 2 1 2 1 101000 f 74 goat snp37369-scaffold456-1892788 1 61698980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804370 Affx-986696537 AX-385290972 1 60571846 TCTCTCTCTTCATCTTCTGTCCTACACTACCCCCT[C/G]CTCCCTCAATAAAATAGCAAACTTGAAAGATCAGT S 4 1 2 1 600010 r 74 goat 1_60571846 1 60571846 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320803838 Affx-986696539 AX-385290574 1 60571880 TCCTCCCTCAATAAAATAGCAAACTTGAAAGATCA[C/G]TAAATGAGATTTGGGAGAAAACTCTAGAAATTTAT S 4 1 2 1 600010 f 74 goat 1_60571880 1 60571880 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 320804374 Affx-986696541 AX-385290975 1 60571892 AAAATAGCAAACTTGAAAGATCAGTAAATGAGATT[G/T]GGGAGAAAACTCTAGAAATTTATAAATATTTTCAC K 2 1 2 1 600010 r 74 goat 1_60571892 1 60571892 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320804376 Affx-986696543 AX-385290977 1 60571919 ATGAGATTTGGGAGAAAACTCTAGAAATTTATAAA[C/T]ATTTTCACTGTATGCTTTATGATTATAAAGTAACA Y 2 1 2 1 600010 r 74 goat 1_60571919 1 60571919 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 38388562 Affx-122969176 AX-123258920 1 60603923 TTGGACTTCTCTGAGCATTGATGGGAAAGACTGGC[A/G]TTGAGCTCTGCTATACCAGACTGAGTAGACTGAGT R 2 1 2 1 101000 r 74 goat snp37368-scaffold456-1844171 1 61748438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414446 Affx-122949949 AX-123284795 1 60659955 AGTGACAGATACAGGCTGCATGATAAGAATGGGGC[A/G]CCCTCCAAATCTAAGCAGAGAAAGTTAAAGAAGGA R 2 1 2 1 201000 r 74 goat snp37367-scaffold456-1788139 1 61804794 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779948 Affx-122942882 AX-385267047 1 60752249 AATAATACATGCATTTATGCCAACTCTAAGCCAAA[C/T]ACTGGATTGCACATTAAAGACTGAAAGATGAATAA Y 2 1 2 1 101000 f 74 goat snp37365-scaffold456-1695845 1 61897520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414401 Affx-122949984 AX-123284750 1 60799586 CCACAAGAAAGAGGATCGAGTCAAGAGGACGGTTA[C/T]AAAAATAGAGAGAAAGGGAGAGCGAGGAGGACAAA Y 2 1 2 1 101000 f 74 goat snp37364-scaffold456-1648508 1 61944890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397180 Affx-122962415 AX-123267535 1 60830950 TGGGACACCCACACTGAAGGTCACAGGGGCAGAGT[A/G]CAATGCAGAAAGACTAAACTTTGATTTGCTAATGA R 2 1 2 1 101000 r 74 goat snp37363-scaffold456-1617144 1 61976563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770635 Affx-122972904 AX-385257799 1 60878587 ATCTTCCCTCAAGCTTCCATACAAAGTGAAACCTT[A/G]TATTAATCACTTTTTCCAAATGAGTTCTTAATGGA R 2 1 2 1 101000 f 74 goat snp37362-scaffold456-1569507 1 62024537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431936 Affx-122935981 AX-123302277 1 60934300 CAGTTTCTAACAAGATACTTCCATAATGCTGTATG[C/T]ATAACAATTATCTTTTATTTAAATATCTGTACAAT Y 2 1 2 1 101000 f 74 goat snp37361-scaffold456-1513794 1 62080632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790279 Affx-122944796 AX-385277283 1 60972778 CTAAGATGATGGAATCATTTGTAGACATGAAATGA[C/T]GAATCATTCACATAGGGAACCCTTGGTTCTAATTT Y 2 1 2 1 201000 f 74 goat snp37360-scaffold456-1475316 1 62119095 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788326 Affx-122944569 AX-385275344 1 61020700 CTAATATGTAGGTTAGGGAAAGGAAAACACTGGAT[A/G]TAATATCTTGTAAATAATACACCTCACAGACATTA R 2 1 2 1 101000 f 74 goat snp37359-scaffold456-1427394 1 62167010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449705 Affx-122922540 AX-123320040 1 61050632 TATGTCTATAGATAGACTTTCAAGGCCCCTCTTCT[A/G]CCTCTGTAGCTCCTGTCTGTGTCCATGACTTGATT R 2 1 2 1 101000 r 74 goat snp37358-scaffold456-1397462 1 62197061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386922 Affx-122970006 AX-123257280 1 61079347 CCATTCACCTCTTTCTTGCTCATCCCAGAAGCTCA[A/G]TAGAGCTCCAGGGCTCTTTAAAAAATCTGCTTAAA R 2 1 2 1 202000 r 74 goat snp37357-scaffold456-1368747 1 62225958 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803442 Affx-122951090 AX-385290272 1 61113649 TTATTTTTTAAGTCTACACTAGATATTGAGGTCAT[A/G]TATTAAAATGAAGGCAAGGCACATGATCTGCTGCC R 2 1 2 1 101000 r 74 goat snp37356-scaffold456-1334445 1 62260177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424449 Affx-122941785 AX-123294795 1 61163027 TCTTCATTCTTTCTCTGGATGAGTCCTTTAGAAAG[C/T]GCTTTCTTCTTGAGACCCATGTTCTCTCTTCTGGT Y 2 1 2 1 101000 r 74 goat snp37355-scaffold456-1285067 1 62309238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799512 Affx-122961189 AX-385286442 1 61214143 AGGATTCAGTCAATCAGCTGTCCCTAGTTTTTAGC[A/G]AATAAAAACAGACAACTAACAGTGTTTATTCCTTC R 2 1 2 1 201000 r 74 goat snp37354-scaffold456-1233951 1 62360114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393848 Affx-122965152 AX-123264203 1 61243471 ATTTATACAGACTCAGCCATAGTCTTAATTTCAGC[C/T]TTACTCACTGGCTCATACTTGTTGAAGATGGTAAA Y 2 1 2 1 101000 f 74 goat snp37353-scaffold456-1204623 1 62389587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445005 Affx-122926642 AX-123315342 1 61286803 CCAGATACTATTTAACTCAAAAACTTTTGGCACAT[A/G]CCTATTATCATCTTCCAGAATACAGTCTTCAGAGA R 2 1 2 1 101000 r 74 goat snp37352-scaffold456-1161291 1 62433181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278376 Affx-1111836391 AX-519551861 1 61290289 GTTTGTAGGGTCAGGGACCAGTGATACAGAGCAGA[C/G]CACGGGAAAGTGTGGGGAATAAATATGAAACAAAA S 4 1 2 1 101000 f 74 goat Random2.2K-69 1 61290289 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772121 Affx-122937647 AX-385259277 1 61323177 TTCCTTTGCAATGTTTGAGATTCTGAAAATAAGAC[A/G]TACACTTTATTGTGGCTTTCTTGACATAACCAACA R 2 1 2 1 101000 r 74 goat snp37351-scaffold456-1124917 1 62470137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272607 Affx-1111832864 AX-519546320 1 61334489 TGAAACTTGATACAACTACACTTGTACCACAGTCT[A/G]TGCCTATGGGATTCCACACTGAAGACAGGAAAGCT R 2 1 2 1 101000 r 74 goat 1_61334489_AF-PAKI 1 61334489 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38391162 Affx-122967444 AX-123261519 1 61360407 ACTTCTGAGGTTTGTACTCAAAATACCTTTATCAC[A/G]TCTTTAGTACAAAGCTGCAGACATTAAGAAAATAC R 2 1 2 1 101000 f 74 goat snp37350-scaffold456-1087687 1 62507128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274709 Affx-1111834376 AX-519548295 1 61439233 AACCAGGCCAATGAACCATTTCTGCAGGAGTT[A/C]TTTCTGCTCCCCAAAGGTTCTAAGCATTTTTGATG M 2 1 2 1 101000 r 74 goat GoatD01.032542 1 61439233 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419465 Affx-122945484 AX-123289813 1 61449683 GCCTGTCTGTCAGCATCCCACAGCTCTGCCACTGT[A/G]TTTGAAGCTTGGCTTCAGTGGATCTTTGAAGACTG R 2 1 2 1 101000 r 74 goat snp37348-scaffold456-998411 1 62596510 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446443 Affx-122925968 AX-123316779 1 61482729 ATCTATCACAATTCTGTGTCTCTCTCTGAATGATA[C/T]ATGATCAGTGATGCTTGTTTTGATTTATCCATAGT Y 2 1 2 1 101000 r 74 goat snp37347-scaffold456-965365 1 62630286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426050 Affx-122941104 AX-123296396 1 61535586 GGTTGTCAGTGTGTCAAATATTTTGAGCAGAAAAA[C/T]GATATTTAAATGCCAACAACAAACACACTCAAAGA Y 2 1 2 1 303000 f 74 goat snp37346-scaffold456-912508 1 62682637 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391092 Affx-122966826 AX-123261449 1 61570292 TTCCCTCACAGCCCCATATGCTTGCTCAGTTTTCA[C/T]TCCCAGTTCTCACAAACCTTTCTCCATCAGCTGCC Y 2 1 2 1 201000 r 74 goat snp37345-scaffold456-877802 1 62717358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770670 Affx-122926369 AX-385257834 1 61604197 AATGTAGACCAGCTATGATAATTCATTGTCTTCTC[A/G]TTAAGAATTGGCCTTTTCAAAATAATCACGGCTGC R 2 1 2 1 101000 f 74 goat snp37344-scaffold456-843897 1 62751446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777171 Affx-122952789 AX-385264294 1 61643291 AGGAGGAAATATATGAGTACTAGATCTTCCTGATA[C/T]GTTTATTCTTTAGAGCTTATATTTAGATTATAAAC Y 2 1 2 1 101000 f 74 goat snp37343-scaffold456-804803 1 62791453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417470 Affx-122947182 AX-123287818 1 61687429 TACGTGGGGAGAAGATTGTCACTTAAACTGTGTCG[C/T]AACTGATTAAACTTGAGGGAGGAGGCAGTCCTTCC Y 2 1 2 1 101000 f 74 goat snp37342-scaffold456-760665 1 62835455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410865 Affx-122952606 AX-123281215 1 61726664 ACATTTTTATATTGTTATCACAGGTGAATATATGG[C/T]AAATATCATTGTTTAGCTTGTTTATAAACTTCAAG Y 2 1 2 1 101000 f 74 goat snp37341-scaffold456-721430 1 62875600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773664 Affx-122964837 AX-385260804 1 61757280 CACTATTAAGGTCTACTGGTGTGAATAACAAATTA[C/T]ATCATCTTGCTACTCAGCAAGAGTAAATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp37340-scaffold456-690814 1 62906322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278560 Affx-1111836400 AX-186382722 1 61763615 CTTCTTTTTCTAGAATGAGAGGAAAGCAACATTCC[A/G]ACACAGACTAGTGATTTCTTTGTTGGTGTTTATTA R 2 1 2 1 101000 r 74 goat Random2.2K-70 1 61763615 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402230 Affx-122959149 AX-123272583 1 61799793 CTAACTCTCCAATTGTGATCTCATGGAGACATTCC[A/G]TTGTACTCAGGGCCCCTCTAACTCTGAGGTATACA R 2 1 2 1 102000 r 74 goat snp37339-scaffold456-648301 1 62949235 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383123 Affx-122973260 AX-123253481 1 61866404 GTTCACTCTGGGGACTATTGTTTTCATAGGCTCTG[C/T]ATTACTGGAACCACTCACACACACACTTTCTTGTT Y 2 1 2 1 101000 f 74 goat snp37338-scaffold456-581690 1 63016100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788774 Affx-122955916 AX-385275789 1 61907537 TTGAATTTGTGTTTGAGAAGTTGTTTAGCACTGAT[A/G]TTTCATACTCCAGAAACCCAGAGAAGACTGTCCTG R 2 1 2 1 101000 r 74 goat snp37337-scaffold456-540557 1 63056899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434149 Affx-122934905 AX-123304490 1 61937729 CTTCATCTTTTCCTATTATAGACACATTTTCTCCA[C/T]AAGGCAAGGAACATGGCCACTTGTGGCCCTGAATT Y 2 1 2 1 201000 f 74 goat snp37336-scaffold456-510365 1 63087371 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382749 Affx-122973598 AX-123253107 1 62031369 GACGGAGTGCCAGGCAGAAGCTATGGCACCTTTTA[C/T]GGCTTAGTTTCAGGAGTCAGATAGCATCACTTCTG Y 2 1 2 1 101000 r 74 goat snp37334-scaffold456-416725 1 63181941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391424 Affx-122966759 AX-123261781 1 62064419 CACAAAATAAATGGGTCAGGGCTCTCAAGGTAGTC[A/G]CTGGCCCTTGGTATAGTCCCTCAGTCATCTTGGGC R 2 1 2 1 101000 f 74 goat snp37333-scaffold456-383675 1 63215144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440443 Affx-122929405 AX-123310780 1 62143344 CTTTTTGTCACTTCAGCAGTGTGCTTGAAAATTTA[C/T]TTCTGTGTACTTTTTAATCCACTGGTTTAGTTGCT Y 2 1 2 1 101000 f 74 goat snp37331-scaffold456-304750 1 63295215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445661 Affx-122926146 AX-123315998 1 62195546 TGGGGAGGGGATGGGAGACTTTTCCAAATCAGTAA[C/T]GTCAGTGAGACTGTTGGTATTGATTTTTGGTCCTG Y 2 1 2 1 101000 f 74 goat snp37330-scaffold456-252548 1 63348656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773861 Affx-122958911 AX-385261001 1 62226929 TGAGATGGAGAATCACAGAATCTAAGCTAGACTAA[C/T]GATTCTCAACTGCAGTTGCCCAGTAGAATCATCTG Y 2 1 2 1 202000 r 74 goat snp37329-scaffold456-221165 1 63378629 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272436 Affx-1111836404 AX-519546162 1 62240760 GCAGATACTCAAAACCTACATGGCTTATGAGTAGA[A/G]GAGCAAACGGAAGATGGTCTAGTTAGTTGATTCCA R 2 1 2 1 101000 f 74 goat Random2.2K-71 1 62240760 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402942 Affx-122958177 AX-123273295 1 62282472 ACAAGACTTCCTTCTTTGAAATCAGCTCTAATCTA[C/T]GACACTCCCCATTCTGACTTAGTTAATATGAACAG Y 2 1 2 1 101000 f 74 goat snp37328-scaffold456-165622 1 63434689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437087 Affx-122932192 AX-123307425 1 62317947 TATGCTTTTTGCCCTCTTCTCCTGCAAGAACAGTC[A/G]TCACAGGAAGTGGCCTCCTGGTTTTCAGACTTCTT R 2 1 2 1 303000 r 74 goat snp37327-scaffold456-130147 1 63470301 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445266 Affx-122925471 AX-123315603 1 62363422 AAAGAATAGGAAATTAGGGTGAATTGTCACTTGGT[A/G]CATTTCTGTTTTGTGTGGGTGGGCTTTTTTCTTCT R 2 1 2 1 101000 f 74 goat snp37326-scaffold456-84672 1 63515259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798784 Affx-122925775 AX-385285714 1 62398934 AGCTGCTGAGAATTCAGGGTTAATTTGCCTAACCA[C/T]AGGGCATGATGTAGTCTATGAAGGTTAATATATTA Y 2 1 2 1 101000 f 74 goat snp37325-scaffold456-49160 1 63550877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770518 Affx-122931268 AX-385257683 1 62433863 TTGAATGCTTACTAGATACTCGCCCTTCAAATATA[C/T]GTGATATAATTAATCTTTACCACACCCTTGAATAT Y 2 1 2 1 201000 r 74 goat snp37324-scaffold456-14231 1 63586237 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783252 Affx-122964673 AX-385270317 1 62455794 ATGTACAAAGTGACATTTGTATGTGCTTTATATAA[A/G]CATGTGCTTCCCAATTAACTTTGTCTGGTCACTAT R 2 1 2 1 201000 f 74 goat snp28579-scaffold306-893870 1 63608252 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418425 Affx-122946530 AX-123288773 1 62490647 GATTAAATTTGAGGCTACTTGTGTGTCTGCAGAGC[C/T]TCAGTGATCTGGAACTGGTTTGAAAACTGAGGTTA Y 2 1 2 1 102000 f 74 goat snp28578-scaffold306-859017 1 63643118 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393605 Affx-122965369 AX-123263961 1 62627971 TGTCGGAGCTTTCAGGAGGAAAGGCCCTTTGATGG[C/T]GTAAAATGTGGGACTGGGTAGAAGTTAAAACTAGA Y 2 1 2 1 101000 r 74 goat snp28575-scaffold306-721693 1 63781802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768565 Affx-122966205 AX-385255745 1 62674431 TATATACACGACTGCTGTTTAAAAGCATTTCAAAG[C/T]TCATTTAGCAATGGCTTCTCCTAAGTGGTGTGGGG Y 2 1 2 1 101000 r 74 goat snp28574-scaffold306-675233 1 63828436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435231 Affx-122934084 AX-123305571 1 62708603 AGGAGGGGGTTGGGCAGCTCCCGAAAGTAAAGCTT[A/G]CAGAGAGAGCCCACACAGTGGATGTCCTGGAGGTA R 2 1 2 1 201000 f 74 goat snp28573-scaffold306-641061 1 63862822 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432318 Affx-122936301 AX-123302659 1 62759584 TTTCAAGTGAATCAAAGGGAATGGAATAAGATGAA[G/T]AAGAGACAAGATGAATCAAGAGGTTCCAGAGAGTC K 2 1 2 1 101000 f 74 goat snp28572-scaffold306-590080 1 63913968 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785260 Affx-122950048 AX-385272305 1 62836461 AGCCTGGCAGACCATCATCCATGGACACAAAACTA[C/T]AGCTGGACCAATCTTTTGCATAAATAGATAACAGT Y 2 1 2 1 101000 f 74 goat snp28570-scaffold306-513203 1 63990873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788474 Affx-122943713 AX-385275491 1 62867930 TAGATCTGCATGGATTCCTCCAATTCCCACTATTA[C/T]AGCCTCTCCTACTAGTTTCAGCACTATTCTCCCCT Y 2 1 2 1 101000 f 74 goat snp28569-scaffold306-481734 1 64022844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789896 Affx-122969371 AX-385276903 1 62928988 GTGATTCTAACAATCAGCCAGTCATTATCATGATT[C/T]CTGCAAGTGTTGGCTCATCTACCCAACAGAGAGGT Y 2 1 2 1 101000 r 74 goat snp28567-scaffold306-420676 1 64084001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799655 Affx-122938168 AX-385286584 1 62959364 GGGAATTGTTAGTAAGTGCACTGAAAGTACAGGTT[A/G]TGGTAGATGTGACAACTACTTGTTGAGTCAGATTA R 2 1 2 1 101000 f 74 goat snp28566-scaffold306-390300 1 64114373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448703 Affx-122923858 AX-123319039 1 63048400 AATAGAATTTGTAAAGAAAATATAATTTACCAATA[C/T]GACGCACAAAGTTCTATAAGTTTTAAGAAAACTGA Y 2 1 2 1 101000 r 74 goat snp28565-scaffold306-301264 1 64204122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381719 Affx-122974699 AX-123252077 1 63179280 CATTCAAGCCCTACCTTTGTTTTGGTTCTGAACAT[A/C]TGTTTCCTCCTCAGTAGCAGTGACCAGTTCCATTT M 2 1 2 1 101000 r 74 goat snp28562-scaffold306-170384 1 64336345 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789488 Affx-122947108 AX-385276498 1 63209040 CCCTTGTTAAGTAAACAACTTGGTAGAAACTCAAA[C/T]GCATACACGTGGTGCCTCTTGTGATATTTGTGATG Y 2 1 2 1 101000 r 74 goat snp28561-scaffold306-140624 1 64366087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404587 Affx-122957358 AX-123274939 1 63247002 CACATTTTCTGTCAGTTATAAGACAAAAGTTAGCC[A/G]TTTAAAATATTAAAATTTTCTTTTTCTGAAATGTG R 2 1 2 1 103000 f 74 goat snp28560-scaffold306-102662 1 64404566 C T 1 parentage parentage not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433528 Affx-122935007 AX-123303869 1 63282387 ATTTTCCCCACCTGGTGTTGCATTCTCAGGGTAGC[A/G]GAGCTGTAGCTGAGCTGAGAGGTGATTGAGAGGGG R 2 1 2 1 201000 r 74 goat snp28559-scaffold306-67277 1 64440251 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382332 Affx-122973890 AX-123252690 1 63365876 GCATTATTTTCACTCATTCCTATTATGAAAGCATC[A/G]CTATGTTAAATGTTCTTGTACATCATCATTTTTAA R 2 1 2 1 101000 f 74 goat snp2241-scaffold1069-462570 1 64524325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427712 Affx-122939282 AX-123298055 1 63409343 AATTATAACCATTAAAATTACAACTTTATATTTGC[A/G]TGTGGTGAAGGACTCTGAGGAATTGTCAGAATAAA R 2 1 2 1 201000 f 74 goat snp2242-scaffold1069-506037 1 64568172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274040 Affx-1111833969 AX-519547644 1 63459407 TCAGCAGAAATGAGGACCCTCTCTTTTGGACCTCC[A/G]TTGTACATCTCAGTCCATCTGCAGCACCAGCACAT R 2 1 2 1 101000 r 74 goat GoatD01.012088 1 63459407 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439208 Affx-122931033 AX-123309545 1 63465928 GTAGCTCACAATCTAGTACAGAAATGAATCCATGG[C/T]TATGTATCCACTGAAGAAAGGGCTCTGCAAGGGTT Y 2 1 2 1 201000 f 74 goat snp2243-scaffold1069-562622 1 64625165 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426952 Affx-122940413 AX-123297297 1 63510325 CCAGCTTTCACAGCTACATGTCTGTGTTGTCTAGA[C/T]CACTGATTGGTAGGTTTCTTTCTTAACTCGTCTCT Y 2 1 2 1 102000 r 74 goat snp2244-scaffold1069-607019 1 64670312 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784994 Affx-122953511 AX-385272041 1 63554283 AAAGAAGCTCTACCTAGCAGAACAAAAGTAGAAAT[A/G]CAGAGAGGTTCAAATTAATCCCAGCAGAAAAGGCA R 2 1 2 1 101000 r 74 goat snp2245-scaffold1069-650977 1 64714301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400671 Affx-122960341 AX-123271026 1 63603000 ATGAGGTCTGTGTGTGTGTATGTGGGGTTGCTTAA[A/G]GATTTGGACTTCTCTGAATGTAAATACTGATTTGA R 2 1 2 1 303000 r 74 goat snp2246-scaffold1069-699694 1 64762989 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398243 Affx-122962197 AX-123268598 1 63637948 GTAGGAGCTTTAAAAAAAAAGACATTCCTCAACAG[C/T]TCATGTTTGTCGTTTTAAGTTTACTTCGAAACTTC Y 2 1 2 1 201000 r 74 goat snp2247-scaffold1069-734642 1 64798036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393575 Affx-122965393 AX-123263931 1 63679693 TCGGTCTCAGCTCCATCGGCATACGTTTCATCCTC[C/T]AGGGCACACTCTGTGAGACCAGAAATAAGGGGCAG Y 2 1 2 1 101000 r 74 goat snp2248-scaffold1069-776387 1 64839355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404170 Affx-122957693 AX-123274522 1 63771780 AAGGAGAAATAATCAAATGAAACAGATAAATAGAC[G/T]AAAATTCTATCCCCATTCCTCCCTCCCCTACCTTT K 2 1 2 1 303000 f 74 goat snp2249-scaffold1069-868474 1 64931597 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271835 Affx-1111832865 AX-186269674 1 63835619 GCTAAGTCGCTTCAGTTGTGTCCAACTCTGTGCAA[A/C]CCCATAGATGGCAGCCCACCAGGCTTCCCCGTCCC M 2 1 2 1 103000 f 74 goat 1_63835619_AF-PAKI 1 63835619 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392524 Affx-122966111 AX-123262881 1 63855152 GACCCAATACCAAGACCTCCCTCTTAGGAGCTCTG[C/T]TCGGAATTGGGCCCCTCGTCTTCTGGTATTATGTT Y 2 1 2 1 201000 f 74 goat snp2251-scaffold1069-951846 1 65013742 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395277 Affx-122964081 AX-123265632 1 63902744 TCAAAAGGCTTGTGACAAACTGAAGGGAGAATCCT[A/G]TACAGCCAGCTGTGGGGAGGAAACAAGGACACACA R 2 1 2 1 101000 f 74 goat snp2252-scaffold1069-999438 1 65060940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766288 Affx-122959549 AX-385253677 1 63945104 TATCCCCCTTCTTAAGGAACAGTCCAGCTGTCTGT[C/T]GCCCAGGCTACCCATTCAATCATTAACACTCAGTA Y 2 1 2 1 101000 f 74 goat snp2253-scaffold1069-1041798 1 65103480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789626 Affx-122938085 AX-385276635 1 63977904 TATTAAGTAATGCTTAAGAGTATGAGTTTCATCAT[A/C]ATAGGTTGGATTTGAATCCTGCCATCACCTCCCAA M 2 1 2 1 101000 r 74 goat snp2254-scaffold1069-1074598 1 65136411 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403559 Affx-122957589 AX-123273912 1 64030909 ATTCATTCACCAAATACTTTTACCATATGCTGGGT[A/G]CTGCTCTAGGCACCAAGAATACAGCAGTGAACAAA R 2 1 2 1 101000 f 74 goat snp2255-scaffold1069-1127603 1 65189519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278417 Affx-1111836413 AX-519551902 1 64063079 ACTCAAATGTAAAAAGAATATCTCCACGAACAAGA[A/G]CAGAATTGCAAAACGGTTCTGGGTTTCAGGTCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-73 1 64063079 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381854 Affx-122974188 AX-123252212 1 64084680 GGCTCCTGTGTGCTGGTGCCTCTCCACCCCCGCCC[A/G]TCTCCATCCTGGTTTTGGCTTTCCTAGTCAGACTT R 2 1 2 1 101000 r 74 goat snp2256-scaffold1069-1181374 1 65243966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787277 Affx-122970158 AX-385274302 1 64118786 TAGAGGATGTAGAAAAGTGGGTAGTTTTCTGATTG[C/T]CAGCATGGAGTCATAAACAACATTAGATGTTGGAT Y 2 1 2 1 101000 r 74 goat snp2257-scaffold1069-1215480 1 65278049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394992 Affx-122964243 AX-123265347 1 64153301 AATACTGATGAGGAACATACTTTGATATTGAGAAC[G/T]CCATTTATAAATAATTTGTACACTTGTTACTGGTT K 2 1 2 1 101000 f 74 goat snp2258-scaffold1069-1249995 1 65312612 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802047 Affx-122924030 AX-385288952 1 64183874 TTGAAAACTTCAGCATGATGTAATTGCATGTGGTT[A/G]CAAAAATTCCCGAAAGTGCCCAGAGGGCAAAGGGT R 2 1 2 1 201000 f 74 goat snp2259-scaffold1069-1280568 1 65343528 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451118 Affx-122921386 AX-123321452 1 64240460 ATATGATAAGCCAACATGTATTGCCAAATTCAATC[G/T]TGAAAATTAAAATCCTTTCCTATAAGATCAATAGC K 2 1 2 1 101000 f 74 goat snp2260-scaffold1069-1337154 1 65401072 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377448 Affx-122977526 AX-123247807 1 64292116 TTTTGTAAATCCAAGATCATTTTCAGAAATAAGTA[G/T]ACAAATTTTATTTTCACATTAGCTGTAAAGTTTTT K 2 1 2 1 101000 f 74 goat snp2261-scaffold1069-1388810 1 65453193 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772397 Affx-122977465 AX-385259550 1 64325436 ATAACATCAGTAGCTATGATAAGTTAAATGAATAT[A/G]CAATGCAATACCTAATGCAACCCTGTTTAAAAAAA R 2 1 2 1 101000 r 74 goat snp2262-scaffold1069-1422130 1 65486489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384384 Affx-122972219 AX-123254742 1 64354038 GGACAAGGTTTAACATCCTTCCCCAAACACACAAA[C/T]ATAAACGGTTGTAATGAATGAAACTGTGGTTTCAA Y 2 1 2 1 201000 r 74 goat snp2263-scaffold1069-1450732 1 65515102 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392883 Affx-122965740 AX-123263240 1 64429992 GATTTACACTTCTGGACTTTTCTTCATCTTCAAAA[G/T]AAGCTGGTGAACTGGATAAGCTGCCTTCCAGATCA K 2 1 2 1 201000 f 74 goat snp2264-scaffold1069-1526686 1 65591382 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411147 Affx-122951884 AX-123281497 1 64463238 TGATGGTCCTTTTGCCACATAATATATGTTCACAC[A/G]TTTTGGGAATTTGGATGTCAACATTTGGGGAGGGA R 2 1 2 1 201000 f 74 goat snp2265-scaffold1069-1559932 1 65625021 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444151 Affx-122926791 AX-123314488 1 64527467 ATTAAATATGAGTGGGCTAAATAATCTATCAAAGA[C/T]AGAGACTGACAGACTGGATTAAAAAAAACAACACA Y 2 1 2 1 201000 f 74 goat snp2266-scaffold1069-1624161 1 65688829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377188 Affx-122978196 AX-123247547 1 64580736 CAAGATATGAATCTAGTCTTTTGTTTCTAGATCAG[C/T]GGCTTAATCTAAAACCTATGCCCTCTGGGCTAGCT Y 2 1 2 1 101000 f 74 goat snp2267-scaffold1069-1677430 1 65742188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784733 Affx-122955407 AX-385271781 1 64626257 ATGTACCACAGAGAAACTCAATCTACCTTCTTACA[C/T]GGCCATTGATTTCATTCATCCAGCTACAGGGAAGC Y 2 1 2 1 101000 f 74 goat snp2268-scaffold1069-1722951 1 65787668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418737 Affx-122946221 AX-123289085 1 64664986 GTCTTCTCTATAGTCTCCCTCTATTTTCTTCAGCT[C/T]CCTGTTACCACAGAGGGCAGATGACACACAGAGAA Y 2 1 2 1 201000 f 74 goat snp2269-scaffold1069-1761680 1 65826455 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414064 Affx-122949765 AX-123284413 1 64704332 ATACTGCCCCCTTTTGCTCACTCTACTTCCAAGAA[C/T]ACTGGCCTTGCTTCTATCTGAAAACATATCAAGGT Y 2 1 2 1 201000 r 74 goat snp2270-scaffold1069-1801026 1 65868141 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423671 Affx-122942333 AX-123294017 1 64772579 AATTTCAGCTTTGTGTGTCAAAGATGGCAAGAAGG[C/T]GTCACCAGGTTTGTACTGAATCATGAGTTAAGTTC Y 2 1 2 1 101000 r 74 goat snp2272-scaffold1069-1869273 1 65936272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451347 Affx-122921260 AX-123321680 1 64890702 ATTTCCACTTCCAATTGAAATAACACAATGTGTCT[A/G]TCTACAGAACTTCACATTCTGATTGTCTTGTACTA R 2 1 2 1 101000 r 74 goat snp2274-scaffold1069-1987396 1 66053211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380677 Affx-122975179 AX-123251035 1 64921155 ATCTCAGACCCATGCTGCGTGTTACTCAAGGAACA[A/G]CTGTAGTAAGGTGACAAGTGGATGGGGGGCAAAGG R 2 1 2 1 102000 f 74 goat snp2275-scaffold1069-2017849 1 66083953 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397989 Affx-122961802 AX-123268344 1 64978949 TCATTCATCAGCACCTCTCTCTATCATTCATTCAT[G/T]AAGACATGACCCAGTTTTCTTTTCTCTAATTATAT K 2 1 2 1 101000 f 74 goat snp2276-scaffold1069-2075643 1 66141335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416174 Affx-122948262 AX-123286523 1 65019963 TCTTCCAGAATCAACATTCAACTATTCTAAATTCT[A/G]CAGGAATAGATCTACGATACCATCAAAGGCTACTG R 2 1 2 1 101000 r 74 goat snp2277-scaffold1069-2116657 1 66180855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390647 Affx-122967144 AX-123261004 1 65082834 AATACTCTACTGCGGCTTTTCAAACTGGAGGTCTA[G/T]CACAAATGCAGACTGACTCAGAAGGTCTGGGGTAG K 2 1 2 1 101000 f 74 goat snp2278-scaffold1069-2179528 1 66244206 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408306 Affx-122953774 AX-123278657 1 65137519 CTGGCCTAACTGATCCCTATATTATTACAGGTGAC[A/G]TCAAGACTAGTACCTGGAGTTAGGAAGGTGAAGGA R 2 1 2 1 101000 f 74 goat snp2279-scaffold1069-2234213 1 66299505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400487 Affx-122961291 AX-123270842 1 65175804 AGTTTGCATCCCACAGAGAACACTGAGGGGAAGGA[G/T]AACAGACCCATGTAGCTTTGGGAAGGAGAAGTGGC K 2 1 2 1 101000 r 74 goat snp2280-scaffold1069-2272498 1 66338189 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384894 Affx-122971925 AX-123255252 1 65209278 TGAGTATCTGCTGGGGTGCTCCTTCCAATGAGGGC[C/T]CAGCACCCTCTGCTAGTGTGACTACTGGAGAAGCA Y 2 1 2 1 201000 r 74 goat snp2281-scaffold1069-2305972 1 66371968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377483 Affx-122977501 AX-123247842 1 65262045 AGAAATGCCTTGTCTACCTCTGCCTGTTCTGGAAC[A/G]TAACCTCTTAGAAACAGAAGCCAGGAAGTCTGGCA R 2 1 2 1 101000 f 74 goat snp2282-scaffold1069-2358739 1 66425008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802919 Affx-986696082 AX-385289816 1 65311203 TAATATAATATGCAGTTAATGTTTAAATTTCCTAG[A/G]TTGTTCCATAGTATCATAGTACCAGTTGTGTCTGA R 2 1 2 1 600010 f 74 goat 1_65311203 1 65311203 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38411125 Affx-122951900 AX-123281475 1 65311936 GAGATGAACAGTGGGGTTGAGGGGCTAATACGTTA[C/T]ACAGGGAGAGCAAGACAGACCTCTCCAGGACATAC Y 2 1 2 1 101000 f 74 goat snp2283-scaffold1069-2408630 1 66475102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454304 Affx-122919258 AX-123324637 1 65342910 TGCTCCTCGTCTTCAGTGACGTCCCCTTCCTTTGA[A/C]AGACTCTCTTATAGGCTGTGGTTCTGCCTGTCTCA M 2 1 2 1 101000 r 74 goat snp2284-scaffold1069-2439604 1 66506209 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383793 Affx-122973194 AX-123254151 1 65372143 AGACACCTGCAGTTGCTAACAAAAATTCCCAGTGT[A/C]TGCTTTGCTTGCTAATTAGGGGAAACTTCATTTTA M 2 1 2 1 101000 f 74 goat snp2285-scaffold1069-2468837 1 66534875 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421004 Affx-122944557 AX-123291351 1 65429177 TCCACAGTGGAAGCAAAAGTTTTACTGGAAACGGA[C/T]GCAAAATAATTTTGTCTCCCTTGTGGCTCAGGGGG Y 2 1 2 1 101000 f 74 goat snp2286-scaffold1069-2525871 1 66591903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781010 Affx-122924480 AX-385268097 1 65472649 TATAAAATTTCCAAAGAGTGATCATTTGATTACCA[C/T]GAGTCTGTTCGTGCTAATCAGAAATTACATACAAC Y 2 1 2 1 101000 r 74 goat snp2287-scaffold1069-2569343 1 66635689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784399 Affx-122955900 AX-385271448 1 65520470 GCATGGTGTCTTGTACATCATGGACTCACTATCAA[C/T]ATTTATTAATTTGAAAGAGATAATTGGACTGAGTC Y 2 1 2 1 101000 f 74 goat snp2288-scaffold1069-2617164 1 66683561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397760 Affx-122962524 AX-123268115 1 65558639 TGACAGGATCAATGGATTCCACATAATGCCACCAG[C/T]GTCTGGGAACAAACAGAACCTGAAAACCAAACAAA Y 2 1 2 1 101000 f 74 goat snp2289-scaffold1069-2655333 1 66721772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791293 Affx-122956123 AX-385278287 1 65568833 AAATCAAGCTACATACATGACTCCTAAACTTTCAT[C/T]GCAAGTCCTTAATTCTCTTCTACTTACCACTAAAT Y 2 1 2 1 101000 r 74 goat snp39045-scaffold495-3419 1 66731850 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278609 Affx-1111836425 AX-519552088 1 65605289 TTAGATGTTAATTATTTGCCACTGACAGACATGCG[A/G]ATAGCACGGACATTTTGTTTTACCAATGAAGGACA R 2 1 2 1 201000 r 74 goat Random2.2K-75 1 65605289 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797871 Affx-122924639 AX-385284809 1 65605655 TGGGGAGAATGACAGTTTAAAAATAGGGTTGAAAG[C/T]TCCACAGACAAGATTCAGAGAATCAATCCTTTAAT Y 2 1 2 1 101000 f 74 goat snp39046-scaffold495-40241 1 66769027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278622 Affx-1111836431 AX-519552101 1 65606257 CTCTCCAGCACTGGCAGAGCCATGTACAGACAACC[A/G]TTTTCCAGAACATTGTGGTTATCTATTTCTCTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-76 1 65606257 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274978 Affx-1111834523 AX-519548560 1 65620903 CTTGATCTCTGGGAATTAGATTGTGAAGAAGTGGA[A/G]GGGCTTGCAACAACAAGCACTCAGATCTTACAGAC R 2 1 2 1 101000 r 74 goat GoatD01.039620 1 65620903 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442233 Affx-122928299 AX-123312570 1 65641056 ATTGGGAGTCAGACCTGGGTCTGAATCTTAGCTTT[A/G]CCTGTTAGCACTTGGGCAAGTTTTTTATGTTTCCA R 2 1 2 1 201000 r 74 goat snp39047-scaffold495-75642 1 66804853 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420393 Affx-122944931 AX-123290740 1 65763844 TTCTCCCCTTCTCCAACTTCCCTTTGTAGTGAAAC[A/G]CTATACTAAATAGCCCCATATACTAACAACCATTC R 2 1 2 1 201000 r 74 goat snp21794-scaffold214-98624 1 66929430 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441202 Affx-122929530 AX-123311539 1 65834281 GACAAATGTCAGGAGGAAAGAAGAGTGTCCTGCAG[C/T]AGGGTTTTCCTTCCCAGACCTCACCCCCCATGAAA Y 2 1 2 1 201000 f 74 goat snp21795-scaffold214-169061 1 67064618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415181 Affx-122949003 AX-123285530 1 65877066 TAGATTAAGGGCCAGGTCAAGTGCTCAACTCCAGA[C/T]GAGTGTGCAAGGGTCACTTTCTGGACATTTGGACC Y 2 1 2 1 201000 r 74 goat snp21796-scaffold214-211846 1 67107054 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382702 Affx-122973632 AX-123253060 1 65936581 TGAAAGGGTGGCAGGAATGTCCATGCAGCATGCTT[A/C]TGCACTCATGCAGCCCATATGGCCTCATACAGAAA M 2 1 2 1 201000 r 74 goat snp21797-scaffold214-271361 1 67166164 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452338 Affx-122920653 AX-123322671 1 65969649 GTGCATGAAGCCGGGGTGGACAGACAGGTGTCCCC[A/G]TGGAGTGACTGAGTGAAGAGTCCACCCTTAGTTGA R 2 1 2 1 101000 r 74 goat snp21798-scaffold214-304429 1 67199102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439304 Affx-122930961 AX-123309641 1 66013425 CTCCACATCCTTGCCAAAAGTTATTTTCTGGGGTT[A/G]TGTGTGTGTGTTGATAATAGCCATCAAAAATTGAG R 2 1 2 1 202000 f 74 goat snp21799-scaffold214-348205 1 67243090 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278462 Affx-1111836437 AX-519551945 1 66042005 ATAATCAAACATGCTTAATATCCTTTCCTGACTCC[A/C]TGTCACCTTTCAGCTATAAATTCTTACTGTTTTCT M 2 1 2 1 101000 f 74 goat Random2.2K-77 1 66042005 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379083 Affx-122976320 AX-123249442 1 66045298 AGAAATGATGTCATAGTGGCAAAGCTACTGACACA[G/T]CTGCAATGCTGGGCAATCCTTGCCGTCTGGCTTCC K 2 1 2 1 101000 f 74 goat snp21800-scaffold214-380078 1 67303006 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782428 Affx-122975595 AX-385269503 1 66080503 TTAAGTTAATAATGAAAATGGGTCTTTTATTTATG[C/T]GATAATGTATTTATGATTTAGCTCTTCACCATTGG Y 2 1 2 1 201000 f 74 goat snp21801-scaffold214-415283 1 67339400 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403713 Affx-122958033 AX-123274065 1 66133191 GGAGAGAGGAGGCTTTGTACCTGAATGATAGGGAG[A/C]TACATACTCTCATTTCCAAGACCAGAAGAGGGCAC M 2 1 2 1 101000 f 74 goat snp21802-scaffold214-467971 1 67392726 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408368 Affx-122953730 AX-123278719 1 66205454 ACTCCCGACACCTGGAAGGCCAGGTCAAGACAGCA[A/C]TGGCCTCAGATCTCAAGAAATCAGTCCACTCACCA M 2 1 2 1 101000 r 74 goat snp21803-scaffold214-540234 1 67464956 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414425 Affx-122949965 AX-123284774 1 66245177 CCAGGTCTTAATAGATGCTAAGATCCCTGTGCAGA[C/T]GCAAAGGTTATGAATGAAGAGAAAGCTTCAGTAAA Y 2 1 2 1 101000 f 74 goat snp21804-scaffold214-579957 1 67504649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443392 Affx-122927393 AX-123313729 1 66304743 TCAAGTCTCAGCCTTCTCTGTAACTGCGTGTGCTC[A/G]TCGATGTTGTTGCTGTTATTATTACTGTTGTACTA R 2 1 2 1 201000 f 74 goat snp21805-scaffold214-639523 1 67564002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438338 Affx-122931338 AX-123308676 1 66389067 TTGAATGCATCAAGCCTAATAATTAGTCTCCTCCC[G/T]CCCTTTCAAATGCAGGCATACCCTCAGCATGCTTC K 2 1 2 1 101000 f 74 goat snp21806-scaffold214-723847 1 67648071 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410311 Affx-122952487 AX-123280661 1 66446999 TTTTCCAAATCCCCTTCTAATTCATCCTATATCTA[A/G]CACCTTAACCTGGGTGGTAGTACTAAAGTAATTTG R 2 1 2 1 102000 r 74 goat snp21807-scaffold214-781779 1 67706153 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410789 Affx-122952666 AX-123281139 1 66547337 AAATGTGGGACTGTGGGTTAGACAGCATCAGTTCA[A/G]TGTTAGATGTCCTGATTTTAAGAACTGCGTTGTGG R 2 1 2 1 201000 r 74 goat snp21809-scaffold214-882117 1 67806759 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447186 Affx-122925002 AX-123317522 1 66578949 CAAAGTAGGCCCACATGGGTTCCTCACCTCCAGAT[A/C]GTCTTTGGAGAGACCGTAACCACATAGTTACCCGT M 2 1 2 1 201000 r 74 goat snp21810-scaffold214-913729 1 67837823 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420598 Affx-122945252 AX-123290945 1 66628549 CCCATTCTGTTAACAGCTCTCCTGCTTTCCTTTCC[C/T]CTCCCCAAGTACCATAACCTAATAAAACTTTTCCT Y 2 1 2 1 201000 r 74 goat snp21811-scaffold214-963329 1 67888110 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271738 Affx-1111832866 AX-519545532 1 66664038 TTCTGCTTCTAGAAAATACTTTTTTTCCTCTCCTT[A/G]TATAGAGACGCAATGGGAAATCCCTTGTAAGGGAA R 2 1 2 1 101000 r 74 goat 1_66664038_AF-PAKI 1 66664038 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396949 Affx-122963178 AX-123267304 1 66664738 CAGGCAATTTTATTGTGCCTTTTAGAAATCACAGA[A/G]GTAATTCCTGCCTACTATTTAAAAAATTCAAGCTA R 2 1 2 1 101000 f 74 goat snp21812-scaffold214-999518 1 67942956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411700 Affx-122951542 AX-123282050 1 66704327 TCAGGCCCCGTGATCAAGGATCACCCAGAAAAGTT[C/T]AGTGCTTATTAATATGTTCCCAGGATAACTCCATG Y 2 1 2 1 101000 r 74 goat snp21813-scaffold214-1039107 1 67982353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405278 Affx-122956858 AX-123275630 1 66747182 GATACTGCTACATATTCACCAGAATGGCTAAAATA[C/T]AAAGTCTGATAATGCTGGGGGCTGGAGCTGACAAA Y 2 1 2 1 202000 f 74 goat snp21814-scaffold214-1081962 1 68023217 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433058 Affx-122935751 AX-123303399 1 66786445 CAACTACCTCTATTTCTCCTGCAAATCAGTGAGGT[A/G]AGGCTGGTAGGATAGATTACCCTTGTAATGGTGAC R 2 1 2 1 101000 r 74 goat snp21815-scaffold214-1121225 1 68062939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433027 Affx-122935774 AX-123303368 1 66818758 CTAACCAGAACCAGACACAGTGTGGCAAGATGCAG[C/T]AGGAATTCCATTAGGGTTGTTCTTTGAAGCCAAGT Y 2 1 2 1 202000 r 74 goat snp21816-scaffold214-1153538 1 68095526 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795100 Affx-122930369 AX-385282059 1 66859940 GTGCTAAATCATATTTCTTGGGAGTTGGCCAAGCT[A/G]CAAGTTTTCTTAGGACAGATCCTTCTCAATCATTC R 2 1 2 1 101000 f 74 goat snp21817-scaffold214-1194720 1 68137187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379147 Affx-122976725 AX-123249506 1 66891193 AAAGTACAGGGATGTAATCAAATGGTTCTCAAATT[A/G]TGCTTATTTATTTATAACTCTAATTTGAAAAGAAG R 2 1 2 1 101000 f 74 goat snp21818-scaffold214-1225973 1 68169324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773699 Affx-122973049 AX-385260839 1 66961583 CATTATTATTACTATCGTTATTAACAAGAGACCAT[C/T]TCAAGAAGTAGAGATGTTCAGCTTAGACTGGAACT Y 2 1 2 1 101000 r 74 goat snp21819-scaffold214-1296363 1 68240008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396423 Affx-122962998 AX-123266778 1 67002224 TGATGGGTTTGCTCTTCACCTTGTGGATGGAGGGT[A/G]CTTTGTTACCAAAGAAACTGTCAAAACAATAAATA R 2 1 2 1 201000 r 74 goat snp21820-scaffold214-1337004 1 68280531 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415300 Affx-122948820 AX-123285649 1 67070477 ATACTGGAAAGCCCTTAGAAAAGCTGAAGAGATGC[A/G]TGAGTGCAGGGCATGTTGATTGTTAAGTGAATGCA R 2 1 2 1 201000 r 74 goat snp21821-scaffold214-1405257 1 68346543 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404203 Affx-122957671 AX-123274555 1 67113279 CCAAGTCCCACAAAGCAGCAAGAACAGAATAGTCA[C/T]GAGGACTTGCAAAAGCAGGAGCTGAAATTTGGGCT Y 2 1 2 1 101000 f 74 goat snp21822-scaffold214-1448059 1 68389643 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439143 Affx-122931079 AX-123309480 1 67147675 TTCTGCTTAGCCCTGGCTTTGGAAAGAAAGGAATC[C/T]GCAGAAATGAACAGCTAGATTTAGGCAGGTGACCC Y 2 1 2 1 101000 f 74 goat snp21823-scaffold214-1482455 1 68424048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782354 Affx-122973773 AX-385269430 1 67191238 TTCCTTCCTAAGTCTTTTCTGAGTTCCTATGGAGT[A/G]TATTCTGCTAGGTGGGATCGGAAGCTGGAAGCATG R 2 1 2 1 101000 f 74 goat snp21824-scaffold214-1526018 1 68467517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773184 Affx-122959885 AX-385260327 1 67225171 AAGGCCTGGGGTATAAAATACTGGTGTTTCTGTGA[C/T]GTTTCATAGTCTCTGATTCCAACCTTAAAGGAATC Y 2 1 2 1 101000 f 74 goat snp21825-scaffold214-1559951 1 68501358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790906 Affx-122963887 AX-385277903 1 67256589 TCAGGAATGCAAGGGTTAATTCAACATAAGCCTAA[A/C]TTTATAATTCTTCAGATGGATTTCATATCCCTAAT M 2 1 2 1 101000 f 74 goat snp21826-scaffold214-1591369 1 68532846 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439009 Affx-122930360 AX-123309346 1 67286967 TTCAGGATACGTAGGCAGATGTCCTTCCAGCAGAC[A/G]TAATGTGGTGGGTTAACCCATCACTGGTACCAAGT R 2 1 2 1 201000 r 74 goat snp21827-scaffold214-1621747 1 68563815 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419338 Affx-122945650 AX-123289686 1 67319659 TCTTCCCTGTTAGCCCTTTTCTGTGGGATATAGCC[A/G]CAGTGTTCTCCCTACCTCCTGGGTCCACATTGTTG R 2 1 2 1 101000 f 74 goat snp21828-scaffold214-1654439 1 68596518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403496 Affx-122957641 AX-123273849 1 67377660 ATCTTCCTGCTGGGCTCTCTCTGGGACTCCAAATC[A/G]CCAGAGGATGGTAGAGGTGAATGGAAAGTAAAAGA R 2 1 2 1 101000 r 74 goat snp21829-scaffold214-1712440 1 68655798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447677 Affx-122924634 AX-123318013 1 67435848 ATTAAAAGCAAGGTTTAAATGTGATACACTGTATT[A/G]TCAGCAATGCATTGAAATAGAGGGGGCATTCACAG R 2 1 2 1 303000 f 74 goat snp21830-scaffold214-1770628 1 68714339 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444321 Affx-122926738 AX-123314658 1 67471068 ACACCAGACCTACACACCCACGCACCACTCTCCAT[A/G]CCTTTCCTTGCTCTCTCTTGCTCTTTAGCACTTAA R 2 1 2 1 101000 r 74 goat snp21831-scaffold214-1805848 1 68749745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273719 Affx-1111833800 AX-519547331 1 67492232 GCCAGCAGCAGCCTTGGGTTGTCAGGAAGAAAGCC[A/G]CCCTGGCTGAGTCTGCAGGCCCAGGAGTGTCCTGA R 2 1 2 1 202000 f 74 goat GoatD01.005508 1 67492232 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422923 Affx-122943041 AX-123293269 1 67527307 CATCACTCCCTACCCTTCCACCCCAGCTCTCCATC[A/G]CACATGACTGGGATTCCCTCCTCCCCTAAACACAC R 2 1 2 1 101000 r 74 goat snp21832-scaffold214-1862087 1 68806469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393698 Affx-122965252 AX-123264053 1 67556171 TCAGGTGGCACGTCACAGTAGTTCACTGGGCTCCC[A/G]GTGGCACTGGCGGACCCCTGACTGAAAATCCTCCA R 2 1 2 1 201000 f 74 goat snp21833-scaffold214-1890951 1 68835371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383182 Affx-122973216 AX-123253540 1 67605120 AATCTTTCTGAGCCTCGGTTACTTTATGTGTAAAG[C/T]GAGACGGATGCTCCCGATCTCACAGGGCTTCTGTG Y 2 1 2 1 201000 f 74 goat snp21834-scaffold214-1939900 1 68884756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383355 Affx-122972669 AX-123253713 1 67621377 CATATTTGCCTTTTCTTCCCTTTTTTCAGGATGGA[C/T]GATGGCCGACTCTTGGACTACCTTATGAATCATGA Y 2 1 2 1 101000 r 74 goat snp21683-scaffold2121-3990 1 68902117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771677 Affx-122956525 AX-385258835 1 67650746 AAATTATTAATGGAAAAAGGGATGATTTCATTGAT[G/T]ATATTGTGCTATTCTTTAATAACTTTCACCAGTCC K 2 1 2 1 101000 r 74 goat snp21684-scaffold2121-33359 1 68931435 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801234 Affx-122962334 AX-385288147 1 67694725 AACAGGGGATAAGGTCAGATAATTTGATTCAGATA[C/T]GGAAAGAGAGAGGCCTTAAAGGGCCCTTCAGGAAG Y 2 1 2 1 101000 r 74 goat snp21685-scaffold2121-77338 1 68975331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383925 Affx-122972973 AX-123254283 1 67729189 CCATTTCCTGACTTGCCCGCAGCCCTCCCAGCTTG[C/T]GGTGCTAAGGAACAGAAAACACCTGCCGAATAACA Y 2 1 2 1 102000 r 74 goat snp21686-scaffold2121-111802 1 69009452 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799870 Affx-122956366 AX-385286796 1 67778715 AGGCAGGAAAACAAATGAGCTATCATCACTGTAGC[A/G]TTACACAACCTTGTAACAACTTCTTTCTTCCCAAG R 2 1 2 1 101000 f 74 goat snp21687-scaffold2121-161328 1 69059264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790090 Affx-122955745 AX-385277096 1 67838295 TGGGGAACGCTGAGGAGACTAAAAGTTAGGGAACA[C/T]AGCCTGCTTCCAAAGTACTCTGTGGGTCCACAGCA Y 2 1 2 1 101000 r 74 goat snp21688-scaffold2121-220908 1 69118889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795561 Affx-122951856 AX-385282516 1 67906075 CATCTAGGGGTTTGTTTGGAAAACGTTGCACAAGA[C/T]GACTTAGGAGCGTGTGAAAACGCTGCATGTTAACC Y 2 1 2 1 101000 f 74 goat snp21689-scaffold2121-288688 1 69188596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399735 Affx-122960453 AX-123270090 1 67950877 ATCAAATAAATCCTTCTTTTCAGAAATGAGGGAAA[C/T]GAGGACCAATTCTTCTTGGCCTAACTGCTTCATAA Y 2 1 2 1 101000 r 74 goat snp21690-scaffold2121-333490 1 69233394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433064 Affx-122935746 AX-123303405 1 67981884 CTACGATTATTATTCCTTGGGTTGGCTGCTCAGCT[C/T]CTCAGCGTCATTTCCCCTTTGGGTGGGAAAGTTCT Y 2 1 2 1 101000 f 74 goat snp21691-scaffold2121-364497 1 69264501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387630 Affx-122969860 AX-123257988 1 68026721 TTGTTACAGCCTAAAAGTTCATTCTCCAGAGAGGA[C/T]GAACCAGAGGGACTTCCAGCTACTGCAATGTGTAG Y 2 1 2 1 101000 r 74 goat snp21692-scaffold2121-409334 1 69309431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431219 Affx-122937152 AX-123301560 1 68068637 AGATACAAGTTCGGTGTCCTTGGGCTCAGGAACAC[A/G]CAGGACATCCAGTGTCTGTTTTTAGAGAATGAGTT R 2 1 2 1 201000 r 74 goat snp21693-scaffold2121-451250 1 69351198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414560 Affx-122949388 AX-123284909 1 68108755 ATTCAATGTGCTTCATCTTTGTCCTATGAGTTCTA[C/T]TGATGAGACTTGATCCTCCAGAAATAATCCTGCAA Y 2 1 2 1 101000 r 74 goat snp21694-scaffold2121-491368 1 69391863 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408028 Affx-122954296 AX-123278379 1 68161546 GCAATTTGAAACGGAAAAAGTTTAAATTAAATTGC[A/G]GAGTCAAAAAGTTTCTCATCGATTATAATAGTGCT R 2 1 2 1 101000 r 74 goat snp21695-scaffold2121-544159 1 69444822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401337 Affx-122959265 AX-123271690 1 68219891 ATAATAAGACCTAGAAGAATAAAGTAGAAGCGAGG[A/G]TACAATTTCACTCCCATATTTAAGAAAACTGAGGT R 2 1 2 1 201000 r 74 goat snp21696-scaffold2121-602504 1 69503729 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774169 Affx-122930703 AX-385261306 1 68267325 ATTAATTGGGACATTTCTGTCATTAACTGAATCAA[C/T]ATTTTGGATCACCTGATATGTATATGCAATACTAC Y 2 1 2 1 101000 f 74 goat snp21697-scaffold2121-649938 1 69551262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770553 Affx-122924018 AX-385257716 1 68329351 CCAAATATGCTAGATATCTTCTCTGGGTCTTTAGT[A/G]TTCACAATGACCCCATATCGGTCTTTCTTTGAGAC R 2 1 2 1 102000 f 74 goat snp21698-scaffold2121-711964 1 69613576 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397152 Affx-122962437 AX-123267507 1 68359699 ATCCTTTTGCTGTTCTATTTCTGTTGAAGAATAGA[C/T]GCAGTTAGACAATACAAACGTGTGCCTGTACAAAG Y 2 1 2 1 101000 r 74 goat snp21699-scaffold2121-742312 1 69643804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778041 Affx-122921481 AX-385265157 1 68391302 AAATAGTAGCAGATTAAATGTTAAAAAGGACATAA[A/G]GTTTTATGACAGTCTATTAAATGATCTTATTTTAA R 2 1 2 1 101000 f 74 goat snp21700-scaffold2121-773915 1 69675342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408506 Affx-122953714 AX-123278857 1 68426134 AGCAAACTCAACCACTGAACTCTGCACTTTGAAAC[A/G]CTGAGCTCAAGCACTTTGTTTCAGTTATCTTCCCA R 2 1 2 1 102000 f 74 goat snp48245-scaffold682-3672712 1 69699837 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434909 Affx-122934324 AX-123305249 1 68454826 AACCCCTTTGGAAAATAATTCCAACAACACAACCA[G/T]CAGAGTGACATATACTGTCTAAGACTCAACTAAAT K 2 1 2 1 101000 f 74 goat snp48244-scaffold682-3644020 1 69728740 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402110 Affx-122958684 AX-123272463 1 68517225 AAATTTTGAAACAGGCCCCATGAACTTATCCAGGG[C/T]ATTCCCCATTTGTGAATCCCCCTCAGTGAATCTGA Y 2 1 2 1 201000 r 74 goat snp48243-scaffold682-3581621 1 69772114 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776207 Affx-122957383 AX-385263335 1 68601050 CAAGATAATCAAGGCTTCAACCATATTTCCTTGAA[C/T]GGAGCACAAAAGAATAGGGACATGATTAACATGGA Y 2 1 2 1 101000 r 74 goat snp48242-scaffold682-3497796 1 69857675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790050 Affx-122937565 AX-385277056 1 68650129 AACACAAACCAAGTCATTAACAAAAGCAATAAGTC[A/G]TAATAAAAGTACTAGCTCAGTCTAAAAACACATTG R 2 1 2 1 101000 f 74 goat snp48241-scaffold682-3448717 1 69907075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794528 Affx-122947894 AX-385281491 1 68695780 ATCTTTCAATTGATGATTCCTATTTAATCTGTGGC[G/T]AAAACCTTGAGCCAATGGGAAACCATATAGCAGAG K 2 1 2 1 101000 r 74 goat snp48240-scaffold682-3403066 1 69952918 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448278 Affx-122924180 AX-123318614 1 68734572 GAAAAGCCAAATTTCTTATATTTCTTTCAGCTAAC[A/G]GCCAGTTTCCATAGCTGAATTAAAGCACTTGTAGC R 2 1 2 1 101000 r 74 goat snp48239-scaffold682-3364274 1 69992232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387357 Affx-122970477 AX-123257715 1 68786662 TCAAAGGTTTGTGTATTTCAGTGTATATAAATTTT[A/G]CCTTAAGAAAGAGAGTGCTGTCAAAAACAAAAATA R 2 1 2 1 101000 r 74 goat snp48238-scaffold682-3312184 1 70045429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378226 Affx-122976916 AX-123248585 1 68856752 TTTTCTTCTTATATTGCTTTTTTCCTCCTTACCCC[A/G]TGAAGATATTTTAAGAATATGTTTTTGTCTCTTAG R 2 1 2 1 201000 r 74 goat snp48236-scaffold682-3242094 1 70115785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450764 Affx-122921842 AX-123321098 1 68963139 CCCCTCAAAAAGCCAGTGCACATTTTAGGGATGAA[C/T]TTGACTCAAGACAAGGGTATCCAGTAAAGCCTAAG Y 2 1 2 1 101000 f 74 goat snp48234-scaffold682-3135707 1 70222494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383790 Affx-122973196 AX-123254148 1 68994805 CTGTCCCCTAGGTCTAGGTCTGGCTAAATATAATC[A/G]ATGTTCATTATACAGGTGGGGAGAGAATGAATGGG R 2 1 2 1 101000 f 74 goat snp48233-scaffold682-3104041 1 70254185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396375 Affx-122963033 AX-123266730 1 69023345 GAGGGAGGAAAAAAAGACTCAAGGTTTCTTGGTTT[A/C]TTTTTGGTTTTGAAGACTTGTGGACCTTAAAGATA M 2 1 2 1 303000 r 74 goat snp48232-scaffold682-3075501 1 70282735 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375483 Affx-122979143 AX-123245842 1 69057177 TTTGCTATGCACGTATGTCTTAGTGTCTTTGCCCT[A/G]TGATTTCATTTGGATCAATTCCTAGAAGTGAATTT R 2 1 2 1 101000 f 74 goat snp48231-scaffold682-3041669 1 70316497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424020 Affx-122942090 AX-123294366 1 69092486 AAAAAATGTTTTTTGGTGAATGATGGCAGAGCTAA[C/T]ACATCTCAGAATTATATTTTATAAGGGGGATACCA Y 2 1 2 1 201000 f 74 goat snp48230-scaffold682-3006360 1 70351246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772217 Affx-122951461 AX-385259373 1 69152598 GTGACACATACAGATAAGCATGTATAGTCTGAAAG[C/T]TAAGGACTGAGGTCAAACCAAAGGACTGCCAATGA Y 2 1 2 1 101000 r 74 goat snp48229-scaffold682-2946248 1 70411133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278471 Affx-1111836442 AX-519551954 1 69169838 GCACTCCTGAAATGCACACTGGTTGGCACATACAC[A/G]AGGATATCTACGAATAAATCAACTGAACAGAGACA R 2 1 2 1 101000 f 74 goat Random2.2K-78 1 69169838 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 463650045 Affx-1110091925 AX-515130960 1 69175701 GACACCAAAATCTGAGAATGCTCAAGTTTCTTATA[C/T]AACAGTATTTTCATGTAACCTATAAGTACCCTCCC Y 2 1 2 1 101000 f 74 goat 1_69175701_AF-PAKI 1 69175701 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396716 Affx-122962810 AX-123267071 1 69191601 CTAATAGAAACTCTCCTCCCTCTAAAACCTACTCA[A/C]GTGTGCTTGGAAGACCAGCTGCCTGGCATCACCAG M 2 1 2 1 202000 r 74 goat snp48228-scaffold682-2907245 1 70450345 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438753 Affx-122930820 AX-123309090 1 69222175 CCTGAATCAGTAAATATAGGACCAGTTAAGAAGGA[C/T]GTGGAAGATCAAACTGCCACATTCAGCTCTTATGC Y 2 1 2 1 201000 f 74 goat snp48227-scaffold682-2876671 1 70481541 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273773 Affx-1111833832 AX-519547384 1 69236173 GTAATGTCTCCAAGATGCTGCTGTTATCACTTGCC[A/G]CACACAGCTCGGGGACTTCTCTGCAGTGTCCTTCC R 2 1 2 1 201000 f 74 goat GoatD01.006351 1 69236173 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792374 Affx-122959395 AX-385279355 1 69273915 AGAGGTTAGATGAGGTCAGATATGGGAACGTAAGA[A/G]GTGCCAGTAAATATCCCACATTGCCTTCCCCTTTT R 2 1 2 1 101000 r 74 goat snp48226-scaffold682-2824931 1 70533390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417105 Affx-122947477 AX-123287453 1 69321170 TTTTCAAGGTCATACAATGATTGTTCTTCTTTTCT[C/T]TCATGGAATAGATTGTCATGGGATAAAGACTGGTC Y 2 1 2 1 101000 r 74 goat snp48225-scaffold682-2777676 1 70580574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768056 Affx-122949680 AX-385255263 1 69350358 TCTAAGAATTAGGTCAGGTTTCTTGTAGATCTTGT[C/T]ATATTGCTCTTTGGAATTTAGCCAGAGGAAAGAAA Y 2 1 2 1 101000 f 74 goat snp48224-scaffold682-2748488 1 70609833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785638 Affx-122952197 AX-385272680 1 69393766 ACTCAAGGAGGAACTGGCCAATGCTGAATACTCTC[C/T]GGAAGAAATGCCTCAGCTCACAAAACACTTATCAG Y 2 1 2 1 101000 f 74 goat snp48223-scaffold682-2705080 1 70652117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804386 Affx-986696553 AX-385290984 1 69424217 ATGAATCTTCTATATAATCATTGTTCACATTCTAT[C/T]ACAGTGTTAATGTGTCTTTTATTGATTCATGAGTG Y 2 1 2 1 600010 r 74 goat 1_69424217 1 69424217 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38411590 Affx-122951614 AX-123281940 1 69426829 TATATCATAAAATATCCAGTGTTCAGCTTTTGACT[A/G]TCATAAAAAATCTTTTTGTATAGTTTGGATTCACT R 2 1 2 1 101000 f 74 goat snp48222-scaffold682-2672017 1 70685244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416518 Affx-122947772 AX-123286866 1 69473904 AGGATTAATAAAGACCCTCAAAGTCCCCTTTTACC[A/G]TGCCCTCCATTCCTCCTCTCTAGAGGTAACTATTA R 2 1 2 1 102000 r 74 goat snp48221-scaffold682-2624942 1 70733094 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433093 Affx-122935722 AX-123303434 1 69525239 TAAAAGAATGAAGAAGCTTTCATGTAACTGTATAG[C/T]AACACAGAGTTATCGCCAAGATGTGTTTTAAAATA Y 2 1 2 1 101000 f 74 goat snp48220-scaffold682-2573607 1 70784310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790180 Affx-122946516 AX-385277184 1 69563504 GTAAGATAGTACAGTCATTACTTCTGACTGAAATT[A/G]CTTCTTTAACTGGAGTTGAAAGTATAATTTCTTCC R 2 1 2 1 201000 r 74 goat snp48219-scaffold682-2535342 1 70823016 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409216 Affx-122953164 AX-123279567 1 69600148 TCCCTAATCTGTTAATTAAACATGTATATTGATTT[A/G]TATTTTCTAACATCACAATAGAACTTTCAGATAAC R 2 1 2 1 101000 r 74 goat snp48218-scaffold682-2498698 1 70860032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798716 Affx-122977533 AX-385285647 1 69699429 GATCCATTTCCTAAGAGTAAAAATTCTCAGTCCAA[C/T]AGTAAGAGCTGAATAATATAGATTATGGTATATCC Y 2 1 2 1 101000 f 74 goat snp48216-scaffold682-2399417 1 70959363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414588 Affx-122949366 AX-123284937 1 69772766 AAAAAATACAGTTAACAACAAGGTAAAAACTAGTA[A/C]GCACAAATACAAGTCAGTAATAATCCCCTCTTCAA M 2 1 2 1 101000 f 74 goat snp48215-scaffold682-2326080 1 71032143 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790646 Affx-122944355 AX-385277648 1 69811501 TAATCTTATCTAATTATTTTAGAGCTCACCAAGGT[C/T]CAAGTCTCTCACTTTGTTAACTCCAAATATTTTTC Y 2 1 2 1 101000 f 74 goat snp48214-scaffold682-2287345 1 71070880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278660 Affx-1111836449 AX-519552138 1 69866677 ACCACATATTAGTCCCAGGTCTTCCCCTAAGGCTG[A/G]TAAGAGTTGATAAAACTAGTTGAGCTGTTCCCTAT R 2 1 2 1 201000 r 74 goat Random2.2K-79 1 69866677 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450625 Affx-122921998 AX-123320959 1 69871820 AAAAAAGCAAACATCTGGCATACAGATTTGAAAAA[C/T]CTCGTTTGCATAATTATGCCTGAAAACCTCAAGAA Y 2 1 2 1 101000 r 74 goat snp48213-scaffold682-2227026 1 71131354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386901 Affx-122970037 AX-123257259 1 69914341 TCCCTGTGAAGATGAAATCAAAAGGTGCTGTAAAA[C/T]GCTGCACAGATAGGTCTGCATTTGCCGGAGAAGAA Y 2 1 2 1 101000 f 74 goat snp48212-scaffold682-2184505 1 71174076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800309 Affx-122976659 AX-385287232 1 69980397 TTCTCCTTCCTGCATGGGCTACTTGTGCTCTGACT[A/G]TATGATCAACTCTCGCCTATCCTATGAAACTCTCC R 2 1 2 1 101000 f 74 goat snp48210-scaffold682-2118449 1 71240423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775141 Affx-122919731 AX-385262273 1 70044618 TTATTTAAGCCTTGCTCTGGAGCTTTATGAAACAC[A/G]TAGCTCTATCCCTATATACAGATGATGATATAGAC R 2 1 2 1 101000 f 74 goat snp48209-scaffold682-2054228 1 71304469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419491 Affx-122945465 AX-123289839 1 70077240 CCTTGCCATCAGACTGTTCAACTTACTGCCTATTC[C/T]TTATGTTAGTCATCTAGTGTCCTCCCCATCAGTGT Y 2 1 2 1 101000 r 74 goat snp48208-scaffold682-2021606 1 71337510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380519 Affx-122975689 AX-123250877 1 70125775 TGAGGTCTTACTGCTCCCAGATGTTCTCTGTAGAC[A/G]GAGCAAGGGTACACATGTATATGTAAACACATATT R 2 1 2 1 101000 f 74 goat snp48207-scaffold682-1973071 1 71386721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382409 Affx-122973829 AX-123252767 1 70159046 GTTTACAGATTCCCAGCCTGGGATGAAAAACATGC[A/G]CTTTTGTTTTCTACCCATTCCTATAATTATGATTT R 2 1 2 1 201000 r 74 goat snp48206-scaffold682-1939800 1 71419997 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446780 Affx-122925311 AX-123317116 1 70197774 ATTCAAATCAGTATTAAATAGGGATGTAAGTCTTC[A/G]TGTGTTTACCAAAAGGAAGCACTGTCCAAACAGTG R 2 1 2 1 201000 f 74 goat snp48205-scaffold682-1901072 1 71458498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395093 Affx-122964168 AX-123265448 1 70230794 ACAGGTGATAGTAGGGTGATGAAGTAGGGATTTGA[A/G]CTCAGCACTGACTATGAAGTATAAAAAGCCTGTGA R 2 1 2 1 101000 f 74 goat snp48204-scaffold682-1868052 1 71491970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416596 Affx-122947644 AX-123286944 1 70260917 ACTACTGTCTTTTGGAGTAGAAGGGGAGGGGGTCA[A/C]CCATCTGAGTGTATGGAAACGTAACATCTAATTTC M 2 1 2 1 201000 r 74 goat snp48203-scaffold682-1837929 1 71522286 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389288 Affx-122968519 AX-123259646 1 70293905 TCTCCTACACCCCCACCTTTGCAAATAAATCCTCT[C/T]CTAATTATCCTATCTTGGGTGTGCCCTCTGCTTCC Y 2 1 2 1 201000 r 74 goat snp48202-scaffold682-1804941 1 71555348 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453744 Affx-122919613 AX-123324077 1 70332779 CAGAACAGAAGTAGAGTCACAGAAGCTTCACCCAA[C/T]TGGGGGAAGAGCATCTGAAGCAAGTCAGAATTCTT Y 2 1 2 1 303000 r 74 goat snp48201-scaffold682-1766067 1 71594202 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436707 Affx-122932321 AX-123307045 1 70362256 CGGGGGACCTTCCAGTGGCCTGGGAGGGCACTGCT[A/G]CTTGAGTTTACTGTGGGTGGGAGGGAAAGGAGGGT R 2 1 2 1 202000 f 74 goat snp48200-scaffold682-1736590 1 71624048 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797233 Affx-122920403 AX-385284172 1 70442654 CAGGGGGTGGAAAGGGATGTGTGGTTTTCAGACAG[C/T]AGAGCAGGTAAGAGGTCAGCATTCTACACCAAAGG Y 2 1 2 1 101000 r 74 goat snp48198-scaffold682-1656192 1 71704361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447758 Affx-122924574 AX-123318094 1 70472305 TTTTTATGCACTTTAAGCTATTTTGATGCCAGCAC[G/T]TTTAGATGTGGCTGACTTGAAGGAAAATAAAGTTG K 2 1 2 1 201000 r 74 goat snp48197-scaffold682-1626541 1 71734212 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388187 Affx-122969432 AX-123258545 1 70506872 ATGCTTAGAGGGAGAAGGCTCCATTCTCGGCACTA[C/T]GCCTTCTCCTTTCCCAGTCTCGCAAATACATTCAG Y 2 1 2 1 201000 f 74 goat snp48196-scaffold682-1591974 1 71768727 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426787 Affx-122940546 AX-123297133 1 70556101 TCACTCTGTAATTACACTATTCTAAGACATTAATT[A/G]CCTTCATTTCTTTGTTCACCTTCAGTCTTTGATTG R 2 1 2 1 101000 r 74 goat snp48195-scaffold682-1542745 1 71817758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393527 Affx-122965794 AX-123263883 1 70587638 CACTCAAATCTCACATTTCAATTTCTATTTGACTG[C/T]TAACTTCTATTTTCACATCTTTCTTGGAATAGAAA Y 2 1 2 1 101000 r 74 goat snp48194-scaffold682-1511208 1 71849228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408469 Affx-122954429 AX-123278820 1 70630569 TATGATGAGATTTTATTTCCTGGCAAATCTGATCT[A/C]GTCTCACAAACGTATACAATATATTAGACTTCTGT M 2 1 2 1 101000 r 74 goat snp48193-scaffold682-1468277 1 71891984 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427011 Affx-122939846 AX-123297356 1 70661229 TTGTCATCCTGCCACAGAAACACGTCCTTAGTCTC[A/G]AATAAATGATGACAGAAAAATCATGAAAATCTTTT R 2 1 2 1 303000 r 74 goat snp48192-scaffold682-1437617 1 71922692 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414663 Affx-122949308 AX-123285012 1 70692257 AAAATGGAAATAATCCACTTGCCCCACCTACCTCA[C/T]AGGACTATTATAAAAATCCCAAATACACTATGTAT Y 2 1 2 1 201000 r 74 goat snp48191-scaffold682-1406589 1 71953985 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446065 Affx-122925825 AX-123316402 1 70745316 ACCATAGTGACAGGTCACACTGACTTAATGGGTAA[C/T]GCTGCACTAAGAAACTGTCCTCAACGGTTTCTTAT Y 2 1 2 1 101000 f 74 goat snp48190-scaffold682-1353530 1 72006567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787814 Affx-122930630 AX-385274837 1 70793556 GAAAGTAGCTCATTTCTGAAAGTTAACCTTTAGCC[C/T]AGGTGTAAAATAAATGGTGCCAATATTCTTTATAA Y 2 1 2 1 101000 f 74 goat snp48189-scaffold682-1305290 1 72054882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379512 Affx-122976080 AX-123249870 1 70862843 AAAGCTCTGCACACACCTGCAGGGAGCTGGGAGGA[A/G]TAACAGTCTGGCCGGGACCGTGCCCAGGTCCAGCA R 2 1 2 1 201000 r 74 goat snp48187-scaffold682-1236003 1 72124350 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768929 Affx-122946949 AX-385256104 1 70901205 GATTTATTTCTGCTTAGTGAATTTCCAGATCCGAA[C/T]GCGCTCTGTTCATCAGCTAAGTTTGCTTTGGTGCC Y 2 1 2 1 101000 r 74 goat snp48186-scaffold682-1197641 1 72162789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382527 Affx-122973796 AX-123252885 1 70940810 TCAAGCTCAGATGGCGCTTTAAGTCTCCTGGTCTT[A/C]GGAGGCAAGTGCAGTAGAGATGGCCACTTCGCATC M 2 1 2 1 101000 f 74 goat snp48185-scaffold682-1158036 1 72202437 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431205 Affx-122937163 AX-123301546 1 70982194 GGGCAAGACTGAGAATCCTAGCAGCCCAAGTCCCA[C/T]GCAAACCCCAGTGAGAACAAAGTCCTTAGCTCATA Y 2 1 2 1 101000 r 74 goat snp48184-scaffold682-1116652 1 72244279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797256 Affx-122927493 AX-385284195 1 71018566 CCAGTTTCCAGCATGTTTCTATATAAATTAATGAG[C/T]ATCTAAAAGTGCTCGACCTCAAAGGGTGTGGAGCC Y 2 1 2 1 101000 f 74 goat snp48183-scaffold682-1080280 1 72280800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399480 Affx-122961187 AX-123269835 1 71050602 CAGGAGGCCTAAGCCCCACAGCTGGTCTTTCCTTC[A/G]CCCCTCAGAGATCCCTGAGAATCACTATTGGAACT R 2 1 2 1 101000 r 74 goat snp48182-scaffold682-1048244 1 72313467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390737 Affx-122967914 AX-123261094 1 71079408 TATGCCCCTTTCTCAGCTCACAGCCATACCTAGGC[C/T]ACACTGCCATGGCAGGCCCTCCTAACACTCATCTA Y 2 1 2 1 101000 f 74 goat snp48181-scaffold682-1019438 1 72342278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415332 Affx-122948796 AX-123285681 1 71118650 TTCATTCATCAATATTTATTCAGATTCTACTATAC[A/G]CTACCATGGGTAAAGCCCTGGGAAGAAGATGAATA R 2 1 2 1 101000 r 74 goat snp48180-scaffold682-980196 1 72381104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424872 Affx-122941332 AX-123295218 1 71172860 GTAATCTTTCCCTCTGGAGAGGCCTTCTCCGAAAA[C/T]ACTCACTTGAAGGTATCTGTGCTGAATTAACCATC Y 2 1 2 1 201000 r 74 goat snp48179-scaffold682-925986 1 72435994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394215 Affx-122964898 AX-123264570 1 71202981 TTGCTGCTGTAGAAACACCAAAAGCAATGTGCTAA[C/T]AAGAAAACACTGAGGTTATTCTTACTGCAGTAGGG Y 2 1 2 1 101000 f 74 goat snp48178-scaffold682-895865 1 72466181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791274 Affx-122955476 AX-385278268 1 71253456 TCATGCTTTCCTCACTCAATGGCTTCTACAAGAAA[C/T]ATACAAGACTCCCAGTTACAGGAACGCCAGCTCCA Y 2 1 2 1 101000 f 74 goat snp48177-scaffold682-845390 1 72515827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411464 Affx-122951806 AX-123281814 1 71365207 CAAGCCAAATGATGACAGCCAATAATAATCTTACC[A/G]TTTATTACAAAAAATATTTTTGAAGTCTAAAAGGA R 2 1 2 1 103000 f 74 goat snp48174-scaffold682-733639 1 72626619 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376880 Affx-122977822 AX-123247239 1 71409224 CCCAGGCCTGACCACACCTGAGTCAACAGATAAAA[C/T]GGAGTTCCAAATTCTGTGAGTTGTGGACTCCTAGG Y 2 1 2 1 101000 f 74 goat snp48173-scaffold682-689622 1 72670911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387678 Affx-122969825 AX-123258036 1 71472190 AAAAACTGAGGAAAGCTAAAGTTATACTGTACCCT[C/T]GAGATGCTGCTGCTGCTGCTGCTGCTGCCAAGTCG Y 2 1 2 1 101000 f 74 goat snp48172-scaffold682-626656 1 72734515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420093 Affx-122945100 AX-123290441 1 71503823 ACCCAGGGCCTTTTAGGAAGTTTTCCCATATTGCA[G/T]AACATTTCTCATCACTGTGGGCCTATCTCATTCTT K 2 1 2 1 101000 f 74 goat snp48171-scaffold682-595023 1 72766967 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779373 Affx-122948231 AX-385266477 1 71544324 CCTAAAAAAGTACAGTACTAGAGTCATCCCACCAA[C/T]GTAAGCTTGTCCCATCAAATCAATATGACCTGAGG Y 2 1 2 1 101000 f 74 goat snp48170-scaffold682-554522 1 72807513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399538 Affx-122961144 AX-123269893 1 71586317 TATCTATACTTACATTTCTATACTCTATACTTAAG[C/T]GAATCCCACTTTCTCATTAATCTCCTCCATGAAAA Y 2 1 2 1 101000 r 74 goat snp48169-scaffold682-512529 1 72849370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404589 Affx-122957356 AX-123274941 1 71624522 TTGAGAGAGACTGACCTGCCTCTGGGTGACGAGCA[C/T]ATGAGCCATCATTCCCTCCCCTATAATTTTTTGTC Y 2 1 2 1 102000 r 74 goat snp48168-scaffold682-474324 1 72887778 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423008 Affx-122942978 AX-123293354 1 71685316 ATTTAGCTGGGCATAAAAGACTTGTTAAAACATGT[A/G]TTTCAAGACCCCATTCCCAGAGGTTCTGAAGGAGC R 2 1 2 1 101000 r 74 goat snp48166-scaffold682-413530 1 72949108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407334 Affx-122955296 AX-123277685 1 71721421 CAGCCGCCCACCCAAAAGCTCTCTGGTCTATTCTA[C/T]ACCCCCATCCTTTTCTAACTGGGCCTTGGATGGAT Y 2 1 2 1 101000 r 74 goat snp48165-scaffold682-377425 1 72984206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271840 Affx-1111832867 AX-519545622 1 71756259 CTTCTAAGATTTTCTCTCTATCATGGATTTTGAAC[A/G]ATTTGATTATGATGTTCTTTGATGTAGTTTTCTTC R 2 1 2 1 101000 f 74 goat 1_71756259_AF-PAKI 1 71756259 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426800 Affx-122940536 AX-123297146 1 71775633 ACATACAGACCACATCAGGAAATTTCACTCTGGGG[C/T]AGAGTGATTTACAAAGCCTGTTCAGAAGTGGAGTC Y 2 1 2 1 201000 r 74 goat snp48164-scaffold682-323213 1 73039055 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393610 Affx-122965364 AX-123263966 1 71806871 TATGGAGCCGGCAATGGGTTTTATTCCATAATCAG[A/G]GGCATGAAATAAATACCACATGATTTTTCTAAAAC R 2 1 2 1 101000 f 74 goat snp48163-scaffold682-291975 1 73068736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800079 Affx-122977083 AX-385287002 1 71866962 TTGACCCAATCACATACAAGGATGGAGTTTAATTC[A/G]TTATTTCAATCAGGTTTTTGGCAAGAAATGAACAG R 2 1 2 1 101000 f 74 goat snp48162-scaffold682-231884 1 73127143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772390 Affx-122976713 AX-385259543 1 71896115 TAGCATCACTAGCAACTTGAGTCCTCAAAAAATTA[C/T]GGGAAGAAACCAAAGGGAGAGATCCTTTAAGAAGA Y 2 1 2 1 101000 f 74 goat snp48161-scaffold682-202731 1 73156401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783958 Affx-122951190 AX-385271011 1 71948142 CTTATATCCCATGAAGATATGCCAAGCTTATCTTG[C/T]GGATTAATGTATTTCACTGGGTCACCATCCCGCCA Y 2 1 2 1 201000 r 74 goat snp48160-scaffold682-150704 1 73208538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385742 Affx-122971082 AX-123256100 1 71977889 TGCCCTGGAACTCCACGAAGGGCTACTGTGCTAGC[A/G]TGGAGAAAGGGGAGGGGTGATCTGTAGGAGAGATG R 2 1 2 1 201000 f 74 goat snp48159-scaffold682-120957 1 73238431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434406 Affx-122934682 AX-123304747 1 72010708 CTCTTCCCCATGCTTGTCGTCTCTGGGTCCCAAGA[C/T]GGCTAGTGTGACTGCAACAGTATGTCCACATTCAG Y 2 1 2 1 102000 r 74 goat snp48158-scaffold682-88138 1 73271739 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426335 Affx-122940271 AX-123296681 1 72042764 TCTAAACAGCCTTTGTTGTTTCTGCTCCTTCAGCC[C/T]CTCTAAGTCAAAGAAGTAGAATCGAAAGCAAGGCC Y 2 1 2 1 201000 r 74 goat snp48157-scaffold682-56082 1 73303581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436847 Affx-122932211 AX-123307185 1 72094585 GCATGCTCAGAAATATTACTTAGGTCAGCCAGTTC[C/T]AGGACCTTCTACACAGGGAGCGAATCTCACCCCTT Y 2 1 2 1 101000 f 74 goat snp48156-scaffold682-4261 1 73354985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776680 Affx-122941565 AX-385263806 1 72102137 GTATGTGAATTAATCCTTGGGATTCCTTGGCTCAA[C/T]TCAGTAAACATTCCATGTACAACTTTCACCAGGTT Y 2 1 2 1 101000 f 74 goat snp37621-scaffold462-3192 1 73362608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418487 Affx-122946445 AX-123288835 1 72148345 ATGAAGGGCTTAATTTGCTGGCTCATTGGTCTCAC[A/G]TGCTCAGCTGTGGCACTCAGCCCCTTAGGCTTGCT R 2 1 2 1 101000 f 74 goat snp37622-scaffold462-49400 1 73409116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773359 Affx-122974262 AX-385260501 1 72190864 TTTGGTTTAAACATAAAGGCATGGACTGATGAAAC[A/G]ATCATTGTTTTTCCTAAGAGAGCTGCTCACTCCCA R 2 1 2 1 101000 r 74 goat snp37623-scaffold462-91919 1 73451660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396132 Affx-122963401 AX-123266487 1 72245839 GAGGCTAAATAATTTGTGGGAAGGAGTGTGTCAGA[A/G]TAAAGCCTGGAAAGAGGGGATAATACAGAGAAAAG R 2 1 2 1 101000 f 74 goat snp37624-scaffold462-146894 1 73506227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432359 Affx-122935872 AX-123302700 1 72276786 GTAACAAACAAGGAAGACCAGAACGGCACGGCTTA[C/T]GAATGCAAAACCACCTGGACATATGAAGGGCCACA Y 2 1 2 1 101000 f 74 goat snp37625-scaffold462-177841 1 73536861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452663 Affx-122920329 AX-123322996 1 72308903 TAATTTGACTCTAGTCTCTCTAGGACATTAACCTG[C/T]GGATCTACATTACAGGATCATCTAAAGCCAAAGCA Y 2 1 2 1 101000 r 74 goat snp37626-scaffold462-209958 1 73568724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380004 Affx-122975606 AX-123250362 1 72340351 GCAGTGTCCCCAGTCATGACAAAAGTGTACCCAGA[C/T]AATACTAAATGTTCCCTGTAGTCCATGGGGTGGTG Y 2 1 2 1 201000 f 74 goat snp37627-scaffold462-241406 1 73599757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388055 Affx-122969533 AX-123258413 1 72361615 TCCTGCACTTTTTCCTTCTGACTGGGTTCCTGAAT[A/G]CACTTGGCAATTCATGTGCCACTGTGGGGTTAAGT R 2 1 2 1 101000 f 74 goat snp36345-scaffold435-3913177 1 73621248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384637 Affx-122972157 AX-123254995 1 72393676 AAAAAATAAAAAAAAAATAAAATAAGTATGTCCTA[C/T]AACTACACATCATTCCTAGAAACACCCTCTTAATT Y 2 1 2 1 101000 r 74 goat snp36344-scaffold435-3881116 1 73653694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797684 Affx-122959480 AX-385284623 1 72426761 ACAATCTAAATATCCATCAATATGACTGTCTTCAA[A/G]ATTATGATACATTTAGAGAAAGCATATTTGTGCGG R 2 1 2 1 101000 f 74 goat snp36343-scaffold435-3848031 1 73686838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390474 Affx-122967602 AX-123260831 1 72521150 AATATACATCAAAAGGAAATGAAATGCATAGGCTG[A/C]TTACCAGGGGCAATTTTAAGAACCAAAATTGGCCC M 2 1 2 1 103000 r 74 goat snp36341-scaffold435-3753642 1 73782563 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448095 Affx-122924321 AX-123318431 1 72619709 ACTGAACCAGGAAGCAATGCTCCATTTCCAGTCCC[A/G]TTTCTTGACAAACTCACATTTGTTGAGAAATTACT R 2 1 2 1 102000 f 74 goat snp36340-scaffold435-3655083 1 73881816 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785707 Affx-122964634 AX-385272748 1 72650400 ATACCCATTTTTAAGCATTCAGCTTTTCAGTCATC[C/T]AGGAATTATAAAATGATAGGTTTTATGCTTCTCAC Y 2 1 2 1 101000 f 74 goat snp36339-scaffold435-3624392 1 73909458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435161 Affx-122933663 AX-123305501 1 72678946 CTTCCATTACCATCTCCCTGCTCAGAACATCATTA[C/T]ACATGCATTAGAGAAGTCTGATAATTATAAGTTGT Y 2 1 2 1 101000 r 74 goat snp36338-scaffold435-3595846 1 73937614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438597 Affx-122930941 AX-123308934 1 72752294 TCTCTCATAAGCAGATGTTACCCTTACCAAAGTCT[A/G]TCTGGAGAGAATCATAAATAATGGCAGGATGGAGA R 2 1 2 1 101000 r 74 goat snp36337-scaffold435-3522498 1 74012046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416807 Affx-122948137 AX-123287155 1 72784147 CTCATTTAAAAATGTTGAAAACTAAGTAAAAATGT[A/G]TTTAGTTACTGTGCTGGCCAACAAAATTTATCTGT R 2 1 2 1 101000 r 74 goat snp36336-scaffold435-3490645 1 74053122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441705 Affx-122929157 AX-123312042 1 72818307 TGCAAAAAAAAAAAAATATGTGAGAGAACTGTTTG[C/T]AGGCATCTGACCCCTGAAAATAGAATAACACAAGA Y 2 1 2 1 101000 r 74 goat snp36335-scaffold435-3456485 1 74087508 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387708 Affx-122969805 AX-123258066 1 72888997 ATCTCAGGGGATGAGACCCAGGCATCAGCACTTTG[C/T]AAAGCTTCCTGGGTGATTCCAGCGTGCAGTCAAGA Y 2 1 2 1 202000 f 74 goat snp36334-scaffold435-3385795 1 74158555 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402485 Affx-122958589 AX-123272838 1 72918171 GGGAAGTCCTTGGATTTTAAAATAGAATGGTTTTA[C/T]GACAATATCCAGAGGTTGAGAAATTGATTCATCAA Y 2 1 2 1 201000 r 74 goat snp36333-scaffold435-3356621 1 74187538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407035 Affx-122954941 AX-123277386 1 72962359 TACCAACATGTCTGGCACTTAGTAAGTATTCAATA[C/T]AAGTCTGATAAATGAAAAAGCAAATGAATGAACCA Y 2 1 2 1 201000 f 74 goat snp36332-scaffold435-3312433 1 74232035 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778106 Affx-122970597 AX-385265221 1 73057096 CCTAAAATGAGTTGTAGCTGGAGGATTCCTAAGGG[A/G]GTATAATCACAGCTTAACAAAATGCATCTCTCCAA R 2 1 2 1 101000 f 74 goat snp36330-scaffold435-3217696 1 74327193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445480 Affx-122925205 AX-123315817 1 73089480 GAAGCATTGGCATACGTTTGCTCTTAAAAGCAAAG[C/T]GAAACGGCCTCCCAGCCTCCCTTTCCGTAATTGAT Y 2 1 2 1 101000 f 74 goat snp36329-scaffold435-3185312 1 74358744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396091 Affx-122963428 AX-123266446 1 73119303 TACAGAGCTAATCTCAGCCTCTCAGACTCTGGCAA[C/T]GGTATTGAGATACATCCATGTCAGTTGAGCTTCCT Y 2 1 2 1 201000 r 74 goat snp36328-scaffold435-3155489 1 74388558 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408785 Affx-122953373 AX-123279136 1 73154493 GTCTGGAAGAATTTAGCTATAGAGGAAGGAATAAT[A/G]AAGTAAATGAGAAAAATTTCAAAAGGCAGAAAGGT R 2 1 2 1 101000 f 74 goat snp36327-scaffold435-3120299 1 74424239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391286 Affx-122967348 AX-123261643 1 73202926 TTCCCTCATCTTCTTTCCCCTGCTCAGCTCAATTT[A/C]AGGGCCCATTTCAAGAGCTATTACTATGTGTCAGA M 2 1 2 1 101000 r 74 goat snp36326-scaffold435-3071866 1 74472653 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453297 Affx-122920370 AX-123323630 1 73244555 GCAGTATATCCTACTAGGAAGGTGTTCAATAAATC[A/G]TTGATAAATGAATAAATGACTTTATATATATATAT R 2 1 2 1 103000 f 74 goat snp36325-scaffold435-3030237 1 74514357 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771957 Affx-122926000 AX-385259113 1 73290159 AAGCTGAAGGTTGGCATTGTTTGTATCACTATACA[G/T]ATGAGAAAAATAATCATAGGGATGTTTTTAAAAAC K 2 1 2 1 101000 r 74 goat snp36324-scaffold435-2984633 1 74559984 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383932 Affx-122972967 AX-123254290 1 73336822 CTTCGATCTGATTCATAAGGATTGGAACATTTCTA[C/T]AAGAGGTTTTTTAAAATAAGGACATGGTATAAATC Y 2 1 2 1 101000 f 74 goat snp36323-scaffold435-2937970 1 74607091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798593 Affx-122925913 AX-385285526 1 73378618 TGCCTCACAGACACGCTGTGTCATGAGAGTTGATG[C/T]ATATGAGTGTTTTCTAAACTATACAAACCAGAGGC Y 2 1 2 1 101000 f 74 goat snp36322-scaffold435-2896174 1 74648851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798740 Affx-122968616 AX-385285671 1 73413442 ATAATAGCATTTCTGGGTATATTAATATTCAGTTT[A/C]TATTAATGCAAGCTCCCTTTGAGCCTCTAAATTCA M 2 1 2 1 101000 r 74 goat snp36321-scaffold435-2861350 1 74683564 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389190 Affx-122969078 AX-123259548 1 73450627 AAAAAAGAAAAACAAAATAAAACAAACCACTACTT[A/G]GGATGTTATCAACACCTGTCAATGAATCTTATCTT R 2 1 2 1 101000 r 74 goat snp36320-scaffold435-2824165 1 74720744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444132 Affx-122926805 AX-123314469 1 73496492 AAAAAAACTTCCTCAAGGTCAAAAAGTCCAATGCC[A/G]TTTTTATGATACTGTTACCTTAGACTGACTCAAAG R 2 1 2 1 201000 r 74 goat snp36319-scaffold435-2778300 1 74767507 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445528 Affx-122925170 AX-123315865 1 73531690 TGTTTGGTAAAAATTAGACTACTCCAGCACACTTA[C/T]AGGGGGCTTTCCAGGTGGCTCAGTGGTAAAGAAGC Y 2 1 2 1 101000 f 74 goat snp36318-scaffold435-2743102 1 74800717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396490 Affx-122963539 AX-123266845 1 73589997 TCTCCATATTTGTTTTACAGCATTTCTATTTTTTT[A/C]TTTCTTCAGCCATCAAGTAAACTATACAAGGCTAA M 2 1 2 1 101000 r 74 goat snp36317-scaffold435-2684795 1 74859693 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802697 Affx-122973369 AX-385289596 1 73658212 CCACAATACAATTCTGCTAAAGTTCTACTGAAATT[A/G]TATCAGGTCACCGGCTAGGATAGAAGAGAACTATT R 2 1 2 1 101000 r 74 goat snp36316-scaffold435-2616580 1 74928047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775623 Affx-122944438 AX-385262754 1 73696677 CGCTCTAACTACAGACTGACTTTCAGCTCATTCAC[A/G]TTTTCCTGGGATCCAAGTGGTTGTTATGACTAAGT R 2 1 2 1 101000 f 74 goat snp36315-scaffold435-2578115 1 74966614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431520 Affx-122936230 AX-123301861 1 73731070 CAAACTTCTGAAAGACAGAGAAAATGTTAAAATGA[C/T]ACAAAGAAGGTACAAAGACACAGGAAACACAGGCA Y 2 1 2 1 103000 r 74 goat snp36314-scaffold435-2543722 1 75000666 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778378 Affx-122937878 AX-385265493 1 73766386 TATTGAGTACATTAAAACAGATTCATTTTACTGTC[A/G]TGAGACAAATGTGACTGTATATGAGCATATGAAAT R 2 1 2 1 101000 f 74 goat snp36313-scaffold435-2508406 1 75036320 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320791324 Affx-122931152 AX-385278317 1 73822337 CCAGAAGACTCACATATTTAACAGATAACTATAGC[A/G]CTTCCCTCACTGTTGTGAAGTAGAGTCTAAATCAC R 2 1 2 1 101000 r 74 goat snp36312-scaffold435-2452455 1 75092836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403730 Affx-122958021 AX-123274082 1 73853746 TGTGGCACCTGGTGTTCTTTTGCAAGTTGAGACAG[C/T]ATATCATATTTTTATTGGATTGACAGGAGACTAGC Y 2 1 2 1 101000 f 74 goat snp36311-scaffold435-2421046 1 75124168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781636 Affx-122967171 AX-385268720 1 73920672 TAAGATGAATATGTCTGGAGCCTTGAGCATTCACA[C/T]ATCAATGCAGTGAATAATAATGTCCTCTATTTGCA Y 2 1 2 1 202000 r 74 goat snp36310-scaffold435-2354120 1 75191822 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447238 Affx-122924963 AX-123317574 1 73976158 GCATCTTAGCAACAGTGATTTTGAGATAGCTATTC[C/T]GTTGAGATCTCAGATTATCAGAGGGTCAAATCTGA Y 2 1 2 1 101000 r 74 goat snp36309-scaffold435-2298634 1 75247307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405738 Affx-122956514 AX-123276090 1 74025414 CTTCATCTTTCTGTATTTTCACTCAATCACTTCAC[A/G]TCGCAGTCATACAAAACTACTCACAATTCCACAAA R 2 1 2 1 101000 r 74 goat snp36308-scaffold435-2249378 1 75297350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792010 Affx-122967361 AX-385278998 1 74062963 TTATTACTCTCAAGCTCTCCTTAAAAACGTTCACA[G/T]CTTTCAGTAAAGCAGTCTATCTTTACGACTAGGGT K 2 1 2 1 201000 f 74 goat snp36307-scaffold435-2211829 1 75335548 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273512 Affx-1111833661 AX-519547127 1 74094908 TGTCAAGTGTGTTGTAGAAGAAAAAGGTTGAGAGT[A/G]GTGCTAGTCAGTCACTCACTTGGCCGCCCTCATTT R 2 1 2 1 201000 f 74 goat GoatD01.000912 1 74094908 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417102 Affx-122947480 AX-123287450 1 74113885 ATTTCCATTCAAAGAGATCTATATTCCCCTTTTAA[C/T]GTTCTCATTTAGGGCTCAGATTAGCCAGTTAATAG Y 2 1 2 1 101000 r 74 goat snp36306-scaffold435-2160907 1 75387515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415668 Affx-122948554 AX-123286017 1 74178773 CTGGGGGGAGTAGGGGCAATATTATCTTCCAAATA[C/T]ATACTTGTTTTCCTAGCTGTAAAATGGGGGTGAAC Y 2 1 2 1 101000 f 74 goat snp36305-scaffold435-2096019 1 75453165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434116 Affx-122934932 AX-123304457 1 74229734 TCATTTAGATTTTTTCACAAATCCCCTATCTCCCA[C/T]TCCACATATTTCTTGAACTTCTGAATTCCCATAGC Y 2 1 2 1 101000 r 74 goat snp36304-scaffold435-2045058 1 75505344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450925 Affx-122921777 AX-123321259 1 74262516 ACTGGAGTCTGGAGGCAGGCAGGAGGCTTATCCTG[A/G]TATGCAGCTAAAGGCTTGACTTCTGTTAACTGGTT R 2 1 2 1 101000 r 74 goat snp36303-scaffold435-2012276 1 75538131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271740 Affx-1111832868 AX-519545534 1 74292981 AAGCCAAAAAAGGAAAAAAAAAAAAAAAGCCCTCA[A/G]TATTACCATGACTTTCTGCTTGGAGTTTGTGGCAA R 2 1 2 1 101000 r 74 goat 1_74292981_AF-PAKI 1 74292981 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381650 Affx-122974754 AX-123252008 1 74307126 GGCCGTGGAGGAAAAGCTACTTGCTTAAGGCCTCG[C/T]ATCTGGTAAGAGCTTAAACTGGGATTTGAACCATG Y 2 1 2 1 101000 r 74 goat snp36302-scaffold435-1967666 1 75583449 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412591 Affx-122951297 AX-123282940 1 74336626 TCATGCTCCTGTTAGAACTCAAGGTCATATGACAA[C/T]CCACCATTTCTCTCGAGTGTCTGGTTGCATGCAGA Y 2 1 2 1 101000 r 74 goat snp36301-scaffold435-1938166 1 75615308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804390 Affx-986696557 AX-385290985 1 74346592 GAAAGTCATCATCTCTCCATCACATCATCCACCCT[A/C]TCTCTTAAGGTATCTTTCTCTTCCATATACCCTGT M 2 1 2 1 600010 r 74 goat 1_74346592 1 74346592 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38440140 Affx-122929686 AX-123310477 1 74387098 TTGGATTCCAATACTCCCTGTGGCCTTTAGGGCTG[C/T]GTTATCCCTGGGGAGGGAGCAGGGGGGATTGCCTC Y 2 1 2 1 101000 f 74 goat snp36300-scaffold435-1887694 1 75666071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421306 Affx-122944095 AX-123291653 1 74422435 ACCAGTTGAATTCCTCTTATTCTCATTCAAATAGT[A/G]TAATTGTTAATTATTGTTGATTTTGAGACTGTAGG R 2 1 2 1 101000 f 74 goat snp36299-scaffold435-1852357 1 75701019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278710 Affx-1111836473 AX-519552188 1 74425506 TGAGATGAGTGCAGTTGTGTGGTAGTTTGAGCATT[C/G]TTTGGCATTTGGAGGGTGGAATCCTTCAAGGTCAT S 4 1 2 1 101000 r 74 goat Random2.2K-83 1 74425506 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429960 Affx-122938070 AX-123300301 1 74463567 AAAGGAAGACGTGAAGGGACCCTTCTATTTACTTC[A/G]TTTGTCTTATTTAAATAAATGAGAGAGCCTATTAC R 2 1 2 1 101000 f 74 goat snp36298-scaffold435-1811225 1 75743955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404147 Affx-122957085 AX-123274499 1 74504259 GAGCACGTCATAAAGTTGTTTGGCAAGGGGTTGTG[C/T]AGGGTGAAGGCTTTCCAGGAAGAAAGACCAGTTAA Y 2 1 2 1 101000 f 74 goat snp36297-scaffold435-1770533 1 75784797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452119 Affx-122920833 AX-123322452 1 74550603 ATCCTATTCCTTAGCAACTCTTTCATTTTCCTTTC[A/G]TTTGGATATTTGTCAGACTCTGCCTGCAATGCAGA R 2 1 2 1 101000 r 74 goat snp36296-scaffold435-1724189 1 75831874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420817 Affx-122944675 AX-123291164 1 74579244 CCTGATTTGAGGGAGGGCAGAAAGGTTTTCTCAGC[C/T]AAACCTACACCAACAACATACAGTGTCTGTGCTTC Y 2 1 2 1 101000 r 74 goat snp36295-scaffold435-1695548 1 75860412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433358 Affx-122935134 AX-123303699 1 74609953 CTGACACAATAGTCAAGCATCTCCTCTAAATTAAC[A/G]TTGAACAAATATTTAAAGGCTATGATATTTAACCA R 2 1 2 1 101000 f 74 goat snp36294-scaffold435-1664839 1 75891278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379194 Affx-122976301 AX-123249553 1 74683286 CAGAGAACATCAGCTCAGCTAGAATGTTCCAAATC[A/G]TCTCATTGAGCTTGGGCGGTTGGGAGGACTGGGCC R 2 1 2 1 101000 f 74 goat snp36292-scaffold435-1591506 1 75964790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412016 Affx-122951745 AX-123282366 1 74713118 CTATGTGGCCTGAAACAAGCTAACATCTGTCATTA[A/G]CCCTCTCAAAAAGACAAAAGAAATGAGCAAAATAG R 2 1 2 1 101000 f 74 goat snp36291-scaffold435-1561674 1 75995421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430297 Affx-122937277 AX-123300638 1 74742740 TGGATCATTTACAAAAGGAACGTAACCCCAGTATT[A/G]ATTCAAAGTATGTCTGTCTTTGGGAGATTTAGAAT R 2 1 2 1 101000 r 74 goat snp36290-scaffold435-1532052 1 76026237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795633 Affx-122935565 AX-385282588 1 74791222 GAATGGGAGCAACCAAGAATAAAGGAGATTTTTGT[A/G]TTCTTTTCCTGTTATAATACAAGAAGTTATTACAC R 2 1 2 1 101000 f 74 goat snp36289-scaffold435-1483570 1 76074658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790657 Affx-122941201 AX-385277659 1 74826682 CCTGACCTGCCAGATCTACCACAGAGGGTTAATGT[A/G]AGGATAAATTGAGTAAAACTTTATGTAAGGTTTTT R 2 1 2 1 101000 f 74 goat snp36288-scaffold435-1448110 1 76110684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452100 Affx-122920848 AX-123322433 1 74864724 TGATGGACAACAAGATAGGAATAAAATTTTATACA[A/C]TCTTTGGTTTCATATTCATACATTCTGTTTTCTTT M 2 1 2 1 101000 r 74 goat snp36287-scaffold435-1410068 1 76149014 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450034 Affx-122922835 AX-123320369 1 74894153 TTGGTTAAGGATGATTTTCATGAACCAGCCTAGAA[C/T]GGAGAGGAAATTAGGAAAACATTTAGATCCATGCC Y 2 1 2 1 101000 f 74 goat snp36286-scaffold435-1380639 1 76178528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406402 Affx-122955224 AX-123276754 1 74964501 TCTTTTGCCATCTTCTCAGATGTTGAGTTCCTGGT[A/G]TATAAAATACTTCAGGTAAAAGAAGGATAAAAACA R 2 1 2 1 201000 r 74 goat snp36285-scaffold435-1310291 1 76247873 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413818 Affx-122949892 AX-123284167 1 74997845 TTTATGTTGATTTTAAAACATTGACAGAAACCACC[A/G]TACATTTCTTCAGAAATTTAAAGTAAAACTAAAAC R 2 1 2 1 103000 f 74 goat snp36284-scaffold435-1276947 1 76281318 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382672 Affx-122973657 AX-123253030 1 75040457 AAGTTGACCAACCTTCCCATGAGGCCTAAGAGAGG[C/T]GACTACAAAACTGTCCCATAGGGCAATGTCCAGTG Y 2 1 2 1 201000 r 74 goat snp36283-scaffold435-1234335 1 76323863 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397482 Affx-122962080 AX-123267837 1 75150738 AGATCACAGATGCATGCCGGAACAGTGGTTCAGTG[C/T]GGATGTAGTGGGTTTGAGGGGAATGGGAAACTGTT Y 2 1 2 1 201000 f 74 goat snp36281-scaffold435-1124054 1 76435841 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429888 Affx-122938125 AX-123300229 1 75183623 TTCACAGTGTGCATTCTAAAGGCCCAGAGAAGTCA[C/T]GTAGAAAAAAGATAACTTTTAAACTTAGTATTTTG Y 2 1 2 1 101000 f 74 goat snp36280-scaffold435-1091169 1 76469291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437387 Affx-122932438 AX-123307725 1 75217332 CAACTTTGCGCCAGGCAACTTGCTAGGCACACCAG[C/T]ACACGCCAGTGGAAAATACAGATTACATTTTGCTG Y 2 1 2 1 101000 r 74 goat snp36279-scaffold435-1057460 1 76502985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779474 Affx-122958704 AX-385266577 1 75277533 CATGATATGTGACCCAGTTATAGACAATGAGACAC[G/T]AGATAAATATGCTATAGGGACACTGATTATAGGAA K 2 1 2 1 101000 f 74 goat snp36278-scaffold435-997259 1 76562542 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416241 Affx-122948210 AX-123286590 1 75310672 TAAGAAATGCTTAGTGTCCAGACCTATTTTGAAGA[C/T]GGAATCAATTTGAAGCATTTCCTGATGTAGGAAGT Y 2 1 2 1 101000 f 74 goat snp36277-scaffold435-964120 1 76595944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799257 Affx-122926763 AX-385286187 1 75350194 TGTATTATGATAGTTTAGTACAAACCATCTCTACT[A/G]TATCCATTTCCCCAGGCTGCCATAGCACATTACCA R 2 1 2 1 101000 r 74 goat snp36276-scaffold435-924598 1 76635763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794079 Affx-122936272 AX-385281046 1 75387094 AGAGACTCAGGATGTTTTACAAGACTACTCTTTGT[G/T]CTGTAATAATAAGTTATAAGCGAAGATGCTTGTTA K 2 1 2 1 101000 f 74 goat snp36275-scaffold435-887698 1 76672891 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386242 Affx-122970968 AX-123256600 1 75450109 ACATTGAGCAATGCAGAACTGCCCCACATAACTTC[A/G]TAATAAAAGAGTAGGTACAGGAAAACTAAACAGAG R 2 1 2 1 201000 r 74 goat snp36274-scaffold435-824683 1 76744885 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412045 Affx-122951721 AX-123282395 1 75496238 ACAAAGCAGGACAAAGAAAGAGAGTGATAGGGTCT[A/G]TTTTGCATATAGTGATCAGACAGGTCTTTCCTGAT R 2 1 2 1 201000 r 74 goat snp36273-scaffold435-778554 1 76791560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444348 Affx-122926718 AX-123314685 1 75529107 GTCCTCGTACACAATTTTATTAACATCTGTTATAG[C/T]AGCTGACATTTCTAAACGCAAGATTTGCTCCTGAA Y 2 1 2 1 101000 f 74 goat snp36272-scaffold435-745685 1 76824494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432323 Affx-122936297 AX-123302664 1 75596679 TATGTTGCTGTATGTATTTCTTTCACTGTCGTTTA[C/T]GTTTTAATCAATGGGAGTAAGTCTTCCCAGGCTCT Y 2 1 2 1 101000 r 74 goat snp36271-scaffold435-678113 1 76891711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432577 Affx-122935523 AX-123302918 1 75633520 AGTGAAAAGTCAAAGTGAAGTCGCTCAGTCGTGTC[C/T]GACTAAAAGCCTGTGCATCATGGAACGGACGTGAA Y 2 1 2 1 202000 r 74 goat snp36270-scaffold435-641272 1 76928550 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420098 Affx-122945096 AX-123290446 1 75682393 TAAGTTGAAACCTACCAGTTCTGGTTCCCGGTTAG[A/G]CCCTGGATGAACTCTTTACTCCCTCACAACCCTCT R 2 1 2 1 101000 f 74 goat snp36269-scaffold435-592399 1 76977227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424725 Affx-122941672 AX-123295071 1 75712798 TTTGGCTCTGAGGCATGTGATTTTAAACTATGATG[A/C]TTAATTAATTCCATGTGCCACCTAGCTCTGGAGAG M 2 1 2 1 101000 f 74 goat snp36268-scaffold435-561994 1 77007576 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412637 Affx-122950798 AX-123282986 1 75776005 GAGAAGCTCAATATAGATTCATAAAAAAGGCAGAT[A/G]TCTGGCTATCAGGTTTCTCCACGATGTCATAATTA R 2 1 2 1 101000 f 74 goat snp36267-scaffold435-498787 1 77070767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794360 Affx-122945163 AX-385281324 1 75812333 GAAATACCCAAACACTGTTGTTTAAACTAAACTCT[A/G]TTGAGTAATGGAGATGACGATGATGAGGTTGATTG R 2 1 2 1 101000 r 74 goat snp36266-scaffold435-462459 1 77107216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775931 Affx-122971868 AX-385263062 1 75851896 CCCTGGATTAGGAGTTTAAACTGCTCTTTCCATCT[G/T]CACCTGAATCTCCTCCTGAACTCTGAAGCTCCACT K 2 1 2 1 101000 f 74 goat snp36265-scaffold435-422896 1 77146955 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380836 Affx-122975065 AX-123251194 1 75889584 AGAGGTATAATAATGAAATCAACACTGCAGTAACG[G/T]TAAGGGTGACCCTGGGAGCTCACGGGAAGAATGGA K 2 1 2 1 101000 f 74 goat snp36264-scaffold435-385208 1 77184631 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801223 Affx-122972497 AX-385288136 1 75932511 GATTCATATAAGAATTCTGCAAGGTAGGTGAGTAA[C/T]ATTCACATTTTATAGATGCAGAGGTATGTATCTTT Y 2 1 2 1 101000 r 74 goat snp36263-scaffold435-342281 1 77228344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423320 Affx-122943182 AX-123293666 1 75962021 TTTCCTGTGACAAAGGTCCATTTGAATTGAAGCAA[A/G]TAAGTTGACTATATGTTGCCAAAGTTACCTCTCCT R 2 1 2 1 101000 r 74 goat snp36262-scaffold435-312771 1 77257661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789027 Affx-122926371 AX-385276040 1 75995323 TATTAATATGAAAAATTGTACAAATGTTAGTAGAT[A/G]CTGTCATTAAATATATCCCCAAGACCCATGTCCTC R 2 1 2 1 101000 r 74 goat snp36261-scaffold435-279469 1 77290761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403889 Affx-122957495 AX-123274241 1 76047056 CTGAGTAATGTTATGATAACTTGAATTTTGCAGGC[A/G]AACCTTTGAAAATGACCCCCCAAAAATAACAGTGA R 2 1 2 1 201000 f 74 goat snp36260-scaffold435-227736 1 77340586 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787783 Affx-122927959 AX-385274806 1 76102928 AATGTAGCTGCCTGCAATGAATTTTATACTGATTT[C/T]GAGCAAGAAATCATAATTAGTTAGCAAGAAATTTC Y 2 1 2 1 101000 f 74 goat snp36259-scaffold435-171864 1 77396503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771450 Affx-122932085 AX-385258608 1 76136354 AAAATTCTATTGGATAATGCTATTCTAGAAAACAT[A/G]CATCTGATACATGCTGACAAAAAAGCAAAACAAGA R 2 1 2 1 101000 r 74 goat snp36258-scaffold435-138438 1 77430308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278539 Affx-1111836477 AX-519552021 1 76176900 GTTTTGTAATGATTGTTACTGGTCTAACTTTTGGG[A/C]TAAACTCCAAAGTGTGTTTAATGGTTACAGATTAT M 2 1 2 1 101000 f 74 goat Random2.2K-84 1 76176900 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784023 Affx-122950181 AX-385271076 1 76195604 GAGAGAGTAAGGACAAGGCTACGCCTCATGATACA[C/T]AGTGTTTCATAGGCGTAACAGTCATTCATGAGCCA Y 2 1 2 1 101000 r 74 goat snp36257-scaffold435-79188 1 77489358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450670 Affx-122921914 AX-123321004 1 76227018 ACAAATGAACTTACGTACAAAAGAGGAAGAGCCTC[A/G]TAGACTTAGAGAACAAACTCATTGCCAGGGAAACA R 2 1 2 1 201000 f 74 goat snp36256-scaffold435-47774 1 77520913 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438757 Affx-122930816 AX-123309094 1 76279644 ATGCAGAGAGAATCCCACGTGATGGCAGAGGCAGA[G/T]ACTGGAGCAGTGCAGTCCCAAGCCAAGGAATACCA K 2 1 2 1 102000 f 74 goat snp40497-scaffold519-4753 1 77574156 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395218 Affx-122964488 AX-123265573 1 76316438 AAATGGGCATCAGGCCTCATTGCACAATGCTGTTT[A/G]CACTGACCCAGTAAACAGAGCAGACAGATAGGTAA R 2 1 2 1 201000 r 74 goat snp40498-scaffold519-41547 1 77611068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772288 Affx-122969188 AX-385259443 1 76359145 GCCAGGGCTAAATACTGTAGTTCATTTCAACCATT[A/G]TGCCTGAGAGCTAGGCTAAATTGTTTGTGAAGGTT R 2 1 2 1 101000 r 74 goat snp40499-scaffold519-84254 1 77653355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278728 Affx-1111836482 AX-519552205 1 76365055 TTTCTGTGCCTTGTCCTGGCAAACACTTAATACAC[A/C]CGATGTTCAGGTGTTTAAAAAGGCTTTTTCTCACC M 2 1 2 1 101000 r 74 goat Random2.2K-85 1 76365055 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769002 Affx-122957405 AX-385256177 1 76404400 TTCTAGGCTAGATTTTACTCCAAAACTAAATAAAG[C/T]AGGTAATTAAGGCAACTGGCTTGATGATTGTAGTA Y 2 1 2 1 101000 f 74 goat snp40500-scaffold519-129509 1 77698457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401201 Affx-122959334 AX-123271554 1 76434159 AAAAAGAATGCCTCTATTTTCCTTTGGAGAGCCAC[A/G]TTCTTCCATTTAGTGCAAATAGCTTAAGTGGAGCT R 2 1 2 1 101000 r 74 goat snp40501-scaffold519-159268 1 77728602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775788 Affx-122938129 AX-385262919 1 76481545 AGAGAAAAGACAGAATAAAACCTGAGTCACATAGG[C/T]GGCATTCCCAGTCTTAAACTCTGAAAGAAACTGAA Y 2 1 2 1 101000 r 74 goat snp40502-scaffold519-206654 1 77776240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387794 Affx-122969698 AX-123258152 1 76510500 CCCCAAAAATTTAAAGTAAAAATCAGGCAGAAATA[G/T]ATGAAGAAACCTCAAACAAAATGGTCATAAGCTTT K 2 1 2 1 103000 r 74 goat snp40503-scaffold519-235609 1 77805126 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376785 Affx-122977954 AX-123247144 1 76547263 GAACAGTTTGGAAATCTCTGAAATCCTGTCCGGGT[A/G]CTCACCGCCTTAGTTCTCACCTTCAGTAGAAACAT R 2 1 2 1 201000 r 74 goat snp40504-scaffold519-272372 1 77842002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779387 Affx-122947100 AX-385266491 1 76602329 TGCAAAGGGAACCTGCCGCACAACATGCCATATCC[A/G]TTTTCAGAGGGTGTCAACACCCTCCTTCCCACACC R 2 1 2 1 202000 f 74 goat snp40505-scaffold519-327438 1 77897755 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444133 Affx-122926804 AX-123314470 1 76636903 TTTTTTTTTTTTATAATATTGTGATGTTTGTACTT[A/G]TGTATTTGTTCCACTTCCTCATTAGATGGTCCCCA R 2 1 2 1 101000 r 74 goat snp40506-scaffold519-362012 1 77932506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783099 Affx-122959690 AX-385270166 1 76665636 TTTCATTTAGTCATTCATTTATTGAGTCAACATAC[A/G]TTAGTTAAGCACCTCTTATGTGCTATTATGGGTGG R 2 1 2 1 201000 f 74 goat snp40507-scaffold519-390745 1 77961097 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415955 Affx-122948429 AX-123286304 1 76703029 ATGGACTGTGCTTCAGAAATGAGAATAACTCTTTT[A/G]TTTTTGTTGTTTGTGCTTTTAATTCATTTTATTGA R 2 1 2 1 103000 f 74 goat snp40508-scaffold519-428138 1 77998494 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476152 Affx-1251763655 AX-586011584 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20000 f 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 539476408 Affx-1251763655 AX-586011812 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20000 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165422 Affx-1251763655 AX-606940833 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 f 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165522 Affx-1251763655 AX-606940933 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165555 Affx-1251763655 AX-606940966 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 38391613 Affx-122966590 AX-123261970 1 76800713 TCAAGGGGTTGGGTTCCAACTATGGAAGATCTAAG[C/T]AGAACAGGTAAGGCAGGGTGGGACCTGAACCCGCC Y 2 1 2 1 101000 f 74 goat snp40510-scaffold519-525822 1 78095314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444145 Affx-122926795 AX-123314482 1 76855354 CTCCTCCCTAGTTTAAGCAGTGGAGCCCCTTAGAT[A/G]GAAAGCAGAATGGTGACTGATGTCAATGACATGGG R 2 1 2 1 201000 f 74 goat snp40511-scaffold519-580463 1 78150398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441390 Affx-122928848 AX-123311727 1 76917656 TTCCAGGCAACTCTAATATTCCATCCCATTATGAA[G/T]AAAGTTTCTCAACTCTCCTATACAATCTCTTTTTA K 2 1 2 1 101000 f 74 goat snp40512-scaffold519-642765 1 78212977 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423426 Affx-122942612 AX-123293772 1 76956378 GTGATGGGAAGCAATATAATAGTGCCTTCAGAACA[A/G]CTGGAGGACAGAAACTCTCTGTCCTTCAAGAGTGG R 2 1 2 1 101000 f 74 goat snp40513-scaffold519-681487 1 78251755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420450 Affx-122944891 AX-123290797 1 77013781 ATGAACAGAGCGTTGCATAGCACCTAGCACAACTA[G/T]AAACACAACTTTACTGCTATTGTTATTGCCAAAGA K 2 1 2 1 101000 f 74 goat snp40514-scaffold519-738890 1 78308976 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404477 Affx-122956726 AX-123274829 1 77070091 TTGGGTTATAGCACAAGCATGAATAAAATACTATG[A/G]AATATTCTATTCTATAAGAACTCAGGCCTCACCAA R 2 1 2 1 201000 r 74 goat snp40515-scaffold519-795200 1 78364229 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773385 Affx-122926686 AX-385260527 1 77101471 AATGAATAAGAATGATAAAAGCTTAGTGGAATTAA[C/T]GTAAATGACTGCATTTCTGATAAAACATTAACTAT Y 2 1 2 1 101000 r 74 goat snp40516-scaffold519-826580 1 78395598 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425388 Affx-122941559 AX-123295734 1 77156340 ACCGCAGCTGGAAAGGAGTCTGCCCCCAAAACAGA[C/T]ACTTAACAGTCACATACTTTGAAGATGAAAACCAG Y 2 1 2 1 201000 r 74 goat snp40517-scaffold519-881449 1 78451066 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442386 Affx-122928008 AX-123312723 1 77227346 GAACCTTCCATAACCCCATTAAAAGGTGGAGTCTA[C/T]GTCCCTTGCCCTTGAACTGGGTGAGTCTTTGTGAC Y 2 1 2 1 202000 r 74 goat snp40519-scaffold519-952455 1 78522449 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272559 Affx-1111832869 AX-519546275 1 77250630 CAGCCATTTTATAAATGGAGCCCTGATATGGTTCC[A/G]AATAGGGGTCACTAAGTGGATGTTTACAATCACTG R 2 1 2 1 201000 f 74 goat 1_77250630_AF-PAKI 1 77250630 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423080 Affx-122942936 AX-123293426 1 77257614 CCTTAAGTACTGGATACCATGGAGTCTCAAAAGTT[A/G]CAGAATTATGCTGAGCAATGCAATGAAATGAGTAA R 2 1 2 1 201000 r 74 goat snp40520-scaffold519-982723 1 78553169 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433448 Affx-122935064 AX-123303789 1 77303017 CCTGTCCTCATTGTCATCAAAATAGCAACAACACC[A/G]CCCCCCTTAAATGACACATCTTCATCTGTAAATGA R 2 1 2 1 201000 f 74 goat snp40521-scaffold519-1028126 1 78598658 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381265 Affx-122974482 AX-123251623 1 77351908 AGTAAGGAAACCGAAGAAGAACGCTGAGGGTGAGA[C/T]ATGAAGATGCAAATTCAGCCTACTGAGCTTTGGGT Y 2 1 2 1 101000 f 74 goat snp40522-scaffold519-1077017 1 78647446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273569 Affx-1111833676 AX-519547182 1 77395837 TTAATTAATTAAGTGATCACTTTAGTTGAGGCAGC[A/G]TACACTAGCTTACCAGACTGTTCTGCAGTCTTGGA R 2 1 2 1 101000 r 74 goat GoatD01.001203 1 77395837 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421437 Affx-122943952 AX-123291784 1 77468750 AAGTCCCAAGGAGAGTAAAATGCCGGTTGAAGGAA[C/T]GCTGGTCTCCATCTCACCTCCACCAGTAAGCAAAC Y 2 1 2 1 101000 f 74 goat snp40524-scaffold519-1193859 1 78763443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387817 Affx-122969678 AX-123258175 1 77539828 ATGAATGCCCTGTAGAACAATGGCAAAAGCACTGA[A/C]CTGGAATCAGGTGACTGGATTCGGTCCTCCGCTCT M 2 1 2 1 101000 f 74 goat snp40526-scaffold519-1264937 1 78834527 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430378 Affx-122937779 AX-123300719 1 77608390 TTGAACCCACCTCTGGTGTCTAGGTCACCTGACTG[A/G]TCCCATGATTTTTCCACCCAGGGAGGAGGCCCTGA R 2 1 2 1 201000 r 74 goat snp40528-scaffold519-1333499 1 78903068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402799 Affx-122958287 AX-123273152 1 77714581 CTCCAGTAAAAATATTTGCACATATACCACCCTCA[A/G]TATTTGCACACACATTATAGTAGTGTGCACTGCAC R 2 1 2 1 101000 r 74 goat snp40530-scaffold519-1439690 1 79009885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386752 Affx-122970131 AX-123257110 1 77746001 GTGCCCTATGAGGTAGATTCTATTACTATCCTCAT[C/T]TTAAGTAACAGACAGGACAGGTTTCTCTGCTAATA Y 2 1 2 1 101000 r 74 goat snp40531-scaffold519-1471110 1 79041355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414419 Affx-122949969 AX-123284768 1 77786902 ATGATAATGATTTAGGAGGACTCACATATGAAAGA[C/T]GGTCTTGTGGGGAGATACAGGAGAGAAGGGGGATG Y 2 1 2 1 101000 f 74 goat snp40532-scaffold519-1512011 1 79082101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778109 Affx-122949302 AX-385265224 1 77818649 GAAAAGAGGAATGTGATTACCCAGCTTGATTCATA[A/G]TGCTGGCATTGGGAATATATCTTCACTAAGGCCTT R 2 1 2 1 101000 r 74 goat snp40533-scaffold519-1543758 1 79113853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420533 Affx-122945304 AX-123290880 1 77868938 CCTTGCAACACACCTGAAATGTCTTGAAGGCAGAA[C/T]GGGAGTTGAACAGTGTGGCAATCATATTATTTTTA Y 2 1 2 1 201000 r 74 goat snp40534-scaffold519-1594047 1 79164135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425402 Affx-122941549 AX-123295748 1 77905331 ATTAATACAAAGGCTTTCTGATCACAGAAAATACT[A/G]TACTAACTCATTTAATCCTGATAGCAGCTTCTACC R 2 1 2 1 201000 f 74 goat snp40535-scaffold519-1630440 1 79200563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443187 Affx-122927599 AX-123313524 1 77937442 TGCACACTTGTGGCTCAGAAGCAAGGCCCTTAGCC[A/G]CTATTCTATACCACCCCCAAAAGATGAAAGGGCAG R 2 1 2 1 101000 r 74 goat snp40536-scaffold519-1662551 1 79233377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428516 Affx-122938757 AX-123298858 1 77985840 CTGTCATTTGCGTTGGGCCTTTGGTACAAAGCTAT[C/T]CTACCTTCCTGTTTTAGTGACTCACCCTTTAACTC Y 2 1 2 1 101000 f 74 goat snp40537-scaffold519-1710949 1 79281700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802819 Affx-122921649 AX-385289718 1 78026255 CTTCACTGAAGGAGGAAAGGCTTCAGCATCACTAA[A/G]GAAATGGCCTTCTAGAAAGGCAGGCGCTAAAGCAG R 2 1 2 1 101000 f 74 goat snp40538-scaffold519-1751364 1 79322063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419858 Affx-122945373 AX-123290206 1 78109262 GTCAGCAGCGAGAGGAGGGAGGATGGATTAGAGAC[A/G]AGAAATAAAGAAGGGCTGCAGTTGGGAGAATGCTC R 2 1 2 1 101000 r 74 goat snp40540-scaffold519-1834371 1 79404791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452799 Affx-122920232 AX-123323132 1 78160686 TATGGCAATGAAGGAATGTTAATATTCCTAAAGAG[C/T]AGAGCTAATCTTTTCGTTATCTTGTTAACCTTGTA Y 2 1 2 1 101000 r 74 goat snp40541-scaffold519-1885795 1 79456413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391711 Affx-122967508 AX-123262068 1 78215896 AGAGAGATGAGGGGTTGGGGTCTCACTGCACTGGA[C/T]AGATACGGTGGGCAGAATTGATTCTCTGAATTAAG Y 2 1 2 1 101000 r 74 goat snp40542-scaffold519-1941005 1 79510272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435362 Affx-122933587 AX-123305702 1 78278435 CATTTTCTGGAGCATGAACTCCAGGTGATGTCCAG[A/G]GGGGTTGAAAGGCAACCATAGAGAAGCCAGAAGAA R 2 1 2 1 101000 r 74 goat snp40543-scaffold519-2003544 1 79573703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440188 Affx-122930708 AX-123310525 1 78329291 GGCCAAGATAGATTGGATTAAACTAGGACTAAAGT[A/G]CAGTCCATCCTAAAGGAGATCAGTCCTGGGTGTTC R 2 1 2 1 101000 f 74 goat snp40544-scaffold519-2054400 1 79625006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392452 Affx-122966166 AX-123262809 1 78363975 GGTCAGTGTATTGAAGGGGTAACTGACCTCCTTGG[C/T]GCTCCTGGAGAGGAAAGAGACAAACAAGCCCATGA Y 2 1 2 1 101000 f 74 goat snp40545-scaffold519-2089084 1 79660095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397888 Affx-122961960 AX-123268243 1 78394495 GCTAACACTACATATTTCTAGATTTTTCTAAAGCT[A/G]CAGTAATTAAGACAATGTGGTACTGGCATAAAGAT R 2 1 2 1 101000 f 74 goat snp40546-scaffold519-2119604 1 79690853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378104 Affx-122977149 AX-123248463 1 78436088 TGCCTCCTTCTGAGTACATTCTTCACAAGACACTT[A/G]TCACACTGTATGATAGCTCTGTCTGTTTTCCGCCA R 2 1 2 1 101000 f 74 goat snp40547-scaffold519-2161197 1 79732428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446920 Affx-122924693 AX-123317256 1 78468000 TCCTAACTGTAGCATCTAACTCAAGAATCTCCGAG[A/G]TTTCATGGAGGAGGCAACACTTTACCTGGGTACAG R 2 1 2 1 101000 f 74 goat snp40548-scaffold519-2193109 1 79764338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777347 Affx-122963464 AX-385264469 1 78531869 AGCATGGAGAAGAGACTGAAATTGAGGGCAAATTC[A/G]TTTTTTGTCTGTGGCTCCCAAGGGTTTGGTACTGT R 2 1 2 1 101000 f 74 goat snp40549-scaffold519-2256978 1 79830482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780032 Affx-122978382 AX-385267131 1 78583997 GGCAGACAGGAAAACACATCTCAGATGACTTAGAC[A/G]AAATCTGCTTGACATGTTTCTTCTCTTCTAAAATC R 2 1 2 1 101000 r 74 goat snp40550-scaffold519-2309106 1 79882334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444645 Affx-122926921 AX-123314982 1 78612850 GAAATAAAAACCAGTTACATTTAGCTTCTAGAGAA[C/T]GAAGTCCAAAAGAAACCAAAAAAAGCAAAAGCAAA Y 2 1 2 1 201000 f 74 goat snp40551-scaffold519-2337959 1 79910816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413588 Affx-122950575 AX-123283937 1 78661072 TTCATCAGGTATCTGGTTACTGGGTCCCCTTGTAC[A/G]TGAAGTGGGGGGCCTGGGTGTTCTCTGAGGCCTAG R 2 1 2 1 101000 f 74 goat snp40552-scaffold519-2386181 1 79959352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383417 Affx-122973484 AX-123253775 1 78704593 TCTTTGGGGCCAGGGTCCTGCTTCATCCTCATCAG[C/T]ACTCCTACGACTCCTACAGACTACTCCAGCGTCTC Y 2 1 2 1 101000 r 74 goat snp40553-scaffold519-2429702 1 80003247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398996 Affx-122960948 AX-123269351 1 78742319 GTTTCTGGATCACTGTGGTGGGTGGGGCAAGCCCA[C/T]AGGAGTGGTATACACACCCAGCTGGGTTGCAGGAG Y 2 1 2 1 202000 f 74 goat snp40554-scaffold519-2467428 1 80041350 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394852 Affx-122964771 AX-123265207 1 78802453 ATGTATTTTAAAACTATGTGTGCTCCCTAGTTAAA[C/T]ATAGCAATTATTACATTTTGATTTTGAAAGACCTC Y 2 1 2 1 201000 f 74 goat snp40555-scaffold519-2527562 1 80101813 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768798 Affx-122927943 AX-385255975 1 78831074 AGTAAGAACACGCGTTTTTGTTGAAATAATAAATT[A/G]CCTCTCAGACCAGTTTTGAGTCACTTTTTCTTGTT R 2 1 2 1 101000 r 74 goat snp40556-scaffold519-2556183 1 80130048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449906 Affx-122922331 AX-123320241 1 78876147 GGGAAGCCCCAGCTAAGGGCTCCTGCCTCAGTGAA[C/T]AAGAACGCTCCAGGGCTGCACAGTGAGCCCCTAGG Y 2 1 2 1 101000 f 74 goat snp40557-scaffold519-2601256 1 80175337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435212 Affx-122933629 AX-123305552 1 78924122 TATACTGACAGTCCTTCTGAAGCCTGATCTAAAAT[A/G]TTCTTTCTTTATTTTGATTTTTGGCCATGCCATGG R 2 1 2 1 103000 f 74 goat snp40558-scaffold519-2649231 1 80223186 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424254 Affx-122942462 AX-123294600 1 78970576 TCTACCACCTGCCAAGGAAAACACTCTAATACTTC[A/G]TGTTCCCTCACAGCCACACCCGAGTATAGCAAGGG R 2 1 2 1 101000 f 74 goat snp40559-scaffold519-2695685 1 80269514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773208 Affx-122933045 AX-385260350 1 79059624 ACATGTGAGTGTCAGGAAGCATGCATCAGAAAGAC[A/G]CATAGAGATGCTTTCTGTTTAGGCTGTGTTTTGTA R 2 1 2 1 101000 r 74 goat snp40561-scaffold519-2784733 1 80358831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438604 Affx-122930936 AX-123308941 1 79125312 CAAGGCTATAACTTGGCTGGGGCCCTTTGCCTCTC[A/G]CTCTTCCTTTCTCTTTCTCGAGCTCCTACCCTCAC R 2 1 2 1 201000 f 74 goat snp40562-scaffold519-2850421 1 80424852 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785248 Affx-122933104 AX-385272293 1 79154035 AATTTACTCAAAAACACAGGAGGAGTCACTGCCTT[A/G]CTCCATCTCCAGGGAGTAATTTAAGCAGGTGTATC R 2 1 2 1 101000 r 74 goat snp40563-scaffold519-2879144 1 80453271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782024 Affx-122942267 AX-385269102 1 79189232 TGATATACCTAGAATGGTAACTTCTAAGAGGTGAC[A/G]TTTGAGACAAGACAGAAATGTTGAGGAAGTAGCTA R 2 1 2 1 101000 r 74 goat snp40564-scaffold519-2914341 1 80488803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379838 Affx-122975814 AX-123250196 1 79231615 CAATTATTGTCACTACCAGTAAAGCTTGTTGGAAG[A/C]GTTAGCTCCAGTCTCAAAGTTGGAATCAGCTTTAG M 2 1 2 1 101000 f 74 goat snp40565-scaffold519-2956724 1 80531379 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779696 Affx-122954547 AX-385266796 1 79273093 TTGATGTTTTGATTTCAGTGGTTCCACCCTCCAGT[A/G]CAAGTATATCAGGTACCCTTAGTAAACCAGAGTCT R 2 1 2 1 101000 f 74 goat snp40566-scaffold519-2998202 1 80572979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771338 Affx-122937279 AX-385258496 1 79308226 CTTTCATAACCATAAAAACAGGAGCTTTACAACAG[C/T]GAAATAGCTGAAGTATACAGGCTGAAAATTGAGAA Y 2 1 2 1 101000 f 74 goat snp40567-scaffold519-3033335 1 80605911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416467 Affx-122947810 AX-123286815 1 79359959 CTCTGACATGGCCCAGCAAGAAAAGCACATTCTTC[A/G]TTCCCAGCACCTTGCAGGCAGATCACAGCTCAAGG R 2 1 2 1 101000 f 74 goat snp40568-scaffold519-3085068 1 80657428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423205 Affx-122942713 AX-123293551 1 79420306 CAGAGCCTGAGAATACACAGATATTTATACTATGT[A/G]CCACCATTTTCAAAGCCCCACCACAGCCTTTATTG R 2 1 2 1 201000 f 74 goat snp40569-scaffold519-3145415 1 80717398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382677 Affx-122973654 AX-123253035 1 79480067 AGATCAGGTCTGAACTGACAAAACCAAAAAGACAG[C/T]GCAGAAGTGGAATTACAACAGAGTAAGAGATCAGC Y 2 1 2 1 101000 r 74 goat snp40570-scaffold519-3205176 1 80777306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447129 Affx-122924462 AX-123317465 1 79545505 TTTCCTTATGTTTAAAATAGGGTTGTTTTTGTTTT[A/G]CCTTTTATCAAGCTGAAGAAAATTTCCTTCTAGCC R 2 1 2 1 101000 r 74 goat snp40571-scaffold519-3270614 1 80842684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785388 Affx-122958726 AX-385272433 1 79601377 TGAAAGTTTATTGAATGGATCACTAGTACTATGTG[A/C]TTAGTACAATAACATAAACAATTAAAGTTACATTA M 2 1 2 1 201000 r 74 goat snp40572-scaffold519-3326486 1 80898157 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794827 Affx-122934679 AX-385281787 1 79630901 ACAACAGGAAATGTTATAGCCCTCATTTGAAACAG[C/T]TGGAGAAGAACTTGTTCACCTTCATGATGATACAA Y 2 1 2 1 101000 r 74 goat snp40573-scaffold519-3356010 1 80927229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803444 Affx-122953920 AX-385290274 1 79675929 AGGTTGAGTGAAAAGTCTTATAATTTCACAAATAC[G/T]GTTTTTTTTGACCCTTGATCTGCTAGAAACCTCAT K 2 1 2 1 101000 r 74 goat snp40574-scaffold519-3401038 1 80972456 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272613 Affx-1111832871 AX-519546324 1 79766752 TATATACCCTTCAGAGGGTGACACTTGTGCCCCAC[A/C]TTGGACGTTTCTGAGCCCCAGTGTCTCTCAGGGGT M 2 1 2 1 202000 r 74 goat 1_79766752_AF-PAKI 1 79766752 C A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388088 Affx-122969507 AX-123258446 1 79790980 TTGTAGGAAAAATTAGAAACAGAAGTCATTTTAAC[A/G]TTATTAGCAGCATCACCATGCTTGCCCGTAGACAG R 2 1 2 1 101000 r 74 goat snp40577-scaffold519-3516089 1 81089634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448364 Affx-122924111 AX-123318700 1 79826718 TTTCTTAAGATCCTGTACTGCTATCTGTCATAACC[A/G]CTTTGTAATATATTGTCACGTTTGATTGAATGCTG R 2 1 2 1 101000 f 74 goat snp40578-scaffold519-3551827 1 81125519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401632 Affx-122959595 AX-123271985 1 79877966 AGTTTAGACTCTGACCTCCCCACTTGTCCAGTTCC[A/G]TCCTGGAGGGCTCACAACTCAAGGAAGCCAGACTC R 2 1 2 1 201000 r 74 goat snp40579-scaffold519-3603075 1 81177161 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432835 Affx-122935379 AX-123303176 1 79914627 AATTGGATTTTTAAAGTATTTACATAGAGCCAAGA[C/T]AGAGTTTGAATATCTTTGAAATCTGCATTTTTTTT Y 2 1 2 1 101000 r 74 goat snp40580-scaffold519-3639736 1 81213960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775092 Affx-122946297 AX-385262224 1 79948007 GCTTTACAGAATTAGAATGGGAAAACTTCAATGCA[C/T]GGCATGGTCTAGTTAGAATCACTTTTTAAAACGAC Y 2 1 2 1 101000 r 74 goat snp40581-scaffold519-3673116 1 81247509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784657 Affx-122920614 AX-385271705 1 79995375 CAAAAGGAGATTACCATCAGCATTATTCTGCAGGG[C/T]AGTTCAGCTGTGTCCCAACTGTACATTCCACTAAA Y 2 1 2 1 101000 f 74 goat snp40582-scaffold519-3720484 1 81295048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804398 Affx-986696565 AX-385290988 1 80041436 TTTAATAGGATCTCAGAAAAGTACAGGTTCCGGGT[C/T]CTATAATGAAGATTGCGTGCAGCCCTAGCTTTTCC Y 2 1 2 1 600010 r 74 goat 1_80041436 1 80041436 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 38376315 Affx-122978358 AX-123246674 1 80044184 GGAGAAACCAGTCTCAGGTACTTTATAGGCTACAA[C/T]GAGAAAGGGGGGCAGAGCCCTCATCTGGAGAGTCT Y 2 1 2 1 102000 f 74 goat snp40583-scaffold519-3769293 1 81344743 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445408 Affx-122925381 AX-123315745 1 80111844 CCTTTCATCCTTCCTAAAGGTTTTCTTTCCCATTC[A/G]TCACCTTTCTTCCTCTTAAGCCACACATCATTCGT R 2 1 2 1 201000 r 74 goat snp13275-scaffold1510-59490 1 81410879 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384077 Affx-122972859 AX-123254435 1 80148940 AGAGGGAGAAATGTCAGCCAGGTTGGTGGGAAGTG[A/C]TGAGAGATGTAGAAGATAGGGCTGGAAAAAACAGA M 2 1 2 1 101000 r 74 goat snp13276-scaffold1510-96586 1 81448069 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782152 Affx-122968416 AX-385269230 1 80179857 GTTAACTGACTTCTGTGGGTGGGAATATTCTTCCA[C/T]GCGTGGGACTTTCCTACATAAGGCAAAATGTTTAG Y 2 1 2 1 101000 f 74 goat snp13277-scaffold1510-127503 1 81478348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799811 Affx-122965773 AX-385286737 1 80232251 ATTATGAATAACAGTTACAATAAGTATTACAAATA[C/T]AGTTATTTAAATGTGCAGATTTAACGGACATGACA Y 2 1 2 1 101000 r 74 goat snp13278-scaffold1510-179897 1 81530768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399074 Affx-122960888 AX-123269429 1 80280032 CTGGAGATTATTATTTGGGTTGGCTGAGACAGGTC[A/G]TAATAGAGTCAGAGAAAAAAATGTATAAGGAGCTA R 2 1 2 1 101000 f 74 goat snp13279-scaffold1510-227678 1 81579399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376319 Affx-122978355 AX-123246678 1 80323862 CTTGGACAAGGCATATACCTTCAGCCAGGATGAGT[A/G]TCCTTGGAGGAACTCAAGCCCTTGGCTTCTCCCAG R 2 1 2 1 101000 f 74 goat snp13280-scaffold1510-271508 1 81623853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452354 Affx-122920639 AX-123322687 1 80355816 ACTAAGAAAAGGCTTCCAGTTGGCTTCCAGCTAGA[A/C]TCTGAAGGAAAGGAGGGGCATTCCTCATGTATAAA M 2 1 2 1 101000 f 74 goat snp13281-scaffold1510-303462 1 81656425 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436778 Affx-122932266 AX-123307116 1 80390812 CCCACTCCCTTCCAGTGCACGTCTTTTAAATATTC[A/G]TTTTTATTAATTTTTTCTGTTATTCTGTATTTTTG R 2 1 2 1 103000 f 74 goat snp13282-scaffold1510-338458 1 81691562 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278763 Affx-1111836500 AX-519552236 1 80401095 GCTGGACCGTTAACAGTGGTCTCCCAATGTACTCC[A/C]GAGGGTACAATGGCATACCTCCTTACACTCCTGGC M 2 1 2 1 101000 r 74 goat Random2.2K-88 1 80401095 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423446 Affx-122942597 AX-123293792 1 80433539 GCATATATTTAAAGAGTACAACTTGATAAGTTTTT[A/G]CGTATGTGCACAGCCCCTAAACAATCAACACAGTC R 2 1 2 1 101000 r 74 goat snp13283-scaffold1510-381185 1 81734720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388699 Affx-122968990 AX-123259057 1 80498452 CACCATGATAAAGTTTAAAGGAGGGTCTAAGTGGA[A/C]CAGAGTCAGGAATGGACTAGGTAAGGTGGCGCCGG M 2 1 2 1 101000 f 74 goat snp13284-scaffold1510-446098 1 81800692 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278775 Affx-1111836506 AX-519552248 1 80521830 GTTAAGGTAAAACCCAGACTGAGCGACTGATACTT[C/G]AGGATAGATTGTGAGTTGGGAGGTTTTGTGGATGT S 4 1 2 1 101000 r 74 goat Random2.2K-89 1 80521830 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402252 Affx-122959131 AX-123272605 1 80547878 CTAAATCCTTTAACTGATTTATAATTTCTATTTTA[A/C]AGTCTTTGACTGCTAATTCAAATATCTAGGTCATC M 2 1 2 1 103000 r 74 goat snp13285-scaffold1510-495524 1 81850290 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780599 Affx-122948475 AX-385267689 1 80595266 ATCCTAAGTAAACACAGTAAACATCCTGGGGCATC[A/G]TTCCACCAGATTATTTCCCAAGGTTACTAGTCAGG R 2 1 2 1 101000 f 74 goat snp13286-scaffold1510-542912 1 81892350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771621 Affx-122957416 AX-385258779 1 80632615 ATTATTCAAGACCCAGTTTGGGCGTATCTGGGAAC[A/G]CTTGTCTGACTTGCTAACACAGTCCGTCATTCTCT R 2 1 2 1 101000 f 74 goat snp13287-scaffold1510-580261 1 81929681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387089 Affx-122969875 AX-123257447 1 80678366 TTCCCTGTTCCTGTCCTTACAGAAAGAAAAAACTA[C/T]AAAACCTAGACATGATATGAAAAGCTACCTGAAGA Y 2 1 2 1 101000 f 74 goat snp13288-scaffold1510-626012 1 81975635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772423 Affx-122921077 AX-385259575 1 80734048 ATACCATTTGATAATGATTCTGCTTTTCATACATT[A/G]CTGATTTCTATTTACTACTATTTCACAGATTTTTG R 2 1 2 1 101000 f 74 goat snp47745-scaffold672-21949 1 82033847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445469 Affx-122925213 AX-123315806 1 80777028 GTCCCACATTCACCACTGCATTCCTAGTGCCTAGT[A/G]CAATGCCGGACACACAATCAGTACTCATTTACTTA R 2 1 2 1 201000 r 74 goat snp47746-scaffold672-64929 1 82077018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447125 Affx-122924464 AX-123317461 1 80807791 CTAACTAAGGGAGGATGCTTCCAGCCCTTGCCCAG[C/T]GGTATGGCCTGCATCCATTCCAATTGGTGGGCCCC Y 2 1 2 1 101000 r 74 goat snp47747-scaffold672-95692 1 82107763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432920 Affx-122935312 AX-123303261 1 80841003 CTACTTTTGGAAAAGGGGAGGTGGGGGCAGGGATA[C/T]GGCAGCACTCAGGATCTGGAATCTGTAGAGGGAAT Y 2 1 2 1 201000 r 74 goat snp47748-scaffold672-128904 1 82141063 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384126 Affx-122972819 AX-123254484 1 80927720 GACAGAAAGCAGGGAGTAGGGATGGGGATTAACTG[A/G]GATGGTACTGGGGCAAGGCTTCCTTATTGAAGGGT R 2 1 2 1 101000 f 74 goat snp47749-scaffold672-215621 1 82227732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437793 Affx-122931688 AX-123308131 1 80959691 CATCTCCAGGCTGGAGCAAGGCTGGAAGGTCTGGT[A/G]TCTTCTAGACCCTTCTAGCTTAGCTCCCCACAGTG R 2 1 2 1 101000 r 74 goat snp47750-scaffold672-247592 1 82259715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781827 Affx-122937318 AX-385268909 1 80992799 GGCATTTTCCTATCTGTTCTTATATTTTATTCAAA[C/T]GCCATACTAATAAAAATAGTAGCTGACATTTTTGA Y 2 1 2 1 101000 f 74 goat snp47751-scaffold672-280700 1 82292922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783472 Affx-122920967 AX-385270535 1 81054482 AACAATATAAGTGATAGCCACTAAGAGCATTTCAC[A/G]TTAATGCTTCTATTCAAATGTACTCATAGAGTTTG R 2 1 2 1 101000 f 74 goat snp47752-scaffold672-342383 1 82354644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441983 Affx-122928440 AX-123312320 1 81089544 ATTGTTTATTTTAACACCAATTTAAATTCTGATGA[C/T]AGCTGGAACCACTCTTTCATTCTTCTGCATTTATT Y 2 1 2 1 201000 f 74 goat snp47753-scaffold672-377445 1 82389814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386495 Affx-122971138 AX-123256853 1 81124467 CAGACCACAATCACAGGTGCCCTCGAAGAGCAGAG[C/T]GGAGGATGCCACACAGATTGTGCCAGTGGTGTTCT Y 2 1 2 1 201000 f 74 goat snp47754-scaffold672-412368 1 82425110 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418234 Affx-122947040 AX-123288582 1 81181298 TGTCCCCACAGTAGGATCGGGGGCTCAACTAGGCA[C/T]GAGAGACTCCAGAAGATGAGGGAAAAGGCCTGGCC Y 2 1 2 1 201000 r 74 goat snp47755-scaffold672-469199 1 82481926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408273 Affx-122953802 AX-123278624 1 81289909 ATGCTCTTGTGGCTGAGAAAGGGTAGATGATGTAC[A/G]ACTGAGAAACTGCTGGATTTCTTTCTTTTGGCATT R 2 1 2 1 101000 f 74 goat snp47757-scaffold672-577810 1 82590887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409195 Affx-122953179 AX-123279546 1 81330330 GTGGAAGCCACACCAGGAAACAAGACGGTGGCAGA[C/T]GCTTTTCCTTATGAAAGATACCAAACATACATTGA Y 2 1 2 1 201000 r 74 goat snp47758-scaffold672-618231 1 82631410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273593 Affx-1111833689 AX-519547207 1 81368940 CCCCTCAGGGCCATGCCACGACTTTCTAGGGACCC[A/G]GCACTCAGAGGTGCCCTCTAACCTTACCTTCTTCT R 2 1 2 1 201000 r 74 goat GoatD01.001650 1 81368940 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782339 Affx-122919800 AX-385269416 1 81376183 AAATATTTTTAAACATAGTTTAGAAAGAAATATAA[A/G]TAGAAAATCAGACCTGTGGTTCCATATTATTGATT R 2 1 2 1 202000 f 74 goat snp47759-scaffold672-664084 1 82677468 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430717 Affx-122936900 AX-123301058 1 81407438 CTACTTTTGCGTTCCAGTTCCCTATAATGAATGGG[A/G]CATCTTTTTTGAATGGGAAAGGCTAAATAAATAGG R 2 1 2 1 201000 r 74 goat snp47760-scaffold672-695339 1 82709138 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775750 Affx-122927190 AX-385262881 1 81449061 GCTATAACGCTGGACTGACAAGGTAAAGAGTTCTT[A/G]TTTTCTATTGGCAACCTATAGAAAAATATAGCAGT R 2 1 2 1 102000 f 74 goat snp47761-scaffold672-736962 1 82750046 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375765 Affx-122978596 AX-123246124 1 81534263 AGTTTTATATAGTGTAAGCATTCATTTTGTCTTTT[A/G]CCCTCCCCCTTCTCCTCCCCTCTGGGAGTTCCTAA R 2 1 2 1 101000 f 74 goat snp47762-scaffold672-822164 1 82835853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411045 Affx-122951959 AX-123281395 1 81575663 CCACCATCATCCCTCGCTGTCCTCTCTCCTAGGGA[C/T]ACTCAAGAGTTGCAGTTCTCTCCATGGTTTTCAGG Y 2 1 2 1 101000 r 74 goat snp47763-scaffold672-863564 1 82878435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408975 Affx-122953911 AX-123279326 1 81626228 CAAACATAAAATAAAACATAAAAGCAGCAGCAAAC[A/G]CAGACACTGCCCCTTCCTTTTCTTTCTAAAGGCAG R 2 1 2 1 101000 r 74 goat snp47764-scaffold672-914129 1 82928530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396212 Affx-122963356 AX-123266567 1 81660214 GAATTAACTATTGTGTCATAAACCTACTAGTCAAT[A/G]CACTTTTTAACTATTTTAACTACTTTGTCAAAAAG R 2 1 2 1 101000 f 74 goat snp47765-scaffold672-948115 1 82963227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769153 Affx-122971631 AX-385256328 1 81714668 GCTTCTCTTGGGAGTAAAAATCAATGTTTTTACAA[C/T]GATTCACAAAGGCCCTATGTGATTTGGCCCCAACA Y 2 1 2 1 101000 r 74 goat snp47766-scaffold672-1002569 1 83017553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476153 Affx-1251763656 AX-586011585 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 4 1 4 1 20000 f 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 539476409 Affx-1251763656 AX-586011813 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20000 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562165442 Affx-1251763656 AX-606940853 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 f 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562166075 Affx-1251763656 AX-606941484 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562166407 Affx-1251763656 AX-606941815 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 38409237 Affx-122953148 AX-123279588 1 81832461 TAACCAGGAAGAGGTCCTCACCCAAAGCACCATTC[C/T]AATGAGGTCAAACCCTACCGGGCTAGGGAGAAAAT Y 2 1 2 1 101000 f 74 goat snp47768-scaffold672-1120362 1 83136052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795783 Affx-122946411 AX-385282736 1 81861044 AAGGAAAGCCAGAAAATGCTGTAACATATAAATTC[A/G]TTATTTAAAAATAACTAGAAAACCATATTTAACAT R 2 1 2 1 303000 r 74 goat snp47769-scaffold672-1148945 1 83164730 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406690 Affx-122955779 AX-123277042 1 81952013 AGACTGGAGAGGAGGACAGAGATATGATAGTAGAG[C/T]AGGCTTTGTTTGTTGTGTTTATCTATATAACTGTG Y 2 1 2 1 101000 f 74 goat snp47770-scaffold672-1239914 1 83256784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423372 Affx-122943140 AX-123293718 1 81984059 GAAAAAGAACAATACTCAGTAAAATTTTCAAAGTG[A/G]GTAAACACCACTGGAATTTCTTATGTAAAGTCCTA R 2 1 2 1 101000 r 74 goat snp47771-scaffold672-1271960 1 83289135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423964 Affx-122942136 AX-123294310 1 82034205 TGGTTAAAGCAGTGAGTATGTGGTACTTGAGCTGC[G/T]ATCTGCTCCCTCTCAGCTCAGTGTAAAGGAAGCTC K 2 1 2 1 101000 f 74 goat snp47772-scaffold672-1322106 1 83339114 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772491 Affx-122922099 AX-385259642 1 82084311 CCTTAATCTAACCTGATGTTTACTGCTGTAAAACA[A/G]TAACTAGTTCATTTCTTGAGGTTCCCTTGGAAATA R 2 1 2 1 202000 r 74 goat snp47773-scaffold672-1372212 1 83389374 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423832 Affx-122942789 AX-123294178 1 82187091 ATCGATACAGCAATGGAGAGTAAATTAGATGAAGA[C/T]AGGCAGGCTGACCACCTGCCAGCAGTTGTCACAGT Y 2 1 2 1 101000 f 74 goat snp47775-scaffold672-1474992 1 83493210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796674 Affx-122974831 AX-385283620 1 82229911 TTTTTAAAATTCACTTTAAACTCTTGGACTGTGTC[A/G]TATCAGCATGATTCAGTCAGCTTCATTCTTTTTAA R 2 1 2 1 201000 f 74 goat snp47776-scaffold672-1517812 1 83536073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446558 Affx-122924843 AX-123316894 1 82289847 TACCCGGAACTCTCCTGATCATCGTCCTTCCTCTT[C/T]GCATTCCTCCTTGTCCGGAGGAGGATACACTCATA Y 2 1 2 1 101000 f 74 goat snp47777-scaffold672-1577748 1 83597154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780506 Affx-122947373 AX-385267597 1 82353267 TTGTGGTAACTTGCTTCTTCTGCAGTTTTATGGCC[A/G]CATTTTCTACTATAGTTCACTTTATTCTGTAGAGC R 2 1 2 1 101000 f 74 goat snp47779-scaffold672-1641168 1 83658324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453579 Affx-122919761 AX-123323912 1 82387617 GGGGCCTCCCCAGAGGGAGATGCCATCACCTGTGC[C/T]GCAGTCTGCCAGTGGGGCACCAGAAAGCTTATCTG Y 2 1 2 1 303000 f 74 goat snp47780-scaffold672-1675518 1 83692690 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409459 Affx-122954076 AX-123279810 1 82433467 GTTTTTTCATTCTGAGCTCTAATTGAAACCACAGC[A/G]TGGGAACTGGTTGGCTCTTCTCTTATATACATTAT R 2 1 2 1 101000 f 74 goat snp47781-scaffold672-1721368 1 83738821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420988 Affx-122944567 AX-123291335 1 82465962 CTCTGCAGCAGCACAAAGGAAGGCTAACCCTTTCA[A/G]GATTTTTCTCATTTATCCTTTCTCATTTTTTTCAA R 2 1 2 1 101000 f 74 goat snp47782-scaffold672-1753863 1 83771283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271741 Affx-1111832872 AX-519545535 1 82502089 CCTCCTAGGAACCCAGGTAAGTCCCCAGTCAAGGG[A/G]GTTAGAGAATATTTCTTTTCTGACTCAGTCCCCTT R 2 1 2 1 101000 r 74 goat 1_82502089_AF-PAKI 1 82502089 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407444 Affx-122954793 AX-123277795 1 82510938 AGCCTCATTACACAGATAAAAAGGTGTAGGAGAGC[A/G]GAAATACAGCCATTTTTATGTTTATAAATATCCCA R 2 1 2 1 101000 f 74 goat snp47783-scaffold672-1798839 1 83816268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783241 Affx-122948745 AX-385270306 1 82550727 TAAATGAAATCAAGAATGTTCAGGAAAATTTACAA[A/G]CTAGATTCACTGTATATATAAGTAGCAAGGCAAGG R 2 1 2 1 101000 r 74 goat snp47784-scaffold672-1838628 1 83856230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440009 Affx-122929782 AX-123310346 1 82585211 TCTTTAGGTTTCCTCAGAAACAAAGGCGACAGTAC[A/G]CCTCGGTAAGCATGGGATATGAAATGTGAAAAAGA R 2 1 2 1 101000 f 74 goat snp47785-scaffold672-1873112 1 83890709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398080 Affx-122961728 AX-123268435 1 82615869 GGAGGAATAGACAAGATACGCTGTTTTGCAGTGCT[A/G]AATTGAACAGGTTAGAGGGGAAACACTTTCTGTGG R 2 1 2 1 101000 f 74 goat snp47786-scaffold672-1903770 1 83921759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792282 Affx-122956729 AX-385279264 1 82655484 AACCAAAATCTAAGGAAAAGTCTGAGTTTCATGGT[A/C]TATTCTTTAGGGCCACTTTTGAATGCATTAACTAT M 2 1 2 1 101000 f 74 goat snp47787-scaffold672-1943385 1 83961402 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424044 Affx-122942074 AX-123294390 1 82717260 CACAACAACACAATACATAGTAGCTATTCATGAAC[A/G]TTTCTTCAAAAAAAAATTGAAATTCTTAAACTTCA R 2 1 2 1 103000 f 74 goat snp47788-scaffold672-2005161 1 84023147 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419843 Affx-122945810 AX-123290191 1 82747321 CACAGTTTTAACTCTACATTTATATATGTGAGTCT[A/G]TGATTAGTGCCTTCTCTCCCAGACTATATGTTTCC R 2 1 2 1 101000 r 74 goat snp47789-scaffold672-2035222 1 84053515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775872 Affx-122973088 AX-385263003 1 82788521 GTGCTCTTAAAGGTCCGTTTCCCTATCTTCAATGA[C/T]AGTTAATGAGGGCACAGACCACTAATAAGCAGTTT Y 2 1 2 1 101000 f 74 goat snp47790-scaffold672-2076422 1 84094923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445237 Affx-122925493 AX-123315574 1 82850318 AAAGTGTTGAGTACAGTTCCTGGCATATGTAATCC[A/G]CTGTTAATTCTAATACTCAGCACCATGCCTAGTTC R 2 1 2 1 101000 r 74 goat snp32733-scaffold377-2162683 1 84159545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394922 Affx-122964311 AX-123265277 1 82894811 AAGGAGACAGAGCCAGAAGTTGCTCTACCAACTGC[A/G]CTCGGATCACCAAGTGCTGTTTCTGCAGAACTTAG R 2 1 2 1 101000 f 74 goat snp32732-scaffold377-2118190 1 84204295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419598 Affx-122945997 AX-123289946 1 82933056 ATCCATAATGGGTTACGGGCCATCTGAGCCCTCAG[C/T]GACACAATGGGCTGGTATTTCCTGAAGTGGAGAAC Y 2 1 2 1 201000 r 74 goat snp32731-scaffold377-2079945 1 84243041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777744 Affx-122929536 AX-385264862 1 82963120 GTTTCCATAAACCAGAGGAGAGAAAAGTGCTTGGA[A/G]CCATCATTATAAACATGACACATCTGTTTTTAATA R 2 1 2 1 101000 f 74 goat snp32730-scaffold377-2049881 1 84272976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378989 Affx-122976392 AX-123249348 1 83010594 TTCAAAATGCTGAATTTCTTTAGAATGACACATTT[A/G]TTGAGAAGAAAAGTGCTAAGAAGAACGAAAAAAAA R 2 1 2 1 101000 r 74 goat snp32729-scaffold377-2002407 1 84320980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275432 Affx-1111834798 AX-519549005 1 83012073 GATTCATTTATATATTGTCC[A/G]TGTGTGCACTGCAGCCTCAGAGTTTGGTCATTCCA R 2 1 2 1 102000 r 74 goat GoatD01.053406 1 83012073 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444753 Affx-122926370 AX-123315090 1 83047000 TGAGTTTAGCATTATGCTGGAAATGATTTTGATGC[A/G]TATAACACAGCTATAAAAAGAACAATAGGAAGAGA R 2 1 2 1 101000 f 74 goat snp32728-scaffold377-1966001 1 84357740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770574 Affx-122941269 AX-385257738 1 83078742 ATCTGGTTTCATCATTCTGAAAATTCCTCATTGAA[A/G]CCATCCCTGTGGAATAGGAATCTATTCCAAGAATG R 2 1 2 1 101000 r 74 goat snp32727-scaffold377-1934259 1 84389437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450122 Affx-122922766 AX-123320457 1 83139374 GGGGGATGAAGAGGATACTATGTCACCCAGAGGAT[A/G]CGTCCACCCACCTTGTTGTCTATAATGTAAAGCCT R 2 1 2 1 101000 f 74 goat snp32726-scaffold377-1873627 1 84444836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429523 Affx-122937844 AX-123299865 1 83168412 GGGGAACTTAGGGAGCAAGACTATATCAAGTCAGA[C/T]GCTTTTTTGCTGAAGCACAAGTGGTAAGAATGGGA Y 2 1 2 1 101000 f 74 goat snp32725-scaffold377-1844589 1 84474198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428911 Affx-122938917 AX-123299253 1 83229154 GCCTTATCTTGCCCATAATTATACAGAAGTCAGAT[A/G]CAGGTTTATGCTAAAAGCATGTACTGTTATCTTTC R 2 1 2 1 101000 f 74 goat snp32724-scaffold377-1783847 1 84535011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775004 Affx-122966516 AX-385262136 1 83267332 AAAAGCACTGTTGCCTTACATCTACAGACCATTCC[A/G]TGTCTTATAAAGGAAAAAGGCAATCCAGTACAGAT R 2 1 2 1 101000 f 74 goat snp32723-scaffold377-1745669 1 84573896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442454 Affx-122927953 AX-123312791 1 83306160 GGAGAACTCACTAGGTACCAAGCACCATTAGAGAA[C/T]ATATGTTATTTTGATTTTTACAACAATTCTGTATG Y 2 1 2 1 101000 f 74 goat snp32722-scaffold377-1706841 1 84612681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778315 Affx-122938412 AX-385265430 1 83373524 TTTGTATCTGAAGAAGGCTTGTGGCCTACATGCCC[A/G]CTTAAGATATAGTGAAAATAACTTGGAGGATAGTT R 2 1 2 1 101000 f 74 goat snp32721-scaffold377-1639477 1 84680880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453718 Affx-122919631 AX-123324051 1 83406572 CAACCTCAGTATTTCCATTTATAAACAGAGAATAA[C/T]AATACCTTCCTTATAGATTTACTCTAAGGATTAAA Y 2 1 2 1 102000 f 74 goat snp32720-scaffold377-1606429 1 84714032 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452992 Affx-122920117 AX-123323325 1 83436546 CCAAAGTTGGACAGACTTTCCAAGTCATAGTACAC[G/T]CAGTATGATCCCTATCATAACCTTCACAGAAATAT K 2 1 2 1 101000 f 74 goat snp32719-scaffold377-1576455 1 84744046 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788205 Affx-122926048 AX-385275224 1 83466558 AGCTAGTAACTGGACTAAAGTTCTCCTGCTCTTGC[A/G]AAATGGCGTTTAGGCTGCTATGTTATTGTGATCCA R 2 1 2 1 101000 f 74 goat snp32718-scaffold377-1546443 1 84774026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407921 Affx-122954378 AX-123278272 1 83498599 GAATTGTGCTTCTTCCATTTCATCCTTGTGGTTAA[G/T]GAATCCTACAGTGGACACCTGGTCTTGCACCTGGG K 2 1 2 1 201000 f 74 goat snp32717-scaffold377-1514402 1 84806521 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437167 Affx-122932131 AX-123307505 1 83540100 CCCCAGTATAGGGAATTATTAAATAAATTATAATA[C/T]GTCCATATGATGGGATAGTACATAGCTATTAAAAA Y 2 1 2 1 103000 r 74 goat snp32716-scaffold377-1472901 1 84848216 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451836 Affx-122921464 AX-123322169 1 83575251 ATGCAGAGAAGTTGAGCTCCTTGTCTTCAGTGAGC[A/G]GCAAAGTGAGGACTGTAAGCTTGTCAGATCCCAGG R 2 1 2 1 101000 r 74 goat snp32715-scaffold377-1437750 1 84883332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408181 Affx-122954199 AX-123278532 1 83642225 TCTTAGAATTTCACACATTGCTTTGCCACATGGCT[A/C]GTGGAATCTTACTTCCTGGATCAGGGATTGAACTC M 2 1 2 1 101000 f 74 goat snp32714-scaffold377-1370776 1 84951808 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792147 Affx-122940854 AX-385279132 1 83723561 TTTGATTCATGTGCTAAATCAAACGTATTTAAGAA[G/T]ATGATTTCCTACTCCTGTTCCTTTTCAATATTTTC K 2 1 2 1 201000 f 74 goat snp32713-scaffold377-1289440 1 85033007 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383315 Affx-122972697 AX-123253673 1 83762267 AGAGACAAAGACAGAAAGTGAACACAAGCTGAGCA[C/T]GAAGGGCCCACTTCATCCTGAGGAGGAGGAGAGCC Y 2 1 2 1 101000 f 74 goat snp32712-scaffold377-1250734 1 85071523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392441 Affx-122966176 AX-123262798 1 83790824 TAGGTGGGCGGAGATTTCTAATAAGTACCTTTACC[A/G]TGTGATACACTAGATACACTAAAGCCAATCCTGAG R 2 1 2 1 101000 r 74 goat snp32711-scaffold377-1222177 1 85100080 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785066 Affx-122938576 AX-385272113 1 83833574 ATGATGGTCAAAATAATCTTTCAAAAGTCAGGGGA[C/T]AACCTTATCTCAAGAGAAAAATACTGTCCAGTGAC Y 2 1 2 1 101000 f 74 goat snp32710-scaffold377-1179427 1 85143025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402687 Affx-122958353 AX-123273040 1 83897021 TCAGTGAGTGCTCTTGTGTACCCACTGGGGCTCAC[A/G]CCCAGTGAATTTCAGACATCCTTCCCCCTGATGTG R 2 1 2 1 101000 r 74 goat snp32709-scaffold377-1115980 1 85206665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424495 Affx-122941749 AX-123294841 1 84000468 AGTTTCCCTTGCATATCTGTCCTTAGTCCGAGCCT[A/G]GTCCCTATACTAATACTGAAGAAATGTAATGAGAG R 2 1 2 1 201000 r 74 goat snp32707-scaffold377-1012533 1 85310982 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773836 Affx-122967371 AX-385260976 1 84044508 GAACTAGTTTAGGGCCAGAAATTGTTCATTCTTGA[C/T]GGCTTCATTCTTATCTGCTTTTCCCCTATTTATTT Y 2 1 2 1 101000 f 74 goat snp32706-scaffold377-968493 1 85355276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428231 Affx-122939432 AX-123298574 1 84073683 CCAGAAGAGTGTGGAAGTGAGGTGAACATGCTCAG[C/T]AGAGGAACTAGAAGGAACATGGGTGAAGAAGGCAA Y 2 1 2 1 101000 r 74 goat snp32705-scaffold377-939318 1 85384075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791438 Affx-122969251 AX-385278429 1 84116774 ATTATAGGTCAGGCTTGAACAAATAAAACATGATT[A/G]CTGGCTTCATGATACTTCCTAACTAGTGTATGGGA R 2 1 2 1 101000 r 74 goat snp32704-scaffold377-896227 1 85427816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441555 Affx-122928694 AX-123311892 1 84176499 TCTGTTCTAAAAATCTAGATTTTTTTTGTTTACAA[C/T]GGAACCAAACCAAAGTCAATACAGTGCAAAAATAA Y 2 1 2 1 103000 r 74 goat snp32703-scaffold377-836502 1 85488116 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428675 Affx-122938642 AX-123299017 1 84278687 TTGGACATTGTAGCTTAAGTCAAATCTGCTTGAGA[G/T]CCAAATGAGAATAGGAATTTGACTAAAAAGAAGAG K 2 1 2 1 101000 f 74 goat snp32701-scaffold377-734314 1 85591981 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796317 Affx-122959375 AX-385283267 1 84309368 AATGGTAATCTCAGTCGCTATGGTGTTTGAACCTG[C/T]AGGCTCTGAAAGGATTTACTCTTTTTTCACAAAGA Y 2 1 2 1 101000 f 74 goat snp32700-scaffold377-703633 1 85620551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402604 Affx-122958418 AX-123272957 1 84365886 GAGCGCTCTCTGTTGCAGGAGAGCAAATGGAACAA[C/T]GGAGGCCAGGTTTTCCAGGCATCATCAGTCTGTTC Y 2 1 2 1 101000 f 74 goat snp32699-scaffold377-647115 1 85677444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770612 Affx-122978188 AX-385257776 1 84410677 GAAAGAAGACCATTCTCAAGTGGATTTAAATTAAG[C/T]TCCACTTCTTGAAGGAGGGAATGTCCACATATATT Y 2 1 2 1 101000 r 74 goat snp32698-scaffold377-602324 1 85722569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401072 Affx-122959639 AX-123271425 1 84448640 GTAGTGAGTTCAAACCACTGAGACACTGCTTAGGA[C/T]AAGGCTGAGGGAGATTGCTTAAGTAAATACTCTTT Y 2 1 2 1 101000 f 74 goat snp32697-scaffold377-564361 1 85761063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787058 Affx-122954851 AX-180660639 1 84482457 CTTAAATTGAATTCACTGAAGCTTTGTGGTAAATA[C/T]GCTTTTTTTCCGCTCATAGCTTTTCTCTAACCATG Y 2 1 2 1 101000 r 74 goat snp32696-scaffold377-530544 1 85794880 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434136 Affx-122934916 AX-123304477 1 84639344 CACAGAGCTGCTGTGAAGCTACAAAAGTAAAAGCC[A/G]CCATTCATCAAACTCTGAATCTGGGCCAGATTTCG R 2 1 2 1 101000 f 74 goat snp32693-scaffold377-373657 1 85954509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398508 Affx-122961554 AX-123268863 1 84676181 ACACAGTTCATGATAGCCTCATCTTTTGGAGTCTA[C/T]TTAATTCTCCAGCCTTATGTCTTCTAGCCTCCTTG Y 2 1 2 1 101000 r 74 goat snp32692-scaffold377-336820 1 85991395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429097 Affx-122938265 AX-123299439 1 84726553 GGAGACATAAACCATTTTCTTGATAAAATGATTAC[G/T]CACAGAAATTTAAAATACAGAAACAACATTTTCAT K 2 1 2 1 101000 f 74 goat snp32691-scaffold377-286448 1 86043145 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788921 Affx-122936218 AX-385275936 1 84770244 TGTAGACATTATGGAAATCAATTGCTTTTTATAGC[A/G]GTTCTCAAAGTATATTTGTTTCAGTTATAGGTCCT R 2 1 2 1 101000 r 74 goat snp32690-scaffold377-242757 1 86086606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389884 Affx-122968134 AX-123260241 1 84799541 AACATTGTTAATTTTCTTAGGAAACCCTTTTTACA[C/T]AGATGGACAAAAAAATTTTAAGCAAATTATCAGAG Y 2 1 2 1 201000 f 74 goat snp32689-scaffold377-213460 1 86116181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440389 Affx-122929628 AX-123310726 1 84837074 AAAAGCGGGGAGACAGACAGAGAAGCGGGTGATGC[A/G]AGAGGAAGGAGTTGGAACTGAATAATCTGAAAGAT R 2 1 2 1 101000 r 74 goat snp32688-scaffold377-175927 1 86153178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379525 Affx-122976072 AX-123249883 1 84870962 TTTTAAATTTAATTTTAAGGAACTGGCTTGCATGA[C/T]CATCAAGAACAGTCAGTCAGAAATCTGTAAAGCAG Y 2 1 2 1 101000 r 74 goat snp32687-scaffold377-142039 1 86187098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400138 Affx-122960706 AX-123270493 1 84906630 CAATAGCAAGAATTTTAAGGAGGCTGCTGAGATAA[C/T]GCAGGCAAGCAATGAGAACCAGAATCAAGGTGCTA Y 2 1 2 1 201000 f 74 goat snp32686-scaffold377-106371 1 86223391 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775156 Affx-122968974 AX-385262288 1 84988811 CCTCATTCTAATACATTATCCATACTCCTCCAAGG[A/C]TGATTTTTCTAAAACCCTAATCTGATTCTATATAA M 2 1 2 1 101000 f 74 goat snp32685-scaffold377-24190 1 86308506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430620 Affx-122936969 AX-123300961 1 85073309 ATGCTATTGACAACTTTTCCCTCTTATTATTTATT[A/G]TTGTTTTGTACCTGGCTTTTATTCCTCCTTCAATG R 2 1 2 1 101000 r 74 goat snp48461-scaffold689-60209 1 86399897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444239 Affx-122927226 AX-123314576 1 85112692 AGAATGATGATGCCAAACTGAAAAGCACATACCCC[A/G]TCTAAAGGGGTGGACATTACTCAGGTCCAACCAAG R 2 1 2 1 102000 f 74 goat snp48462-scaffold689-99592 1 86439698 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774714 Affx-122979203 AX-385261848 1 85168222 GACAATAAAGATACAATGTCAGAGATAAGCACAAT[A/G]TCCAGTGATATGGATAGTTCAGTAAATTATGTATT R 2 1 2 1 201000 r 74 goat snp48463-scaffold689-155122 1 86495591 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770924 Affx-122921706 AX-385258087 1 85201142 GAGATTCTGCACTTTGAGAGTTTAAAATTGTCAGA[C/T]GAAATCATCAATTGAATACAAAACTACAATGTAAC Y 2 1 2 1 101000 f 74 goat snp48464-scaffold689-188042 1 86529269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767250 Affx-122927168 AX-385254531 1 85257032 CAAGCATGAATTTGTTGTGTAACACTTCAGTTCAT[A/G]CATCTGTTAATTTACTACATATAATGTGCAAATAT R 2 1 2 1 101000 f 74 goat snp48465-scaffold689-243932 1 86584934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449173 Affx-122923534 AX-123319508 1 85287025 GGAGATCTGAGAGAACAAAAGATACTCTTTAACCA[C/T]GGCCCAGGCAAGGAGGCATTCACATCTGCCACCCA Y 2 1 2 1 101000 f 74 goat snp48466-scaffold689-273925 1 86615554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405371 Affx-122956310 AX-123275723 1 85396740 TTTGCATTTCCACATAACAGAACTCTTGCCTTCTG[C/T]ACACTGACTATTTCCTCATCCTTTATATTCCACCC Y 2 1 2 1 101000 r 74 goat snp48468-scaffold689-383640 1 86726067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792939 Affx-122965267 AX-385279917 1 85453955 GGAAAAAGAAGATTCAGACATATTATCTCTCTCCC[A/G]TAACACAACAGTAAAACTGTTGGCATGATCTGTGT R 2 1 2 1 101000 r 74 goat snp48469-scaffold689-440855 1 86783809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790003 Affx-122927194 AX-385277009 1 85507180 GTGCCTGGCAATGTTTGCTTACTGGCTGACTTATT[A/G]CTCTCTACTCCATAATCTTGCACACAACAAATCAC R 2 1 2 1 101000 r 74 goat snp48470-scaffold689-494080 1 86836696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423689 Affx-122942899 AX-123294035 1 85536648 TGATATCCTACTAGATGGGTTCATTACACTAAGTA[C/T]GGAGAATTAAAAGGGCAAGTTCTACCAAGAAATAT Y 2 1 2 1 101000 f 74 goat snp48471-scaffold689-523548 1 86866171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447955 Affx-122923774 AX-123318291 1 85568683 AAGGCTGTAAATTACTTCAAGTAGTTATCCACAAA[C/T]ATTAGTGGCTGTCTATACATGTTGGCTGCTGAACT Y 2 1 2 1 101000 r 74 goat snp48472-scaffold689-555583 1 86897921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434329 Affx-122934738 AX-123304670 1 85635619 CCTAACCTTAACCTGGATAACTGGTGGCCATTCCG[C/T]GGACTTCTAGCATATCAGATATACATTACCAAGAT Y 2 1 2 1 101000 r 74 goat snp48473-scaffold689-622519 1 86964109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416962 Affx-122948015 AX-123287310 1 85672458 GGCTCCCCATTTTACTCTAGAGCCACACCCTTCCA[A/G]TGCCTCTTCGGCTAAGGCAATCTGGCTCCTACTCT R 2 1 2 1 101000 f 74 goat snp48474-scaffold689-659358 1 87001193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771050 Affx-122961530 AX-385258210 1 85703281 ATGGCATCTGTCTTACTGCGGCTCTTTCCAAAGCC[A/G]CACTAACTGCAATGCTACCTTCTCCACCAACTGTA R 2 1 2 1 101000 r 74 goat snp48475-scaffold689-690181 1 87032144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790210 Affx-122931915 AX-385277214 1 85750268 GAGTTTCTCACTGAACAGGTATATCCTTGTTGGGG[A/C]GAAGGAAACCAGGATGATTGGATCATACCACCATT M 2 1 2 1 101000 f 74 goat snp48476-scaffold689-737168 1 87078969 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422858 Affx-122943091 AX-123293204 1 85779983 CCTTCCTTCCAAAGACCATCACCTCTGTGCCTGCA[G/T]CAGTCACCACTAGAAATCTACAAGGCTTAAGAAAC K 2 1 2 1 201000 r 74 goat snp48477-scaffold689-766883 1 87106738 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432613 Affx-122935496 AX-123302954 1 85808941 GAAATGAGTTGTCACGCTGTCCCACTTCACACCCA[C/T]GAAGGAGAAGAACAGTAAAAGTGGTCACACCACAC Y 2 1 2 1 201000 r 74 goat snp48478-scaffold689-795841 1 87135732 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781578 Affx-122978651 AX-385268662 1 85846879 TAAACTCTATGTGGGGTTTTAGGGACAACTGTTTA[C/T]GAATGCAAGCATTAACAAATACAGAAACTGTAACA Y 2 1 2 1 101000 f 74 goat snp48479-scaffold689-833779 1 87173544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770974 Affx-122971499 AX-385258137 1 85899646 GCTTTAAGATATACTCCTCTACATGAACAAAGGGA[C/T]GTTTATTCTGAAAATCTAAATCATACATGAATATG Y 2 1 2 1 101000 f 74 goat snp48480-scaffold689-886546 1 87225330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804371 Affx-986696538 AX-385290973 1 85904559 TCATTTCTTAAGGATAATATTTTAGCATCTATTAA[C/T]TTCAGCATCTATTAATATTTTAGCATCTTTCTAGG Y 2 1 2 1 600010 r 74 goat 1_85904559 1 85904559 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320792455 Affx-122952932 AX-385279436 1 85981002 TGTACGGCACAGTACTGAGTGATGGCATCACTGCT[A/G]TTTGCCAATCCTGTTAAGATCCAGCACTCCCATTT R 2 1 2 1 101000 f 74 goat snp48482-scaffold689-967902 1 87307131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453187 Affx-122920458 AX-123323520 1 86020950 GATGTTGCTGCCACCACCAGAATAGATTCTCCAGC[A/G]TCTCTTTATCTCACTTGTTCCAGATCCTGAGCAGG R 2 1 2 1 101000 f 74 goat snp48483-scaffold689-1007850 1 87347598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799899 Affx-122936221 AX-385286825 1 86050656 GTAGATGAGTTTGATGGTTTCACAGAGTTATGACC[A/G]AAACATTCCAGTGTTAGTGGTTAAAGGAATAGAGT R 2 1 2 1 101000 f 74 goat snp48484-scaffold689-1037556 1 87376742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444476 Affx-122926532 AX-123314813 1 86148154 TATAATAGCTAGTTATGGCAAACCTGGTTAGAAGC[A/C]GATTTCTTCATTCCAAATCTGATTCTGAATCCTGG M 2 1 2 1 101000 f 74 goat snp48486-scaffold689-1135054 1 87473937 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421948 Affx-122943820 AX-123292295 1 86204394 TGATGTTTACACCTTTTATAAATGATGTCTCTTGA[A/C]TAGGGTTAGCAAGTACTGTGTATACAAATATAAAT M 2 1 2 1 101000 r 74 goat snp48487-scaffold689-1191294 1 87530249 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802527 Affx-122970344 AX-385289431 1 86257263 TACACTCCAAAACTAGCATAACTGTCCATCTGTCT[A/G]TTTCTGCTCTTCTCCATATCTGCTGTGTGGTGACA R 2 1 2 1 101000 f 74 goat snp48488-scaffold689-1244163 1 87582608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435825 Affx-122932830 AX-123306164 1 86288098 GTTAATATTTATTCATTTTCTCTTTATTTCCCCCA[C/T]GATGCTATGACTGTTACCATGTGTTATCACTTCTT Y 2 1 2 1 101000 r 74 goat snp48489-scaffold689-1274998 1 87613463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799377 Affx-122921480 AX-385286307 1 86317307 AGAAAAAGCTAAAGGTCAATAGAATCATTGTGGAC[A/C]CCATGCCTTGTCTACTGTTTGTCATTTTGAGTATG M 2 1 2 1 101000 r 74 goat snp48490-scaffold689-1304207 1 87642468 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416003 Affx-122948390 AX-123286352 1 86349215 CTTTTACTTTATTTTATTAACTTTTAAATGTGAAT[A/G]CTTTTATTGTATAAAACGCTTAAAAATTTCTGCAT R 2 1 2 1 101000 r 74 goat snp48491-scaffold689-1336115 1 87670327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431691 Affx-122936779 AX-123302032 1 86395836 GTTTAATGTGTCAAGAATATAATAGCATAGTTTCT[A/C]TAGTTTGGGTCTCAGGCCACCTGCATCAGGAAGGG M 2 1 2 1 201000 f 74 goat snp48492-scaffold689-1382736 1 87716802 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794864 Affx-122960122 AX-385281824 1 86425495 CCCAAGTTAGAAAGTTGGGAAGAGTCATGACTACT[C/T]TCTTCAATGTCTTCATCCAGTCAGTCACCAAGTAT Y 2 1 2 1 201000 r 74 goat snp48493-scaffold689-1412395 1 87747146 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463660402 Affx-1110097185 AX-515141214 1 86442752 CTCTCCCTCACTGCAGTCTACTCAGTCCTGGTGCC[A/G]CAGCATGGGCACCCATGTCCCAGATGCTAGCATTG R 2 1 2 1 202000 f 74 goat GoatD01.051133 1 86442752 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435628 Affx-122933774 AX-123305968 1 86486082 GATGGCAGCAGGACAGTCTGTTTGTTTGCTCACCA[C/T]GGGAAGGAGCTAAGTGTCAGGGCTTGCAGCTGCCT Y 2 1 2 1 101000 f 74 goat snp48494-scaffold689-1472982 1 87807773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802520 Affx-122946465 AX-385289424 1 86516757 GCTAGTAATCTCTAGTTACTGGGCATGTGGCCCCT[A/G]CTCAATTCCTATTGGTCTTCCTAGACCGACATGAA R 2 1 2 1 101000 f 74 goat snp48495-scaffold689-1503657 1 87838642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777244 Affx-122932992 AX-385264367 1 86545447 TTTAAGCTGCAGGTAAAAGGCAAATGGATCTAATT[A/G]TAAGAGAAAGTTTTACAATTCAAAATGCACTAAGC R 2 1 2 1 101000 f 74 goat snp48496-scaffold689-1532347 1 87867105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782897 Affx-122942784 AX-385269967 1 86597150 TTCAAGGCATTCACAGTCTGTTACAAGAGGACAAG[C/T]AAGCAGGTACTATCAATACTGCATGATAGGTGCAT Y 2 1 2 1 101000 f 74 goat snp48497-scaffold689-1584050 1 87918800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417844 Affx-122946785 AX-123288192 1 86627540 AAAAGTGGCGGTACTTGCCAGATTATGGGGACATT[A/G]TTGATAAACTTCACACTGAGGAAATGAAAGACTAG R 2 1 2 1 201000 r 74 goat snp48498-scaffold689-1614440 1 87949422 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379828 Affx-122975821 AX-123250186 1 86661189 GTCACTGACTGGCATTACTACTTGTGCATTGCAGG[C/T]GTGAACTCAGTCAGCCAAGATCCACATGTTGGTTG Y 2 1 2 1 201000 r 74 goat snp48499-scaffold689-1648089 1 87983013 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414858 Affx-122949151 AX-123285207 1 86717835 TTCTCCACTTCTGATAGGAACCTTCTCTATTGATG[C/T]GTAACTTTTAGGCAAAGGCCAAATTTACCGGAGCT Y 2 1 2 1 201000 f 74 goat snp48500-scaffold689-1704735 1 88039569 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407222 Affx-122955381 AX-123277573 1 86754857 ACATGTCCTTGGCATGCTTTTTAAGTCATACATCA[A/G]CCATTCCTCTATATAGCCTCTGAAGTTGAACTTAA R 2 1 2 1 101000 f 74 goat snp48501-scaffold689-1741757 1 88076628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388008 Affx-122969570 AX-123258366 1 86784620 GGCTTCACTATTAAAAACATAGTTCCTTCCATGCC[A/G]CACTCTGTTTCTGAGGTGCATGACTGAGTTATCCA R 2 1 2 1 101000 f 74 goat snp48502-scaffold689-1771520 1 88106525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380492 Affx-122975709 AX-123250850 1 86815677 GTGCACACAGAGCAGACACTTATTTCAGATCCATT[C/T]TGAGTACAAATAGACTGTTGCCCTCCTAATTGAGT Y 2 1 2 1 101000 r 74 goat snp48503-scaffold689-1802577 1 88137621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420178 Affx-122945568 AX-123290526 1 86852312 GTGGCATATTAGTACCATGGGATACAATACAGCAA[C/T]GTAAATGAATAAACTGCAGTTCTGCCACAACATGT Y 2 1 2 1 101000 f 74 goat snp48504-scaffold689-1839212 1 88173828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781771 Affx-122941743 AX-385268853 1 86943152 GGTTAAAGTGTTAAGGAAAGTACCAAAACATGGGC[A/G]TCCTAATATCCCTGCTCTCATGAGTTTATTTAGCA R 2 1 2 1 101000 f 74 goat snp48506-scaffold689-1930052 1 88263467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765261 Affx-122974742 AX-385252796 1 86994434 AATATTGAACTAATAGTGTAATTTTGAAAATTAGA[C/T]GAGTGAAATCACTTGAGAATGAATGATAAGCCCTA Y 2 1 2 1 201000 f 74 goat snp48507-scaffold689-1981334 1 88314924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412564 Affx-122951320 AX-123282913 1 87035856 TAAGATAGATAGCTGTGTCAAGGAGACATTAAGAG[G/T]GTTGCAGGGTAGAGATATAGAGTAGCAGAAGCGCT K 2 1 2 1 101000 r 74 goat snp48508-scaffold689-2022756 1 88356720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452286 Affx-122920693 AX-123322619 1 87102509 ATTGTTGGCTCCGTACTTATAGAAATTTTTCCAGA[C/T]GGTGTGGAAGGGCTTTAACATATCCATAGTTTAGA Y 2 1 2 1 101000 f 74 goat snp48510-scaffold689-2089409 1 88424002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400255 Affx-122960138 AX-123270610 1 87146410 CTGGCTGGAGTGAATTATGAAGGCACAAAATTAGG[A/C]GGCAAGAGAGGTAGACAGGCTCCAAGGCTGTGAGA M 2 1 2 1 101000 f 74 goat snp48511-scaffold689-2133310 1 88467909 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427189 Affx-122939603 AX-123297532 1 87178401 AAAACAATTTCTAGAGCATAAACTTCCATAGTCAC[A/G]GTTTCTTAAAATCAGTTTGCTTGACAGCTTACATC R 2 1 2 1 101000 r 74 goat snp48512-scaffold689-2165301 1 88499826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452223 Affx-122920799 AX-123322556 1 87232472 ATGCCAGTACCAGCTCAAATATTGAAAGGGGTTTT[A/G]CATGATTTGACCTTGATGGTGTAGCTGAGACTTGT R 2 1 2 1 101000 r 74 goat snp48513-scaffold689-2219372 1 88555090 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786239 Affx-122947334 AX-385273274 1 87285145 ATTATTTAACTACTTTTCAGAGTTTGACTCAATGT[A/G]CATATATGAGAATGCTTTACCAGGGAATCCTCAAA R 2 1 2 1 202000 r 74 goat snp48514-scaffold689-2272045 1 88607732 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451769 Affx-122921513 AX-123322102 1 87325829 TTAGAAGGGAAACTATTTGAATAAATACCAAACAG[C/T]AAATAGTTTTAAATAAAAATAAGCAATGCTAATTC Y 2 1 2 1 103000 f 74 goat snp48515-scaffold689-2312729 1 88648508 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419381 Affx-122945619 AX-123289729 1 87384307 ACACAGTGGATGCTCAGTACTTCTTTCAACTGAGT[C/T]AACAGTCCTGAGACTTGACAAGGGAGATCCAATGA Y 2 1 2 1 101000 r 74 goat snp48516-scaffold689-2371207 1 88714498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769192 Affx-122933217 AX-385256367 1 87420712 CTTTGTGAGTTGGTAGTGGTGATGTTGAAACCTCA[C/T]GAGGTTTGACCACCAGGTTTATTTGGAATTTTTCC Y 2 1 2 1 101000 r 74 goat snp48517-scaffold689-2407612 1 88751395 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399132 Affx-122960664 AX-123269487 1 87459390 TTACTCTTTCTAAATTTAGCTATTGGCAAACAGTT[A/G]CTCTTACATCTAATTAAATTTGGTAAGACTTTCCA R 2 1 2 1 101000 f 74 goat snp48518-scaffold689-2446290 1 88790472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798629 Affx-122933339 AX-385285561 1 87552429 AAAATGCTGTATAGCACAGTAGCATTTTATACATA[C/T]AAAAGAGGTAAACTTTTATTCTTGTAATATTCCAG Y 2 1 2 1 202000 r 74 goat snp48520-scaffold689-2539329 1 88884470 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773590 Affx-122958086 AX-385260730 1 87590720 TTTTGTAAGAACAATTTAACCTCGAGCTCTATACC[A/G]TATAAGACTTTCTTGTTCTTCAATCAAAGGTGGCA R 2 1 2 1 101000 r 74 goat snp48521-scaffold689-2577620 1 88922721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444363 Affx-122926707 AX-123314700 1 87632932 AACTTCATGGACTGTTTGCTAGTTTGCTTAGCTAT[C/T]GGTTACTCTCTCCAAATGTACTGGCAGACAAAAAC Y 2 1 2 1 101000 f 74 goat snp48522-scaffold689-2619832 1 88965345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400957 Affx-122960116 AX-123271310 1 87677945 ATACAGTGTGGAAGTGTGGATGAGCAGGCTTAGGC[A/G]GGCTGACGAATGATTCCAAGGGCTTTAGAGACTCT R 2 1 2 1 101000 r 74 goat snp48523-scaffold689-2664845 1 89010341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770478 Affx-122956146 AX-385257644 1 87758748 GCACAGAGATGATCCTTATCAGTGGAGGACTGTGA[G/T]ATGAGATGACAACACCCTATGGGTTCAGACAAACT K 2 1 2 1 101000 r 74 goat snp48525-scaffold689-2745648 1 89092240 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434574 Affx-122934118 AX-123304915 1 87802980 AGTTGTCCAGAGCTCTGAAATTGTCCTCAGTATTG[C/T]TCATGCACAGACAATGGATGTACTATCCTCTCCTT Y 2 1 2 1 101000 r 74 goat snp48526-scaffold689-2789880 1 89136936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453339 Affx-122919961 AX-123323672 1 87837359 TGTGGGGCAGCCCCCATAGGTGCTTCAGGTTCCAG[C/T]ATTGTGATGGATGAACACTCTTTGCAGAACTCAGG Y 2 1 2 1 101000 r 74 goat snp48527-scaffold689-2824259 1 89171089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399663 Affx-122960511 AX-123270018 1 87911540 ACAACTCATGAGGAACCAAATCCTGCCACCTGACA[C/T]GGATGAGCTTGAAAGATTGTCCCTCAGTCTAGACG Y 2 1 2 1 101000 r 74 goat snp48529-scaffold689-2898440 1 89245781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427756 Affx-122939246 AX-123298099 1 87940819 GTCATTGACCATAACCCTGCCATCTAATGAATTAA[A/G]GAATTTCTATTTGCTTGTGCCCATGCATTATTTTT R 2 1 2 1 101000 f 74 goat snp48530-scaffold689-2927719 1 89275015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383273 Affx-122972729 AX-123253631 1 87973848 AGATATTAAGCTAGTGCTGAGAAATGTATCTTTTC[C/T]AAGGTGTTAGCTCAAGGTAGCCAAAGACTATACAA Y 2 1 2 1 101000 r 74 goat snp48531-scaffold689-2960748 1 89307578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423684 Affx-122942322 AX-123294030 1 88013865 TTGCCATGTTCAGTTCTTTCACAGCATGTAGAAAG[A/C]AGAGGGGAGTCCCCTGGTGCCTCCTTTCTGACATC M 2 1 2 1 303000 r 74 goat snp48532-scaffold689-3000765 1 89348366 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404274 Affx-122957046 AX-123274626 1 88064968 GGGATTTGGGTACAGATTATACTAGGGTTCATTAC[A/G]TTATTCCCTACATTTTGAAGTCTGTTTGAACATTT R 2 1 2 1 101000 f 74 goat snp48533-scaffold689-3051868 1 89399920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423124 Affx-122942906 AX-123293470 1 88098853 TTTCTTCTGCCTTCCCAGATATCCCCCAGGCTACC[G/T]AATATCCTTTATTAACCTATTTCAGTGAAGACTAG K 2 1 2 1 201000 r 74 goat snp48534-scaffold689-3085753 1 89433588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384271 Affx-122972308 AX-123254629 1 88128695 TCCTGAACCCCAGAATCTGAGTCAGAGGGAGAGTT[A/C]TAGAAGGGGAACAGAGTAGAGAAAGTTGATACTTC M 2 1 2 1 201000 f 74 goat snp48535-scaffold689-3115595 1 89463514 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432932 Affx-122935302 AX-123303273 1 88162582 TTGGGTCTTAATTCTGACCTCTTCTTCTGACCTAC[A/G]GCTATCCACATTCTAACATGAGGTTACCCTAAACT R 2 1 2 1 201000 r 74 goat snp48536-scaffold689-3149482 1 89497379 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786033 Affx-122976141 AX-385273069 1 88254361 TCTCAAAGCAAATATGCTGCAAAAATACAAACAGA[C/T]GAAAAGCAAACGTGCTGCTGTTTTGTATGTAGCTT Y 2 1 2 1 201000 f 74 goat snp48538-scaffold689-3241261 1 89589169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442813 Affx-122927712 AX-123313150 1 88288787 AAGGAATAGATAGGATATTGAGCCTTCAATTTTGA[C/T]TTGAAACTCCAGTTATTCTTCTTCCAGGGCTTTGT Y 2 1 2 1 101000 f 74 goat snp48539-scaffold689-3275687 1 89623652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436872 Affx-122933238 AX-123307210 1 88331549 ATAAAATTTGCCACCCACCCATTTTCTGACACTAA[C/T]GGTTATTTCAAAAGGAGTCACTTAGTAATTTGTGG Y 2 1 2 1 101000 r 74 goat snp48540-scaffold689-3318449 1 89666343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385754 Affx-122971073 AX-123256112 1 88378087 CCATCATGTCCTCTGCCCTTCTTCTCTCATCACAT[A/G]CTTCCAGCTCTGTCTTAATTTTTGGCCTTCCCTCA R 2 1 2 1 101000 r 74 goat snp48541-scaffold689-3364987 1 89714012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381282 Affx-122974468 AX-123251640 1 88428426 CGTGGGCTCCCAGAGGCCTCTGGACTGGCCTGGTC[A/G]CCTACAGATGGGCACCTGGGATATGGTGTTTGCCA R 2 1 2 1 103000 r 74 goat snp48542-scaffold689-3415326 1 89763695 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773268 Affx-122931267 AX-385260411 1 88472429 GACATAGATGGCTTTGCTAATCAGTGGGAGAAAGA[C/T]AGAATATTCAAAACCTGTGTAGGATAATTATCCAT Y 2 1 2 1 101000 f 74 goat snp48543-scaffold689-3459329 1 89808282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442252 Affx-122928285 AX-123312589 1 88516578 TTTTATGTTGCTAACAAAGAGAAGCCCAGTGGCAG[C/T]GCACACTGTGGCATTTGCTTTGGGTTTTAAAGACA Y 2 1 2 1 201000 r 74 goat snp48544-scaffold689-3503478 1 89852361 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411795 Affx-122951263 AX-123282145 1 88549465 AGCTCCTATGGAACTGAAAAGCAAAAATATACTTG[C/T]AAAATAAATACAAATTCCAAAACTGATAAAGTTCA Y 2 1 2 1 101000 f 74 goat snp48545-scaffold689-3536365 1 89884997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780419 Affx-122963118 AX-385267511 1 88559852 TAGTAGGTATCTGGAATATATGAATCTCTAATAAA[A/G]AGACCCAAACCTTTCAGGAAGTTCTCTCATGTTTG R 2 1 2 1 102000 r 74 goat snp26306-scaffold276-1558 1 89895197 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437895 Affx-122931665 AX-123308233 1 88630384 TATTGTGTGCATGTGTATGTGTTTGCTTTAAAGCA[A/G]GGAGACTACTGGGGTTCTGTTCTGTATACGAGTGA R 2 1 2 1 101000 r 74 goat snp26308-scaffold276-72090 1 89966221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768481 Affx-122964321 AX-385255661 1 88678918 TTATTGTTTTTAATAAGCTCTACAGATATCTGTGT[A/G]TACCTTTCTGTGAAAGATATATTTTGCATTAGTGC R 2 1 2 1 201000 f 74 goat snp26309-scaffold276-120624 1 90008487 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795879 Affx-122968537 AX-385282831 1 88709256 AGAAGATTGATCTGATGTTGATGTGCGGAGGAGCT[A/G]TATATTTACATCACCTTCCATTAGTGGGAAATGAT R 2 1 2 1 101000 f 74 goat snp26310-scaffold276-150962 1 90038519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271742 Affx-1111832873 AX-519545536 1 88732772 AACACTAATCAGAAGAGACTCCCTGTGGCCTCTGC[A/G]TTTGCTCAGTACACCCCCGGCCATCCTGGGGGTTG R 2 1 2 1 202000 r 74 goat 1_88732772_AF-PAKI 1 88732772 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320767491 Affx-122979068 AX-385254755 1 88766967 TGTCTCTGCTCTTAACATAACTCACTGATGAAAGC[C/T]GACTATTGTCGGCATTTTTATGGGCTATGTATAAA Y 2 1 2 1 101000 f 74 goat snp26311-scaffold276-208673 1 90096310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274036 Affx-1111833967 AX-519547639 1 88767344 TGCAGATGCTCAAAGTCTTTCTTTCATATAATGCG[A/G]GTTTGAAAGCTTTTCCATAAGTCATGTCAAATGGT R 2 1 2 1 101000 r 74 goat GoatD01.011992 1 88767344 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786254 Affx-122939688 AX-385273289 1 88799789 GTCCTTCCTCTGTGGAAAGACCTTAGTGTTTTATC[A/G]TCCTTCCATTCAGGAAACTTTACCTCTATAAAGCA R 2 1 2 1 101000 f 74 goat snp26312-scaffold276-241495 1 90128829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771252 Affx-122960456 AX-385258410 1 88862532 ACATTAACAACAGTGGGTGTGTAGACACTGCATAT[A/G]ATAATAATGCTATTAAATTCACTTTTTTTATCTGA R 2 1 2 1 202000 r 74 goat snp26313-scaffold276-304238 1 90191647 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448470 Affx-122923628 AX-123318806 1 88912946 GGATGCAATAGCTCACAGGAAGCTACAGAGGAGAA[C/T]GCCAGGGGCATACATTGCTAAAGAGGAATTGAATG Y 2 1 2 1 201000 f 74 goat snp26314-scaffold276-354652 1 90243406 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438691 Affx-122930867 AX-123309028 1 88963238 CATTTATTTAAAATAGTTTTAAATATCAGTTTCTA[C/T]GCTGATGACTTCTAAATATATAATCTAAAGAATGC Y 2 1 2 1 101000 r 74 goat snp26315-scaffold276-404944 1 90294667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781412 Affx-122953947 AX-385268497 1 88997027 ACTTTCAATTCATTTAAACAAATTCTATGAAAATA[C/T]GATATTCTGCCATTCAAGGACAGATTATTGTGTGA Y 2 1 2 1 201000 f 74 goat snp26316-scaffold276-438733 1 90330182 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382948 Affx-122973374 AX-123253306 1 89029471 ACATTAAAAATGCCAGGGTGGTGACTTTAGACTTT[A/G]TTCTCTGGGAAAATGAGAATCACCAAATTCTAATG R 2 1 2 1 101000 f 74 goat snp26317-scaffold276-471177 1 90364079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430643 Affx-122936952 AX-123300984 1 89084143 ACTTATTTAAAATGACAGTGTTACAATCCTGCTAC[G/T]AGGTTGTAAAAAATTATTGCTTGTATGTATTTTGT K 2 1 2 1 101000 f 74 goat snp26318-scaffold276-525849 1 90418475 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408059 Affx-122954271 AX-123278410 1 89186913 TCCTAAGTAATAAGAATCTCAAGGAATTCGAAGTT[A/G]TAACATATGAGAGCTTCTCACATGGGAGATTTAAA R 2 1 2 1 201000 f 74 goat snp26320-scaffold276-628619 1 90522295 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394031 Affx-122965000 AX-123264386 1 89236473 GAGAGAATTATCCAGATTTCATCCCTTTGCAGATC[A/G]TCCTTCAGATCATCTGATTATGGTTTTCCTCTGCC R 2 1 2 1 101000 f 74 goat snp26321-scaffold276-678179 1 90571978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779645 Affx-122979072 AX-385266747 1 89276824 GCTCGACAAACTGTGAATGGCTTCTTATATCATTC[A/G]CATTGAAAATCTAAGCCCACAGTGATGTGTAAAGC R 2 1 2 1 101000 r 74 goat snp26322-scaffold276-718530 1 90613037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776331 Affx-122924290 AX-385263459 1 89399881 ATATCTGTTTTAACATAAGTAATTGCAAAACTATC[G/T]CTGAAAAAATGAGTCCATCTAGAGTTAAATAAAAG K 2 1 2 1 101000 r 74 goat snp26324-scaffold276-841587 NW_017199709.1 12632 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773740 Affx-122955047 AX-385260880 1 89450821 CCCCAGTTCCAATAAACTTAATCTATCACAACTGA[C/T]AGTATATGATTTCTGAGACCAAGTTCTAAAAAGCA Y 2 1 2 1 201000 r 74 goat snp26325-scaffold276-892527 1 90790907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383652 Affx-122972524 AX-123254010 1 89479582 ACTCTGTATCTGGGCTTCTTTCTATTCCATACAGA[C/T]GTAATCTGATCACTTTCCCTGGCTAGAACAGTAGT Y 2 1 2 1 101000 r 74 goat snp26326-scaffold276-921288 1 90820159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386329 Affx-122970881 AX-123256687 1 89511858 TGTAATACCATAAACAGGTTAAAGTAAAAATCTTA[C/T]GAGATTATGGGAAGGAAGAGACCAGTTCTAGGGGG Y 2 1 2 1 201000 f 74 goat snp26327-scaffold276-953564 1 90852445 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448983 Affx-122923114 AX-123319318 1 89548153 AAAACTGCCTTTCAGCAAGGAGTTTCAGAAAAGAT[A/G]CATGAATGAGGAGCAAAGTGAGATGCTTTCATTTT R 2 1 2 1 101000 r 74 goat snp26328-scaffold276-989859 1 90888912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785189 Affx-122962015 AX-385272234 1 89578619 TATACTGAGCAATATCCTAAGAATTTTGCATACTA[C/T]GGCACATGTAATCCTTAAAACAACTTAATGCAACC Y 2 1 2 1 201000 r 74 goat snp26329-scaffold276-1020325 1 90919369 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380079 Affx-122975550 AX-123250437 1 89609794 AACAAATGTACTACATTGCTATAAGATGTTAATAA[C/T]AGGGAACTTTGTGTTGGGAGCTGAGGGAACTGTGC Y 2 1 2 1 201000 f 74 goat snp26330-scaffold276-1051500 1 90950522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418775 Affx-122946190 AX-123289123 1 89641809 ATAAAGTGCACATTTATTTGCAAATTGGGAAATTC[A/G]TCTTACATTACTCAGAAAGGGGGGAAAAAAGACAT R 2 1 2 1 201000 f 74 goat snp26331-scaffold276-1083515 1 90982717 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790359 Affx-122922629 AX-385277362 1 89699062 AATTCCTGTTTCTATATCCTTAAAAATCTGATAGA[C/T]GAAATGGGAGATTGAAGAGGACTAAATTTATTTAT Y 2 1 2 1 201000 f 74 goat snp26332-scaffold276-1140768 1 91039777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426885 Affx-122940469 AX-123297230 1 89740466 AGAATATATTTAATACTAAAAGGCTATATAATAAT[A/G]CTATAATGCCACAAACATTGTAAAACTTCTACCAC R 2 1 2 1 101000 r 74 goat snp26333-scaffold276-1182172 1 91080697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275543 Affx-1111834868 AX-519549115 1 89779351 CAATGATGAGTCTCAGACTGCAGTGTGTTTCTGAG[A/G]AAGTTTTGACCAGGCTGATGGGAAGCCCTTGGGCA R 2 1 2 1 101000 r 74 goat GoatD01.057124 1 89779351 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432597 Affx-122935507 AX-123302938 1 89787698 TGCAGCGTAGTTTCACAGTAGGAAGGAAAAATTAT[A/G]TATTATTATATATTGTTATATTTTATACTCACTTT R 2 1 2 1 103000 f 74 goat snp26334-scaffold276-1229404 1 91127894 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418788 Affx-122946182 AX-123289136 1 89829495 GTAACAAAGGTGTTCCTCCAAGGTAGTAAACAACA[G/T]CTGCACTCAAGGCCTTCACATTGTTGAACAAAATG K 2 1 2 1 101000 f 74 goat snp26335-scaffold276-1271201 1 91169789 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453949 Affx-122919476 AX-123324282 1 89887496 AGTTTGCATTTTTGTTTCAAATACATAGAGTTAAA[C/T]AGTGATGCATTTCCTTGTTCCGACATAGAACAACT Y 2 1 2 1 101000 r 74 goat snp26336-scaffold276-1329202 1 91228808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444261 Affx-122927211 AX-123314598 1 89927427 AGTTGTCCAAGAGATTCTATCTCATAGGTCTCCGC[A/G]TATACTTTAAAGAGAGCATTGCATTTTTAACCTTG R 2 1 2 1 201000 r 74 goat snp26337-scaffold276-1369133 1 91269366 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795506 Affx-122953868 AX-385282460 1 89997600 AGGCTTTGTCAAAATAACTTCTTAGAAGTTTCAAC[A/G]CTATTTACTTGAGAGTCACAGAACACTAATATATG R 2 1 2 1 201000 r 74 goat snp26339-scaffold276-1439306 1 91339816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791169 Affx-122924554 AX-385278164 1 90038692 TTTGCATTCTAGCAAGAAAGTAAGGAATTACTAGA[C/T]GAAAATATAGGTTGTGATGGGAACCCAGATAAGTA Y 2 1 2 1 201000 f 74 goat snp26340-scaffold276-1480398 1 91381905 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410442 Affx-122952392 AX-123280792 1 90090652 CATGTATCTCTTTCTATTCATCAGGTAATCTCTAG[A/C]TGATTTTACCTCCATTTATCTTTGCCTTTAAAGTA M 2 1 2 1 101000 f 74 goat snp26341-scaffold276-1532358 1 91434455 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789573 Affx-122926965 AX-385276582 1 90136982 TTATGGTAGCTGGATTAACCCAATTATTTTTAGGA[A/G]GTTAAGGGAAACTGCATTTGGAGAACATCATCCTT R 2 1 2 1 101000 r 74 goat snp26342-scaffold276-1578688 1 91481575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767402 Affx-122975249 AX-385254675 1 90169147 TTCAGTTTCTTGCTTGGATTCAAACAAGAGGGGCA[C/T]ACTTTCTGCTTCTAACAAGTTGCTGAAATTTGAGC Y 2 1 2 1 101000 f 74 goat snp26343-scaffold276-1610853 1 91513077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385930 Affx-122971562 AX-123256288 1 90206227 TTGCTAAAATGTTGAAATACTTTCACAATGGCAAA[C/T]AGCCACTGCCTTGATCCTCCTGAGAGCTCCCACTG Y 2 1 2 1 101000 f 74 goat snp26344-scaffold276-1647933 1 91550566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444011 Affx-122926897 AX-123314348 1 90258423 GGATACCATCTAAAGTTACTTTAACGTTTCTAACA[C/T]GTAAGAGAAAAAAACAAATACAACTTTCTAGTTTC Y 2 1 2 1 103000 f 74 goat snp26345-scaffold276-1700129 1 91603605 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434768 Affx-122933894 AX-123305109 1 90290978 ATAAAATGCCAAGTCATTTTTCCCCAACCATTCTT[A/G]TTGCTACAGTGAACCTCTTCTTATTGTGTGTATTC R 2 1 2 1 101000 r 74 goat snp26346-scaffold276-1732684 1 91636763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421685 Affx-122944416 AX-123292032 1 90332048 AGCACTCCAAAAATCCAGCATTAAACCTTTGGAAA[C/T]GCAAGTCAACTTGTAATATAATATCTGGCAATAAC Y 2 1 2 1 101000 f 74 goat snp26347-scaffold276-1773754 1 91677713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400266 Affx-122960130 AX-123270621 1 90409499 CTGTAGAAATTAATAAGAAACTGAACTGCAAATAA[C/T]GCACTGGAGGCTTATAGCTAGGGGTCTACTGCAAA Y 2 1 2 1 201000 f 74 goat snp26348-scaffold276-1851205 1 91756049 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798078 Affx-122957616 AX-385285014 1 90448152 AGAGAAAGGACACCACAAACTATAAAATAAATGAG[A/C]GGATAAAAACTCTGATCATGTAAGGAAAGTCACTG M 2 1 2 1 101000 f 74 goat snp26349-scaffold276-1889858 1 91794697 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426180 Affx-122940583 AX-123296526 1 90501621 GTGTGTTTATGGTATGAATATCTGAACAAATGAGG[C/T]AACAGAAGGCAACACCAACACACTAAGAGCAGAAT Y 2 1 2 1 201000 f 74 goat snp26350-scaffold276-1943327 1 91848526 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437267 Affx-122932001 AX-123307605 1 90531895 ATTGTATTCATTCAGAAAGTAGTCATAAAATACTA[C/T]AGACCTAAAATCATGCTTGAGTCTGGAAAAGCAAT Y 2 1 2 1 101000 r 74 goat snp26351-scaffold276-1973601 1 91878929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451561 Affx-122921699 AX-123321894 1 90582130 TACACTAAAAAAGTATGCACAGACACACACAAATA[G/T]AGTGTGCCATTAGTATGGTAAGTAAGATAGATGAA K 2 1 2 1 201000 r 74 goat snp26352-scaffold276-2023836 1 91929208 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380222 Affx-122975479 AX-123250580 1 90622625 CTTCCACCCTCACTTTTTCCCCTCTCTCCTTTCCT[A/G]ATACAATTCTTTCTTCCCTCACGCTTTACTTTCTT R 2 1 2 1 201000 r 74 goat snp26353-scaffold276-2064331 1 91970698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388781 Affx-122968929 AX-123259139 1 90657448 ATCATAGCAAATATATGTGGTCATCTGGTACAATT[C/T]TGACCAATGAGATATAAATATTCATTCATCGGTGA Y 2 1 2 1 101000 f 74 goat snp26354-scaffold276-2099154 1 92006317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765442 Affx-122921261 AX-385252943 1 90690383 TCTAACCAGACACACTAATTATGAGAAATAGAATC[A/G]GATATCAGATATGATGTCTTTAATGAATAGCAGAG R 2 1 2 1 101000 f 74 goat snp26355-scaffold276-2132089 1 92037773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416550 Affx-122947677 AX-123286898 1 90728360 CTACAAGTGTTAATGCAGGACTATTCACTGACTTA[C/T]AAAATATTTAACACATTATTGTGGTATAATTTGTA Y 2 1 2 1 101000 f 74 goat snp26356-scaffold276-2170066 1 92075525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448160 Affx-122924268 AX-123318496 1 90821110 AAAAGCAAAAAACATGCCATATCATGAGATAAACT[A/G]CACTGCTGTCATGATTTTAAAATAAAATACTGAAT R 2 1 2 1 101000 f 74 goat snp26358-scaffold276-2262816 1 92169330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789905 Affx-122977023 AX-385276911 1 90873881 CACATCGACCTTTCCAACATAATCCCTGTTGTATT[A/G]TTTATCTATACTTTTTCAACTAAGAAACAAAATAA R 2 1 2 1 102000 f 74 goat snp26359-scaffold276-2315587 1 92222825 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779782 Affx-122943458 AX-385266882 1 90906735 CCTTGTTTTGGAATACCATCTCTGTGCCTTTTTAA[A/C]TTGCCAGTTTTCTATTATACCTTCAAGACCCAAGT M 2 1 2 1 101000 f 74 goat snp26360-scaffold276-2348441 1 92256307 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387178 Affx-122970620 AX-123257536 1 90971281 ATTTGTGAAATAACAGAGGATGAGTATGGATGAAT[A/G]ACCAAGGGGATTAATGCTGATTTTATTTAAATGAT R 2 1 2 1 201000 r 74 goat snp26362-scaffold276-2412987 1 92321401 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380833 Affx-122975068 AX-123251191 1 91001747 ATGTTTACGTATTCTGGACTCCATCAGCGAAGCCA[A/G]GAGAAATGTAACTGTCATCTGCACTAGGCACTTAT R 2 1 2 1 101000 f 74 goat snp26363-scaffold276-2443453 1 92352247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445735 Affx-122926093 AX-123316072 1 91055733 TTTACCATCTGAGCCACCAGTGTTTTCTTAAACTG[C/T]AATAAATCACACCCATTCATCTGACTACATGCTGA Y 2 1 2 1 202000 r 74 goat snp26364-scaffold276-2497439 1 92406788 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436062 Affx-122932706 AX-123306401 1 91119950 ATTGAGGGAAGGCAGATGAGTGTTGTTGAATCAGA[C/T]GGTTCCTAATATCAAAAAATTTCAGAAAGTCAAGA Y 2 1 2 1 101000 f 74 goat snp26365-scaffold276-2561656 1 92471764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440588 Affx-122929290 AX-123310925 1 91157153 TAAGGCGGTGATTTACAGATCATTTAGTCTGGCCT[A/G]TTCTGGGGTAGACAGGAGACCCTTGGTGATTAGGT R 2 1 2 1 201000 f 74 goat snp26366-scaffold276-2598859 1 92509032 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803844 Affx-986696542 AX-385290576 1 91162282 TACATCAAAAACTTTACCCAGCTGTCTTGGTCTTA[C/T]GCCCTCACCTGGCAAGATGTATTTGTCATCCTGGG Y 2 1 2 1 600010 f 74 goat 1_91162282 1 91162282 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320803847 Affx-986696544 AX-385290578 1 91162327 TGGCAAGATGTATTTGTCATCCTGGGGTCCACTAC[C/T]ACCCCAGAGAAAAGAAAGGCCATTTGGGCCGCAGC Y 2 1 2 1 600010 f 74 goat 1_91162327 1 91162327 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 320769682 Affx-122927585 AX-385256852 1 91187368 TTGTTTTATATTGCTAGTATTGAGGTCTCCAGAAA[C/T]ATTTGCCTGAACTGCTCTGCACATAGAAGTTGTTG Y 2 1 2 1 101000 r 74 goat snp26367-scaffold276-2629074 1 92539331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399472 Affx-122961193 AX-123269827 1 91218201 AGCCCATAGATACAGAAACAACTGCCTCCCCCTTC[A/G]CAGGTGGTATTATCACCCTTGTATTAGCAGCTGGA R 2 1 2 1 201000 r 74 goat snp26368-scaffold276-2659907 1 92570207 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782606 Affx-122950768 AX-385269679 1 91249657 TCATCAGAGAGATGTGTATAGAATAGAAGACAAGC[C/T]GGACCTGTGCCCATTCACATAAATGACCCTTGTTT Y 2 1 2 1 101000 r 74 goat snp26369-scaffold276-2691363 1 92601685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793779 Affx-122964128 AX-385280751 1 91296330 AAGATAAGCCTACATTGTTTCTTGTGTCTGTAAGT[A/G]CTGAATTATTCATATGAATCCTTCAGAGCAGCCTT R 2 1 2 1 101000 f 74 goat snp26370-scaffold276-2738036 1 92645086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787165 Affx-122949044 AX-385274191 1 91355992 ATGAGAAAATGTGATGTTTCTTGTAAAGAGGGACT[C/T]GATTCTTAATTACTGTTTTCTCTAAACTAAAAATT Y 2 1 2 1 101000 f 74 goat snp26371-scaffold276-2797698 1 92705385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439762 Affx-122930520 AX-123310099 1 91393520 GAATTTAGTAACAACAAACTTTGTGATGTTCTTCC[A/G]TACCATGGTTTGAAGTATGTGTTATAATGCACAGG R 2 1 2 1 101000 r 74 goat snp26372-scaffold276-2835226 1 92743160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271847 Affx-1111832874 AX-519545630 1 91393638 ATGTATGGTGTGAGAGTTGGATCATAAAGAAGGCC[A/G]AGCACCAAAGAATTGCTGTTTTTGAACTGTGGTGT R 2 1 2 1 303000 f 74 goat 1_91393638_AF-PAKI 1 91393638 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791694 Affx-122944101 AX-385278685 1 91438326 ACATCACTAGGAACTCTTTACCGTCCCTATGTTAC[A/G]CATATAAATTATAGCCAAATGATATCCATATTAAC R 2 1 2 1 101000 f 74 goat snp26373-scaffold276-2880032 1 92789231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796380 Affx-122932564 AX-385283330 1 91496816 TTAGTCATTCTATTAAACCACTGTTGATCTTACAT[A/C]TTAGCTTCTCACCTACATAATAATCATCTTGCTAG M 2 1 2 1 101000 r 74 goat snp26374-scaffold276-2938522 1 92847698 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794162 Affx-122924096 AX-385281128 1 91574844 ATTTAATGCATTAAATTATATGCTATAAGAAGAAA[C/T]ATGGCTATTCACTTCAAGTTAAAAAATGAACAGGT Y 2 1 2 1 101000 r 74 goat snp26376-scaffold276-3016550 1 92926166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794820 Affx-122962363 AX-385281780 1 91606571 TGAGACAAATTACACATGATGGCTTTGCAATCTGG[A/G]TAAATGACAGGTTCAGGTGGATGTGCAACTTACAA R 2 1 2 1 101000 f 74 goat snp26377-scaffold276-3048277 1 92958344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771019 Affx-122936733 AX-385258181 1 91640853 GAAACAAAACATAGAAAGTGTCATGGAAATGTTTA[C/T]AAGCTTCTGGATTCAAGCCTTGATATAATATTTTT Y 2 1 2 1 202000 r 74 goat snp26378-scaffold276-3082559 1 92992347 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439419 Affx-122930237 AX-123309756 1 91695865 TTCTCAAAAAAACTCCTGAAATCAAGCAGATGAGG[C/T]ATATATTGGAATCCTGCTATCAGATCACCTTATTG Y 2 1 2 1 101000 f 74 goat snp26379-scaffold276-3137571 1 93048412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388952 Affx-122968810 AX-123259310 1 91736866 ATTGGCATAGACAGAATGCTTCATAAACAGAGGTA[C/T]GCATATTTAATCTGTGAATTACTAAGGGACCTTTG Y 2 1 2 1 101000 f 74 goat snp26380-scaffold276-3178572 1 93089584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432669 Affx-122936051 AX-123303010 1 91781411 CTGACTGTTTAATGCAGACCAGGGGACTTTCTTGA[C/T]GACTGCCTTCCATGAGAGGGAGGCAACTTCCCATG Y 2 1 2 1 101000 f 74 goat snp26381-scaffold276-3223117 1 93134172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435419 Affx-122933547 AX-123305759 1 91810480 ACTGAGCTCCGGGTCTCCTGTTACCTGCTGAGACC[A/G]TACCCTTGTAGGCCAGAGAATCTAATGGAGTGAGG R 2 1 2 1 101000 r 74 goat snp26382-scaffold276-3252186 1 93163309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420067 Affx-122945120 AX-123290415 1 91854319 TGCTGCACTCTTTCCCTGCCCTCTTTACCCAACAG[C/T]GTTTGAGGTAAACTGACTGTAAAAGGTTCCTAAGG Y 2 1 2 1 101000 r 74 goat snp26383-scaffold276-3296025 1 93206953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770731 Affx-122943343 AX-385257895 1 91895885 TTCCAAGCATTTAATCAAAGACTTTGATATTAAGC[C/T]GATATTTCTTGGCTCATTGCTATCAGGTTGGTCTT Y 2 1 2 1 101000 r 74 goat snp26384-scaffold276-3337591 1 93248874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388657 Affx-122969107 AX-123259015 1 91925780 GTATTACACTCCCACCACCCAGGTGCTCTGCTTTG[C/T]AGGAAAGACTTCAGGCTTCCTACCAGACAGTACAA Y 2 1 2 1 202000 r 74 goat snp26385-scaffold276-3367486 1 93278915 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770836 Affx-122945647 AX-385258000 1 91990839 AGATCAAATGGGACCACTTCAGTACACTTTAAAAA[C/T]TGAGTTCTTTGGACATCACAAGCATATTTTCCTTT Y 2 1 2 1 201000 f 74 goat snp26387-scaffold276-3432545 1 93343467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784732 Affx-122922753 AX-385271780 1 92030140 TTCAGTGGAGAAGATTCATCTCTATAAGTATAAGA[C/T]GGGATAACTCAGTTGGGCTAAAGGACTTACTTATG Y 2 1 2 1 101000 r 74 goat snp26388-scaffold276-3471846 1 93382581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426306 Affx-122940292 AX-123296652 1 92063017 AATGAACAAGCTAATTTCATATAGAGATAAAAATG[C/T]AATGCAGGAGATAACCAAGGGGATGTAAGACAATA Y 2 1 2 1 103000 r 74 goat snp26389-scaffold276-3504723 1 93415460 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406480 Affx-122955169 AX-123276832 1 92108674 GAAAAAGAATATGATGGAGAGGAAATGGTAAGAAA[C/T]CCTGTAGGTAATTTAAATTAGTTTTAAGATCCAAT Y 2 1 2 1 101000 f 74 goat snp26390-scaffold276-3550380 1 93461237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387595 Affx-122970256 AX-123257953 1 92153669 GTTATATATATTTATAATGATATATGACTTTGAAA[G/T]AAATCATCAGAAGACTCATAGCCCACTAAGAAAAT K 2 1 2 1 202000 f 74 goat snp26391-scaffold276-3595375 1 93506393 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409411 Affx-122954132 AX-123279762 1 92184941 AATTAAAGGCAGACTTTCTCAAAATGCATTAAAAA[C/T]GAAAGGAAGCACACAGCAGCCACAAAAAGATACAT Y 2 1 2 1 303000 f 74 goat snp26392-scaffold276-3626647 1 93537993 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402036 Affx-122958736 AX-123272389 1 92277447 ATGATACCATTCACTCTTGTACATGTATCTATACA[C/T]GTACATACATAGACTTTCTCCTTCCAAAAGTAATT Y 2 1 2 1 101000 r 74 goat snp26394-scaffold276-3719153 1 93631840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452651 Affx-122920338 AX-123322984 1 92311069 TTATTACTCCTTATTCAGTACGTTGGGAAGTGTGC[A/G]CCATGTGTGTGCTACCTTAGGAAGCTTTTTATTAA R 2 1 2 1 101000 f 74 goat snp26395-scaffold276-3752775 1 93665360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771739 Affx-122941532 AX-385258896 1 92365620 CCTGGATTTTATTAGAATCAGTGAGATAATACATG[C/T]AATATACTTTACAACATCTTATATGTAGTAAACAC Y 2 1 2 1 101000 f 74 goat snp26396-scaffold276-3807326 1 93719435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398633 Affx-122961464 AX-123268988 1 92423943 TGAGTACATAAATAAGCAAACAAACAAAGCAGTCT[A/G]GGGGTATGGTAAAGAATTGATATTGTCCCCAGTAC R 2 1 2 1 201000 r 74 goat snp26397-scaffold276-3865649 1 93780028 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439535 Affx-122930113 AX-123309872 1 92466570 CCTTCAAAGCCACTGTCTCCCTATAAATCAGCAAG[C/T]AGAAGGAACATGTCTGACAAAAATCCTGTCTCTCC Y 2 1 2 1 101000 r 74 goat snp26398-scaffold276-3908276 1 93823282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796070 Affx-122979030 AX-385283022 1 92513153 CATAAAAGTTATCTACTCAGAGGTGAGGCAGGAAT[A/G]CTATTCAGGTCTAAGACCAGGCCCAATCTCCTCAT R 2 1 2 1 101000 f 74 goat snp26399-scaffold276-3954859 1 93868739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799913 Affx-122936812 AX-385286839 1 92569963 ACAGAGTTAGGAAAAAGAGTAGTGAGAAAAATCTG[C/T]GAGAAGTGTTATGATAGGATGATTCAAGGCACTAC Y 2 1 2 1 101000 r 74 goat snp26400-scaffold276-4011669 1 93924525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442995 Affx-122928185 AX-123313332 1 92637780 GATGTTGTACAGTTTAGAAGAACCTAGTCCAGTTT[A/C]GCAACAGTGACTTCCAAACTCATGTCCTCTACTGT M 2 1 2 1 101000 f 74 goat snp26401-scaffold276-4079486 1 93992564 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798183 Affx-122936984 AX-385285118 1 92676550 CCTCCAAAGAAACGTCAGTGTTTCCTCAAATCAAT[A/G]CCATGAACCAGTTCAAGGGTGCAAAACTTCTCCTA R 2 1 2 1 101000 r 74 goat snp26402-scaffold276-4118256 1 94032221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278843 Affx-1111836540 AX-519552314 1 92696418 TGGCATAATAACAGAATGCTCTTTTCATTCTGAAA[A/C]AGGACTAACTCTTTACATTAAAGTGCAAGAAAATC M 2 1 2 1 101000 r 74 goat Random2.2K-96 1 92696418 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794976 Affx-122973006 AX-385281936 1 92705755 CTCCTGTTGTTTTTCTTCTTGATACTGCAAAATCA[G/T]CCCAATATTAGTCATTCACCTAATAAAAACTTATG K 2 1 2 1 101000 f 74 goat snp26403-scaffold276-4147461 1 94061238 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274868 Affx-1111834543 AX-519548452 1 92751185 TGTGCAACCAACTAACCTGCAGGGGTGAATGCCTG[A/C]GTCCTCCAGTCACTCTCTGCCCACTTCACGACCCT M 2 1 2 1 102000 f 74 goat GoatD01.040952 1 92751185 C A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785126 Affx-122952659 AX-385272172 1 92759921 CAATCATGGTAAGAACCCGCAGAGGGAAAACTGGT[A/G]TCAGGAGACGTGAGAAGAAAACACTGTTCCATTTA R 2 1 2 1 101000 r 74 goat snp26404-scaffold276-4201627 1 94115584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278674 Affx-1111836547 AX-519552152 1 92792868 TCCAGAGATCTTATTAAAGGTTGTAGGAGGTGAGA[A/C]ATGTTGATGGAAAAGTGAATAAAAACTTAAAAGAT M 2 1 2 1 101000 f 74 goat Random2.2K-97 1 92792868 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396866 Affx-122963244 AX-123267221 1 92796145 CCTGGAATGAACAACCCCACTGTGTCCAGCACAAT[A/G]TCCTGCACCCCAGCACCCCTTTCTGTGCACATCAT R 2 1 2 1 202000 f 74 goat snp26405-scaffold276-4237851 1 94151712 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421992 Affx-122943788 AX-123292339 1 92858762 GTGGGGAATGGGCCTTATACCTGTTTCAAGCCCAT[A/C]CAGAAATCCTAAGCAATTTTCCAAAATTTAACTAA M 2 1 2 1 101000 r 74 goat snp26406-scaffold276-4300468 1 94214610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427606 Affx-122939363 AX-123297949 1 92887827 TAACTACAAGGACTAGACAGCAAAGCCTATGAGAA[C/T]GCCATGAAGTGTGTTACAGACAAGATTCTGAAACA Y 2 1 2 1 101000 f 74 goat snp26407-scaffold276-4329533 1 94244276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433512 Affx-122935017 AX-123303853 1 92918028 AACTTGCAAGCTCAAAGAAAGGGTAGGGCACAGAA[G/T]AGCAGCCTCATTCTCAGTGTGCTCACAACAGGCCC K 2 1 2 1 101000 f 74 goat snp26408-scaffold276-4359734 1 94275913 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765052 Affx-122959489 AX-385252621 1 92998541 TGCAGTGATCCATAAACTATTTTCAGCCTTTCTCA[A/G]TCAAGATCTGGTAGTCCTTAGAGAACACTGACTTA R 2 1 2 1 101000 f 74 goat snp26409-scaffold276-4440247 1 94356598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278688 Affx-1111836555 AX-519552166 1 93020108 AAACCAAATTGTGATGAAAATAATATGTATCTCAA[A/G]TATTAGTTTACAGTACTCAAAGTTAAAAATGTTCA R 2 1 2 1 101000 f 74 goat Random2.2K-98 1 93020108 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788305 Affx-122958836 AX-385275323 1 93034024 ACCATAGAGAAGTAACACTCCTTTTCAGGGAAATT[A/G]CAGTGCCATCCAAGATATTGGTAGAACTACAGAGC R 2 1 2 1 101000 r 74 goat snp26410-scaffold276-4475730 1 94392080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409781 Affx-122952980 AX-123280132 1 93071444 GTCACATTCCCATCTCAGTTGCACTCTCAGACACA[C/T]GCTCATGAAGTACAGTGGAAGGTGCACTGCCAGCG Y 2 1 2 1 101000 f 74 goat snp26411-scaffold276-4513150 1 94429539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407811 Affx-122954554 AX-123278162 1 93103943 GTGGGTAGAGGGGACTATCTTTGCGGCCTCTGTCT[G/T]TAAGAGGAGAGTAAAAAGCAACTACCACCTGCAGT K 2 1 2 1 201000 f 74 goat snp26412-scaffold276-4545649 1 94459068 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770274 Affx-122938683 AX-385257440 1 93133307 AGTGAGAGAACTCCTCCTCCCACATAGGAAGTCTT[A/G]TACCCTCCTTTAAAAGTCACTGCCATAATAAGCAA R 2 1 2 1 101000 f 74 goat snp26413-scaffold276-4575013 1 94488764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417346 Affx-122947728 AX-123287694 1 93190358 AGAGTTCTTGACTCGAATTCTCGGGCAAGAGAGGA[A/G]CTGCCTCAGAGGAGGACTGTGTCTGCTTTTGCTTT R 2 1 2 1 101000 f 74 goat snp26414-scaffold276-4632064 1 94546464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412955 Affx-122951049 AX-123283304 1 93242618 GGGTTGGATTTTTTTCATTTTTGGAAATGACTGTT[A/G]TATGAGAAAGAACTTTTGAATAATTGCTTTTAGGA R 2 1 2 1 201000 r 74 goat snp26415-scaffold276-4684324 1 94598872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392539 Affx-122966100 AX-123262896 1 93315922 TGGTTGGGAATCTTCTGGTCTCTTGTGTCAGTAAA[C/T]ACCCAAGTCCAAGTAGCTTAAACACAAAGGGGCAG Y 2 1 2 1 101000 f 74 goat snp26416-scaffold276-4757628 1 94671245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773173 Affx-122944150 AX-385260315 1 93355497 AATGCCAAGTGTTTCTCCCTAATCTTCAGTAGTCA[A/G]GAGCCAAAATCAAAGGCTTGGATTCATGGGACCAT R 2 1 2 1 101000 r 74 goat snp26417-scaffold276-4797203 1 94710861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778496 Affx-122943411 AX-385265610 1 93391262 ACTGCTCCTTTCCATCATCACTGTGGGCCAGAAGT[C/T]TGGCAGCTATAGCAAAAATAGGGCCAGAATCCCAT Y 2 1 2 1 101000 f 74 goat snp26418-scaffold276-4832968 1 94746690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788121 Affx-122933942 AX-385275141 1 93429561 TTATTGGACAAGGCCCAATGTGACATTTGTTTCAG[A/C]GCTAGAGATATAAAAGAGTCTACTGTGAAGGTTAC M 2 1 2 1 101000 f 74 goat snp26419-scaffold276-4871267 1 94785046 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425084 Affx-122941246 AX-123295430 1 93461828 GCTATCCTGTGGTGTGTGTGGTTGGGCAAATGAAA[C/T]TTAAAAGAAAAGCCAAGGCTGGTCACAGCAGAGAG Y 2 1 2 1 201000 r 74 goat snp26420-scaffold276-4903534 1 94817358 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413526 Affx-122950621 AX-123283875 1 93496663 AAGAATCAAGAAGGGCCTTGTGGTGCCCAAGTCCA[C/T]ACACAAAAGAATTAAAAGCCCAAACAAACAAAAAC Y 2 1 2 1 101000 f 74 goat snp26421-scaffold276-4938369 1 94852412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421071 Affx-122944242 AX-123291418 1 93546246 AAATATCTGACTTGTCCACAATCCTGAATATTCTA[C/T]ACTCAACTCAAGAGTGACAATGAAGGTACGGCCAG Y 2 1 2 1 101000 r 74 goat snp26422-scaffold276-4987952 1 94901997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776880 Affx-122975532 AX-385264004 1 93581234 CCTATTCCCACATTCTATATTGATATGTTCTAGCC[A/G]TCTGGAGTGAAGCATTCGCTCACTCACACTGGAAC R 2 1 2 1 101000 r 74 goat snp26423-scaffold276-5022940 1 94936886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775353 Affx-122922746 AX-385262484 1 93616757 ATAGCTTATGTTTTATGAGTGATTACAAGTTTCTT[A/C]ATGACTCCCAAAGAAAAACCCAAGCCTAATAAAAT M 2 1 2 1 101000 r 74 goat snp26424-scaffold276-5058463 1 94972442 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798866 Affx-122965777 AX-385285796 1 93665166 ATGACCTGAAGTAACACAAGAAGACCTGTTCCATA[C/T]GAATTACAGATCCATTAAAACAGAAGGGTTTCTAT Y 2 1 2 1 101000 f 74 goat snp26425-scaffold276-5106872 1 95021266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376335 Affx-122978343 AX-123246694 1 93693812 TGAGAGATAGGTCAAAATAACATCATTGTTGGAAC[A/G]TTACAGTCAATATGATTTTTAAAAGTATGAATGAA R 2 1 2 1 101000 f 74 goat snp26426-scaffold276-5135518 1 95050067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767294 Affx-122953847 AX-385254575 1 93781901 AGAAGGAATGCCTGAACTGGAATTAAAGAACAACA[C/T]GACTATGTAGTTTTCTTCATATCAAAACTGGACAT Y 2 1 2 1 101000 f 74 goat snp26427-scaffold276-5223607 1 95138092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448885 Affx-122923263 AX-123319220 1 93814451 TACTCTGGATCAGACATATTGGGTAAAATTGACAA[A/G]CAAAACAGAAAGATGATTTCTGCTCTGATGGTGCT R 2 1 2 1 201000 f 74 goat snp26428-scaffold276-5256157 1 95170617 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446886 Affx-122925228 AX-123317222 1 93850996 AACTTAAGTGTGTCACCGGCAAACTTGTGCAGCTC[A/G]CTGTTGGTTGGCTTTCCCCAGCCCTGCAGCTGGAA R 2 1 2 1 101000 f 74 goat snp26429-scaffold276-5292702 1 95206948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376940 Affx-122977776 AX-123247299 1 93915599 TAATGGTGAGCTGTTCAGGTTTTCTCTTTCAATTT[C/T]ATTGACATATAACTAACACAACAGCACTGAATAAG Y 2 1 2 1 201000 r 74 goat snp26430-scaffold276-5357305 1 95272425 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411722 Affx-122951526 AX-123282072 1 93947690 AGTTCCCAGTCCTATCTCTGCGGAAGCTGAAGTTA[C/T]AAAGTTATGTCTGCATGCCATCTCAGAATTGCAAA Y 2 1 2 1 101000 f 74 goat snp26431-scaffold276-5389396 1 95304851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786940 Affx-122951602 AX-385273969 1 93980043 TACTTAGAGCTAGTGGACTTGTTTCCATATGCTAT[A/C]TGTAAGCCTGGATTCAAATAATAGAATAAGGCTTA M 2 1 2 1 201000 r 74 goat snp26432-scaffold276-5421749 1 95337361 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419836 Affx-122945815 AX-123290184 1 94026823 ACTAAGAGAGAAAAATGATAGTGCTTTCCTGTACT[A/G]CCAGCTGTTGGACATTCTTTTTGATGGTTAATATT R 2 1 2 1 101000 f 74 goat snp26433-scaffold276-5468529 1 95383818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272615 Affx-1111832875 AX-519546326 1 94041880 GCTATGAAAGGAGGAAACTGAGGTTCCTCAGATTG[A/G]GGATATTAGTTTTCCAAAAGTGGTGAAAAGATCAG R 2 1 2 1 201000 r 74 goat 1_94041880_AF-PAKI 1 94041880 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795163 Affx-122964997 AX-385282121 1 94078292 GACAAACAAAGCTTTTGAAGTATTTAAGGCACTGA[C/T]ATAATGTTTGATTTGGTTTTATCCACTTCATTTGC Y 2 1 2 1 101000 f 74 goat snp26434-scaffold276-5519998 1 95435489 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416759 Affx-122948184 AX-123287107 1 94138237 ACATCTCTGGACCTCAATTTCCTCATGTATAAAAA[C/T]ATGAAAGTGAATGGCTCGTTGTAAAAGAGTGCATA Y 2 1 2 1 103000 r 74 goat snp26435-scaffold276-5579943 1 95495879 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796273 Affx-122933796 AX-385283223 1 94190862 TTGGCTGTAAGTTTCCTTGCAGCAAATACAAAGAA[A/C]GTAAACCAGCTACATGATTCATAAGATAAAACATA M 2 1 2 1 201000 r 74 goat snp26436-scaffold276-5632568 1 95548614 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772677 Affx-122928503 AX-385259824 1 94239394 TTCTAGAACTTTATAGTTGTTATAGTAATTTCCTT[C/T]AAGGTAAGGTCGATATAACTTATCTCTCCTTCCAA Y 2 1 2 1 101000 r 74 goat snp26437-scaffold276-5681100 1 95597525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399081 Affx-122960883 AX-123269436 1 94270966 ATTGATTTAAAAAAAACCACCCAAAACTCTTGTCT[A/G]TTTGTTTTCTTAGTTTCTTCTGTGCTCATCCCTTG R 2 1 2 1 101000 r 74 goat snp26438-scaffold276-5712672 1 95629099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413757 Affx-122949940 AX-123284106 1 94309968 CTATTTGTTAAAAATTTCCTTCTTTGAATCTTAAA[C/T]GTCTCTTAGTTGATTTAATTATTGAAGTCCGCCAG Y 2 1 2 1 101000 r 74 goat snp26439-scaffold276-5751674 1 95667724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439872 Affx-122930049 AX-123310209 1 94382869 ACTCTGAAGCAGTCTGCAGTTGCAACCTGGCCCAG[A/G]ACAGCTGAAGCCCCATTATGAAAAATGTTATCTTT R 2 1 2 1 101000 r 74 goat snp26441-scaffold276-5824575 1 95740928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770477 Affx-122959851 AX-385257643 1 94423258 TATCTGTCCTACAGGCTGCTAGAATACTGCTGTCT[A/G]CTCCTCTCTGTAGTCCTATAGCTCAACCTTCCTTC R 2 1 2 1 101000 f 74 goat snp26442-scaffold276-5864964 1 95781176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409376 Affx-122954156 AX-123279727 1 94507503 TTCCACACAGGCAAAGCAGTGTTCGACTGAGCTCA[C/T]TGGAAAAGTCGTAACTGCTTATCTCTGGGAAGAGA Y 2 1 2 1 101000 r 74 goat snp26444-scaffold276-5949209 1 95864728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410639 Affx-122952080 AX-123280989 1 94587913 GTAACATCTGTATAGAAAAGAGTTAGAACCAGTAA[C/T]GGCAATTTTACTAAAATTATGATGAAAATGCAAAA Y 2 1 2 1 101000 f 74 goat snp26446-scaffold276-6029619 1 95945242 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418992 Affx-122946060 AX-123289340 1 94620426 TTCTGCTGCTGAACAATAGGATCTTCGCAAATTCC[A/G]TGCCACAAATTCAGCAATAACGTTTGGGATCGAAT R 2 1 2 1 101000 f 74 goat snp26447-scaffold276-6062132 1 95977695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419346 Affx-122945645 AX-123289694 1 94663893 CCTACCCTCTGTCCTTGTGTAGAGAAAAAACTTCA[C/T]AGAGAAACACCCCTATGTTTGTCTACTCTCCAGTT Y 2 1 2 1 101000 f 74 goat snp26448-scaffold276-6105599 1 96021061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787049 Affx-122957306 AX-385274077 1 94696407 CACAAACTCACAGAATTTTCTTCATTAGCATTTTC[C/T]TGAACTATGATGTGGAGTGCTGTGATGTGGACAAC Y 2 1 2 1 101000 f 74 goat snp26449-scaffold276-6138113 1 96049885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395698 Affx-122963731 AX-123266053 1 94796824 TCTAGATCAGCAATTTCTCATAAATCATTGGAACA[C/T]GGAACATGAAACAAGAAGAAGAAATCAGGAATTCA Y 2 1 2 1 101000 f 74 goat snp26451-scaffold276-6238530 1 96150950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387219 Affx-122970587 AX-123257577 1 94844914 CTGCATGAAACACAGAGTCTTAACTACTGGATTAC[C/T]AGGGAAGTTCCCATGATGTATACTTTGATTACAAA Y 2 1 2 1 201000 r 74 goat snp26452-scaffold276-6286620 1 96199432 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781399 Affx-122977005 AX-385268484 1 94901451 GTTACCTGAGGGGTATGGGTGTGAGGGATAAATTG[A/G]GAGACTGAATTGGCACGTATGCATGGCTATATATA R 2 1 2 1 101000 f 74 goat snp26453-scaffold276-6343157 1 96256638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401699 Affx-122959547 AX-123272052 1 94978247 CATCAGAGCATATGCAGAGAATCCATTCCTTGGCC[A/G]TGGCCATCCTAAGACTTAGCCTAGCAAGCACATGG R 2 1 2 1 201000 r 74 goat snp26455-scaffold276-6419953 1 96334092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425108 Affx-122941229 AX-123295454 1 95007910 CACACGCATGTGGCCAGGTATGTGAGATGACCCTC[A/G]TGTACCATCTCTCCATCCAGCTCCCTACTGTCCAG R 2 1 2 1 101000 r 74 goat snp26456-scaffold276-6449616 1 96364460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418581 Affx-122946373 AX-123288929 1 95038583 CTCAACTAGAGTGGTGTCCTCACTCCTTGTATATC[A/G]CTCTATTTTTTTTTTATCATGGTTCTTGTCTCCAC R 2 1 2 1 102000 f 74 goat snp26457-scaffold276-6480289 1 96398563 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425403 Affx-122941548 AX-123295749 1 95108722 GAGCCAGGCACAACAACCAAGGATAACCACCTGAT[A/G]CAGGAGTGCACATGGAAACCGTGAAGAGCAGTTGT R 2 1 2 1 101000 f 74 goat snp26459-scaffold276-6550428 1 96468553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452709 Affx-122920299 AX-123323042 1 95140184 GGAAGGACTTTAAGGAGGCAGAATTTGAACTGGAC[A/G]ACAAGATAGGTTTTAGACAGAGGGAAGTGGGGGGC R 2 1 2 1 201000 r 74 goat snp26460-scaffold276-6581890 1 96500113 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272451 Affx-1111835351 AX-519546177 1 95189909 GGACATGTGTTAAAAATGCACATTCCCTGTCTCCA[A/G]CCCCAGAATTTCTGATGTAGTGTGACAGGACCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-100 1 95189909 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800344 Affx-122954575 AX-385287266 1 95234236 GCATTGAATGGAAGTATTCCCAGGACCTTTAAGAT[A/G]TGAAGCTGGTCTGATGTACATCTGGAGCAATAAAT R 2 1 2 1 201000 r 74 goat snp26461-scaffold276-6675942 NW_017189517.1 9999612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377953 Affx-122977205 AX-123248312 1 95273319 GGGGAAGATTTCAACAGGTGAAAAGGAAGGAGGAA[C/T]AGAGAGGCAATGTTAACAGCATGCTATCAGGGAGT Y 2 1 2 1 101000 f 74 goat snp26462-scaffold276-6715025 1 96635727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411206 Affx-122952363 AX-123281556 1 95305311 TACCAGTTACGTGATGGCTGAGTTTCAGTCTCTCT[A/G]TACCACTGCCCACCTCTGAGGCTTGTTAACGTTTA R 2 1 2 1 201000 f 74 goat snp26463-scaffold276-6747017 1 96668034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449971 Affx-122922884 AX-123320306 1 95338965 TTTTCCAGTGCAAAGTACAGAGCTATTGTTTTCAA[A/G]TCAAGACTTCCTTGATCAATTTAAGCAAAACCACT R 2 1 2 1 101000 f 74 goat snp26464-scaffold276-6780671 1 96701692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404591 Affx-122957354 AX-123274943 1 95377851 CTGAATGGTAATGAAAAATTGTGCTGACAATAGAA[A/G]AAATAAGTATATTCAAATAAGTTATTCATTTTTAA R 2 1 2 1 101000 f 74 goat snp26465-scaffold276-6819557 1 96740910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771457 Affx-122938996 AX-385258615 1 95433621 TTTTAAATGCTTCTCTGAAATCAGACATCAAAGTC[G/T]TCTTTTTGGAGTCCTCATTTTCTCCAGGTAGAATT K 2 1 2 1 101000 r 74 goat snp26466-scaffold276-6875327 1 96796711 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417794 Affx-122947380 AX-123288142 1 95470528 GGATGCAGCGGGAGTTTGGAATTAGCAGATGGAAA[C/T]TACTATATAAAGGATGGATAGACAAGGCCTAGGAT Y 2 1 2 1 101000 r 74 goat snp26467-scaffold276-6912234 1 96833797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433032 Affx-122935770 AX-123303373 1 95537305 CACAGACCGTGAAGGAGCTGTTGTTACACACAGTA[C/T]GGATCCCCTCAATGTTGAAAAGTTCAGCATGAAAG Y 2 1 2 1 101000 f 74 goat snp26469-scaffold276-6979011 1 96901245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403367 Affx-122957792 AX-123273720 1 95599505 ACACTGAGACACATCTGTTCAAGTGAATCATGTAC[G/T]AGCTCAACTGACTCATGTAGCAGGGATAAGAAATT K 2 1 2 1 101000 f 74 goat snp26470-scaffold276-7041211 1 96964371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775378 Affx-122943665 AX-385262509 1 95633878 TAGTGATTTTTAATGACCATAAAATGGCAAGCACC[A/G]TGAGAATTGTATTCTGAAAACATGGTTCTTGCTTC R 2 1 2 1 101000 f 74 goat snp26471-scaffold276-7075584 1 96997427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411068 Affx-122951942 AX-123281418 1 95668644 GGTTGGTCAGTTTCCTACATAGGTGTCCTTCCACC[C/T]ACCTCCACTGGGTGGGGGAAGAGGGTGACTAAGTT Y 2 1 2 1 101000 f 74 goat snp26472-scaffold276-7110350 1 97032543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792323 Affx-122928781 AX-385279305 1 95699311 AAGTCAAAGGTATACCAGCTTGTGGGCTGTTTAAC[A/G]TGATTTATGTTACAAGAGCTTTGTAAATATATGTT R 2 1 2 1 101000 f 74 goat snp26473-scaffold276-7141017 1 97063520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453561 Affx-122919773 AX-123323894 1 95739321 ATAACACTAGAAGCTGAATTGAGTTGGACTAATAA[C/T]GACAAGCTATAGCAGAAAGCAACTAGACTTGAATC Y 2 1 2 1 201000 f 74 goat snp26474-scaffold276-7181027 1 97103252 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418570 Affx-122946382 AX-123288918 1 95796085 GCTTATGTTCTAGAATCAGAAATTCATCCACCTCA[C/T]GTGCTTTATCTATTCTGCGATCTCCTGATAGTCGC Y 2 1 2 1 101000 r 74 goat snp26475-scaffold276-7237791 1 97160638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408636 Affx-122953482 AX-123278987 1 95827435 GAATGTGGCACATCTTTTCATGGTTCTGTGTCTCC[A/G]CAAGTGCTGTCTCCTTCCTCAGAATGCTTCTCCCA R 2 1 2 1 101000 f 74 goat snp26476-scaffold276-7269141 1 97192383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438729 Affx-122930838 AX-123309066 1 95860266 TTTCCTTCCCCCGCGTAGTGCGTGCGTTTCCGAGC[G/T]CAGGGCGGAGATAGTCGCTGACCCCTGCTGTGAAG K 2 1 2 1 101000 f 74 goat snp26477-scaffold276-7301972 1 97224989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381774 Affx-122974301 AX-123252132 1 95932336 AAAAGGATGAATAAAACTTCATTTCTGCCTCCAGA[C/T]GGTAGCTTCATTTTTCATTTTTATTGGTTATAGAT Y 2 1 2 1 101000 f 74 goat snp26478-scaffold276-7374042 1 97297113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386231 Affx-122970976 AX-123256589 1 95980351 GTGGATGCAGCAGTTAGGATATTTTTTTTTCCTGA[C/T]GGTTGTCTATTCTTTAAAGGCAGGGCTGTCTAGAG Y 2 1 2 1 101000 r 74 goat snp26479-scaffold276-7422057 1 97345143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395390 Affx-122963966 AX-123265745 1 96020679 TAGAAGACAAAAAATGATAAAAGCAACTTTAACTA[C/T]AATAAACAGGGATAAATGTGAAGATGTAAAATATG Y 2 1 2 1 101000 f 74 goat snp26480-scaffold276-7462385 1 97385386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765568 Affx-122946004 AX-385253048 1 96051039 GATTAGGGAGAACAAAGCTGGCAAAAGTGGCATCA[C/T]GCCACAAATTCACTTTAGCCATATTTAGTGCAAAC Y 2 1 2 1 101000 f 74 goat snp26481-scaffold276-7492745 1 97415960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410500 Affx-122952188 AX-123280850 1 96110722 CGTACTAGAGAGAGGGCAGGAATTAGACTGATTGA[C/T]GGGGACTATCAGACTATCTGATAGTGCACTATCAG Y 2 1 2 1 101000 f 74 goat snp26482-scaffold276-7552428 1 97475669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401054 Affx-122959652 AX-123271407 1 96161019 AATGTCTTGATGGTGTCCTATCTGTGGTGCCTGTG[A/G]TGTTGTCCAACGCTAAGTATATTATTCAAAATAGT R 2 1 2 1 101000 r 74 goat snp26483-scaffold276-7602725 1 97526489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387163 Affx-122970630 AX-123257521 1 96273650 CACCTGGGAATAGCTGTCCTGTGGGATTGACTCCC[A/G]CTGGAGAAATGAGACTAGTCCCTATCACTGTCCAC R 2 1 2 1 101000 r 74 goat snp26485-scaffold276-7715356 1 97639400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779722 Affx-122931142 AX-385266822 1 96305674 GGGTAGTGACACAAACTGGCATTTCTTGAAGTTTT[A/G]TCAAATGTCCCCACATTTCATGGTTTTATGGATTA R 2 1 2 1 101000 r 74 goat snp26486-scaffold276-7747380 1 97671099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386018 Affx-122971497 AX-123256376 1 96338441 TAACTGATGTAGTTTGGTTGCTTATGTTTTTTATG[C/T]CTTCACACTGTTCTAGAAGGCTGTGCAAATGGTAA Y 2 1 2 1 101000 r 74 goat snp26487-scaffold276-7780147 1 97704458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384238 Affx-122972367 AX-123254596 1 96395839 TATTAAAGGAAATGATGCATAATAAGCACTTGACA[C/T]AGTGTAGACACTGATATTTTATGATCTTACCATCC Y 2 1 2 1 101000 f 74 goat snp26488-scaffold276-7837545 1 97762011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444095 Affx-122926832 AX-123314432 1 96440200 GGAGGCATATAATGGATTGCCTAGATTAATTAATT[A/C]TTTAGGTGCTGCAAAATGAATGTGTTCTAATTCCC M 2 1 2 1 202000 f 74 goat snp26489-scaffold276-7881906 1 97806337 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779892 Affx-122929540 AX-385266991 1 96475287 ATGGTACAAATAAGAAATATCGAACAAAAAGCACC[A/G]TTTGTGTTCTGAGACACCTATTCAGATTTCAAACC R 2 1 2 1 101000 r 74 goat snp26490-scaffold276-7916993 1 97840365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425601 Affx-122940922 AX-123295947 1 96504996 GGAACTTTTGGGTGCTAATATATCCTGGCTCTTAA[C/T]CTGGGTGATGGTTTCATGGGAGTGTTCATTTTATG Y 2 1 2 1 201000 f 74 goat snp26491-scaffold276-7946702 1 97870267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399835 Affx-122960256 AX-123270190 1 96549595 AAAATCACTCTTAAAGTGTCTGACTGAATGAATCA[A/C]ATTTTACAAATAAATATCTGTCAAAGGTGCAATTA M 2 1 2 1 101000 f 74 goat snp26492-scaffold276-7991301 1 97914078 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272617 Affx-1111832876 AX-519546328 1 96556498 CATAGTACTTGTGATTTACGATCCATATCTTAAGA[A/G]TGTTGAGTAGGAAGTTTTGTGTTTCCTGAAATCCT R 2 1 2 1 101000 r 74 goat 1_96556498_AF-PAKI 1 96556498 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795117 Affx-122973360 AX-385282076 1 96597496 CATCCTAATTTCTACAAGCTTCATATCATGTGATA[C/T]GAGCAGTTAAACCACTAGACTCAATTCTGAAAAAC Y 2 1 2 1 101000 r 74 goat snp26493-scaffold276-8039202 1 97961756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424208 Affx-122942499 AX-123294554 1 96627154 CCAGAGGGGTTCTCTGTGAAGCAAACCTTTCAACA[A/G]TTGCCTGTGATTTAGTTCAGTTCAGTTCAGTCACT R 2 1 2 1 201000 f 74 goat snp26494-scaffold276-8068860 1 97991597 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276470 Affx-1111835357 AX-519549982 1 96654492 TATTGATACTTGACATTTTCCATAATAAAAAGGTA[A/G]CCCAGAGTAAAACATAATACACTTATCAAACAATG R 2 1 2 1 101000 r 74 goat Random2.2K-101 1 96654492 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417995 Affx-122946670 AX-123288343 1 96665188 TAACTTGCATTGATTCCTGTTGAATGGGAGAGCTA[C/T]GAAAGTCAAACTCAGTTTGTCTACAGGGTCACATG Y 2 1 2 1 101000 f 74 goat snp26495-scaffold276-8106894 1 98031155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433872 Affx-122934422 AX-123304213 1 96697446 TGACTTACTTTGACTGCAGTCAGCCCCGATGAAGC[C/T]AGGAAGGCAGTCACAGGTTCCAATCATGGTGTCAC Y 2 1 2 1 201000 r 74 goat snp26496-scaffold276-8139152 1 98064098 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428277 Affx-122939398 AX-123298620 1 96760186 TCTCCTTCTGATTTTAAACAAGACTGCTTTGGATC[A/G]CTTCACAGGCAAAAAGTTCACTTGCCATTAGTTGT R 2 1 2 1 101000 r 74 goat snp26498-scaffold276-8201892 1 98127175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410502 Affx-122952186 AX-123280852 1 96812544 TAAGGTCATGTCCCTCCCAGGTCAGGCTGCAGGTT[A/G]TTATAGGCTATTGAGTCCCTGTTGCTTTGCCTCAA R 2 1 2 1 101000 r 74 goat snp26499-scaffold276-8254250 1 98179823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432333 Affx-122936288 AX-123302674 1 96947709 GACAAAATACCTTCACTGTGGAGAAAAATCATTTG[C/T]AAGTTATCAGTTTTCTACAACTTCTACACCTTTAC Y 2 1 2 1 101000 f 74 goat snp26502-scaffold276-8389415 1 98314148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409822 Affx-122952950 AX-123280173 1 96980351 ATATGAGAGGTCACACTGTAAATTGTACTTCTTTG[C/T]GGATCTTGTTCAAAAGAGTTGGAAAGCTTCTGAAT Y 2 1 2 1 101000 f 74 goat snp26503-scaffold276-8422057 1 98346991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381815 Affx-122974272 AX-123252173 1 97074803 GACTCAGAAATGTTTTACAAATTGGCTTCAGCCTA[C/T]GAATCTTTAAAATTTATGGTCATATTTGCTTTACT Y 2 1 2 1 201000 r 74 goat snp26505-scaffold276-8516509 1 98441832 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391434 Affx-122966752 AX-123261791 1 97204521 TTTAATTAAAAACACCTGGCCCATAAGTACTGCTG[C/T]ATTACCATACTAGATTTCAAAATACTCCTTTATAC Y 2 1 2 1 101000 f 74 goat snp26507-scaffold276-8646227 1 98572362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428999 Affx-122938848 AX-123299341 1 97252334 CTGTAACAAACCGAGCAGTTTAAACAACAGAAATG[C/T]ATTGTCTCTCAGCTCTACAGGCTGGAAGCCTGAGA Y 2 1 2 1 201000 r 74 goat snp26508-scaffold276-8694040 1 98620472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766213 Affx-122960271 AX-385253612 1 97309292 TAAATCAAACTTTGGATCACCTCAGACCATGTGAC[A/G]TTCACATATGTAGACAAAATTAGTTTAGCCTTTCA R 2 1 2 1 101000 f 74 goat snp26509-scaffold276-8750998 1 98677572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417608 Affx-122946873 AX-123287956 1 97345953 TATGTATATTTATGAGATAGGACACAATTAGAAGA[C/T]ACATTTAACTTGTACTTTTTTGGAAACCATACTTT Y 2 1 2 1 101000 r 74 goat snp26510-scaffold276-8787659 1 98714199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780678 Affx-122929964 AX-385267768 1 97378633 GGCTGACAGCAATCTATTGAAAATGCATTTCAGAC[G/T]ATCATTTTTCCAGTCTAATTTACTCTTAATAAAAT K 2 1 2 1 101000 f 74 goat snp26511-scaffold276-8820339 1 98747074 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398702 Affx-122961854 AX-123269057 1 97412844 GGATAAAAAAAACCAATAACCTAGCCCTGAAGAGA[C/T]GGAAAGGGGGAAAAGTAGTCAGAAACACAAATAGA Y 2 1 2 1 101000 f 74 goat snp26512-scaffold276-8854550 1 98781565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797399 Affx-122962120 AX-385284338 1 97627715 TGGAGTATTTTAGGTAAGTTCAGCCTAGCCTGATG[G/T]TATATGGGTTAGCAATAGCTCTGCTTCATTGTTGA K 2 1 2 1 101000 r 74 goat snp26517-scaffold276-9069421 1 98992253 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387788 Affx-122969703 AX-123258146 1 97670214 TATTGAGAAAAGAGCATTTAAAAAAATTTTTAAGA[C/T]GTTTTTTATGCAAAAGAGAGCTAAAAGCTACCCTT Y 2 1 2 1 103000 r 74 goat snp26518-scaffold276-9111920 1 99035156 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387388 Affx-122970424 AX-123257746 1 97712111 TTTAGAACACTTCAAATATTAATATTTCCAAGGCA[C/T]ATGTGTTGTGTCTCATTCTAATTGCCCTTTCTCTA Y 2 1 2 1 101000 r 74 goat snp26519-scaffold276-9153817 1 99076878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428783 Affx-122938413 AX-123299125 1 97767429 ACTGGCCAGCACAGAGCGTGCAAGTGTCAACACAG[C/T]GGTGAAGTTGATATAATGGTTAAGTCCAGCAAGAA Y 2 1 2 1 101000 r 74 goat snp26520-scaffold276-9209135 1 99132489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397346 Affx-122962298 AX-123267701 1 97797689 CATAAGACAGAGCATATGGTGCCCCCAAAATGATG[C/T]AGGGAATAAATGCTATTGAATTTAGAGGAATGGAG Y 2 1 2 1 101000 r 74 goat snp26521-scaffold276-9239395 1 99162718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791150 Affx-122945749 AX-385278145 1 97863426 CTAAGTATCCCTCTATCATAAAAAGCATTTTTACA[C/T]GATTGCTGGCAAAAGTTATACTTCTGATAGGTTCA Y 2 1 2 1 101000 f 74 goat snp26522-scaffold276-9305132 1 99227577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400767 Affx-122959880 AX-123271122 1 97921128 CTCCTGGCTCACAGGCTTGCCAACAGCAGGAGAGA[A/C]GTGAGAACTGTCAGATTTTTCCTCTCTACTCACTG M 2 1 2 1 101000 r 74 goat snp26523-scaffold276-9362834 1 99285884 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419756 Affx-122945877 AX-123290104 1 97952018 AGACCTTTACACCATGGGCTGTGTGCTTCCTCAGT[C/T]ACTTCAGTCGTGTCCAACTCTTTGTGACCCCACGG Y 2 1 2 1 101000 f 74 goat snp26524-scaffold276-9393724 1 99316827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796800 Affx-122962563 AX-385283743 1 97995639 ACATTTTATTACCTGAGAATGTCTGATAATGATGC[A/G]TTAAGATGTGCAGCATATATGAGCTACATTGGGGT R 2 1 2 1 101000 f 74 goat snp26525-scaffold276-9437345 1 99360577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276328 Affx-1111835362 AX-519549861 1 98018826 TGTTCTCTCCCAATTCCCAACCAGGTTCTTAAAAA[A/T]AGAATGAAAAAAAAAAAAAATCCCTAGGGTGATTT W 4 1 2 1 101000 f 74 goat Random2.2K-102 1 98018826 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418927 Affx-122946512 AX-123289275 1 98102587 TACTTATATCTTTTTTGCCCCCAACTCCTCTTTCC[A/G]CTAGAGATATCACCAAACTCCATCTTTTCCACAAT R 2 1 2 1 201000 r 74 goat snp26527-scaffold276-9544293 1 99468042 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788708 Affx-122941604 AX-385275724 1 98196876 AGGCAGTGTCAACAATAGAGCAGGTGTTGAATAAA[C/T]ACTGGTTGAAAACGACATGCCCATTGAAAAAGCTT Y 2 1 2 1 101000 f 74 goat snp26529-scaffold276-9638582 1 99563005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415094 Affx-122949451 AX-123285443 1 98263154 CATCAACTATATATAGTTCTTTAGCCATGATGTGG[A/G]CAAAATAGCTCATCTATCTACTTGGGGTCGATATA R 2 1 2 1 101000 f 74 goat snp26531-scaffold276-9704860 1 99628781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382060 Affx-122974927 AX-123252418 1 98300631 GAGACAGAGCATACTTTTAGGGATCTAAGGTTTCC[A/G]CAGAGGTCTCAGTTCTAATTTCTCACTTTGAAAAG R 2 1 2 1 101000 f 74 goat snp30205-scaffold332-1463418 1 99666864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385051 Affx-122971831 AX-123255409 1 98330312 TAAAATCATAAGGGATTTGATTTAGTATAGAAGTA[C/T]AGAAGCTGTCAAAGAACTCTGGTCTTTTGAATAAA Y 2 1 2 1 101000 r 74 goat snp30204-scaffold332-1433737 1 99696374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431178 Affx-122937184 AX-123301519 1 98361459 TTACATTTTGATAATATTATAGAATCTCATGAACA[C/T]GTGCTTGAATTTAATTAAAAAACCTTATTGATAGA Y 2 1 2 1 101000 f 74 goat snp30203-scaffold332-1402590 1 99727700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452768 Affx-122920255 AX-123323101 1 98410127 TCCACTGGAATATGTCAGAGACTGAGAAAACAGTC[A/G]CCAAAGCTTGTCTCTAAGCAATTTCCACATATTAA R 2 1 2 1 101000 r 74 goat snp30202-scaffold332-1353922 1 99776399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385320 Affx-122971669 AX-123255678 1 98457712 ACATATCCTGCATTCTGACCATTACTGACCTCTCC[C/T]CTAGGTATCTAATGCACCACAGGTTCATTTTAAGC Y 2 1 2 1 201000 r 74 goat snp30201-scaffold332-1306337 1 99824531 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391904 Affx-122966953 AX-123262261 1 98511688 CTGACAGATAAAAAGATATCTCTGCAAAGTTCTAA[C/T]GGAAGAGCATTTCAGGTAGAGAAAAACTAAAAAGA Y 2 1 2 1 101000 f 74 goat snp30200-scaffold332-1252361 1 99879308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771776 Affx-122946898 AX-385258933 1 98546397 GTTTCACAACTGCTAAATAATCCTATTGGGACATC[A/C]CTTTGTTAATGAGATAAATAGTAATCTAACCGTGG M 2 1 2 1 101000 r 74 goat snp30199-scaffold332-1217652 1 99914986 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438517 Affx-122931203 AX-123308855 1 98620925 TGTTTATTTAAAGATAACAGTATTGATGTAATATT[A/G]CATTCTTTATCAAGTGTGGCAGTCTCCCCCAATCA R 2 1 2 1 101000 r 74 goat snp30197-scaffold332-1143124 1 99991863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427304 Affx-122940147 AX-123297647 1 98673867 TGCACATATATTAATATTCATCTTATTTGCAAGAA[C/T]GATTAATTGTTATCAGCAGACAGGGACTCTAAAAG Y 2 1 2 1 101000 r 74 goat snp30196-scaffold332-1090182 1 100044856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782943 Affx-122942934 AX-385270014 1 98703635 TATAGGAAACCACACAAAAATACATACTTCTCTTC[A/G]ATTCTAATTTCTAGTATAACAATTTTCCCAATATT R 2 1 2 1 101000 f 74 goat snp30195-scaffold332-1060414 1 100074281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399050 Affx-122960909 AX-123269405 1 98749524 AATATGATAGCTATTTTTAGTTTTAGAGCTCTTTC[A/G]TTCACTTCCTACTCACTTCTTGCACAGGTCCCAGA R 2 1 2 1 101000 r 74 goat snp30194-scaffold332-1014525 1 100120292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396842 Affx-122963264 AX-123267197 1 98797269 AAGATCAGTTAACAAAAGCAGCAGACAATATAAAC[C/T]ATTTTTAGTTAGCTTTTTTGAATTCATTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp30193-scaffold332-966780 1 100168322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383687 Affx-122972495 AX-123254045 1 98881949 GGACTACTAAACAAAAAGTTGACTTGGGAGCCCAA[C/T]GGTGTCTCACTCATTTCTGGTGATCCTGGAATATC Y 2 1 2 1 303000 f 74 goat snp30191-scaffold332-882100 1 100243780 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419018 Affx-122946043 AX-123289366 1 98939212 AAAGGACCCCTGCTGGGTTCAGAGAGAGCTAAATT[A/G]CATTCATAAAGGAAATCAGAATGAATTTTGTTAAT R 2 1 2 1 101000 f 74 goat snp30190-scaffold332-824837 1 100301088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396363 Affx-122963043 AX-123266718 1 98971419 TTAAGTAAATATTAGTTCCAGTTTTTCAATTGGCC[A/G]AACATCATTTTGTATTCCTGGTAAGCTATTCAGTT R 2 1 2 1 101000 r 74 goat snp30189-scaffold332-792630 1 100333304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414058 Affx-122949770 AX-123284407 1 99021773 GACTTCTATGTGAATTATCTCTACATACAAGAAAC[A/G]TCTCTGATTATGTTGTACTCTTATAAGTTCAGTTA R 2 1 2 1 101000 f 74 goat snp30188-scaffold332-742276 1 100383617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406025 Affx-122955492 AX-123276377 1 99063921 GTTAGCAAAACATTAGCAAGGAAAAGGAGCTGTGC[A/G]GTCTGAAGGCAGAAGCCACCTGAAGCCTGGTAGGG R 2 1 2 1 101000 f 74 goat snp30187-scaffold332-700128 1 100426578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433406 Affx-122935099 AX-123303747 1 99092942 CAAGAATCTATTTGGAATATAAAAATCTGTAAATA[C/T]GTAGAGTAATAGCTTGGAATCAAATTGCCTAGGTT Y 2 1 2 1 101000 r 74 goat snp30186-scaffold332-671107 1 100456200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396338 Affx-122963063 AX-123266693 1 99128985 CTACCTGATTTTCAGTTCTTACTATCTCTCTTTGA[A/G]GACATTTTTTCAAAGCTTTACTGCGAATAGATGAC R 2 1 2 1 101000 f 74 goat snp30185-scaffold332-635064 1 100493318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380163 Affx-122975967 AX-123250521 1 99159735 ATTATGAGCCACCACTTAAGAATTTGTCCACACTT[C/T]ATTTTTATTATGATCCATGTTAAATGCTACTGTTG Y 2 1 2 1 201000 r 74 goat snp30184-scaffold332-604314 1 100524380 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783757 Affx-122976209 AX-385270813 1 99190885 GTATAAACTAAAGGAAATAGAGAATACCAAAAGGA[C/T]ACATATTGTGGACTTCTTACTAACCTTTGCAAATG Y 2 1 2 1 101000 f 74 goat snp30183-scaffold332-573164 1 100555676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446054 Affx-122925833 AX-123316391 1 99224987 GCAAAGAAAGGAAATCAAAAATTATTTCTACATTC[A/G]TAACTCTGGAAGAACTTTTGCTGGAATAAGAAACA R 2 1 2 1 101000 r 74 goat snp30182-scaffold332-539062 1 100590961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393831 Affx-122965164 AX-123264186 1 99273949 GAGGGACCAAGGAAAAGAGAGAATAGTGAGAGTGT[A/G]GAGGAGAGAGAGAAGATAGGGTGTGAGAGTGTAAA R 2 1 2 1 101000 r 74 goat snp30181-scaffold332-490100 1 100639919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441469 Affx-122928755 AX-123311806 1 99314044 GCAATAGCACGTTGGAGTTCCATAAACTCGAAAAA[C/T]GGAGCCCATGGAGGACATTGCTGAGCTCCTGAACT Y 2 1 2 1 103000 f 74 goat snp30180-scaffold332-450005 1 100681774 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405322 Affx-122956829 AX-123275674 1 99346035 AGAAATAAACATAATTTAACATTGTAGTAAAGAAA[C/T]AGGAATAAAGAAAATGTTTGGCCTGGAAGAGCTAT Y 2 1 2 1 101000 r 74 goat snp30179-scaffold332-418014 1 100714073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789235 Affx-122948634 AX-385276246 1 99399193 ATTTAAGACATTTTGATGGTCTTAATCTCACTAAC[A/G]CATAGATTTTTCATTTCACGTTTAGTCCAATACTC R 2 1 2 1 101000 f 74 goat snp30178-scaffold332-364856 1 100768105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272568 Affx-1111832877 AX-519546283 1 99427524 TAGAGAAAACTTACAAAGTGCCAGATTCCATGTAA[A/G]TTATTATGATAATGATTTCTTCTAATTGTTCTTGC R 2 1 2 1 101000 f 74 goat 1_99427524_AF-PAKI 1 99427524 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790122 Affx-122974281 AX-385277128 1 99444157 CTCTTCTAATCCTTATATGGTTAAATTTATTATTT[G/T]AGAAGCCTGTTGTAGTAAAATTCTTTAACATTAAG K 2 1 2 1 202000 f 74 goat snp30177-scaffold332-319892 1 100813411 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380379 Affx-122975337 AX-123250737 1 99492139 AAAAGTGTTTTCATGGCATTATCTCTTTTGATTAA[C/T]AGAAGACCCTTCATTTGACCTATTCTGTCTTTATC Y 2 1 2 1 101000 f 74 goat snp30176-scaffold332-271910 1 100861790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423034 Affx-122943405 AX-123293380 1 99521903 AAGTCACTTTCCCCTGGGGCATTTGCTGATTCTTA[A/G]GAGAGGGAAGAGTTTGATAATACTTGCTTTGCCCA R 2 1 2 1 201000 r 74 goat snp30175-scaffold332-242146 1 100888418 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771481 Affx-122952511 AX-385258639 1 99571306 AACTTTAAACCTAACCTATGATAGATTTTATATGC[A/G]TATTATTAATAGAAGCTTTAAGTGCTGGGAGAACT R 2 1 2 1 101000 r 74 goat snp30174-scaffold332-192743 1 100937622 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795439 Affx-122965457 AX-385282395 1 99615013 TCTATTCATTCAGTATCCAAAACTTTTTCATAGCT[A/G]TTTGCCTGTAATCTATGGTTCTGGTATCATTTAAA R 2 1 2 1 101000 f 74 goat snp30173-scaffold332-149036 1 100982156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776742 Affx-122920594 AX-385263867 1 99698840 CTTTCATCTCAAAGGGCAACCTGTGGCAAGATCAA[C/T]ATAAGACTGAGGGAAACTTCTGGACAAGCAGACAA Y 2 1 2 1 202000 r 74 goat snp30171-scaffold332-65209 1 101065184 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437573 Affx-122931879 AX-123307911 1 99760334 ATGTCTGTACTTAAAAGAGGTTTCAATATTTTTCC[A/G]TTATTGATATTTTTAGTAAGACTGTTCCCATAATG R 2 1 2 1 101000 r 74 goat snp30170-scaffold332-3715 1 101127527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795712 Affx-122948060 AX-385282665 1 99790416 CATTGTCTGCTATCACATGACTACAGAGTAGTGAA[A/C]ACAGCATTTAAACCCAGTTGTCTATCTGCTTTCAG M 2 1 2 1 101000 f 74 goat snp11326-scaffold1409-832959 1 101158863 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393720 Affx-122965236 AX-123264075 1 99848865 CTAAATCATAGGACTTTTATTGGGTCACATAATTA[C/T]GTCTCTGTTTCCATTTTGGGGGGATTCTATTGACT Y 2 1 2 1 201000 f 74 goat snp11325-scaffold1409-774510 1 101218319 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410937 Affx-122952044 AX-123281287 1 99890505 ACTACCTCTTTCCCCTAATCACACTGCATTTGAAC[A/C]AGAGCAATGATATCTGACATTTTCAAATGCTCAAT M 2 1 2 1 201000 r 74 goat snp11324-scaffold1409-732870 1 101261462 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780059 Affx-122974334 AX-385267156 1 99923271 CACTATCACTTTTGCAGGAAAGACTAGAATAAGCT[A/G]TTTTTCACAGATCTAATAGAGAAAATATGAGTGTC R 2 1 2 1 201000 r 74 goat snp11323-scaffold1409-700104 1 101294434 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799881 Affx-122949463 AX-385286807 1 99952088 CAGATGGGACATCAGTTTTACCATCATTCAGATTT[A/C]TCCCCACATTAACCCTTGATGAACTAATGACTGTC M 2 1 2 1 101000 r 74 goat snp11322-scaffold1409-671287 1 101323092 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380549 Affx-122975290 AX-123250907 1 100058091 ACTCAAAAATGCCTCAGATGCATTTTTCCAGTAAA[C/T]GTTTTATTAAAAAGAATGTATCCTTTATAAAGAAC Y 2 1 2 1 103000 f 74 goat snp11320-scaffold1409-565284 1 101430324 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775154 Affx-122973816 AX-385262286 1 100087841 ACTAACACTTTCATTTTACCTTTGTATCCTGAGGT[A/G]CTTCTGTGTCTCTTAGTATCACTTACTCCATTTTT R 2 1 2 1 101000 f 74 goat snp11319-scaffold1409-535534 1 101459994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776155 Affx-122966846 AX-385263283 1 100135816 AGTTTTGAACTTGACTGGTTTCCTAGCATCCCACT[A/C]TATTTCTAGCAAGCTTTGACCTTTACATTTTTAGA M 2 1 2 1 101000 f 74 goat snp11318-scaffold1409-487559 1 101509454 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386819 Affx-122970101 AX-123257177 1 100170030 ATTACAGTTAGAAATTAAAGAGCTGAGTAAACTAG[C/T]AGAGTTGAGTGATGGGAAAGTGAAAGTGAAAGTCA Y 2 1 2 1 201000 f 74 goat snp11317-scaffold1409-453345 1 101543519 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793752 Affx-122941188 AX-385280724 1 100213869 CATAGCCTAGGAAATGCCTAGCAGAGTAATCAATA[C/T]GTGATAAGCTCATATTGATACAGTGTCATGTTTAA Y 2 1 2 1 201000 r 74 goat snp11316-scaffold1409-409506 1 101588073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439360 Affx-122930281 AX-123309697 1 100291525 TATTGAAAAATCATTTAAAACTGTAATATGAATCC[A/G]CAAACTTTCTTTGATGAGCACTTGGTCTTGTGATA R 2 1 2 1 101000 r 74 goat snp11315-scaffold1409-331850 1 101666979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417515 Affx-122946946 AX-123287863 1 100329005 ACCTGCCGTGTACTCTGTCCAATATCCCTTTTCCA[C/T]AAATATCAGCATGGCTAGCACCATCATGGGCATTC Y 2 1 2 1 101000 f 74 goat snp11314-scaffold1409-294370 1 101703986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439525 Affx-122930122 AX-123309862 1 100390890 TTCCCTGATCTCAAAAGTCTAACACTAAATGCCTC[A/G]TAAATGCTAAATCAAATGACACTTTCTCTGTCATC R 2 1 2 1 101000 f 74 goat snp11313-scaffold1409-232485 NW_017214269.1 24061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781989 Affx-122963164 AX-385269069 1 100432606 TATAGAACAATTCAACTAAACTTTCTATCATTCTA[C/T]GTGGGTCTGACAATTTTAATGAATAGCTGGGCAAA Y 2 1 2 1 101000 r 74 goat snp11312-scaffold1409-190769 1 101808411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803264 Affx-122959801 AX-385290113 1 100507100 GTGTTTCTTCTATTCCAATCACAAACACAAAACAG[A/G]ACTCAAATTCAATCATGCCAAAAGCTCTGGGATTT R 2 1 2 1 201000 r 74 goat snp11311-scaffold1409-116275 1 101881767 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377977 Affx-122977617 AX-123248336 1 100554270 GATAAAAATAATTACATAATTTGCCCAAAGTCATG[C/T]ACTTAATAGTCACAGTAATGCTTGTTGATATTCAG Y 2 1 2 1 101000 r 74 goat snp11310-scaffold1409-69105 1 101928176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377988 Affx-122977608 AX-123248347 1 100625726 AAGTTAATTAATATCATTTAACAAATGAGACAACT[G/T]AAGGCCATTTGAGAAGAGCTAGAGATGGAGCCAGG K 2 1 2 1 101000 f 74 goat snp16781-scaffold1758-299848 1 102000881 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801466 Affx-122946686 AX-385288375 1 100668969 TTGCCACAATAGTAACATTTTCTGTGCCTGCTAGA[C/T]AATTTGCATTAAAACCTTAATATGATCAGATTTTG Y 2 1 2 1 101000 f 74 goat snp16780-scaffold1758-256605 1 102044394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779375 Affx-122950895 AX-385266479 1 100720126 CTTTCCCATTCTATATCCATACAGTTAAAATAATA[C/T]GATCATCTTAAGTCATATTTAGTAAACTTTCTTTT Y 2 1 2 1 101000 f 74 goat snp16779-scaffold1758-205448 1 102094214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794455 Affx-122934815 AX-385281418 1 100752309 TGAATAAAGTCTAAATCTGTTTTCATCTCAGCCAT[A/C]GGACCTACATTAGAGTCATACAAAATAGTTCCTTT M 2 1 2 1 101000 f 74 goat snp16778-scaffold1758-173265 1 102127057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396103 Affx-122963420 AX-123266458 1 100780930 ATGGAGCAGTGTAAAGGAATATCACAAAGTTAGGA[A/G]AGAAAGAGAAAACGTGATTAATCACTCTGCTATTT R 2 1 2 1 101000 f 74 goat snp16777-scaffold1758-144644 NW_017197173.1 3959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411470 Affx-122951802 AX-123281820 1 100822114 TCTTGATTTTCACTAAACACATAATAAATAGATTT[C/T]GTTATGAATTAAAAAACAAGATAACTCCATCTGAG Y 2 1 2 1 303000 r 74 goat snp16776-scaffold1758-103460 1 102199061 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768149 Affx-122960279 AX-385255348 1 100858117 TGATAGTTTAGGTCAGGTGAAAATTGAGATTTGAT[C/T]ATTGAATTTACCAGTAAAAAACTTGTAGGAACTTT Y 2 1 2 1 101000 f 74 goat snp16775-scaffold1758-67457 1 102235149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453193 Affx-122920454 AX-123323526 1 100894370 AACAGGCCTCATTTCTCTCTTCACTAACCTCCTTT[A/G]TAATTCTCATCAGTATTTTCACTGTTCTTGCAATT R 2 1 2 1 101000 f 74 goat snp16774-scaffold1758-31204 1 102271564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801074 Affx-122961050 AX-385287988 1 100929642 TAAAATTTTAACCATCTGGTACATATAATTCCATG[C/T]ATGTACACAGACTCATCTATTTATCCTAGCTCAAA Y 2 1 2 1 101000 r 74 goat snp23565-scaffold2379-3969 1 102511470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387466 Affx-122970361 AX-123257824 1 100982960 AGAATCAGCTCCATAACCAAGGCCTCCCACCCCCA[C/T]CCCTTAGGTTCCTTAAGCCCAGACACCTAGGACAA Y 2 1 2 1 201000 r 74 goat snp23566-scaffold2379-57287 1 102566207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799490 Affx-122974613 AX-385286420 1 101013357 TAACTCTGTCTGAAAATGTGAGGCCTCAGTCCTTG[A/G]CTCTTTGAATGTGCTTTCTGGCCACTCCTTACAAA R 2 1 2 1 101000 f 74 goat snp23567-scaffold2379-87684 1 102596487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792326 Affx-122970325 AX-385279308 1 101045550 TATATTGCAAAAATTGTACAAGTCATCAAAGCAAG[C/T]GAGAAATTTCTCATGTATTAATGGAAAATCTTACC Y 2 1 2 1 201000 r 74 goat snp23568-scaffold2379-119877 1 102628257 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444883 Affx-122926269 AX-123315220 1 101088190 TTAACTGGGAAAGCATTCATTTATTTAGGCTAAAG[G/T]AAAAATCAAGTCTCTATTGGTAAATGGTTGGATGG K 2 1 2 1 201000 r 74 goat snp23569-scaffold2379-162517 1 102670601 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378855 Affx-122976523 AX-123249214 1 101120147 TGTCTCCTAATTTAGAGTTTTCAAAACATAGGAAA[G/T]ATTTATTATTTTCTGTTTGGCTAGAGAACAAAAAG K 2 1 2 1 103000 f 74 goat snp23570-scaffold2379-194474 1 102704110 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440966 Affx-122928991 AX-123311303 1 101150938 CCTTTCCTCCCCACCTTCCTCACTTCTCTGCCAGT[A/G]TCTCCTGCACTTGAAGCATGGTCTACCTGCACTGA R 2 1 2 1 101000 r 74 goat snp23571-scaffold2379-225265 1 102734131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384003 Affx-122972914 AX-123254361 1 101176005 TATGCATCTGTCTTTGTCAATTTTGCCCAAGAGAG[C/T]CACCTACTAGAAATAAGATATTGCTTTAGTAATAG Y 2 1 2 1 101000 f 74 goat snp6965-scaffold1257-239 1 104174879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422086 Affx-122943587 AX-123292433 1 101266392 CTAGTCTGTAGCTTGACCCAGTTCGTGTCCAGAAG[A/C]CTTCTCCTGTGACTGTGTGCTTCTTTTTACTTCAA M 2 1 2 1 101000 f 74 goat snp6966-scaffold1257-90626 1 104084475 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786601 Affx-122920958 AX-385273633 1 101318645 ATATATGAAGACAAATTCTACAAGCTTTCACTGCT[A/C]TGTCCTTCATCTATGATTATATGTCCTATGTTCTT M 2 1 2 1 101000 r 74 goat snp6967-scaffold1257-142879 1 104031749 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793671 Affx-122944697 AX-186719019 1 101371482 AGTAATTCATTAGTATTACTAATGTACTGTCCTGG[C/T]AGGAGAGCATACAGTAGGCTTTTAATAAATGTTGA Y 2 1 2 1 201000 r 74 goat snp6968-scaffold1257-195716 1 103978156 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411589 Affx-122951615 AX-123281939 1 101400148 ACAGAGAACTGAGCAAAGAAGTGTTTGTTAAAGGA[A/G]CAAATAAAGAAATGAATACTATTTCAGTTTTTCTA R 2 1 2 1 101000 f 74 goat snp6969-scaffold1257-224382 1 103949486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421442 Affx-122943948 AX-123291789 1 101446612 AAGCCCAGTAGAAACAGGTTCAAGAAGCACTAAAA[C/T]AGTGATCCATCAGACTACAAAATGGGAGAGGCTTA Y 2 1 2 1 101000 f 74 goat snp6970-scaffold1257-270846 1 103907140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439927 Affx-122930009 AX-123310264 1 101515524 TGGTAATCATAATAAAATATTATTGTGATAGGGAA[G/T]AACAAGTCTGACCCCATATTAGACCCTTTCCTTTT K 2 1 2 1 103000 r 74 goat snp6971-scaffold1257-339758 1 103840418 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384277 Affx-122972304 AX-123254635 1 101558427 GAAGTATAGCAGTGAGGATGATCTTGACTGGATCT[A/C]GGTGTAACTTTCAGGGTTGTCATCTGTTTGTTTCT M 2 1 2 1 101000 f 74 goat snp6972-scaffold1257-382661 1 103797477 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421771 Affx-122944352 AX-123292118 1 101597885 AGGCAGCTAGTGATAATGTAGGAGGTGGGGTGCCT[A/G]CTGGAAAGTCCACCATAGTGAGTAGAAAAAAAGAT R 2 1 2 1 101000 r 74 goat snp6973-scaffold1257-422119 1 103757944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276349 Affx-1111835372 AX-519549881 1 101629228 TTGATATTTACTAACTTGAAAATGAGAGCTTGACA[A/C]ATATTTTTTTCTTTTGTCCTTAGAAAGGTGTATTT M 2 1 2 1 201000 f 74 goat Random2.2K-104 1 101629228 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437926 Affx-122931640 AX-123308264 1 101635571 GCTGTCAATCACTCTGTACCACTTAATTTGTGGCA[A/G]AAATGACTTGACCTTCATTTTCAGAAAAATTGTCA R 2 1 2 1 101000 f 74 goat snp6974-scaffold1257-459805 1 103720380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413557 Affx-122950599 AX-123283906 1 101668450 TTGCATTGCAGAAATAAATCCCCTTCAGCTATGAT[A/G]TATAATCTGACCAATTAACTGTTGAGTTAGTTTGC R 2 1 2 1 201000 r 74 goat snp6975-scaffold1257-492684 1 103686836 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794317 Affx-122926406 AX-385281281 1 101714367 TTGCTAGTGAACAATTTATTATACCTGAAAAATCT[A/G]TTCTTGATCAATAATGTATTTTCTCAAACACACTG R 2 1 2 1 101000 r 74 goat snp6976-scaffold1257-538601 1 103640088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790660 Affx-122975211 AX-385277662 1 101757470 AAGATACCTTAAGTAGTTAGTAGAGCTTTGCTGAA[C/T]GAAAACCTCAGTAAAATGCAAACGTAACAGGTGTG Y 2 1 2 1 101000 r 74 goat snp6977-scaffold1257-581704 1 103597193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769451 Affx-122950470 AX-385256621 1 101813056 TATTTTCATGTAATTATTTTTCCCATCCATATTAC[A/G]TTTAATGTGCTCATCTGTTTTCACAAGAAAGTAAG R 2 1 2 1 202000 f 74 goat snp6978-scaffold1257-637290 1 103541242 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800099 Affx-122957660 AX-385287022 1 101842821 AACCCTATCAGTTTCTCACAGTGAATGTAGAGCAA[A/G]TAAATCTCTCATGCTTTTGACAACACAAATAAAGC R 2 1 2 1 101000 f 74 goat snp6979-scaffold1257-667055 1 103511221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425625 Affx-122940902 AX-123295971 1 101872057 TAAACTCAGATGCACAGTTAGTCAGTGTTGTAAAA[C/T]GGACACTAGGTCAACTCAACTATAAATTCTGAGGA Y 2 1 2 1 101000 f 74 goat snp6980-scaffold1257-696291 1 103481804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799631 Affx-122977588 AX-385286560 1 101910090 TATGTTGTGGTTTCTGTTTCAGCAATACAGCTTTT[C/T]TAGAGCCAAATTTTTGTAGCTACATATTGTTAAAT Y 2 1 2 1 101000 f 74 goat snp6981-scaffold1257-734324 1 103443466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272455 Affx-1111836713 AX-519546180 1 101941444 TGAAAGTGAATTCGCTCCGTCATGCCCGACTCTTT[A/G]AGACCTCATGGACTGTAGCTTACCAGGCTCCTCTG R 2 1 2 1 103000 f 74 goat 1_101941444_AF-PAKI 1 101941444 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437842 Affx-122932092 AX-123308180 1 101945943 CATATTGTTTCTGACCTTACTAATTTTCAAAAGTA[A/G]CAGAAAAAATGCAAATAGAGAAAAGAACAGTCCCT R 2 1 2 1 202000 f 74 goat snp6982-scaffold1257-770177 1 103407638 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799862 Affx-122977085 AX-385286788 1 101987942 TGAATTTCAATTAATGATTTCTGTTGGTTTCAATC[A/G]TTCTTATTAAATTGATCTCAAATACTTATGATGGT R 2 1 2 1 102000 f 74 goat snp6983-scaffold1257-812176 1 103365326 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418269 Affx-122947013 AX-123288617 1 102063360 CAAGTAGAAATCCTGAATTTTTTGGTTTTCTTTTA[C/T]GGAATAATAAAGGTTTGTTTGTTGTTATTTGATTT Y 2 1 2 1 303000 r 74 goat snp6984-scaffold1257-887594 1 103288682 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400728 Affx-122959911 AX-123271083 1 102100621 GGAACAGCAACAGGGTTTGGTGAGAGAAAAAGAAG[C/T]AATTTTACTGGAGAGAAACTTGGCAGACATCACAC Y 2 1 2 1 101000 f 74 goat snp6985-scaffold1257-924855 1 103251264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402188 Affx-122959177 AX-123272541 1 102141402 TTGATCTATTCAAGATAAGTGGATTCAGCACCTAA[C/T]GTTGAATTGGCAGACATGGCATTGATAAATCTGAC Y 2 1 2 1 101000 r 74 goat snp6986-scaffold1257-965636 1 103210408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399681 Affx-122960498 AX-123270036 1 102184497 CCTTCTTATTCCAGCACCTTAGACCACTCGGCCAC[A/G]CTACCTCCCATTATAGCTTTCTGTTTTAGAAAACA R 2 1 2 1 201000 r 74 goat snp6987-scaffold1257-1008731 1 103166950 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798317 Affx-122939953 AX-385285252 1 102286494 ATCAACTGTATTTATATTGTAGTAAATATTCTGAT[A/G]TCTCCAACTCTAAGCCATAGTCATGTGTATCTTTC R 2 1 2 1 101000 r 74 goat snp6988-scaffold1257-1110728 1 103064675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417375 Affx-122947705 AX-123287723 1 102319345 AAGGCAGACTGAGCATGGATCAACAGGGAAGCCAA[C/T]AAGAAAATATTTAAATAAGGAAGGAATGACAGACT Y 2 1 2 1 101000 f 74 goat snp6989-scaffold1257-1143579 1 103032015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798038 Affx-122952376 AX-385284974 1 102354075 AGCCTTTTACACTTTTTCAGTTCAAGTGTTCTCCA[A/G]AATTGCTGAATTCAGTGAAAGCAGCCTAATGTTAG R 2 1 2 1 201000 r 74 goat snp6990-scaffold1257-1178309 1 102996619 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442456 Affx-122927951 AX-123312793 1 102389546 AGAGACAGGTCTGTATGGAGAGTATTACCTTAAAC[G/T]AGTGGGAAGGCATAGCTAGCCTTCAATAATTTCTC K 2 1 2 1 101000 f 74 goat snp6991-scaffold1257-1213780 1 102961211 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403157 Affx-122958093 AX-123273510 1 102435910 TTCCAAATATTAGACATATATAGAGAGATGCAAAA[C/T]GCAATTCAACCACAGTATTAAACCTTGGCCATCAC Y 2 1 2 1 101000 r 74 goat snp6992-scaffold1257-1260144 1 102914890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387883 Affx-122969625 AX-123258241 1 102493999 CTGTTTGGCACTTTCTATTTATTCCTTATGCTACA[G/T]CCAGAGTGATCTTTCACAAAACAAATATTATTCTC K 2 1 2 1 101000 f 74 goat snp6993-scaffold1257-1318233 NW_017192230.1 13525 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404793 Affx-122956669 AX-123275145 1 102526031 TGTTCAAGAGTTCTCAATTAATATCTGAATCTATG[C/T]ATTATGTCTCATTTGGCCTCCAAGGTATTCCAGGG Y 2 1 2 1 101000 r 74 goat snp6994-scaffold1257-1350265 1 102819448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796654 Affx-122973434 AX-385283600 1 102569430 ATTATCAACAATTATAGTACTTGTCCCTATTATCC[C/T]TATGATGAATACACAAGCATTACAGCATTGCTTGT Y 2 1 2 1 101000 r 74 goat snp6995-scaffold1257-1393664 1 102775573 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393022 Affx-122965644 AX-123263379 1 102610519 CTCCTTCTGTGCTCACTCTACAATCTTTGTCTTGG[C/T]AATCTCATGATCTCTTTAATACCAGTGTGTTTAAT Y 2 1 2 1 101000 r 74 goat snp46637-scaffold65-82482 1 104194587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442749 Affx-122927840 AX-123313086 1 102697159 TGTTCTATTTTCTCTCGTAGTGGGAAAGCATCGCC[A/G]TTCAAGTCACATAAACATATGTGCAAAGCTGGGTT R 2 1 2 1 101000 f 74 goat snp46639-scaffold65-169122 1 104282287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424194 Affx-122942512 AX-123294540 1 102774805 AAGCTATTAAAATGTTACACTGTCATTTGTTTCCA[A/G]ATATCTTTAACACCTCCTTTCATACTTCAGTGACA R 2 1 2 1 101000 r 74 goat snp46640-scaffold65-246768 1 104363174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428178 Affx-122939028 AX-123298521 1 102803378 GTGTTCTTCAAGAGAATTAATAGGCCAGGCATAGC[C/T]AGAGGAAACTCTTCAGATAAAGAGACATTTAAAAC Y 2 1 2 1 101000 f 74 goat snp46641-scaffold65-275341 1 104391750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379979 Affx-122975624 AX-123250337 1 102845039 GTGAATCTCTATGTGTTACATCTGGTTTATGTGGG[C/T]AAAACTTCAGGATAACTCAAAAGATGATTGTGACC Y 2 1 2 1 101000 f 74 goat snp46642-scaffold65-317002 1 104433935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394343 Affx-122964662 AX-123264698 1 102875009 ATTTTCCTCAGTTATATAGGTGAGAAGGGGGAGGC[A/G]TTAAACATCATAATGAATACTAAGGACTATAAGTT R 2 1 2 1 201000 r 74 goat snp46643-scaffold65-346972 1 104464784 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787176 Affx-122941687 AX-385274202 1 102915602 TTCTTAATAGCCTTTCATCTCACTTACAAAAGAAA[C/T]GTCTATCACTCAATGAATTCAGATCATATCATTCT Y 2 1 2 1 101000 r 74 goat snp46644-scaffold65-387565 1 104506940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453291 Affx-122920375 AX-123323624 1 102949121 TATGGTATTTTCTACACAAAACAAGTACTATGTTC[G/T]AGGTAGAAGTTAATTGAGATCATATTTGGCTTATT K 2 1 2 1 101000 r 74 goat snp46645-scaffold65-421084 1 104541287 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276384 Affx-1111835390 AX-519549912 1 102958686 CTACAGTTTTGTCTTTTCGAAAATGCCATGCAAAC[A/G]AAATGATTTGTAAATATATGCCTTTTCAGACAAGC R 2 1 2 1 101000 f 74 goat Random2.2K-107 1 102958686 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778136 Affx-122952574 AX-385265251 1 103031962 CTATATTCTGCGTGTTCTTATGCATTACAAAATAT[A/G]TCCACATCAAGAACTTTCATAGAATTTGTGCCACT R 2 1 2 1 101000 r 74 goat snp46647-scaffold65-503925 1 104625709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788710 Affx-122928336 AX-385275726 1 103062902 TTTCCAGACCAAAGTTAAAAGAAAAGACAAGTTAA[C/T]GGTAACTGAAGTGTCTAAATTCGTGGAAATTTAAA Y 2 1 2 1 101000 f 74 goat snp46648-scaffold65-534865 1 104657505 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453107 Affx-122920027 AX-123323440 1 103093925 AGAATCTTGAAAATAGGTTTAAGTTTATTATAATT[G/T]TGCATTTGCTGCAAGAAAGGAGGATAGTGTTCATG K 2 1 2 1 202000 f 74 goat snp46649-scaffold65-565888 1 104689293 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383661 Affx-122972516 AX-123254019 1 103133040 AGTGTTGTGGGTGTTACATTCATGATGGCCCACAG[A/C]TGAGAGAGAGAGAGTTAAGAGATAGAAATAGAGGT M 2 1 2 1 101000 f 74 goat snp46650-scaffold65-605003 1 104729579 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429430 Affx-122938510 AX-123299772 1 103166746 AATGCAGCAATTTGGATTAACCCCATACCCATTAC[A/G]CTGAGTAAAATAAATAAGACTAGAAAATTTACATC R 2 1 2 1 201000 r 74 goat snp46651-scaffold65-638709 1 104762755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794304 Affx-122963229 AX-385281268 1 103220400 GCTCAAGGCCACATACTTAATTAGTAGCAAAGATG[C/T]ATCTAGAATGAAGTTTCCTGACTTCCAGTCCATTT Y 2 1 2 1 101000 r 74 goat snp46652-scaffold65-692363 1 104816114 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404202 Affx-122957672 AX-123274554 1 103250664 AGTGGAAGAAATACCACTTGATGGATAAGGAAAAT[A/G]TGTTCTCTAAATACAATGGAGTCACTTGACTGCCA R 2 1 2 1 101000 r 74 goat snp46653-scaffold65-722627 1 104846416 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423087 Affx-122942930 AX-123293433 1 103287344 ACAGTTTCCAGAAAGCATATTATCCATAAATACTT[A/C]ATGAATTGATTTACTATGATTTTAAGAACACTGGG M 2 1 2 1 101000 r 74 goat snp46654-scaffold65-759307 1 104883367 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786681 Affx-122974895 AX-385273714 1 103352668 GATACTATAAATAAATTTAACTACTTTCCAGTTAC[A/C]TAAGGAATTTAAAAGCTTAAAAGTTAGGGTAATGT M 2 1 2 1 201000 r 74 goat snp46655-scaffold65-824631 1 104949406 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775272 Affx-122946893 AX-385262403 1 103398431 TCTAGGTGATTCATGGACACATCAGAGTACGAGAA[C/T]CACTACTCTACAGAAAAAATAACCCCCATTTAAGT Y 2 1 2 1 201000 r 74 goat snp46656-scaffold65-870394 1 104992417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443652 Affx-122927201 AX-123313989 1 103438369 ACCATTCACAAAATAAACTGTCAAAAAATTTCTAG[C/T]AGCTTTTCCCTCCTCCCAAATCTATCAAAAATAAA Y 2 1 2 1 101000 r 74 goat snp46657-scaffold65-910332 1 105032208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428446 Affx-122938812 AX-123298789 1 103467000 GAGCACATAGAAAATGAAAAGCCAAAACTTCACAG[C/T]AGCTATTTTTGTGTGTGCTAAGTTGCTTTGGTTGT Y 2 1 2 1 201000 f 74 goat snp46658-scaffold65-938963 1 105061986 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416768 Affx-122948177 AX-123287116 1 103508963 TGGAAGCCACCAATTCAAATATGGAAATCAACACT[A/G]CACACTGAGATTATTTTGTTCTAAGTTCACCATCA R 2 1 2 1 101000 f 74 goat snp46659-scaffold65-980926 1 105104279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788772 Affx-122972269 AX-385275787 1 103549287 TGATGTCTTAGATCAGCACTTTTGAAACCATTTTA[A/G]CAGTAAAGCCATTTTATCAAAAAATCTCCTACACA R 2 1 2 1 201000 r 74 goat snp46660-scaffold65-1021250 1 105142293 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441616 Affx-122928648 AX-123311953 1 103580318 ATGACCACCAACTAAACTTAATAGACTAATCTGCC[A/G]TGTGATTTGAGGGTGCAGCAGAAAAACAAATAAGA R 2 1 2 1 101000 f 74 goat snp46661-scaffold65-1052281 1 105174455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450514 Affx-122922501 AX-123320848 1 103632606 AACTGTAAAACTTTATGTTACAAATAGATTCATAA[C/T]GGTTTTAAGATAAACCTCTTGGGAAGAAAAAATGT Y 2 1 2 1 101000 r 74 goat snp46662-scaffold65-1104569 1 105228884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436923 Affx-122933197 AX-123307261 1 103664741 GTTTTATCATAATTTTTTCTCACCAATTTTATTTC[G/T]TATAGGACATCTAGATTGCTTCATACGGTTCACCA K 2 1 2 1 201000 f 74 goat snp46663-scaffold65-1136704 1 105261369 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431891 Affx-122936012 AX-123302232 1 103718868 CACTATAATTTTTCCAGGAATCAGAGATCAAGATG[C/T]GATCCTGAAAGCTTCCAGAGGTACATTTAACAAGA Y 2 1 2 1 201000 r 74 goat snp46664-scaffold65-1190831 1 105316122 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276393 Affx-1111835395 AX-519549921 1 103732995 ATGCTTAACAAGATATAAGTAAATTGAGCACAGCT[A/G]TATATGTGAAAAAGAAAATATACCATGAAGAAGTA R 2 1 2 1 101000 f 74 goat Random2.2K-108 1 103732995 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384444 Affx-122973100 AX-123254802 1 103769606 CGAGAGTGAAGTGAATAAAGATCCAAGAAAATGCA[G/T]CCCGTGTCTTTGTGGTAGCTTCTCTGTACCTTGTC K 2 1 2 1 201000 f 74 goat snp46665-scaffold65-1241569 1 105366950 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429563 Affx-122937815 AX-123299905 1 103801231 CAAGTTTAGATAAGTTATGTTTTTCTTTTTTAAAC[G/T]AAGTTGCTAAATATTTTTTCAAAGGGACTTCTCTT K 2 1 2 1 303000 f 74 goat snp46666-scaffold65-1273194 1 105397841 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769090 Affx-122952408 AX-385256265 1 103830056 TGTCTCCTTTATCTCCTTTGGTACCATTGGCACTC[A/G]TGTCCCCCTTCAAGCCTTTTTGTCCTTTCACTCCC R 2 1 2 1 101000 f 74 goat snp46667-scaffold65-1302019 1 105426753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422118 Affx-122943559 AX-123292465 1 103862840 CTATACCACAACTTTCCACGCTTCAAAACATCAGT[A/G]CAAAAATTGGATATAAGACAGCAGAGGAAAGACTG R 2 1 2 1 101000 r 74 goat snp46668-scaffold65-1334803 1 105460312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426315 Affx-122940285 AX-123296661 1 103907765 CAGAAGGCCTATGGGACTGTAGCCTAGTCTATAAG[C/T]AAAGATGAATATAAAATCTGAATTATAAAACAATT Y 2 1 2 1 101000 f 74 goat snp46669-scaffold65-1379728 1 105505645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769640 Affx-122951639 AX-385256810 1 103937426 GTTCTAACTCTTGAGGCAGGCATTGTGGAAGGAAT[A/G]TACTCTCCTTACAGGAAATGGCTTTGTGCTCTCTT R 2 1 2 1 101000 f 74 goat snp46670-scaffold65-1409389 1 105536119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441696 Affx-122929165 AX-123312033 1 103968062 GGAGGTCATAATTTTACTTACTAACCATGAGGAAA[C/T]GCTACCAAATGTTAAAGTGGAAAAATACCTTATAA Y 2 1 2 1 101000 f 74 goat snp46671-scaffold65-1440025 1 105567454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385282 Affx-122972065 AX-123255640 1 104004062 TGAAGACCTGGGGATGAAAAGAGAAAATCAGAATC[A/G]TTATGATGCACATGGCACATAGTTGCCAGTAAAGG R 2 1 2 1 101000 f 74 goat snp46672-scaffold65-1476025 1 105603413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775061 Affx-122964667 AX-385262193 1 104052633 GACATAATGATGACAATGGAATTCATTAAATTTAG[C/T]GATTGAAATATGTACAGGATGTTACAGGAGCACTT Y 2 1 2 1 201000 f 74 goat snp46673-scaffold65-1524596 1 105651989 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384902 Affx-122972348 AX-123255260 1 104087392 TTCCCAAGATCAGCCAGTGGTCCATACAGCTCAGC[A/G]TGGAAGATGCCTCAAGACACTGGTCAGTTCAAGGC R 2 1 2 1 201000 r 74 goat snp46674-scaffold65-1559355 1 105686917 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320800271 Affx-122942419 AX-385287194 1 104120191 CAGACAGTGTAAATCTAATAGTTTTCACCACAATC[A/G]CCACATGTTAAAAGCAAATAGCATACAAACACAAA R 2 1 2 1 101000 r 74 goat snp46675-scaffold65-1592154 1 105719714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440219 Affx-122930686 AX-123310556 1 104177654 GGACCAAATGAGAGTGACACCTGGCAAACAGCTGG[C/T]GACTGAACCTCCTATTTTATATATCCTGGTTATTA Y 2 1 2 1 101000 r 74 goat snp46676-scaffold65-1649617 1 105777647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389094 Affx-122968580 AX-123259452 1 104232794 CTTCACCCCATCTGGAAGATAACTATCAATCTGAA[C/T]TTCTCTAATCAGTTTGCTCCTGTTTTCTAGCTGAA Y 2 1 2 1 201000 r 74 goat snp46677-scaffold65-1704757 1 105833294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378183 Affx-122976949 AX-123248542 1 104262462 TTGAGTCCTGGAAATTTGATGAAAAAGTTTTGACT[A/C]TGGGGTACAGTAGGGATCAAAAACTGAAATGCCTT M 2 1 2 1 201000 f 74 goat snp46678-scaffold65-1734425 1 105863983 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428097 Affx-122939090 AX-123298440 1 104309467 TTTGTGTACTTTATAAGTCCTGATCTGTTTCAGAA[C/T]GTTGTTATTTCATCTTCATTTCACCTGAACTCTCT Y 2 1 2 1 201000 f 74 goat snp46679-scaffold65-1781430 1 105911209 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447057 Affx-122924517 AX-123317393 1 104350215 ACGTTGGCCATGAAGAAGGGCAAATTCAGTGGCCA[C/T]GCATTTGATGGGAAACATTACAAAGTCCAGTCCCA Y 2 1 2 1 101000 r 74 goat snp46680-scaffold65-1822178 1 105951949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783978 Affx-122961953 AX-385271032 1 104420774 GGAGAAGGTGGAGGCAGGTTGGAAATGGAAAACCA[C/T]AGCTGTATACAAACACTACTATAGTAAATGGATTT Y 2 1 2 1 101000 f 74 goat snp46681-scaffold65-1892737 1 106022999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400505 Affx-122961278 AX-123270860 1 104450543 TCAATTCTGTAAATGCTGAGTAGAAAAGAGCTAAA[C/T]TTTAGAACAGTAACTCAGGGATGATGGCTACGTAT Y 2 1 2 1 101000 f 74 goat snp46682-scaffold65-1922506 1 106052836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272459 Affx-1111836715 AX-519546184 1 104453302 GTACCAGCAAAGTGCAGCCGCTGCTCCTTCACTTG[A/G]ACAAGGGGTATCTCCTCACCACCGCCCCTCCTCAC R 2 1 2 1 103000 f 74 goat 1_104453302_AF-PAKI 1 104453302 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404110 Affx-122957115 AX-123274462 1 104488780 CATAACTAAGCACTGTGGGAATACTCAATTGACTG[C/T]GCCTAAGACAATAATTTTTTTCATAGGGCAGAAAT Y 2 1 2 1 101000 f 74 goat snp46683-scaffold65-1960743 1 106092190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770907 Affx-122969619 AX-385258070 1 104549729 CCTACAAATGCCCTCTGTGGCACCCAGACAGGTAT[A/G]TCCTAAAAATACCTTTACCTTGTACACTTAACACC R 2 1 2 1 101000 f 74 goat snp46684-scaffold65-2021692 1 106152827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412510 Affx-122951362 AX-123282859 1 104611949 GGGTGCTGAAAGGGTAATGTGAATGGACTGAGCAA[C/T]GTAAACGTCAGGCAACAGCTGGTGTGGTAGACTGC Y 2 1 2 1 101000 f 74 goat snp46685-scaffold65-2083912 1 106215675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802631 Affx-122971493 AX-385289532 1 104659384 CTTAACCTCTCAGAGCCTTAATTTCTACTTATGTA[C/T]GTAGATAACACAGTACCTACCTCAAAAAAGTGTCA Y 2 1 2 1 101000 f 74 goat snp46686-scaffold65-2131347 1 106262965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376171 Affx-122978836 AX-123246530 1 104750455 CTTACGTGTGGTTTTCTTTTTGAAATCTAGGAAAC[A/C]GGAGGACTAGGTTTAGTAAGTGCTTAATCATTTCT M 2 1 2 1 101000 r 74 goat snp46687-scaffold65-2222418 1 106353702 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772291 Affx-122978986 AX-385259446 1 104783969 AAGTTCAAAGTATTATGAAATCAAATATAAAATAA[C/T]ATGGTCTTATTCATTAGCCGTATAACAAAGATTTA Y 2 1 2 1 303000 f 74 goat snp46688-scaffold65-2255932 1 106386642 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375447 Affx-122979170 AX-123245806 1 104830876 TCATGAATGACCAGACATTTCTCTTCTGAGTAGGA[C/T]AGAAGAATATTTCTGAGCTCTCATCCAATGACCTG Y 2 1 2 1 101000 f 74 goat snp46689-scaffold65-2302839 1 106428851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404657 Affx-122957300 AX-123275009 1 104875301 CCTACCTTTCTGTTCCTGGCTTCTCATGTTCTTCA[A/G]CAGATCCTGCACGACATCGTTTATGCATCTCTGTT R 2 1 2 1 201000 r 74 goat snp46690-scaffold65-2347264 1 106473927 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772269 Affx-122934069 AX-385259424 1 104911625 TAGTACCATCTGCAGTCATCATTCTTCAGAAGATA[G/T]CCATTTTGCATATTCTCTTCAGTTTCTTCCCTTTT K 2 1 2 1 101000 r 74 goat snp46691-scaffold65-2383588 1 106510449 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385883 Affx-122971596 AX-123256241 1 104946320 TTCCTTGCATACCTGGTTCTCACACACTTGTACAC[A/G]TGAGGACCTATGTGTCCTGTTGTGATCCCCTGCCT R 2 1 2 1 101000 f 74 goat snp46692-scaffold65-2418283 1 106545999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407211 Affx-122955391 AX-123277562 1 104979465 CAAAGCCATGTATTTAGTATGAGAGACCCATATAT[A/G]TATTTTAAGAGTTCACCTGTTGTGTTACCTTTAAA R 2 1 2 1 101000 r 74 goat snp46693-scaffold65-2451428 1 106579185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427391 Affx-122940080 AX-123297734 1 105014852 ACTTGGTTAAAAAAAAGTTAGCACTTATGTGGGAT[A/G]TATGAAAAGAGAAAGAGACTGAGATCAAGCATGGC R 2 1 2 1 201000 f 74 goat snp46694-scaffold65-2486815 1 106614605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450345 Affx-122922115 AX-123320680 1 105063445 AATTAATTAAAAGTGGGGAAGAGGGATTATGTTTA[A/G]TAACCTGGAAAGCTATATATAGTAATTTATTTAGT R 2 1 2 1 101000 f 74 goat snp46695-scaffold65-2535408 1 106663203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792811 Affx-122958313 AX-385279789 1 105119453 CTGTCAGAATCCAATTATCTACCTGCCTATTGAGC[A/G]TTCCCATTGGATGTCTCATATGTTTGAGTTCAAAT R 2 1 2 1 101000 f 74 goat snp46696-scaffold65-2591416 1 106720153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382366 Affx-122973864 AX-123252724 1 105155775 AAGCTGGTACAAGAAAAACATCTCGATTCATATCA[C/T]GTGTATTTTCACAAGATTTGTTGTACAGTTCAAGA Y 2 1 2 1 101000 f 74 goat snp46697-scaffold65-2627738 1 106757188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771980 Affx-122929067 AX-385259136 1 105208609 GGAAGGGAGTTCTCTAAAGATGAATTGCACTTAAC[A/G]TCCTTGTTTTTTCCACAGCCAAACCAATGCGATTT R 2 1 2 1 101000 f 74 goat snp46698-scaffold65-2680572 1 106810286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451325 Affx-122921276 AX-123321658 1 105262165 AATATATTATCTTCTGAGTCTAAAAGGGCTCAGAA[C/T]AGAGATGTGCAGATTCATCTTGAAGACACTGCCTG Y 2 1 2 1 101000 r 74 goat snp46699-scaffold65-2734128 1 106864329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434414 Affx-122934676 AX-123304755 1 105305766 GGAGGAGGATGAGCAACTGTCCCTTTTTGCCTGAG[A/G]AGTTTCCTCAGCACATGGCACTTTCCGTGCTAAAG R 2 1 2 1 101000 r 74 goat snp46700-scaffold65-2777729 1 106906595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434277 Affx-122934778 AX-123304618 1 105343434 CCTTCCTGTGTTAACAGACCGAGATACCAACATGA[C/T]GTTCAAAGTCTTCCATGTTAAAAGTACTGGGGCCT Y 2 1 2 1 101000 f 74 goat snp46701-scaffold65-2815397 1 106944354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430175 Affx-122937364 AX-123300516 1 105390780 CAATCTCTTGAGTGATAAGCTTCCTTATAAACTGC[A/G]CATCTACCAGTAATGCAGATATGCCTTCAACAAGG R 2 1 2 1 101000 f 74 goat snp46702-scaffold65-2862743 1 106991831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387773 Affx-122969715 AX-123258131 1 105420634 GTCTGCCATACTGTCTTAAGCTTCCTGTTCTTCAT[C/T]TGCAAATGAGGATAACCATATCTACCACATAAGGT Y 2 1 2 1 201000 r 74 goat snp46703-scaffold65-2892597 1 107021537 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452192 Affx-122920825 AX-123322525 1 105498797 TTGGCAGACTGCTACGTGCAAAAAGCTGCTTGACA[C/T]GTGTCTTGCCTTGGATTTGATTTCTGGAAGGTCTG Y 2 1 2 1 101000 f 74 goat snp46704-scaffold65-2970760 1 107099865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771625 Affx-122919605 AX-385258783 1 105535467 GAAGCAGTAATTGTACCAGTCAATAGGTTTTCTAA[C/T]GTGAATTCTTGACCAGCTTCAATGCTGTTAAGAAC Y 2 1 2 1 101000 r 74 goat snp46705-scaffold65-3007430 1 107136658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775852 Affx-122970025 AX-385262983 1 105583841 TCGTATTTTTATTTCTAAGACAAAACCTTGAGAAC[A/G]GAGCCACTTGGAACAGTAGAAAGAACAGCATCCTT R 2 1 2 1 101000 r 74 goat snp46706-scaffold65-3055804 1 107185022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390949 Affx-122967061 AX-123261306 1 105628109 ACACAGAGCTAACCGCACAGGCAAAAGTCGAGAGG[C/T]GGGAATAGCTTAATTGGGTCTCCTCACAGAGGAAA Y 2 1 2 1 201000 r 74 goat snp46707-scaffold65-3100072 1 107229275 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432807 Affx-122935403 AX-123303148 1 105659998 CCAGCATTGTGTGTGTTAACAAGCCTTGCTGATGC[A/G]TGCTCTCTCTAGTTTGGGAAGCACTGCAGTAGGGA R 2 1 2 1 101000 f 74 goat snp46708-scaffold65-3131961 1 107261417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382700 Affx-122973633 AX-123253058 1 105715197 AAGAGAAACGTCCACTGAACAAGTAAACTGCGGTA[C/T]GTCAGTGACTTAATGAAATATTCTTCAGGCACCAA Y 2 1 2 1 101000 f 74 goat snp46709-scaffold65-3187160 1 107316338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426750 Affx-122939861 AX-123297096 1 105756410 ATATGGCTATCACTACATTAAATGTGTTAAAGACC[A/G]CCTCTGAATGCCTCAGCAAAAAATAATAAATGCAA R 2 1 2 1 101000 f 74 goat snp46710-scaffold65-3228373 1 107357625 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786384 Affx-122936500 AX-385273418 1 105830289 TTCTGGTTCACTTACTGATACTTTGACTAGTACTT[A/G]TTTGAAAAATGCTGACATGGAACACGAGAGAATAC R 2 1 2 1 101000 r 74 goat snp46711-scaffold65-3302252 1 107430715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411723 Affx-122951525 AX-123282073 1 105872247 AGTGGGAATTTCAGGCTCTCCGAGCACATGTCCCC[A/G]GGCTTCATTAACCTCCTACTACAACCAGGGCCAGT R 2 1 2 1 201000 r 74 goat snp46712-scaffold65-3344210 1 107473030 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395325 Affx-122964048 AX-123265680 1 105906409 TGTCTCTGTGTGTGTGTGAGTGAGAGATGGTGGTA[A/C]ATAGGGGTAGGGCTGTGCTTTAATTAAGAAATCAC M 2 1 2 1 103000 r 74 goat snp46713-scaffold65-3378372 1 107507496 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382247 Affx-122973953 AX-123252605 1 105937501 TAGCTCAGAATGTTGGCTCTTTATATCAGATTACT[A/G]TTAAAAATCCCCTTGAATAGGTAAGTGTTCCTGAG R 2 1 2 1 101000 r 74 goat snp46714-scaffold65-3409464 1 107538971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399319 Affx-122961375 AX-123269674 1 105968071 AGCAATACCGTAGAGAAAGTTAGCTGTGCCCGGTT[C/T]TCATGTGTGAGCATGCAGCAAAGCAAACAGATGAG Y 2 1 2 1 101000 f 74 goat snp46715-scaffold65-3440034 1 107568920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396138 Affx-122963395 AX-123266493 1 106001784 AGGAAGAGCAAAGACCTGGTAAGAGAAGACCTTCT[A/G]TACTAAGGAGTTTGGACTTTGGAGTCTCATAAATT R 2 1 2 1 201000 f 74 goat snp46716-scaffold65-3473747 1 107602975 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417403 Affx-122947682 AX-123287751 1 106057794 CTGCAGAATAATGTCCCCATGACAGAAGCTACTGA[C/T]GCCCTAGAGAAGAAAAACCCAATGCAAAAAAGCAT Y 2 1 2 1 101000 r 74 goat snp46717-scaffold65-3529757 1 107657487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797818 Affx-122952854 AX-385284757 1 106114698 AGAGACAGTTTTAAGAAATCATCTTAGTGTAGAGC[A/G]TTTCCACAACAGGTTTACAAAAGAAACAACAAAGT R 2 1 2 1 101000 f 74 goat snp46718-scaffold65-3586661 1 107714492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773425 Affx-122939354 AX-385260567 1 106151314 CCACTTGCAGGCTCTCCTTTAGTGAGACTGCTCCT[A/G]TTGGAACTGTAGCTGGGAGAGTTGCTTCTGGCTGG R 2 1 2 1 101000 f 74 goat snp46719-scaffold65-3623277 1 107752002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394665 Affx-122964373 AX-123265020 1 106202160 AAGAGTCAGTCCACACATGAGTTGAAATAAAACAA[C/T]GATAAAGATATTTTTTTAAAGCAGAAGCAAAAGGG Y 2 1 2 1 101000 f 74 goat snp46720-scaffold65-3674123 1 107802974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387174 Affx-122970623 AX-123257532 1 106250701 AGCTGCCAGCTAGGTAGGGCCATGGGACATGTTCT[A/C]ACCACATGATACATGTCACTTTCAGGCCTGGGCAT M 2 1 2 1 101000 r 74 goat snp46721-scaffold65-3722664 1 107851656 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378852 Affx-122976526 AX-123249211 1 106279213 CTCTCTAGGATGACAAGAGAAAATAAGACTCTCTT[A/G]TATTTAATGCACAGTTATTTTGGGTTTCAATCTCA R 2 1 2 1 101000 r 74 goat snp46722-scaffold65-3751176 1 107883410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381348 Affx-122974416 AX-123251706 1 106329592 AGTATGATCAAAAATGTTCTTTTTACTGAACAGGG[C/T]GCACAATTCAAAAAATCACGAACATCACTGTTCTA Y 2 1 2 1 101000 r 74 goat snp46723-scaffold65-3801555 1 107931346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447004 Affx-122924556 AX-123317340 1 106376501 CTGTCCTCATGGGCCCTTTCATCCCACCAGCAAAA[C/T]GTTCTGATTCCTGGCCTCACTGTTCTACATCCAAG Y 2 1 2 1 101000 r 74 goat snp46724-scaffold65-3848464 1 107978889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407831 Affx-122954537 AX-123278182 1 106422824 TATTAAATTATTACAATAGGCTTTTAACTGTTCTC[A/G]CTGCTTCCACTCTTACTCTTCCCCAACCCCATTTG R 2 1 2 1 201000 f 74 goat snp46725-scaffold65-3894787 1 108027785 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430597 Affx-122936986 AX-123300938 1 106480604 ATAAGCACCCCCAAAGAGCATGTTGTCAGAGTGGT[A/G]CCAACACAAAAAAGAGAATTTAGATGGCCTCGACC R 2 1 2 1 101000 f 74 goat snp58241-scaffold945-12446 1 108096270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430390 Affx-122937769 AX-123300731 1 106511597 GATCTTAGGTTCTGCCACCTAGAACTGTGAGACAA[C/T]GCATTTCTGTTATTCAGTTACCTACCTATTGCGGC Y 2 1 2 1 101000 r 74 goat snp58242-scaffold945-43439 1 108127105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394850 Affx-122964773 AX-123265205 1 106558542 AAACACCATCTCAGGTAACCCTAAGAAAGATGGTT[A/G]TAAGAGGTAAACTTGTCACAGAAAGAGGTAACAAT R 2 1 2 1 101000 r 74 goat snp58243-scaffold945-90384 1 108174596 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446746 Affx-122925335 AX-123317082 1 106644421 CTTCTCTGACCCCTCATCCACATCTCCCTTGGACC[A/G]AGTATGAGCAGCATTATTTAAGTCCCCTATTTCCT R 2 1 2 1 101000 r 74 goat snp58245-scaffold945-176263 1 108259487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794576 Affx-122955554 AX-385281538 1 106673661 GGAGATAATGCTGCCTCTGTTTCTCCACTAACTCC[A/G]TCTAGAAGTATACAGGAGAAACAACCAGTTCAAAA R 2 1 2 1 101000 f 74 goat snp58246-scaffold945-205503 1 108288773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375760 Affx-122978600 AX-123246119 1 106703279 CTATATATCATTTATTTGAAAAATATTTATCATTA[A/C]GCATTTGATCTTTTTCATTTCCAACCATATATAGT M 2 1 2 1 101000 r 74 goat snp58247-scaffold945-235121 1 108318988 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776673 Affx-122959332 AX-385263799 1 106778516 ATTTATGCGAAAGATTATTTTACCAAGAAGGGTTC[A/G]TTTCCTAAGTAAGCTGTCACATATTAAACTATTAT R 2 1 2 1 101000 f 74 goat snp58249-scaffold945-310358 1 108393850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450556 Affx-122922470 AX-123320890 1 106836048 GCAGTTGTTCCAACAAAATCTACAGAACGAATGAA[C/T]AGATTGATGAATAAAAGTAGAAAAAGAGATATTAC Y 2 1 2 1 101000 f 74 goat snp58250-scaffold945-367890 1 108451718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275458 Affx-1111834911 AX-519549031 1 106856950 GACTCATCATCTTGTCACTAGCTGCAGTTCCAGCC[A/G]TGCATCAGCGCCCCAGGAGACAAAAAGAGAAGGGA R 2 1 2 1 202000 f 74 goat GoatD01.058473 1 106856950 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320781849 Affx-122967340 AX-385268931 1 106893132 AGGTATAAATATGGTAAAGTCCAATAAGCTTAAAC[A/G]TACAGTTCAGTAAGATTTACATATGAATAACCCTA R 2 1 2 1 101000 r 74 goat snp58251-scaffold945-424974 1 108508730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780020 Affx-122930981 AX-385267119 1 106965690 TAAAGAAACAAACATTAGGAGAGTATAAAAAATAT[A/C]AGCCTAAATTCTCTCTCTGGGTGATGGGATTACGT M 2 1 2 1 101000 r 74 goat snp58252-scaffold945-497532 1 108582124 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400769 Affx-122959878 AX-123271124 1 106999256 AGAGGATATGGTTGAGGAAGACTTCCAGGAAGAGG[C/T]GATACTTGGGCTGCCTATTGTAGGATAACTTAGTC Y 2 1 2 1 201000 r 74 goat snp58253-scaffold945-531098 1 108616721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779729 Affx-122945503 AX-385266829 1 107050360 TTTTCTGCACTGATTAAAATGTACTACATATCTGT[A/G]CTGCCCAGATAAGACAGCTTCTAGCCACATGTGTT R 2 1 2 1 101000 r 74 goat snp58254-scaffold945-582202 1 108667531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448551 Affx-122923427 AX-123318887 1 107080716 AGCACAAAGAGATATCCAATACCACAGTGCAAAAG[C/T]ATCAATTCATCGGTGCTCAGCTTTCTTTACAGTCC Y 2 1 2 1 103000 f 74 goat snp58255-scaffold945-612558 1 108698026 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272461 Affx-1111836716 AX-519546185 1 107080965 GTGTCCAAACAAAACACCAAGTAATAATTAAAGAA[A/G]AAAGGAGGTGATCACAGAAGTAAAGCACAGGAGAT R 2 1 2 1 201000 f 74 goat 1_107080965_AF-PAKI 1 107080965 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430153 Affx-122937381 AX-123300494 1 107142087 AGGGAAGATATCATTTTAAGAAACGTTTAAAGGCT[A/G]TGTTTTAGCAGGATATGGTGTTTAAATGGATATGG R 2 1 2 1 101000 r 74 goat snp58256-scaffold945-673929 1 108761210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411364 Affx-122952247 AX-123281714 1 107176872 TCATATAAAGTGAAAATACAAAAGAAGAGTCTTTT[A/G]GGAGTAACTTTCTTACCACAAGTGGTTTTATATTC R 2 1 2 1 102000 r 74 goat snp58257-scaffold945-708714 1 108795931 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414874 Affx-122949141 AX-123285223 1 107235351 TAAAAAAAAAATCCTTTAATAGATCCAAAGAAAAA[G/T]AAGGCACAATTTGAAGGTTTGTGTGGATTCTACAT K 2 1 2 1 102000 r 74 goat snp58258-scaffold945-767193 1 108854471 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800456 Affx-122932989 AX-385287377 1 107277667 TTTGAGATTATATTCCCTGACAAGTACCTGGTAGG[C/T]AACTATTTTATGTGACTACCATAGGTACAGAAACC Y 2 1 2 1 101000 f 74 goat snp58259-scaffold945-809509 1 108897412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399332 Affx-122961367 AX-123269687 1 107321577 ATATGTGAGTGTATGTGTATGTGCACACGTGCGTG[C/T]GCTTGTCTTACCATCCCAATCTAAATGCTTTGTGC Y 2 1 2 1 101000 r 74 goat snp58260-scaffold945-853419 1 108941244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785780 Affx-122942972 AX-385272820 1 107376995 CATTTGGATTATTTTCAGGCTTATGCAAAAGGTAC[A/G]TATAGCAATGAGGCTGAGTGTACTCACCAAAAACT R 2 1 2 1 101000 f 74 goat snp58261-scaffold945-908837 1 108997025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436868 Affx-122933241 AX-123307206 1 107445093 CTGGTGACCAAGCCTGCACTGGCTATGTCAGTCAG[C/T]AAAAATAATATATTTTCTTCTGAAAATTAATCACA Y 2 1 2 1 103000 f 74 goat snp58262-scaffold945-976935 1 109066339 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794782 Affx-122922915 AX-385281742 1 107485400 TGACTCCATAGGTACTGAAAGCTACTGAAAATGGC[A/G]TAAAACTTTGGAATAATTCATTGCTGTGTAAGTAA R 2 1 2 1 101000 f 74 goat snp58263-scaffold945-1017242 1 109106705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451184 Affx-122921336 AX-123321518 1 107582547 TTCCATGGCAACACAGCAGAGTAAATATTTAATAA[A/C]CATTGGTTCAATGTTGCACACATATTGTGAGGCTA M 2 1 2 1 201000 f 74 goat snp58265-scaffold945-1114389 1 109209428 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383429 Affx-122973475 AX-123253787 1 107642933 ACATGGAAGAAATAGTCTTTAGAAAAGGACAGCAG[G/T]AGTTGTTTGAAAAACAGTTAAAATGCAACTCAAAA K 2 1 2 1 101000 f 74 goat snp58266-scaffold945-1174775 1 109269954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396183 Affx-122963375 AX-123266538 1 107675447 TATTATTTTATTTTTATTTTTTGCTCTCTATGATC[A/G]TTTATATTCCATATGAATTTAAGACAGCTTTATTT R 2 1 2 1 103000 r 74 goat snp58267-scaffold945-1207289 1 109303461 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411290 Affx-122952301 AX-123281640 1 107716349 TCTATGCCCAGGGCTCTCTGGAGCAGTGCCCACAG[C/T]GGCTCAACATTCTTCCAAGGAACATGGATGGATGG Y 2 1 2 1 101000 r 74 goat snp58268-scaffold945-1248191 1 109344406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451058 Affx-122921431 AX-123321392 1 107751739 GTCACTAGCAGACACCTGGTTCAGAGTAAGAGCTC[C/T]CTTTACCAGGTGACATCGATCTGTCTGTGGGCTAA Y 2 1 2 1 101000 r 74 goat snp58269-scaffold945-1283581 1 109379955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769089 Affx-122940041 AX-385256264 1 107781884 ACTTGATTATGAAATTATGTAGAAGTTATAAGAAA[C/T]GTATATTTGAGGAGTTACTTAGCTTGGTCATGAGA Y 2 1 2 1 101000 r 74 goat snp58270-scaffold945-1313726 1 109409915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437131 Affx-122932157 AX-123307469 1 107823894 AGTGTATTTATACTGGAGGGACATAGGCAGGTCAT[A/G]CCAAACATAGTCACTCTTTTCTTAACATTTAAAAT R 2 1 2 1 101000 f 74 goat snp58271-scaffold945-1355736 1 109452264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431830 Affx-122936096 AX-123302171 1 107875997 ACAGTGGGATATTTGTCATGCCCAGTGGTGGGAAT[A/G]CCACTGCTTCTCTCAGTCCTGTCTTCTCTCTCCTG R 2 1 2 1 101000 f 74 goat snp58272-scaffold945-1407839 1 109497716 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411581 Affx-122951622 AX-123281931 1 107963683 CTGCATTGCAGGCAGATTCTTTACCATCTGAGCTA[C/T]GGGGAAGTCCACAAAGGAACCTCCGTGCTCTTGCC Y 2 1 2 1 303000 r 74 goat snp58274-scaffold945-1495525 1 109586270 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426713 Affx-122939888 AX-123297059 1 108002313 AGCTGCTGAAAGATAAATAACATGCCTTGTTGATT[A/C]TTGTCCAGAAAAGGGCAGACTGGATGCCGGCCACT M 2 1 2 1 201000 r 74 goat snp58275-scaffold945-1534155 1 109625403 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768607 Affx-122948263 AX-385255787 1 108061414 AAATACACCAGACAATGTGTAAAGCCTTCTTAAAT[A/G]TGGATGTGATTTGGAACTGATTTGTAATTGTATTA R 2 1 2 1 101000 f 74 goat snp58276-scaffold945-1593256 1 109690340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397001 Affx-122963142 AX-123267356 1 108091945 AGTTATGGCTGCATCTTTGCCCCATTTTCATGTTA[A/G]TATCAATATCCACCACTTGAAAAACAACACCAAGG R 2 1 2 1 201000 r 74 goat snp58277-scaffold945-1623787 1 109721132 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772926 Affx-122974665 AX-385260070 1 108165663 GTCCTTCACTTGTTTTACTAAGAATTGATGTCATT[A/G]TACTTTGGACCATCTTTTCTCTACTAAATCTACAT R 2 1 2 1 201000 r 74 goat snp58279-scaffold945-1697505 1 109794886 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404663 Affx-122957295 AX-123275015 1 108206386 TGTTTATGCTGCTCTTTTTTTTCTCTGTTCTTTTT[A/G]CTGGAATGTTTCCTTTCTTTTTCTACACCTTTGAT R 2 1 2 1 101000 r 74 goat snp58280-scaffold945-1738228 1 109835798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377963 Affx-122977197 AX-123248322 1 108227014 GGTGTAAAGATGAAGGCATTTGGGGGGATGTAATG[C/T]GATTTATAAATGGAAGCCTTAAATGGGGGAGGGTA Y 2 1 2 1 101000 f 74 goat snp38090-scaffold4745-95947 1 109855360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775533 Affx-122925310 AX-385262664 1 108262127 AAGTTGTTTTCTTATAATGTACAATGCCATAGGTA[C/T]AGAAGTTTCTAGATCCCTTCTCTCCCCTTTCTGGC Y 2 1 2 1 101000 r 74 goat snp38089-scaffold4745-60834 1 109890327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786964 Affx-122971093 AX-385273993 1 108292150 TCTGAAAGAGTATTCTGGGAAATGAGTCTGAAAAG[A/G]TAAGTGGTATCCAACAGTGGGTGGCCTAGATGTCA R 2 1 2 1 201000 f 74 goat snp38088-scaffold4745-30811 1 109920528 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783269 Affx-122952956 AX-385270334 1 108328216 CCTGCCTTATTTTCATTAGTGATTTTCTGCATCAT[A/G]CCCATGCGTCATCCAGACAGGATTACTTCAAGCTC R 2 1 2 1 101000 r 74 goat snp25508-scaffold263-5156 1 109966062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773443 Affx-122961507 AX-385260585 1 108378971 TTCTATTTTTAGTATGTGTAGCATGAATTCTACCA[G/T]TGGAAACAGCAGCTTAAAATGGGCACCATTCCCAT K 2 1 2 1 101000 r 74 goat snp25509-scaffold263-55911 1 110017241 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409335 Affx-122953076 AX-123279686 1 108480880 TCTATGATTTCATACCGTTAACAATGAAAAGAAAG[C/T]GTAAATGACTTATGAGAACAAAGACTTTATTTCAA Y 2 1 2 1 101000 f 74 goat snp25511-scaffold263-157820 1 110117679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771159 Affx-122925227 AX-385258319 1 108518734 CAGGTCTTATGAAAACAAGGGAACCTTGTCAAAAC[C/T]TTATATTTTGTTTAGTAAACATTATTTAAGAAATT Y 2 1 2 1 202000 r 74 goat snp25512-scaffold263-195674 1 110155473 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413315 Affx-122950186 AX-123283664 1 108587905 ATTGGAGATTGCTATCCCAGGAGGGAGAAGCGGAA[C/T]ACCCTTGGGGCTTGTGCTCTAGTCCATTAGGCCCT Y 2 1 2 1 101000 f 74 goat snp25513-scaffold263-264845 1 110225650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774758 Affx-122938347 AX-385261892 1 108662572 TAATGAGCACTACTTTAAAATTTGAGGGATTTTAC[A/G]TAAAGATGCATATTCTCTGCTTTTCTGTACAAGTC R 2 1 2 1 101000 r 74 goat snp25514-scaffold263-339512 1 110302016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774804 Affx-122962658 AX-385261938 1 108701041 GCATTTGTCCTATGAAAATAAAAGCACAAGTTCAC[A/G]TAAAAACCTGTACACTAATATTTACTGCAACTTTA R 2 1 2 1 102000 f 74 goat snp25515-scaffold263-377981 1 110340492 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443862 Affx-122927516 AX-123314199 1 108736980 GAAAATGAGAGAGAAGCCATCTGAGTCTGTTTTAC[A/G]TTCCTTTAAATTTTGCTTCAAATAACACTTTTTTA R 2 1 2 1 201000 r 74 goat snp25516-scaffold263-413920 1 110376570 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424470 Affx-122941768 AX-123294816 1 108803157 CTGATAAGAAGTGCAAGAAGCCCTGCCACAGACCA[A/C]GTGATGCTAGAGCCATGTCCACCCCAAGAAGTCCT M 2 1 2 1 101000 r 74 goat snp25517-scaffold263-480097 1 110442872 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428011 Affx-122939155 AX-123298354 1 108849810 TCAAGGATTTTTGTTTATATTTTGTTTTTAATGTT[C/T]CCTTTGCAATCTAAGAATTAGAATCATTAAGACTA Y 2 1 2 1 101000 r 74 goat snp25518-scaffold263-526750 1 110489500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442391 Affx-122928004 AX-123312728 1 108890711 CATGAAATCTAACCTGGGATGCAGGGAGGCAGGAC[A/G]TGTCCTGTGGTGAAAGTGAAGGGAAGCATGGATTA R 2 1 2 1 101000 r 74 goat snp25519-scaffold263-567651 1 110530773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410139 Affx-122952804 AX-123280489 1 108919616 GGCTTCATGATCCAATACACAGGTGAGCTGCTGCT[A/C]CTGGCTTCAGCCCTGAATTCTCTTCAAGGGAAAAA M 2 1 2 1 201000 f 74 goat snp25520-scaffold263-596556 1 110559332 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417590 Affx-122946888 AX-123287938 1 108960127 TGCCTCTCCCAGGGTGACGGCTGCAGGATGGTGCT[A/G]TGGTAAAGTAGGCAGGGAGGGAGATATGGGTCTTC R 2 1 2 1 202000 f 74 goat snp25521-scaffold263-637067 1 110599971 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385330 Affx-122971661 AX-123255688 1 109055568 AGCCAGTGACTCTAGTCGGGCTGATTGTGTTAACA[C/T]AATCCAGAGCTCACCTCAGAACTGAGGTCCAGCCA Y 2 1 2 1 101000 r 74 goat snp25523-scaffold263-732508 1 110695471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385371 Affx-122971632 AX-123255729 1 109096434 GGAAGGACAGACCCTTCTCACCAATGTGTCAGCAA[C/T]GGTCTGGGGGGAGTCTCTGGGGCCCAGAACTGAGA Y 2 1 2 1 101000 f 74 goat snp25524-scaffold263-773374 1 110736508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406120 Affx-122956204 AX-123276472 1 109125670 CATGGTGTCTGGCACCTCGCATGCAGTCCTTGGAC[A/G]CACAAATGAAGGAGAGGAGTGCAGATCCCATGCTT R 2 1 2 1 101000 r 74 goat snp25525-scaffold263-802610 1 110766262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276458 Affx-1111835429 AX-519549971 1 109126162 AGGTTTTCACCCAGTTAAAACTGAAAAACAAATCA[A/C]ACACACACACACACACACACACACACACACAAACA M 2 1 2 1 303000 f 74 goat Random2.2K-114 1 109126162 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415015 Affx-122949029 AX-123285364 1 109210559 TCAGGGAAAGGAAGCTTGGAGAGTTGCTTACTTTC[C/T]AAATTTGAAAAATAAGAACTTCCTGGGTTTATAAA Y 2 1 2 1 303000 r 74 goat snp25526-scaffold263-887499 1 110851415 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445539 Affx-122925162 AX-123315876 1 109256497 AATGAGACAATATGTGTAAAGTGCTTCACACCACA[C/T]GCAGCACATAACGAATCCTCAATAAATGAACATTC Y 2 1 2 1 201000 r 74 goat snp25527-scaffold263-933437 1 110893983 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773451 Affx-122953620 AX-385260593 1 109285218 AAATTCATATCCCTGCAAGAAACTCCTACTTTCCT[A/G]TCCCCAACACCACCATTAATTGACAACACTAAGGA R 2 1 2 1 101000 r 74 goat snp25528-scaffold263-962158 1 110922640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803206 Affx-122930500 AX-385290065 1 109328920 GAAATAAGATAGATTTTACAAATACAAGCCTAGCA[C/T]GGCAACCTGCGTTCTATGTACCTTCTCTGTATATA Y 2 1 2 1 101000 r 74 goat snp25529-scaffold263-1005860 1 110964225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276620 Affx-1111835435 AX-519550130 1 109338632 GACAGGTATGCACTTACAAATAACTAACTTTAAAC[A/G]CCAATGAGATTCAGTTCTATTATCAGTCACTCACT R 2 1 2 1 101000 r 74 goat Random2.2K-115 1 109338632 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800403 Affx-122956449 AX-385287324 1 109427054 GACAACTCCCAAATGTTCTGCCAACTAAATCACTA[C/T]AAATATAAACTGGTTCATAAAACTCCTAAAATGTC Y 2 1 2 1 101000 f 74 goat snp25531-scaffold263-1103994 1 111063662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416997 Affx-122947988 AX-123287345 1 109465902 AGATAGATTCAGGGAAGATAGGTGAGGAATGACAG[C/T]GTCTCCTCGATCCCAGGCTGTGGGACCACGGATTC Y 2 1 2 1 101000 f 74 goat snp25532-scaffold263-1142842 1 111103048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420447 Affx-122944893 AX-123290794 1 109515915 AGAGCTTGATCTTTATTCTAAAAACAATATGAAGC[A/G]CTGAATCTGTTTTGTTCAGAAGAGTGACCTGAACA R 2 1 2 1 101000 f 74 goat snp25533-scaffold263-1192855 1 111153490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776373 Affx-122936471 AX-385263500 1 109563944 TTGGTTCTTGCACTTATCTTTCAGTATAAAGCAGC[G/T]CATTCATTCTCTTCTCTTCAACCAGCACCTCTGCA K 2 1 2 1 201000 r 74 goat snp25534-scaffold263-1240884 1 111201788 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780530 Affx-122974079 AX-385267621 1 109599694 ACATCTCATTCCAAAGGGTATGAAATAGAACCTAA[A/G]TCTTATTAGCTTCAAGGCCCTTGCTTTTGCCATGA R 2 1 2 1 101000 r 74 goat snp25535-scaffold263-1276634 1 111237824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411706 Affx-122951536 AX-123282056 1 109628240 TAAGATAGACTACAGAGGGACGTAGAGTGAAACTA[C/T]GATAGGACAAATCCTAGGTGACCACACTTAGTTAA Y 2 1 2 1 101000 f 74 goat snp25536-scaffold263-1305180 1 111267033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389933 Affx-122968097 AX-123260290 1 109696167 ACTGTCCTCTGAATCAATCTCAAATATGTCACTGA[A/G]AGAAATCAGACATCTCTGAAATCATGCTATATCTT R 2 1 2 1 101000 f 74 goat snp25537-scaffold263-1373107 1 111334972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786867 Affx-122934931 AX-385273896 1 109782549 GGTGAGAATTGAGAATTGGAGTATGGGGAACCTGT[A/G]TGGTTATTAAAAGTAATAATTAAGTCCTACTCCAG R 2 1 2 1 101000 r 74 goat snp25539-scaffold263-1459489 1 111448954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430308 Affx-122938237 AX-123300649 1 109822677 GCTGGCGATGGAAGGAAACACCAACACTGCAGAGT[A/G]GTTTGAATCTTTGTATTTTAACTCCTCGCTTTTTA R 2 1 2 1 103000 f 74 goat snp25540-scaffold263-1499617 1 111489728 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271720 Affx-1111832829 AX-519545516 1 109839943 TAATGAGAAGAATAATTCATAAAATAAAGATAGCT[A/G]AAAATCAATTTGATTGGGAAATACCTGGGCTGATA R 2 1 2 1 101000 r 74 goat 1_109839943_AF-PAKI 1 109839943 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417080 Affx-122947500 AX-123287428 1 109855040 AATGTTGGGTACAATAGAAAGATTTTTTTTTAAGT[A/G]CAATACTCTATAAGAAAGTAATGACTACTCAGGCC R 2 1 2 1 101000 r 74 goat snp25541-scaffold263-1531980 1 111521337 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434792 Affx-122933877 AX-123305133 1 109899091 TGCTTCAGAAATGTTAGTAATCCTCAAAGTTCTCC[A/G]TTGTTTAACACACCAGTGGGAAAGGATTATCTCCC R 2 1 2 1 101000 r 74 goat snp25542-scaffold263-1576031 1 111574344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430727 Affx-122936892 AX-123301068 1 109930416 TTTTAAACATAGCCTCTGTTTCAATATTCTTTTCC[A/G]TTTATAGTTTTTTGTTCATTTATGGTTTCTCATTT R 2 1 2 1 202000 r 74 goat snp25543-scaffold263-1607356 1 111605789 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804402 Affx-986696569 AX-385290991 1 109960672 CCTTCCAGCGCGTAAGCTGGGCCTCGGTCTTACAC[G/T]GGCTAACCAAACTTAACACCAGTGTTCAGATAGCT K 2 1 2 1 600010 r 74 goat 1_109960672 1 109960672 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 38410631 Affx-122952088 AX-123280981 1 109968624 TGTAAGTTTCCTGTCAAGGTATCTTTTTAAAGAGG[C/T]GACTCTGGATGGGATGTAGGTGAGATCAGATAAAA Y 2 1 2 1 101000 f 74 goat snp25544-scaffold263-1645564 1 111643988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783215 Affx-122946578 AX-385270281 1 110005953 CTATGCCCTGGTGATATTTGATCACCTTGGCCTGC[A/G]TTTCAGGAAGAATCCTATTAGGCTGGGTTAGCCAA R 2 1 2 1 202000 f 74 goat snp25545-scaffold263-1682893 1 111681527 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402392 Affx-122959022 AX-123272745 1 110052644 GCTTCTCCAGTTTCTTCCATTTCTGCCCTTATATT[A/G]CTGGAAAAATGAAAGTCTCCTCCTGCAAAATGATG R 2 1 2 1 101000 f 74 goat snp25546-scaffold263-1729584 1 111728323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771236 Affx-122935388 AX-385258394 1 110084522 CTTACAGAATGCTTGCTGGTGATGATAACAGCAAA[C/T]GTTTTAGTGTGTGAGAAGCACCGCTTTATTGGGGT Y 2 1 2 1 101000 f 74 goat snp25547-scaffold263-1761462 1 111760712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795091 Affx-122922922 AX-385282050 1 110123141 GATTCTTTAAGGAAAGTATCATACTAAACAAACGG[A/G]CAAAAATGGATCAAAGTACCATGCTGCAGATTCTG R 2 1 2 1 101000 r 74 goat snp25548-scaffold263-1800081 1 111809578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437614 Affx-122931850 AX-123307952 1 110168450 CATTTGTGAGAAGACTAGTTAATATAGAAAATTAG[C/T]AAATCAAGAAAAGTATCAAAAGTATATTATTTAGA Y 2 1 2 1 101000 f 74 goat snp25549-scaffold263-1845390 1 111855035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775633 Affx-122957138 AX-385262764 1 110214956 ATAGCAAGTGTGGGGCATCAATTCACCACTATCTA[C/T]CTCAAATTTCTCTACAGATTATTGCTATCAACCAA Y 2 1 2 1 101000 f 74 goat snp25550-scaffold263-1891896 1 111901781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770557 Affx-122978540 AX-385257721 1 110263574 AAGGCCTCAAGAGGCATGAACAGACTAGACTCATA[A/G]ATATCGTAAAGAGTCATATTACAGCCACCTCATCA R 2 1 2 1 101000 f 74 goat snp25551-scaffold263-1940514 1 111950316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388661 Affx-122969104 AX-123259019 1 110294474 GGGTTGAACTTTAAAAATGGGATGTCCCATCTTGA[C/T]ACATTGCTAATAAAAACAAGATTATGACTGTTCGC Y 2 1 2 1 101000 f 74 goat snp25552-scaffold263-1971414 1 111984607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377374 Affx-122977640 AX-123247733 1 110327037 CATCTGTTTTCCTTGAGCCAGAAAATCACACAACC[A/G]CTTAAGAATATAAGAATTTCTATACCATTTGACAG R 2 1 2 1 101000 f 74 goat snp25553-scaffold263-2003977 1 112017210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405942 Affx-122955558 AX-123276294 1 110363427 AGTCAACCAGGATGCTTTAAGAAATATTGACAAGG[C/T]GGGGGCCCATCTCCAAAAGTTCTGAAGCAATTGGT Y 2 1 2 1 101000 f 74 goat snp25554-scaffold263-2040367 1 112053639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404842 Affx-122956629 AX-123275194 1 110404927 GGATCCAGCCTGGCACACTTTTCATTCAAGGACTA[C/T]GCATCCTGAGGCTGAAACTAATGATCCTCTTTACT Y 2 1 2 1 201000 f 74 goat snp25555-scaffold263-2081867 1 112089593 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796278 Affx-122974993 AX-385283228 1 110443900 TGATAGGCTGCATTCTTATATACTCATTAATAGAC[A/G]CATATTCTTATATTGAAAGTGTCAATTGAAAAATT R 2 1 2 1 101000 f 74 goat snp25556-scaffold263-2120840 1 112128637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424638 Affx-122942173 AX-123294984 1 110494155 CTAGAAACCAGCTACTGGTCTACCTCAAGAAGAGG[C/T]AATCCATGGTCTGCCTTTGAATGCCAATAGCTTCC Y 2 1 2 1 101000 r 74 goat snp25557-scaffold263-2171095 1 112179032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799272 Affx-122954901 AX-385286203 1 110539975 TGGGGTTGCCTGACATCACAAAGATAAGGAATAGG[C/T]TCAGTCTCATTCTTGCTAAATTGAGTCAGTATCTG Y 2 1 2 1 101000 f 74 goat snp25558-scaffold263-2216915 1 112225044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383696 Affx-122972487 AX-123254054 1 110571570 ACACTAAAGCCATAAATGAAAAAGTTTAAAAATTG[C/T]ACTGCAAAAAGACTGTAAGAGCGATTTTACAAGAG Y 2 1 2 1 101000 r 74 goat snp25559-scaffold263-2248510 1 112256671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797658 Affx-122920589 AX-385284597 1 110605907 AAGGGAGAGTGAAAATCGAAGGGTGGTTGGAATCC[A/G]TTTAAACTGAAGGGATCACCAACTTGAAGTCATGT R 2 1 2 1 101000 f 74 goat snp25560-scaffold263-2282847 1 112290825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382723 Affx-122973617 AX-123253081 1 110663697 CATTCTAGTAAGAGGAGCTGTTTGAAGAGTTTAGA[C/T]ATCTAATTTTCTTTGAGTAGATATTTAGATGAAAG Y 2 1 2 1 101000 f 74 goat snp25561-scaffold263-2340637 1 112348685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793529 Affx-122968093 AX-385280505 1 110694450 TCTGTGGCCACAGTATACTGGAGGTACAATTTGGG[C/T]GGTCCATAGTTTCATAGGCAAAAAGAAGTTTGATT Y 2 1 2 1 101000 f 74 goat snp25562-scaffold263-2371390 1 112379926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441843 Affx-122929047 AX-123312180 1 110752468 GTCTCAATTTACTTATTTCCCTATTCTTACAAACT[A/G]CTGACCTGTGTTATCTGTTGTTCAATGCCTGAAAA R 2 1 2 1 201000 f 74 goat snp25563-scaffold263-2429408 1 112439098 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413646 Affx-122950538 AX-123283995 1 110870010 TTTCATCATCAGCTTTATAAGCATCACTTTATGAT[A/G]CTAAATTCATTTGAACTTAACATTCAAAAGTGCTG R 2 1 2 1 103000 f 74 goat snp25565-scaffold263-2546950 1 112558348 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794623 Affx-122976749 AX-385281584 1 110921584 AAATGTTAGAACACTCCAATTTTTTTGTAAGAGAG[A/G]CAAAAAATGGCTTCTATGGTTAACACTGAACTTTT R 2 1 2 1 101000 r 74 goat snp25566-scaffold263-2598524 1 112610676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772031 Affx-122949803 AX-385259188 1 110956660 GTATTGTACTCCATAGCTAGTCACCTTGAAAAAAT[A/G]TTTAAATATATTGTCTCTACATCTTCACCTACATT R 2 1 2 1 201000 r 74 goat snp25567-scaffold263-2633600 1 112645538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780495 Affx-122943068 AX-385267586 1 111005625 TTTTGAGAAAAGATTTAGAAGTTGTAGAATGCAAA[C/T]GTACAGACTCAGAACAAGATCAAGCTGGACCTTCT Y 2 1 2 1 101000 r 74 goat snp25568-scaffold263-2682565 1 112695128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412536 Affx-122951341 AX-123282885 1 111057463 GGTATCAGCATTTGTGTGGGAAGAAGTAGAGAAAA[A/G]GCACGCAGGCTTCTGTTAACTCTGAGCAAGGAAGC R 2 1 2 1 201000 f 74 goat snp25569-scaffold263-2734403 1 112747530 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764665 Affx-122937435 AX-385252300 1 111126935 CTTCTGTTCCCATATACTCTACTTTCCCTCCGGTT[A/G]CAACATATATTCTTAACCTTTTGTGTGTGTGTTGT R 2 1 2 1 101000 f 74 goat snp25570-scaffold263-2803875 1 112819660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417713 Affx-122947446 AX-123288061 1 111159418 TGTCATTCTCAATGCAACATTTATCGCATTGGGTA[C/T]GTCTAAGCAATCCAGAAGGCTCATGCCACACATCA Y 2 1 2 1 102000 f 74 goat snp25571-scaffold263-2836358 1 112852198 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773651 Affx-122935061 AX-385260791 1 111193557 GCTACGGTATAAACCTTAAAGGCTTTGTGTTGGAA[C/T]GGCCCAGTTATGGCTTAGATCTCTTCTACAGCTCC Y 2 1 2 1 101000 r 74 goat snp25572-scaffold263-2870497 1 112886368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433580 Affx-122934968 AX-123303921 1 111244752 CTGGATGAGACAGATTCTGTGATTGGACTGCATTC[G/T]ACCACCTTCATCCATAAATATATTTTGGTTTTTGA K 2 1 2 1 101000 f 74 goat snp25573-scaffold263-2921692 1 112938093 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445441 Affx-122925356 AX-123315778 1 111280185 TTCGTTGTTCTCAAACAGTATACAAAAGTTGTCCT[A/G]TAGACAAAGCCGTATTTATGATTTATAACATAAAT R 2 1 2 1 101000 r 74 goat snp25574-scaffold263-2957125 1 112973498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414397 Affx-122949987 AX-123284746 1 111316932 TGTCAAACAGCCTTTTTGTCCTTCCCTTCCTGTTT[A/G]CTTGTCCATGTGTCCCCTCCTCTGTGCAGCCTTGT R 2 1 2 1 102000 r 74 goat snp25575-scaffold263-2993872 1 113010373 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779296 Affx-122949718 AX-385266400 1 111347053 TTGATCAAGCCTGTTTGTTGCTAGGGTAATAATCT[A/G]TATTAACTGGAAGTTCACATGGCAACATCATCTCT R 2 1 2 1 101000 r 74 goat snp25576-scaffold263-3023993 1 113040102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798212 Affx-122946409 AX-385285147 1 111384917 AATTCTGAACACAATACTATGGATGAGTATAAAGA[C/T]GACATTAAAATAGGAAATAGTCTTTAAAAGCATAG Y 2 1 2 1 101000 r 74 goat snp25577-scaffold263-3061857 1 113077614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795863 Affx-122960016 AX-385282815 1 111416969 GCAAGAAACAAAATGAGTAAGACCCACATAGCTTC[A/G]TGCCACATCTGAACACTCAATTTGTCTCTCCCTCT R 2 1 2 1 101000 f 74 goat snp25578-scaffold263-3093909 1 113109501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380542 Affx-122975669 AX-123250900 1 111460195 CAGTTATGGGAACTCTTTCCTACCTACAAATGCTG[C/T]ACCCAAACTCACATCACATAAACTAAGCATCACAC Y 2 1 2 1 101000 r 74 goat snp25579-scaffold263-3137135 1 113153335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387432 Affx-122970390 AX-123257790 1 111525567 GGGTTACCTTCATATGGGCATCCTCTGTGTGCAAG[C/T]GGCTCCCTCACTTCTCATTTTGAGTTGCCCCTGGC Y 2 1 2 1 101000 f 74 goat snp25580-scaffold263-3202507 1 113218662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777686 Affx-122934503 AX-385264805 1 111577655 TTCGGTATGAAGAATCACAATTTGTTCCTTGAAAC[A/G]TGGAGATGAGTCATTAGTAGCTGAATTTGATCAAA R 2 1 2 1 101000 f 74 goat snp25581-scaffold263-3254595 1 113270622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434752 Affx-122933906 AX-123305093 1 111610854 TTGAAGCAACTTGGAAATTATTTTTAGTAAACTAG[A/G]CTTTGATGTTGTGGTTTATGTTTTTCTTCTAAAAT R 2 1 2 1 101000 r 74 goat snp25582-scaffold263-3287794 1 113304084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394606 Affx-122964419 AX-123264961 1 111653657 ATCACTGGATTGGAGATAAAAACATGGGGGGAGGC[A/G]TACATGGGGAACACCCTGATGGCGGTGGCAGTCAT R 2 1 2 1 103000 f 74 goat snp25583-scaffold263-3330597 1 113347813 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429340 Affx-122938579 AX-123299682 1 111699042 AATTTTGCTACCCTCCATCTGTATTTTTGGTAATG[C/T]AATCAAAAATTTCTGGTTGACTGAATTCAATTTTC Y 2 1 2 1 201000 r 74 goat snp25584-scaffold263-3375982 1 113393304 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420238 Affx-122945073 AX-123290586 1 111728971 AGAGATTGACAGTGGTGGGAAACTACACTCCTGCC[A/G]TGAACTCTCTCTGTGGATTTTTAAAAAAGAACCTA R 2 1 2 1 101000 f 74 goat snp25585-scaffold263-3405911 NW_017191590.1 8076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393488 Affx-122965823 AX-123263844 1 111763681 TTTTAAATGAATCATTTAAATAGCTGACTGTTAAA[C/T]AGCCTGTGTCCGCTAATTCTCCCTTCTAACTTCCC Y 2 1 2 1 201000 f 74 goat snp25586-scaffold263-3440621 1 113460657 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765050 Affx-122937157 AX-385252619 1 111848799 AGTAACAAAGTCATCAGGTCTAGAAAAAGGAAGAT[A/G]TTTCTCTTTCTAAAGCTACATTACTCTTTTGCTTG R 2 1 2 1 101000 f 74 goat snp25588-scaffold263-3525739 1 113546508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789924 Affx-122961472 AX-385276930 1 111913477 TTTGCCAATACTACCACTAACTCTTTCATATTACC[A/G]TGAATATACTGAAATTACTTGCATTTAGAAATGAA R 2 1 2 1 101000 f 74 goat snp25589-scaffold263-3590417 1 113612516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802085 Affx-122946745 AX-385288989 1 112000320 ATTTTCTGTTTTGAGCTACAGCTAAGACTGCTCCT[A/G]CATCTGGTTTTCTGCTTCAAAACTTTTATTCCTAT R 2 1 2 1 101000 f 74 goat snp25591-scaffold263-3677260 1 113699599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775059 Affx-122957628 AX-385262191 1 112031135 TTAAAAATAACTTACTTAAATCTACCCAATCAGAT[A/G]TCCCCTTAAAAGATATCCAAATTCTTATTTCTGCA R 2 1 2 1 101000 r 74 goat snp25592-scaffold263-3708075 1 113731458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380356 Affx-122975354 AX-123250714 1 112070197 GAACTTTGGAATGAAATGGTCTTCTTCAGTAAACA[C/T]ACTTAAAATCTGAAAAGAATATAAGCAAATGCTAT Y 2 1 2 1 101000 f 74 goat snp23439-scaffold236-4492 1 113770884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800793 Affx-122968212 AX-385287709 1 112132712 TCTCATTAAGCTCAAAATAAAGTCCTCATCAAGAC[A/G]TCTACGGCCTTCCATGAGATGCTTTCTTTTGCCTT R 2 1 2 1 201000 f 74 goat snp23440-scaffold236-67007 1 113853175 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792643 Affx-122925358 AX-385279623 1 112165187 GATGGAAATGTCTCTCTTAGAGGTAGAAGAATTTT[A/G]CTAGGTAATTTCACAGAAGTTATTCCTGTCTTAGG R 2 1 2 1 101000 r 74 goat snp23441-scaffold236-99482 1 113887304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389876 Affx-122968141 AX-123260233 1 112201651 CCCACTGGAAAAGCTGTAGTGCCCTGTTGGAGGAC[A/G]CATGTGAGACATACTCTGGGACTTCCTAGAAGGTC R 2 1 2 1 101000 r 74 goat snp23442-scaffold236-135946 1 113923292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447828 Affx-122923910 AX-123318164 1 112270731 AAGATGGTGCTTCTGCAGCCATTTGTGAATGAGTG[C/T]AGGGTGGCAAAAAAACTTGCAGCTCAGCAGATGTC Y 2 1 2 1 101000 f 74 goat snp23443-scaffold236-205026 1 113992906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443263 Affx-122927492 AX-123313600 1 112301140 AGATGAAAAATGGGGCTGGGGAGGACTTGAATCTC[A/G]GAGGGAAAAATCAAAGCAAAGGCTCTGGTTGTGTC R 2 1 2 1 101000 r 74 goat snp23444-scaffold236-235435 1 114023567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403071 Affx-122958517 AX-123273424 1 112348741 AGCCCTCATGGAAATGTCAACTGTACCCTTCAGCT[A/G]ATATTCTGAAACAATGGGAAAAGGACCTTTTTACA R 2 1 2 1 101000 f 74 goat snp23445-scaffold236-283036 1 114070740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413802 Affx-122949904 AX-123284151 1 112377629 ATGTGTAACTTTCATAATTAAAACCCCTCTTCACT[A/G]TAGAGTCTGCATGCATGCATACATGTTCAATCAGT R 2 1 2 1 101000 r 74 goat snp23446-scaffold236-311924 1 114099496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784020 Affx-122967250 AX-385271073 1 112414563 TGAAGGAATACCTGTAATCAGTAAAACCTACTCAA[G/T]CCCTGATCAAACATAAGATTTGCAAATATTTTCTC K 2 1 2 1 101000 r 74 goat snp23447-scaffold236-348858 1 114136324 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387474 Affx-122970355 AX-123257832 1 112456928 GCTGTTTTCTTTCAAGTAATGAAATAAGTGAACAT[A/G]AAAGAGGAGGCCAGGTTAAAAACAGAAGGGAAGCT R 2 1 2 1 201000 f 74 goat snp23448-scaffold236-391223 1 114178820 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271721 Affx-1111832830 AX-519545517 1 112457804 AAAATCCAGCCCAGGTTGATCTGCTCTGTTGATTG[A/G]TGAAGAGAAACTGACCTACAGCTTGAAGGAGAAGC R 2 1 2 1 101000 r 74 goat 1_112457804_AF-PAKI 1 112457804 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427602 Affx-122939365 AX-123297945 1 112490962 CAACAGTAAAATTTTGCTCTGTGCTTCTGGAGGAA[C/T]ACCCTACAACAGAAAACCAAAAATTAAAAAAAAAA Y 2 1 2 1 101000 f 74 goat snp23449-scaffold236-425257 1 114212902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423875 Affx-122942306 AX-123294221 1 112533553 ACTAAGGAAATGTTGATTTTAAGACTTTAAGAACG[C/T]ACAGTTGTGTTAGAGCTGTTCCCATCCACACCTCT Y 2 1 2 1 101000 r 74 goat snp23450-scaffold236-467848 1 114255882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396684 Affx-122962834 AX-123267039 1 112563299 GGTCGCAAAGAGTAGGACACGACTGAGTGACTGAA[C/T]AACAACGCGCACAACCAGTTTTCAATTTTCTCATC Y 2 1 2 1 101000 r 74 goat snp23451-scaffold236-497594 1 114285701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390818 Affx-122967850 AX-123261175 1 112574839 TTTTTGCCTGCTAGCAGAACAATCCAATGGTAAAA[C/T]AGCAGGAGGGAAAAGGAAAGGAAAAAAAAACCCTG Y 2 1 2 1 201000 f 74 goat snp403-scaffold1009-1550238 1 114297514 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402309 Affx-122959087 AX-123272662 1 112614027 AACGTGACCAAAACTCATGCATATACAGATAATCA[C/T]GCCTTTCTGTGTACCAGCGAATCAGAGGTTTTTTT Y 2 1 2 1 101000 f 74 goat snp402-scaffold1009-1511050 1 114336981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406567 Affx-122955098 AX-123276919 1 112655499 TATGGGCATTATTTTCATTACTTTTGAACTGTAAC[A/G]ATTCTGGTGCCCAGTAATTAGTAGCAAATGTAAAA R 2 1 2 1 101000 r 74 goat snp401-scaffold1009-1469578 1 114378951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399368 Affx-122961341 AX-123269723 1 112721894 AAAGTGACCACTGCTTTCTCCTTCCTTCCTTCAAT[A/C]TTTCCTGCCTCCCTGCCTTCTTTTTCTTGAGTCAA M 2 1 2 1 303000 r 74 goat snp400-scaffold1009-1403183 1 114445151 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773189 Affx-122947625 AX-385260332 1 112791564 GCTTTTGTAAAATCCAGTTAGTGGTTAATAGACCT[A/G]TCTAACTTAGGCTTTGCACTTCTCATACGTATTCT R 2 1 2 1 201000 r 74 goat snp398-scaffold1009-1333513 1 114514997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433421 Affx-122935087 AX-123303762 1 112823404 AGATTTGGAAGTGACAAGAACATCATGAGAAAAGC[A/G]TGAGAAAGAATGCATTGCTAAGGAGTTCTGTGCAA R 2 1 2 1 201000 r 74 goat snp397-scaffold1009-1301673 1 114546836 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422494 Affx-122943309 AX-123292840 1 112930287 TTAAAGAGTCGGGCACAACTGAAGCAACTTAGCAT[A/G]CAAGCACATACATAAGACAAGGAGAAAAAAGCTCC R 2 1 2 1 303000 r 74 goat snp395-scaffold1009-1194790 1 114654763 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406677 Affx-122955787 AX-123277029 1 112960571 CACATATATGCTGAGCTCATGAGTAAGAGGCATGA[C/T]GTGATTTGTTTCACTTTTAGTCAGAACACAAAATT Y 2 1 2 1 101000 r 74 goat snp394-scaffold1009-1164506 1 114685459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392078 Affx-122966378 AX-123262435 1 112998395 GCACAAATTTGTTTAAACTTGTTTCCTTAATTTAC[G/T]AGAGTCATTACTCTGTGCCAGTAAGAGCATATTCT K 2 1 2 1 101000 r 74 goat snp393-scaffold1009-1126682 1 114723104 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790194 Affx-122973824 AX-385277198 1 113060421 CTTTTTGCCTCTTCATATTGTTTATACTATTCATG[A/C]TGGAGGGTAGTCCTTGGAAAAGGGACCTATAATCT M 2 1 2 1 102000 r 74 goat snp392-scaffold1009-1064656 1 114785123 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423921 Affx-122942270 AX-123294267 1 113100521 CATCTTAGTAAAATATTTTTTGAATAGAAGAGTTT[A/G]CAGCAAGAGACAGACAGCTGGGAAAGGAGTTACCA R 2 1 2 1 103000 r 74 goat snp391-scaffold1009-1024556 1 114826280 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401373 Affx-122959235 AX-123271726 1 113146255 GAGAGGAAGCTGACAGGTTCTGACCAGCATGATGT[C/T]AGCTCCAGTCTTCTCTCAGAAAGCCAAGTCCTGAC Y 2 1 2 1 201000 f 74 goat snp390-scaffold1009-978822 1 114872015 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425946 Affx-122941185 AX-123296292 1 113175449 GTAAAAAATTATAATTGTCTGAAGGAGGATGCAAG[A/C]GAATTTGGGGGATCTGGAGATGGAGAACAACATAT M 2 1 2 1 101000 f 74 goat snp389-scaffold1009-949628 1 114901320 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776860 Affx-122944134 AX-385263984 1 113207793 CTTGTTAAAGGTTATTAAGTGTTATGTCCTCTAAA[C/T]GATTTATCCATCACAGCAGAAACAGGAATACCAAG Y 2 1 2 1 101000 r 74 goat snp388-scaffold1009-917284 1 114933911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444389 Affx-122926596 AX-123314726 1 113248142 GCAAACCAAACAGCACACCGTAGCTATAGTTGTTA[C/T]GTGATTGTTTTTTAATTGCTGTAGGAGCCTGTTCT Y 2 1 2 1 101000 f 74 goat snp387-scaffold1009-876935 1 114974732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276658 Affx-1111835455 AX-519550168 1 113285837 GCTGCACATAACTGCCTAGGAAGCAAATGTGTGCA[A/G]TTCATAAGACCACCACCAATATTGACTCTTTCCTT R 2 1 2 1 101000 r 74 goat Random2.2K-118 1 113285837 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396951 Affx-122963176 AX-123267306 1 113338591 CTCAACCAGTGTCTCTTAACCCAAGAGCCAATTTT[A/G]TTTTCTTTCATACATTTTCTTCTAAGATAATGGGC R 2 1 2 1 103000 f 74 goat snp386-scaffold1009-786486 1 115064979 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798894 Affx-122935879 AX-385285824 1 113379010 CTTCGTATTTTTGTCACTTAATGAAATACTTGTTA[C/T]GTAGTAGACTCCATCAAAAAGAATGTCTGAATGGT Y 2 1 2 1 101000 r 74 goat snp385-scaffold1009-746067 1 115105280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794653 Affx-122959953 AX-385281614 1 113411999 CTTGCTTTTGGAATTCTAATCTTTAGCAACAATGC[A/G]TCACTTAACTAACTTCCTTCAGTATCCTTCCAGTA R 2 1 2 1 101000 r 74 goat snp384-scaffold1009-713078 1 115138277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782562 Affx-122977130 AX-385269636 1 113466015 GTAAATTCTCCTACATATATTGGTTTGTTAATTTT[A/G]CATATTATTCGTTGAACATTTTCTGGGGAAAAGAT R 2 1 2 1 101000 r 74 goat snp383-scaffold1009-659062 1 115192345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387117 Affx-122970663 AX-123257475 1 113523164 GTTGATGAGGATGTCATTTGTTGCTTCTATTTGTC[A/G]CAGGCACAGAGCTGGGGCCTGGAGGTGAGCTCAGA R 2 1 2 1 101000 f 74 goat snp382-scaffold1009-601913 1 115249959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276528 Affx-1111835462 AX-519550039 1 113548317 GGAACAGTACCGTGCATTATGTGGTCCTATGATAC[A/G]ATGAGTGGCACAGATGTGGGCTGGTAGGACCAGGA R 2 1 2 1 101000 f 74 goat Random2.2K-119 1 113548317 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785035 Affx-122947390 AX-385272082 1 113581625 ACAAACAAATTAATGAAATAGATATTCTCATTTCA[C/T]ATAAAATCACAGTGTCGGGTGAGTTCTGTTCTGTC Y 2 1 2 1 202000 f 74 goat snp381-scaffold1009-543452 1 115308758 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379356 Affx-122976159 AX-123249715 1 113650049 GCAAGTTTTGATATTTCATTCCTGCCCTTTACAAC[A/G]ATGTTGGTGAAGAATGAGCATTAATTAAGCAATAG R 2 1 2 1 101000 f 74 goat snp379-scaffold1009-475028 1 115377569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276543 Affx-1111835469 AX-519550053 1 113670826 TTATCCCTTTTGTGGCCCTGAATTGTGAGGGAAAA[A/G]AATGATAGTATTCCCACCTCAAATGTATTAAAAAA R 2 1 2 1 101000 f 74 goat Random2.2K-120 1 113670826 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386308 Affx-122970896 AX-123256666 1 113696159 GAGGGAGTGTTATGACTTCTGTCGGTTTCCATAAT[A/G]CAGTAGAAGAATAACTTGCTAGCTTCCAAGCAGAG R 2 1 2 1 101000 f 74 goat snp378-scaffold1009-428918 1 115421806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393317 Affx-122965955 AX-123263673 1 113728652 CAACCTTTTAAGTTCTGCCTAAATGTTACTATTAC[A/G]TCCATTATATTTTATGTTCACTGGTTGATATTACT R 2 1 2 1 101000 r 74 goat snp377-scaffold1009-396425 1 115456614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421859 Affx-122944285 AX-123292206 1 113764573 AAAATGAATTTTGAAAAGAAAATGTATGTCTTGTG[C/T]TAAGTATTTCAATCTTGACTCTTCTCCCTTTCACA Y 2 1 2 1 103000 r 74 goat snp376-scaffold1009-360504 1 115492907 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796342 Affx-122935113 AX-385283292 1 113845590 GAGTAGCTAATTCAGATTTGCTAGTGAGAATCTGT[A/G]CTAGTAAAGCAAAGAGGATACATGAGCACTGGGTA R 2 1 2 1 101000 f 74 goat snp374-scaffold1009-279487 1 115574426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402839 Affx-122958256 AX-123273192 1 113901792 AATTTTACAGTGAAGGATCTACTGTGTGCAGTGCC[A/G]TGGGCTGCAGGGCAAATTCTGGCCCTGACATTCGG R 2 1 2 1 101000 f 74 goat snp373-scaffold1009-223285 1 115631113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399776 Affx-122960301 AX-123270131 1 113937631 TCTTTTATATCCATTGCAATCTGTGTTTTACCTCA[C/T]AAATTCTTGAAAATACTCTTGGGACTATCATCAAT Y 2 1 2 1 101000 r 74 goat snp372-scaffold1009-187446 1 115664752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785845 Affx-122952398 AX-385272882 1 113975281 TAGGAGAAATATAGAACAAGAATTATTCTACTATC[A/G]TGAAATAAACTGAATCATCATTTTAATATTTTTAC R 2 1 2 1 202000 r 74 goat snp371-scaffold1009-149796 1 115703280 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445615 Affx-122925105 AX-123315952 1 114065642 TGATTATCTGTGACCTTTCTAATGTTCTCATAACC[A/G]CTGTATTTTGTTTGTCTTTTTAACTCAGCAAATTC R 2 1 2 1 101000 f 74 goat snp370-scaffold1009-59435 1 115796286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793129 Affx-122940246 AX-385280107 1 114115182 TGTTTTTCTTCAGCTCAATTTAAGCACTTGAAGGA[C/T]GAAAAATAACTCCATGACTATCACAAATGAAAACA Y 2 1 2 1 101000 f 74 goat snp369-scaffold1009-9895 1 115846519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794769 Affx-122962840 AX-385281729 1 114149354 CATTTCTTTGCCTCACCTTTGTATGGAAAGTTGAC[G/T]AGCTTATGCCAGGTCAAATTAGTGGCTATGGTCAA K 2 1 2 1 101000 f 74 goat snp26955-scaffold285-1887635 1 116040333 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422545 Affx-122943266 AX-123292891 1 114196154 AAGGAAACAAGCTATGCTGTGTATTGATTTGTATC[G/T]ACACCATCTCTTGAAATTTTAGCCTCTGTGGTATG K 2 1 2 1 101000 f 74 goat snp26954-scaffold285-1840835 1 116088951 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797542 Affx-122972467 AX-385284481 1 114270879 AACTTAACAACAAGCCAAAAATCAGCTTCTTCCCT[C/T]TTAGACTTAATCTGATTAGAGAACATTTACCAAAA Y 2 1 2 1 101000 f 74 goat snp26952-scaffold285-1766110 1 116165633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425783 Affx-122940713 AX-123296129 1 114301189 ATAACAGCAAGAGCTGATCTGATCACAAGCTTGAG[A/G]CTAATAGAAAAATTAAAAGGTCACTGTCCAGAAAT R 2 1 2 1 101000 f 74 goat snp26951-scaffold285-1735800 1 116196617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800954 Affx-122937909 AX-385287869 1 114336385 CAATCATCACACACGCTATTTTTTCACTTCTTCCA[A/G]TAGAGAATTTTATTAACACACTCTGAGAACAACCA R 2 1 2 1 101000 f 74 goat snp26950-scaffold285-1700604 1 116233205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418116 Affx-122947126 AX-123288464 1 114369375 AATGAGATCTCTGTTAAAATGAGTATCCTTTGACC[A/G]CTTGTGGTCACTGGATACCAAAATCAGAGAAAGTA R 2 1 2 1 101000 f 74 goat snp26949-scaffold285-1667614 1 116265923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384548 Affx-122973018 AX-123254906 1 114434694 GATGCTCTAGATATAGTCCATCAGTTGTCTGATCC[A/G]TTTTCAAAAACATATATGACAAAAATACCAATGAA R 2 1 2 1 101000 f 74 goat snp26947-scaffold285-1602295 1 116331047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397197 Affx-122962401 AX-123267552 1 114485164 TACAGGCATATAATGTTTAAGCTGAATTTAAAAAA[G/T]AAAGTTGAATATTCTATTGCTATGCCTTAGAATTT K 2 1 2 1 303000 f 74 goat snp26946-scaffold285-1551825 1 116381966 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407941 Affx-122954363 AX-123278292 1 114542772 TAAGGGAAGCCCAAGAATAGTGGAATGGGTAGCCT[A/G]TCCCTTCTCCAGCGGATCTAGCTATCAGAGAAGCC R 2 1 2 1 103000 r 74 goat snp26945-scaffold285-1494217 1 116439901 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397218 Affx-122962385 AX-123267573 1 114584958 GATGAAATTAACAAAGCTCTTGACAACATTAAAGT[A/C]TTTCTTCAATTACCTTTTTAAAAATTTGGACCAAT M 2 1 2 1 102000 f 74 goat snp26944-scaffold285-1452031 1 116481720 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377459 Affx-122977518 AX-123247818 1 114630349 TTGTTTTAATACAGTGTTGTTCTACCAACGGTGTG[A/G]TGGAAAAACACAAATGATCTTTTTGGTCAACCCAG R 2 1 2 1 102000 f 74 goat snp26943-scaffold285-1406640 1 116527022 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392931 Affx-122965705 AX-123263288 1 114689226 TTTTCATTGTATATCGATCTCAAGGAACAGGAGAT[A/G]CCAATTCACATTAGAAAAGTTGTACCAGTTATTCG R 2 1 2 1 101000 r 74 goat snp26942-scaffold285-1347763 1 116586299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792344 Affx-122966685 AX-385279326 1 114741608 AAAATAAAATAGCAATCATAATCCGCTTTCAGCTC[C/T]TATTTGATCTCTCTTCTCACCTTCAAAGGTCAAAT Y 2 1 2 1 101000 r 74 goat snp26941-scaffold285-1295381 1 116638791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409471 Affx-122954065 AX-123279822 1 114780998 AACTGTAGTGTTTTTCACCCTTAGGTGTCTTGAAT[A/G]CCCAAACTTTTCTGAGACTTCCACGAGACAAATTG R 2 1 2 1 101000 f 74 goat snp26940-scaffold285-1255991 1 116678181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773186 Affx-122953226 AX-385260328 1 114814129 CTGTTAAAAAGATTGAAACTGTTGCAAGGTCAACG[C/T]GGTGGAGAATCCTTGCTGAGGGATAAGTAATATTT Y 2 1 2 1 101000 r 74 goat snp26939-scaffold285-1222860 1 116711379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399796 Affx-122960287 AX-123270151 1 114863779 ACCTCGGGAAGGAGTCTGCCATATTCATCATTGCC[A/G]TGGTGAAATAATTATCATAGTGTAAGTAACTAAGT R 2 1 2 1 101000 r 74 goat snp26938-scaffold285-1173210 1 116761086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416202 Affx-122948241 AX-123286551 1 114900273 AGAAGTCCAGAGTCAGTTTTAACCTCCCAGTCCCC[A/G]CTTCCTTGCCTATGAAATATGGATAAGAAAGATGA R 2 1 2 1 101000 r 74 goat snp26937-scaffold285-1136716 1 116797191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425682 Affx-122940861 AX-123296028 1 114939106 CTTACCTGAGGAAGTTACCGTCTTTTCCCTTCCTT[A/G]TAAACAGCAGGTATTTAATGATGGATCCTTGTACA R 2 1 2 1 201000 r 74 goat snp26936-scaffold285-1097883 1 116835961 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420592 Affx-122945257 AX-123290939 1 114971515 GTGAGGGTAACACCTGGGCAGCTATTTAATAGTCT[A/C]GTGGTGTCTGCACCAAGAAGGTGGTGATGCAAATG M 2 1 2 1 101000 f 74 goat snp26935-scaffold285-1065474 1 116867779 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774493 Affx-122923853 AX-385261628 1 115005901 ATTTGATGAAAGCTAGTCTCTCTCCAGGAAAGTTC[A/G]CAAAATGTGTGGATATTCGGAATGCTCCCTACAGC R 2 1 2 1 101000 f 74 goat snp26934-scaffold285-1031088 1 116902566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271804 Affx-1111832831 AX-519545592 1 115032820 TCGCTTCAGTTGTGTTCGACTCTTTGTGACGTTGT[A/G]GACCACAGTCCGCCAGGCTCCTCTGTCCATGAGGC R 2 1 2 1 103000 f 74 goat 1_115032820_AF-PAKI 1 115032820 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387161 Affx-122970632 AX-123257519 1 115072113 GCCTTCTGAAACTCTTCTGTGAGTGATGAGTGAGA[C/T]ACTTCTGCCAACTGTTTAAAAACACACATCCAACA Y 2 1 2 1 101000 f 74 goat snp26933-scaffold285-964876 1 116969120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423995 Affx-122942111 AX-123294341 1 115101339 GCCAGAGTCAGGAGGTAAGAACAGAAACACTTGCT[A/G]TGGTGGAGTAGGGGGCACATCAGAGCGTAAGTGTT R 2 1 2 1 101000 f 74 goat snp26932-scaffold285-935650 1 116998709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786325 Affx-122960205 AX-385273359 1 115182980 TTCTATTGCTGATGATCTCTTTGCTTATATTTTTC[A/G]TTTCTTCGTATATCAGTTTCGTATTTTGTGTTTGC R 2 1 2 1 101000 f 74 goat snp26931-scaffold285-854009 1 117080492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383742 Affx-122972450 AX-123254100 1 115232611 GTGATGTCACCAGAGAGACACTTTCATTGTGCCCC[A/G]TCTTCTTTGCTTTTGTGTCCCTTCCCCTCTTCTTC R 2 1 2 1 202000 r 74 goat snp26930-scaffold285-804378 1 117129970 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421429 Affx-122943958 AX-123291776 1 115289443 TACAATAGAATTAGTTAACCAAGAGGGAAACAAAC[A/G]CAGGGGTTGATTTCCTCGGTGAGAAAGGCAGGTTA R 2 1 2 1 201000 f 74 goat snp26929-scaffold285-747546 1 117186670 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767533 Affx-122934202 AX-385254790 1 115374236 AGTAGAGAGGTTAGGTTCATGTAAAAATGTAAGCT[A/C]TACTACAAATTGTATGGAAACATTGAACTGAGAAT M 2 1 2 1 101000 f 74 goat snp26928-scaffold285-662753 1 117271956 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796094 Affx-122966130 AX-385283046 1 115408441 GTTCCATAATAAAAGAAAGTAGGCTTTAATAGGAT[A/G]TTATATTTATTATTTAGTTCAAGATGCACCCTTTT R 2 1 2 1 201000 r 74 goat snp26927-scaffold285-628548 1 117305769 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791190 Affx-122960848 AX-385278185 1 115440428 ATTTCTGCTCAGCCAAGTGCAAAAGACATTAGCCT[A/G]TTCATCACAAATCCATCTTCCTTATTTTGATTACA R 2 1 2 1 101000 f 74 goat snp26926-scaffold285-596561 1 117338322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777754 Affx-122921240 AX-385264872 1 115470542 CCTCTGCGGCAAAATAGCATCAACCCTACTTTAGT[A/G]TAGTTATAGGCTCACTACTCCATTTATCATCACTT R 2 1 2 1 101000 f 74 goat snp26925-scaffold285-566447 1 117368427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775024 Affx-122955029 AX-385262156 1 115502604 AGATATAGGTTAAGATATGGATATGGGTAAAGACA[C/T]AGATATAGGAAGACATAGATATCAGTTCAGTTCAG Y 2 1 2 1 101000 r 74 goat snp26924-scaffold285-534385 1 117400400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442026 Affx-122928407 AX-123312363 1 115548951 CACCAAGGAAGTGCTGCGTGATAGACATCTTGAAG[C/T]AGGAAGCCACAAAGTGAACCCCAAGACCCAAAGAG Y 2 1 2 1 201000 f 74 goat snp26923-scaffold285-488038 1 117447153 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398111 Affx-122961708 AX-123268466 1 115601201 AGATCAACTCCCCTAGACGAGGAGTCCCTGATTCT[A/G]CTTGAAATTGCTTTCCTAGACCTCTGGTTCCAGTC R 2 1 2 1 101000 r 74 goat snp26922-scaffold285-435788 1 117499075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440483 Affx-122929372 AX-123310820 1 115635139 ACATTTTAATTAAAAATAAAAAACCTCTTCGCTTA[C/T]AAACTCTACATAATTCCACCAATGCCTGCAGCCAC Y 2 1 2 1 101000 r 74 goat snp26921-scaffold285-401850 1 117533249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384568 Affx-122973002 AX-123254926 1 115670525 ATGGTGAGACATGGGATGTACACTGACACATATTC[A/G]TATATGTATATATGCATGTTTACACCATGAGCAGA R 2 1 2 1 103000 f 74 goat snp26920-scaffold285-366464 1 117568940 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800466 Affx-122945726 AX-385287386 1 115732389 ATTTCATAGGGAGGAATTATAGAAGATTAGTAACC[G/T]CCTAAATTACATTGGTCTTACTGTTGGCTAGTGAA K 2 1 2 1 101000 r 74 goat snp26919-scaffold285-304600 1 117626656 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396491 Affx-122963538 AX-123266846 1 115801338 GTCTAGGTAGGCTTTCATCTCAGCTTCCCAGAGAG[C/T]AGCCAAGGCTCCTGTTTTTAAAGATCTGCAAGTAA Y 2 1 2 1 201000 f 74 goat snp26918-scaffold285-235651 1 117697041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420932 Affx-122944996 AX-123291279 1 115872235 TTTAAAAATAAAATTTCAACTAGGAAAAAAAGGGT[A/G]TCACTGACAAAAGTTTTCTTGATAAAACTGGGCAG R 2 1 2 1 101000 r 74 goat snp26917-scaffold285-164754 1 117768269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776504 Affx-122973065 AX-385263631 1 115903579 TGGTGTATCTGCAGGAGTGTACTTCATTTCACTAA[C/T]AATAGACTGGTGCTGTAACTCAAGCATCAAATCAA Y 2 1 2 1 101000 f 74 goat snp26916-scaffold285-133410 1 117799739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418998 Affx-122946056 AX-123289346 1 115966310 ACGATGTTCATGGAGTATCGTCTGTCTGAAATAAT[A/C]CTGGTTTTTAGCTTGCCTTTTCACTATTGTTCAAA M 2 1 2 1 101000 f 74 goat snp26915-scaffold285-70679 1 117862647 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383222 Affx-122972768 AX-123253580 1 116057118 GAAAATGTTTATTAAGGCATTTCTAGAGTGTATTT[A/G]TAGAACTGCTACTCAATCTCTACAGAATAATTCCA R 2 1 2 1 101000 r 74 goat snp27138-scaffold29-20030 1 117952805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447172 Affx-122924427 AX-123317508 1 116125609 CGAGTTCTAGTGTCCTCTCACAACACACACTCACA[C/T]GTGTTGTAGCTCTCTTGGGTGTGACTGCATAGACA Y 2 1 2 1 202000 r 74 goat snp27140-scaffold29-88521 1 118021451 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404415 Affx-122956774 AX-123274767 1 116177880 AGGTTGAGGAAGCAACTGTGACAATCCGTTAATCC[A/G]TCAAAATCAGTAGAAAACACAAGCAAAAGAAATAT R 2 1 2 1 101000 f 74 goat snp27141-scaffold29-140792 1 118072995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783403 Affx-122968649 AX-385270466 1 116217126 ATTAGGATTATTATGAAGGAACTGTCTTTTGAATC[A/G]TTTTGAAGCTAAAGAAATCATAAACCAGTATTTTT R 2 1 2 1 101000 f 74 goat snp27142-scaffold29-180038 1 118112217 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775692 Affx-122977427 AX-385262823 1 116247820 ACCTCACAGTGTCTTACCCTTAGTAGGAGCTGTGT[A/G]ATGTCATGTTTACGGGATTGGTTTCAAGGGCCCTG R 2 1 2 1 101000 f 74 goat snp27143-scaffold29-210732 1 118142843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273587 Affx-1111833708 AX-519547201 1 116300609 TTCATCTGTATCAACTGCTGCTGCGATGTGATGGC[A/G]TGCAGAGAGGGCGGCTGCATCATGGCCCCCGAGCG R 2 1 2 1 202000 f 74 goat GoatD01.002114 1 116300609 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431259 Affx-122937120 AX-123301600 1 116301222 TAATGAAGGTTATTTCCTGAAGGATCTTTGCATTT[A/G]CTGTCTATAAAGGACTATAAAGGACTAAAAATTAC R 2 1 2 1 101000 r 74 goat snp27144-scaffold29-264134 1 118196341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400199 Affx-122960184 AX-123270554 1 116330643 GTAAAGAGCTCAGTGGCTGAGAGTGTAGAGATTCT[C/T]ACCCTCAAATAGTCAGACTCTCTGGGCTTAGATCC Y 2 1 2 1 101000 r 74 goat snp27145-scaffold29-293555 1 118225947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801773 Affx-122968615 AX-385288681 1 116361703 GAAGTTAAAGGTAGGAATGTATAATTTATCATTGG[A/G]GTTCTTTTAGATGGACAACTGACTCTGGAGATTAG R 2 1 2 1 101000 r 74 goat snp27146-scaffold29-324615 1 118257096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766813 Affx-122937403 AX-385254138 1 116429857 GACTGATAATTATGTACTGTAACCAGGAGCAGCTG[C/T]GTATATTTCCTTATTCACAAACCACACTAAGAAGT Y 2 1 2 1 202000 f 74 goat snp27148-scaffold29-392769 1 118325492 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400824 Affx-122959799 AX-123271179 1 116496266 AAAATAATACAGGGAAGCCGTAATTTCCACTCTGT[A/G]TTTGGGAAACGTAAGCACACAACATCTACTTAGTC R 2 1 2 1 101000 r 74 goat snp27150-scaffold29-459178 1 118392885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404359 Affx-122956817 AX-123274711 1 116526061 GCTTTTAACACAGTGCCTAGGATAAAGATACTCAA[C/T]GGATGTCAATTCATTATGATAATTTTGAGGGGGGC Y 2 1 2 1 101000 r 74 goat snp27151-scaffold29-488973 1 118422707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419341 Affx-122945648 AX-123289689 1 116559452 TAAGTCTCAGGGAGGTTGAGTATCACCAATTAATC[C/T]TAATGGAGAATGATTTCTATTTTGTTCATTTACAC Y 2 1 2 1 101000 f 74 goat snp27152-scaffold29-522364 1 118456097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423307 Affx-122942633 AX-123293653 1 116595496 CAAGAACATATAAATCCCATTGCATGGGAAATCCT[A/G]TACGAGGGCCAACCATTTGAATATGTACTATGTAC R 2 1 2 1 101000 f 74 goat snp27153-scaffold29-558408 1 118492153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420319 Affx-122945016 AX-123290666 1 116636809 TGTTGGCTCCTCTGTTCTTGCATCATCCTAGTCTA[C/T]GCAGAGTGCAGAAATTCTCAATTGCAACATTATTC Y 2 1 2 1 101000 f 74 goat snp27154-scaffold29-599721 1 118534679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398730 Affx-122961831 AX-123269085 1 116667758 TAGTACTATCTGCTTGTTTGAGTATTTGACAAATC[A/G]TGGGTAATAATTCTAAGCCTTGGTCAGAACTTTTC R 2 1 2 1 101000 f 74 goat snp27155-scaffold29-630670 1 118565708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377889 Affx-122977252 AX-123248248 1 116703793 TCTCCTTGGGACTGGAATTCACAGAATTCTCTACA[C/T]GATCACACCTGTGGCTCCAAGAGGGGGGAAATGGC Y 2 1 2 1 101000 f 74 goat snp27156-scaffold29-666705 1 118600327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770964 Affx-122951102 AX-385258127 1 116735413 CATCGTTTCTCTGAGGTCCAGGAATCTTTTTAAGC[C/T]ACCCTAGGTGATTCTTAAACACCAGTAGAGGCATC Y 2 1 2 1 101000 f 74 goat snp27157-scaffold29-698325 1 118631978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446813 Affx-122925287 AX-123317149 1 116766846 TGTGTTCCCTGTATTGGCAGATTCTTAACCACTGG[A/G]CCGCTAGGGAAGTCCTAATTATAGTTTTAAATGGT R 2 1 2 1 303000 r 74 goat snp27158-scaffold29-729758 1 118663522 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792760 Affx-122954824 AX-385279739 1 116814544 AAAGCAGGTGGAGTTGGTTTGAATCTTTCTGCAGC[G/T]TCTCGAGTTTTTTTAATGGATCCAGTAAGTAATTT K 2 1 2 1 101000 f 74 goat snp27159-scaffold29-777456 1 118712082 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426047 Affx-122941106 AX-123296393 1 116864170 AAATATAAATAAATAAATGACATTTAAAAAAAGAA[G/T]AACCACAAGCTCCTATCTACATAGTTGAATTTTCA K 2 1 2 1 103000 r 74 goat snp27160-scaffold29-827082 1 118761957 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416895 Affx-122948070 AX-123287243 1 116910899 AAGTGAAAGTGGATGGTGTGTTACAAAGTTTGGCT[A/C]GAGTTCAGGGTACATTGCATGTGAGAATTATATGA M 2 1 2 1 101000 f 74 goat snp27161-scaffold29-873811 1 118808657 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395676 Affx-122963749 AX-123266031 1 116947095 ACCATGGAAGTCCTACAACAGTTTTAGATGTCCAC[A/C]CAGTGAGCAGCGATGGTGGAGCGTGTTTAGAATAT M 2 1 2 1 101000 f 74 goat snp27162-scaffold29-910007 1 118845656 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416940 Affx-122948034 AX-123287288 1 116996190 GTTGAAAACAGTTGACTGAAGTCAGAAGGACAATT[A/G]TAACCTCTAAAAAATTAAAAAAAATTTTTTGAGGC R 2 1 2 1 101000 f 74 goat snp27163-scaffold29-959102 1 118894841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397253 Affx-122962359 AX-123267608 1 117040977 TGGAAGTCTTCTTATTACTCCACTTTCTTGAGAAA[A/G]GAGCTCTGTTAAGGGTCTAGCTCTTCCTGCTAAGT R 2 1 2 1 101000 f 74 goat snp27164-scaffold29-1003889 1 118940979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446810 Affx-122925289 AX-123317146 1 117104293 TTCAAATTCTTCTCTTAGTTGCATTTATTCACTCT[A/G]CTACAGTGTAACTCACTTTTATATAGGGCTTGCAG R 2 1 2 1 101000 f 74 goat snp27166-scaffold29-1067205 1 119005729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386789 Affx-122970918 AX-123257147 1 117136085 GCAAGCCACAAAGTCTGTCTAGATGTTTGTGTGTG[C/T]ATAGGAGGGACAGCCTTGGTGGATGGGGAGTTGTT Y 2 1 2 1 101000 f 74 goat snp27167-scaffold29-1098997 1 119038932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787351 Affx-122965851 AX-385274376 1 117166805 AGATTGGTTCATGGTTGCAAGACAAAATTAAAAGC[A/G]TACTTTGCTGTTAGGGAGTCAAGATAACATCAATA R 2 1 2 1 101000 f 74 goat snp27168-scaffold29-1129717 1 119069591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449591 Affx-122923217 AX-123319926 1 117253511 AAAAACCACCCCAAACAGGGAATTGTTTACCCAGA[C/T]GGAATAAGTCAAGTCAAAGGTAACTGAAACTAGTG Y 2 1 2 1 101000 r 74 goat snp27170-scaffold29-1216423 1 119156679 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799249 Affx-122922723 AX-385286179 1 117292248 TTATTTCAAAACTGAAAGTAAGTTACAAGAAATGC[A/G]TAAGGAAGCATTGTAGTTTCAAATAAATGCAAAGT R 2 1 2 1 101000 r 74 goat snp27171-scaffold29-1255160 1 119193521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399406 Affx-122961242 AX-123269761 1 117328942 AGTATTTTCATATGTGTTATTTCAATTTATGTTCA[C/T]GACTACCCAGTAGATATAGGTACTATCCTTTTCTA Y 2 1 2 1 101000 r 74 goat snp27172-scaffold29-1291854 NW_017211682.1 14321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436998 Affx-122933139 AX-123307336 1 117380044 TCACTTTCTTCTTCTCTCCTTTTGTCTCCCTGCCC[G/T]ATTTTGACTGACACCCCCCCTCAAATTGCCTATTG K 2 1 2 1 102000 r 74 goat snp27173-scaffold29-1342956 1 119276500 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376746 Affx-122978945 AX-123247105 1 117436656 ACATGCAGAGGGACACAAAATTCAGGCAGGATTGT[A/G]GGGAAATAAGGATTTTAAAATGAGATTGTTAAAGA R 2 1 2 1 101000 f 74 goat snp27174-scaffold29-1399568 1 119333356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408938 Affx-122953939 AX-123279289 1 117468272 TTGGGTGGAGAGAAAATTTTTTGAGGAAATAATTA[C/T]GCCTAATTTCCCAGAATTAAAGCAAGGTTAAATAA Y 2 1 2 1 103000 r 74 goat snp27175-scaffold29-1431184 1 119365068 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441425 Affx-122928822 AX-123311762 1 117501325 ATCCATTTTAAATGTCAATGTTTTAAATTCATCTC[A/G]TCTAGTTTGAAATGTCAGTGTCATTCAATTGCTTT R 2 1 2 1 101000 r 74 goat snp27176-scaffold29-1464237 1 119398757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428425 Affx-122938827 AX-123298768 1 117546970 CAGGTGAGTTGAATTCTAAGGGTAAAATGGAGTAT[A/G]TATTTCCTCAGTTCAGTTGCTCAATTGTGTATGAC R 2 1 2 1 201000 f 74 goat snp27177-scaffold29-1509882 1 119445912 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394797 Affx-122964815 AX-123265152 1 117583016 GACTTCTTATATTTTAGCTAAGGGTTGTGAATCTT[C/T]CCTACAAATGGCAAGATAGTAAATATTTTAAGATT Y 2 1 2 1 201000 f 74 goat snp27178-scaffold29-1545928 1 119482417 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429780 Affx-122938240 AX-123300121 1 117624753 ATTTCCTTATTTCTTCTGAAACCCTGTAATTATAG[C/T]GGAATTTGATCTATTCTCCTCCTGTTCTAGGATAG Y 2 1 2 1 101000 f 74 goat snp27179-scaffold29-1587665 1 119524632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438363 Affx-122931320 AX-123308701 1 117693350 TGACTATACTCCACTTTATTCATTCTATTATTTAT[A/G]TTTCTGTGGTTGACTGTCTCTCTTTATGCCACTGC R 2 1 2 1 101000 r 74 goat snp27180-scaffold29-1656262 1 119596928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415753 Affx-122948936 AX-123286102 1 117735663 TTTTGAAACATACCTTTCAAAGTTGGGGAGGAGAA[A/C]ATGCCCTTTCACAGCAGACTGATCCAACTTTATGC M 2 1 2 1 101000 r 74 goat snp27181-scaffold29-1698575 1 119638383 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452681 Affx-122920316 AX-123323014 1 117781370 AGTACTATTTTAGATTTTGGAGCTATGACAATATG[C/T]AAGATAAAATCCCTGCCTTCAACAAGCTTATCAGT Y 2 1 2 1 201000 f 74 goat snp27182-scaffold29-1744282 1 119684625 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410283 Affx-122952509 AX-123280633 1 117818144 TATACAGTCATGTTTCTTAAAGAAATCCTGTGGTC[A/G]ATCCTTTGCTGCTAATTAATCTCTCTTAGTAGATT R 2 1 2 1 101000 r 74 goat snp27183-scaffold29-1781056 1 119722041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378930 Affx-122976438 AX-123249289 1 117850292 GACAGATTGTACAAATTAACATCCCCATTAGTAGC[A/G]TATGAAAAGTCAAAGTGATAGTCACTCAGTCATGA R 2 1 2 1 101000 f 74 goat snp27184-scaffold29-1813204 1 119754434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786311 Affx-122941233 AX-385273345 1 117888781 CTGAGACACATTGTATAGAAGAAGTAAAGTAGTGA[C/T]ATCAATGATTCTTTAATATAGTAAATTATCATTGT Y 2 1 2 1 201000 r 74 goat snp27185-scaffold29-1851693 1 119793784 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382224 Affx-122973984 AX-123252582 1 117927174 TGTCTCTCTTCTACCTTTCACCAAACCCCAAAGAT[A/G]TTAGATGTTAGTTATTAAGGGTTGTTTAAGCATAA R 2 1 2 1 201000 r 74 goat snp27186-scaffold29-1890086 1 119832489 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271807 Affx-1111832832 AX-519545594 1 117945786 AAGCAAACCGAGGCACCATGGTAAGAGATAGATAC[A/G]AAGTGTCTTACTTTTCAATAAAGAAAACACATAGA R 2 1 2 1 101000 f 74 goat 1_117945786_AF-PAKI 1 117945786 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320775191 Affx-122961658 AX-385262322 1 117956673 AACAATGGCTTAACTACTGTGGTTCAGAATGATCC[A/G]TCTTATTCCACTCATTTATGCTATTCCTGTTGGAA R 2 1 2 1 101000 f 74 goat snp27187-scaffold29-1919585 1 119861809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802777 Affx-122963620 AX-385289676 1 118021713 AGACAAATCCACAAATACAGAATCATGAATAATAA[A/G]GATCAACTGTGCCAAAACCCTTACTGCTCCTAATA R 2 1 2 1 101000 r 74 goat snp27188-scaffold29-1984625 1 119928850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383494 Affx-122973428 AX-123253852 1 118055872 AAAAAAAGAAAAGTATGAGATATGATCATTCATGA[G/T]AGCCTGGATGATCTCTGAAGTCCTTTCCAACTTGG K 2 1 2 1 201000 f 74 goat snp27189-scaffold29-2018784 1 119963723 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770355 Affx-122936536 AX-385257521 1 118133288 TCTCTGAACACCCTGCCTGTGGGCATATATAAAAT[A/G]CTCACTCTTACCTAATAAGACCTGAAATTCTATAT R 2 1 2 1 101000 f 74 goat snp27191-scaffold29-2096200 1 120042039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450326 Affx-122922130 AX-123320661 1 118168385 TTTGTATAGTTCTTTTGCTTAGTGACTGCATTATT[A/G]TTATTTTGTCTCCTTTGTTTTCCTTTGCTTCAGCA R 2 1 2 1 303000 f 74 goat snp27192-scaffold29-2131297 1 120077695 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784426 Affx-122942024 AX-385271475 1 118214800 CCATTTTTAGAGAGAAGATAACTGGAAAGGTCCAA[C/T]CTATTGGATCTTTTTCTTAGGATTAGGACCAACCT Y 2 1 2 1 201000 r 74 goat snp27193-scaffold29-2177712 1 120124419 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439267 Affx-122930989 AX-123309604 1 118248260 TGGAAACAATCAATGGGAGAAATTCTTGTGCTGTT[A/G]TTCTTTTGTTCATAGTCAACTCAATTTCTTTCAAA R 2 1 2 1 201000 r 74 goat snp27194-scaffold29-2211172 1 120157911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764844 Affx-122937259 AX-385252443 1 118300479 ACTTTTTCTTCTCTACACAGATGATGGGGTGAGAG[C/T]ACATTCTAGGCCTAGGGAATGGTAAGTATCCCATT Y 2 1 2 1 101000 f 74 goat snp27195-scaffold29-2263391 1 120209874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784623 Affx-122958656 AX-385271671 1 118360605 TGGCTCTTCATATGCCCTGATCCCTATAATTTTTC[A/G]ATCTTGTTGTCTCACCACCATGTTGATTCTACATT R 2 1 2 1 101000 r 74 goat snp27196-scaffold29-2323517 1 120270412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804406 Affx-986696573 AX-385290995 1 118381310 CATTCGCTGGTGTGGCTCGCCATCCTCTGCATTGT[C/G]GCTAATATTTTGCTTTACTTTCCTAATGGGGAAAC S 4 1 2 1 600010 r 74 goat 1_118381310 1 118381310 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38405463 Affx-122956035 AX-123275815 1 118413261 ATCCAACAAATAAATGAAAGAGAATTCTTTCTTCT[A/G]TCTTTAAAGCCCAAATCTTTTCCACTGCACTATGT R 2 1 2 1 101000 r 74 goat snp27197-scaffold29-2376173 1 120323597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416469 Affx-122947809 AX-123286817 1 118493069 AAAATGAGTAAACACCTTATGCCGGATTCAGTTTT[A/G]CAATTTGCAATCTCAGCTCTCCACTGTCATTAGAA R 2 1 2 1 101000 f 74 goat snp27198-scaffold29-2455981 1 120405168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476157 Affx-1251763660 AX-185682401 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 4 1 4 1 20000 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 539476412 Affx-1251763660 AX-586011815 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20000 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 560378498 Affx-1251763660 AX-605230913 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20000 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562165977 Affx-1251763660 AX-606941386 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562166139 Affx-1251763660 AX-606941547 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562166237 Affx-1251763660 AX-606941645 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 38403534 Affx-122957611 AX-123273887 1 118531770 CACAGAATTTCACTAATGCTTCCTAAATCATGCCA[C/T]GTTCTGGTGTGACCATATTCTTCAGAAAATAACTT Y 2 1 2 1 101000 f 74 goat snp27199-scaffold29-2494682 1 120444417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420590 Affx-122945259 AX-123290937 1 118565327 GGATTTGTGGAGTTCACAGTATAAGGAAAAGGGCA[G/T]ATATACAAACAAACAAGTTATAAAACAACATGATA K 2 1 2 1 101000 f 74 goat snp27200-scaffold29-2528239 1 120478571 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396589 Affx-122962906 AX-123266944 1 118638327 ACAGCTGTGTAAGAAAAGAAATGAGAGAGAGAAAA[C/T]GGAAGAAAAAAAATTACTTCAGGATGTAAGTTGAT Y 2 1 2 1 102000 f 74 goat snp27201-scaffold29-2601239 1 120551161 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404937 Affx-122956433 AX-123275289 1 118676534 TCAAGTTACTTAGATCTCCAGATTTCTGTTTCCTC[A/G]TCTGTAAAATGGGAAGGATGTTACTTCCTTATAGA R 2 1 2 1 303000 r 74 goat snp27202-scaffold29-2639446 1 120589055 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408173 Affx-122954206 AX-123278524 1 118707412 TGCTTTGAAATATAAATTTAGGGAGTTTTTGCTAA[G/T]CATAATTTATAAAGGCAAATATTTCTCCATTTAAT K 2 1 2 1 101000 f 74 goat snp27203-scaffold29-2670324 1 120619878 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771001 Affx-122946000 AX-385258163 1 118761754 TAAAACAAGTAAATAGACTGTTCTGTGTCTACTAC[A/G]TTTGTCTTGATTTCTCTAATAAAAAAGGCTTTTGT R 2 1 2 1 101000 f 74 goat snp27204-scaffold29-2724666 1 120682320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792599 Affx-122963058 AX-385279580 1 118800641 GGGGGTGGGCAGGGCTCGGTAGAGAACATTTTGTC[A/G]TATCTGTTTTTCATCTTTGTGTCATGCCATCTGCC R 2 1 2 1 101000 r 74 goat snp27205-scaffold29-2763553 1 120722058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390301 Affx-122967721 AX-123260658 1 118830647 GACTACTCTCTGGGCTTTCAGGAAGAGGTGAAATT[A/G]AACTGAGTCTTCAAAAATGATAAAGTTTCATTTAG R 2 1 2 1 101000 f 74 goat snp27206-scaffold29-2793559 1 120752761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398485 Affx-122961575 AX-123268840 1 118860711 ATTACTTGTATAAAGACAGACATAGAGCAATGGAA[C/T]GGAAAAGAGAGTCCAGCAATAACCTTTGTGTATTT Y 2 1 2 1 101000 r 74 goat snp27207-scaffold29-2823623 1 120784516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780361 Affx-122960732 AX-385267456 1 118927884 TTAAGGCATTATGGCATTCAACTAAAATATGCCTA[C/T]AAGCCAGCCAGTTGCCTTTTTGATACTCTGGGGGT Y 2 1 2 1 101000 r 74 goat snp27208-scaffold29-2890796 1 120852507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276550 Affx-1111835473 AX-519550062 1 118946303 GTTCAGCTGCTTAGCAGCATTAATTCCATAGCAAC[A/C]AAATTCCATCTACATTCCTAACTTTTCTTTGCCAT M 2 1 2 1 101000 f 74 goat Random2.2K-121 1 118946303 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387759 Affx-122969726 AX-123258117 1 118979763 TCTGTGGTCAAAGAATGAGAAATCCAGCTGCTTCT[A/G]TTGCTGCAGTAGATTTAGAATAAAAGCTCTAATGT R 2 1 2 1 201000 r 74 goat snp27209-scaffold29-2942675 1 120904588 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404655 Affx-122957301 AX-123275007 1 119021606 CCTATTTGCTAGTTATGGATCTTTAGCCCAAGGGG[C/T]AGGCTTCTGGGCTGGCACCCTTCTAGTGACCTACG Y 2 1 2 1 101000 f 74 goat snp27210-scaffold29-2984518 1 120946554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786005 Affx-122961891 AX-385273041 1 119057467 GGAACCATTTAATTCTAAAATCCCATAGCTAAAAG[C/T]ACATCTTTTAAGAAAAGTATATTTTAGAAATGTAT Y 2 1 2 1 201000 r 74 goat snp27211-scaffold29-3020379 1 120984438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433350 Affx-122935141 AX-123303691 1 119087221 TTCCGATTCGTCCGTCTCCCCCAATGATGACATAC[A/G]CTGTCATCATTTTCTTGTGTTTTCTTCCAGAGAAT R 2 1 2 1 303000 f 74 goat snp27212-scaffold29-3050133 1 121014512 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430426 Affx-122937745 AX-123300767 1 119120079 TACTTCTGTTCAATAAAACATCAATTAAGCAAATG[C/T]AGAAGAAACACTTCATTGCATTTCTATATTTCTAC Y 2 1 2 1 201000 f 74 goat snp27213-scaffold29-3082991 1 121048869 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451136 Affx-122921372 AX-123321470 1 119167801 AAGACCTAAATGAAATACTTTTGGTATCTTGAACT[A/G]TTGGGCTGTGTGGACTAGAGGGAAGACACCAGAGG R 2 1 2 1 201000 f 74 goat snp27214-scaffold29-3130713 1 121097376 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771683 Affx-122965096 AX-385258841 1 119199195 TCTTATTTTGATTAGGTCACATTGTATAATGGCCC[A/G]TTAGCTTTGACTTTCAGGACATGATAATAAAATGC R 2 1 2 1 101000 f 74 goat snp27215-scaffold29-3162107 1 121129312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387323 Affx-122970503 AX-123257681 1 119230177 TATGATAAATGAATTCTATTTACCTTTCCTTTGTT[A/G]CATCTGTTTACTCTTTCATGGATGTTTGCTTCATT R 2 1 2 1 101000 r 74 goat snp27216-scaffold29-3193089 1 121158151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410664 Affx-122952762 AX-123281014 1 119264585 ACCTCTTTTTTCTTCATCTCTTATATTCAATTCTA[C/T]CAATAATTTTGATTCCTCCTTTTAAGTCTCCCTAA Y 2 1 2 1 101000 r 74 goat snp27217-scaffold29-3227497 1 121192649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449253 Affx-122923471 AX-123319588 1 119317996 AAGGGTGAATATTTGCTAAACAATAAAATTATTGC[C/T]AATTTCATCTGACTCAAGGCAGGCAGTTAATACTC Y 2 1 2 1 101000 r 74 goat snp27218-scaffold29-3280908 1 121246295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419976 Affx-122945188 AX-123290324 1 119365743 GTAGCACTTGACACTATAAACAGAGATATCAAATA[C/T]ACTCATTTCATCTTCATAAGAATTTCAAACCCCTG Y 2 1 2 1 101000 f 74 goat snp27219-scaffold29-3328655 1 121293822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453828 Affx-122919552 AX-123324161 1 119429385 TGATTGTTGTTTGCAATGCATTGATTCAGGCATGG[C/T]AAATGCAAATATATCTATATTTAGGAGGCAGTAAA Y 2 1 2 1 101000 f 74 goat snp27220-scaffold29-3392297 1 121358705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393217 Affx-122965493 AX-123263574 1 119490301 GCCTAGGGTGTTCCTGATGCTCTCTCCCAGCATCC[A/G]CATTAGAACTCATGATCAGGTAACCTTCATTCTGA R 2 1 2 1 101000 r 74 goat snp27221-scaffold29-3453213 1 121420959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417051 Affx-122947521 AX-123287399 1 119535994 TTGTTTCTGCCTTGGACTTTACAATCTACTGATTA[C/T]GGGATATGCCTTGTTCCAGGGAATCTGTGTACAGG Y 2 1 2 1 201000 f 74 goat snp27222-scaffold29-3498906 1 121465951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394996 Affx-122964240 AX-123265351 1 119612931 CCTCAACAGGTATGTAGGATCCACTGTCTCAGGTT[C/T]GATACCCCCAGGCATCTCACACTTGCCTAATCTAA Y 2 1 2 1 201000 r 74 goat snp27224-scaffold29-3575843 1 121544152 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419062 Affx-122945808 AX-123289410 1 119663884 AGCACCATGTAGATGTGTATACATATGTATACATA[C/T]ATTTGCATGTATTGCATTTACTTAGTGCTTACTCT Y 2 1 2 1 103000 r 74 goat snp27225-scaffold29-3626796 1 121595226 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786302 Affx-122966660 AX-186931094 1 119733838 ATTTGTATTGTCATAAAGGTACAAAAGTTCTTGGC[A/G]TATTGGATAATAAACAGTTTTGGTGTGATTTGTGC R 2 1 2 1 101000 f 74 goat snp27226-scaffold29-3696750 1 121666874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782327 Affx-122945025 AX-385269404 1 119800880 AGCAACCAAGCACACATAGCTTCAAGTCAAGTCCA[C/T]AAGACTCCCCTTCCCACAAAACGGTGATCTCCTCA Y 2 1 2 1 101000 f 74 goat snp27227-scaffold29-3763792 1 121734383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405642 Affx-122956586 AX-123275994 1 119879452 GTGCTACCAGTTAAGACAGGGAACATACAAGAAGG[C/T]ACCTAAGGTAAAATCAGTTTTGTTTTAAATCTGTT Y 2 1 2 1 101000 f 74 goat snp27229-scaffold29-3842364 1 121812783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790405 Affx-122956111 AX-385277408 1 119946308 TTTTAAGCACAGGCTTACTGAGTCTACAGTACTTC[A/G]TTACACCATACTAATTTCATACAGGTCATCTAACT R 2 1 2 1 101000 f 74 goat snp27231-scaffold29-3909220 1 121879669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380752 Affx-122975127 AX-123251110 1 120003170 ATTCACCATTCAGGAAGGGGCTAGACACCTCCAAA[C/T]GGGAGTTAAAGGTATAAGCTTGCCTGACTTACTGG Y 2 1 2 1 101000 r 74 goat snp27232-scaffold29-3966082 1 121936805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800146 Affx-122965714 AX-385287069 1 120043093 AATTGTCGTTAGTTTACACTTACTTGATTGTTTTA[A/C]AGATAGATTTCGGCCTTGTTAATACTCTGCCACTC M 2 1 2 1 101000 r 74 goat snp27233-scaffold29-4006005 1 121977146 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802429 Affx-122970457 AX-385289333 1 120083352 GTTTTGTTGAATATCTACAGCATGCCAGATAAGTG[C/T]AGACACAAATAAAATTCCCCTTAATATAGTTCTGG Y 2 1 2 1 101000 r 74 goat snp27234-scaffold29-4046264 1 122016851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411557 Affx-122951641 AX-123281907 1 120140330 AGGCTTTCTACAATGATTAAATGTGTCAATTCATA[C/T]GAAAGGACTTAGAACAGTGCCTTAGAATTAATTTA Y 2 1 2 1 201000 f 74 goat snp27235-scaffold29-4103242 1 122073434 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411098 Affx-122951921 AX-123281448 1 120179602 ACATAGATGGTGATACACTCATTCAGTGGAATTCT[A/G]CACTGCAATGAAAAATTACTGTTTGCAACCACATA R 2 1 2 1 101000 f 74 goat snp27236-scaffold29-4142514 1 122112797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406598 Affx-122956255 AX-123276950 1 120208994 GATGGGGCGCAAAAAAATGAAAGGGATGTTGTGAA[C/T]AGTGTCCAAAAAGTGACAACACTTGGTGGCAAATG Y 2 1 2 1 101000 f 74 goat snp27237-scaffold29-4171906 1 122141743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769588 Affx-122959459 AX-385256758 1 120317123 TGTTCTAGGAAACATTTGAGTATGTTCTGCCAGTG[C/T]ATGATATTTGGATCTGTTCTTATTCTGTGTATGTT Y 2 1 2 1 101000 f 74 goat snp27239-scaffold29-4280035 1 122252351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391703 Affx-122967513 AX-123262060 1 120356741 ATATTTATCTCAGCTATCTGGGGCCAGTTTCCTGT[A/G]TCTTGTCTTTTCATATCCCCCTAAGCTCCTCAGTG R 2 1 2 1 201000 r 74 goat snp27240-scaffold29-4319653 1 122294386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788327 Affx-122932141 AX-385275345 1 120370639 CAAAACTTTTTGTTAATCTTCATAAATGACTTATA[C/T]GAGCAAAGTAAATCTTGGATAATAAAAGCTGAATG Y 2 1 2 1 101000 r 74 goat snp14652-scaffold1590-683424 1 122325202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793217 Affx-122969594 AX-385280195 1 120426454 CTTACTGGTTTCAAGAAATTAACCTGGAAATTATT[A/G]TGTCATTCCATGATAATTATACAATCCAGAATCTA R 2 1 2 1 101000 f 74 goat snp14651-scaffold1590-627609 1 122380371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427783 Affx-122939776 AX-123298126 1 120458177 TAGCAAAATAAATTTCCAGAAAGAGTTTTGTACTC[A/G]TAGAAATCAATTTTCCCAATGTAATAAACCAGCCT R 2 1 2 1 101000 r 74 goat snp14650-scaffold1590-595886 1 122411571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389890 Affx-122968129 AX-123260247 1 120493043 ACTAACCCACTGTGACACCACCCTGTTACCTCACC[A/G]TCAACCAATGAGAGGACTATGCATGAATTGATCAA R 2 1 2 1 101000 r 74 goat snp14649-scaffold1590-561020 1 122447646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787716 Affx-122932713 AX-385274739 1 120542757 AGATAACTTAGGAGATAACTGTATTCAAAATGTTG[C/T]AATACAGACTATTCTTTACTCAAAAACATGTCAAA Y 2 1 2 1 101000 f 74 goat snp14648-scaffold1590-511306 1 122506755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404627 Affx-122957325 AX-123274979 1 120600162 ATACAATTGAATATTTCTTTCTCCTTTGAAAGATT[A/G]CAAACAGGTCAACCTGTTGTTGTACCACGTTAAAG R 2 1 2 1 103000 r 74 goat snp14647-scaffold1590-453901 1 122564348 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411613 Affx-122951595 AX-123281963 1 120658886 AATAACCAGAATGGGAATGACATTGTACTTCTCAA[C/T]AGCAGCACAAGTTGCTCTAAGAGAAATGAATAATG Y 2 1 2 1 101000 f 74 goat snp14646-scaffold1590-395177 1 122623602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440398 Affx-122929619 AX-123310735 1 120690904 GGCACACTTAGTGGCATTTTTCTAAGATTATTCCA[C/T]GCAACTTACTCATGATAATAGTAGTATAGTCATAT Y 2 1 2 1 101000 f 74 goat snp14645-scaffold1590-363159 1 122655516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428262 Affx-122939410 AX-123298605 1 120724276 AATTATTGAGGCAGAAGATTCTGCATCATTCTCCA[C/T]TGAATGCAGACTGGCTGACTCTTCAGATGTTAAAT Y 2 1 2 1 202000 r 74 goat snp14644-scaffold1590-329787 1 122688253 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775027 Affx-122953115 AX-385262159 1 120760763 GAAAGAGAGGAAATAAAAACCTACTCATTAGCAAA[C/T]ATAAGCTATTTCTTTTGGAAAAGGAAGGATATTTC Y 2 1 2 1 101000 r 74 goat snp14643-scaffold1590-293300 1 122724539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379192 Affx-122976303 AX-123249551 1 120827698 ACCATGGATAAGCCACAGTTTCTTCATTTATAAAT[C/T]ATGCTGTGGAACATAACTCAATTAAATTAAATAAC Y 2 1 2 1 102000 r 74 goat snp14642-scaffold1590-226365 1 122791525 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394526 Affx-122964530 AX-123264881 1 120858649 CATATGAAGAAAGGAATGATGAAGAAAATAACTAA[C/T]GATTCAAGAATGTGTCACAATTTATCCGACTCTGG Y 2 1 2 1 101000 r 74 goat snp14641-scaffold1590-195414 1 122822407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403077 Affx-122958512 AX-123273430 1 120900385 CTAACTCTGGTTGGTATCAGAATTGAACTAAATTG[C/T]AGAATACCCAGCTGGTGTCACAGAGAATTGTTTGA Y 2 1 2 1 101000 f 74 goat snp14640-scaffold1590-153678 1 122864426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380423 Affx-122975305 AX-123250781 1 120946741 CTGAGTTGATTTTTGTCTTTTCTAGTGTTTCTTAT[A/C]GATTGAACTGCAGAGCAGGGACACACTTTGTCCAC M 2 1 2 1 101000 f 74 goat snp14639-scaffold1590-107322 1 122911826 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398579 Affx-122961501 AX-123268934 1 120987096 ATTATACTCCCCTTCTATAGAAAAAGCAGCAAACT[A/G]CTGAAAAGAGTACTTCCATTAAAAAGCAGAAGCAT R 2 1 2 1 201000 r 74 goat snp14638-scaffold1590-66967 1 122952220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271724 Affx-1111832833 AX-519545520 1 121035617 TAAATGAAACCTCAGATTATGAAGCCAATTAAGGT[A/C]AAAAAAATTAGTGTAAGAAGCTGCATGTCATGATT M 2 1 2 1 101000 r 74 goat 1_121035617_AF-PAKI 1 121035617 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387908 Affx-122970456 AX-123258266 1 121048966 GCTACAGAAGTGAAATAATTGGGGCAAATGATGGC[A/G]TTAATCAGCAGATTCTCTACCTGGAGAGGAATTCT R 2 1 2 1 101000 f 74 goat snp14637-scaffold1590-5097 1 123015156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417922 Affx-122946724 AX-123288270 1 121098939 TCCTCTTAGGAAAATAATGTAACTCTCTGCTAGAT[A/G]TAAAACAGAAGAAAAGATGTGGCCATTTCCAAGCA R 2 1 2 1 101000 f 74 goat snp16955-scaffold177-1087146 1 123067362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803168 Affx-122933351 AX-385290031 1 121136119 AACGCATAATCATTCCAAAATGATTAAGTTTGAAA[C/T]AAATACTTAAACATTTCCAGTAATAATTGTTTATT Y 2 1 2 1 201000 r 74 goat snp16954-scaffold177-1049966 1 123104454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406322 Affx-122955455 AX-123276674 1 121166200 TCTCTTAATATATGCTTCTGTGGTGATCCAGAAGA[C/T]AATGCAATAATAAAAATATTTATGGGAGCAGATGT Y 2 1 2 1 201000 f 74 goat snp16953-scaffold177-1019885 1 123134772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777781 Affx-122941442 AX-385264899 1 121204522 AAAAAGTTATGTACTACATCTATTTTGTTCTATTC[G/T]ATATTTGGAAGCATGTAAGTCTTCTGTAATATAAT K 2 1 2 1 101000 f 74 goat snp16952-scaffold177-981563 1 123173848 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406622 Affx-122955831 AX-123276974 1 121233953 GACTTCAGATCTCAAAGGATTGAAATTATTTGTCA[C/T]ATTTTCTCTGACCACAGTGAAATCTAGAAGGAAAA Y 2 1 2 1 303000 f 74 goat snp16951-scaffold177-952132 NW_017207670.1 4161 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799731 Affx-122977405 AX-385286658 1 121316305 ATACTCAGTCTTTTATTGTATGAATTAATTAGCAT[A/G]AAGTCATAATTTTGACTCTTTTGTGAATCTAGTAC R 2 1 2 1 101000 r 74 goat snp16950-scaffold177-869780 1 123284237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388155 Affx-122969457 AX-123258513 1 121346925 TTCGACTATAATAAATCTTCCTTGCAGGAGATTTT[A/G]CTATGACATATATACTAGCCTACTTTCAGTGAGAC R 2 1 2 1 101000 r 74 goat snp16949-scaffold177-839160 1 123315079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276724 Affx-1111835487 AX-519550234 1 121389214 GATTTAAAAGGAGGAAGGAAGGGGATGATGCCATT[A/G]TTCTTTGTATGTAGTTGTAGCATGATACATGGGCA R 2 1 2 1 201000 r 74 goat Random2.2K-123 1 121389214 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409881 Affx-122952907 AX-123280232 1 121405734 AAAGAAAAGTGCTGTTTGTATTGTTTCTGTTTAAA[C/T]GAAGGAGAAGGAGTCGTGTCCAGTATGGAGCAGAG Y 2 1 2 1 202000 f 74 goat snp16948-scaffold177-780351 1 123373118 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437765 Affx-122931709 AX-123308103 1 121447986 CATTTCTTACTTGCACCTATAAATAAACCAAGCAC[A/G]CATATTTTTTAAAACAAGCTACAAGAAACAAAGCA R 2 1 2 1 101000 f 74 goat snp16947-scaffold177-738099 1 123415504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441711 Affx-122929152 AX-123312048 1 121479956 CTTAGTTTCTCACGGTTCTCACCATCTCCCCTCCC[A/G]CAGTCAAAACCAGATCCTGTTAACACTGACGACAC R 2 1 2 1 101000 r 74 goat snp16946-scaffold177-706129 1 123447547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443994 Affx-122926911 AX-123314331 1 121574699 TCTTATTAACTGTGATACTGAGAATATAATAGACA[C/T]AGGTGAGGTCTGTATGGGTTCTGTTAATGGCAGGG Y 2 1 2 1 201000 f 74 goat snp16944-scaffold177-611386 1 123542876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433746 Affx-122934505 AX-123304087 1 121607128 CAAATAATATAATCATTCTGATTTCAGTATTGATC[A/G]TCTGGTGATATCTGAATTTGGTAACTGGAGATATA R 2 1 2 1 102000 r 74 goat snp16943-scaffold177-578957 1 123575192 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436693 Affx-122932332 AX-123307031 1 121664137 AAGATTCAGAATTTTGACATTTCTTTTTATTTTTA[C/T]ATTGCTTTTTACACAGTAAAATTGAAATGAGCTAA Y 2 1 2 1 103000 r 74 goat snp16942-scaffold177-521948 1 123632639 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409203 Affx-122953172 AX-123279554 1 121703953 TTTTTTATTGTATTGGCCTCCTGGTGAGAATTTAA[C/T]GGGAATGGATCTGCAGAAAACTTATTTTGGTTAAT Y 2 1 2 1 101000 f 74 goat snp16941-scaffold177-482132 1 123673382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450505 Affx-122922509 AX-123320839 1 121739933 AATGTGTAATAAGGAAACTGCAAGAAAGATTCTTT[C/T]ACCTGCAGAAATAAAATTCCTTTATTTGAGAGTAA Y 2 1 2 1 101000 r 74 goat snp16940-scaffold177-446152 1 123709920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437361 Affx-122931931 AX-123307699 1 121864474 TCTGAAAAATAGCTTGTTGAAGAGCATTACTAATT[A/G]CATCAATCTCTTGGGGCTACATGTTGTTAAAAATC R 2 1 2 1 201000 f 74 goat snp16938-scaffold177-321611 1 123836018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423194 Affx-122942720 AX-123293540 1 121896227 GATTTGTGTTCTTTTATTATTAAAGACCTGGTTGA[C/T]AATGAAGAGAGGTTCAATAATTAGCCCAGAAATAG Y 2 1 2 1 101000 r 74 goat snp16937-scaffold177-289858 1 123868225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434557 Affx-122934132 AX-123304898 1 121943419 AGACAAAAATCGCTTACACAGGACTGGCGATGTTC[A/G]TTGGAGAGAAGTGGACAGACTTGAGAGCTTTTCTA R 2 1 2 1 101000 f 74 goat snp16936-scaffold177-242666 1 123915386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426559 Affx-122940173 AX-123296905 1 121974254 ATGTCATATTTATCTCCTTCAATTCTCATTAAACT[A/G]CTCTGCTCACAGTAGAATTTAAGCTGTATTTTTAA R 2 1 2 1 101000 f 74 goat snp16935-scaffold177-211831 1 123946108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424474 Affx-122941764 AX-123294820 1 122020403 AAGTTAATTAAAAACCTGAGATGAAATAAAATATC[C/T]AAAGATGGTTCTCTGGCTTCTTATTTTTAGGACTG Y 2 1 2 1 201000 f 74 goat snp16934-scaffold177-165682 1 123992775 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769169 Affx-122954586 AX-385256344 1 122050419 TTTTGCTCCTCTTTCTCAAGTTTTAAACATTTCCC[A/G]CTAGCATCCCTGTTCCAGGCTTTTCATTTTTCTGT R 2 1 2 1 101000 f 74 goat snp16933-scaffold177-135666 1 124023566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784672 Affx-122963313 AX-385271720 1 122092899 CCACTTGAATTTCATTCCAGGAAGTAACACAAACT[A/G]CAGAGATAGTTGTGTATACTTTTGTTTGTCAGAAA R 2 1 2 1 201000 f 74 goat snp16932-scaffold177-93186 1 124066756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801886 Affx-122937937 AX-385288793 1 122133651 GAAGAGAGGGATAATCTATGATTGAATAGCCAAAA[C/T]GACATGATTCCTTTTTGCCCAGTTTGTGCAGAACT Y 2 1 2 1 101000 r 74 goat snp16931-scaffold177-52434 1 124108131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381621 Affx-122974774 AX-123251979 1 122163298 TCACTCTCAGGTAATGGAATATCTTCCAGTCATTC[A/G]TGTATATTAAGATAATTTTTAAAGATAGTTTTATT R 2 1 2 1 101000 f 74 goat snp16930-scaffold177-22787 1 124137808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451993 Affx-122920927 AX-123322326 1 122233791 GGGCCTTATCTCAAAGCAATATTTTCAAAAGTTTG[A/C]TGCACTGGACTTTCCTATTACACAGTAAAAAATGT M 2 1 2 1 101000 r 74 goat snp25854-scaffold266-3258613 1 124180025 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801284 Affx-122930928 AX-385288196 1 122266559 GGCCAGATGCCATTTATCCTCTAATAACTCTTTAG[C/T]GGAAAAATTCAGCACTAAGAGAAAAATATGTTAGA Y 2 1 2 1 201000 r 74 goat snp25853-scaffold266-3225845 1 124213199 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434003 Affx-122934238 AX-123304344 1 122296181 CAAGATCCCTAGGAATATGAAAATATATAAATGAC[A/G]CTTTTCATCAGCACCACCTGTGTCACAAAGAGGAT R 2 1 2 1 101000 r 74 goat snp25852-scaffold266-3196223 1 124243258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423313 Affx-122942628 AX-123293659 1 122353075 GTTTCTTCCAATATAAGATATAAATAAATAAACAG[C/T]AAACTCTAGTTGGGAACTATTTCATTGCATGGTTG Y 2 1 2 1 103000 r 74 goat snp25851-scaffold266-3139329 1 124298595 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798089 Affx-122940680 AX-385285024 1 122382460 GACATTACCAAGTTTTTGGCTCTTGCCCAGTCTAA[C/T]AGGTAAAAAATTGTGTTGCAGTGCAGTTTTAATGT Y 2 1 2 1 101000 f 74 goat snp25850-scaffold266-3109944 1 124328326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779636 Affx-122966950 AX-385266738 1 122424034 TTGGGTTCTGAAACTAAGCATCTAGATCAGTTGCT[A/G]TTCTTTTCTTTCAGTGGTTGTGTTTCAGTTTCATT R 2 1 2 1 201000 r 74 goat snp25849-scaffold266-3068370 1 124370469 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425231 Affx-122941007 AX-123295577 1 122469927 CATTATGATGTGAAAAATCCATCAGCTGAAGCTGA[C/T]CCAGAACTGGATTAAGATAAGGACATTAAACCATA Y 2 1 2 1 101000 r 74 goat snp25848-scaffold266-3022477 1 124416139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399506 Affx-122961168 AX-123269861 1 122509026 TAACAAATTCCAGAATTTATCATTTATATATGTTT[A/C]TAATCATCTTCCCAACTCAGGCTAAAAAGCCTTGC M 2 1 2 1 101000 r 74 goat snp25847-scaffold266-2983378 1 124455396 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434974 Affx-122933838 AX-123305314 1 122548666 GGTATAATTCAAATGTTCTATTTTTTCTATTTCTT[A/G]CAAATTCTCTTCAGGATACAGAAGGTGATAAAACT R 2 1 2 1 101000 r 74 goat snp25846-scaffold266-2943738 1 124496094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433520 Affx-122935011 AX-123303861 1 122581667 CTTTCTAGTTACTTTGCATAATAGTTTGCTTTGTT[A/C]GCCAAGTTTAACTGTACAAAACAATCTTATTTTCT M 2 1 2 1 101000 r 74 goat snp25845-scaffold266-2910737 1 124529280 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402283 Affx-122959109 AX-123272636 1 122618296 TATTTCTGCATTGCATAAAACTTTATACATTTTCT[A/G]TAAATGATGATGCTTGGTGTATGCGTTGTTAGAAA R 2 1 2 1 101000 r 74 goat snp25844-scaffold266-2874108 1 124565261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437674 Affx-122931777 AX-123308012 1 122664834 CCCCGTGTTGTACAATACCAAGCCATCTTGATTAA[C/T]GTAGCTTTACAGGTAGTGTTGAAGTTGAGTAGTTT Y 2 1 2 1 101000 f 74 goat snp25843-scaffold266-2827570 1 124611483 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402754 Affx-122958324 AX-123273107 1 122698863 GAGTGAATGTACTCCTACCCAGTATTATAAGAGAG[C/T]AGGTGACAGATAAAGAGGGACTGCTAATAGGAAGA Y 2 1 2 1 101000 f 74 goat snp25842-scaffold266-2793541 1 124645776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777644 Affx-122930146 AX-385264763 1 122749603 TTACCATGATGGCCTTTATGTCTCTAAATCTGGCA[A/C]TAGCCATGTACTATCAATTTCATCTCCCAAGCAGC M 2 1 2 1 101000 f 74 goat snp25841-scaffold266-2742801 1 124696182 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383096 Affx-122973281 AX-123253454 1 122802107 TATTGCCTAAACCACTTGCTCTTATTAATCAACCC[A/G]CTTGAAAAATACAACAAAATATCCCTAATTTTAAA R 2 1 2 1 101000 f 74 goat snp25840-scaffold266-2690297 1 124748552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449007 Affx-122923098 AX-123319342 1 122842771 AAGCTATCAAAAGGAAAAACACATGCATAACTGCT[A/G]CCTCACTTGCCCTTGCCCTTCTTGCTCTCCCTGGG R 2 1 2 1 101000 r 74 goat snp25839-scaffold266-2649633 1 124789007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410806 Affx-122952650 AX-123281156 1 122890862 CATGTGAAAGCTATTTGAGTTTGTTGAAAGAGATA[C/T]GTAATATAAGTTCAAGCTGCTCTTTTTATTTCTGG Y 2 1 2 1 101000 r 74 goat snp25838-scaffold266-2601542 1 124836595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426846 Affx-122940499 AX-123297191 1 122920561 TTTTTAAGTTAAGCAGATTTATGAGAAATATTGTA[A/C]TTTTTGGCTGGAATAACAGTTTTGGTTCAAGCTCA M 2 1 2 1 102000 r 74 goat snp25837-scaffold266-2571843 1 124866999 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769886 Affx-122974707 AX-385257055 1 122951902 AACCCTGAACCCTCGTGAATATGCATGAGTGCAGC[A/G]CAGTTAGACAGAATATTGGCTGCAAGGTAGAAGCA R 2 1 2 1 101000 r 74 goat snp25836-scaffold266-2540502 1 124899199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400652 Affx-122960358 AX-123271007 1 122985327 AAAATGAAATGGGATCTTCAAAAGGCAAGTCCTCT[A/G]TCACTGGAGATGCTTAAGCACAGAATGAAAGCATT R 2 1 2 1 101000 r 74 goat snp25835-scaffold266-2507077 1 124932532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410423 Affx-122952409 AX-123280773 1 123024303 TACCTTCTAAACCTTTGCCCCTTTCAGAAAGGAAA[C/T]AGTGGCTACCTCTATAATATCTGCTTCAGCTTTTC Y 2 1 2 1 201000 r 74 goat snp25834-scaffold266-2468101 1 124971657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779277 Affx-122966376 AX-385266381 1 123057179 TTAATCACAGCTTTCTTTCCCATTGATTTTGGGAA[C/T]AGCTATAAACTCCACCTTTATCTTATGTTGTCAGT Y 2 1 2 1 202000 f 74 goat snp25833-scaffold266-2435225 1 125003697 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776142 Affx-122941287 AX-385263272 1 123121250 GTAAGGCACCTATATTTGATCACATTTTACGATAG[C/T]AGGCTAATGAATACCCTTCAATAGAGCAGAATGTT Y 2 1 2 1 101000 r 74 goat snp25832-scaffold266-2371154 1 125067107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442001 Affx-122928425 AX-123312338 1 123178145 CTATATCCTTTGGTGAGAATGGACTTTTAGGAGAA[C/T]GAAAGATTAAAATGAAGAGATTAGTTGAAGATACC Y 2 1 2 1 101000 f 74 goat snp25831-scaffold266-2314259 1 125124047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416229 Affx-122948219 AX-123286578 1 123223584 TACTTCTCTGTCAAGTCAAAATTGCTCTCTATGGT[A/G]TCATTTCCAGAAAAATAACTATGGGATGAAGTACT R 2 1 2 1 101000 f 74 goat snp25830-scaffold266-2268820 1 125169503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436734 Affx-122932301 AX-123307072 1 123260964 TCCCTCCTGGATCATTTCCATCAGCTACAGACAAA[C/T]GTGATCTGGTGTCTTCCATATTTAACTCTCCTCCA Y 2 1 2 1 101000 r 74 goat snp25829-scaffold266-2231440 1 125207289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773667 Affx-122965151 AX-385260807 1 123369820 GTTTCCAATAGCATCTGCAGGCTCTCAAATTTGTC[A/G]TTCCTTCTCCCTAGAATTCTCTGAGCTCTAGACTC R 2 1 2 1 101000 f 74 goat snp25827-scaffold266-2122584 1 125316857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439138 Affx-122931083 AX-123309475 1 123439457 GACTGAGCGACTGAATTGAACCAGATAAAATGGTG[C/T]AGGAAATGAGTGTAAATTCAAAGTCACGAAGAAAT Y 2 1 2 1 201000 r 74 goat snp25826-scaffold266-2052947 1 125386355 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390280 Affx-122967736 AX-123260637 1 123485061 GGGTGTCTGGGAGGTGGATATATGGCTTGTACTCT[A/G]TGGGCTTTGCAGGTAGGAACTTGGTGGGCAGGTGG R 2 1 2 1 101000 f 74 goat snp25825-scaffold266-2007343 1 125431929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796680 Affx-122930637 AX-385283625 1 123516406 AAGTTGGGACTTAAAGGCAAAGACAAAAGAGACGA[C/T]AGGACACTATCCTTGAGGTACTTGCTGAGATCCTA Y 2 1 2 1 101000 f 74 goat snp25824-scaffold266-1975998 1 125463671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449249 Affx-122923473 AX-123319584 1 123549273 TTTCCTACTACTAGCTGTGTGATCATTTGGAATCT[A/G]TTTTCATCTGTAAAATGGCAGTAATCTTGCCTGTT R 2 1 2 1 101000 f 74 goat snp25823-scaffold266-1943131 1 125496583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375808 Affx-122978563 AX-123246167 1 123614451 TACACTTTGAAGACCGCTGATTGAGAATAGGGATA[C/T]GACAAAGAGCTGTTGTGAACTCAAGAATGCTCTGA Y 2 1 2 1 101000 f 74 goat snp25822-scaffold266-1877953 1 125561884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463688289 Affx-1110107313 AX-515168538 1 123634970 CATAGTAAGTATTGGATTGGTGAAGCAAAAATACC[A/C]AAGCCAAGGGATCTCTGATTCTCTAGACTTCCTCT M 2 1 2 1 201000 f 74 goat 1_123634970_AF-PAKI 1 123634970 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453026 Affx-122920092 AX-123323359 1 123672498 CATACATTCAGCAAGTATTAAACAAGTGCCTGCAA[C/T]ATGCTAGGCACTGTACTGAGTGCTGAGGATCCAAT Y 2 1 2 1 201000 f 74 goat snp25821-scaffold266-1819906 1 125620409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783391 Affx-122920873 AX-385270454 1 123713016 TGGGCTTGATGTTTCTCTAATAGAAAAACAAAGTC[A/G]TGTAAGCAAAGAGTCATTTTTACAAGTTTAAAAAA R 2 1 2 1 101000 f 74 goat snp25820-scaffold266-1779388 1 125661326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795240 Affx-122968249 AX-385282198 1 123800765 TAGCAAAGAGTTGGTTTATTCTCATGCTAAGTTCT[A/G]TCCTGAAATTAATATCTGAAAGTGGTCCCCAGAAA R 2 1 2 1 101000 r 74 goat snp25819-scaffold266-1691639 1 125749280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435095 Affx-122933714 AX-123305435 1 123847304 AAAAAGAAGGGGAAAAAAGCAAGGTAATAGGATCA[C/T]GTAGGACCTTGTTGGCTCTTTTATGGACTCTGGGC Y 2 1 2 1 101000 r 74 goat snp25818-scaffold266-1645100 1 125795901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781158 Affx-122947850 AX-385268243 1 123925237 ACAAGTTCTGGGTCAAATGATCTATTCTGCCTGCC[A/G]TTCTTTAAGCATTCAATAGGGCCACTGTATTTTTA R 2 1 2 1 101000 f 74 goat snp25816-scaffold266-1567167 1 125874006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802892 Affx-122978098 AX-186977875 1 123963534 TGCAAACACTGTGAAACAAGGGATTTACTAATAAA[A/G]TTATTATGTGGCCACTAAATATTATGTTGATACAT R 2 1 2 1 201000 r 74 goat snp25815-scaffold266-1528870 1 125912185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428250 Affx-122939418 AX-123298593 1 123995551 TTCCTGGGCCCAGCCTTATATGGAACAGTGGAGAC[A/G]TGGACCTTGACACTTGTTTGATTATATGACTCTAG R 2 1 2 1 101000 r 74 goat snp25814-scaffold266-1496853 1 125943991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415461 Affx-122949167 AX-123285810 1 124056440 TCAGTTTCACATTATGAGCTTCTTCTCACCATCTA[A/C]ACCTTCTCTAGTGGCTAATGTTGCTGCTCTGCAGT M 2 1 2 1 101000 f 74 goat snp25812-scaffold266-1435964 1 126004373 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398896 Affx-122961023 AX-123269251 1 124097886 GCTTCTTTCTATCATGAAAACAAATACAACTCAGT[G/T]TGCAATCAACTAACTCCTGAGGGTCTTAGGCTCTC K 2 1 2 1 101000 r 74 goat snp25811-scaffold266-1394518 1 126046344 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447035 Affx-122924534 AX-123317371 1 124143094 ATCCTCCCACTCTGGCAGAAACAAGGTTACATCCT[A/G]TAGAAGAGAACACAGAATACTCACTTAAGAAAATC R 2 1 2 1 201000 r 74 goat snp25810-scaffold266-1349310 1 126091255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409431 Affx-122954115 AX-123279782 1 124211012 AGCAGAATTGGACCGAAGCAGAGAACTACAGAAAC[A/G]ACTGAAACAGACAGAGAAGCTATGATCCTTGGAAA R 2 1 2 1 101000 f 74 goat snp25809-scaffold266-1281392 1 126159397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414288 Affx-122949596 AX-123284637 1 124276659 TTTCATACTAAAGGCACTACTAATATACAAATATC[C/T]TATTAACATTTGGAGAAACTCTTAACATTTAGCAG Y 2 1 2 1 101000 r 74 goat snp25808-scaffold266-1215745 1 126224885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442227 Affx-122928303 AX-123312564 1 124339628 TCAACCCACCACACATACTTCAGGGTGACTCCTAT[C/T]AAATTTCACTAGTATGGGGAGTATGCAGTGTGTAT Y 2 1 2 1 101000 f 74 goat snp25806-scaffold266-1152776 1 126288313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388533 Affx-122969198 AX-123258891 1 124387492 GATTTGTCTGATGAATCTTCCACCACGATCATCGG[A/G]ATATCGCTACTTATGTGTACATATGTGAAGCAACA R 2 1 2 1 101000 f 74 goat snp25805-scaffold266-1104912 1 126336392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406696 Affx-122955775 AX-123277048 1 124422883 TATGTAGAAAAATTCTTTTAAAATATGAACTCAAA[C/T]GAGGAGTCATCAAGGGAAGAAAACTGATATAACTA Y 2 1 2 1 103000 r 74 goat snp25804-scaffold266-1069521 1 126371812 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436327 Affx-122933252 AX-123306666 1 124484447 TAATTAAAATATAGTGCAGATGCAGAAATAGGGCA[A/G]TACAGGGTTTCACAGGAGCACAGACATGACAAATT R 2 1 2 1 201000 f 74 goat snp25803-scaffold266-1007957 1 126434640 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408367 Affx-122953731 AX-123278718 1 124603296 TGGAAATGGGGAACCTATCTGGGAAAATGGCCCTC[A/G]GGTAGTCTTTAGCTCCACTAAAGTCAGTCATACAC R 2 1 2 1 101000 r 74 goat snp25801-scaffold266-889108 1 126551137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273982 Affx-1111833932 AX-519547587 1 124616291 TCCTTTGCCGCTGGAGCCTTGTCCCAAGCAAAATT[A/G]TTTGTTCCCAGTTTTGTGAACTGTACAGTCTAGGT R 2 1 2 1 202000 r 74 goat GoatD01.010903 1 124616291 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437786 Affx-122931694 AX-123308124 1 124643070 AGCACGTTAATACAGCCCTGCTGTGGCATGTTCTT[A/G]TTGTTCAGTCGTTAAGTTATGTCCTGTTCTTGGCG R 2 1 2 1 103000 f 74 goat snp25800-scaffold266-849334 1 126590513 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384233 Affx-122972371 AX-123254591 1 124683449 GGGGAAATGTCATCTGCCCAGGAAGGAGAGGAAAC[A/G]TATTTGGGGAGTCACAGCTCACCTCTGGCATAGGT R 2 1 2 1 102000 f 74 goat snp25799-scaffold266-808955 1 126630832 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798908 Affx-122935200 AX-385285838 1 124713236 GTTTTTTCTGTGAAAGACATGATAGTAAATATTTC[C/T]GATTTTGTGGATGGAAACTACTTAACTCTGCCTTG Y 2 1 2 1 101000 r 74 goat snp25798-scaffold266-779168 1 126660500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789881 Affx-122922826 AX-385276888 1 124748543 TCATCTGAAGTGAAAGCAGATCAGAGGAGATTCAT[A/G]TGGATTGTGGTTGTTTGCAATCCCGGTGAAAGATG R 2 1 2 1 101000 f 74 goat snp25797-scaffold266-743861 1 126696327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444050 Affx-122926864 AX-123314387 1 124797258 CTTACCGATATCCAAGGAGTTATTGAAGTGGTTCC[A/G]TTCAGAAGAGAATTTTTTGCATGCTTATGGTTGAT R 2 1 2 1 101000 f 74 goat snp25796-scaffold266-695146 1 126745796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773518 Affx-122960361 AX-385260659 1 124832092 TGAAATCATAAAAATGGCATGGCAGATAGTTATAT[A/G]TTAGCCCTCAATGGGTCTTGAAGACCTCATTAGAA R 2 1 2 1 101000 r 74 goat snp25795-scaffold266-660312 1 126780546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447062 Affx-122924513 AX-123317398 1 124883357 CATTGTATAAAGGCAACATACTTTTGATACCCAGC[A/G]AGAAGCAAGAAAAGAACTCAGAGATAGTCTTGCCC R 2 1 2 1 101000 f 74 goat snp25794-scaffold266-609047 1 126831533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773104 Affx-122938509 AX-385260247 1 124923677 ACTGCCAACATTGTGTTTTACTAGGAAAATTTCAA[C/T]CCATGACTATTCAGAGCTTTCCGTTTAGTTCATCT Y 2 1 2 1 101000 r 74 goat snp25793-scaffold266-568727 1 126872579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408560 Affx-122953675 AX-123278911 1 124964034 GGCTATGGAATGGGGGTGGTACACTTAATACCTGC[C/T]TCCCAACATTAGAGGATGAATTGGTTTCACGTAAA Y 2 1 2 1 101000 f 74 goat snp25792-scaffold266-528370 1 126913220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410306 Affx-122952491 AX-123280656 1 125002753 ATGAGGAAGAAGTTTTAATGAAAAAGATATGTTTT[A/G]TTAACTCAGAGGAGAATCCTTAGAACTGTGTGATT R 2 1 2 1 101000 r 74 goat snp25791-scaffold266-489651 1 126952028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771596 Affx-122964927 AX-385258754 1 125032239 AGTCTCCATATGCCTATTTGTGACTCATTCTCTGC[A/G]TGAATAATATCACAAGTATAAATGTCTATCTCTTC R 2 1 2 1 101000 f 74 goat snp25790-scaffold266-460165 1 126981505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423579 Affx-122942402 AX-123293925 1 125091647 TCGCTCTGAATTGATTGCAAACTAAACAGAAGTGC[A/G]CGTGTCTTACAGGTCTTTTGTTGTTTAAGCAAAAT R 2 1 2 1 101000 f 74 goat snp25789-scaffold266-400757 1 127040891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398187 Affx-122962645 AX-123268542 1 125126749 TTTTCCTTTCTTTGAGCCAAAGCAATAACAGTAAG[C/T]AGTTTTTTGGTGCTTCAGAGCTGTGTTTCATTGTT Y 2 1 2 1 101000 r 74 goat snp25788-scaffold266-365655 1 127075969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436016 Affx-122932742 AX-123306355 1 125170430 TTTGACTTGAACCCACAGGACTGAAAATAAAATGA[A/G]CTCAGACTGTAGAAGGAGGCTGTAAGCAAGCAAGG R 2 1 2 1 202000 f 74 goat snp25787-scaffold266-321974 1 127119577 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772617 Affx-122956960 AX-385259765 1 125210642 GAAAGCCACGAGTCTCCTAGACTTATAAAATTTAC[A/G]CATCAAGGATGTCAAAGAGGTCCTCTATGATGTTT R 2 1 2 1 201000 r 74 goat snp25786-scaffold266-281762 1 127159995 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448981 Affx-122923115 AX-123319316 1 125284118 TGAGAAGGACATTTCCCCATATGCTTTCTGCTCCC[A/G]TTTTCTTATTTAATATCTTACCACCCTCCTCAACT R 2 1 2 1 101000 r 74 goat snp25785-scaffold266-208286 1 127230859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423852 Affx-122942772 AX-123294198 1 125332086 TGGCTTGGGGTTCCCAGGCCCATTGCCCTTGGAAT[G/T]TGGGTTACTTATGAGATAGCACTGACCAAATGCAG K 2 1 2 1 101000 r 74 goat snp25784-scaffold266-160318 1 127280688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380984 Affx-122974681 AX-123251342 1 125386322 GCAACCTAGTTCCTGACAAGATGGAAAGATGAACA[C/T]AGGATCCTTCCCCCTCATTGCTTCGTTCATAGTAG Y 2 1 2 1 101000 f 74 goat snp25783-scaffold266-106082 1 127334851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448658 Affx-122923344 AX-123318994 1 125416460 GCTTCTCCAGTCTGCCTCTGCTTGGAGGTTGAGAT[A/G]CCTCAACAGGGGCCAAGGCCATGAAGCCCCCAGGA R 2 1 2 1 103000 f 74 goat snp25782-scaffold266-75944 1 127364980 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443531 Affx-122927775 AX-123313868 1 125464043 TGGCCTGGATCAAGGTAGAGACTGCTTCACAAGAC[A/G]CTGTTGATGGTTCGCTTTGACTTGTTATAATCGTA R 2 1 2 1 101000 r 74 goat snp25781-scaffold266-28361 1 127412067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440479 Affx-122929376 AX-123310816 1 125498689 ACAGGCAGAGAATCGGAGTTACCTAGGCAAAATCC[A/G]TGCCAGGGAGCAAGGTCAGCGCGTTCGAAGGCTGG R 2 1 2 1 101000 f 74 goat snp11826-scaffold1438-1284450 1 127446515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792894 Affx-122949208 AX-385279872 1 125574632 TAACGATACATGAATGAAGGCAATGTCTCTTCAGT[A/G]ACTTAACTGATTATGAACTTAAATTGTCACCCATC R 2 1 2 1 101000 f 74 goat snp11825-scaffold1438-1208507 1 127522708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385366 Affx-122971637 AX-123255724 1 125609910 ACTTGTTTGTTTAAGGGGCAAGGGCACAAGTAACC[G/T]CTTCTTTGTGCTGGTCCTGTGTGAAGCACTTGAAG K 2 1 2 1 101000 f 74 goat snp11824-scaffold1438-1173229 1 127558025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802385 Affx-122944002 AX-385289289 1 125663188 ATGGTAGACTAATATAAACGTAGCTACAGGCAGCC[A/G]CATTTGCAGCTTCAATGCCAGATACAGTATCTTTA R 2 1 2 1 101000 f 74 goat snp11823-scaffold1438-1119951 1 127610396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775377 Affx-122934156 AX-385262508 1 125698770 GTCTCTAATCCACTGGTATTTAACTAAAGTTAGCT[A/C]AAATAATTCCCCTCATTCTGTGGAAAACCTAATGC M 2 1 2 1 201000 r 74 goat snp11822-scaffold1438-1084369 1 127645635 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418988 Affx-122946063 AX-123289336 1 125730109 GTAACTTCAGGACCAGACCTCACACCTCCTCCCCA[A/G]TCTAAGAAGGTAGCACCATAATTCTAGCCTTCACT R 2 1 2 1 101000 r 74 goat snp11821-scaffold1438-1053030 1 127678022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454064 Affx-122919388 AX-123324397 1 125769618 TGTGTAACAGGTACTAGACACCTTAGTCTAAACAA[G/T]TGTATGAGAGATTTGGCTTGAGGTGACCCAGGAGC K 2 1 2 1 201000 f 74 goat snp11820-scaffold1438-1013521 1 127718415 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399164 Affx-122960640 AX-123269519 1 125804966 ACAAATTCCACTGGATTTATTCTCTTGGTCAGAGT[A/G]CTCAAAGTCCAGACTGGAATCAAGAACTGAGAAAT R 2 1 2 1 101000 f 74 goat snp11819-scaffold1438-978173 1 127754149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385025 Affx-122971861 AX-123255383 1 125853679 ATGAAATTTCTGCTCCTTTAATCTTTGCAAGCTGC[A/G]TAAAGTGGAAAGCAAAATTCTCCCCTAAAATAGAA R 2 1 2 1 101000 f 74 goat snp11818-scaffold1438-929460 1 127802923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417290 Affx-122947241 AX-123287638 1 125885480 TGTGTTGCAGCGCTTGCACCTGGACAAATGTCTCC[A/G]TGGGCAACAAAATACGAAGAAAGTACAAGAGACTG R 2 1 2 1 101000 r 74 goat snp11817-scaffold1438-897659 1 127834801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419015 Affx-122946045 AX-123289363 1 125936999 AATCCCCCAGCCTTGGCTCTTGGAATCCTCAGGCA[C/T]ATCCCTCTGACCTTGCTCAGGACCTGCAATCCAGT Y 2 1 2 1 101000 r 74 goat snp11816-scaffold1438-846140 1 127887216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396100 Affx-122963422 AX-123266455 1 125981722 CAAAACAGATTAAACCCTTAAAGATGGATGCCCAG[A/C]TCCCACAGCTGAAGACATCCTGCAGTAAAGCAGTG M 2 1 2 1 101000 r 74 goat snp11815-scaffold1438-801417 1 127931852 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445494 Affx-122925195 AX-123315831 1 126015056 TCACCCGTTCATCCTCCCTGGGACTCTGAGGAGAA[C/T]GTTGGATAACATGAGGGATACTTTGAAAATAATAA Y 2 1 2 1 201000 r 74 goat snp11814-scaffold1438-768083 1 127963519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429811 Affx-122938190 AX-123300152 1 126067658 TCCCAGTGTGCTGCGTCTTCCGGGCCAGAGTACCC[C/T]ATTTGTCCCCATCCCCAGCTCATTCCCATCCCTAT Y 2 1 2 1 101000 r 74 goat snp11813-scaffold1438-715481 1 128016064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415204 Affx-122948984 AX-123285553 1 126131419 CTGCTCTGGATAGCTTTTCCTACAAGGCCCTGTGG[C/T]GTAGCTGATCTGTCCCCACCACACACACACACAGG Y 2 1 2 1 101000 f 74 goat snp11811-scaffold1438-651720 1 128080007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271812 Affx-1111832834 AX-519545598 1 126138111 TCTTCTTAAGTTAGCATATCAAATAAATGACCTCA[A/G]TTCTAGAACTTACTTAATTTAATTAACTGTCACCC R 2 1 2 1 101000 f 74 goat 1_126138111_AF-PAKI 1 126138111 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778348 Affx-122934389 AX-385265463 1 126160729 CCATGTGTTTTGGCCATGTTCACAGAGTTAGGAAC[A/G]TTGGAGCTGGTACTTGAAGCCAAATCATCCTGATT R 2 1 2 1 101000 f 74 goat snp11810-scaffold1438-622410 1 128109455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440249 Affx-122930662 AX-123310586 1 126222287 GACCTGGTGACCCATTTGGTGGCTACAGCTGGAAA[C/T]GGAGCAAGACACATGGCAGACTCATCCATTAAAGA Y 2 1 2 1 101000 r 74 goat snp11809-scaffold1438-560852 1 128171721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381135 Affx-122974566 AX-123251493 1 126262831 CTACACGTGCATCCAATGTTCTCTGTTCCCATTAG[C/T]GGCACCTAATTAGCAGTAATCCAATTAAGCCTGGT Y 2 1 2 1 101000 r 74 goat snp11808-scaffold1438-520308 1 128209609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438047 Affx-122931546 AX-123308385 1 126299714 ATAAGTCCATCACTGGTTGAGCATTGCCTTTGGGG[A/C]TAGGCACTTCTGGGCTGCCCCACATAAACAATTGA M 2 1 2 1 101000 f 74 goat snp11807-scaffold1438-483425 1 128246318 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790775 Affx-122973806 AX-385277776 1 126385530 CAATCCATCCGGTTCTCCAAGAGCTAATCAAAAGC[C/T]GCATGTGCAATGATTTATCTTCTGCTCATCTTCCA Y 2 1 2 1 101000 f 74 goat snp11805-scaffold1438-397609 1 128332279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770724 Affx-122979110 AX-385257888 1 126429075 ATAAAAATGTATCACACATTCGCTACCCTCTAGAA[C/T]GAAGTTGATAGCAAAAGCCACAAAGGTTTTATTTA Y 2 1 2 1 101000 f 74 goat snp11804-scaffold1438-354064 1 128375725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424186 Affx-122942518 AX-123294532 1 126492454 GAGTTCCTGGAATGAAGGCATAGTATCCTAAGTCA[G/T]CTAGAAACTGTCTCAAGCCAAACATTTGAAGGTCC K 2 1 2 1 101000 f 74 goat snp11803-scaffold1438-290685 1 128439507 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421133 Affx-122944197 AX-123291480 1 126525306 GGTGCTCTTCTAGGCCCTAGGGGAACCTCAGTGAG[C/T]GAAGCAGATTAACATCCCTGTTATTATGGAGCATT Y 2 1 2 1 101000 r 74 goat snp11802-scaffold1438-257833 1 128472620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408961 Affx-122953921 AX-123279312 1 126559305 CAGAGTTTTGAGGATTAAATGAGATCACCTGTATG[C/T]GCTGTTAGCACAGTGACTGACCCACAGTGAAGTCT Y 2 1 2 1 101000 r 74 goat snp11801-scaffold1438-223834 1 128506679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439847 Affx-122930456 AX-123310184 1 126610922 GAACAGGGTATACTGCCAGGAAATGGGGCTCCCTG[C/T]GCTTAGGAATCATGTGCACCTGGCTTTGCATCTTT Y 2 1 2 1 101000 r 74 goat snp11800-scaffold1438-172217 1 128566484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416813 Affx-122948131 AX-123287161 1 126644443 AAGTAACATTTCCAGGAAGCTGATATTACTCACTG[A/G]CAGGTTTCTGGGAAAGGATGGAGCCTGTGGTCATG R 2 1 2 1 101000 f 74 goat snp11799-scaffold1438-138696 1 128600199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793551 Affx-122962926 AX-385280526 1 126726793 AAACTGGCAGGCAAAGATGGTCTCCTTTTTCATAG[C/T]CTTGATTACATGTTGAGCCCTATTCTAGGACGTTA Y 2 1 2 1 102000 f 74 goat snp11797-scaffold1438-56346 1 128676575 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778750 Affx-122960030 AX-385265861 1 126761244 ACCCCCATATAGGTCAAATATTCTAGCAAGAAAGT[A/G]TAGCAATCATGAACACATATGCCATGATATATCAT R 2 1 2 1 101000 r 74 goat snp11796-scaffold1438-21895 1 128710957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440507 Affx-122929354 AX-123310844 1 126785109 ACAGCTCATGGTATAAACTGGAGTTTAAGTTATTT[A/C]GTTGCTAGAACAGAGAAAAGAGGAGAATTGAATCA M 2 1 2 1 201000 f 74 goat snp24410-scaffold2473-1871 1 128735061 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791506 Affx-122968090 AX-385278497 1 126828395 GGCTCCTTATGGGTCTCCATGAAGCCTGACATGCC[A/G]TCATTGAAGTTTATGTTACTCTGGACAAAACATCA R 2 1 2 1 101000 f 74 goat snp24411-scaffold2473-45157 1 128778251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431208 Affx-122937161 AX-123301549 1 126878282 CTGATACTAAATCACTTTTGTGGGTGTTGCAGAAT[C/T]TGGGGTGTCCAGAGTTTAGGGAGGGGCATAAACAT Y 2 1 2 1 201000 f 74 goat snp3462-scaffold1105-1973710 1 128848272 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440300 Affx-122930218 AX-123310637 1 126910700 CACATCTTTTCATTTCCATCATCCCTTGGTTCACA[A/G]ACACCTTCAAGCTTCTGTTCTGTGCTCTGAGACCT R 2 1 2 1 101000 f 74 goat snp3461-scaffold1105-1941292 1 128881789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379805 Affx-122976236 AX-123250163 1 126961918 TTAGTGAGCCCCTATGCTTTTAAACTTTTGCATAT[A/G]CAGAGTTAGTTAGGTTAGGCTATGCTATGATGTGG R 2 1 2 1 101000 r 74 goat snp3460-scaffold1105-1890074 1 128932771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421019 Affx-122944548 AX-123291366 1 126990549 TAGCACACCCCACAAATCTTAAGTCAAATATTATG[C/T]GTTTCCCCCATCCCAATCTCTAGCTTAGAGGAAAG Y 2 1 2 1 201000 r 74 goat snp3459-scaffold1105-1861443 1 128961014 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777990 Affx-122946224 AX-385265106 1 127023559 GTGCCTCAAAATTGAGTTACTCAATTTGCAATTTG[C/T]GGACACAATACTCAAACATTTACAAGTGAGCAAAA Y 2 1 2 1 101000 r 74 goat snp3458-scaffold1105-1828433 1 128993746 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775375 Affx-122972862 AX-385262506 1 127074054 TGAGCTAAAACTCCGTCTTGCCCGCTAAATGGTTA[C/T]GAATTTAAGTGTTTATCCTTCCCTACAATCCTACA Y 2 1 2 1 101000 r 74 goat snp3457-scaffold1105-1777938 1 129045102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770395 Affx-122956170 AX-385257562 1 127107655 ATCCTTGCTTTCAGAGAACTTGATGTTGCTATTGA[A/G]TCAGTCATTTCAAGAGTGATGAAATTCTCTCACGA R 2 1 2 1 101000 r 74 goat snp3456-scaffold1105-1744337 1 129078685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427532 Affx-122939511 AX-123297875 1 127137282 GAGTCCTGCCATAGAACAAAGCCATCAGGAGGAAA[C/T]GAAACAAGGGTTTGGAAGGACTTGTTTTAGAGCTG Y 2 1 2 1 201000 r 74 goat snp3455-scaffold1105-1714710 1 129108226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799362 Affx-122938962 AX-385286292 1 127175486 TGTTTTATTGTTCCTTTGATTCATAAGCAACCAAG[C/T]ATTGTTTCTCAGGTACTCATTAGCATGTCTTAATC Y 2 1 2 1 101000 r 74 goat snp3454-scaffold1105-1676506 1 129146430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423459 Affx-122942588 AX-123293805 1 127249346 GAAAGAAAGGGGTGGTGGGTGGTGGTGGGAGAATT[C/T]ACTGCTATTGCTGGGTCCTGTGAAGCAAGGTCCTT Y 2 1 2 1 101000 r 74 goat snp3453-scaffold1105-1602646 1 129220979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441024 Affx-122928945 AX-123311361 1 127315297 GGTTTTCTTAATTTTTTTCTGAAAAATGACAGTCA[A/C]GTTTGGAAACTTCTGGTGTTTGGAATTAGGTTGCT M 2 1 2 1 101000 r 74 goat snp3451-scaffold1105-1536695 1 129287209 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398147 Affx-122961683 AX-123268502 1 127355351 CACTTTGTTCATGTCTCAGGGCTGTCCAAATTCAT[C/T]ACTGTTTTGTGATAACCACATCACATAGGTGTCCG Y 2 1 2 1 101000 r 74 goat snp3450-scaffold1105-1496641 1 129327673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401283 Affx-122959870 AX-123271636 1 127384052 GAATGTTTGTGCTTCTCCAGTTCCTACCTAGGGCG[A/G]TTAAGAGGTGGTCTCACACAGCGGTCATATCACTA R 2 1 2 1 101000 r 74 goat snp3449-scaffold1105-1467940 1 129356087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774450 Affx-122974841 AX-385261586 1 127431105 GGTCGCATTAAGGTGGCTCCTGAATGCTCTCTGTA[C/T]GAGGTAGATTCCATCACTCCATTATACAGAGAAGG Y 2 1 2 1 101000 f 74 goat snp3448-scaffold1105-1420887 1 129402132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769943 Affx-122967425 AX-385257112 1 127505387 ATGTTGATTTTAGTATTGCTGTAAGTTTCACAGCA[G/T]ACATAATCCAGGGCATGATGGAAATCCTAAAGAGA K 2 1 2 1 101000 r 74 goat snp3447-scaffold1105-1346605 1 129475511 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381942 Affx-122974123 AX-123252300 1 127541961 CTCATCCCACATCTGCAAAGGAGGAATTACTCTTC[A/G]TACTTCTTTAGATGAGGAAATTAAGGCCAAGTGGT R 2 1 2 1 101000 f 74 goat snp3446-scaffold1105-1310031 1 129512966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401280 Affx-122959872 AX-123271633 1 127591732 ACCCAACTTTACAGATCAATGAGGGTGTCATTGTC[C/T]ATTTCTCTCCGCTTGTCTCTGGGGCAAAGAAAGGT Y 2 1 2 1 201000 f 74 goat snp3445-scaffold1105-1260260 1 129562610 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447481 Affx-122924345 AX-123317817 1 127640552 AATAGCTAAGGAACTCAATGCAATGAGAGACCTCA[A/G]ACATGGCATGGACTTTACACATTGGTGTGGACATT R 2 1 2 1 101000 f 74 goat snp3444-scaffold1105-1211440 1 129611514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791025 Affx-122929224 AX-385278021 1 127704874 ATATATACATAAGTTGATCGTGTAGCAGTTGCTAA[C/T]AAGACACTCAATTCTAACATTGCTTTCCCTTTCAA Y 2 1 2 1 101000 r 74 goat snp3443-scaffold1105-1147118 1 129672870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413186 Affx-122950330 AX-123283535 1 127758399 GGCAGTCAGAGGCTGGTAAGCGGACCATTGGAGGA[C/T]GAACAGGAGTTAGCAAGGTGCCGAGCTGGGGAGTC Y 2 1 2 1 101000 f 74 goat snp3442-scaffold1105-1093593 1 129726382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778749 Affx-122946966 AX-385265860 1 127802752 GTGAGATTTATATTTATGGGGTAAAACACGTTTAT[A/G]CTTTATAGATGCATAATGACATTTGAATATCATGT R 2 1 2 1 101000 f 74 goat snp3441-scaffold1105-1049240 1 129770913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416805 Affx-122948138 AX-123287153 1 127867176 TGCTCTGTTTATGGGGTTTTAGTTCATGACTAGGG[G/T]TTGACAGTGACAGCACCAAGTTCTAACCACTGGAC K 2 1 2 1 201000 f 74 goat snp3440-scaffold1105-984816 1 129835578 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387770 Affx-122969717 AX-123258128 1 127902575 ATGGCTTGAGGATGTAACACAAGCCAATCAAAGCA[C/T]AGAAACCCAGAGTTCACCCTGCAAGAGCATCCTGA Y 2 1 2 1 201000 f 74 goat snp3439-scaffold1105-949417 1 129871123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780482 Affx-122960338 AX-385267573 1 127985256 TTTGGTATTTGTGAGGCTCCTGGAATCAAACCTCT[A/G]CAGGTAATGAAGGTGAACCCTAATGAAAAGTTACA R 2 1 2 1 101000 f 74 goat snp3438-scaffold1105-866736 1 129955047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768358 Affx-122921197 AX-385255538 1 128036519 ATAGCACCTGAACTTCATTCACTACCTGTCAGAAA[C/T]AACCTCCAGTGAGTTGAGACAAATAAGAAAACTTT Y 2 1 2 1 101000 f 74 goat snp3437-scaffold1105-815473 1 130006675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778786 Affx-122958833 AX-385265895 1 128090087 TTTGGAAAGTAAGAACAGCTACTAGTCCCCAGGTA[C/T]GGATAAGTTGGCTGAGTGATAACACTTGGTCACAA Y 2 1 2 1 201000 r 74 goat snp3436-scaffold1105-761905 1 130060016 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785560 Affx-122934211 AX-385272604 1 128144081 AGACACAAACTTCTAGAAATATACTCAGAGACCTA[C/T]ACCAAGAAGTACTACAATCAAGTTTTTGAAAGAAC Y 2 1 2 1 101000 f 74 goat snp3435-scaffold1105-707911 1 130113992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452901 Affx-122920210 AX-123323234 1 128179561 AATACTAATAGAAAAAGCTAGCAATATATTCCATG[C/T]AATCTATGTTGATATATTAAAGAAAAATAGGTAAA Y 2 1 2 1 103000 f 74 goat snp3434-scaffold1105-672431 1 130149544 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792971 Affx-122928094 AX-385279949 1 128315980 CACTCACAGCCTGTAAACTGGAGAGAAGAGAGATG[C/T]GTTTACCCAGAAGGCTTTACTGTGGTTTAGGATAC Y 2 1 2 1 101000 f 74 goat snp3432-scaffold1105-536012 1 130287224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451634 Affx-122921613 AX-123321967 1 128377110 TACAGGAAGGGATTTGGCTGTTCAGCATGTGGTAA[G/T]AGAAGGAGGTGGCAGGGGATGGAAGTCCTCAGCTC K 2 1 2 1 101000 f 74 goat snp3431-scaffold1105-474882 1 130348195 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774996 Affx-122946039 AX-385262128 1 128452746 AATACTTCAGGCTTTCGACTGGTATTTAGGAAGAC[A/G]TTAGTAATGAAGTGGTGGTTCAGAGACTGTCATTC R 2 1 2 1 101000 r 74 goat snp3429-scaffold1105-399246 1 130422701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404186 Affx-122957683 AX-123274538 1 128535812 CCTTTCTCCGCTCTGCTGTGGAGGTCTCAGCCCTG[C/T]GAGTCTGAAGGAACTGTGCTTGGCATTCCTCTTTC Y 2 1 2 1 101000 r 74 goat snp3427-scaffold1105-316180 1 130505864 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396655 Affx-122962856 AX-123267010 1 128601696 GTACTGTAGATGGCATGGATTCCCTGATGATAAAC[A/G]TTAAGTCGTTACTGTTTTCAGATGAATGAAATCTT R 2 1 2 1 101000 f 74 goat snp3426-scaffold1105-250296 1 130572253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403540 Affx-122957606 AX-123273893 1 128665888 TGAGAGCTCTGCAAATCGGAGTCAGTCACTGAACA[A/G]AGTGAATAAAAGTGGCAGGCTCCCAGGGCTCCGCA R 2 1 2 1 101000 f 74 goat snp3425-scaffold1105-186104 1 130635602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272537 Affx-1111832835 AX-519546255 1 128682158 AGTGTGCTCAGTTGTGTCTGACACTTTGCAACCTC[A/G]TGGACTGCAGCCCTCCAGGCTCCTCTGTCCATGGG R 2 1 2 1 103000 f 74 goat 1_128682158_AF-PAKI 1 128682158 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395564 Affx-122963850 AX-123265919 1 128698173 TAAGGATTTTTACCTACCTCCTGTCCCTGACACTG[C/T]GAATTCTCCTCTGGAGGCAGAGTGGCTGGCAGGCA Y 2 1 2 1 101000 f 74 goat snp3424-scaffold1105-153819 1 130668188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413715 Affx-122950075 AX-123284064 1 128729907 GTAAAAACCTGTTGCTAAGACTCACTGCACTTTAA[A/G]GAGGCACTAGAAACCACTTTAGAAGTGTCTGGAGG R 2 1 2 1 101000 f 74 goat snp3423-scaffold1105-122085 1 130700297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802803 Affx-122934241 AX-385289702 1 128764101 CCCTCTTTCAGGTCTCATGGGAGAACTTCCTGCCC[C/T]ATCCTTTTTAGTTGAGCACAACCATAATCATCACT Y 2 1 2 1 101000 f 74 goat snp3422-scaffold1105-87891 1 130734757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393949 Affx-122965063 AX-123264304 1 128800091 GGCGTGCTCTTCCCAATTTGACAGGACTCTTGGTA[G/T]CTCCTCAGCAACATGTTTGGAAACACTGTTGGTGC K 2 1 2 1 101000 f 74 goat snp3421-scaffold1105-51901 1 130770932 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772039 Affx-122939404 AX-385259194 1 128848028 AAGAAAAATGATCTATGATTCTCATAGAGAGAAGA[A/G]CTGAGAATATGTAGTCTATTTCATTAAAAATAGTG R 2 1 2 1 201000 r 74 goat snp3420-scaffold1105-3964 1 130818247 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782029 Affx-122964156 AX-385269107 1 128853926 TCTGAATATTCCTTGGCCCACAGGAATGAACCCAT[A/G]CTTATTAACAGCTTCTGCTTTCCATATGTCTGAGG R 2 1 2 1 101000 f 74 goat snp34570-scaffold4083-25330 1 130824043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396789 Affx-122962757 AX-123267144 1 128894857 GCCATCCCTCTTTTGACATCGGTATAATATTCTAT[A/G]CTATAGCTGTACTACAATTAATTTAGTCATGCCTT R 2 1 2 1 101000 f 74 goat snp23083-scaffold230-4296149 1 130868713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448546 Affx-122923431 AX-123318882 1 128948377 TCAGTGTCTCTTACATAGAAAATGGAAAGAAAAAT[A/G]AAAGCTTCTACAAAAAAATTAGATGGCATTTAAAA R 2 1 2 1 201000 r 74 goat snp23082-scaffold230-4242629 1 130923008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417469 Affx-122947183 AX-123287817 1 129013502 TTCTCCTATGTGACAGCAAAGGCTGATGCTGATGC[A/G]TTTTCTGTTTTGCGTACCTTTGCTTTAAACACACA R 2 1 2 1 201000 r 74 goat snp23080-scaffold230-4177504 1 130999816 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766182 Affx-122947195 AX-385253583 1 129083350 GTAGAACTGGGCAGAAAGTATAAAAGAAAGTGTAG[C/T]CTGTTATTATCCTTATCTTATAAAGCTAGTAGTAG Y 2 1 2 1 101000 f 74 goat snp23079-scaffold230-4107656 1 131069752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779813 Affx-122961742 AX-385266913 1 129115113 AGAACTGGCAGGGAAGTAGGAGAAACATTTTAATA[C/T]GTATTCCAACTAAATAGACTGCCTGAGTTAGACAC Y 2 1 2 1 201000 f 74 goat snp23078-scaffold230-4075893 1 131102595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775674 Affx-122954419 AX-385262805 1 129147921 CTGAGCTTAGGACTTCAATAAAGCTTTTTGGGAGA[C/T]GCAGTTCAACCCATAGTAATATTTATAAGCAATAC Y 2 1 2 1 101000 f 74 goat snp23077-scaffold230-4043085 1 131136061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789831 Affx-122941686 AX-385276838 1 129180349 GGTGACCTCTTATTTTCTACCCTTATTTTACCTTG[C/T]CCCTGTTTTCTCGCTGACTAATGTTTTGTGTGTTT Y 2 1 2 1 101000 f 74 goat snp23076-scaffold230-4010657 1 131168311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423509 Affx-122942554 AX-123293855 1 129233480 AAGATGATAAGAAGCAGAAGAGCATGCCAGGCAGA[C/T]GGGACAATGTATATGAAGCTCCTAAGTTGGACAAG Y 2 1 2 1 201000 r 74 goat snp23075-scaffold230-3957526 1 131222828 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792519 Affx-122958686 AX-385279500 1 129267668 AAATGATTCAGCTTCTCAACTGAAAAGAGCAGAGC[A/G]TTAAACCAAGCATGGTCTCCCTTGTAAGGGTGGAG R 2 1 2 1 101000 f 74 goat snp23074-scaffold230-3923338 1 131258128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803917 Affx-986696579 AX-385290625 1 129286054 ATGAAGATATTTTGGACGACTAAATAATGTTTCCC[A/G]TTTACTCAGCTAAACAGATCATTATTATGGACAGG R 2 1 2 1 600010 f 74 goat 1_129286054 1 129286054 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320804414 Affx-986696581 AX-385290999 1 129286068 GACGACTAAATAATGTTTCCCGTTTACTCAGCTAA[A/G]CAGATCATTATTATGGACAGGTATTGATCGTCACC R 2 1 2 1 600010 r 74 goat 1_129286068 1 129286068 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320803925 Affx-986696583 AX-385290632 1 129286150 GCTTTGGACTCTGAGAAACTCCTTACATTTTTTAT[A/G]TATAGACGTTGTTGCCCACTAGGAGCACAATCCCC R 2 1 2 1 600010 f 74 goat 1_129286150 1 129286150 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320804424 Affx-986696591 AX-385291009 1 129286180 TTTATGTATAGACGTTGTTGCCCACTAGGAGCACA[A/G]TCCCCTCATCTTCAGAGGAGTTTATGTGCAGCATC R 2 1 2 1 600010 r 74 goat 1_129286180 1 129286180 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320803945 Affx-986696593 AX-385290651 1 129286575 GCCTTCCTCTGACTTTGTCTGGTAGTACCTATTTC[C/T]AGAGTCAGCTCCCCTGACCTCATTAAGCTGGGCTC Y 2 1 2 1 600010 f 74 goat 1_129286575 1 129286575 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320804428 Affx-986696595 AX-385291013 1 129286579 TCCTCTGACTTTGTCTGGTAGTACCTATTTCTAGA[A/G]TCAGCTCCCCTGACCTCATTAAGCTGGGCTCTGTT R 2 1 2 1 600010 r 74 goat 1_129286579 1 129286579 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 38450796 Affx-122921816 AX-123321130 1 129303982 GCTGCTTCAGAAGTTTGGATTTCTGTCAATCTACA[A/G]TGGCCAGGTAAAGTAAATGAAAAAAAAAAAAATGT R 2 1 2 1 101000 f 74 goat snp23073-scaffold230-3887024 1 131295570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774653 Affx-122950763 AX-385261787 1 129382079 ACCTAGGCTGTCTGATTCCAGAGCAAATAACCACT[A/C]TTCTGTGATCTTACTGCTATGAAGATGTCATAAAC M 2 1 2 1 101000 f 74 goat snp23072-scaffold230-3808927 1 131374326 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276346 Affx-1111835291 AX-413837232 1 129434939 A[A/G]TCACTACGAACAAAGCTAATGGAGGTGATGGAATT R 2 1 2 1 103000 r 74 goat INRA-CHI1-PIS2 1 0 T C 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region PIS PIS-variant SNP associated with polled intersex syndrome multi-breed 320791267 Affx-122937260 AX-385278261 1 129445690 TTACTCTTCCAAATAACGTCACAGTTAGGAATCTT[A/G]CATCTTTTTATTACTTTTGTCAAGGTGGCCTTGTA R 2 1 2 1 101000 r 74 goat snp23071-scaffold230-3745316 1 131438712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400380 Affx-122960014 AX-123270735 1 129502861 AATAGTTTTCAGATTTCGTGGTCATCATGAGATTC[A/G]TGATAAACATTTTTGGCAAGAATACCACATAGAGT R 2 1 2 1 103000 f 74 goat snp23070-scaffold230-3688145 1 131496198 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451057 Affx-122921432 AX-123321391 1 129535097 AGCATACAGTCCATGGGGTCACAAAGAGTCAGACA[C/T]GACTGAGCGACTTTTACTTTTTAGTGAGGCTAACC Y 2 1 2 1 103000 r 74 goat snp23069-scaffold230-3655909 1 131528543 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782179 Affx-122972966 AX-385269257 1 129564489 ATTTTAAGTATGTTTTGCTGTGATAAGATCCCTAA[C/T]GAATATCCCAAGTATTTTAGGATTAGGACTGCTAG Y 2 1 2 1 101000 r 74 goat snp23068-scaffold230-3626517 1 131557973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412392 Affx-122951453 AX-123282741 1 129602469 TTACCTCTCAGTCATCAGTTTTTTCCTGAGAGTAA[G/T]TTCTTAACAAATCAGCTTCATGAAATCCTTGGCTC K 2 1 2 1 101000 r 74 goat snp23067-scaffold230-3588537 1 131596098 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442452 Affx-122927955 AX-123312789 1 129682502 TGAATATAATCCCTACAGTTTCTACTCCTCAGAGC[G/T]CAGGTCAGGAAGGACTGAACATTTCTTTCTGCTGT K 2 1 2 1 101000 r 74 goat snp23065-scaffold230-3508504 1 131675988 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381463 Affx-122974980 AX-123251821 1 129770149 GATTTAGAATTTAGCAGACACCATATCCTCACTCG[C/T]GCTCAGAAGCGCTCTGCTCAGTGCTCCTGTGGCCC Y 2 1 2 1 101000 f 74 goat snp23063-scaffold230-3420857 1 131763512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773482 Affx-122958922 AX-385260624 1 129811814 TGTTGCACTCTAAAATTCACGTTCTTTTTACTAAT[A/G]CATTTGCACATGTAGAGTATTTAGAGACTTTAAAA R 2 1 2 1 101000 r 74 goat snp23062-scaffold230-3379192 1 131805668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786858 Affx-122951705 AX-385273887 1 129894158 AAAGGCCCTTAACTTGCATAACCCACTCTTGCTTA[C/T]ACTTTGTCATCTTTTGCTCTAGCAATATTCTACTG Y 2 1 2 1 101000 f 74 goat snp23061-scaffold230-3296848 1 131888025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390717 Affx-122967931 AX-123261074 1 129936450 GCCCTGAGTCACAGAGCAGAGTGCTGAGTGGGTCT[C/T]GAAGGACATGGGGAAAACCAGCAGTCACTTCCTAT Y 2 1 2 1 201000 r 74 goat snp23060-scaffold230-3254556 1 131931194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793834 Affx-122938065 AX-385280803 1 129975195 TGATGATTTCAGCATGGACCCTGAAGAGAATGGAC[A/G]TTCATGTTTCCAGCGGAGCCTGATGACAGCTGGGA R 2 1 2 1 101000 f 74 goat snp23059-scaffold230-3215811 1 131970293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276615 Affx-1111835504 AX-519550125 1 129977048 GTAAGCATTGTGTCTCGTTGGATACAATGTGGTAT[A/G]AATAATACTACTACTAAGTACCAATGTAAAGAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-126 1 129977048 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435073 Affx-122933728 AX-123305413 1 130023268 AAGTGAGAAAGTCTTGCCAACAGCTAGATAGAAGA[C/T]GGTGACTCCAGTCATACAGCCACAAGGAAATTCTG Y 2 1 2 1 101000 f 74 goat snp23058-scaffold230-3167738 1 132018470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414114 Affx-122949732 AX-123284463 1 130075544 TTTTCACAAGTGTATACTTACGTCAAAACTTAATT[A/G]TACAATTTAAAGTGTACAATTTAAATACATACACT R 2 1 2 1 103000 f 74 goat snp23057-scaffold230-3115462 1 132071474 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401117 Affx-122959398 AX-123271470 1 130171599 TGAGGTATGAATATATAATAATCCCCATCCTTTCA[C/T]AAATAATGAATATCAACATACGTGGGGTAGCTTAA Y 2 1 2 1 102000 r 74 goat snp23055-scaffold230-3019407 1 132167788 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448299 Affx-122924164 AX-123318635 1 130211629 CACTAGTAATTAGGAACCTCCTATACATTAAAAGA[C/T]GCTTACTCCTTGGAAGAAAAGTTATGACCAACCTA Y 2 1 2 1 103000 f 74 goat snp23054-scaffold230-2979377 1 132207904 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424030 Affx-122942084 AX-123294376 1 130281185 AAATTTCCAGCTTGGATCTGGTAGACAGGGCCTGA[A/C]GATTAACTGACAGCCAACAGACTAAGTGGAGAAGA M 2 1 2 1 201000 r 74 goat snp23053-scaffold230-2909821 1 132277390 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376732 Affx-122978956 AX-123247091 1 130312990 ATAACAAGAAACTTAGGACTGATTCAACAGATTAA[C/T]ATCCAAGTAAAATATATTCAGCAGAGAGTAATGAA Y 2 1 2 1 101000 r 74 goat snp23052-scaffold230-2878016 1 132309208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787554 Affx-122961466 AX-385274578 1 130349762 TAATATTTAATTCTCTGCTCTAATAAATTTTAGTG[C/T]CTTCTAAGTCCATGTCATTGCTTAAAAAATAAAAA Y 2 1 2 1 101000 r 74 goat snp23051-scaffold230-2841244 1 132346261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411882 Affx-122951197 AX-123282232 1 130395222 ACTTTTTGGTACAAAAAGAGAAAAACTAATTTAGG[C/T]AGATCTCTTAATCTTATTTCACCTATAATTCATAT Y 2 1 2 1 201000 r 74 goat snp23050-scaffold230-2795784 1 132391733 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784251 Affx-122921193 AX-385271302 1 130471776 ATGTATATCTTAATCTTTGAAATATACTGCAAAAT[C/T]ATATTCCAAGAAGGTAGGAGAAATTGCTTTCACAA Y 2 1 2 1 101000 r 74 goat snp23049-scaffold230-2719230 1 132468894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390233 Affx-122967772 AX-123260590 1 130504607 CCTTAGCTTGTGTCCAACTACTGTTTGTGACTGAG[A/G]TGCCAAAATAGACAGATAAGAAAACATCTCTTTTA R 2 1 2 1 101000 f 74 goat snp23048-scaffold230-2686399 1 132501737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417419 Affx-122947221 AX-123287767 1 130544819 TTCATAGCAGGCACCACAGACAGGCCATGGGGTGG[C/T]ACAGAACCAGGGCACTGAGGAACATGTTGTGGGAA Y 2 1 2 1 101000 r 74 goat snp23047-scaffold230-2646187 1 132542375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378585 Affx-122976588 AX-123248944 1 130586709 TTAGTGGCTCTTGGAGCAGCTGGTTTGCCTTGATT[A/G]CCTTACTGGCTGAATTCTACTGATAACACCTGTGT R 2 1 2 1 201000 r 74 goat snp23046-scaffold230-2604297 1 132584726 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387313 Affx-122970511 AX-123257671 1 130622723 ATCTAATTACTGCCTATTTTCTAGGCCCTGACCCT[A/G]TCTTACCTCTCCTATGAAGATTGCTATGGAGGTCA R 2 1 2 1 201000 r 74 goat snp23045-scaffold230-2568283 1 132621078 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419655 Affx-122945954 AX-123290003 1 130680983 GATCACAAAGAGGAAGAAAATGTCTTTCAGTCTGA[C/T]GGGAAATAAGTAGATGCATGTGTAGAATTAACTCT Y 2 1 2 1 201000 r 74 goat snp23044-scaffold230-2510023 1 132678692 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387840 Affx-122969657 AX-123258198 1 130737951 AGACTAGCAGTGTATTTATTTTTCTTTTTCAGTCC[A/G]CTTGCAATATATTTCTTAGTGTACACTTTACAGAC R 2 1 2 1 201000 r 74 goat snp23043-scaffold230-2453055 1 132736269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444606 Affx-122926949 AX-123314943 1 130770195 CTCATTATGTGCAAAGCCCTATTATTTGCAAAGTC[A/G]CTATTTTCTGTTATTAAGCAGTTATCAGCTACCTG R 2 1 2 1 101000 r 74 goat snp23042-scaffold230-2420811 1 132768890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275521 Affx-1111834949 AX-519549093 1 130823139 TCCCCATTCATATCTGCAGTTTCCAGAACTGAAGT[A/G]GACTATCAAGAATCCATTTGAGAAGGAAGCATGGA R 2 1 2 1 201000 f 74 goat GoatD01.059663 1 130823139 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434870 Affx-122934357 AX-123305211 1 130825807 TACCACTTTTGAGGATAAAATCCAAACCACTATTC[C/T]CTGTATCCACCTGACCACCTGCGCCTGCCCCTGCA Y 2 1 2 1 101000 f 74 goat snp23041-scaffold230-2365199 1 132825442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779987 Affx-122933175 AX-385267086 1 130854753 AGTTACCAAACCTCAAATTTTGATGATTTCCCTTC[A/G]CGGGAAAGGTCATTATTTTGTAAGAAACCACTGAA R 2 1 2 1 101000 f 74 goat snp23040-scaffold230-2336253 1 132854651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393092 Affx-122965592 AX-123263449 1 131005765 TAGCTACAGGTGATGAGTGGGGGTGGTGGCGGTGA[C/T]GGGGGGCGGGGGAATGTACTGTCAGCCCGAGACTG Y 2 1 2 1 103000 f 74 goat snp23037-scaffold230-2185241 1 133004084 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386134 Affx-122971409 AX-123256492 1 131095400 TTCCAGGGCTAGTCTTGGCCAGAAGTGGATGGTAA[C/T]GGAGCTGAGGCCAACTGCAGGGGAGAAGCACCGTG Y 2 1 2 1 101000 f 74 goat snp23036-scaffold230-2095606 1 133093227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781594 Affx-122958871 AX-385268678 1 131144390 CTGGGAGGATGCCAATGGTTTCTATAAATTTCTCA[C/T]AGAAGAATGAGTGAGTATGATAGTTAATTTTATGT Y 2 1 2 1 101000 f 74 goat snp23035-scaffold230-2046616 1 133142464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394457 Affx-122964581 AX-123264812 1 131203099 CTGTGAAGAATCTCGGTTTACTAACTGATCTGAGT[A/G]GTGTGTTATATCTACATAATCAATTTAGCAATACT R 2 1 2 1 101000 f 74 goat snp23034-scaffold230-1987907 1 133202007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426711 Affx-122939889 AX-123297057 1 131255363 ATAGATACAGATATAGATATAGATAAGATATAAAA[C/T]GTCACACTTGCAGGCAGAGGTGTGTTTGTAATTGC Y 2 1 2 1 103000 r 74 goat snp23033-scaffold230-1935643 1 133254186 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429229 Affx-122937922 AX-123299571 1 131290392 CTTTAGGAGAGCACTGTGGGTGGAGTCAGCTAAAT[A/G]CCCAGTAAGTGGCAAGAGGAAGGACGCAGACTGAG R 2 1 2 1 101000 f 74 goat snp23032-scaffold230-1900614 1 133289412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380845 Affx-122975448 AX-123251203 1 131327388 GTTTCAGATTTACAGTAAAGTTGCACAGATAGCAC[A/G]ATGAGTTCTCATACACCCCACTGTCTCCACTAGCA R 2 1 2 1 101000 f 74 goat snp23031-scaffold230-1863618 1 133326277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801383 Affx-122954151 AX-385288294 1 131383827 TATGAACACCTGTACAAATGCATTCTTGCACATAC[A/G]TGTATGTTAGGGTATGGCATTTTTAGAAACAGAAA R 2 1 2 1 101000 f 74 goat snp23030-scaffold230-1807179 1 133383315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416975 Affx-122948006 AX-123287323 1 131423872 TATTGCCCACCTGGCCCCATATACGTTTGAATTGG[C/T]AACCTTAGGCAAGATTTCCTCTAAGGTTTTACTAC Y 2 1 2 1 102000 f 74 goat snp23029-scaffold230-1767134 1 133423420 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272469 Affx-1111832837 AX-519546191 1 131450616 GGGGAAACAATGGAAACAGTGAGAGACTTTACCTT[A/G]GGGGCCTCCAAAATCACTACAGATGGCGACTGAAG R 2 1 2 1 103000 f 74 goat 1_131450616_AF-PAKI 1 131450616 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422601 Affx-122943733 AX-123292947 1 131464397 AAAAGTTAACTATTGGCACTAACAAGAGAGAAGAA[C/T]GAACTTCAAGAAAAATGTAAATGGTCACAGAAGGT Y 2 1 2 1 201000 f 74 goat snp23028-scaffold230-1726609 1 133464390 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396452 Affx-122962977 AX-123266807 1 131504660 GAGAATAAAATAGAATGGTAGGGAGAGGCATGAAC[A/G]TCAGAGCAAAATTTTCCCTGGGTCCCCTGTCAGCA R 2 1 2 1 101000 f 74 goat snp23027-scaffold230-1686346 1 133504793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434934 Affx-122933868 AX-123305274 1 131542606 CATCCCAAGATGACACTGATTTCTTCCTGGCAACA[C/T]TGTAATGAAAGACAAGCCAGCACTCACATAAGATC Y 2 1 2 1 201000 r 74 goat snp23026-scaffold230-1648400 1 133543054 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438846 Affx-122930769 AX-123309183 1 131571886 TTGCCCTTTGGAAAATGTGTTGAATTTGGGGGAAA[C/T]GATTTAGGAGGAAGTCCCAGTGAGAAATGATGATG Y 2 1 2 1 101000 r 74 goat snp23025-scaffold230-1619120 1 133572464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420742 Affx-122944760 AX-123291089 1 131626865 AGATACCCAAATAAAAGAGGACAATGTGGACTCCC[C/T]GAATGGCCTAACTGCTGTATAGCAATCCTAGAACA Y 2 1 2 1 101000 f 74 goat snp23024-scaffold230-1564141 1 133627527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408825 Affx-122954025 AX-123279176 1 131737480 CAGGAGACACTCCTGGCTGGAGTCAGTCTCTCTCT[A/G]TCCTCCAATTCTTCCTCTCTGTCACCACTCCTGCT R 2 1 2 1 101000 f 74 goat snp23021-scaffold230-1453526 1 133737751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803434 Affx-122939385 AX-385290265 1 131769671 CACTTTTTAGTTCTGTTTGGTCTGAAGATTTTCTT[A/G]CATATAAAACATGAGATTTAGAGGTGGCATTTGCA R 2 1 2 1 201000 r 74 goat snp23020-scaffold230-1421335 1 133769875 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403779 Affx-122957986 AX-123274131 1 131850019 TCAGTTCAATTGAAAACAAAACCTTCTTGTGTTCT[A/G]TTGGATCAAGCCAAGCCTTCTTGTGGGTCATCAGT R 2 1 2 1 101000 r 74 goat snp23018-scaffold230-1340987 1 133848471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801310 Affx-122954218 AX-385288222 1 131908517 CCTTTCATATCCTGGCTGCCCATAAATGACCTCGA[A/C]TGTTTCCAGCAATGCTCATTGTAATTCTTTTTAAT M 2 1 2 1 101000 f 74 goat snp23017-scaffold230-1282489 1 133907258 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443889 Affx-122927063 AX-123314226 1 131961617 TTTATGGCTTCTGAGTTTCGTGTCGTCATTACTAT[A/G]CATACATTGTCTCTATGGTTTCTTTTAGTATTTTT R 2 1 2 1 101000 f 74 goat snp23016-scaffold230-1229389 1 133959006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777746 Affx-122927039 AX-385264864 1 132030081 AAATTGTGGAAGAGAAAAGACAAGTCTGCAGAACT[A/G]TTGTACAATGATTTATATCCAAATCTAGACTGATG R 2 1 2 1 101000 f 74 goat snp23015-scaffold230-1160925 1 134026984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399380 Affx-122961329 AX-123269735 1 132086882 GAGACTGGTCAGCACAGTCCTGGGCACACATGGAC[A/G]CTGAGTCAGTGTGTGGTCCCCAGATTGGCTAATGA R 2 1 2 1 202000 f 74 goat snp23014-scaffold230-1104124 1 134082080 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449992 Affx-122922869 AX-123320327 1 132141988 GTTAACATACAAACTTAACACTTGACTTGAGGCAA[C/T]GTAACAGCATGCCACAATACTAATGTAATGGAGAG Y 2 1 2 1 101000 f 74 goat snp23013-scaffold230-1049018 1 134136722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779382 Affx-122963884 AX-385266486 1 132191826 CTGACACATGGAGATTACATAAGGTTCACAGCAAA[C/T]GGACCAGTAAAGGCATTAACAAGAAAATGCAAGGA Y 2 1 2 1 101000 r 74 goat snp23012-scaffold230-999180 1 134186305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442872 Affx-122927666 AX-123313209 1 132233830 ACATCATTTTAGGGTTGGAAAAAACCGAAGTGACT[A/C]GACAATCTGCACACAGCTGGCACAGCATGTCTTGC M 2 1 2 1 101000 f 74 goat snp23011-scaffold230-957176 1 134228496 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415661 Affx-122948560 AX-123286010 1 132291560 TCTAAAATGGGACTGAAAACCCTATTATTAGTTTT[A/G]CCCTTTCTTGGTTTCATTTTACAATATCTGAACAT R 2 1 2 1 202000 r 74 goat snp23010-scaffold230-899446 1 134286400 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275300 Affx-1111834823 AX-519548875 1 132300059 TTGCTCCATTTCCTTCACCTTTTCCTCTATTTTTC[A/G]CATTGGAACCAAAAATAAATTTTTAAAGCTCATAG R 2 1 2 1 303000 f 74 goat GoatD01.055148 1 132300059 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382124 Affx-122974472 AX-123252482 1 132354993 TGCTGATTCGATTCTTGAAAGGATGTTGACTGTCC[A/G]TTGTCAGGTGGTAGGGGGAGGTGCTGTGTGGCCAA R 2 1 2 1 101000 f 74 goat snp23009-scaffold230-836013 1 134348470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396921 Affx-122963202 AX-123267276 1 132386140 TTCAGTTAAATTTGAACCAGCTTAAAAAATGCAGC[A/G]CCGTGTGCTCACTGTGCTCACCCCATCCTCACGCC R 2 1 2 1 101000 f 74 goat snp23008-scaffold230-804866 1 134379200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380161 Affx-122975969 AX-123250519 1 132426265 TTTATTCACCTCTGTTTTAGAGTTCCGTAAACTTG[C/T]AGTTAAAAGAGCAAACCTGGAATGCCCTTTCCCCC Y 2 1 2 1 101000 f 74 goat snp23007-scaffold230-764741 1 134419132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416105 Affx-122948312 AX-123286454 1 132456001 GAAGGAAATTTCTCCAAGATCAGGGTGGGAAAGAG[C/T]AGATTCATTTAATCATTTACTCATTCAACAAATGT Y 2 1 2 1 101000 f 74 goat snp23006-scaffold230-735005 1 134448822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795422 Affx-122964357 AX-385282378 1 132488373 TTCTGAATAGCAAACAGTAACAGCTGCTTGGTACA[C/T]GCTTATTTGACTAATGGAATAAAATATGCTGACAT Y 2 1 2 1 101000 f 74 goat snp23005-scaffold230-702633 1 134481510 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381858 Affx-122974185 AX-123252216 1 132550535 GGGGCTGGGAGCATGGAATGAGGGGGTGAATCTGA[A/C]GCAGCCCACTTCAATCTTCTATTTCACAAGAAAGG M 2 1 2 1 201000 f 74 goat snp23004-scaffold230-640471 1 134543743 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437862 Affx-122932073 AX-123308200 1 132588244 CAACAGATAGATTTGTCCTGGTTTATAAACCAGAA[C/T]GAAGGGAGAAAAGAGTTTTTACAAACTGCCAAGAA Y 2 1 2 1 101000 f 74 goat snp23003-scaffold230-602762 1 134581196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275254 Affx-1111834684 AX-519548831 1 132615543 AGGCTACAAGAGGCCCTAGAGAGGAGCACTGCAGT[A/G]GTTAGGAGTTAGTAAAGGGTTTCTGGCACAATGAA R 2 1 2 1 101000 r 74 goat GoatD01.045838 1 132615543 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394504 Affx-122964547 AX-123264859 1 132631554 TAGAGGCACCTTTAAACTGAAATCTTGAAAGATGA[A/G]TGTTTTCAGTAAACTCACATTTCTCATCTACCCTT R 2 1 2 1 201000 r 74 goat snp23002-scaffold230-559452 1 134624235 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421237 Affx-122944118 AX-123291584 1 132692696 ACACTTCTAGATACAGGCATCCACTGCCTCCGAAG[C/T]GGCACATCCTAACTGAAAAGCTCTAACTGCTCCGA Y 2 1 2 1 101000 r 74 goat snp23001-scaffold230-498310 1 134684117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799836 Affx-122921565 AX-385286762 1 132744490 TAGATATTGTGGTGGGAAGGGAGGTTACATTACTT[A/G]TGACTCTGAATGAAGTTTTACAGCCCAAAAGTAGA R 2 1 2 1 101000 f 74 goat snp23000-scaffold230-446516 1 134736026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764753 Affx-122919405 AX-385252367 1 132808626 AAACAAGGCCCGTTCTTCCGTAACTTTGACTTTCT[A/G]TGGACAAAATTTATCTCTTTGCTAGATAATACAGC R 2 1 2 1 101000 f 74 goat snp22999-scaffold230-382380 1 134800898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452424 Affx-122920584 AX-123322757 1 132840309 ACAGTCTACCCAGAAAGAAGATTGATTCCATGTGG[C/T]AGCGAAGAAGTCTGGCTTGGCAGTCACCCTGGCCT Y 2 1 2 1 101000 f 74 goat snp22998-scaffold230-350697 1 134832638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452527 Affx-122920546 AX-123322860 1 132897256 TGTGCCCCTTCCCAGCTGTCATAAGTGTGCATGAG[A/G]CCGTGCTAAGTCCCCAGTGCTCGTGCGGGAGTTGC R 2 1 2 1 101000 f 74 goat snp22997-scaffold230-293750 1 134890090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276778 Affx-1111835516 AX-519550287 1 133010643 TTAAACCAAAAACCCCACAGTGAGAATAGAAACTT[A/G]TTTGGTACTTGTAACTACCTGCCTTGGAGAAGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-128 1 133010643 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403169 Affx-122958084 AX-123273522 1 133012042 CCACGTGGGTGTCTCTTTCCTTTCCCAAACTGCCC[C/T]GGGGTGTTCTGGGGCAGCATCATTCACACGGAAAC Y 2 1 2 1 102000 f 74 goat snp22994-scaffold230-178964 1 135005898 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403090 Affx-122958502 AX-123273443 1 133042518 GCATAGCAGTCCATTCCCGACGTTTATGAATTCTG[C/T]AGTTCGACCTAACCTTTCCTCACCTTCTGCAACGC Y 2 1 2 1 101000 f 74 goat snp22993-scaffold230-148488 1 135034718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383795 Affx-122973193 AX-123254153 1 133075319 TCCCATTGGCCCAGCACATGCCCAAGGAAAGAGAT[A/G]TTTCCTGAGGCACTTGTTGAAATCGTTTTTGCTAT R 2 1 2 1 101000 r 74 goat snp22992-scaffold230-115687 1 135065110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381928 Affx-122974134 AX-123252286 1 133105727 ACTAGAAATGACCATTCTAGTGGTTTCCCTTAACT[A/C]GGGAACCTAGGGAGATTTAGAAGCTGTTCTGTTTT M 2 1 2 1 101000 r 74 goat snp22991-scaffold230-85279 1 135095900 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379390 Affx-122976137 AX-123249748 1 133135910 AAAATTTATGTTGTGAGTGTGAATCAGTACCAAAA[C/T]ATTAATATTACTGCTGCCATCCTTAGGGCACTAAC Y 2 1 2 1 101000 f 74 goat snp22990-scaffold230-55096 1 135126105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445557 Affx-122925150 AX-123315894 1 133184002 CAGAATCCCAAAACTTTCTTGCTTTTTATTTAAAG[A/G]CTTGTATAGGTATATATTGGGCTTCCCTGGTAGCT R 2 1 2 1 101000 r 74 goat snp22989-scaffold230-7004 1 135174495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439624 Affx-122930626 AX-123309961 1 133201624 GATAGTAATAGAGCAGTGAACTTGGGGCTCTTTCT[A/G]TTTAGCAATTGCTTTACATACATTGGGCTTCCCTG R 2 1 2 1 201000 r 74 goat snp48965-scaffold699-939219 1 135204267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384719 Affx-122972057 AX-123255077 1 133253330 AATTTCTCAGTTGCCTAAGAAAACAGTAAGCAGCT[A/G]GGAAAAGCCTTATCCCTTTCCTTCAGAGCAAAGCT R 2 1 2 1 101000 f 74 goat snp48964-scaffold699-887513 1 135255901 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436915 Affx-122933203 AX-123307253 1 133288345 GTGAGTCTGAGCTGGGGTCCAATTTCTCAGGCCAC[A/G]GTGATGCTACTGGGGGAGACACTACCCCTACATCC R 2 1 2 1 101000 f 74 goat snp48963-scaffold699-852498 1 135292903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412175 Affx-122951066 AX-123282525 1 133318650 TACACAACATACTCCTCATAAATATTATAAGACAT[A/C]CAGCGAAATGCTAATTTGTATGCTTTTCAGTAAGT M 2 1 2 1 101000 f 74 goat snp48962-scaffold699-822193 1 135323768 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422446 Affx-122943347 AX-123292792 1 133373749 GTTGGAGCACATTCTCTCTCTACATACTTTTCTGC[G/T]AATCTTTTAAATGCACATTAAATTTAAAGTCCACT K 2 1 2 1 101000 f 74 goat snp48961-scaffold699-767094 1 135378111 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423002 Affx-122942983 AX-123293348 1 133410875 CAACTGCTCTTTATGTGTGTTGGATTTAGGGGGGT[G/T]TTCATAGTTATATTAATGTTCGAACTAGATTCAGC K 2 1 2 1 201000 r 74 goat snp48960-scaffold699-729968 1 135414107 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774620 Affx-122927418 AX-385261754 1 133470119 GGTGAATAAAGGCCTACAAGAAGGGATGAATGAGT[A/G]TAGGCACAACCTCAAATTAAAGAAGTTTAGACCAA R 2 1 2 1 101000 f 74 goat snp48959-scaffold699-670724 NW_017198025.1 17773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409343 Affx-122954181 AX-123279694 1 133513697 CTTGGTTCGAAATTCAAAATGTACAAAATAATAAA[A/G]AGTGAAAAATGTCACCTCACCCATGTCCCAGGCAC R 2 1 2 1 102000 r 74 goat snp48958-scaffold699-627146 1 135519152 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451148 Affx-122921364 AX-123321482 1 133590475 GCTGAGCCACTGGGGAAGCCCTGTTCCTCCCTGAC[A/G]TCTCCACAAAGAACCTGATGCAGTCACTCGGGACC R 2 1 2 1 101000 r 74 goat snp48956-scaffold699-550368 1 135595758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426055 Affx-122941101 AX-123296401 1 133622514 AAAACCTCGTCCTTGAGGGATGTCCCCAGGAAAAA[A/G]ACAATGATCTCAGATTCCTTGATGGGCAAAGAGAA R 2 1 2 1 101000 r 74 goat snp48955-scaffold699-518329 1 135628029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419264 Affx-122946257 AX-123289612 1 133691112 GTTTTATGAATTTGGGAGTGGAGGGCCCGGAGAGG[A/G]TGTTTTTTCTTGAACCGTGGGTAACAAGTAGAAGT R 2 1 2 1 201000 r 74 goat snp48953-scaffold699-449731 1 135695117 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770124 Affx-122926459 AX-385257291 1 133727678 TTTACTGACAAACGTACATGCTATCTCTTTCAAAT[A/G]TTGAGAGCAGCATAATTCATTCAAATCTCTTCTTG R 2 1 2 1 101000 r 74 goat snp48952-scaffold699-413165 1 135732399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442674 Affx-122927893 AX-123313011 1 133761215 AACTTAGGAATTATTTATAAACTTCGGAGGGATTT[A/G]TAGTATAATTATTAAGGAAGGAAGGAAGTCTTTAT R 2 1 2 1 303000 f 74 goat snp48951-scaffold699-379628 1 135766400 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451202 Affx-122921324 AX-123321536 1 133800252 TCTGCTACAACAATATCAGGAAATTTCACATAAAA[C/T]AGTCCTAGGAGTGTAGTCCCCATAGAGGTGGTTCT Y 2 1 2 1 201000 r 74 goat snp48950-scaffold699-340591 1 135805374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416861 Affx-122948094 AX-123287209 1 133829157 GTTTATTTTTTAGGGGATTCTTGTGTGAGTCACTT[A/C]TTTTGTTAACTCTGTCTTCATACTAGAAGTATTTT M 2 1 2 1 201000 r 74 goat snp48949-scaffold699-311686 1 135833985 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406419 Affx-122955210 AX-123276771 1 133881094 CCTGAGAACATGTAGCAAGTGGGAGGCAGGCCTCT[G/T]GTTCTCAGTCATGTGCTTTGTCCACCCCAGAGGCT K 2 1 2 1 201000 r 74 goat snp48948-scaffold699-259749 1 135885973 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392968 Affx-122965678 AX-123263325 1 133915359 TCTAGCCTCATCTGTTGATACTTGCCTATTTATAA[G/T]CCTGGCTTCAGTCTTCTTAAATTACAGTGTAAACC K 2 1 2 1 201000 f 74 goat snp48947-scaffold699-225484 1 135918715 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788584 Affx-122930040 AX-385275601 1 133944266 CCTTCTCTTTTATACATTATTCTTTATGAGGTTGT[A/C]GGAAAGATAGGATATTATTTAGTCCACTCTGTGTT M 2 1 2 1 101000 f 74 goat snp48946-scaffold699-196577 1 135947715 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272471 Affx-1111832838 AX-519546193 1 133973968 ACATTTTATTGGGCTACAATAACCCTAAACTGAGC[A/C]TCTCCTGAGCTCAGAGCCCTGTGTTGAAGATGCAG M 2 1 2 1 201000 f 74 goat 1_133973968_AF-PAKI 1 133973968 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413138 Affx-122950365 AX-123283487 1 133978557 AGTGTAACTACTTTGAGTGGAGAGATATTATAGGC[A/G]TGCAGCAGGAGCCTCCCACCCTCTTCTCTCCATGA R 2 1 2 1 101000 f 74 goat snp48945-scaffold699-162286 1 135981948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780076 Affx-122941878 AX-385267174 1 134016241 AGCGTCAGCATCTTCCTTGACCCTGTTTAAAATGT[A/G]CATTCCCAGCACTCACAGCGAACTTACTGAATCAG R 2 1 2 1 201000 r 74 goat snp48944-scaffold699-124602 1 136019303 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386280 Affx-122970939 AX-123256638 1 134060498 CAAATCCCCTCCTCAATGGCAGGCAATTGTCTTTT[A/G]GCCCTCTCTTGGGATTATCACACTGTAAATTCCAC R 2 1 2 1 201000 r 74 goat snp48943-scaffold699-80345 1 136064580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389521 Affx-122968291 AX-123259879 1 134122869 CTCATATCCCTTTTCTCCCCTCTTCCCTGGAACCT[A/C]TTCCCAACCTGAGGTCCCATTTCTATGCCCAGCTC M 2 1 2 1 303000 r 74 goat snp48942-scaffold699-17974 1 136128514 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783736 Affx-122919489 AX-385270792 1 134144946 ATCATATAGCGTTTGCCTTTTAGGGACTGGCTTAT[G/T]TCGCTTAGCAGAATGTCTTCAGAATTCGTCTATGT K 2 1 2 1 102000 r 74 goat snp37475-scaffold458-4004 1 136225466 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441174 Affx-122929551 AX-123311511 1 134191760 CAACCCAGTATTATGGGGTCCTGGCTCAATGTGGC[A/G]AGCACTGCACTCATTGATGGTGGTAAACAATGCAT R 2 1 2 1 101000 r 74 goat snp37476-scaffold458-50818 1 136272847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440192 Affx-122930706 AX-123310529 1 134249106 GCACCCCAACATTAAAGTAATTAAATAAACAGATA[C/T]GTTTGTTCATTCACTTACTGCCTATTTTCCCCATT Y 2 1 2 1 101000 r 74 goat snp37477-scaffold458-108164 1 136330861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436842 Affx-122932215 AX-123307180 1 134301684 GGTTTGCTTCTCAGGAAATCATTTAATTTTTATAA[C/T]AGTTTGTTTCCTTATCTATAAAAGGAGGGCTTGAC Y 2 1 2 1 201000 f 74 goat snp37478-scaffold458-160742 1 136380977 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431522 Affx-122936229 AX-123301863 1 134338891 CAACATTATTCTTTTCTTTAAGCATCTTAAAGCAT[A/G]TTGCTAAAAAATAATCCTGTGGCATCTACTCTACT R 2 1 2 1 101000 r 74 goat snp37479-scaffold458-197949 1 136419816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775663 Affx-122927305 AX-385262794 1 134425682 CAAAACAGTTCAGTGGCTAACCTACAATTAATCCT[C/T]TGAAGTTTTCTTACTAGAATGAAACATGAGTTTTA Y 2 1 2 1 101000 f 74 goat snp37481-scaffold458-284740 1 136507519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409352 Affx-122954174 AX-123279703 1 134471183 CAGGACTGATTTCCTTTAGGCTGCCTACATAGCTG[C/T]AAACATATGTGACCTTTATCAGGACTGATGCTTTT Y 2 1 2 1 201000 r 74 goat snp37482-scaffold458-330241 1 136552939 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404499 Affx-122956710 AX-123274851 1 134481587 CTATTTTCCTCCATCCTCTTCCTACAGGAAAAGAA[C/T]ATGAAACCCAGAAGCTCAGCACGCGAATTTAGAGC Y 2 1 2 1 202000 f 74 goat snp55184-scaffold848-520062 1 136574462 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386317 Affx-122970889 AX-123256675 1 134511268 GTTCCTGGTGGCAGTGCCTAAAAGTACTGCTGAAG[C/T]AAAAGCAAATTCACTCTGGAGGAAAAGTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp55183-scaffold848-490381 1 136604119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773302 Affx-122963566 AX-385260445 1 134540117 ATGAACAACTCTTTAGCTCTTACTCCAGCAGCATC[A/G]TGGAGTTGTATTTATAGCCTCAAACTTTCACATCA R 2 1 2 1 101000 f 74 goat snp55182-scaffold848-461532 1 136632416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276678 Affx-1111835535 AX-519550188 1 134591452 TTATTCCTCTAACCACACTGTAAGCTCAGCTCTGA[A/G]AGAGGATGAGGATTATTGAGTCACACAGCAATTAC R 2 1 2 1 101000 f 74 goat Random2.2K-130 1 134591452 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773510 Affx-122945640 AX-385260651 1 134602152 CACTGATTTTGGCTTCCCTGACTTGGCAGAGAGGT[A/G]ACTTGTGAGCTGGTGCATGTACAATTTTTTATCTT R 2 1 2 1 101000 f 74 goat snp55181-scaffold848-399497 1 136694945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400147 Affx-122960700 AX-123270502 1 134682326 AAACTCTAACTTGCTGACAGCTTGTTGTGGGGAGA[A/C]AGCTGTAAAACTTTGAAATTTTTGGTTTATTTCAA M 2 1 2 1 201000 r 74 goat snp55179-scaffold848-319323 1 136775752 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769672 Affx-122963713 AX-385256842 1 134730851 TCCCCATTGATTTTCTAAACCTGAGGGAAGGTATT[A/G]CTATTATAGTTTAGTTTGAGTGTGGGGTTAAGCAG R 2 1 2 1 202000 r 74 goat snp55178-scaffold848-270798 1 136824715 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401124 Affx-122959392 AX-123271477 1 134808550 ATTTTTAAAAATATTGATGCCCAGCTCACACCCCA[C/T]AGTACATCAGCATCTCTGAGTGTGGGACCCAGGCA Y 2 1 2 1 102000 r 74 goat snp55176-scaffold848-193099 1 136903242 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387372 Affx-122970466 AX-123257730 1 134870382 ATTTAGAGAAACGTACCACAGAGGGGGAGGGGGAG[C/T]TGGGTATTAATCACCAGTACTGATGGCAGCACAAA Y 2 1 2 1 201000 r 74 goat snp55175-scaffold848-131267 1 136965713 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383427 Affx-122973476 AX-123253785 1 134932459 GCTTCCTGGTAGAGGGACTGGGGCCTGTGTTGTGG[A/G]TGGAGCTGGATCTTGTTCCTCTGATGGGCATTGCC R 2 1 2 1 202000 f 74 goat snp55174-scaffold848-69190 1 137028313 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771871 Affx-122957801 AX-385259027 1 134984769 GGCAGAGATAAGATTCAAATACAGAGTGACTTCAG[A/G]ACTCATGTCTGGTGTAACACTTACCCATGGGGCTG R 2 1 2 1 101000 r 74 goat snp55173-scaffold848-16880 1 137081138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450202 Affx-122922292 AX-123320537 1 135029781 CCCACATTGCAATTGCTTATTTACCTGTCTGGAGG[C/T]GCCTTACAGCAAGGACTCTTTCTTTCTCCTTCTTT Y 2 1 2 1 101000 r 74 goat snp414-scaffold1010-28033 1 137123894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779456 Affx-122931976 AX-385266559 1 135100432 TCTGTCACTATACTGAAAAGGATGCTAGCTGATTT[A/G]TTAATGAACTCTCAGATTATTAAATATGTCATGCC R 2 1 2 1 201000 r 74 goat snp415-scaffold1010-98684 1 137195527 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789347 Affx-122951589 AX-385276357 1 135137336 TTACCAAGTACAGAGAGGAGGGTTTTTAGACAGGA[A/G]TGTGGTTAATTCACATGTTAGCAGATGAACAGATA R 2 1 2 1 101000 f 74 goat snp416-scaffold1010-135588 1 137232670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388632 Affx-122969124 AX-123258990 1 135173099 CCTGCTGTTATCTCATGGGGATGGTCTGGAAGAGA[A/G]TGAGGAGCTCCAGTGAGCTTCTGGGGTGGAGCCAG R 2 1 2 1 101000 f 74 goat snp417-scaffold1010-171351 1 137268823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771513 Affx-122961540 AX-385258671 1 135214569 GGTGAGCAGCTTGGCAGTAGACCCAATGAGCTTAT[G/T]CTCCAGGCTCTCTTTGAGGTCTAGAGAAACATCAA K 2 1 2 1 101000 r 74 goat snp418-scaffold1010-212821 1 137310626 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395012 Affx-122964227 AX-123265367 1 135260650 TGCCTGGGAATTAATTGAGTGGGATGAAATCCTCA[A/G]ATCCTCAGGTCTAGGAGACAACCACCTCTTGTAGC R 2 1 2 1 101000 f 74 goat snp419-scaffold1010-258902 1 137356557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382698 Affx-122973635 AX-123253056 1 135314149 ATTTCTCTGCTAGAGCTCTGCAAGTCTTTCTCATG[C/T]TCTGAGACATCACATTTTCTATTCTTGAAGTCCTA Y 2 1 2 1 101000 f 74 goat snp420-scaffold1010-312401 1 137405419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410818 Affx-122952641 AX-123281168 1 135370939 TTTACCATGCAAATGTATGCAAATAAGAAAATAGT[A/G]TTCTTAGCCAAGTGCATTAGCACCTATTTCTTTGG R 2 1 2 1 101000 r 74 goat snp421-scaffold1010-369191 1 137461470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802924 Affx-986696084 AX-385289820 1 135395880 ACATAACAGGGGGCCATCCCTGATCACCTTCCTCT[A/C]AAAGGAATTAACTTAGGGCTCCAGTTAACAGTCTC M 2 1 2 1 600010 f 74 goat 1_135395880 1 135395880 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320800273 Affx-122933693 AX-385287197 1 135418063 GTTTGCCCCTACTCTACAATGTCTGAAGTCTTTAG[C/T]AGAAAATTTGAAGGCTAAGGGCCGAAATCACTTGA Y 2 1 2 1 202000 f 74 goat snp422-scaffold1010-416315 1 137509150 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396894 Affx-122963224 AX-123267249 1 135466364 TAACAAATATTTGTAAAATGTAAAGGAATAAAACA[G/T]CATGACCAAATGGGTCAAAGTTGTTTCAAAACTCA K 2 1 2 1 103000 r 74 goat snp423-scaffold1010-464616 1 137557930 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428087 Affx-122939098 AX-123298430 1 135512746 GATTGTGCAACTTGTCCAATTCCAAGGCCATCCAG[C/T]AAGCTAACAGCAGAGCCGCATTTGAATTCACATTT Y 2 1 2 1 201000 f 74 goat snp424-scaffold1010-510998 1 137604549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275387 Affx-1111834768 AX-519548961 1 135520262 TGATGGAACTGGAGGCCCGCCTCCCAATTCCTAGA[A/C]GTTACATCTCTGTCCCTTCTTCACTGCAGCTGGGT M 2 1 2 1 101000 r 74 goat GoatD01.052126 1 135520262 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38433420 Affx-122935088 AX-123303761 1 135570066 ATCACCTAAAACCACTCCTGATCTGCAGCCAGCCA[C/T]GAATCTTTCATCAATAAGCTCTCCTGTGGTTCATG Y 2 1 2 1 101000 r 74 goat snp425-scaffold1010-568318 1 137662082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412393 Affx-122951452 AX-123282742 1 135646359 ACCTTCCCTCAGATCCCCACCTTACTGCTTCTCCT[C/T]TCATCCAGGATTGACCCTGCCAATCATAAATGTCA Y 2 1 2 1 101000 r 74 goat snp426-scaffold1010-644611 1 137738561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788934 Affx-122955575 AX-385275947 1 135681113 AGCAGTTTTAAACTATTCACTTTATGGCTTCTCAT[A/G]ACTTCTTTCCACTTAGTCACACACTCCAACTGATT R 2 1 2 1 101000 f 74 goat snp427-scaffold1010-679365 1 137773402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432453 Affx-122935804 AX-123302794 1 135718707 TTAACTGAGTTCATGGTGAGGTGAGCACAAGCAAG[A/G]CAGAACCAGGAGAAATAAGTAGCAGAAAAGAAAGA R 2 1 2 1 201000 f 74 goat snp428-scaffold1010-716959 1 137811059 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435429 Affx-122933486 AX-123305769 1 135781523 GGACGGACCTTTGCAGTAGTCCAGAGAATATGATA[C/T]GGGGCTTAAGGTGAGGGTTATAATAAAGACTAGCA Y 2 1 2 1 101000 f 74 goat snp429-scaffold1010-779775 1 137874506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381695 Affx-122974718 AX-123252053 1 135837954 CTAATCTGTCAATGTTGAGAAATAGAATTAATGAG[C/T]GGACTAAGGATCTTCTCCTACATGGAATCTGTGAG Y 2 1 2 1 101000 r 74 goat snp430-scaffold1010-836206 1 137931757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447941 Affx-122923784 AX-123318277 1 135875385 TAAGGCAGCTGACTTTCCTTTTCATAGCCAGGCTC[G/T]AGCCCAGCTCAAAAGAATAGTAAAAATAACAGCTA K 2 1 2 1 201000 r 74 goat snp431-scaffold1010-873637 1 137969108 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793303 Affx-122933467 AX-385280281 1 135906396 CAAAACAGTTCTTTCCTCAAAAAATCTTATCCTCA[A/G]AACAGATCTGCTCCCTCACCATCATTATCCCTATT R 2 1 2 1 101000 r 74 goat snp432-scaffold1010-904648 1 138000817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409493 Affx-122954049 AX-123279844 1 135946067 TTGGGCCTGAATCCACACTTTGTTCTTGTTGCGTA[C/T]GTGCTCGTAAAACCAGTTTCTGTGCCTGAGTCTGG Y 2 1 2 1 101000 f 74 goat snp21243-scaffold2074-35471 25 41907407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387299 Affx-122970523 AX-123257657 1 135993048 GGCCAGCCTCGCCACTGTGATGGTTACTGAACAGC[C/T]GGACTCTGCGTTTACAGACCCAGGGTGTGCTCAGC Y 2 1 2 1 201000 f 74 goat snp21244-scaffold2074-82452 25 41951912 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402831 Affx-122958262 AX-123273184 1 136041433 TTTTTCCCATCAAATAAAAACAAAATAAATATTCA[A/G]CCTGGGATTTAAGTCAACATAATACAAAATGAGAG R 2 1 2 1 103000 r 74 goat snp53685-scaffold819-57603 1 138047555 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428203 Affx-122939453 AX-123298546 1 136095034 ATGCCCTGGATCAAATTAGGGCATGACTAAAGAGT[A/G]CAACTGCTCTCAAGTGAAGCTCCTCTGGGTACCCC R 2 1 2 1 201000 r 74 goat snp53686-scaffold819-111204 1 138099764 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384935 Affx-122972326 AX-123255293 1 136157770 GCCCTCTGCCCATCTCTAAGGCAGGTCAAAGTCCA[A/G]CGTTCATTAGTTGAGCTCAAATTCTGCTGACATTC R 2 1 2 1 101000 r 74 goat snp53687-scaffold819-173940 1 138163195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386071 Affx-122971456 AX-123256429 1 136211746 GCAGCTCCCTGAGGACCGCCTTTCCTATTCCTCAG[C/T]AAGGACTGCATGCTAAATGCCTCCTTAGAGGAGAA Y 2 1 2 1 202000 f 74 goat snp53688-scaffold819-227916 1 138217396 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441578 Affx-122928678 AX-123311915 1 136284233 AGGTAAACTCAAGTTTAAAAGAAACTCTTTCATAA[C/T]ATTGGCATAGATACACTATCATGTGTAAAATAGTG Y 2 1 2 1 103000 f 74 goat snp53690-scaffold819-300403 1 138292030 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476159 Affx-1251763662 AX-507596443 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20000 f 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 539476414 Affx-1251763662 AX-586011816 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20000 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165086 Affx-1251763662 AX-606940498 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165974 Affx-1251763662 AX-606941383 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 f 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165985 Affx-1251763662 AX-606941394 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 320781069 Affx-122955414 AX-385268156 1 136294294 AATTTGACATTAGTTTTGCCTGATGCAGAAGCCCA[A/C]TTTCTTCCCATTACCTGTTTTGTGAGTTTGTTCTC M 2 1 2 1 101000 f 74 goat snp27914-scaffold2997-194539 1 138308231 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379451 Affx-122976093 AX-123249809 1 136341865 CAAATTTCAAAGAGTAAAATTTATTCATCTCGAGA[C/T]AAGACAAAGTCAGAGTTACATTTGCAATTCATTAT Y 2 1 2 1 101000 r 74 goat snp27913-scaffold2997-146968 1 138356136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402635 Affx-122958393 AX-123272988 1 136420438 TTGTCCACCAGCCCCACACCTGCATTCTAGAACAG[C/T]GTAGATCTCAGGTTTACCTCTGAATATATTATGGC Y 2 1 2 1 101000 r 74 goat snp27912-scaffold2997-68395 1 138432806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405209 Affx-122956905 AX-123275561 1 136455683 GTCCCAGCACCCGGTGATGTCTCCTACCCTTGGAA[G/T]TGGCAGCCCCAAGAGGGAGTCGTACTTTACTCAAG K 2 1 2 1 101000 f 74 goat snp27911-scaffold2997-33150 1 138469529 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432918 Affx-122935313 AX-123303259 1 136486915 CTTCCTGTGTAAGTGTGAGGATGGATGCATTTTAT[G/T]ATAATGCTAGTTCTCACTCTTGGGTTTTTAAAGTT K 2 1 2 1 101000 f 74 goat snp27910-scaffold2997-1918 1 138500754 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790535 Affx-122932451 AX-385277538 1 136505765 CAGAAATTTCGTTTTAGACGTTTATCTTGTGAGAA[G/T]GGTAATGAACGGAAGTAGAGCGATGTTTCTCCTTC K 2 1 2 1 101000 r 74 goat snp8576-scaffold1309-1459353 1 138519063 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423505 Affx-122942557 AX-123293851 1 136534729 TCCTACTGATCCTTGAACAAGAGCTTTTGGAAAAT[A/C]GATCAGAGATGTTTGCTGCTACTGTTGCTGCTAAG M 2 1 2 1 201000 f 74 goat snp8575-scaffold1309-1430389 1 138548003 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441416 Affx-122928829 AX-123311753 1 136574710 ATATGGTAAATATCAGTAGCTATTAGTCACATAAA[C/T]GAAAGCTGGTCCTCAGTTTGTAAAGGGATCCTGAG Y 2 1 2 1 201000 f 74 goat snp8574-scaffold1309-1390408 1 138568103 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421338 Affx-122944070 AX-123291685 1 136623744 TAAATGGGCTAAATGCCTTTTTTTGGAAGGTTAGT[G/T]TAAGGAGAGAATGAAGCCTGGTATGTAAAGTGCCC K 2 1 2 1 101000 r 74 goat snp8573-scaffold1309-1341374 1 138617473 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391974 Affx-122966518 AX-123262331 1 136706417 ATGTGATTGTTTTCTCTTTTGCTTCCTGTAAACAA[C/T]GGTCTACCAAAGAGAAATCAGAGCATTTCACCAGA Y 2 1 2 1 101000 r 74 goat snp8572-scaffold1309-1258701 1 138701430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385364 Affx-122971639 AX-123255722 1 136748205 TCACTCACCTAGCAGGTATGGGATTTGATTTTATC[A/G]TGATTGATCCCCTCCTACTGTTCTGCTGCAGTTTC R 2 1 2 1 303000 r 74 goat snp8571-scaffold1309-1216913 1 138743182 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434177 Affx-122934882 AX-123304518 1 136801943 TGGCTCACATCTGAGGGCTGTTAATTGCTGATGAC[G/T]GTGACATCCTTAAGTTTCTTGAGTAGGGAGTGGTG K 2 1 2 1 201000 f 74 goat snp8570-scaffold1309-1163175 1 138797866 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780168 Affx-122947759 AX-385267265 1 136839784 AAAGACACTGACAGCCTAAGATACTTTGCAGATTT[A/G]CTGCATTTTCAGCGAAAGAACAGTGGCTCCCTATT R 2 1 2 1 101000 r 74 goat snp8569-scaffold1309-1125334 1 138836636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406106 Affx-122956215 AX-123276458 1 136955655 GTGCCATGTGCCCCATGTGTATGATAAGCCAAGAT[G/T]GTGATTTTCTTTGAATTGCTGGTTTTTGGTAGTTA K 2 1 2 1 201000 r 74 goat snp8567-scaffold1309-1009463 1 138952998 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790475 Affx-122976999 AX-385277478 1 137007904 GCTGAGAGGAAAGAGAGAGGTATCTTTTCTAGAGT[A/C]TGGAATTTGTGAATGATAACTAGTTTCATGTAACT M 2 1 2 1 101000 f 74 goat snp8566-scaffold1309-957214 1 139005293 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272473 Affx-1111832839 AX-519546195 1 137034442 CATAGATTCCAGCCCACCAGGCTCCCCAATCCCTG[A/G]GATTCTCCAAGCAAGAACACTGGGGTGGGTTGCCA R 2 1 2 1 303000 f 74 goat 1_137034442_AF-PAKI 1 137034442 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446805 Affx-122925293 AX-123317141 1 137093647 AATACCTGTAACGTAACCCTTTTTCTATCAATCTT[G/T]TCTAAAACAGTATATTGTTATAATTAGTGTCCACT K 2 1 2 1 303000 f 74 goat snp8565-scaffold1309-871471 1 139092420 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771440 Affx-122974265 AX-385258598 1 137172068 GTTTACTACAAAATGATACTGTGACAAATAACATC[A/G]TTTCCATAAATCACCAGGTGTCTGTCTTCCCAAAG R 2 1 2 1 101000 r 74 goat snp8564-scaffold1309-793050 1 139169588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784171 Affx-122969409 AX-385271223 1 137218819 TTCAGTTTGTGGGGAGACAGATGAAATGGTGCTTC[A/G]TGGTTTGGGTTTCCTAAAAGAAAGGGAAGATATTA R 2 1 2 1 101000 f 74 goat snp8563-scaffold1309-746299 1 139216743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse317 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320772020 Affx-122941694 AX-385259176 1 137285746 GCCCCAAATTTAGAAACATGAAGCTATTAAGACAT[A/C]CTTGACCCCTAAAATATCTTTTGAGTTTCCTGGAC M 2 1 2 1 101000 r 74 goat snp8562-scaffold1309-679372 1 139283581 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse318 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410584 Affx-122952124 AX-123280934 1 137318510 AACTGTCCCGTAGTTAACTTCGAAAAAACCAAAAC[A/G]CCCTCTGTGCGGGAAGGCCCCGCGGTCCCACACTT R 2 1 2 1 101000 f 74 goat snp8561-scaffold1309-646608 1 139317139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse319 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38439062 Affx-122930319 AX-123309399 1 137354861 TGGGCACCACTTGGATAAAGCCATGTGAATGAGGC[G/T]CTCTACAACTGCCCCAAGCCCACGCTAGGCCACAG K 2 1 2 1 101000 f 74 goat snp8560-scaffold1309-610257 1 139354044 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse320 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421016 Affx-122944550 AX-123291363 1 137386709 TGAACCAAGGAGTGATGTGGGAAGCCAGGGCCCAG[A/G]AAAGTTTCCAAGAACAACCTGGTGAGGGTACTGGC R 2 1 2 1 102000 r 74 goat snp8559-scaffold1309-578409 1 139385717 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse321 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320770761 Affx-122960304 AX-385257925 1 137445103 CTTCCATTATATGGATGGGAATGGATGCTCTAATC[A/G]CTGAGAAAAAGCAATCCTACCCACAAGTTTACATT R 2 1 2 1 101000 f 74 goat snp8558-scaffold1309-520015 1 139444127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse322 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392389 Affx-122966224 AX-123262746 1 137488373 GAAGCTGAAGTGAACATCAATGCCAGGAGAGAAGG[A/G]TGGGTCTTCGAAGGCACGCACTCAGCAGTAGCGCC R 2 1 2 1 101000 f 74 goat snp8557-scaffold1309-476745 1 139486766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse323 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410601 Affx-122952110 AX-123280951 1 137516937 TGACCCTGAAAAGATAAACAAGTTTAAAGCCTGTC[A/G]CATTCATTCATTTTTAGGTCTAGTTACCCCCGTGG R 2 1 2 1 101000 f 74 goat snp8556-scaffold1309-448181 1 139515537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse324 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377000 Affx-122977731 AX-123247359 1 137582393 CCCCTCACGGTTGGGGAACAAATTGCCTTCTGTAG[C/T]AGTAAGGGTCCCAGGGCATCCCCAGGGTCCCCAGC Y 2 1 2 1 101000 f 74 goat snp8554-scaffold1309-382725 1 139582025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse325 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320802254 Affx-122946497 AX-385289158 1 137628443 ACTTGACTGAAAGTCATAAAATGCTATAAAGACAA[C/T]AATATAAAGAAATCCATTCTTCCCTAACTATGCCC Y 2 1 2 1 101000 r 74 goat snp8553-scaffold1309-336675 1 139627942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse326 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432986 Affx-122935263 AX-123303327 1 137701495 CCTTCAGACAAGGGTCATGTATTGAGACCCAGGTA[C/T]GGTGTGACTACAATATTTGGAGGGGCCCAAGTATT Y 2 1 2 1 201000 f 74 goat snp8552-scaffold1309-263623 1 139701259 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse327 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410843 Affx-122952619 AX-123281193 1 137765601 CCTGTCCAACATCTAGTTCTGTGATTTTTCATGGC[C/T]ATTTCCTGTCAAGTTCTCTAAAGTGAATTTCTAGC Y 2 1 2 1 201000 r 74 goat snp8551-scaffold1309-199517 1 139765433 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse328 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380437 Affx-122975297 AX-123250795 1 137794316 TGTCACTGGTCTCGGTACAGAGAGCGCCTCGTCAC[A/G]TCCTCAAGTCCAGCCTTTCATTCCCCGGAAACGAG R 2 1 2 1 101000 r 74 goat snp8550-scaffold1309-170802 1 139794306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse329 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433147 Affx-122935679 AX-123303488 1 137846228 TCTTTCATATCCAGTGCTAATAATAAGGGGAGATG[C/T]GATTGATTGTGGAAGGTCCTGCCTCAGGTATATCA Y 2 1 2 1 101000 r 74 goat snp8549-scaffold1309-118890 1 139845521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445718 Affx-122926105 AX-123316055 1 137876678 TACAGGGGAAAATGGCTTAGTTTGTCATTTAAAAA[C/T]AAAACTGCCTTATTGCCAATGACCTTCATAGCAAC Y 2 1 2 1 202000 f 74 goat snp8548-scaffold1309-88440 1 139875525 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse330 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38436723 Affx-122932310 AX-123307061 1 137922493 GATGCCTGCATGATTATACACACGTGCACTCTGGC[A/G]CTTACAGAAGAATGCACACACGTGCACATGATCTC R 2 1 2 1 201000 f 74 goat snp8547-scaffold1309-42625 1 139921398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse331 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412522 Affx-122951352 AX-123282871 1 137961901 GTTATATATATAGACTGATCAACTGGTCCCGGTTT[A/G]CCTGAGAATTCTGGTGTTAGCCTTAAAAATTCAGT R 2 1 2 1 101000 r 74 goat snp8546-scaffold1309-3217 1 139957414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse332 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425441 Affx-122941522 AX-123295787 1 137975026 GAAAGGTAAGGAAAGGGCGCAGTGCGTGGAATGAC[G/T]CGGGCTCTTAAGATCAGTGCTGATAAGGAGACCCT K 2 1 2 1 101000 f 74 goat snp4724-scaffold11542-14597 25 42007035 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse333 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38428021 Affx-122939148 AX-123298364 1 137991024 ATGCTGATGAACATTTGCAATGCAAGGGTGGGTCA[C/T]GGAGGGGTGCCTGTGGCCACCAGGGCAGGGACCAG Y 2 1 2 1 101000 f 74 goat snp27437-scaffold292-1261810 1 139961892 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38436766 Affx-122932276 AX-123307104 1 138020133 TCTTCATCAGGGCCCACAGGGACTTGAATCTTTTG[C/T]TTAGAAATCCACAGGAAAAACATCTGACACTGGCA Y 2 1 2 1 201000 r 74 goat snp27436-scaffold292-1232701 1 139990820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse335 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402585 Affx-122958435 AX-123272938 1 138076107 CCCTCTCAGGGAAGAAAAGGCTCTCCCTCTTTGTC[A/G]CTTATGCTTTCTTCCATTCTTCTCTCTCTGGCTAC R 2 1 2 1 201000 f 74 goat snp27435-scaffold292-1176727 1 140047297 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse336 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320785275 Affx-122963610 AX-385272320 1 138110014 TCTCCCTGTCTTTCCTACAAGTACTATATATTTTA[C/T]GATAACCAAACAACCCTAGTTCAGGAAGAAAAGTT Y 2 1 2 1 102000 r 74 goat snp27434-scaffold292-1142820 1 140081733 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse337 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453169 Affx-122920470 AX-123323502 1 138142122 GTTGAGTGAGCATTGCGATAATGTGTGTGGTGACC[A/G]TTGAATAAGAAACAGTGCAGGCAACAAAGCGGCGT R 2 1 2 1 101000 f 74 goat snp27433-scaffold292-1110712 1 140113796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse338 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424205 Affx-122942502 AX-123294551 1 138172279 TGGTTGGCTTGCTCGCCTCTGTGGTCAGGTGTCAG[C/T]TCCCTCTGGATAGTGAAGACACAGACTGTTCCCAG Y 2 1 2 1 101000 r 74 goat snp27432-scaffold292-1080555 1 140141842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse339 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420349 Affx-122944965 AX-123290696 1 138216211 CCATATTTATGCACAGACACACCATTTCTTTGACA[C/T]GTCTAAGTGACAAATAGATGTCACTTTGTCTAAGT Y 2 1 2 1 101000 f 74 goat snp27431-scaffold292-1036623 1 140185652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse340 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392900 Affx-122965728 AX-123263257 1 138275303 CGTGAATTCCAATGAGGATATCGAGGATGGAGCAT[A/G]TCTGAAAGTAAAGCATCTTTAAATATATAATGCAT R 2 1 2 1 101000 f 74 goat snp27430-scaffold292-977531 1 140244752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse341 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320768621 Affx-122963127 AX-385255801 1 138375750 TTTCAAAAAGAGGGGAGATGAAGGGAGGTCTTAGT[C/T]GTTATTGGATAACCTAGAATCAGAGTCAAAGTCAT Y 2 1 2 1 101000 f 74 goat snp27428-scaffold292-877084 1 140345224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse342 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320788214 Affx-122942099 AX-385275233 1 138417308 ATATTCTATAAGGAAACATTGAAGAATGCACACCT[A/G]CATAACACACCATGATCATTTTTTATTTGAACCTT R 2 1 2 1 101000 r 74 goat snp27427-scaffold292-835526 1 140387562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse343 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38385442 Affx-122971316 AX-123255800 1 138465188 TTATGTATTTTGGTGCAAGTCCATGGTCAGATATC[C/T]ATTGCTGACTTTTTATATATTAACTATCCCTGAGA Y 2 1 2 1 101000 r 74 goat snp27426-scaffold292-787646 1 140434838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse344 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423196 Affx-122942719 AX-123293542 1 138498480 TTCCTAGAAGTCAGTCTCTTTGGGTAAGTTTTGCC[A/G]TCCAGCTGGGCTGTGGAACAAGAATAAGTAGATTG R 2 1 2 1 101000 r 74 goat snp27425-scaffold292-754354 1 140468063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse345 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410686 Affx-122952744 AX-123281036 1 138533195 GAAACGTTTCTGAAAGAGGAACTATGAAGTGGGAA[C/T]TGAATGATTTGTATCTATTATTCAGCTTGTCTTAG Y 2 1 2 1 101000 f 74 goat snp27424-scaffold292-719639 1 140502732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse346 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453110 Affx-122920024 AX-123323443 1 138591460 GTCAATAAAGCAGAAGTAGATGGTTTGTCCTTTGC[A/G]TTAGCATAATGGGATAGTCTGGTTACAAGAAAGGT R 2 1 2 1 201000 r 74 goat snp27423-scaffold292-661374 1 140559740 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse347 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38383926 Affx-122972972 AX-123254284 1 138627525 GCTCTCCAGCTCTAGGTTCATCAAGCACTGTCCAG[C/T]GTAACTTCTGCAATAATGGAAACCCTTTCAACTCA Y 2 1 2 1 201000 r 74 goat snp27422-scaffold292-625309 1 140596042 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse348 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420614 Affx-122945239 AX-123290961 1 138674421 TAGTTTTGTTTACAGAGTTGCAATCCAACATGCCT[A/G]CTGATCCATTAATCGGGGGTGACAGTGACCCAGGG R 2 1 2 1 101000 f 74 goat snp27421-scaffold292-578413 1 140643058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse349 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432912 Affx-122935317 AX-123303253 1 138710283 CTTTGATAATAAGACACCCTATTATTTTATGTGCC[A/G]TTTTATGTGTTTTTAACAAAGAAAAGATACAGAAG R 2 1 2 1 103000 f 74 goat snp27420-scaffold292-542551 1 140678900 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse350 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38397060 Affx-122962732 AX-123267415 1 138740524 AAAATCTCTGGGTGCTCAGTTCCTTATATGTTGGG[A/C]TGGCCAAAAAGTTCATTTGGGTTGTTAATAAGATG M 2 1 2 1 101000 f 74 goat snp27419-scaffold292-512310 1 140708752 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse351 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447484 Affx-122924091 AX-123317820 1 138794764 AGAGACCAACACAGACAAATTAAAAGGCCAACAGA[C/T]GAGAGAAACTAAAGAAAGCACAAGGGAATCAGGTT Y 2 1 2 1 101000 f 74 goat snp27418-scaffold292-458070 1 140763357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse352 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38383459 Affx-122973453 AX-123253817 1 138865579 AGGTGGACCTGGAGAGACTTTGTTCATTAGAATTC[A/G]CTTGAATTTTTGATTCTTGTATTAAAGTCTATTTT R 2 1 2 1 201000 r 74 goat snp27417-scaffold292-387255 1 140843053 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse353 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320775306 Affx-122943006 AX-385262437 1 138917290 CTTTGGCATCAACCACAGGCAGACAGGAGAAACTC[A/G]TGGGTCAGGGTAGGAGGTTTACTCTTTCATGTATC R 2 1 2 1 202000 r 74 goat snp27416-scaffold292-335544 1 140894087 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse354 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38397915 Affx-122961939 AX-123268270 1 138947073 TGACTCTCACATCAGTGAGTCTCACAGGAAAGCCG[G/T]CTGGGCTCTGGTCATTACCTGCTGACCATCACTCA K 2 1 2 1 101000 f 74 goat snp27415-scaffold292-305761 1 140923846 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse355 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412196 Affx-122950942 AX-123282546 1 138996059 AACTCAGTGCCTGTCCTCAGGGAGATTCCAGGCAA[C/T]GAAATAGTTCACGGTCCTCACTGCTGCCCAGGAGA Y 2 1 2 1 102000 f 74 goat snp27414-scaffold292-256775 1 140972331 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse356 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400609 Affx-122960386 AX-123270964 1 139041683 GGCTGATTGGAAGGAAGAGGTGTCTGTCAAGGTCC[C/T]GGAGGAAGAAGTCCATGAGCTAAGTTGAGCAGTAG Y 2 1 2 1 201000 r 74 goat snp27413-scaffold292-211151 1 141017992 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse357 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410643 Affx-122952777 AX-123280993 1 139075264 CCAAAGGGAAGCAGCATGTGGGTCAGCTGCTCGTC[A/G]CACCTGGTTAAGCTGTTTCAGCTGGGTGTACTTGA R 2 1 2 1 101000 r 74 goat snp27412-scaffold292-177570 1 141051692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse358 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38398543 Affx-122961528 AX-123268898 1 139109166 CATTGCCTAACAACCATCATGCCAAGGAACCTGGC[A/G]TATTCTTTTCTCATAATGGAAACTTTCCTTTTAAA R 2 1 2 1 201000 r 74 goat snp27411-scaffold292-143668 1 141087410 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse359 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320792879 Affx-122949814 AX-385279857 1 139144711 TTAATAACTATGATCCCTAAGTTCCGTCTACTTGT[A/C]TCCATGAACTTCCTTGCTTCCGAAGTTTAATTCTC M 2 1 2 1 101000 r 74 goat snp27410-scaffold292-108123 1 141123033 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse360 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400602 Affx-122960390 AX-123270957 1 139177402 AAACATATCAAATGCAGTTTTATGTATTTAATATG[A/G]TTTCAATAAGATTCAAATACATTTTTATGTTGAGA R 2 1 2 1 103000 f 74 goat snp27409-scaffold292-75432 1 141155587 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse361 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38439915 Affx-122930016 AX-123310252 1 139207085 CCTAGTGCTCTCATGGTAAGTGACCTGGGTTCCAC[A/G]GTGGGGTCACGTGAGGGGGGCAGCACGATCAGATC R 2 1 2 1 101000 f 74 goat snp27408-scaffold292-45749 1 141185777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse362 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418661 Affx-122946322 AX-123289009 1 139244110 TTGAATGGTCTGGTATTGAGAATTCTGTAGTTCCC[A/G]TCATGTGACCAGAGTTGGGAGGGAATCCGGTGGTG R 2 1 2 1 101000 f 74 goat snp27407-scaffold292-8724 1 141221804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse363 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38436262 Affx-122932546 AX-123306601 1 139258064 ATTATCCAAGGAGAATGGGCTCCTGGGCACTGTGT[C/T]TTCAAGTGAGAAAGCAGTGATATGGGAAAACAGAC Y 2 1 2 1 201000 r 74 goat snp40269-scaffold514-5131 1 141236847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse364 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38422796 Affx-122943209 AX-123293142 1 139316127 CCTCGAAACAGCACACCTGACTTACAGGTGCAGAC[A/G]CTACTGTCAGACACCTGGGGTGAACTGTCTGAGGC R 2 1 2 1 101000 f 74 goat snp40270-scaffold514-63194 1 141294910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800355 Affx-122947711 AX-385287277 1 139370104 TAGATGCTCAAGATGTACCCATGCATCGAAGAACC[A/G]TAAATTAAGGATATTCACTGCTTACATATGTGAAC R 2 1 2 1 101000 f 74 goat snp40271-scaffold514-117171 1 141349092 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402848 Affx-122958251 AX-123273201 1 139422228 GCATTGGTCATTTTTGATCTCCCTGGGTCATCTTG[A/C]TGTTCAGCCAGGGTTAAAGTCACTGTGCTGTCTAA M 2 1 2 1 201000 r 74 goat snp40272-scaffold514-169295 1 141401573 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273890 Affx-1111833876 AX-519547498 1 139425875 CACCAGCTCAGGCTGCAGAGGAGAAAGAAGGAAGG[A/G]CTCTGTGAACTGGCCCAGAATTTTTGCCTCTGGAC R 2 1 2 1 202000 r 74 goat GoatD01.008855 1 139425875 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437679 Affx-122931773 AX-123308017 1 139454003 AACAGTGGCTTCCAACTAAACTCTGCTATGCCATC[A/G]TTTGGAAGTTGTCTCCCCATTTCAGAGATGTTAAA R 2 1 2 1 101000 f 74 goat snp40273-scaffold514-201070 1 141433682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409072 Affx-122953344 AX-123279423 1 139539276 TCATTCCTTTTTCTTTCTGGCTAATATTCCACTAA[C/T]GGATGTTCCATTGTCTGGCCATGTCCCGTGGTTAG Y 2 1 2 1 201000 r 74 goat snp40275-scaffold514-286343 1 141519187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272522 Affx-1111832840 AX-519546240 1 139541154 CCTGAGCCTGGCAGGACCAGCGCATCCTCAAAAAG[A/G]CGGTGGTCAGACAGCTTATCAGCTATGCACAGAAA R 2 1 2 1 102000 r 74 goat 1_139541154_AF-PAKI 1 139541154 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276713 Affx-1111835553 AX-519550223 1 139558608 AGAGCCCACTCCAGGGAGCATTTAGCCACTGGGGA[A/G]CCTCTCCTCCCAGCCCAGCTGTGAACCTCAGAATT R 2 1 2 1 202000 f 74 goat Random2.2K-133 1 139558608 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391652 Affx-122966561 AX-123262009 1 139588375 ATTAAAACGCAAAACCAGAGCACAGACCCTGATGG[C/T]GCCAAAGACACAGTGGTGAGAACATCACCTGAAGA Y 2 1 2 1 201000 r 74 goat snp40276-scaffold514-335442 1 141568586 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403371 Affx-122957789 AX-123273724 1 139633165 GTCCATGGGGTCACAAAGAGTTGGACACGACTTAG[C/T]GACTGAACAACACAAGTCACTTAAGGATCAGAAAT Y 2 1 2 1 103000 r 74 goat snp40277-scaffold514-380232 1 141612835 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448936 Affx-122923152 AX-123319271 1 139737108 ACGTTTCTGCTCATCCCTGGCTCCCTTACCCGTGA[C/T]GTATATGTTGAAGGAGTCACAAAAGCACCTCTGGA Y 2 1 2 1 201000 r 74 goat snp40279-scaffold514-484175 1 141716330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383755 Affx-122972440 AX-123254113 1 139765868 GCACAAACACCCACAAAACCCTCACTCTGCCTGTC[G/T]GCTTACTCAGAGGCTCCTTCTGCTTCGTCAGGAGG K 2 1 2 1 201000 r 74 goat snp40280-scaffold514-512935 1 141746337 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395886 Affx-122963621 AX-123266241 1 139812547 ATTCCTGCCTCTCTACTTTTCTCTCTGTGCCCCAG[C/T]GGCATCATTTTCTCTCACAAACACACCCAAATCAT Y 2 1 2 1 101000 f 74 goat snp40281-scaffold514-559614 1 141792726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410078 Affx-122952848 AX-123280428 1 139844549 TGAGACTAACAGCTGCCCACCCTATGGGATTCTTA[C/T]GAAGGACAACGAACGCAGTATGTCTGCAAGTTTCC Y 2 1 2 1 201000 r 74 goat snp40282-scaffold514-591616 1 141824597 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423018 Affx-122943418 AX-123293364 1 139894079 CATGGGTTCTGCATCCTCGGAGGCAGAGAGCTGGC[C/T]TCATAGCTCGTACTCGATAAACAGTGGTTTGCAGG Y 2 1 2 1 101000 r 74 goat snp40283-scaffold514-641146 1 141864810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453768 Affx-122919595 AX-123324101 1 139934921 CTTTTTTTTATGAACTGTGATTTTGTAAGAAAACA[C/T]GGTATTTCCTCCGGAATGAGTAATGTGCACATCAT Y 2 1 2 1 101000 r 74 goat snp40284-scaffold514-681988 1 141905709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425448 Affx-122941518 AX-123295794 1 140031637 TGTCCTGTGGCTGAAACACATCAGCACAAACTTGG[C/T]GGTTTAAAACTACACAAATCGATCATCGTACATGT Y 2 1 2 1 101000 r 74 goat snp40286-scaffold514-778704 1 142002582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768291 Affx-122961659 AX-187158319 1 140064692 AACCATGGCTCACAAAGAATGCAATATTGTTGTCC[A/G]TTCTCTGAATTAAGTTGAGATGTAAGTGACATTTA R 2 1 2 1 101000 f 74 goat snp40287-scaffold514-811759 1 142035966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418317 Affx-122946973 AX-123288665 1 140161533 GCATCAGCTTGAGAATTAAATGCTTCCAAAGCTTC[A/G]TACGTGTGACATGGGAAGGAAAGACACCAGATAAA R 2 1 2 1 201000 f 74 goat snp40289-scaffold514-908600 1 142132966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799760 Affx-122923627 AX-385286687 1 140203316 CAAGACAAAATAAACTCACATTAGAATAACATATC[A/G]CAAAATGTTGATAAGAGTATAGAGAATTAAGAACT R 2 1 2 1 101000 f 74 goat snp40290-scaffold514-950383 1 142174751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442101 Affx-122928356 AX-123312438 1 140245191 GAGGGTGATTCAGAGAGAGACGCCCACACCACGCC[A/G]GGCACAGGGTTAGCAGTGGCCATGGGCTTCCCCCA R 2 1 2 1 303000 r 74 goat snp40291-scaffold514-992258 1 142215445 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394471 Affx-122964570 AX-123264826 1 140320986 AGAGCCGGGGACAGGACCCTGCACGCATTCCCCTC[A/G]GCCGTGCCTCTGGTTCTCCACTCTTCCATCAGCTA R 2 1 2 1 101000 r 74 goat snp40293-scaffold514-1068053 1 142289169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426935 Affx-122940428 AX-123297280 1 140415818 TCTTTGAAACTGGATATTCTTACACTTTTCCCTGC[G/T]GTGGTGGTGTGAGTTCCAGGTGTCTGTTAAGAGCC K 2 1 2 1 201000 f 74 goat snp40295-scaffold514-1162885 1 142385069 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385398 Affx-122971346 AX-123255756 1 140447513 AAGTACCATGGATGATGACCCCTCCCCAGGGTGGG[C/T]GGTGGCTTCTGGGGGATGAGTTTAGAAGAGACTTG Y 2 1 2 1 303000 r 74 goat snp40296-scaffold514-1194580 1 142416711 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769605 Affx-122961252 AX-385256775 1 140493157 TCAGCACAAGCGGTAATTTTGAAAGCAGGGGTAAC[A/G]CTAGAAAGAGAGTCCACTCTTGCAGGGTTATGTTT R 2 1 2 1 101000 r 74 goat snp27918-scaffold3-21710 1 142462719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403406 Affx-122957764 AX-123273759 1 140535710 TGTCTATCTCCCCACCAGAATATAAGTCCCAGGTA[A/C]GTGTTTGTTGTCTGTCTTCCCACTAGAATTAAAGT M 2 1 2 1 102000 r 74 goat snp27919-scaffold3-64263 1 142505324 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423886 Affx-122942296 AX-123294232 1 140579857 GAAAAGGGAAAAGGAAACCCTGAATTCATCACCAG[A/C]TGATATAAATGTTCATTTCTACTTTACCACAGTTT M 2 1 2 1 101000 f 74 goat snp27920-scaffold3-108410 1 142548452 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392561 Affx-122966081 AX-123262918 1 140643356 TTATTTCCCACTGGGGGACATTCAGGTAGCTTCTA[C/T]TCTGGTTTTTGCAGCAGTAGATAACGCTGTGGTAA Y 2 1 2 1 101000 r 74 goat snp27921-scaffold3-171909 1 142600261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412797 Affx-122950490 AX-123283146 1 140682501 ATGCAAGAAAATGTGTCCTTTGCACTTTTGAGACC[A/G]AGTGTGCTTTTAAATGGGGCCCCTTGGCAGCCAGG R 2 1 2 1 101000 f 74 goat snp27922-scaffold3-211054 1 142638865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393018 Affx-122965647 AX-123263375 1 140728323 CAATCAATAGGACAGAGGCCCTGGAGTTTGTAATC[C/T]GGTTCCTTAACATCATAAAGTTACATCACCTGTCT Y 2 1 2 1 101000 r 74 goat snp27923-scaffold3-256876 1 142684760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449500 Affx-122922626 AX-123319835 1 140760441 TTCAGGATGCCCCAGCCCTCTTCAGGACGGGAGTC[C/T]CCCCGCCACTGAGAGCCCAGTTTAAAGGTTACCCT Y 2 1 2 1 101000 r 74 goat snp27924-scaffold3-288994 1 142716767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476160 Affx-1251763663 AX-586011589 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20000 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 539476415 Affx-1251763663 AX-586011817 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 4 1 4 1 20000 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562165249 Affx-1251763663 AX-606940661 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166082 Affx-1251763663 AX-606941491 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166268 Affx-1251763663 AX-606941676 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166316 Affx-1251763663 AX-606941724 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 38431318 Affx-122937074 AX-123301659 1 140790014 ATGATACTGGGTGTTAATGCTGTCCTCTAGGGCAC[A/G]GATATTTACATGTCTGTTTCAGTGTGTTGTAACTT R 2 1 2 1 101000 f 74 goat snp27925-scaffold3-318567 1 142746200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448357 Affx-122924118 AX-123318693 1 140840457 TGTGTCTGGCAGAGGAACTGCCTTTTTCAAATTCC[A/G]CCAAAGTTGCACTGTTGTGTTGGCAGATGGATCAA R 2 1 2 1 201000 f 74 goat snp27926-scaffold3-369010 1 142796576 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405118 Affx-122956973 AX-123275470 1 140930277 AACCTGGACATCCATAGGATTTCACACTTATTCTC[C/T]AGGAACTGCCAACAGGCGGCCCACCCTGCTGGAGC Y 2 1 2 1 101000 f 74 goat snp27928-scaffold3-458830 1 142887188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405248 Affx-122956879 AX-123275600 1 140979606 TCCATCCATCCAGCACATCTCTGAGCCCTTGCCAC[A/G]TACCAGGTGTTGTTCTGCATATCTGGGATCCACAG R 2 1 2 1 101000 r 74 goat snp27929-scaffold3-508159 1 142933758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276879 Affx-1111835566 AX-519550388 1 140986624 CAATGTTGGCAAAGAGATTGGAGCAGTGAAAAGCC[A/G]GCGACTGTCAGAATGCTAGACCCTTGCTCTTTGAG R 2 1 2 1 101000 r 74 goat Random2.2K-136 1 140986624 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787072 Affx-122929242 AX-385274099 1 141015296 GGCCCTCTCTCTTAAAAATGTTTAATAGACTCTTT[G/T]TAAGAGTAGTTTTAGATTCGCAACAAAATTGAGTG K 2 1 2 1 101000 f 74 goat snp27930-scaffold3-543849 1 142969566 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773071 Affx-122929769 AX-385260214 1 141054410 GAAGCTCAGTCTCACAGACTTAATTTGTGTTCAAA[C/T]GAGATCTGGATAAGTGTTGCTCCCCTAAAAGAGGG Y 2 1 2 1 201000 r 74 goat snp27931-scaffold3-582963 1 143008578 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273977 Affx-1111833963 AX-519547582 1 141099375 TCATTTTCAGAGCTGCCAAGATTAAATGAAGTAAT[A/G]TACCAGCACAGACCATCTGCAGCTAGCAGGCACTT R 2 1 2 1 202000 f 74 goat GoatD01.012317 1 141099375 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410514 Affx-122952178 AX-123280864 1 141102428 CCAAATCTCTCCTTTTAATGCTGTATTTTTGCTTT[A/G]TTTCTATTAACTTTTAATTACCCTGAGATAAACAT R 2 1 2 1 201000 r 74 goat snp27932-scaffold3-630981 1 143053173 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429128 Affx-122938005 AX-123299470 1 141132454 CACAGCATCTTTTCCAGAGACTCCTGCATCCCTCC[A/G]TCCGATCCTGCCCAGCAGAAAGGACACTGCTGAGT R 2 1 2 1 102000 f 74 goat snp27933-scaffold3-661007 1 143083234 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429401 Affx-122938531 AX-123299743 1 141173769 CCTCAGTATCTTTCAGCTCAAGGATAACAGCACCA[C/T]GAGGTTCCTGATAAGAAAGGGCTGCATAGCTCTGG Y 2 1 2 1 101000 f 74 goat snp27934-scaffold3-702322 1 143124704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787153 Affx-122972486 AX-385274179 1 141205239 AATACCTATATTTTAGAATGCTGGTCCACGTGACA[C/T]GCGAAATAAATGCATCTGCATATATTGGGAGTGTT Y 2 1 2 1 101000 f 74 goat snp27935-scaffold3-733792 1 143155775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425710 Affx-122940771 AX-123296056 1 141260937 CCACATGCACACAGACACACACTCCCAGACAAGAA[C/T]TGTGGCTGCAACCACTCATGGTCATGCCAGGGACA Y 2 1 2 1 201000 r 74 goat snp27936-scaffold3-789490 1 143210901 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276889 Affx-1111835571 AX-519550398 1 141264582 GAATTTATGGCATGCCAATTAAATCTTAATTTTTT[A/T]AAATGCCTTTCAGAAAGTATCTCCTGACCAAAAGA W 4 1 2 1 103000 r 74 goat Random2.2K-137 1 141264582 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419180 Affx-122945721 AX-123289528 1 141332981 TCTCTTCCCCTGTGAAGTTCCTTGACATGTGTGTG[C/T]ACATGCTATTAACATCTATTTTATATATACAGATA Y 2 1 2 1 103000 f 74 goat snp27937-scaffold3-861534 1 143283606 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424922 Affx-122941293 AX-123295268 1 141373140 ACTTCAGTTGGTACTTCTTTATGGGGGCTGGTGGT[A/G]AAATTGTAGGTGAAATATGACGCACAGGTCAGCCA R 2 1 2 1 101000 r 74 goat snp27938-scaffold3-901693 1 143324182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276770 Affx-1111835580 AX-519550279 1 141398879 TAGATTTAAAACCGCTCTGATTGGAGAGCCTGGAA[A/G]TTAAAAATTAAGTTAACCTGAAGAATGCATTCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-139 1 141398879 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427330 Affx-122940126 AX-123297673 1 141443923 CACTGTTGCTTTCTCACCCAGCCCCCAGCTTCTGG[C/T]ACAAGGAAGGTGAGTGGGGTCATGACCAGGATGGA Y 2 1 2 1 103000 r 74 goat snp27939-scaffold3-972476 1 143394463 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409178 Affx-122953192 AX-123279529 1 141491749 TCCTTGTTAACATTTTGCCATATTTGCTTGTGTAC[G/T]CCATGCATGTCATCATTTATCCATTTGTTGACATC K 2 1 2 1 201000 r 74 goat snp27940-scaffold3-1020302 1 143443612 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402357 Affx-122959049 AX-123272710 1 141512827 GGGGCTAACAGTGTTGCAGAGGGGCTCTGAAATTA[C/T]AGTACTGTTTCTCGTCAAACTGCTACTTATTCACT Y 2 1 2 1 101000 f 74 goat snp21323-scaffold2083-3122 1 143465553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419854 Affx-122945375 AX-123290202 1 141570967 GCATTTCCTTGAACCCACTCAAAACATTACTCAAG[C/T]GGCCCTTTCCCCTACTTCTCAGGAATCAGGTGGCA Y 2 1 2 1 101000 f 74 goat snp21324-scaffold2083-61262 1 143524189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408480 Affx-122954420 AX-123278831 1 141609200 GTTGAAAATTTCTTCATTGCTTAATTCATGGGCAC[C/T]GTTTGTGAACGCTTCTGTGAGCAGCTGAGAGAAAG Y 2 1 2 1 201000 f 74 goat snp21325-scaffold2083-99495 1 143562895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430315 Affx-122938233 AX-123300656 1 141641238 TGAGATGATATCTCTCTACTGTCCTCTGTTTCAAA[G/T]AGTCAGTCCAGTTCATAGACTTTTCCCTCCAGTAT K 2 1 2 1 101000 f 74 goat snp21326-scaffold2083-131533 1 143592279 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449045 Affx-122923067 AX-123319380 1 141689926 TGAAACTCTCTGTGGCTCAACGTGTTGTCAACGTC[C/T]AAGAATGTTCCAGGGCCACATGGAGAGGCAGTGCC Y 2 1 2 1 101000 f 74 goat snp21327-scaffold2083-180221 1 143641237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400168 Affx-122960682 AX-123270523 1 141727421 GGAGCAGTGTGTGTGCAGGGAGGCACTCCTGTGGC[A/G]CAGTGACGGGAATCCTCCAACATCCAGATTGGATT R 2 1 2 1 101000 r 74 goat snp21328-scaffold2083-217716 1 143678723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381294 Affx-122974459 AX-123251652 1 141756443 GAGACAGGAGAGAGACGGATAGATTCAGAGACAGA[C/T]GGAGCTCTCTGGTGCATCCTCCTGTAAGGGCATGA Y 2 1 2 1 101000 f 74 goat snp21329-scaffold2083-246738 1 143707820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400409 Affx-122959990 AX-123270764 1 141797136 CTCCTGAAACAAAATTCCTGTGTTAATTTGACTTC[C/T]CCAGTACATGCAGCTATACAGTTCTCGTCTTTACA Y 2 1 2 1 101000 f 74 goat snp21330-scaffold2083-287431 1 143749941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453826 Affx-122919554 AX-123324159 1 141914329 GGAAGATGCACCATGTACCTGGATTTAATTTCCTA[A/C]TTGCATTTTAAAAGGCAATTCTTCATATCTACAAA M 2 1 2 1 201000 r 74 goat snp28928-scaffold3111-232523 1 143867864 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399107 Affx-122960865 AX-123269462 1 141983550 ACCCTCTTCCAGCCTCTGATCCCCCAAAGGGAGGT[A/G]CTGGACCCTCAGGGGAGCCGAGCTCATGAGCAGTA R 2 1 2 1 303000 r 74 goat snp28927-scaffold3111-163302 NW_017204900.1 9611 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392075 Affx-122966379 AX-123262432 1 142016282 TCTGTAACCCCAAGTTAATTCCGAAGTCCCTTCAC[A/G]CATCCTCCCGCGGATGAGTAGCAGGCCCCACGGAG R 2 1 2 1 101000 f 74 goat snp28926-scaffold3111-130570 1 144265013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271816 Affx-1111832841 AX-519545603 1 142041543 CACTTTCCATTTCTTATTCTGGGGTTCATCAGGAG[A/G]AAACCACCCCCATCCTCATGCTCTCATGGGCCTGT R 2 1 2 1 101000 f 74 goat 1_142041543_AF-PAKI 1 142041543 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413454 Affx-122950676 AX-123283803 1 142045578 GGTACTGGTGCCAGTCTTCTGGAGTTCAGAAATGC[A/G]AGAGTACACTTCGGTTGCTTTAAGCCATCAGTTCT R 2 1 2 1 101000 r 74 goat snp28925-scaffold3111-101274 1 144294155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771212 Affx-122927531 AX-385258371 1 142082475 TTGTTGCTCTTCTGCAAGAGTTGAGTTTTGAATAT[A/G]TTCACCATGCCAATTCTCAATTTTTCCCTCTTTGG R 2 1 2 1 101000 r 74 goat snp28924-scaffold3111-64377 1 144330717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415488 Affx-122948700 AX-123285837 1 142128895 ACCCAATGAATAGAGGAGCAGACGAGAGGCCACAC[A/G]ATTTGCTCAGAAGCCAGGAACTCCGGGAGCTGAAA R 2 1 2 1 101000 f 74 goat snp28923-scaffold3111-17957 1 144376801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412842 Affx-122950456 AX-123283191 1 142157746 ATCCTTGGGAAGAGCCAACCCATGTCCTAAGACTT[A/C]TGAATATTTCCCACAGGCAGGTGGGGGCAGGTCCT M 2 1 2 1 103000 f 74 goat snp59164-scaffold971-10795 1 144397617 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414800 Affx-122949220 AX-123285149 1 142233618 AATATGTCCCATTCATTAGCTAATAAGCAATACAG[C/T]GGATCGTCCCATCCAGGAATAAAAGCTTCATCCAC Y 2 1 2 1 201000 f 74 goat snp59166-scaffold971-86667 1 144513690 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781509 Affx-122969919 AX-385268594 1 142272452 AATGCTGTTGCACCTCAGTTGATATGATTTCACAT[A/G]TTTTCTATCTTACATTGTCAGTGGAATTAATCGCA R 2 1 2 1 101000 f 74 goat snp59167-scaffold971-125501 1 144553336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442558 Affx-122928518 AX-123312895 1 142302374 CTTCCTTCCCCTCCCAAGCTGCAAAGAATGGTTTT[A/G]TCCCAACAGTCATAGTTGCTGCCACAGCCACTGTG R 2 1 2 1 101000 r 74 goat snp59168-scaffold971-155423 1 144583805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380444 Affx-122975748 AX-123250802 1 142358371 AACCAGGCACATGTGACTGTGACAATATGTCCTGC[A/G]ACCCCTGGATCCGCATGAACGCCCCTACCTATTGT R 2 1 2 1 101000 f 74 goat snp59169-scaffold971-211420 1 144639015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435555 Affx-122933383 AX-123305895 1 142413380 TGTTAAGCATCATCAGCCGCGTCCACCAAGCAGCA[A/C]GGTCACGGTCAGCCTGCTGGAGGGGATGAGGAGAG M 2 1 2 1 103000 f 74 goat snp59170-scaffold971-266429 1 144694701 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422127 Affx-122943553 AX-123292474 1 142493459 CGTTGACTGGACACAGCCAGCTTCCCCTGCCTCCA[C/T]GGAGGCTTAGGAGTTGCTTCTTAAATATTTAATGG Y 2 1 2 1 103000 r 74 goat snp59171-scaffold971-346508 1 144774353 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444973 Affx-122926667 AX-123315310 1 142538563 AAAGTAAAATTAAAAACAAAGATTCAATTGATTCC[A/G]TTGCAGTTAGATGTAGTTGAAGAAAGAACTAGTAA R 2 1 2 1 101000 r 74 goat snp59172-scaffold971-391612 1 144818903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416887 Affx-122948077 AX-123287235 1 142589723 CCCATGGACTGCAGCACACTTGGCTTCCCTGTCCA[G/T]CATCAACTCCCAGAGCCTGTTCATTTATTAACAGC K 2 1 2 1 103000 r 74 goat snp59173-scaffold971-442772 1 144869800 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378739 Affx-122977032 AX-123249098 1 142629300 CTCTGGCCCCACTGTCCCACCATGTGTGCCCTTTG[A/C]CTCAACTGTGGTCTCTGCAGAGCACTCCTTGCACT M 2 1 2 1 102000 r 74 goat snp59174-scaffold971-482349 1 144909427 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432778 Affx-122935427 AX-123303119 1 142659820 ACCGGGAAAGGAACATTTTTTTTTTTTGCAAGACA[C/T]AGTCAGTCATGTTGTAAAGAAGAGTTTGACACATT Y 2 1 2 1 201000 r 74 goat snp59175-scaffold971-512869 1 144939665 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378628 Affx-122977113 AX-123248987 1 142694340 TGAACCGTAAAGGAAAGTAGACGCATGCGCCCCCC[A/G]CGTTCACAGCAGCACTGTTTACACTAGCTAAGGTA R 2 1 2 1 303000 f 74 goat snp59176-scaffold971-547389 1 144974871 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428622 Affx-122938681 AX-123298964 1 142752193 CGTGGAGTGGGCCAGGGTCAAGCGTTCACAAGGGA[C/T]GCCCCCCGCCCTGGACACACACAGAGTTCAGCCAG Y 2 1 2 1 101000 f 74 goat snp59177-scaffold971-605242 1 145032410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378322 Affx-122977344 AX-123248681 1 142801516 GACCCCACACACAGGCCATGGCAAGTCCTGTCCAC[A/G]TGGCTCAGAGCCCAGGAGCCCCTCGAGGCTGCGCC R 2 1 2 1 101000 f 74 goat snp59178-scaffold971-654565 1 145081289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392940 Affx-122965699 AX-123263297 1 142834375 TGTGCTCCCCAGGACTCAGAAGCCAGAAGTCCTTC[C/T]TTCTTCCACAGACACCCTGGCCTGGGCTTCAAGGG Y 2 1 2 1 102000 f 74 goat snp59179-scaffold971-687424 1 145113328 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450984 Affx-122921733 AX-123321318 1 142862899 ATAGTCTTGTTTGCCCACTATGGCTGTGCCACCCA[A/G]TGCTTGGTGTGCTGAGCTGAATGGTGTCTCCACAA R 2 1 2 1 201000 r 74 goat snp59180-scaffold971-715948 1 145141134 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793679 Affx-122942476 AX-385280651 1 142916438 GAGTGAAATACTCAGTGAGAACTCAAACACCGGCA[G/T]AGTCGCTGGAGAGTTCGGTTCTAGTCCATGGAGAC K 2 1 2 1 101000 f 74 goat snp59181-scaffold971-769487 1 145191476 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392684 Affx-122966418 AX-123263041 1 142964084 TGAGGGACTAACATTCTCACTAGAATTCTGCATCC[A/G]GTGAAGACATTCTTCCATAGGAAGAGGAAGCGGGC R 2 1 2 1 101000 f 74 goat snp59182-scaffold971-817133 1 145239454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440221 Affx-122930685 AX-123310558 1 142997989 CCGTCTGGCCATCCCTACTGTGGACATCAAACCCA[A/C]AAGTTGAAAACCCCCTGGACATGCTGGTCATCTTT M 2 1 2 1 101000 r 74 goat snp59183-scaffold971-851038 1 145273759 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798466 Affx-122954942 AX-385285399 1 143131758 AAAAGCTTTTAGACTCTGGCTCTGTTTCAAGGGCA[C/T]AGATTTAAGATGACTCCCGATCTTTCTCCATGTAG Y 2 1 2 1 101000 f 74 goat snp59185-scaffold971-984807 1 145407619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398396 Affx-122961642 AX-123268751 1 143214056 GGCAGGCTGCCTGGACCTCCCTCCAGCACTTCCCT[A/C]GGTGGAACCTACCAGAAGTCAGCCCAGGACGAGGT M 2 1 2 1 101000 r 74 goat snp59186-scaffold971-1067105 1 145490320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432934 Affx-122935300 AX-123303275 1 143242847 TCCCAGTTCGCAGGGGTGCACTGACAGCTCTTTGT[A/C]GGTTCTCCTCTCTCCTCCTGACTTCTCAGTGCTTG M 2 1 2 1 201000 f 74 goat snp59187-scaffold971-1095896 1 145520670 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449800 Affx-122922418 AX-123320135 1 143344660 TAAACTATAAAACATTTCAGCTGGTATTAGACCAG[C/T]GTTAACAGCGCCAGCTCTGGGGAAGATCTAGAATG Y 2 1 2 1 101000 f 74 goat snp59189-scaffold971-1197709 1 145622448 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798238 Affx-122956713 AX-385285173 1 143399821 TAACACATTGGAGGCATACTTTGGCAGAGGTAATG[A/C]CTCCCAAGGATGCTGAGAACATAATATTTGATGGG M 2 1 2 1 201000 r 74 goat snp59190-scaffold971-1252870 1 145685638 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804403 Affx-986696570 AX-385290992 1 143400881 TCTGCCCGAGCAGAAATGCGTGAACGTATCTGAGT[C/G]CATCTAGAACTAATGCTCCAGGGTCAGATTTTCTC S 4 1 2 1 600010 r 74 goat 1_143400881 1 143400881 Ancestral_priority_1043 ancestry 0.772 recommended IMAGE 10K 10K ancestral 38377721 Affx-122977393 AX-123248080 1 143443682 ATTAAATTTATGTGGAAGGAAGAAAGCAAGGCTAA[G/T]CCTGAAGTCTCTGAAGTGAGTTCCTTGAGGCCAGG K 2 1 2 1 101000 r 74 goat snp59191-scaffold971-1296731 1 145728897 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385374 Affx-122971630 AX-123255732 1 143521433 CCTAACAAGTGCACGCATGCTTTTTGGTTTTCCCA[C/T]GTGCATAGCCCGTCTGGAAGGAATTTCAGGGTGTG Y 2 1 2 1 101000 f 74 goat snp59192-scaffold971-1374482 1 145806577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443428 Affx-122927368 AX-123313765 1 143554685 TAGAGAAACAGAAAACAAAAGAATAAAATTGAAAA[C/T]GAGAAAAGCCAGATAAGAATGACCAGGAAGACAAT Y 2 1 2 1 103000 r 74 goat snp59193-scaffold971-1407734 1 145839443 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800488 Affx-122973944 AX-385287408 1 143628286 CACCATCAAGTCTTAAATACTTCTGGACAAAGACC[A/G]TTGCCAACTGTACAAGATTAAAATGTGAATGACCT R 2 1 2 1 101000 f 74 goat snp22395-scaffold2210-27252 1 145909196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414335 Affx-122950032 AX-123284684 1 143742243 TGTTCTCTGTGATGCTTGTAAGCTTTATCATTAAT[A/G]ACATTTTTGCCTTCCATGTACACGGAAACGACAGC R 2 1 2 1 101000 r 74 goat snp22398-scaffold2210-141209 1 146019858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424911 Affx-122941301 AX-123295257 1 143803889 AAACTGCATCTGTGTTCCATGTGAATGTGAAATGG[C/T]CCTGATCCTTTTTTTCTGACGGGGACAGAAAAGAA Y 2 1 2 1 101000 f 74 goat snp22399-scaffold2210-202855 1 146081892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276781 Affx-1111835585 AX-519550290 1 143848171 GAATATGTGATCCTGAGTCCAGCCAAAGCCAGTCT[A/G]CAAACCTAAGCAGCAGCTGTCAGCAGACGTGGAGG R 2 1 2 1 201000 f 74 goat Random2.2K-140 1 143848171 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415203 Affx-122948985 AX-123285552 1 143858387 TGTTTCTGGGCATCAGTCACTGCTTGTGACCGACA[A/G]CTAGCATATTTGATAGAGAAGGAATGTTGAGAAGG R 2 1 2 1 101000 r 74 goat snp22400-scaffold2210-257353 1 146136046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444181 Affx-122927270 AX-123314518 1 143907757 CCCACATTCAGTGTTGTTGGGAGGAAAGGTCTCAG[A/G]AGAACCACAGTCACGGTCCTGACCAATGCCTGCCG R 2 1 2 1 101000 f 74 goat snp22401-scaffold2210-306723 1 146184948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424860 Affx-122941340 AX-123295206 1 143959775 AACATGTAAAAGACTGAGGTTCCTGTGAGGGGTTG[A/G]GTGGCACCTATAAACATCTGCCCAAAGATTAATTT R 2 1 2 1 201000 r 74 goat snp22402-scaffold2210-358741 1 146238663 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376024 Affx-122978399 AX-123246383 1 144014937 AGGCTCACAGGTGGAGCTGCAGTGCAGTGCTGCCC[A/G]AGTCCCGATCCTGCCAGAACCCAGACGTAGCATTT R 2 1 2 1 101000 r 74 goat snp22403-scaffold2210-413903 1 146294100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382449 Affx-122974225 AX-123252807 1 144050869 TTCAGAAACCTGAAATTCAGCTCTGAACAGTCACC[A/G]CTCCAGCTTCAAGGGTGATACATAGTGACCAGTGT R 2 1 2 1 101000 f 74 goat snp22404-scaffold2210-449835 1 146330700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378394 Affx-122976797 AX-123248753 1 144112284 GTGTTTGTTGAGCCATTTTTAAGCCTATACAGTCC[G/T]CTGTGCTCTGGTTGGGACCAGAGACTCGAGTGGGA K 2 1 2 1 101000 f 74 goat snp22405-scaffold2210-511250 1 146395126 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766525 Affx-122961086 AX-385253885 1 144142073 TCCTGGTTCACATCGCGGATTACATTATCAAATAA[C/T]GTATCATAACAGATCAAGCTGGAAAAAACATTCTT Y 2 1 2 1 101000 f 74 goat snp22406-scaffold2210-541039 1 146425331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778363 Affx-122968912 AX-385265478 1 144171376 CCATGTGCTCTCTGACATTAGTTGGTAAAATGTGC[A/G]TAATATTGCAGATTGTACCAGCTATTTCACAAGAG R 2 1 2 1 101000 f 74 goat snp22407-scaffold2210-570342 1 146454808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803904 Affx-986696572 AX-385290616 1 144193528 TTAAGTTACCTCTGAAGATTGCTAAAAATAGCCAC[A/G]GTATACAGAAATGGTCTGGTATTGTATTAAACTTT R 2 1 2 1 600010 f 74 goat 1_144193528 1 144193528 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320767726 Affx-122948059 AX-385254959 1 144236918 TGACTCATTCATCATGGAATGGGAAATAAAGGACC[A/G]TAGTAGACAATTTATGTGAAAGCACAGAAAGATAC R 2 1 2 1 101000 f 74 goat snp22408-scaffold2210-635884 1 146519136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787393 Affx-122956628 AX-385274418 1 144278669 TAGAAATAATGCAAGGTGATTAGCAATGCTAGGAT[A/G]TGTCTGTAAGATTTACCTATTCATATAATCATCAC R 2 1 2 1 101000 f 74 goat snp22409-scaffold2210-677635 1 146561256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769851 Affx-122928605 AX-385257021 1 144339450 CCTTTCCAATAAGGACTGACACATCTATTCATCCA[C/T]ATTGGAAATCTTCCTCCTCCTCTAGCCTAAGGGAG Y 2 1 2 1 201000 r 74 goat snp15149-scaffold1619-19073 1 146701519 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430734 Affx-122937510 AX-123301075 1 144433512 GTGTGAACTGTCTAGCTCTGTTCCAGGAGCCCATT[A/G]TTCCTGAAGAACCTCCTCCAAAAGACTCCTTGACC R 2 1 2 1 201000 r 74 goat snp15152-scaffold1619-113135 1 146795979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797069 Affx-122951501 AX-385284009 1 144459107 ATAGCATATTTTCATTAGGGGTTATCAAGTTTTCC[A/G]CTGATAGAAAGTTTAGAGAGCAGAGCAAAGTACCA R 2 1 2 1 101000 r 74 goat snp12298-scaffold1461-17289 1 146821420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421195 Affx-122944151 AX-123291542 1 144488312 TTCATTGGGAAGGGTCCTGGTCCCCAACACCACAT[A/C]CTCTTCACCTTTCTTCCCTTAGCCAGGGAACATGC M 2 1 2 1 101000 r 74 goat snp36351-scaffold436-1810 1 146851572 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770466 Affx-122921019 AX-385257632 1 144521193 CAGTACTGGAAGCCCCTGATCAGTTTTCATATCTG[C/T]GACCACAGTGAACTGTGTTCGGCTTCATTGGCAGT Y 2 1 2 1 102000 f 74 goat snp36352-scaffold436-34691 1 146884606 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272539 Affx-1111832842 AX-187183534 1 144546271 AACTAGTAGAGTCTTACAGTCATGGCTCACCCTCC[A/G]TCTGAGGGCAGCGGGCCCCACTATGGGGAGCAGAA R 2 1 2 1 102000 f 74 goat 1_144546271_AF-PAKI 1 144546271 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412524 Affx-122951350 AX-123282873 1 144557873 CTCAAATAGGAAATGACTTCTGCCCTGTTGTCTAA[A/G]GAGAGGCTTCAGGGAACAGCAGAAAAGGGTTACGT R 2 1 2 1 101000 f 74 goat snp36353-scaffold436-71371 1 146921283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378152 Affx-122976973 AX-123248511 1 144601558 AGCTGAGATGACATTTACTGCATAGCTAGGAGACC[A/G]TGATCTCACCGACAGAAACGTTACTTCTTTCTTTC R 2 1 2 1 101000 f 74 goat snp36354-scaffold436-115056 1 146964989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397239 Affx-122962370 AX-123267594 1 144643092 CTGCACTGCAGATACAATCTTTACTGACTGAGCTA[C/T]GAGGGAAGCCCATGTATTGTAGTAAACTGTACATA Y 2 1 2 1 303000 r 74 goat snp36355-scaffold436-156590 1 147006487 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385570 Affx-122971845 AX-123255928 1 144673829 GCTCTTCCACCTTCAGATTCACCCGTATGCACTTC[A/G]CTTGGTCCTATCGTGGTCTGTAATCAATTATTTAT R 2 1 2 1 101000 r 74 goat snp36356-scaffold436-187327 1 147038064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797702 Affx-122925507 AX-385284641 1 144733106 TTGTGACTGTATAACATAAGTGTCCACAGTATAAC[A/G]TGTCTGCAAATTATCCCAATCATAATATACATTTT R 2 1 2 1 101000 f 74 goat snp36357-scaffold436-246604 1 147097270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442961 Affx-122928213 AX-123313298 1 144770436 CTTTATGTCACTGTAAGAAAAGGCATCATTTCAGT[A/C]GTCTTTGAGGTGCATGGTCTTTCCACCTGAATTCC M 2 1 2 1 101000 r 74 goat snp36358-scaffold436-283934 1 147134672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429243 Affx-122937910 AX-123299585 1 144842391 ACTCACATGTTATCATAGGATACCCTTGACATCCA[C/T]TTATTCAGAGGATGTGGGGTGGGAGTCACAGTTTG Y 2 1 2 1 101000 f 74 goat snp36360-scaffold436-355889 1 147207614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445259 Affx-122925476 AX-123315596 1 144874530 ACATTATGCATGATATTAATATATGATAAAGGATC[C/T]GTGGAAAAGTGGAAAAGCACAAGCGTGCCATGCAA Y 2 1 2 1 101000 r 74 goat snp36361-scaffold436-388028 1 147239720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446304 Affx-122925646 AX-123316640 1 144965888 CAAAAGTACTGGCATTAGGGCTCCTTCCCCTTCCC[A/G]TATTCCCTCTTTTCTAGATTATTAGGTACCATACA R 2 1 2 1 101000 r 74 goat snp36363-scaffold436-479386 1 147331232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382499 Affx-122973817 AX-123252857 1 145001694 TGGGAAGCAATGGAAAGGCAAGTTGCTCTCCCCTT[A/G]TCCAACAATGATCTTAACTTTCTAGATATACGATC R 2 1 2 1 201000 r 74 goat snp36364-scaffold436-515192 1 147365588 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387080 Affx-122969881 AX-123257438 1 145037345 CCCGTTCCTCTGAGGTCACCCTGATCACTCTGTTC[C/T]CAGATCGCAAAATTACCGTGACCTCTGCCACACAT Y 2 1 2 1 101000 r 74 goat snp36365-scaffold436-550843 1 147401327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450152 Affx-122922741 AX-123320487 1 145075408 CCTTGGTGAATTGGTAAAGTTTGAAAGATCTGAAA[G/T]ATAACTGTGTAATCATTTAATCTTTGTGGAAGATA K 2 1 2 1 101000 f 74 goat snp36366-scaffold436-588906 1 147439114 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427205 Affx-122939590 AX-123297548 1 145115074 GTTTTCTATCTCTCTGTAACAAATTTCCAAAAGCA[C/T]AGCTGCTTTAAACAACACCCATTTATTACATTACA Y 2 1 2 1 101000 f 74 goat snp36367-scaffold436-628572 1 147478744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442459 Affx-122927948 AX-123312796 1 145154668 AGGGAGGTGCTGTCTCTAGGGAACTTTCTATCCCA[C/T]GCTTCAAAGTATCATATATGTCTGGAACTCCTTGA Y 2 1 2 1 101000 r 74 goat snp36368-scaffold436-668166 1 147517992 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38407744 Affx-122954987 AX-123278095 1 145207697 AGAACTAAGGTGATGATGCCCATAAATGCTCAGCA[C/T]GGGGCTGGGCACCCAGCTGTGCTCAGAAAATGTTA Y 2 1 2 1 101000 f 74 goat snp36369-scaffold436-721195 1 147571154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800188 Affx-122968626 AX-385287111 1 145239224 TCTCTGAGGATTCATCCTGGTTTGCTCTCAAACAT[A/G]CTCATGTCTACTGTTGATTTCCGTTCTAGGAACCT R 2 1 2 1 101000 f 74 goat snp36370-scaffold436-752722 1 147602702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406216 Affx-122956124 AX-123276568 1 145268152 TGATTGTCTGTTTCACTCTTCCACTGGAATGAAAG[G/T]TCAATAAAAACAGAAACCCTGCCTGTCTCCTTCAC K 2 1 2 1 201000 f 74 goat snp36371-scaffold436-781650 1 147631984 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386143 Affx-122971403 AX-123256501 1 145326929 GGCTCTGTTCTCAAAAGTCCCACTTTCTCTCTCAC[A/G]TCCTCAGTCCCCTAAGACCTAGCCTTTGAATTCAG R 2 1 2 1 101000 r 74 goat snp6737-scaffold1244-1457031 1 147692948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443508 Affx-122927794 AX-123313845 1 145362221 TGGTTGTTTAAATTTTATTTTAAAAGCGAAGAGCA[C/T]GGAGGATTTGACAGCTAAGTTCTCAGTTTCATGAT Y 2 1 2 1 101000 r 74 goat snp6736-scaffold1244-1421739 1 147728303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388240 Affx-122969791 AX-123258598 1 145403049 ATCTTCGGGGCTTGACTCAGTGTCTGGTCCATAGA[A/C]GGACTTCCAAAAATATTTGTTGAATAAGCCACAGA M 2 1 2 1 101000 f 74 goat snp6735-scaffold1244-1380911 1 147769259 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412519 Affx-122951354 AX-123282868 1 145467271 TGGGGAAGAGGGTTGTGAGGTGGAAAAGGAAATGG[C/T]AACCCACTCCAGTATTCTTGCCTGGAAAATTCCAT Y 2 1 2 1 101000 f 74 goat snp6734-scaffold1244-1316689 1 147834039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411715 Affx-122951530 AX-123282065 1 145521550 ACACAGCTGGCCCTATTGCTCCAACTTCCTCTTCC[A/G]TCACTCTCTGCCATGGTCTTCTTCACCAACCAACT R 2 1 2 1 201000 r 74 goat snp6733-scaffold1244-1262410 1 147888174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771990 Affx-122927006 AX-385259146 1 145589611 AATATTATCTAACATGGGGACTCTCAAATGCTATC[A/G]TGCTTAAGAATTACCCAGAGAGCTTCTTAAAATGC R 2 1 2 1 101000 r 74 goat snp6732-scaffold1244-1194349 1 147956450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383199 Affx-122972787 AX-123253557 1 145623967 GATTACTTCTTTTTCTTTCCTCCCGCCCTTCCCCC[A/G]CTGTCCCCACCTGGCCTAAATGCTTATACACACTT R 2 1 2 1 303000 r 74 goat snp6731-scaffold1244-1159993 1 147990515 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440593 Affx-122929288 AX-123310930 1 145655990 TGATCTATAGTACAGAGGTAGTGCTGAGGATCAGC[A/G]TCTGAAATTTAGAGACTGCCTCACTGCCTGTATTT R 2 1 2 1 101000 r 74 goat snp6730-scaffold1244-1127970 1 148022658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379306 Affx-122976200 AX-123249665 1 145717128 CAGTGACAATACTGAGATCCTGCAGCAGGCCAGCA[C/T]GTGACCCACATGGACAAACCCAAACCCAACATGCA Y 2 1 2 1 101000 r 74 goat snp6728-scaffold1244-1066832 1 148083864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450106 Affx-122922778 AX-123320441 1 145783167 ATCTCCCCCCGCAGGACCCTGCTGAAAAGCAGATG[C/T]GGTTTCTGCTCCCTGGCTCATTTTGCCTTGTGCAT Y 2 1 2 1 101000 r 74 goat snp6727-scaffold1244-1000793 1 148149528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450897 Affx-122922201 AX-123321231 1 145813249 TGGCTCCAATCCAAAGCACACTCAATTTCAGAACA[C/T]GCCTCCCCAGATCTTACCACGCCGAATCCTCTCGG Y 2 1 2 1 101000 f 74 goat snp6726-scaffold1244-970711 1 148179447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383246 Affx-122972749 AX-123253604 1 145886802 TTTCAGGTGGACAGCACAGGGACTCAGCCACACAT[A/C]TTCATGTATTGGTTCTTTACAATCTCCCCTCCTTC M 2 1 2 1 101000 r 74 goat snp6724-scaffold1244-897158 1 148252735 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452420 Affx-122920588 AX-123322753 1 145937514 TTTCATGTTTAATTTAAAAATTTGTTTTACAGTAC[C/T]AAGAAATGGTTGATGTAAACTATGTTTTGAAATAT Y 2 1 2 1 103000 r 74 goat snp6723-scaffold1244-846446 1 148310403 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430899 Affx-122936867 AX-123301240 1 145979871 GATCCAATGGCACCATCTCAGCTACGCTCACCAGG[C/T]ACTGCCTTCTTTACCATTCCCACCACACTCATCAC Y 2 1 2 1 101000 r 74 goat snp6722-scaffold1244-804089 1 148352257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433074 Affx-122935739 AX-123303415 1 146008373 TTCCACCGTCTGAGAGCCTGGGGAATGCCACTTAC[A/G]CTATCCCGTCTTCAACATTCAGAGAACACTGCCCA R 2 1 2 1 201000 f 74 goat snp6721-scaffold1244-775587 1 148380537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403735 Affx-122958019 AX-123274087 1 146039340 TGGGGCTTTGAGATGATTCAAAACATGTTTCTCTT[A/G]TTTAAAAAATTTTGTAAATGGGACTTTCCCTGTGA R 2 1 2 1 303000 r 74 goat snp6720-scaffold1244-744620 1 148413501 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420475 Affx-122944872 AX-123290822 1 146071676 ATCACTGGAAATGCAGAGTGAGCCATCGGGAGGTC[A/G]CAGAGGGTGAGGCCAGGGGTCACCCAGCAGGAAGC R 2 1 2 1 101000 f 74 goat snp6719-scaffold1244-712284 1 148445116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385124 Affx-122971775 AX-123255482 1 146105414 TCCTCACAGAGATGCTGCAGCTGGGTTGGGGTGAC[C/T]TAAGTCATCAGGCAGTGCTGGGACCAGCAGGATAC Y 2 1 2 1 101000 r 74 goat snp6718-scaffold1244-678546 1 148478665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399425 Affx-122961230 AX-123269780 1 146147156 TCTGTTAAACATGTGCCCAGCTCTCAGTTAGCTCC[A/G]CATGGTCTCTTCTGCTCCCTTTGTTTGAGCTGTGT R 2 1 2 1 201000 r 74 goat snp6717-scaffold1244-636804 1 148520480 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405135 Affx-122956962 AX-123275487 1 146190197 AGGGAGGAAGTTTACCAAACGCTGTTGGCCACTCT[A/G]GGCACGCTCATCACCAGGCAGGAAAACAGAAGTGT R 2 1 2 1 101000 f 74 goat snp6716-scaffold1244-593763 1 148563929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790931 Affx-122945366 AX-385277928 1 146248669 ATGCCTCCTGGGAAACGGTTTAGGATTTTACGGTC[A/G]TGGTAACTTAAGCTTGTAGATTTCACTAAATCAAT R 2 1 2 1 101000 f 74 goat snp6715-scaffold1244-535291 1 148622833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414601 Affx-122949357 AX-123284950 1 146295731 TGTGCTCCCTGCAGTGCTGGCCACCACACACTGGC[C/T]TCAGCCCTAAGGAGGCTACTGACGTGTAGACGCGA Y 2 1 2 1 101000 r 74 goat snp6714-scaffold1244-488229 1 148670021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412691 Affx-122950760 AX-123283040 1 146331824 AACAGTGAAGATATATGAGTATGTATGACGGAGTC[A/G]CTTTGTTGTACAGCAGAAACTAACACAATATTTTA R 2 1 2 1 101000 f 74 goat snp6713-scaffold1244-452136 1 148706944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781024 Affx-122921754 AX-385268111 1 146405538 CATCTTAACCATCTCCTACATCTACCTGGCACAGA[C/T]GCTGTCAATATTCCCCTACTCTAAATTACCCTAGA Y 2 1 2 1 101000 f 74 goat snp6711-scaffold1244-378422 1 148780410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452972 Affx-122920155 AX-123323305 1 146462126 CCTTCCTCTCCTATATTTCAGATAGACTCTGTACC[A/G]CTGAGCCACCTGGTACCCTTCCCTTCGCTCTCTTT R 2 1 2 1 102000 f 74 goat snp6710-scaffold1244-321834 1 148837415 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436629 Affx-122932498 AX-123306967 1 146504701 TTCACCTGAAACTATCTTAATATTGTTAACTGGCT[A/G]CACCTCAATAACAAAGTAAAAAGCCTGAAAAAATA R 2 1 2 1 101000 f 74 goat snp6709-scaffold1244-279259 1 148879955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802235 Affx-122952092 AX-385289139 1 146534752 GAGCTTTAAGCTAGCTTCGGGCTTCCTTTGAAATA[C/T]AGAGCATTCCTGCAGGACTATATAGACGCACACAG Y 2 1 2 1 101000 f 74 goat snp6708-scaffold1244-249208 1 148910087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427917 Affx-122939226 AX-123298260 1 146591028 TCAGACAAATGTTGGAAAACTGATCACGACCACGG[C/T]GCAAGCAATGGCTTCTAGAAGATGAAAATACCATA Y 2 1 2 1 101000 f 74 goat snp6707-scaffold1244-192932 1 148966329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803911 Affx-986696576 AX-385290620 1 146674504 GTCCTTGAACTGCGGGATCTAATTGCTTTGATAGA[G/T]AAATGACAGGGGTGAAGCAGGGGCCAAAACTCCTC K 2 1 2 1 600010 f 74 goat 1_146674504 1 146674504 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38404112 Affx-122957113 AX-123274464 1 146713017 AGATTTGGCTTAAGGTGGCTGCAGATTCCTTCCTC[C/T]TAATGGACAAGTGGAATTTTATATTCCTCCCTTGA Y 2 1 2 1 101000 r 74 goat snp6704-scaffold1244-70943 1 149089077 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424422 Affx-122941804 AX-123294768 1 146808163 AACAGTGTTTAAAGAGCATTTGGCCCTCCAGTCGT[C/T]GTCCTCAGCCTTTAAAGCTGAGAGACAAACCCTCC Y 2 1 2 1 101000 f 74 goat snp29563-scaffold320-1673275 1 149183747 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418642 Affx-122946338 AX-123288990 1 146867272 CAGCCCATGGGGTCACAGAGTCAGACATGACTTAG[G/T]GACTAAACCACCATCCACTTTAATAACCTCATGAA K 2 1 2 1 103000 r 74 goat snp29562-scaffold320-1614166 1 149242626 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452257 Affx-122920770 AX-123322590 1 146897255 GAATTGAAGAACGTGTCTAACTCTGGATGTCAACT[A/G]TCATATCCACCTTCATGTTCACAGCCGGGCATGGA R 2 1 2 1 101000 f 74 goat snp29561-scaffold320-1584183 1 149272940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382816 Affx-122973559 AX-123253174 1 146929656 TCTTATGGAAGGCCACTGTTGAAAAGCCTCAAAAA[C/T]GTGATCTTCATTCCAGGAATTTATTCATTGCATGG Y 2 1 2 1 101000 f 74 goat snp29560-scaffold320-1551782 1 149305587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453774 Affx-122919591 AX-123324107 1 146973824 TAAGTGGCTAGTAGAAAATTTTAAATTACACATTC[A/G]CTTCTTCACATTTGTGGCTCACCTCATGTTTCTGT R 2 1 2 1 101000 r 74 goat snp29559-scaffold320-1507614 1 149349691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439380 Affx-122930266 AX-123309717 1 147020690 CGACCTGAAAGCTGAGACAGGTAAAGATGAGGGCA[C/T]GATGCCAGATGTGGAGATGAAACACAGCGAGAGGC Y 2 1 2 1 201000 f 74 goat snp29558-scaffold320-1460748 1 149396646 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436968 Affx-122933162 AX-123307306 1 147062954 ATCCCACTCCCTCCTCCCAGTGTGACTGCGTTACA[A/C]AACACGGATCAATAAACTGTCATGTCCAGGTTGGA M 2 1 2 1 101000 r 74 goat snp29557-scaffold320-1418484 1 149439377 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386115 Affx-122971423 AX-123256473 1 147219943 CTCTGCACATGGCCTGCTCATGTACCAACAGACCA[C/T]GGCCCAGAGACTCTTTGGGGAGCAGAGATTGTTTC Y 2 1 2 1 101000 f 74 goat snp29553-scaffold320-1261495 1 149596828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272541 Affx-1111832843 AX-519546258 1 147259623 AAACTTTTTTGTTTGTTTGAAAGAAAGTGTTAGCT[A/G]CTCAGTCATGTCTGACTCTTTGGGATAGCGTGGGC R 2 1 2 1 303000 f 74 goat 1_147259623_AF-PAKI 1 147259623 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397331 Affx-122963298 AX-123267686 1 147260103 CCCTCCGTCACCCACCCCCCAGGAACTCTGGAGAG[A/C]GTCCAAGAGAGGTGTTTCCATTTGGTGGAAATCTC M 2 1 2 1 101000 r 74 goat snp29552-scaffold320-1221335 1 149634299 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377236 Affx-122978158 AX-123247595 1 147298119 CCCAAAGCAGAGGGCATTGAGAAGAAAGCAGGGGC[C/T]GAAACCCACATGGGAATTCCCAGTGGCCACTGAGG Y 2 1 2 1 101000 r 74 goat snp29551-scaffold320-1183319 1 149672725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438003 Affx-122931579 AX-123308341 1 147329636 ATGAGCTGAAAGACATCTCCACTAGTCCTAGGGAA[A/C]GTACAAACTCGGGTGGGTTTCCTTTCCAGCCTTAT M 2 1 2 1 101000 f 74 goat snp29550-scaffold320-1151802 1 149704230 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427215 Affx-122939582 AX-123297558 1 147360186 GGGGTCCATTCCTTGATGGTCAGTCTCACCACGTT[C/T]TTTCCCTCTTCCACCCATCCACTGATGTACTGAGC Y 2 1 2 1 101000 r 74 goat snp29549-scaffold320-1121252 1 149735173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780543 Affx-122968069 AX-385267634 1 147389485 GATCAGAAAATGTGTTCACGTCTTGACCCTGCCCT[A/G]TCCTCGACCAAGATACCTGATTCAGACAGACCCCC R 2 1 2 1 101000 r 74 goat snp29548-scaffold320-1091953 1 149764529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423170 Affx-122942740 AX-123293516 1 147436985 GCCACATCACGCCACTCCCCAGCTTTCCCATCACA[C/T]AGCCTTCTCTGCCTGTCCTTTTCTGTCTCCTATAA Y 2 1 2 1 101000 r 74 goat snp29547-scaffold320-1044453 1 149809199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797372 Affx-122941951 AX-385284311 1 147476863 CTGGAGAGTGGGGCACCACTCATTCAACCAGAAAA[C/T]CGGAAAGAGCTCTGATCCAGAAGCCTCTCAATGAA Y 2 1 2 1 202000 r 74 goat snp29546-scaffold320-1004575 1 149849592 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449627 Affx-122923192 AX-123319962 1 147526282 TAGACTCCCAAAACAGCCAGCGCTCTGCCCCTTGA[C/T]GATGAAGTCAATCTTTCCCTGGGTTCATAGGTTTA Y 2 1 2 1 303000 r 74 goat snp29545-scaffold320-955156 1 149899346 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387909 Affx-122970455 AX-123258267 1 147563120 AACCTTCTAATGCTCCTCACACTTCACTTTACTTG[C/T]GATTCTCAAGCCCATTATAAGGCTATTCATACTGG Y 2 1 2 1 101000 r 74 goat snp29544-scaffold320-918318 1 149936710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429422 Affx-122938515 AX-123299764 1 147593387 GGTCTGCCTGCTCTACAGGGTCTCTTGCTCATCTA[C/T]GTGGAGACAGGAAGCCAGGATCAGAGAGGGTGAGT Y 2 1 2 1 101000 f 74 goat snp29543-scaffold320-888051 1 149967013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791008 Affx-122946118 AX-385278005 1 147626104 AATCCCTCTAAAGGCAACAACAGTCACAATGCTAT[A/G]TGACATTATAACTTCAGGCACAGGAATAATTCAAT R 2 1 2 1 101000 f 74 goat snp29542-scaffold320-855334 1 149999627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396686 Affx-122962832 AX-123267041 1 147663352 TCCAACAAAGAAGGACAATGTTATCTTAAAAAGAA[C/T]ATTCAGTATTCCCTAAACTACGGCTTTGATCTAAC Y 2 1 2 1 101000 r 74 goat snp29541-scaffold320-818086 1 150037066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441056 Affx-122928920 AX-123311393 1 147704741 ACCCCCACCACCTGCTGACCATCAGAGGTTCATCA[C/T]GTGCTTTGATGGTGACAGCCCTGGAAAAGGACACG Y 2 1 2 1 101000 f 74 goat snp29540-scaffold320-776697 1 150078563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389121 Affx-122968559 AX-123259479 1 147744657 CTGAGAGCCATATGATCCTTCCAGATCGGACAAAG[C/T]AATGAGAAATAGAGAATGCCATCAAGTTCAGAGAT Y 2 1 2 1 101000 f 74 goat snp29539-scaffold320-736781 1 150118910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433289 Affx-122935208 AX-123303630 1 147801281 TAGTGATATTTCAGGGAATTGCACAAGAAAAGTTA[C/T]GGTAAATTACTGATTATAACTCATATAATTAAAAG Y 2 1 2 1 101000 f 74 goat snp29538-scaffold320-680157 1 150175723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786494 Affx-122922661 AX-385273528 1 147833361 GTTTTGATGGAAGAAAGCTTCCAGGAGGTTTCACA[C/T]GGCACGAAGATAAAGATATGGCTCCTGAAAAGCAA Y 2 1 2 1 101000 f 74 goat snp29537-scaffold320-648077 1 150207831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276955 Affx-1111835603 AX-519550463 1 147882442 GAGAGAAATAGCTAGAGAGAAACTCAGAAGTCCCA[A/G]TCCAGAGAATTGTGACTCTTCTGTTAAGGCAGGCA R 2 1 2 1 101000 r 74 goat Random2.2K-144 1 147882442 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786979 Affx-122965797 AX-385274007 1 147929662 GCAGGTTAACAAGAGGAAAACAGAAGGGTATTAAC[A/G]TGTGTAGTTTGTACATACATGGGAAATACCAGGGC R 2 1 2 1 202000 f 74 goat snp29535-scaffold320-551776 1 150305283 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776145 Affx-122973463 AX-385263274 1 148048360 ATCCGTCCATGCATTTTCCATTAGGCATAGATGCA[A/C]GTGCGTGGATTCCTTTGAGTATCAAGTAATACTCT M 2 1 2 1 202000 f 74 goat snp29533-scaffold320-433078 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435383 Affx-122933573 AX-123305723 1 148080530 GCCCAGAACATGTGAGCAGTTTCATTGCATGTATC[A/G]TGCCAGGCGAAGTTTTTAAATGGCTTCTTTGAAGT R 2 1 2 1 101000 r 74 goat snp29532-scaffold320-400908 1 150457102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389907 Affx-122968115 AX-123260264 1 148111764 TACATTATACAATTAAAAAGTTTAATAATTGAAAG[A/G]GCTAATATCCAACTACACTAATGTGATTTTTTAAA R 2 1 2 1 101000 r 74 goat snp29531-scaffold320-369674 1 150488663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768323 Affx-122941093 AX-385255503 1 148143653 TGCAAGACCAAAACTCTATAGTTATACATATGATT[A/G]TGAATATGTTATATTGACAGCCTGGGTGTCTCAGA R 2 1 2 1 101000 r 74 goat snp29530-scaffold320-337785 1 150520518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394633 Affx-122964399 AX-123264988 1 148256884 ACTTAAAACCTCAGAAGAATGGTCCAACCATGGCA[C/T]ATTGCTGTTTCTTTTCAACAAATCATGCAAAATGA Y 2 1 2 1 101000 f 74 goat snp29528-scaffold320-224554 1 150635131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430993 Affx-122936688 AX-123301334 1 148291881 ACTGAAGTGGAATTCAAGTTTGTGTGTCCTGTCCT[A/G]TTTCTTGGCCTTTCCTCCTGAGAAATTCTTCATTT R 2 1 2 1 202000 r 74 goat snp29527-scaffold320-189557 1 150669945 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439100 Affx-122931115 AX-123309437 1 148383848 TTAGATATATAAGATAGCTTTTTTAAAACATAAAT[A/G]CTCTGTATTGAACAACTCATTTTAACATAGCTTGT R 2 1 2 1 101000 r 74 goat snp29525-scaffold320-97590 1 150761309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437132 Affx-122932156 AX-123307470 1 148424629 TCTTTGCAAAAGTATACGTGGACCTCAGTACGTCC[A/G]TTACAGCTTGGCCTTTATCTCATTCCTAATTTTTG R 2 1 2 1 10000 r 74 goat "ins-del_015;snp29524-scaffold320-56809" 1 150801933 T C ins-del_015 1 preexisting CNV preexisting recommended GoatSNP50 chip candidate gene ou candidate region PIS 10.1371/journal.pone.0086227 38450206 Affx-122922289 AX-123320541 1 148478485 CAAACGCTCACTTGTTAATACTCACTTGTTTCTCC[A/G]TGTTTCAGGTAGAATGTTCCTCCCTTTAGGCCGTT R 2 1 2 1 101000 f 74 goat snp29523-scaffold320-2953 1 150856109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433619 Affx-122934595 AX-123303960 1 148483663 CTGACTTAATTGGTCTGTGATGGGCCCTGGGCATC[C/T]GTACTGGGCAGCCAAGACAGAGAACTCTGGGTTCA Y 2 1 2 1 201000 f 74 goat snp21980-scaffold2163-2126 1 150859549 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770568 Affx-122962690 AX-385257732 1 148574464 TAGGCCTACCAAGAGGGATTGAGACCTGCTGAAAG[A/G]CGTCCTATGAGTAAGTATGTAAGCTTACAAGGTAG R 2 1 2 1 101000 f 74 goat snp21983-scaffold2163-92927 1 150948608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445775 Affx-122926063 AX-123316112 1 148626429 ACAGCATAATTCCTGGAAAGCATTTATGTCCCCCC[A/G]TGTGGGGAACAGACCTTCAGCCCTGCCATAGCCCA R 2 1 2 1 201000 r 74 goat snp21984-scaffold2163-144892 1 151000629 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425531 Affx-122941457 AX-123295877 1 148657624 CTGCAAAACTGGTCACCAAATCCTGCCAGGTAGGA[C/T]GCACGATTTAGAGGGGCACAAGCCTGCTGTGTTCC Y 2 1 2 1 101000 f 74 goat snp21985-scaffold2163-176087 1 151031573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798119 Affx-122941428 AX-385285054 1 148707231 CAGTAATGGAGGGAAAAGGGTGAATAGAAAATGGA[C/T]AAAAATATTGTGTATCAGCCATGATTCATCTCCAT Y 2 1 2 1 101000 f 74 goat snp21986-scaffold2163-225694 1 151081229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436780 Affx-122932264 AX-123307118 1 148743092 CTATGAAGGGCAAGTATCTGGATTGGTGGCTAGAG[C/T]ATTTATTGTGTACAGGGTTCCCACCTGGGATTTCC Y 2 1 2 1 101000 r 74 goat snp21987-scaffold2163-261555 1 151117036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408744 Affx-122953404 AX-123279095 1 148778498 AGCAACCTCCTCCCTTTGCTGATAATCACTCTGCA[C/T]ACCCCTTGCCCCTTCACCCTGAAAGCGTTTGCCCA Y 2 1 2 1 101000 f 74 goat snp21988-scaffold2163-296961 1 151165203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409479 Affx-122954058 AX-123279830 1 148811530 TTGATGTTCAAAATATGTATTTACATGCATGCATT[A/C]TGGTCTCCACTTTATAGAGTAGAAGACTAAGACCT M 2 1 2 1 101000 r 74 goat snp21989-scaffold2163-329993 1 151197865 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391696 Affx-122967580 AX-123262053 1 148853218 CATCTCAGGTTTAAATCTTTCCCCCAGAACTAGAC[A/G]CTGACTCAAGAATGGTCTAAACAGCCCTTCCTCAA R 2 1 2 1 201000 r 74 goat snp21990-scaffold2163-371681 1 151239390 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451871 Affx-122921062 AX-123322204 1 148896183 TCAGAGGACTTTCCCCAGTTCAGTAATCAGCAGGA[A/G]TTTATCTAACTGCATGATGCCAGCCATGCTGACTA R 2 1 2 1 101000 r 74 goat snp21991-scaffold2163-414646 1 151283056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406380 Affx-122955406 AX-123276732 1 148926402 CCAAGACCACCATGTACAGTTGCTCAGGTTGTGCA[C/T]AATGCAACATATAGCCATTGGGTTATGGTGCCTCT Y 2 1 2 1 201000 r 74 goat snp21992-scaffold2163-444865 1 151313160 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430093 Affx-122937531 AX-123300434 1 148971281 TTTAAACAGACCCCGAGTGGGAAAACAGGTCAACA[A/G]TGAAAGCTGTTGCTGGAAGTTCAAGGTCACCTTGG R 2 1 2 1 201000 r 74 goat snp21993-scaffold2163-489744 1 151358235 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390131 Affx-122967999 AX-123260488 1 149022417 CTGTGGACTGTAGGATGCTAGCAGTATCCCTGGCC[C/T]CCACCAAATCCCAGGAGTGTCTTCCTAACCGTGAC Y 2 1 2 1 103000 r 74 goat snp21994-scaffold2163-540880 NW_017191234.1 13885 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421882 Affx-122944270 AX-123292229 1 149037907 GATCTTGCAGGAAAGCAAAGCACACAAGCACGCAC[G/T]GCTGTGCACACACGCAAACCTTTACCCCGGGGCAG K 2 1 2 1 202000 r 74 goat snp12152-scaffold145-841841 1 151374628 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446621 Affx-122924796 AX-123316957 1 149067676 TAGATCTCAAAATGTCAGATGACTTTCCAGATCTA[C/T]GAAGTATCTGAAGTTCGCAGGTCTAACAGCCAAAA Y 2 1 2 1 101000 r 74 goat snp12151-scaffold145-812072 NW_017205255.1 12913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429221 Affx-122937927 AX-123299563 1 149111957 TGAGATGTGGATGGAGAAGTTTCTGTGCTAACAAT[A/G]ATCGATAAATCTGAAGGGTTCATTTTAGCGGGGAA R 2 1 2 1 101000 f 74 goat snp12150-scaffold145-767791 1 151473795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395011 Affx-122964228 AX-123265366 1 149143491 ACGGCCCTCCATACCTTTATATCCTTATACTTTTT[A/G]TATAAATGCTTCAGTCTGTGCCCTCTGGTTGCTTG R 2 1 2 1 201000 r 74 goat snp12149-scaffold145-736257 1 151505265 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439211 Affx-122931031 AX-123309548 1 149182752 TAGGCATCCCATCACACGGATGATTCTATGGCAAC[A/G]CAGCGGGGACAGTTCAATTGAAATACTCTTAACTA R 2 1 2 1 101000 f 74 goat snp12148-scaffold145-696996 1 151545083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435830 Affx-122932827 AX-123306169 1 149238996 TATTGGTTTGCTATCAACATCAAACAGGAGAACAC[A/G]TGTAAAGCTGCTGGGACAGGGCATGGCACATGGTC R 2 1 2 1 101000 f 74 goat snp12147-scaffold145-640752 1 151602067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388356 Affx-122969342 AX-123258714 1 149282601 CCTCGCTCTCCTTCCAAACTTGTCTTTTCTCGGGG[C/T]GACCCCAGGGTGCTGACAGGGAAATTTGGATGAAG Y 2 1 2 1 101000 r 74 goat snp12146-scaffold145-597147 1 151646075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421372 Affx-122944044 AX-123291719 1 149365535 TTCCCACAACCATGAAAGGCATCATAGCTCCACAG[C/T]ATCGCAATCCCCGTCCAGATGGTCCAGCCCTGTAG Y 2 1 2 1 101000 f 74 goat snp12144-scaffold145-514213 1 151727335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774748 Affx-122955242 AX-385261882 1 149414958 GAGAAAATTAGCATATTTCAATTTACAGATAAATG[C/T]GAAATTAGCTTATTGATTAAGGGCTAAATTAGTTT Y 2 1 2 1 201000 f 74 goat snp12143-scaffold145-464790 1 151776312 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379857 Affx-122975799 AX-123250215 1 149450102 ATGACCCCCATCAGTCAGGGAACTTTGACTGGAAG[C/T]GCGATAACCTTTGTGGATCCATACTTCACCGAGTC Y 2 1 2 1 201000 r 74 goat snp12142-scaffold145-429646 1 151811805 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439631 Affx-122930620 AX-123309968 1 149494557 CTCTGAATTGAAAAGGATCGAATAGTGCTATTCGG[C/T]GTGTCCAAGGACAAGTAGCAGCTCCATCCCCTGGC Y 2 1 2 1 101000 f 74 goat snp12141-scaffold145-385191 1 151856454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794626 Affx-122927704 AX-385281587 1 149525918 TTCTTTAGGGAGTTTGGCTCATGTTGAGTTTGGGG[C/T]GATTAAAAACAGTAAGGAGTGAACACGGAGTCTCC Y 2 1 2 1 101000 f 74 goat snp12140-scaffold145-353830 1 151889129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400884 Affx-122959754 AX-123271237 1 149584567 GTATTGGATGGGGCTGATATAGAATGTTTCCCTCA[C/T]GGCACCAAGTTCTGCTGGGTAGTGCTACCCTAAGA Y 2 1 2 1 201000 f 74 goat snp12139-scaffold145-295181 1 151949029 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802616 Affx-122944609 AX-385289517 1 149620463 ATTCTGGATTTTTTTCTCCTAGAAATCATAAAGAA[G/T]AATACCATTATCTTGACCACAAAGGAAAAAAGTTT K 2 1 2 1 101000 f 74 goat snp12138-scaffold145-259285 1 151985193 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427966 Affx-122939192 AX-123298309 1 149652912 GGGAAGTCAAGACAGTCTGCACGCTGACCTCTATG[A/C]GAGGCACATACAGGGTGTTCCAGGCCATCAGCTGG M 2 1 2 1 101000 f 74 goat snp12137-scaffold145-226836 1 152017708 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408753 Affx-122953398 AX-123279104 1 149703271 AAATTGAGAAAGGGCTTATGTGGACACAGCAGTAC[A/G]TTGCCATCTCACCAAACAAACAAGTTCGTTAAGAA R 2 1 2 1 201000 r 74 goat snp12136-scaffold145-176477 1 152068247 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793245 Affx-122939786 AX-385280223 1 149736946 GTTCTGCAACATAAACCCAGTCAGGACTGTCACTG[C/T]GGTTTTCAGGATCTTAAATAAGTCCCTAGGGTACG Y 2 1 2 1 101000 f 74 goat snp12135-scaffold145-142802 1 152102117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377159 Affx-122978217 AX-123247518 1 149805738 CAGTGGTTGCCAGATAGGAATGGGGGCCCAGTGTT[A/G]CCTGATCATCGGATTTAAAAAAAATAAAAATTTTG R 2 1 2 1 101000 f 74 goat snp12134-scaffold145-74010 1 152170948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272595 Affx-1111832844 AX-519546308 1 149807157 ACACATTGTGGGGACAGCCGGAAGAAAAGTGATGC[A/G]TCCTTTCCCTCTTTCGTGGACTTTCCAGGTGGCTC R 2 1 2 1 201000 r 74 goat 1_149807157_AF-PAKI 1 149807157 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768079 Affx-122919685 AX-385255283 1 149924303 AGAGGTCCAGTGTAAAACTTAGTTTCCTGAGCCAA[C/T]GGGGAAGAGCGCCAAGTATACCCGAAATCCAGAAG Y 2 1 2 1 101000 f 74 goat snp37579-scaffold46-3395473 1 152300137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802075 Affx-122951891 AX-385288979 1 149960852 GTCTAGGTTTTCATTCTGTGTATCAGAGAGCAATA[C/T]ACTCCTGTAAAATTAAATATGACAGCTTCTCTGTT Y 2 1 2 1 101000 r 74 goat snp37578-scaffold46-3358924 1 152336132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773790 Affx-122948830 AX-385260930 1 150017950 TGGCTGCCCTAGCAAATGAATATATTGGGCTAATG[C/T]ACTTTCCAGACACTTTGTGGAGAATCACAGACTGT Y 2 1 2 1 101000 f 74 goat snp37577-scaffold46-3301826 1 152393440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776290 Affx-122973693 AX-385263418 1 150047598 AAACGTAGATTTAAGAGTGACTGTGATGAAGTTCC[A/G]TATCAATGTATGAAGAAAGTTGGAAACCAGTTAAA R 2 1 2 1 101000 f 74 goat snp37576-scaffold46-3272178 1 152423873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781867 Affx-122972998 AX-385268949 1 150083903 TTCAAAAGCCATGTGTTAACAGAAACCATTTGACA[C/T]AGGTTACAGCATCATAGTTTCTGAAATCTTTGGCA Y 2 1 2 1 101000 r 74 goat snp37575-scaffold46-3235873 1 152460114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276827 Affx-1111835606 AX-519550336 1 150129185 GAGTCCGTCATAATGGAACTGGGCAGGTTGGTAAC[A/G]GAGATGTGATCCTTGAAAGCTATTTAAAATTTTGA R 2 1 2 1 101000 f 74 goat Random2.2K-145 1 150129185 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398599 Affx-122961489 AX-123268954 1 150136519 AACATACATTCCCAAATAGCCTTCCAGAAAGACCA[C/T]AGCAAAATTCAGTCCCTCCAGCAGAAAAAGCATTC Y 2 1 2 1 101000 r 74 goat snp37574-scaffold46-3183257 1 152512656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276975 Affx-1111835613 AX-519550483 1 150146496 AGCTCCTTTCAACCCTGCTTGGGACTCCGTTTGAG[A/C]TGAGTTCCGATAAATTCACCGTTCGTCCTCCTCCT M 2 1 2 1 101000 r 74 goat Random2.2K-146 1 150146496 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383192 Affx-122972793 AX-123253550 1 150190500 CCTTGAAATCCATAATTAGAGATTAAATCATTTAT[A/G]TACGTTCTGATACTGTGACGTTCTCCCAAACATTC R 2 1 2 1 101000 r 74 goat snp37573-scaffold46-3129276 1 152567105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392587 Affx-122966062 AX-123262944 1 150223746 AGTGTTTTTCAAGAAAAAGTGGTCAGCCTTTGAGC[C/T]GCTTAGTGACCCATGGCCTCTGATTGCATGACTCC Y 2 1 2 1 101000 f 74 goat snp37572-scaffold46-3096030 1 152600356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414704 Affx-122949276 AX-123285053 1 150265965 AGTACAGACATTCATGCCTAGGTACTATCCTTGGT[A/G]CTTAAATGCAGTTGATCCTTGAACAGCATGGGAAT R 2 1 2 1 101000 f 74 goat snp37571-scaffold46-3053811 1 152642766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393284 Affx-122965445 AX-123263640 1 150312623 GATTTACTGTTCCCTTCTCCAGTGGACAACGTTTT[A/G]CCAGAGCGAAAGTACCTGAAGAAATACTGTGCCGA R 2 1 2 1 101000 r 74 goat snp37570-scaffold46-3007153 1 152689514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413674 Affx-122950107 AX-123284023 1 150344609 CCTTTGTGGCTATAGGTGCAGTCTCAGGTGGGAGG[C/T]GCCCTTGAAATTGTGTGATGTTGGTGACCGAGGCA Y 2 1 2 1 101000 r 74 goat snp37569-scaffold46-2975167 1 152721678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407798 Affx-122954563 AX-123278149 1 150373752 TCTAGCCTAATATAAAATTCAGTGAATGCACTCTC[C/T]GTGGGCTAGAATAAGACGCACCTGAAAATGTTGTG Y 2 1 2 1 101000 r 74 goat snp37568-scaffold46-2946024 1 152751405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384237 Affx-122972368 AX-123254595 1 150433892 TGAAGCTCACAGTGAGAACCATTGTGGGGACTGAT[G/T]ATGTTTGCACATATGCAGATCTTCCTTGCTGTTTT K 2 1 2 1 101000 r 74 goat snp37567-scaffold46-2885884 1 152811692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449925 Affx-122922918 AX-123320260 1 150472573 ATAATACTTAGTTTAGGCTTTAAGATCTTCTAAAC[A/G]TTATCTTTTACAAAGGATTCCCCATTATTTTCTGC R 2 1 2 1 101000 r 74 goat snp37566-scaffold46-2847203 1 152850179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416667 Affx-122947590 AX-123287015 1 150508565 TAAGTTACCTGGGGCTTAGCTGTGATTTCATTCCC[A/G]TCTCTGTGCCTGGGCAACTTGCTGGCATCTGCTCC R 2 1 2 1 101000 f 74 goat snp37565-scaffold46-2811211 1 152884271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436732 Affx-122932303 AX-123307070 1 150552092 CATTGCCCCCTCCCTGCACGTGTTAATCCCCATCC[A/G]TGCTTTAAGACCCAGCTTCCGTGTTACGTGGGCTG R 2 1 2 1 201000 r 74 goat snp37564-scaffold46-2767684 1 152927226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790895 Affx-122942157 AX-385277892 1 150592421 GTTAACTGAGTGCTTGTTTGGACCTCCTGAGCCAA[C/T]GTTCTCAGATCTCCCAGCTGTTTCCACCTAAGTCG Y 2 1 2 1 101000 f 74 goat snp37563-scaffold46-2727355 1 152968447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770240 Affx-122942170 AX-385257406 1 150622162 CAAAACTGGTTATTTTTCCTCAAGGCAATAAAGCT[A/G]TAACCTTGTGTGTTATCTTCTCCATAAACAGAACA R 2 1 2 1 101000 f 74 goat snp37562-scaffold46-2697614 1 152997668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450713 Affx-122921883 AX-123321047 1 150665603 CCATCTTGATCAAAGCTCTCTACATGCTAATTATT[A/G]TTCTGATTAATATTGTAATTATTATTGAAGAAGGG R 2 1 2 1 101000 f 74 goat snp37561-scaffold46-2654173 1 153040045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432964 Affx-122935278 AX-123303305 1 150724692 GCATAGAGCAAGAAGAAAAGGTGCCCGAGTCCAAA[C/T]GTCCCAGGAGACATTGAAGGCACGCGTGATCAATG Y 2 1 2 1 101000 f 74 goat snp37560-scaffold46-2595084 1 153099091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277003 Affx-1111835627 AX-519550511 1 150824408 CTTCCCGTGGCAGAGGTACCCTCTCAAAGAAAAGC[A/G]TTTTAGGTAATTCATGTATAAATTAAAAGTGTAAC R 2 1 2 1 201000 r 74 goat Random2.2K-149 1 150824408 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791857 Affx-122927155 AX-385278847 1 150843914 GACATCAGCTGTGTCATGCTGGGCATTCCAATACT[C/T]GGAGTGCGTTGGCACATTTAAAGGACTTGGAGGCT Y 2 1 2 1 101000 r 74 goat snp37557-scaffold46-2475862 1 153217991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381799 Affx-122974285 AX-123252157 1 150876734 TTTTTTCTGCCCTGAGATTCCTCTTCTTCTGAAAG[C/T]GGCTTTGTTCCCACAGTCCAGCTGTGTGATTTCCA Y 2 1 2 1 201000 r 74 goat snp37556-scaffold46-2443042 1 153251756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779990 Affx-122973328 AX-385267089 1 150914623 AAGAGGTCAGAGTCAATCTCAAAGACGTTGGCTTA[C/T]GTGCTACTCATAAACATTGCTTAGAGCCAACATTT Y 2 1 2 1 101000 r 74 goat snp37555-scaffold46-2405153 1 153290013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375979 Affx-122978430 AX-123246338 1 150963379 ATGGTGGAATTTTCCACGGGTTATGTGATGTGTGA[C/T]GACATCATCACTAATTAATGTGTGCTCAGATACTC Y 2 1 2 1 101000 f 74 goat snp37554-scaffold46-2356397 1 153339072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387552 Affx-122970291 AX-123257910 1 151012727 GGTCATTTGCAGTGTCTAACGTCCTGTCCTTGCAG[C/T]TGGGCCTCAGAACCCCCGGTGGTTACCTGAGTCTC Y 2 1 2 1 101000 f 74 goat snp37553-scaffold46-2307049 1 153388796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429805 Affx-122938194 AX-123300146 1 151098952 TACCTGCTAAATGAGGAACGCTCAGCTGCACTTTT[C/T]TCCTGAATGTGGCGTGGTTGCAGCTCGTTATTTTG Y 2 1 2 1 101000 f 74 goat snp37551-scaffold46-2220824 1 153474222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435771 Affx-122932873 AX-123306110 1 151225269 TGCCCAAAAGAAAGACCTTATTTCTCAGACTCCCA[C/T]GTGACTGAATTCTGACCAGTGAGGTATACGCAGAA Y 2 1 2 1 101000 f 74 goat snp37548-scaffold46-2094507 1 153598765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397493 Affx-122962071 AX-123267848 1 151256141 GGGGCAGATTCTTTACCAGCTGAGCCACAAGGGAA[G/T]CCTGTAGTAAGGGCAGTACTCGCTGAATAAACATG K 2 1 2 1 101000 r 74 goat snp37547-scaffold46-2063635 1 153629960 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395684 Affx-122963743 AX-123266039 1 151305295 TGGTCAATGCCTGACGACCCTAGGGGGTGTTCTCT[C/T]GCCCACAAGCCTGACCACATTCTCCTGCTCTGGGC Y 2 1 2 1 101000 f 74 goat snp37546-scaffold46-2014481 1 153679766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378849 Affx-122976528 AX-123249208 1 151342083 TGGCATCTCAAGTTGCCCTGGGTGCCCCAGCGCAG[C/T]GACCAGGAGCCAGGAAGGGAAGAGCTGCCTTCATC Y 2 1 2 1 201000 f 74 goat snp37545-scaffold46-1977693 1 153716818 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785112 Affx-122950911 AX-385272159 1 151371167 CCCTCCGTGCTGACCAGGGGCTCTCTGCGGTCTTC[A/G]CTCAGGCCCTCTAAAGGTTAGAGGCCTAAAGGTTA R 2 1 2 1 202000 f 74 goat snp37544-scaffold46-1948609 1 153745989 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452938 Affx-122920184 AX-123323271 1 151403609 TTACCACGACTGTCCAGTAGGTATTATTATTCTCA[C/T]TTTGCAGAGAAGAAAGCTGAACTTAAAAGACACTG Y 2 1 2 1 103000 r 74 goat snp37543-scaffold46-1916167 1 153778150 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401140 Affx-122959380 AX-123271493 1 151440752 TGTAAAAGGATAATTTGGAGTGAAGAAAACAGAAC[A/G]TCTAAAGAGAATTTAAGACAAGATGGCACCACACA R 2 1 2 1 101000 r 74 goat snp37542-scaffold46-1879024 1 153814773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792364 Affx-122967377 AX-385279345 1 151500405 CCAGTTACGAGTACCTCCTAAATTTCTGGAACTAA[C/T]GTGTTAGGAAAATCTATAGATTTAACGTAGCCCAG Y 2 1 2 1 101000 r 74 goat snp37540-scaffold46-1819371 1 153874172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448322 Affx-122924146 AX-123318658 1 151559875 GGCTGACAGAATTTTTAAAATTCTCCAGATGGTCT[C/T]GGGTAATTAAGGTGGTAATAACAAGAGTTCTCTAT Y 2 1 2 1 101000 r 74 goat snp37539-scaffold46-1759901 1 153934390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401360 Affx-122959244 AX-123271713 1 151614435 GAATTTTTTGTTCTCAGTGCTCTGCTCAGTGACAG[C/T]ATACTGCTGATGAGAACTTTTAGGGTAAGTCCATT Y 2 1 2 1 101000 f 74 goat snp37538-scaffold46-1705341 1 153967041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402783 Affx-122958301 AX-123273136 1 151669166 CTGTAACTTTTGTACCGCGTCTCGTTTTCAAAGCC[A/G]CGTGCAGAAGCGCTGCTCTCGCTCCTGGAAGCTCT R 2 1 2 1 101000 f 74 goat snp37537-scaffold46-1650610 1 154022794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423904 Affx-122942282 AX-123294250 1 151701785 TTGCTTCCAAGGTCAGGGACACGGATCCCTTGAGC[A/G]TAGAACACCACTGTATATGGTTTCAGTTCCGCCTC R 2 1 2 1 101000 r 74 goat snp37536-scaffold46-1617991 1 154055390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435541 Affx-122933395 AX-123305881 1 151748940 TGCATATTATATAGAGGAAAATATATTTTGCTTTA[A/G]TTTAATATCCTTACATGTACAACCCACTAAGAGTC R 2 1 2 1 101000 r 74 goat snp37535-scaffold46-1570836 1 154103353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427755 Affx-122939247 AX-123298098 1 151789185 GGAGTAAAGTGCAGTCTGCAGGCAGCATCCTAATC[C/T]GCTTTGCACTAGAGCTGCAGTCTCTTTTCCTAGGT Y 2 1 2 1 101000 f 74 goat snp37534-scaffold46-1530591 1 154143950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793892 Affx-122971607 AX-385280861 1 151837502 TCCTGTACTTTAAATGTTGATCAATTAAGTTGAAT[A/C]GGAATTATTACCTTTGTTTCTATCAAGTAAAAATG M 2 1 2 1 101000 f 74 goat snp37533-scaffold46-1482274 1 154192252 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276878 Affx-1111835634 AX-519550387 1 151856897 ATGAAACCCACGAGGAATTAATGGTCCAGCTCAAC[A/C]CCCGCCTCCCCCCCCCCCCACCCCCCGGCCGGTGG M 2 1 2 1 101000 f 74 goat Random2.2K-150 1 151856897 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440922 Affx-122929024 AX-123311259 1 151904749 GCAGGGTTGTTGATGTGAACATTAGGCCTTTTGAT[C/T]TCTGCAGCTGTGTTCTAGGTGCTTAGAATACACCA Y 2 1 2 1 101000 f 74 goat snp37531-scaffold46-1415027 1 154260025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379178 Affx-122976314 AX-123249537 1 151991828 TATATCCATCAAATCAATTTTTAGGAAAGTTTTTC[C/T]CTGTCAGTAATACTTACTGATTGTCCTTCACTTGC Y 2 1 2 1 101000 r 74 goat snp37530-scaffold46-1327948 1 154347914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392405 Affx-122966211 AX-123262762 1 152035178 TTAGTTCACAGCAGTATCTCTGATCCTTCCACAGC[A/G]TTCTTTCTTGTCTCCACTTCTCCGTATTTACACGT R 2 1 2 1 201000 r 74 goat snp37529-scaffold46-1284598 NW_017214946.1 17626 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769473 Affx-122939640 AX-385256644 1 152064114 GTAGACTAGGGCAGCAGATTTAAACAGAAAACTCT[C/T]GTTCCTTGCAGTTCAGGTTTTTTCTCTCCTCTCCT Y 2 1 2 1 101000 f 74 goat snp37528-scaffold46-1255662 1 154420128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377108 Affx-122978255 AX-123247467 1 152094847 CTAGTTTTTGAGAGGAGGCAGCAGGGGAGCCTGCC[A/G]TGGGGATAGCAGGCGTTTATTGAGCACGTACTTCG R 2 1 2 1 303000 f 74 goat snp37527-scaffold46-1224929 1 154450823 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791521 Affx-122938838 AX-385278512 1 152174942 ATGAACTAAGTGATATAAGTCATGTTGCTCATCGA[C/T]GCTTTTCTTGGCATATTCTAAGCCTGCACCTAGAA Y 2 1 2 1 101000 f 74 goat snp37525-scaffold46-1144834 1 154531335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391293 Affx-122967342 AX-123261650 1 152216029 CCTTGCTTTTCTTCTTTTCCGTGTGATAACGTTTA[C/T]GTGTATGAATTTCCTCTGCGTGCGGTTTTGGTGGG Y 2 1 2 1 101000 r 74 goat snp37524-scaffold46-1103747 1 154572098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439802 Affx-122930490 AX-123310139 1 152247982 CTGCGCACAGCTTCTGAACCTGAAAAGAGAGCGCA[C/T]GAAAGTTAGGGAATCAGAGTGTGTTATAAAAGTAA Y 2 1 2 1 101000 r 74 goat snp37523-scaffold46-1071794 1 154605226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432498 Affx-122935582 AX-123302839 1 152286686 ACTGTGTTCTCATCCCTTTCTTCAGCAAGCATTCT[A/G]TCCAGTGAATTCTTTATTTCTTCTCACTTAAAACT R 2 1 2 1 101000 f 74 goat snp37522-scaffold46-1033090 1 154645750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798710 Affx-122957134 AX-385285641 1 152329746 TCAACTGCCATCCTAATCTAGGCAACATTCACAAA[C/T]GTCAGATTTTTTAACGTAAAAATTACTGTAAGATA Y 2 1 2 1 101000 f 74 goat snp37521-scaffold46-990030 1 154688706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272545 Affx-1111832845 AX-519546262 1 152361551 CTGCACGTGGGGGTGTGGAGCGGGGTCGGCACTTC[A/C]TGCTGGTAGCCAGACGTCCAGAAGTCTCCAGGGTC M 2 1 2 1 202000 f 74 goat 1_152361551_AF-PAKI 1 152361551 T G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390573 Affx-122967202 AX-123260930 1 152376840 TTGTCACGCCTGAAACAAGGGACCTGGACTAGACC[G/T]CTGGTCGGGGAACTGGATCCCATATGCCGCAAGTG K 2 1 2 1 101000 f 74 goat snp37520-scaffold46-942936 1 154735424 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277039 Affx-1111835647 AX-519550546 1 152417645 CGAGTAACTGACCAGCACTCCCACGAGTCTAAGTC[A/G]ATTGCCAAGAAGTCCGTTTTTCTCACCGGGACCAC R 2 1 2 1 101000 r 74 goat Random2.2K-152 1 152417645 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395303 Affx-122964064 AX-123265658 1 152440649 AGGCTCCCGTCTGTTGGCATATTTGTGGCATGGAT[A/G]TTGCTGGAATTCTCAGAGTGCTGGGGTGCAGGCAA R 2 1 2 1 101000 f 74 goat snp37519-scaffold46-879127 1 154799871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769944 Affx-122927077 AX-385257113 1 152471353 AATCTGTTATTTGGGAAAAGCCAAGTTCAACGAAC[A/G]TAGCAGTAGTCTTGACTTAACAGTGTCTGGAGAAT R 2 1 2 1 101000 f 74 goat snp37518-scaffold46-848423 1 154830369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803919 Affx-986696580 AX-385290627 1 152480696 AGATTGGGAGCGGTCTGTGACCTTGTGTGTGAGCT[A/G]ACTGGTGAGCCAGAAAGGGGTGGGCATGGAGGAAG R 2 1 2 1 600010 f 74 goat 1_152480696 1 152480696 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 38398038 Affx-122961764 AX-123268393 1 152503967 CTCTTTTGTTTGCTTGCTTGCTGGCTTCCTATCTG[C/T]ACCCTGACCCCACCCCAGTAAAGTTCTTACTTTAC Y 2 1 2 1 303000 r 74 goat snp37517-scaffold46-815809 1 154863243 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772367 Affx-122977300 AX-385259520 1 152534794 AGATTCAAGAAGTAGGGGGGAAAAGCTGGGAAAGA[C/T]GAAAAAGATAGGGAGCCATTATATTAAGCAAAATG Y 2 1 2 1 101000 f 74 goat snp37516-scaffold46-784982 1 154893878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773757 Affx-122958504 AX-385260897 1 152566524 CAACTCTTTCTTGATTCTTATTGATAACTGTGTAC[A/G]TGAAAATTCTAGCTTTTGATGTGGTCTACATTGTA R 2 1 2 1 101000 r 74 goat snp37515-scaffold46-753252 1 154925648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407279 Affx-122955336 AX-123277630 1 152626228 CAGCAACAATGAGTCAGCGATTTGGACTCTGAAAG[C/T]TCTTTATCTGCAGAATGGGGAGAGTAAAACTTGCT Y 2 1 2 1 101000 f 74 goat snp37514-scaffold46-693548 1 154985531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398728 Affx-122961832 AX-123269083 1 152669904 ATGTCTTCCGAGAAAGCATTTACAGCTTCTGTTTA[C/T]GTGGCATCAGAGCCACCTGAAGACTTGTCCTCTGT Y 2 1 2 1 101000 f 74 goat snp37513-scaffold46-649872 1 155035179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380770 Affx-122975114 AX-123251128 1 152701473 GATAACAGGTGGCCTGGGCTGGCCCTCACCACATG[C/T]ACTATGGAGCAGAGCCTTGTTCGGAAGCTGGTAGA Y 2 1 2 1 101000 r 74 goat snp37512-scaffold46-618303 1 155067257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382077 Affx-122974912 AX-123252435 1 152733464 TTGTTCTTCTCCGACTTATGTCACTCAGTATGACC[A/G]TCTCTTGGCTCATCCGTGTTGCTGCCACGGGCACT R 2 1 2 1 101000 f 74 goat snp37511-scaffold46-586312 1 155099731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417208 Affx-122947305 AX-123287556 1 152764079 CCCTTTCCTGCCAAGACTCATTCATCCTTATCCAC[A/G]GACTGGATCCTACCCCTTACAGCTTCAGCTATGGT R 2 1 2 1 101000 f 74 goat snp37510-scaffold46-555697 1 155130941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402402 Affx-122959014 AX-123272755 1 152811098 TTAAAGTCTTAGCAGGAAACCTCGGGGTGCTGCTC[A/G]TAGGAAGCCCACTAACAGAGGCAACTAAAAACCAA R 2 1 2 1 201000 r 74 goat snp37509-scaffold46-508678 1 155178697 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779218 Affx-122952310 AX-385266322 1 152867863 TAATGAAAGCATTGCCTGTTGACAACATACACTGT[C/T]CTATCTCTACTGAGAAATGACTTCGTTCTTAACTC Y 2 1 2 1 101000 f 74 goat snp37508-scaffold46-451913 1 155231686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419686 Affx-122945931 AX-123290034 1 152911628 CATGTGTTTCATGGACCATGATAAATTGCCATTGC[A/G]TTGTCATTGAATCTGTTTTGCCTTTTTTCAGTAGT R 2 1 2 1 101000 f 74 goat snp37507-scaffold46-408148 1 155275220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449289 Affx-122923017 AX-123319624 1 152950925 ACCTTTATTCTTGTGCTGTGTGCAGTGTTAACATC[A/G]TCTCCTGCTCTCCATATGATCTGTTCCTGGGGGTG R 2 1 2 1 101000 f 74 goat snp37506-scaffold46-368851 1 155314464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449523 Affx-122922607 AX-123319858 1 153004715 ATTTGTGGCCAATTACAATATTTCATTAACTTCTT[A/G]ATTGGGTAAGTATTTAATGTATTCCTACTATGTGC R 2 1 2 1 101000 r 74 goat snp37505-scaffold46-315061 1 155367936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780746 Affx-122938074 AX-385267836 1 153101257 CCACAGTATATGAAAATGCCTGAGTTTCATTGTAC[A/G]TTTGTACTTTTGCTCCAAGCAATGACTAAAAAAGC R 2 1 2 1 101000 f 74 goat snp37503-scaffold46-218519 1 155464693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276919 Affx-1111835654 AX-519550427 1 153231240 CGCTGCTTGGGTTTTCTTGATAGGCAACACGCAGC[A/C]TAGCAGAATGCTGGCCTTTGATGCCCTGCCTGCAG M 2 1 2 1 201000 f 74 goat Random2.2K-153 1 153231240 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791352 Affx-122961857 AX-385278345 1 153236133 AACGAGGCCTTTGTGCTTTCCAGGTTAAGGAGAAA[C/T]AGAAAGTAGATTTAGGACGCAAGGAGGCTCCATGG Y 2 1 2 1 201000 r 74 goat snp37500-scaffold46-83643 1 155601607 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453516 Affx-122919808 AX-123323849 1 153328131 ATCCTCAATCAACGAAGGCTTTGAACTTTAAAGAC[A/G]CAAACTGGGTCATATGGAAATGACAAGATCCTCCC R 2 1 2 1 101000 f 74 goat snp59780-scaffold993-8256 1 155693663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783754 Affx-122960173 AX-385270810 1 153376351 TTAAAAAGCAACAACACACGTACTTTTTAACAAAG[C/T]ACAAGTAGGCATTCAGCTCTCCAGATTCATCATCT Y 2 1 2 1 101000 r 74 goat snp59781-scaffold993-56476 1 155741583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401839 Affx-122959437 AX-123272192 1 153410264 GCAGATAATCATTCACAGTTCTGTGGGGCTTGGTC[A/G]TTCTTGAAATGATCAATGAGAGCAAGCTAAATACT R 2 1 2 1 201000 r 74 goat snp59782-scaffold993-90389 1 155775871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447267 Affx-122924942 AX-123317603 1 153449969 CCTCCTGCACAAACTGGACCCCACGAGGACAAACT[A/G]GAGCCGTGTCTGTGTCTCCCTGCCCCCAGTCTTGA R 2 1 2 1 101000 f 74 goat snp59783-scaffold993-130094 1 155816589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378240 Affx-122976904 AX-123248599 1 153500331 GGAAGAGTTGGTGGTCGTGAAGGTTGCTCAGTCAC[A/G]TCCGACTCTTCGTGACCCCATGGCCTACACAGTCC R 2 1 2 1 103000 f 74 goat snp59784-scaffold993-180456 1 155864994 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451281 Affx-122921308 AX-123321614 1 153539790 TACTTGAATTATTCAGGTATTCAGAAAGGGAACGC[C/T]GATGTCATTAGCATAGAGAAAGTCATGATATAAAT Y 2 1 2 1 101000 f 74 goat snp59785-scaffold993-219915 1 155904219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796398 Affx-122939635 AX-385283348 1 153572961 AAATAAAACATATTTCATAAAGGCTATGAAAACAC[A/G]ATAATGAGATAAATTATTCTAGTCATCTTGCTTTA R 2 1 2 1 201000 r 74 goat snp59786-scaffold993-253086 1 155936546 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448269 Affx-122924187 AX-123318605 1 153602983 GCTGCAGGCCGTGGGGCTGCAGAGTCGGACATGAC[C/T]GAGCGACTGAACGCCAGCAATTCAGAATACTTGCA Y 2 1 2 1 103000 r 74 goat snp59787-scaffold993-283108 1 155966732 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407052 Affx-122954928 AX-123277403 1 153648499 TCAGGCGTTTTATCCTCAAAGTTCATCTGAAAGAG[A/G]GGGTGGTGGTGGAATCTCACACTTAGCCAGTCACT R 2 1 2 1 101000 f 74 goat snp59788-scaffold993-328624 1 156012971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414143 Affx-122949699 AX-123284492 1 153680889 AATCAACTTAGCTCTGACTCACCCTGCTGTGCTGC[C/T]GGGAAATTTAATCACAGTTACGACGTGATTGTAAC Y 2 1 2 1 101000 r 74 goat snp59789-scaffold993-361014 1 156045121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792854 Affx-122941862 AX-385279832 1 153722582 TAGGTTAAAGGAAATTAAATCAGTTGAAAGGGAAG[A/C]AGTGTCTGTTAACGTAACTGGAAGTATTGGCACAT M 2 1 2 1 101000 f 74 goat snp59790-scaffold993-402707 1 156087056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429664 Affx-122937660 AX-123300005 1 153794202 AAACTTGAAATTTTATAAATTTCATTTTCATGATT[A/C]ACCTTAACCTTGACCATCTAGTTTTTAATAGAATT M 2 1 2 1 101000 r 74 goat snp59792-scaffold993-474327 1 156159567 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377466 Affx-122977513 AX-123247825 1 153824356 GCTGTTCCGTGGAAATGTTGGCAGAAACACACAGC[A/G]CTGCATAGATGTCTCCCGCGAGCGGCTGTCTGTAC R 2 1 2 1 101000 f 74 goat snp59793-scaffold993-504481 1 156190026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787863 Affx-122924287 AX-385274886 1 153859829 TCGTTAATTCAGTTTTGCCACACTTGTAGTTACTG[A/C]ATTGGAACAGGTCATTATACATTAGAAGGTGGTGC M 2 1 2 1 101000 f 74 goat snp59794-scaffold993-539954 1 156225837 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384677 Affx-122972130 AX-123255035 1 153901676 TTACGTATAGAATGGGCAGGCAACAGAGTCATAGC[A/G]TAGCACAGGGAATCTAATCTCCTGTGATAAATGAT R 2 1 2 1 101000 f 74 goat snp59795-scaffold993-581801 1 156268114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383449 Affx-122973461 AX-123253807 1 153933663 CTGCAAGAAGGCGATGGTCAGGCTGAGAACTCAGG[C/T]GTCCTGACCTGCTGTGATTTTCCCCTTAGCATCAA Y 2 1 2 1 201000 f 74 goat snp59796-scaffold993-613788 1 156299930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788459 Affx-122957966 AX-385275476 1 154032197 TTTTTTCTATTTTAGGCAAATTTGACTTTTAAAAA[C/T]GTTTGACAACTGAAAAACGAATTGAAGCACCAGAT Y 2 1 2 1 201000 f 74 goat snp59797-scaffold993-712322 1 156398759 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441450 Affx-122928768 AX-123311787 1 154075604 CTGTAGGGAACAGAAATGCCACTCTTAAGGGCTCA[A/G]CTGCAGACCTAGACAGCCTGGGACTGAGTGCTCAA R 2 1 2 1 101000 f 74 goat snp59798-scaffold993-755729 1 156442380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392193 Affx-122966290 AX-123262550 1 154108246 GGCTAAATGAAGATAGTAATTATTTGTATTTGGTA[C/T]GTATGCCCTCATGAACACCATTATATTTTAATTCA Y 2 1 2 1 101000 r 74 goat snp59799-scaffold993-788371 1 156475240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792438 Affx-122931699 AX-385279419 1 154137128 CGAGCGCATGCTTGGTGAATACTGTAAGCAAGTCA[A/G]TTCTGCTGGGCATTCTTTACCGATATTGTGGGCAT R 2 1 2 1 101000 r 74 goat snp59800-scaffold993-817253 1 156503947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411381 Affx-122952233 AX-123281731 1 154181285 CTGGCCATTCTCGGTAGGTCTTGTTGAAAAGCCCC[A/G]TGAAATTCTACTCTGAAGCATGAATTAAGGAGATT R 2 1 2 1 102000 r 74 goat snp59801-scaffold993-861410 1 156549080 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276928 Affx-1111835659 AX-519550436 1 154197112 ATTTGGAATTGACACTACTTTACTCCTTCAAGGAT[A/G]AATGCTTTAAATTGATTTCAATTTTTTCTTAATTG R 2 1 2 1 101000 f 74 goat Random2.2K-154 1 154197112 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408770 Affx-122953385 AX-123279121 1 154211708 TATTGGAATTTGATTCATTCCTCTGTATATAGACG[C/T]GTTTCCATATCCACAAAATAATAGAATGTTAGAAC Y 2 1 2 1 101000 r 74 goat snp59802-scaffold993-891833 1 156579680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431707 Affx-122936767 AX-123302048 1 154244153 AAAAGGTTTGTAGGTCAGGCTCAGAGGGCTTCCTC[A/G]TCTCCGAAATCTGGGTGACCCAGAAAGACTCCACG R 2 1 2 1 201000 r 74 goat snp59803-scaffold993-924278 1 156612798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790236 Affx-122960182 AX-385277240 1 154288393 GGAAGATGCAAGACCTGTATTCACTGATGTGAGCG[C/T]GCTACGTAAGCATATACTTTTCTCGCCCTCAAGTT Y 2 1 2 1 101000 f 74 goat snp59804-scaffold993-968518 1 156657013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799278 Affx-122925336 AX-385286208 1 154346557 CTATTAACCATGGAAGGATACGTTATAGGGAAGGC[A/G]CCTTAATGAGCTCAGAGACCTCCGTTTATCCTCAA R 2 1 2 1 101000 r 74 goat snp59805-scaffold993-1026682 1 156714363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410483 Affx-122952202 AX-123280833 1 154377317 GAAAGCCAATTCCTGCCTTACCGCCACTGGATTTC[A/G]CAGACACTGGGAAAGTCACGTAACTCTAGAAAGCA R 2 1 2 1 101000 r 74 goat snp59806-scaffold993-1057442 1 156745800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434977 Affx-122933836 AX-123305317 1 154407601 AGTGTTGCCCTGAGCTCTTTCATGTCATCGCCACA[A/G]AACTGTAAGCACACAGTTATCTCACCCTCGTCATC R 2 1 2 1 201000 r 74 goat snp59807-scaffold993-1087726 1 156776150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404740 Affx-122957236 AX-123275092 1 154444699 CTGAACTCAAATCTTCCAGGGTCTTCCGTGTTCTC[A/G]TGTGGACTGCCCCTTTCCAGCCCCTAAAGCAGCAT R 2 1 2 1 101000 f 74 goat snp59808-scaffold993-1124824 1 156814393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450654 Affx-122921973 AX-123320988 1 154477212 AGTTTCTTCCAAGAAATACTCCTGAAGAAAAAGCT[A/G]TAACAGATTTGTGTGTAGGAAAATGACAAGCTAGG R 2 1 2 1 101000 r 74 goat snp59809-scaffold993-1157337 1 156847333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395161 Affx-122964115 AX-123265516 1 154521982 CAGCATTTTCTCAAAAGCCTAAGGAGTGAGGTGTT[A/C]GTCACTCAGTCGTGTCTGACTCTTTGCAACCCTGT M 2 1 2 1 101000 f 74 goat snp59810-scaffold993-1202107 1 156892864 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444682 Affx-122926445 AX-123315019 1 154559993 GGAAAATCAGGTAATTACCAGTGAAATAAGGACTG[C/T]AAGCTGTAGATTACTCTCAGGAAACATTTTCTGAG Y 2 1 2 1 101000 f 74 goat snp59811-scaffold993-1240118 1 156930332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768257 Affx-122965483 AX-385255438 1 154607056 TTCTGAAGAATGTTAACCACTTTGGTCGTCCTGAG[A/C]CACATGCCAAGCCCAATTAATTTCCCAATTTTGAG M 2 1 2 1 101000 f 74 goat snp59812-scaffold993-1287181 1 156977663 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793068 Affx-122924125 AX-385280046 1 154639837 TACTTTGCAAGAGGTGTGTAATTAAGCAGGACCGT[A/G]TTTTTTCAGGTGTTCACGAATATATTTTTAACCCC R 2 1 2 1 101000 f 74 goat snp53422-scaffold809-29101 1 157013272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419393 Affx-122945609 AX-123289741 1 154677530 TAGCACTCTTCGTCTCCTGCCCTCATGAGACAAAA[A/C]TTATAAAGCGTTTTTAGGCTTGTACTGTGTAAAGA M 2 1 2 1 201000 r 74 goat snp53423-scaffold809-66794 1 157050828 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438876 Affx-122930744 AX-123309213 1 154784514 ATTTTTCAAAACATCTGTAACAATTTTTTTTAGAA[C/T]GGCTCTGCTGGGTGAAGGTATCCACGTTTAATTTG Y 2 1 2 1 201000 f 74 goat snp53425-scaffold809-173778 1 157154991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392521 Affx-122966114 AX-123262878 1 154815506 ACCAAAAAAGAACAGTCCAGCTAAAGAAGTGGTCT[C/T]GGTTTTAGAAGCAGCCACCTCATGTCCCAGTTTTT Y 2 1 2 1 101000 f 74 goat snp53426-scaffold809-204770 1 157185801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380017 Affx-122975597 AX-123250375 1 154898732 ACTCTCCCGCTCTTGGGCTTAGATCCAGAGAAAGT[A/C]GGAATTTGAGATGACAGGCAACTCCTGTTTTGTTT M 2 1 2 1 101000 r 74 goat snp53428-scaffold809-287996 1 157268892 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376026 Affx-122978397 AX-123246385 1 154928905 ATTAAGGACAACAAATTGTATTCTTTAGTTCTTGC[A/G]TCCTCTAAAAGTCTCAAAAGCAAACTTCATGCCTT R 2 1 2 1 101000 r 74 goat snp53429-scaffold809-318169 1 157299737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272599 Affx-1111832846 AX-519546312 1 155042557 TTGAATCTCCGTGTTTCTTCATGGTAACTGTGGAG[A/G]AAATGATCTTGGACAGAATTAAGTGGGCACAGGTG R 2 1 2 1 101000 r 74 goat 1_155042557_AF-PAKI 1 155042557 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350603090 Affx-1002479389 AX-413837288 1 155256793 ATATGAACACACACTCAGCCAAATGCAATTCATTA[C/T]AGGAACGCAGTTTACAATCATGTTGAGATATTATG Y 2 1 2 1 101000 f 74 goat 1_155256793_RH-map 1 155256793 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603186 Affx-1002479390 AX-413837372 1 155299798 GCAAGTCACACAAAATACATTCAAACTATATAATC[G/T]TGACTGAGGAATCAATATCAATCCCTTTGGTAAAA K 2 1 2 1 101000 r 74 goat 1_155299798_RH-map 1 155299798 G T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603188 Affx-1002479391 AX-413837374 1 155347735 CAATGTGATGGGTTAAATTGGGAATTTCCAAGATG[C/T]ATATTTTAATAGTTGCTTCACACTGGTGATGCCTG Y 2 1 2 1 101000 r 74 goat 1_155347735_RH-map 1 155347735 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603096 Affx-1002479392 AX-413837294 1 155384297 CTTGCTTCCCTGATGGCTCAGATGGGAAAGAATCC[A/G]CCTGCAAGGTGGAAGACCTGGGTTTGATCCCTGGG R 2 1 2 1 103000 f 74 goat 1_155384297_RH-map 1 155384297 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603098 Affx-1002479393 AX-413837296 1 155519634 TAGTGCCATTTAAATCTGGGTTGGTTTTCACTAGC[A/G]TTGCAGGAGAAGAAGGGTTTCAAAGCAGATGTATC R 2 1 2 1 101000 f 74 goat 1_155519634_RH-map 1 155519634 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603100 Affx-1002479394 AX-413837297 1 155559180 AGGTGGATCGAAATCACCACAGTGTACACCTTACA[C/T]GTATATGTTATATGTCAATAAAATCTCAGTACAGC Y 2 1 2 1 101000 f 74 goat 1_155559180_RH-map 1 155559180 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603102 Affx-1002479395 AX-413837298 1 155575234 GCAGCTGGTCTGGAGTCTACACTTTGAGACTAGAG[C/T]TTAGTTTATCACAAAGTTAAGAAAGATCACTCTGA Y 2 1 2 1 101000 f 74 goat 1_155575234_RH-map 1 155575234 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603104 Affx-1002479396 AX-413837300 1 155662486 ACAGCTGGCTAGGAGAAAATTCAGCAATTGCTTTC[C/T]AGGCCAGCTACACCCCCAAATTGTCAAAGCTTCTT Y 2 1 2 1 201000 f 74 goat 1_155662486_RH-map 1 155662486 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603199 Affx-1002479397 AX-413837384 1 155722058 GGGGGGCAGAGGGAGAGAAGCAGAGTCTAAGTGTC[A/G]TGACACAAGTGGAAGAAGAGTCATTTATTTAGTAG R 2 1 2 1 101000 r 74 goat 1_155722058_RH-map 1 155722058 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603108 Affx-1002479398 AX-413837304 1 155831223 ACCTTTTCTGCCTCCTGAGAAACCTGTATGTGGAT[C/T]AAGAAGCAACAGTTAGAACCAGACATGAAACAGCA Y 2 1 2 1 303000 f 74 goat 1_155831223_RH-map 1 155831223 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603203 Affx-1002479399 AX-413837388 1 155920183 TAAGAGGAAAATAATGACATTCCAGACATATCAAC[A/G]AAATCATGACCTCCTGTCACCTTTCAGAAACTCAA R 2 1 2 1 400000 r 74 goat 1_155920183_RH-map 1 155920183 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468277086 Affx-1111835673 AX-519550593 1 156353835 GGTCACAAAGAGTCAGACAGGCCTGAGCGACTCTC[A/G]CTCACTCACTCTGATTTTCTGCATCTGAGTTCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-156 1 156353835 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276964 Affx-1111835678 AX-519550472 1 157187893 CTCAAAAAAAACCCTCAAACTTAAGACAAAAACTG[A/G]TAACCTTCAGTTCAGCTCAGAAAATTACACACACA R 2 1 2 1 201000 f 74 goat Random2.2K-157 1 157187893 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320803509 Affx-986696087 AX-385290328 1 157379917 GTGGCGGATGTATTCCCTATGAAGAAGCTCTCTTC[A/T]TGTCAAAACCTTTCCAGACAACCAAATGTTTGATT W 4 1 2 1 600010 r 74 goat 1_157379917 1 157379917 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320765479 Affx-122974531 AX-385252974 1 TGAAGGGATGCATAGTGATTGACCTTAGGGCAGGA[C/T]GAAATTGGACAGAATTAATAGAAACCTTATATAAG Y 2 1 2 1 101000 f 74 goat snp19065-scaffold1917-222828 5 9412898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405647 Affx-122956581 AX-123275999 1 GGGCAGTGTGTTGGGGACATTGGCTAGGGTGTATG[A/G]CTAGGATGGGGCAGAGGGCTGAAGTAGCTTCTTGG R 2 1 2 1 201000 f 74 goat snp4303-scaffold1134-142270 25 36460678 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602987 Affx-1002479334 AX-413837230 1 CCAAAGCAAAAATAAGAAAAATAAGGGTATAACTC[A/G]A R 2 1 2 1 10000 f 74 goat "INRA-CHI1-PIS1;ins-del_011" 1 "0;129424781" A G ins-del_011 1 preexisting CNV preexisting not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region PIS 38441951 Affx-122928573 AX-123312288 2 1982 CAGAGGGAAAGCCACAGATTCCTTGATCCACGTGA[C/T]GGGAAGGGTGACACTGCTGCTAAAGCACGGGCGGA Y 2 1 2 1 303000 r 74 goat snp38036-scaffold474-1982 NW_017189900.1 3631 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271857 Affx-1111833160 AX-519545640 2 14356 TGGTGAAATCAGCAGTGTCCTCAGTCAGGACTGAG[A/G]TGTTACACCACTTGTTCTGGTGTAAGAACCTGGGG R 2 1 2 1 101000 r 74 goat 2_14356_AF-PAKI 2 14356 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804419 Affx-986696586 AX-385291004 2 14633 CGAGCCCCAGGCTAGCTGCTCCTGAACCTCATCCA[A/C]CATTCCTAGGTAAAACACCCGGATATGAGCAAAGA M 2 1 2 1 600010 r 74 goat 2_14633 2 14633 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38391700 Affx-122967516 AX-123262057 2 35123 GTACTTATAGATTCTCCACAGGGGAGTCAGTCCTC[A/G]ACTGGAGTGGGGGCATACAGTTCCGTTTTCCTCCC R 2 1 2 1 303000 r 74 goat snp38037-scaffold474-35123 NW_017189588.1 54672 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380593 Affx-122975258 AX-123250951 2 64813 GTTTCAAGAGCCCTTTTGGGGCTCAGGTAGGAAAG[C/T]GGGATTTCTCTTGAGACGAAGCACTGGAAAAGGGC Y 2 1 2 1 101000 f 74 goat snp38038-scaffold474-64813 NW_017189588.1 24983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397634 Affx-122962621 AX-123267989 2 100362 AGCTATACTGCTAACTTGTGGGAGAGGGTGTGCTT[G/T]TATTTTTCCCCAGGGTGCTGCATTACCAATTTGGA K 2 1 2 1 101000 r 74 goat snp38039-scaffold474-100362 NW_017197087.1 1590 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395609 Affx-122963814 AX-123265964 2 167028 ATGGACTTTGAAGAGTAGCATCTCTTCATGTAACC[A/G]AGATAAGAATATAAGTGAAAGGGGAAAGAAACTAG R 2 1 2 1 101000 f 74 goat snp38040-scaffold474-167028 2 136405967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399627 Affx-122961077 AX-123269982 2 231997 AGGAAAGCTAATAAGAAAACATCTGGTGGTCTCAT[C/T]AGCTCTTCCACAGTTTGTGGCTTTTGTTTTATGTA Y 2 1 2 1 201000 f 74 goat snp38042-scaffold474-231997 2 136340323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376614 Affx-122979046 AX-123246973 2 348087 GAGAACACTGAACCAAAAAACTCTGACTGGACCTC[A/C]CTCAGGACTGTATAGGAGAGCAGCCTCATCGTGTA M 2 1 2 1 101000 f 74 goat snp38043-scaffold474-348087 2 136224720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402538 Affx-122958471 AX-123272891 2 382955 TGCAGTGGACCACTTCCTACATTAACTCTGCATAC[A/G]TCATCAAATAAGATGAAAATTAAATAAAATTCTCA R 2 1 2 1 101000 f 74 goat snp38044-scaffold474-382955 2 136190741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377730 Affx-122977386 AX-123248089 2 427937 AAATCATAAATATAAGCTTATTTAGAGCATGGTTT[A/C]TTGATATCAGCCTAAAGAGATGTTAGGAACAAAAT M 2 1 2 1 101000 r 74 goat snp38045-scaffold474-427937 2 136144554 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799712 Affx-122927198 AX-385286640 2 483824 TTTTCATAGATCAGAAGTATGATGAGCGTGGCTGA[G/T]CTCTAATTAGGGCCTCAAAACAAAATCAATGTGTT K 2 1 2 1 101000 r 74 goat snp38046-scaffold474-483824 2 136086650 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276982 Affx-1111835687 AX-519550490 2 491452 TACTTTCCAAAGGCAGAGAAAACCCTTCTTGGAAG[A/G]GGGAGCCCCGAGTCCCGAGCTTACCGTTTCCATCT R 2 1 2 1 102000 f 74 goat Random2.2K-158 2 491452 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437046 Affx-122933103 AX-123307384 2 554191 GATTGCTTGCATTTAAAGTACCACTTTTATATCTA[C/T]AAGGGCACTCCAATTTTTGTGCAATCAATACATAT Y 2 1 2 1 101000 f 74 goat snp38047-scaffold474-554191 2 136014197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387733 Affx-122969745 AX-123258091 2 590016 TTCCTGTGAAAATAGGTCTCTCTCTCATGTGTATG[C/T]AACCTATCCTGGGTGACAGATTACAAAGCAAATTA Y 2 1 2 1 101000 r 74 goat snp38048-scaffold474-590016 2 135977152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378872 Affx-122976511 AX-123249231 2 631056 GACTCAGGCTGGCAGGCATAATCACGGATAACACA[C/T]GGACAAGTTCCAAAGACATGAATTTGGTGTTTGAG Y 2 1 2 1 201000 f 74 goat snp38049-scaffold474-631056 2 135936180 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428835 Affx-122938369 AX-123299177 2 683983 TTGTGGGAGGGGAGAAGCAATATAGTAGGGACCCA[C/T]GTGTTTAGCAGGGGACTCAGATGTAGAGGGGAATA Y 2 1 2 1 201000 f 74 goat snp38050-scaffold474-683983 2 135882177 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38413308 Affx-122950190 AX-123283657 2 772637 CACAGCATCACTTCTGATACAACCAGCTCTGAAGA[G/T]GTGGAGGAAAGCTGCTGAGAAGCAGCAAGCGTCCT K 2 1 2 1 101000 f 74 goat snp38051-scaffold474-772637 2 135792964 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427396 Affx-122940077 AX-123297739 2 814959 ATGTTGATTGTCTTTAATTCAATTAGGTTATTTAG[C/T]GAATTTCCACCTAGGAAATAAAGGGGCAGGGGCAT Y 2 1 2 1 201000 f 74 goat snp38052-scaffold474-814959 2 135749923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796907 Affx-122965299 AX-385283849 2 858281 AAGATAAAGTGAAGATTAGTTATGATTGTGAAATA[C/T]GTCAGTTGAAAGATCTATAGCACAGCTAAAATACT Y 2 1 2 1 101000 r 74 goat snp38053-scaffold474-858281 2 135706661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403915 Affx-122957478 AX-123274267 2 911352 CCATAAATGGCATGTGAAGGAAGACAGAGGAGGAA[A/G]AGAAGATTTGCCTAGTGCCCCTGGGAGGGTCAAAA R 2 1 2 1 103000 f 74 goat snp38054-scaffold474-911352 2 135653317 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397213 Affx-122962389 AX-123267568 2 1002815 GCCAGTTGCAATATTAGAATTCCTGTGCTGGTAGA[C/T]AGGCTAGGATGGAGCCTCTTAGCTAGGGGGATGGT Y 2 1 2 1 101000 f 74 goat snp38056-scaffold474-1002815 2 135565544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778054 Affx-122955885 AX-385265170 2 1055039 CTATGATGTGTGAAGGAATTCACTACCCAGTGACT[A/C]TCTTCTGATACAATGAAATGATGTATTAAAGAAAA M 2 1 2 1 201000 r 74 goat snp38057-scaffold474-1055039 2 135513238 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804421 Affx-986696588 AX-385291006 2 1090376 CGCAATAGTCACTGAGTCCGAGGGGAGCCGAGAGG[C/T]AGCCAACACCCCGGGAGCGGTCGCGACAGTCACTG Y 2 1 2 1 600010 r 74 goat 2_1090376 2 1090376 Ancestral_priority_1043 ancestry 0.454 neutral IMAGE 10K 10K ancestral 38421095 Affx-122944224 AX-123291442 2 1099357 GGGTCACTTAGACATTTTCTGGAATTCTGTTGTGA[C/T]GTAACTGTGGTATTTTGGGGAGCATCTCTTTGCAC Y 2 1 2 1 201000 r 74 goat snp38058-scaffold474-1099357 2 135468712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399307 Affx-122960530 AX-123269662 2 1133378 GTGAGAATAGCTAAGAATTCTTGAAGAGAGAAAGA[C/T]GTACTTTACAAGACACACGTAACTACTGTAATTAA Y 2 1 2 1 101000 r 74 goat snp38059-scaffold474-1133378 2 135434648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386621 Affx-122970231 AX-123256979 2 1165920 ATCCCAGCCGAACACCAGGGAGCGGGTGCTTTGCA[C/T]AGGCTTTAAAATAGAACTGCCAAGGCAGCTTGATG Y 2 1 2 1 101000 r 74 goat snp38060-scaffold474-1165920 2 135402296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767957 Affx-122976169 AX-385255172 2 1263606 AATAGGATTCTAGACCAGTGCCAGGTTTTGTACAT[C/T]ATTTTTAGTGAAACAGGTTTACAGACTACATTTAC Y 2 1 2 1 101000 f 74 goat snp38061-scaffold474-1263606 2 135304194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386532 Affx-122970731 AX-123256890 2 1355472 CTGCTGCATCACCACCCTCAGGTCTTGGCTCAAAT[A/G]CTCCTTCCTCAATGAGATCTTCCTGGACCTCACCC R 2 1 2 1 101000 f 74 goat snp38062-scaffold474-1355472 2 135211669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443322 Affx-122927448 AX-123313659 2 1405504 CTTGGAAATCAGAAAACCACTTGCACTAGCTAAAT[A/G]CCTTTATCCAATGGAATCATAAATTTCTATTACAA R 2 1 2 1 101000 f 74 goat snp38063-scaffold474-1405504 2 135161171 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776454 Affx-122976360 AX-385263581 2 1485062 TAGGTTAAAGATCTTAGTCTTTATGTTAAGAGCAA[C/T]GAGGAACAAGTGGAGAGCTTTATTTAATGGAAGCA Y 2 1 2 1 101000 r 74 goat snp38065-scaffold474-1485062 2 135081120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445676 Affx-122926137 AX-123316013 2 1514043 CATGGCTGGCAAATAATGGGAGAGTATCTCTCAGG[C/T]TCCCCCCTAAAAGGGTGTTTAGCCACAGGATAACA Y 2 1 2 1 201000 f 74 goat snp38066-scaffold474-1514043 2 135051585 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415646 Affx-122948573 AX-123285995 2 1600819 TTACTCTACTAGTGCCTTGAATCTCTTTGACCCTC[A/G]CTGAATCTGTTTTTGTACATCTACAAACTTTTCCT R 2 1 2 1 101000 r 74 goat snp38067-scaffold474-1600819 2 134963693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386201 Affx-122971357 AX-123256559 2 1634633 TAACAATCTGTCAGATCACGAGTTGGTAAGCTCAC[A/G]TTTGTAAAATGCGTGGCCTGTGTACCTTGAGTCTA R 2 1 2 1 101000 r 74 goat snp38068-scaffold474-1634633 2 134930016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273872 Affx-1111833904 AX-519547480 2 1656849 AGAGGTGGCGGTACAGATCCACGTGGGGGCTGTCA[A/G]CGCCGAAGGAGGACCCCGGGGGGAAACACAGCTTC R 2 1 2 1 202000 f 74 goat GoatD01.009963 2 1656849 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382885 Affx-122973418 AX-123253243 2 1741591 CATTGGAGATTGAAGAAAGTGAGATGAAAAGTGTA[C/T]GCCTTTTCTCAGGGTCCCTCAGCCAGACAGTGATG Y 2 1 2 1 101000 f 74 goat snp38070-scaffold474-1741591 2 134823736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438943 Affx-122930409 AX-123309280 2 1791989 TTTGAAGGCAGGAGTTACTGAGAAGGAACCTGTAG[C/T]TGGCTCCCTGCTCCCTGTTCAATTCTCTGTTCATG Y 2 1 2 1 101000 f 74 goat snp38071-scaffold474-1791989 2 134773103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391226 Affx-122967398 AX-123261583 2 1832926 AGGCACCCTCAAATGGAAGCGACAACCTTTTTATC[A/G]CCTAATCTTGGAAATGATATTTCATTCTGCCAAAG R 2 1 2 1 101000 f 74 goat snp38072-scaffold474-1832926 2 134733162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401810 Affx-122959461 AX-123272163 2 1928042 GACAAGAAAAAAGGGCTGGAGATGGGCCTTCCTTC[A/G]TGGGAAGCTACAGGCCTGAAGGGCCCCTGCCCAAG R 2 1 2 1 101000 f 74 goat snp38074-scaffold474-1928042 2 134636556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429580 Affx-122937805 AX-123299921 2 2039417 TTCATCGAGTGCTCCCTGAGGCTGGGAACGGATGA[C/T]GAAGGGTCAATACGCCCAGCCTTGAGGCATTCAAA Y 2 1 2 1 303000 f 74 goat snp38076-scaffold474-2039417 2 134525302 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780220 Affx-122947169 AX-385267316 2 2081972 ACTGAAAGACTTGCCTTGTTTGGATTTGAAGAGCT[A/C]GGTGAGTCAGAGGAGGTTGTTTCTTAATCTGTATG M 2 1 2 1 101000 r 74 goat snp38077-scaffold474-2081972 2 134486511 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416211 Affx-122948234 AX-123286560 2 2141670 CATCCCTCCATCCATCCAGTCTTCCCTTACACAGG[A/C]GTCTGTGGCTGCATGTCTTACTGAGTCAGTAAGGA M 2 1 2 1 201000 r 74 goat snp38078-scaffold474-2141670 2 134426851 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393366 Affx-122965919 AX-123263722 2 2196842 CCTTGTGTCCACTGGGGTAGTGCCCCTGCATGCCC[A/G]CAATTCTTCCCACAGGGACTCCTTGATGGCTGCCT R 2 1 2 1 101000 r 74 goat snp38079-scaffold474-2196842 2 134371874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767380 Affx-122966430 AX-385254653 2 2256208 TCTCCACCATGGGAAAATGCTGGTGACAAATGAAT[G/T]CTGCATAATCTTCTTAATGTGGCAGTTTTCCATTT K 2 1 2 1 101000 f 74 goat snp38080-scaffold474-2256208 2 134321282 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794199 Affx-122973697 AX-385281165 2 2361272 TATATACATGTGTGTATGCAGTTCTGTGCAGTTAC[A/G]TACATGTGTAATTTCATGTGACAGTGACCACATGA R 2 1 2 1 202000 f 74 goat snp38082-scaffold474-2361272 2 134217722 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428305 Affx-122939377 AX-123298648 2 2407871 TGTTTCCACCCCACTGAACAAACAGGCTCAGATGA[A/G]TTACAAGACTCCTTTCACCCAGCTTGTTAGGGGAG R 2 1 2 1 201000 r 74 goat snp38083-scaffold474-2407871 2 134170650 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444127 Affx-122926808 AX-123314464 2 2447852 TACTTTATTTGATGAAGAACACTGCAAATATGAAA[C/T]ATTACAATCTCACTTACCAGATCACTCAGTGTTGA Y 2 1 2 1 101000 r 74 goat snp38084-scaffold474-2447852 2 134130843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413786 Affx-122949917 AX-123284135 2 2485892 TGTGACTCTTGATTCACAATCGAGGGAGTTGGAGA[C/T]GAAAGGAGGGCAGTAACATTCCCATATGACAAGTG Y 2 1 2 1 101000 f 74 goat snp38085-scaffold474-2485892 2 134091501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778741 Affx-122949587 AX-385265852 2 2541566 TATTTCATAAGCAGAATGCCCAACCAAAAGAAAGC[A/G]TTCTAGAAGAATTAATGTCACATAGGGATTAGAAT R 2 1 2 1 202000 r 74 goat snp38086-scaffold474-2541566 2 134034468 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421565 Affx-122943852 AX-123291912 2 2573831 TCAGTTTTTCATCTTCTTCTTTGTTGCTTCAGCTT[A/G]TTAATTTTACTCCAGAGCTCTCCCAAGACAATTTT R 2 1 2 1 201000 r 74 goat snp58419-scaffold948-993256 2 134002375 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412909 Affx-122950406 AX-123283258 2 2624821 TGTATATATTATGATTTTTTTTTCCAAATTGGTTA[C/T]ACCAATTTTGATTCTCACTAAAAGTATAAGGAATA Y 2 1 2 1 103000 r 74 goat snp58418-scaffold948-942266 2 133950218 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442758 Affx-122927750 AX-123313095 2 2654670 CATAGCAGCCCTCTTCCAAGGGTAATCAGAGGCAC[A/G]TTTACAGGGAATGGGATATCTAAGCCTTAAAGAAT R 2 1 2 1 101000 r 74 goat snp58417-scaffold948-912417 2 133920474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432096 Affx-122936479 AX-123302437 2 2688074 CCTGTGGGTTGTCAGAGAGCACTACAAGGTGCAAA[G/T]AGTTTACACCAGATTCAGTTCTTCAGTGCATATGC K 2 1 2 1 101000 f 74 goat snp58416-scaffold948-879013 2 133885555 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439073 Affx-122930309 AX-123309410 2 2719168 GTAACTGTCACGTGTTATTGGTGTGCATGTACAAC[A/G]TGTATGAGAGTGTGTGTATGAACGTGCAGTTGGTA R 2 1 2 1 101000 f 74 goat snp58415-scaffold948-847919 2 133854521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427998 Affx-122939167 AX-123298341 2 2749602 CGTGTTGCCAAGGACCAAGCTCTTCCTAGGGTCTT[A/G]CAGAATTAATACTGCCTTGTGTCCACCATTTGTCA R 2 1 2 1 201000 r 74 goat snp58414-scaffold948-817485 2 133823726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272030 Affx-1111833165 AX-519545796 2 2782624 AATTGCCTCATCTGTTCAACTTAAATTATTTAAGC[A/G]GAAGGATTTCCCTGGTGGTCCAGTGGCTAAGACTC R 2 1 2 1 101000 f 74 goat 2_2782624_AF-PAKI 2 2782624 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802261 Affx-122974017 AX-385289165 2 2823278 TGGCTGACATTTCACAGCTGTGGAATTAAGCAAAT[A/G]TAATTTGCAGATCCTCTACAAGGTTTAGTAATAAA R 2 1 2 1 101000 f 74 goat snp58412-scaffold948-743809 2 133749920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791023 Affx-122930705 AX-385278019 2 2863486 CCCTGATGCACCTTTCCGCAGGCTCATTTAAACTT[A/G]TTAAATCAACTCTTGTCCCCACTTTGCCCTGCCTA R 2 1 2 1 201000 r 74 goat snp58411-scaffold948-703601 2 133708844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408040 Affx-122954286 AX-123278391 2 2895745 TGCTGCAGCAGGTGCTCCATCTTCACATGTTGGAA[C/T]GTACATTCTGATGCTTCTTTTATTGTATAGAGAAT Y 2 1 2 1 201000 r 74 goat snp58410-scaffold948-671342 2 133676381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379360 Affx-122976156 AX-123249719 2 2932291 TCTAAAGATGAAAAAGTTTTCAAATCACAGAATGG[C/T]AATAAATAACCATAAACAATCTCTTATTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp58409-scaffold948-634796 2 133639875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791765 Affx-122936257 AX-385278756 2 2978432 TCACCCAGTCTGTAGTTTGTTTTTCATCGTATCTA[C/T]GTGAGTTTTTGCATAGCAACCATTTTGGGTTTTTT Y 2 1 2 1 101000 f 74 goat snp58408-scaffold948-588655 2 133592012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421447 Affx-122943943 AX-123291794 2 3012471 TTCCATATATAATTTGAGAACAAAAGGGGAGACAG[A/G]AAGAATGAGTTAGAAGAAACGTATGTGAGAGTGGG R 2 1 2 1 101000 r 74 goat snp58407-scaffold948-554616 2 133557239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451906 Affx-122921032 AX-123322239 2 3051820 AAATATAATGTCTGCACATCCAACCTAAAGAATAT[A/G]TGGATTTACATGGATTTGAGAATCGAAGAGAGGGC R 2 1 2 1 101000 r 74 goat snp58406-scaffold948-515267 2 133520292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380149 Affx-122975975 AX-123250507 2 3085660 AGCTGTAGGTGTACAACAACAGCTCTGGCCTCCCA[A/C]ACTGCCTGCTGTGGTCCCTAGCTGTTGGACATAGA M 2 1 2 1 201000 f 74 goat snp58405-scaffold948-481427 2 133486315 A C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765008 Affx-122964287 AX-385252582 2 3121017 TGGTTGTTTGGTACAGATATAAATACAAATTGCAG[A/G]GACATGTATTATGTAAACTGGTAAAAAAAAAAAAA R 2 1 2 1 101000 f 74 goat snp58404-scaffold948-446070 2 133454858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431346 Affx-122937053 AX-123301687 2 3178888 TTCCTTTGATTCATTTACTGAGGGTTACCCCAAAT[A/G]TTATGAACTTCTCTGTCTAGGCCAATGGGTAAAAT R 2 1 2 1 201000 r 74 goat snp58403-scaffold948-388199 2 133397948 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403795 Affx-122957974 AX-123274147 2 3222036 GGACCAACTACTTAACTTCTCTGAGCCTCACTCTT[C/T]TATGTTTAATTGGGAAAAACTGAGGAACTGCCTGA Y 2 1 2 1 303000 r 74 goat snp58402-scaffold948-345051 2 133356489 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424514 Affx-122941734 AX-123294860 2 3251090 TACGCTGTTCCCAGGCAAGTGTGCCCCCACCTCTG[A/C]ATCATGCCTCACTGAAGACCCCTCATGGAGCATCT M 2 1 2 1 101000 r 74 goat snp58401-scaffold948-315997 2 133327263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404250 Affx-122957063 AX-123274602 2 3305696 GACAGCAGGAAAGTGGAAAGTGTTTCAAATTTACA[A/G]CAAAATTCTCATATGCACACAAGTACAGCAGGTGG R 2 1 2 1 201000 r 74 goat snp58400-scaffold948-261391 2 133270846 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448634 Affx-122923366 AX-123318970 2 3337443 GTTGCAGTCTAAGCCTGGTGCATAGCTGCTGTTTC[C/T]GCGACCTTCACTTCCCATTATACTCGGAAGTCCCT Y 2 1 2 1 101000 r 74 goat snp58399-scaffold948-229644 2 133237923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804423 Affx-986696590 AX-385291008 2 3405670 GGCTCCATCAGCAGCATATAATAGATAGAACTGAT[A/C]ATTTCCTGAACCTTTCCAGCAAATCTGAGTTTTCA M 2 1 2 1 600010 r 74 goat 2_3405670 2 3405670 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320803943 Affx-986696592 AX-385290649 2 3406468 CTCACACTAATCGAAGAAAAGCAGAGAAAGTCGAT[A/G]CTATATGACATCACTTATATGTGGAATCTTAAAAA R 2 1 2 1 600010 f 74 goat 2_3406468 2 3406468 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 320767772 Affx-122956429 AX-385254999 2 3417224 TGTCAGCCTCATAGGATAAGTAGAAAATGTTTCCT[A/C]TGCTTCTAGTTTATGGATGTAATTATGAAAATTAT M 2 1 2 1 101000 f 74 goat snp58397-scaffold948-149863 2 133166106 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803946 Affx-986696594 AX-385290652 2 3421931 CCTGGAGGGTCCTGGTGAGTGGTCATGACGGAAGA[A/T]CCTGCCCCACCCCGCCCCCAGACCCTGCCACCCAT W 4 1 2 1 600010 f 74 goat 2_3421931 2 3421931 Ancestral_priority_1043 ancestry 0.464 neutral IMAGE 10K 10K ancestral 38439386 Affx-122930262 AX-123309723 2 3482109 TAAATAGAAACTAGCCTAAAGTAGAAAGGAAAGAA[C/T]GGCACAAAGTTAAAAGCACTGAGAGGCGAAACACT Y 2 1 2 1 101000 r 74 goat snp58396-scaffold948-84978 2 133108815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786608 Affx-122956461 AX-385273640 2 3521685 TTATGTAGCAGAAGGTAAAATGTGTATTTTATATA[A/C]ATTTTCTCTAATTCTCATGATGGCCTGATAGGTAG M 2 1 2 1 303000 f 74 goat snp58395-scaffold948-45402 2 133069358 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401920 Affx-122958824 AX-123272273 2 3563671 GTGATAAATATTTAACAGCATTTATTTAGTGAAGG[A/G]GATGATATACTTTAAAAAAGGTATAGAAATGTAGA R 2 1 2 1 101000 r 74 goat snp58394-scaffold948-3416 2 133027554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387942 Affx-122970020 AX-123258300 2 3572292 CCTTCAATTAGTATAAAGAATAAGAACAAAACAAC[A/G]TAGAAAAAGCAGTAAAAACAGAAAAGCCAAAATTA R 2 1 2 1 103000 f 74 goat snp9808-scaffold1350-344637 2 133003589 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397738 Affx-122962539 AX-123268093 2 3602401 CAACATGGGATGAGTTACAACAAAGTGATTTCACA[C/T]GCCACATTATTTTGTTTAGATTTTCAGTAGTTCGC Y 2 1 2 1 101000 f 74 goat snp9807-scaffold1350-314528 2 132973320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397842 Affx-122962467 AX-123268197 2 3636598 ACTGGAAACACTTGGGGCCAGGGCTTTATCACCAG[C/T]AGGGTTATAGTGTCTCTACCAGAGCTCTTTACCCA Y 2 1 2 1 201000 r 74 goat snp9806-scaffold1350-280331 2 132939114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802311 Affx-122962191 AX-385289215 2 3684835 GCCTATACTTAGTTATACTGACTCTGCACCTTTTG[C/T]AAAACAATGTTCCCTCTAGCCTGAAGTATACAGGA Y 2 1 2 1 101000 f 74 goat snp9805-scaffold1350-232094 2 132891058 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392029 Affx-122966473 AX-123262386 2 3719323 GCAAAAATTTCAGTAAAGAACATTTATCAGAAACA[C/T]AGAATAAGTATTACATTTAATGTTATTGCATTATT Y 2 1 2 1 101000 f 74 goat snp9804-scaffold1350-197606 2 132856325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423414 Affx-122942621 AX-123293760 2 3821212 TGGAGCTCTGGCATGTTTCACACATGATGAAGTGG[C/T]GGTCAGTCTCCTGCAGGCTGTGAACAGAGAGAACA Y 2 1 2 1 101000 f 74 goat snp9802-scaffold1350-95717 2 132752709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423739 Affx-122942860 AX-123294085 2 3875461 TATAAACTCTTAGGTTTCCAGCAGCTTTATCAGAT[A/G]ACTTAGGAAGGAAGGCTTACCTCATCAGTACAGAA R 2 1 2 1 101000 r 74 goat snp9801-scaffold1350-41468 2 132698754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433794 Affx-122934466 AX-123304135 2 3908725 GTCAGTTGTCAGAATCTCTAGGTTGATCTTCTCTA[C/T]GATTTATCTTTATTTTGCTAATGTTTCTGTCTACA Y 2 1 2 1 101000 f 74 goat snp9800-scaffold1350-8204 2 132671435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416906 Affx-122948062 AX-123287254 2 3922626 GCCTCCCAACCTTGCAGTTGCCCACACTCCCCGTC[A/G]CCCACCCTGTGTGGTTTTCTCTGCTGTACTTGTTT R 2 1 2 1 101000 r 74 goat snp19013-scaffold1910-120802 2 132656324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386151 Affx-122971397 AX-123256509 2 3967148 AAGGATGAATTTTTTTGACTCAGAACCTCAGGCTT[C/T]GCCTAGGGTGGGTAGGAGAGGGGACTCATCCATCA Y 2 1 2 1 101000 f 74 goat snp19012-scaffold1910-76280 2 132611713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449317 Affx-122922998 AX-123319652 2 4005445 AGGATTGGCAGCCAGCTCAGGGAGGGAAAGCAGAA[G/T]CCATGGGCTTACAGCTGGCAGGCCCTCTCAGTGTG K 2 1 2 1 201000 r 74 goat snp19011-scaffold1910-37983 2 132572867 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387060 Affx-122969899 AX-123257418 2 4040490 CTAATGATCTTGTAAGTAACACGTTCTGTCTGGTC[C/T]CGATACACACTAGAAGCTCGACTATGGGGATGGTT Y 2 1 2 1 101000 r 74 goat snp19010-scaffold1910-2938 2 132537168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426032 Affx-122941118 AX-123296378 2 4086276 ATAAGAAAAGTGATCCTATAGAATTGCACGACCCT[A/C]GGGTTTCTTCCCTTGGGGGAACCATACTGAATGCT M 2 1 2 1 101000 f 74 goat snp13900-scaffold1540-42749 2 132487140 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386552 Affx-122970716 AX-123256910 2 4122276 CTAATAAAGCACTGGTACTCAGTCCTTCCTGGGGA[A/G]CTCAGACTCACACACTGTTCTGATTTTTGTCTTTA R 2 1 2 1 101000 r 74 goat snp13901-scaffold1540-78749 2 132449957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427810 Affx-122939753 AX-123298153 2 4178836 CAGTGGCCCCTAGAATCTTTCCAAACGTGAGTTAA[C/T]GTCCCTTTGGGACATTCCAGGCATGTGAACTTTGC Y 2 1 2 1 102000 f 74 goat snp13902-scaffold1540-135309 2 132392378 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438982 Affx-122930381 AX-123309319 2 4218446 CGGCCCCCAGCCATGGTCCTGGGGGCTCACCCCCA[G/T]CTGTTCCATGTTGCCCTCAAAAGGGCCGTTGTCCC K 2 1 2 1 101000 r 74 goat snp13903-scaffold1540-174919 2 132352924 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444269 Affx-122926777 AX-123314606 2 4235195 TGAGACAGTGAGCCAGCCGACCCCACCTCCTGCAG[C/T]GGTGATGCAAACACAAAGCCTCCATGTGCACAGGC Y 2 1 2 1 101000 r 74 goat snp21081-scaffold2062-610374 2 132336227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442449 Affx-122927956 AX-123312786 2 4264913 ACAGCCCTTCTAGAGTCTGCATGTGGTTACGCCTG[C/T]GGGGGAAAGTGCAGGTACTGGTTTCCTGGCCCTAC Y 2 1 2 1 101000 f 74 goat snp21080-scaffold2062-580656 2 132306704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424456 Affx-122941779 AX-123294802 2 4302703 AGCAATAACTTTCTCACTCTTATTTGTTTAGTTTT[C/T]TGTGCATTAATTTTGCCCCAAGTGGTTCAGGAGCT Y 2 1 2 1 101000 r 74 goat snp21079-scaffold2062-542866 2 132268439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413653 Affx-122950532 AX-123284002 2 4337349 ACATCAGTAACTCAGGTTGCCGTTGCCATTTCAGA[A/G]CATCTGGAGGATGCCAGTTCCTTTTTCATTATTTG R 2 1 2 1 101000 f 74 goat snp21078-scaffold2062-508220 2 132232685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801869 Affx-122972088 AX-385288776 2 4385201 TATTGAAGAATCGTTGCATTCTGGGATATGCAGAT[A/G]TGTGAGATTCAAAGTGTGTATAGAGAGATACATGA R 2 1 2 1 101000 f 74 goat snp21077-scaffold2062-460368 2 132185267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380802 Affx-122975090 AX-123251160 2 4442615 CTCCCGCATCCACGGCAGACATTGATGGTGGGTCA[C/T]AGCACGTCCATGGTGGGAGGCTGAAGGGTCAGATA Y 2 1 2 1 201000 f 74 goat snp21076-scaffold2062-402954 2 132128046 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419616 Affx-122945985 AX-123289964 2 4480198 GGGTTTTCACTCCCTGTGGATTCCCCAAGCACACA[A/G]CTCTCTTATTCTGGGCTCACCCACCTGGCCAACAC R 2 1 2 1 201000 r 74 goat snp21075-scaffold2062-365371 2 132090228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421210 Affx-122944141 AX-123291557 2 4539754 AGTAAGTGAAACTAGGTGGCGGGAGACAGGGGCAT[A/G]GATTGTGTTCCCTAAAATGAGCCACTGGGGTCCTA R 2 1 2 1 101000 r 74 goat snp21073-scaffold2062-305815 2 132030791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447889 Affx-122923818 AX-123318225 2 4570173 GTAGGCTCACCAAATGTGCCACTGTGGTGAGGGAC[A/G]CTGAGAGTGAGGGAGGCTGTGCATGTGTGGGGACA R 2 1 2 1 101000 f 74 goat snp21072-scaffold2062-275396 2 131999783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414097 Affx-122949743 AX-123284446 2 4607367 CATATGCTGCTGTCTGTTGCTGCTTTTCTTTGGGA[C/T]GTATACAGTCTGTGATAAAACAGCCAGAAAATACA Y 2 1 2 1 201000 r 74 goat snp21071-scaffold2062-238202 2 131962036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409348 Affx-122954177 AX-123279699 2 4641694 TTAGGAACGAGGAAGAAACGAGAGCAATTTGTGCC[A/G]TAAATGTGGAAGGGCCTGTGTCTTACTATCTCGTC R 2 1 2 1 101000 f 74 goat snp21070-scaffold2062-203875 2 131927238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401891 Affx-122958846 AX-123272244 2 4691933 CTTCTCATCTAGCTCGCCTTTTTGAATTCCAGTCT[A/G]TTTGGTGGGTACTCAATAAAATACGTTGAATGAAT R 2 1 2 1 101000 f 74 goat snp21069-scaffold2062-153636 2 131877071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410114 Affx-122952824 AX-123280464 2 4772544 GCCTGGTGTTGGAACCTTGGCATATGGAAAAACCG[C/T]GGAGGAGAACCAATTTCTGTAGCCATGGTGATGTT Y 2 1 2 1 201000 f 74 goat snp21068-scaffold2062-73025 2 131796669 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377881 Affx-122977258 AX-123248240 2 4801415 GGACTTCAAGTTGGAGAGGAAAGCACAAAGCTTGC[A/G]CCAGTGCCACACTATGACCCTGGAGAGAGGACAAA R 2 1 2 1 101000 f 74 goat snp21067-scaffold2062-44154 2 131767824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426291 Affx-122940304 AX-123296637 2 4845448 TCCAAGAGTCCTTATAAAAGTTTCAGCAATCAAAA[C/T]GTCTATCTGATCAAGCATTCTTATGTAAATCAGGC Y 2 1 2 1 101000 r 74 goat snp21066-scaffold2062-121 2 131724032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380560 Affx-122975282 AX-123250918 2 4871485 TTGCCAGATGCAGGGCTGCCTCCAGATGAAATATG[C/T]GATGCTCTGAATGCTGGATTTGAATGTCAGATAAG Y 2 1 2 1 101000 r 74 goat snp6587-scaffold1235-25817 2 131695475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406744 Affx-122955739 AX-123277095 2 4951357 CTGGAAGGATTTACTGGTGTCAAGGCTGCCCCAGG[A/G]CAGATGGCCAGGGTGGTCAGACTTCCTGCTGTCCC R 2 1 2 1 202000 r 74 goat snp6589-scaffold1235-105689 2 131617753 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437258 Affx-122932009 AX-123307596 2 4990894 CAAGGAGAGTGACGAGAGCTGGCATAAGCCCGGGC[A/G]TGGAGGTTAGCCCAGATGGCATCTGGGTTGCAGTA R 2 1 2 1 101000 r 74 goat snp6590-scaffold1235-145226 2 131579265 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382920 Affx-122973393 AX-123253278 2 5051283 CCACCCCAATTCTGACCGTTGAAGCATAACTTTTC[A/G]TTACACTTCCAATTTTTTTTATTATGACCTTATAA R 2 1 2 1 103000 f 74 goat snp6591-scaffold1235-205615 2 131521228 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792593 Affx-122942567 AX-385279575 2 5102369 TTTAACTTAAACAACCTCACAGTCACCTGATAACA[G/T]AATCATCTTTGTCATACCAATATTCAAAAAGTCAT K 2 1 2 1 101000 f 74 goat snp6592-scaffold1235-256701 2 131470107 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392603 Affx-122966051 AX-123262960 2 5141643 CGGTGGCAGGCTGCTTAGCCCCAGAGGTGCCCAGG[A/G]AGCCTCCATGTGTGTCTGAGGAAGCTGTCCAGGAA R 2 1 2 1 101000 r 74 goat snp6593-scaffold1235-295975 2 131430509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277129 Affx-1111835694 AX-519550635 2 5164716 CCTTGGCCTGAAACGTCCCACCCCTCTGCCTCCCG[A/C]GTCTTTGCCAGCCTACTCCTATTCATTGTTTATGA M 2 1 2 1 101000 r 74 goat Random2.2K-159 2 5164716 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796448 Affx-122959129 AX-385283398 2 5207127 CCCTGAAATAGTTTTTGGCAATTTGTCCAGTTTTA[G/T]TCTTATTTTTGGAGACGAGGATATGCTGACTTCAG K 2 1 2 1 101000 r 74 goat snp6595-scaffold1235-361459 2 131365898 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780354 Affx-122961806 AX-385267449 2 5241773 TATACCAATAATGAGGTAAACATATGTACATTAAC[A/G]TTCAATAACTCTGTTTTTGGAAAAGTAGTGTGTTT R 2 1 2 1 201000 r 74 goat snp6596-scaffold1235-396105 2 131330554 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376272 Affx-122978756 AX-123246631 2 5273170 CAACCAAGCTTGGGAGCAAAAGCAAATACATTTGC[C/T]GGATGCAGACTCTTTGGCCCACAGCAGAGTTCTTT Y 2 1 2 1 101000 r 74 goat snp6597-scaffold1235-427502 2 131298940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389114 Affx-122968564 AX-123259472 2 5312888 GCAGAAGAGTACAATGCCTTCTTCTACTCGCTGGT[A/G]TCCCAGGACACACAGGAAATGGCTTACTCAACCAA R 2 1 2 1 201000 f 74 goat snp6598-scaffold1235-467220 2 131260855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271875 Affx-1111833173 AX-519545658 2 5328081 GAGAACCACAGGGAAGCCTGGAGGCAGAAAGGACC[A/G]TGGCACAGACCCTTGGGTGATCCCAGGGAGAACCT R 2 1 2 1 102000 r 74 goat 2_5328081_AF-PAKI 2 5328081 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417802 Affx-122947372 AX-123288150 2 5343497 GGAGCAAAAAGCACGTGGGTTGTGACCACAAGTAA[C/T]GTGATTGATTTCTCATTTTTAAACTCTTTTAATTT Y 2 1 2 1 101000 f 74 goat snp6599-scaffold1235-497829 2 131230620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791286 Affx-122924169 AX-385278280 2 5385459 GGGAAAAAAGCCCTAATAATGAACCCTATGCTTCT[C/T]AAATCATTCAGGTGGCTCCATCTGGTATCATGGTC Y 2 1 2 1 101000 r 74 goat snp23434-scaffold2358-26243 2 131188027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786350 Affx-122958542 AX-385273384 2 5417964 CCCAAATTCAAGATAAGCACACAACCAAGAGTCAT[C/T]AAACATGGAGGAAAAACACAACCGTGAAAGCGGCA Y 2 1 2 1 202000 r 74 goat snp19057-scaffold1914-6163 2 131155931 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766022 Affx-122929241 AX-385253441 2 5446756 ACTCTAGGGGCTTTACATCTATTGTTCTCTATTTG[C/T]ACAATAATCTACAGAGTGTAATATACCTCCCGTAA Y 2 1 2 1 101000 f 74 goat snp19058-scaffold1914-34955 2 131127068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421805 Affx-122944324 AX-123292152 2 5485076 GGTACAGCCTGAAGCCTGGGCAAGCACAGCAACCC[A/G]TCCTGTGGGTGACCCCTTTCTCTGGGTGCCTTGTA R 2 1 2 1 201000 f 74 goat snp19059-scaffold1914-73275 2 131090120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782394 Affx-122933240 AX-385269470 2 5517984 CCTGTCACTCTTAAATCTGGCCCAGCTTGGACCAA[C/T]GACCTATGTGAGTCACCTTATCCATACATAATGGC Y 2 1 2 1 101000 f 74 goat snp20929-scaffold2050-369335 2 131041723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792360 Affx-122949058 AX-385279341 2 5549545 AATTATTTTCAGAAATCAAAGTTTAATGACTTGGT[A/G]CTTTGACAGTCACAATACAGGTGCAAATGTCAAAA R 2 1 2 1 101000 r 74 goat snp20928-scaffold2050-337774 2 131010655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277009 Affx-1111835700 AX-519550517 2 5557403 TGCAGGTACGTGAGAAACCACACAGATGAGTTAGA[A/G]CACCGTAGGTCCGGATCCATATGACTACCTCCTCG R 2 1 2 1 101000 f 74 goat Random2.2K-160 2 5557403 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793716 Affx-122950343 AX-385280688 2 5584236 AGTGAGCCAGAATGCGTATCAGGTCTGCCAAATCC[A/G]TATGAACAAACATACATGTAGGTTCTAGTCGTCTA R 2 1 2 1 101000 r 74 goat snp20927-scaffold2050-303083 2 130976321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380532 Affx-122975679 AX-123250890 2 5646001 AAAGATTCATGGAATGATAACTCTGGCTTTTTAGA[A/G]ATGGGGAGAAGACATTAGTATTATCCATGTAAAGC R 2 1 2 1 201000 f 74 goat snp20926-scaffold2050-241318 2 130914376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385194 Affx-122971723 AX-123255552 2 5691962 GTCCATTTAAATTTACTACAGTGACTGATGTTTTG[A/C]ATTTATTTCCTTTATTTTGTATTTCTTCCCTTCCC M 2 1 2 1 303000 f 74 goat snp20925-scaffold2050-195357 2 130868973 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380932 Affx-122975012 AX-123251290 2 5801467 GGAAACTAACCCTGAGGCCAGGCTTCTTCAAACTG[C/T]GGGTTAGGAAATCAGTTCTGTTGAGTGGATGAGGA Y 2 1 2 1 201000 f 74 goat snp20922-scaffold2050-85852 2 130759736 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392429 Affx-122966192 AX-123262786 2 5836510 TCAGTCTTGGCAAGACTAGTCTTGTGATGATGGAT[A/G]TTGGTTTTCTCATCCATAAAATGAGAATAATAATC R 2 1 2 1 103000 f 74 goat snp20921-scaffold2050-50809 2 130724554 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400707 Affx-122959929 AX-123271062 2 5897847 AAAATCTGAACCGTCTTCTAAAGTCGACCTAAACA[C/T]ACACCCAACTTCCTGAATCCAATTCAGAGGTGTTT Y 2 1 2 1 101000 f 74 goat snp40701-scaffold520-288891 2 130659415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384743 Affx-122972039 AX-123255101 2 5954016 GGCTTGGTGTTTACTGGGTGTGATGGGCAAAATCA[C/T]GGCCTCCTAGAGATGTCCATGTCCTAATCCCCGGA Y 2 1 2 1 101000 f 74 goat snp40700-scaffold520-232722 2 130606349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402572 Affx-122958445 AX-123272925 2 5998395 TGAATCTACTTTCGTTTTTTCTTTTTAATATTCTA[C/T]ATGATTTCAGGTTTCATTTCTGACACCTTGGTGGT Y 2 1 2 1 103000 r 74 goat snp40699-scaffold520-188343 2 130562043 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400721 Affx-122959917 AX-123271076 2 6042334 GTCACAGCTGCGTTCTGGTTATGTTACGGCTGCTG[C/T]TATGACTGCTGCATCAGCCAGAAGAGAGGCTGTGT Y 2 1 2 1 303000 r 74 goat snp40698-scaffold520-144404 2 130516971 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418419 Affx-122946536 AX-123288767 2 6086234 GGGATTGAGCAGAGGGCAAGCCCCAAGCAGTAAAG[C/T]GAAGTTCCTGGTTAGTAAATGGAAGCACTCCCCAA Y 2 1 2 1 101000 r 74 goat snp40697-scaffold520-100504 2 130472249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450665 Affx-122921918 AX-123320999 2 6139761 CCTTTACTTTCCAGGGGAGTAGTACAAGGATGTCC[A/G]CCAGATCGTAATCTAGCTAGAAGCCTAATCTCTGT R 2 1 2 1 101000 r 74 goat snp40696-scaffold520-46977 2 130418727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773697 Affx-122937667 AX-385260836 2 6169441 ACAGAACTTAATTCATGTGTCATTAGTACAGTTGC[A/G]TCGTTGAGTTAGAACATGACATGACCGAGAAATGA R 2 1 2 1 101000 r 74 goat snp40695-scaffold520-17297 2 130388704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426375 Affx-122940244 AX-123296721 2 6189525 TTGCTGCCTAGGATGCTCCCTTCTGGTACAGAGGA[C/T]GTGAGGTTTACACCCAGAGACTCCTCAGATCAGGA Y 2 1 2 1 101000 r 74 goat snp38176-scaffold479-94944 2 130359220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780977 Affx-122976727 AX-385268064 2 6228410 CAGGAGAATGAGAGGAAAAGAATTTAGTATGAGCA[C/T]GCTCCACATCTATGCATACCCCAGTTGTAGCCCTA Y 2 1 2 1 101000 f 74 goat snp38175-scaffold479-56059 2 130319063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767604 Affx-122958109 AX-385254854 2 6276967 AGTTCCACCTTTGAAACCACTTCTAGAAACTTCAC[A/G]TTCTTAGTTTATAGACACTGAGCTTTTTGGCTTGC R 2 1 2 1 101000 f 74 goat snp38174-scaffold479-7502 2 130269662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378600 Affx-122976578 AX-123248959 2 6287492 TCCACCATTCTATCAAGGTAGCTTCTCCCTCTGGA[C/T]GGGAAACCATGTCTTCAATTCTTATTCTTTTAATA Y 2 1 2 1 201000 r 74 goat snp14410-scaffold1572-692179 2 130259429 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421139 Affx-122944192 AX-123291486 2 6326521 ATCTGGTAAAAGCAAGGTGGGGCTCACTAGTCACA[A/G]TCTACCCTCCCCTATCAGCAAAGGAGAGAGCTCTG R 2 1 2 1 101000 f 74 goat snp14409-scaffold1572-653150 2 130220175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785206 Affx-122928079 AX-385272252 2 6382855 ACATAGCTGTAATATTCATCAGTCTTTACTATAAA[C/T]AAGTTACTTTTTCGTTCCATCAGTTTAGGACTTGA Y 2 1 2 1 201000 f 74 goat snp14408-scaffold1572-596816 2 130163229 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795743 Affx-122927580 AX-385282696 2 6469408 CTAGGCTTGTATCTGATGCCATTTGGAAACAAACT[A/G]AAGTGTTAGCTATTCCTAAAATAGTTTTATCTATA R 2 1 2 1 101000 f 74 goat snp14407-scaffold1572-510263 2 130066629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391413 Affx-122966770 AX-123261770 2 6503532 TCTTCACAGAAAATGGTGGCTGAAAAGAAAAGGAT[G/T]AACAGCTGGAGTAAAGTTACAATATAAGGAAAGAA K 2 1 2 1 101000 f 74 goat snp14406-scaffold1572-476139 2 130031994 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392848 Affx-122965765 AX-123263205 2 6532834 ATCTCTTCCAGCTCTATCATACTAGAATTCCTCAG[A/G]ATGTTGATGGATGGAGGCTCATCCTGCTAATATAA R 2 1 2 1 201000 f 74 goat snp14405-scaffold1572-446837 2 130002813 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443430 Affx-122927366 AX-123313767 2 6616297 TACTTCTCCAGATACTTTATCCGATCCTTGGAGTT[A/G]TACTATACTGTGTTGCCAGAAAAAAAAGCAGTGAT R 2 1 2 1 101000 r 74 goat snp14404-scaffold1572-363374 2 129921528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438931 Affx-122930419 AX-123309268 2 6669096 GTTTTTTGTCTTTAAATTCTCATTACACCTACAGC[A/G]CTTTGTTGTTATTTAGTCATTAAGTTGTGTCTGAC R 2 1 2 1 201000 f 74 goat snp14403-scaffold1572-310575 2 129868770 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438530 Affx-122931196 AX-123308868 2 6699059 AATGATACCAAGTAGCCCTAAAGTATTACTTCAAG[C/T]GACACAGGAGCTACAGCAACTGAGGGGAAAGATAA Y 2 1 2 1 101000 f 74 goat snp14402-scaffold1572-280612 2 129833950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse392 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399272 Affx-122960555 AX-123269627 2 6732389 CAGCTACCTAGCCAAGCACAGACTCAGAAGCTGGC[A/G]TTTATTTGGGGCGTGAAGGAGTAACGTGTGGCCGG R 2 1 2 1 101000 r 74 goat snp14401-scaffold1572-247282 2 129800081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432605 Affx-122935501 AX-123302946 2 6761737 GAGTCTCATTTTATCCTGAGTCATCCAAAATTACT[A/G]CAATCCACAGAACAACATTTGATTGTCCGCTGCAC R 2 1 2 1 201000 f 74 goat snp14400-scaffold1572-217934 2 129770781 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413806 Affx-122949901 AX-123284155 2 6815851 GTCTCCAAGAAAGTGCATGAATGGTTAAGGCAAAG[C/T]ATGCCGCTGGTATTGGCATGCTGCAAAATGACTTG Y 2 1 2 1 101000 f 74 goat snp14399-scaffold1572-163820 2 129718047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse393 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423628 Affx-122942368 AX-123293974 2 6860840 ATCTCTCAAGTGGCTTTTATATACTGAAAGCTCAC[A/G]CATTCATATCTATAGTCCAGACCTAGGATAGCCAA R 2 1 2 1 101000 r 74 goat snp14398-scaffold1572-118831 2 129672023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436762 Affx-122932279 AX-123307100 2 6890467 TTTGTCTGACACTATTTAGCCCCCAGCTTTTATTC[A/G]TCCTTATAACAACACCTCCTTAGCCCAAGTTTGGA R 2 1 2 1 201000 r 74 goat snp14397-scaffold1572-89204 2 129642335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse394 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273836 Affx-1111833848 AX-515586065 2 6920977 CCTACTGCAG[A/G]GATCACTGCCTACCTTCCATTATTTGTGCCTATTC R 2 1 2 1 101000 r 74 goat GoatD01.007141 2 6920977 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776701 Affx-122963986 AX-385263827 2 6923032 AAACTGTGGAAGAATTCACGGAAGTCCTGCTTGTT[A/G]CCATATGGCATAAGTCAAATACTGGAAAGTGGCAG R 2 1 2 1 101000 f 74 goat snp14396-scaffold1572-56639 2 129609623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791764 Affx-122976923 AX-385278755 2 6975646 ATTATTAGCAGCTAAGAGAGTGGCTAAATTATTTT[C/T]ATATTTTTTGTTATCATTGGAACATTATTCACTGA Y 2 1 2 1 201000 r 74 goat snp14395-scaffold1572-4025 2 129556696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450055 Affx-122922818 AX-123320390 2 7081216 GGGGTAGGGATGAGGTGGGGGCAGCAGGGAAGTTT[A/G]TATAACTATATTCTTCTTGTCCCTGGGCCATCCTT R 2 1 2 1 101000 r 74 goat snp12485-scaffold1478-361135 2 129451522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse395 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400497 Affx-122961284 AX-123270852 2 7125710 GTGAGCTGAACTATATATGCTGTTACTGGCCAGAC[A/G]TTGGGACAGGAATAGCTAGATTTAGAAAAAAAAAT R 2 1 2 1 103000 f 74 goat snp12484-scaffold1478-316641 2 129406161 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse396 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38379132 Affx-122976738 AX-123249491 2 7177958 ATCTTGAGTTCTTACACATTAAGGAAAAGGCCATA[C/T]ACAAAAGAAAAAAAATTCTGAAAAGGCTAATAATC Y 2 1 2 1 103000 f 74 goat snp12483-scaffold1478-264393 2 129354308 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse397 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38443828 Affx-122927541 AX-123314165 2 7236823 GGTATGTCCTGGTTTAAAGAAACAATATTTTTACC[A/G]TCAGTGAAATCACTGAAGTAATAAACAGTTTTTAC R 2 1 2 1 101000 f 74 goat snp12482-scaffold1478-205528 2 129294879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse398 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449630 Affx-122923190 AX-123319965 2 7270442 TAATCAAAAGAGTATTTCTCTTCCTTATAACATTT[A/G]TAAAACTGTATTTCTTTCCATGTTGCCAAACAAGG R 2 1 2 1 103000 r 74 goat snp12481-scaffold1478-171909 2 129261508 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788132 Affx-122949264 AX-385275152 2 7312610 ATTTCTATATAAGTATGTATGTAACTAATAGTTGC[A/G]TATTCATTATCTTGAGTTAAAGAGAGAAGCATTCT R 2 1 2 1 201000 f 74 goat snp12480-scaffold1478-129741 2 129220004 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse399 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320776479 Affx-122972832 AX-385263606 2 7361654 GTGATGTTCTGGGAGGCTTCTTTTGATAAAAGGCG[C/T]AAGAAGGTCATCTGAGTAATGGCTGCATTAGGTGA Y 2 1 2 1 101000 f 74 goat snp12479-scaffold1478-80697 2 129170679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse400 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771508 Affx-122936476 AX-385258666 2 7404620 TAATTTCCAATGGCAAATTCTTCCCACTGGATTGA[G/T]AGTTGGTCATAATATTTGCTTGGAGTGATGCCTCA K 2 1 2 1 101000 f 74 goat snp12478-scaffold1478-37731 2 129127940 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse401 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771226 Affx-122945547 AX-385258384 2 7441725 AAAATCTAACCTATTATTGAGTCATTTTAATTGTT[A/G]CAGTTAAAGCAGAAAATTGGGATGATCCCTTGGGG R 2 1 2 1 101000 r 74 goat snp12477-scaffold1478-626 2 129090917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431728 Affx-122936750 AX-123302069 2 7442917 TCTCCTCATTGTACGCAGATGCTTTACTGTCTGAG[C/T]TACCAGGGAAGTCTCATGCTTAGGGCTGTGACAGA Y 2 1 2 1 303000 r 74 goat snp23361-scaffold2337-467 2 129078196 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441125 Affx-122929589 AX-123311462 2 7485214 ATGTTTTAAAAAGTTTCACAGTCTAGCTCTAGCTC[A/G]TATTAAGGGCTGGGTCTAGCATAACTTGACTTTTC R 2 1 2 1 101000 r 74 goat snp23362-scaffold2337-42764 2 129035927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396088 Affx-122963429 AX-123266443 2 7548918 TGTGTCTCAGAGCTGTGACATTCACAAATTCTATC[A/G]CCAGTGATAATTTTTTTTTCCCCATTCCCTAACTC R 2 1 2 1 101000 f 74 goat snp23363-scaffold2337-106468 2 128970647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse402 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447033 Affx-122924535 AX-123317369 2 7581467 GTTTGTCCACAGCAGTTATGAAAACCTAGGTATTT[A/G]TGATAACCACTATTTCTGAGTTGGTCATTGCTTTT R 2 1 2 1 101000 f 74 goat snp23364-scaffold2337-139017 2 128937631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404701 Affx-122957264 AX-123275053 2 7618206 CCCAGTGCAAACTTTTATAATGTGCTTGGATAAGT[G/T]GATGGTGGGCATGAGACCATTAGTTTTGCTTTAGA K 2 1 2 1 101000 f 74 goat snp30384-scaffold3341-1197 2 128901152 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793830 Affx-122958082 AX-385280800 2 7658415 ACATAACAGCATTCTATTTGTGTCACTGGCAAGAA[G/T]CCCTACTTGACTTCAAGCTTACACAAATAGACAGA K 2 1 2 1 101000 f 74 goat snp30385-scaffold3341-41406 2 128860692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450381 Affx-122922088 AX-123320716 2 7684459 CTCTCTGCCCAGTCCTGCTTCCTATAATCCTGGGC[A/G]TTATCTCTCACTAAATCTCTTACACAACTAACTTC R 2 1 2 1 101000 r 74 goat snp32359-scaffold367-2390405 2 128832750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse403 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432102 Affx-122936475 AX-123302443 2 7778906 TCATATGGACAAGGAAAACTGTTTGTGTATACTTG[C/T]GTATATTCTCAGAGAAAACAGAGTTTGGAATTCAA Y 2 1 2 1 101000 f 74 goat snp32357-scaffold367-2295958 2 128738034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416830 Affx-122948118 AX-123287178 2 7812010 AGAATTCATTGAGCCAAACATTTCCAGTTTGCAAG[C/T]AGCTCTATAGGCAATTTGGAACTTGCATTAGACTT Y 2 1 2 1 201000 r 74 goat snp32356-scaffold367-2262854 2 128704135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse404 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277163 Affx-1111835711 AX-519550669 2 7825934 GTGGAGGTGTAGGTTATAGGGTATACGTGTGTCCA[A/G]TTTTAGTAGAAATTGATCAGTTTTCCAAGTTCAGC R 2 1 2 1 101000 r 74 goat Random2.2K-162 2 7825934 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272951 Affx-1111833180 AX-519546637 2 7844574 AGGGCAGCAGGTATTAATTTGCTGAGAAGTAAGGA[A/G]ATTGGCGGGCCTGGAGGAACCCTTCCAGTGCTGAT R 2 1 2 1 101000 f 74 goat 2_7844574_AF-PAKI 2 7844574 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764617 Affx-122975530 AX-385252259 2 7854510 ATGCACACTGAAATTACAATATGGGGGGTTGTTAT[A/G]TAGGATTAATTTGGCTTCAAACTCTCCATGAGTTT R 2 1 2 1 101000 f 74 goat snp32355-scaffold367-2220354 2 128660747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426213 Affx-122940363 AX-123296559 2 7903842 TCTGATCGCAAGGTAGACTCCTTACATAAACAGAC[G/T]CACTGATAATGCCGATTCAGGGTGGCCCTCTCATC K 2 1 2 1 101000 f 74 goat snp32354-scaffold367-2171022 2 128611465 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453482 Affx-122919837 AX-123323815 2 7961292 GCTTTCTTAATCTCTGTATTAGTATTATTCTCAGT[A/G]TTAATACCATGACTGAAAGCACAATGTTTGTAAAG R 2 1 2 1 101000 r 74 goat snp32353-scaffold367-2113572 2 128552956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397398 Affx-122962260 AX-123267753 2 8020297 CATCTTTAGTCTATAATTTGAAAAAGTGAAAAATA[C/T]AGGTCTGGCTTTACCAGTGGTCTGTATTAGAGTTA Y 2 1 2 1 102000 r 74 goat snp32352-scaffold367-2054567 2 128493546 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385873 Affx-122971604 AX-123256231 2 8050333 ATTGAGCAGATGATATAGATATCTTGGCCATTAGA[C/T]ACTAAATGCTAAATATTGTATGCAGCATTCAAAAT Y 2 1 2 1 101000 f 74 goat snp32351-scaffold367-2024531 2 128465987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441246 Affx-122929498 AX-123311583 2 8079680 ACTAACACAACATTGTAAAGCAACTATACCCCGAT[C/T]TATAAAAGAGAAGGAAGAATGAGGAGTAGATGCTT Y 2 1 2 1 201000 r 74 goat snp32350-scaffold367-1995184 2 128436637 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441566 Affx-122928685 AX-123311903 2 8114946 TTTAGGCTGCTTAATCTACTTTTATACTTTCTTGT[A/G]TCTTTACCGAAAACTTGTTATTGCAACATACATAC R 2 1 2 1 101000 r 74 goat snp32349-scaffold367-1959918 2 128401320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388128 Affx-122969479 AX-123258486 2 8149415 ATCTCAGTATTCACACATTGGCCCAATAGGTAAGG[C/T]CCTGCTGCTTCCAAGTTTCAGACTAGCTGGGAACT Y 2 1 2 1 101000 f 74 goat snp32348-scaffold367-1925449 2 128366699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417410 Affx-122947227 AX-123287758 2 8193088 GCCAGTGCATGGTTTATCAGATTCTCTTTCTTCCT[A/G]TCACTATGACTGTCACTGTTTCTGCTAGAAGTTGC R 2 1 2 1 101000 f 74 goat snp32347-scaffold367-1881776 2 128322932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778335 Affx-122932295 AX-385265450 2 8234709 CTGAAGGTTGGGTTGGATGTGTCAGTTTCTTAAAA[C/T]GAGACAACAGTGAAGTTCGACACGTTGACTGACTA Y 2 1 2 1 202000 r 74 goat snp32346-scaffold367-1840155 2 128280578 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405486 Affx-122956015 AX-123275838 2 8271302 TCGAGCCAGTTCCACCACGGCAGATTGAATACCAC[A/G]TGCATACAGCAAACGTAAGTGGAATGAGAGCAATC R 2 1 2 1 201000 r 74 goat snp32345-scaffold367-1803562 2 128243655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385126 Affx-122971774 AX-123255484 2 8319728 AATCCAGGAGCACACACATTTTATCCTATAGGAAG[C/T]ACAAAAGACTGCAAAAAAGAGGATGTGAAACTGCT Y 2 1 2 1 102000 r 74 goat snp32344-scaffold367-1755136 2 128194520 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791917 Affx-122965776 AX-385278907 2 8363892 GACTGACAGAATCAGATCTCCTCTTGTAAATGATC[A/G]TGCATTTGTTATCAAAATCTTCTTTTTGTTCTCCT R 2 1 2 1 101000 f 74 goat snp32343-scaffold367-1710972 2 128150167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428705 Affx-122938471 AX-123299047 2 8394154 GGAGAAATTCAATAGGCTACCTTTCCTTAGGAACA[G/T]ATACTGGGGACAATTTCAGTGTTGTCCTCTTAACT K 2 1 2 1 101000 f 74 goat snp32342-scaffold367-1680710 2 128127436 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438622 Affx-122930922 AX-123308959 2 8446342 TTATTTCACCAAAATTAAATAGAAAAAATCCTAAA[G/T]CTCAAAAAACTGAGCAGGAGTTGTTGAAAAGGCTT K 2 1 2 1 102000 r 74 goat snp32341-scaffold367-1628522 2 128076370 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405675 Affx-122956560 AX-123276027 2 8479380 TCCCAAAGCATTATGTTAAGAAGGCAACTGAGGCC[A/G]TAACTGGAGACAGTGGAAAGAAAACACCTTGATCT R 2 1 2 1 101000 f 74 goat snp32340-scaffold367-1595484 2 128041937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427247 Affx-122939558 AX-123297590 2 8508167 AGAAGCCAAGAAATTATTTGCATAAAAATGAATAG[A/C]TTTCCCTTCTCTTTGGTGGAAGAGAAATGACTCTT M 2 1 2 1 201000 f 74 goat snp32339-scaffold367-1566697 2 128012457 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408217 Affx-122953845 AX-123278568 2 8551307 AGCATTTGTGATCCTTAGAATTTACTTTCCTCTAC[A/G]TACCTGCCTTTGAACTGTGGTATTGGAGAAGACAC R 2 1 2 1 101000 f 74 goat snp32338-scaffold367-1523557 2 127968606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443960 Affx-122927009 AX-123314297 2 8585568 ATCATCAAAATGAATGAACTGCTATACTTTGTACA[C/T]AGCTTCTGGCAGCTTCGTTATTGACATGATTTATC Y 2 1 2 1 101000 r 74 goat snp32337-scaffold367-1489296 2 127934583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429183 Affx-122937960 AX-123299525 2 8624930 TGAATATGAACCCCATTCAGCCTTTTTGAACATTG[A/C]TGTGAGGTTGCCTTTGTCTGAAGTGCATATTCTTA M 2 1 2 1 201000 r 74 goat snp32336-scaffold367-1449934 2 127894750 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433677 Affx-122934554 AX-123304018 2 8659455 AGTATGACACAGTTTTGAATTTTCCTCTGAGCACT[A/G]CTTTAGCTCTATTCTATACAGTTTGGTATATTGCG R 2 1 2 1 201000 r 74 goat snp32335-scaffold367-1415409 2 127858924 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425854 Affx-122940659 AX-123296200 2 8697046 ATCAAAGTTATTATTCTTGTCATTTTCTCATCTTC[C/T]GCATCTCTCCAAATACTTATATTAATATATTTTAG Y 2 1 2 1 101000 f 74 goat snp32334-scaffold367-1377818 2 127821438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410950 Affx-122952034 AX-123281300 2 8743010 ACATATACTCAAATATATGTGTGGAACTGAGGTTC[A/G]TGGAACTAAGTATCTGTGTGTGTGGTGCAGGAAAA R 2 1 2 1 201000 f 74 goat snp32333-scaffold367-1331854 2 127775131 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277049 Affx-1111835718 AX-519550556 2 8754453 GAGGGGCCATGGAGGACCTCTCTCATGGACCTCGT[A/G]CCTGCCCAGGCCCAGCCTAGTATGCAGCAGCATTC R 2 1 2 1 202000 f 74 goat Random2.2K-163 2 8754453 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778521 Affx-122934691 AX-385265633 2 8797993 TGCTGGGTAAATACAGAGAAAATCTAGTTGTTATT[A/C]TCCACAGAGAATCTCTAAAATGACTAAAGTAGTCC M 2 1 2 1 101000 f 74 goat snp32332-scaffold367-1276871 2 127719723 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274343 Affx-1111834146 AX-519547938 2 8839041 GCATGCATACATGTGA[A/C]GAGTCGGCTGCAGGACAAGACTGGAAACAAGCAGT M 2 1 2 1 102000 r 74 goat GoatD01.021443 2 8839041 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793301 Affx-122974918 AX-385280279 2 8858042 CTTTTATATCAATTTCTAACCACTTGAACTTCAAT[A/G]TCTATGGTAGTACCCATATACCAAGACCCTTAATG R 2 1 2 1 101000 r 74 goat snp32331-scaffold367-1216822 2 127659675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395819 Affx-122963637 AX-123266174 2 8911065 TAGTGCTTATACTTATTATTATGTAAATATTTCCG[C/T]GTCACTCTATCCATATATATGCGTAGGGGTTTTGG Y 2 1 2 1 101000 r 74 goat snp32330-scaffold367-1163799 2 127607931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791758 Affx-122925666 AX-385278749 2 8972537 CAGTTAGCTCTAAACATATGTAATAAAGTAAACAG[C/T]GATTCCTCATCCCTCAGACTTCCACATCCAGCTTT Y 2 1 2 1 101000 r 74 goat snp32329-scaffold367-1102327 2 127545933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444267 Affx-122926778 AX-123314604 2 9014226 AGTATACAGTGTCATTTTCCCCCAGTAAAGGAAAC[A/G]CAGGAACTATCTTAATAGGATTATGTTGAGGAATA R 2 1 2 1 201000 r 74 goat snp32328-scaffold367-1060638 2 127504003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406808 Affx-122955691 AX-123277159 2 9052981 GTGGTACAGACAGAATCCTGTGGTAGGCAGAATAA[C/T]GAGCCTCCAAAGATTCCCATATATAATCCCCAGAA Y 2 1 2 1 202000 r 74 goat snp32327-scaffold367-1021883 2 127464085 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416826 Affx-122948122 AX-123287174 2 9107165 TTGCTGATAATTTGACATTTTCTATTGTCATTTAT[A/G]GCTGAGACTTGATAGTTTGTCTGGTAGAATGCTGA R 2 1 2 1 101000 r 74 goat snp32326-scaffold367-967699 2 127409679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780954 Affx-122954763 AX-385268041 2 9171721 ATTCAAAATGATGTGAGGCAGAATATTATCATATA[C/T]GATTTTAATCAAACCAGGAGACTAATTGGATCCAT Y 2 1 2 1 101000 r 74 goat snp32324-scaffold367-903143 2 127344546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776910 Affx-122927242 AX-385264034 2 9202260 GGTGAATATTCTTGTAACTAGAATGTGATCAAGTG[A/C]TGACATAGAAATATGGTTACTTCACAAGAAATTTT M 2 1 2 1 101000 f 74 goat snp32323-scaffold367-872604 2 127313560 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435265 Affx-122934057 AX-123305605 2 9240831 GTTTGCACACTTCTTTTAAAGTATCCCTGAGGTTT[A/G]CACCTGAAAGGATGTTTGTTTGTAAAAAGGAGGGG R 2 1 2 1 101000 r 74 goat snp32322-scaffold367-834033 2 127271173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796514 Affx-122963939 AX-385283462 2 9280023 GTCTCTATGTTTCCAGTGTAAAATCTCTATAACTT[A/C]TCAGTGGAAAAAAGGAATGTGTACTCAGTACTTGA M 2 1 2 1 101000 f 74 goat snp32321-scaffold367-794841 2 127233928 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444039 Affx-122926875 AX-123314376 2 9315663 ATTAAAGATTTATCTTTTGCTCACAGTACATTCCT[A/G]CCTTTTTTGTTATAGATTAGTTGATCATGTAAATG R 2 1 2 1 101000 f 74 goat snp32320-scaffold367-759201 2 127197718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430703 Affx-122936911 AX-123301044 2 9352731 CTTGTGTCTTTCTTTAGAACTTAACCATCACACTA[C/T]GGTTATGTTTTAAATTTGTGGCAAATGGCAACATG Y 2 1 2 1 101000 f 74 goat snp32319-scaffold367-722133 2 127160014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776345 Affx-122929519 AX-385263473 2 9409673 TGATGTAGGATTCCTCTAATATCCATAGGATATAC[C/T]AATATTTGATCAAATTTGGGCCACGATACAAATCT Y 2 1 2 1 201000 r 74 goat snp32318-scaffold367-665191 2 127102303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438937 Affx-122930415 AX-123309274 2 9452580 GGGGTTTCCAATCAGGAGAGAAAAGATATTTTGTC[A/G]AATTCAAAAGAACTTGATTTATGAGACATGGACAT R 2 1 2 1 201000 r 74 goat snp32317-scaffold367-622284 2 127058786 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795806 Affx-122960454 AX-385282759 2 9491535 TTAGCAACTTGAAGATTTTTAGCACAGCAGCCAAG[C/T]AAAGATCACATCCATATATTTGATACATAAAAGAC Y 2 1 2 1 101000 f 74 goat snp32316-scaffold367-583329 2 127020034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440202 Affx-122930698 AX-123310539 2 9522671 TAGGAAGTTCCAGCGTGGCTTCAACCACTACGAGG[C/T]ATGACTCGAGGTAAATAAGAACTTCTCTAGGAATA Y 2 1 2 1 201000 r 74 goat snp32315-scaffold367-552193 2 126988708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406969 Affx-122955053 AX-123277320 2 9578428 TCCTTTACAACTTTTGTTCATCTTCTGGCTTTGAC[G/T]AGTGTGGTGTTTTTTATTTATACATGGGTTTTTCA K 2 1 2 1 101000 f 74 goat snp32314-scaffold367-496436 2 126933301 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802873 Affx-122958315 AX-385289771 2 9610581 GACCCCTGTAAAACATTTAGAAACGAAACTGTATT[A/C]CTCTTGTGAAATGTTACTATTATATTCTCCACTGC M 2 1 2 1 101000 f 74 goat snp32313-scaffold367-464283 2 126902269 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379859 Affx-122975797 AX-123250217 2 9643635 CCTTCCTCTCCCTGTTCCATTCATCTAGAAGCTAC[A/G]TGCTAACTACCCTTAGTAAACCCTGGCAAAACACT R 2 1 2 1 101000 r 74 goat snp32312-scaffold367-431229 2 126869525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798096 Affx-122968917 AX-385285031 2 9681041 TTTTTTTTTTTCTCAACTAGGTTTCTATATCATAA[C/T]GCTTGAGGGGCTAATTTAAAATTAAACATTTGCCA Y 2 1 2 1 102000 r 74 goat snp32311-scaffold367-393823 2 126831472 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387793 Affx-122969699 AX-123258151 2 9716637 GTAGTTGATTGTCTTTGGTATGACTTGTATAGTTA[C/T]GTCAAAGTTCTTCTAATAATCCTGACCTTTTCCCC Y 2 1 2 1 101000 r 74 goat snp32310-scaffold367-358227 2 126795606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793949 Affx-122937180 AX-385280918 2 9751656 CAGAAAGAACTTTGGGGAATACAGAAAGTATTTAA[C/T]AGTTAATTATCTTATAATTTAGTAGCTGGAAAATT Y 2 1 2 1 101000 f 74 goat snp32309-scaffold367-323208 2 126760563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393946 Affx-122965065 AX-123264301 2 9781755 TGCCCCTGCATTAGGTAAGCCCTTGTGACTTTTGC[G/T]AGCCAGTGAAACATGAGCAGCAGTGTAGGTGGAAG K 2 1 2 1 101000 f 74 goat snp32308-scaffold367-293109 2 126730371 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424113 Affx-122942022 AX-123294459 2 9811038 TGTCCCAGTTCAACAATAAATTACATGATTAGCTA[C/T]AGTTGACTGGCTGACACATCTCTTACATTTCCTGG Y 2 1 2 1 101000 r 74 goat snp32307-scaffold367-263826 2 126701201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797080 Affx-122968337 AX-385284020 2 9840527 TAGATGTCTTTCTGCAAGGACCAAAGGGCATCCTC[C/T]AGTCGTTCCACCTTTTTCTGCCCTGTTTTTTTTCC Y 2 1 2 1 101000 f 74 goat snp32306-scaffold367-234337 2 126671339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797377 Affx-122937159 AX-385284316 2 9893647 CATTTTTAATTTCTCATATTTAAAAACCAGTCTTT[G/T]GATCCCATTTACAAAGACTAAATGGCAGCAAATCC K 2 1 2 1 202000 f 74 goat snp32305-scaffold367-181217 2 126618270 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790769 Affx-122971553 AX-385277770 2 9922741 AAGTATGTTTGCAGATGCTTATTTCCCATAATTAA[C/T]GTTTTTACGTATTTTAATTTACACTAGAACTGTAA Y 2 1 2 1 101000 f 74 goat snp32304-scaffold367-152123 2 126589289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791082 Affx-122929983 AX-385278077 2 9996677 CTAAACTGCATTTCCTTCATAATCTCATGTTTAAA[C/T]ATTATTTACTTTTATGACCACTCCCTATTAGATGT Y 2 1 2 1 101000 r 74 goat snp32303-scaffold367-78187 2 126513704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798302 Affx-122964372 AX-385285237 2 10088461 GTGGCAGAATCATTTGCATGAATTGGCTTTGGTCT[A/G]TCTGTAATTTAATTCATCTGTTCTGCTTTTCAGTG R 2 1 2 1 101000 f 74 goat snp20609-scaffold203-13498 2 126406723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413821 Affx-122949890 AX-123284170 2 10139425 GAAAATTACATGTTGATGGATTGGTCCTCTACAAG[C/T]TCAGCTTCATTTGAACTTTCAGTACCCTTTATCTG Y 2 1 2 1 101000 f 74 goat snp20610-scaffold203-64462 2 126356623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764572 Affx-122966469 AX-385252227 2 10198377 CTTAATCACCTGGCTACTTATTTTCTAGTGTCTGT[A/C]GTATATAGGGATTTCAAAAAAAGCTATTGAATTTA M 2 1 2 1 102000 f 74 goat snp20611-scaffold203-123414 2 126300578 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421964 Affx-122943807 AX-123292311 2 10226914 TCATTTGCAGGTAATCACTTCATTGTGACTGCACA[C/T]GAGAATTCTTGGAGTACTTTAAAAAAAATACCAGT Y 2 1 2 1 101000 f 74 goat snp20612-scaffold203-151951 2 126272265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410085 Affx-122952843 AX-123280435 2 10284408 GTATTTACATTTAGGTCTTTAGACTGAATTTTCAA[C/T]GTTGTGACTTTATTCTTTTCTATAGAGAGTTAGTT Y 2 1 2 1 202000 f 74 goat snp20613-scaffold203-209445 2 126213162 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426201 Affx-122940373 AX-123296547 2 10331892 TTACTTTGGAACTACCTGAGCATAATCTTGGGAGA[C/T]GCATTATTGTAAAATTCTTTGGGTGGAATTGGTTT Y 2 1 2 1 101000 f 74 goat snp20614-scaffold203-256929 2 126165777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791212 Affx-122973254 AX-385278206 2 10371625 TGGACACAAGAGGCTTAACTAAGAGTGAAGTTTTG[C/T]ACATATAAGTTTACTCTTCATCCAAAATAGGGAAA Y 2 1 2 1 101000 f 74 goat snp20615-scaffold203-296662 2 126125981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277064 Affx-1111835725 AX-519550571 2 10404168 ATTTGCTATATAATACTCCACTAAGTTGATCTAGT[A/G]AATTTTATGTAAGCATTCCTTCTAGATTGTTCTAT R 2 1 2 1 101000 f 74 goat Random2.2K-164 2 10404168 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376014 Affx-122978406 AX-123246373 2 10450322 GGAGGTCTTCTAGATTTCACACTTTGCCCTGTATA[C/T]GTAGTTGATCATCTTCTGCCATCCTGTGACTTCCT Y 2 1 2 1 101000 f 74 goat snp20617-scaffold203-375359 2 126046961 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383776 Affx-122973206 AX-123254134 2 10535534 TCTTGAGAGAATAGGGACAAAACTTTACTGAGAAG[C/T]ACAAACCTTGAAGGATCATTCAGACCATTGTGAGA Y 2 1 2 1 101000 f 74 goat snp20619-scaffold203-460571 2 125960704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464112637 Affx-1110318147 AX-515588612 2 10555813 AAGGTGGGATCTGTCCAAGATTTCCTCACTAGTGC[C/T]CCCTAATGTTAATTCCATATTGACTGTTTAAAGGT Y 2 1 2 1 201000 r 74 goat 2_10555813_AF-PAKI 2 10555813 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789964 Affx-122949823 AX-385276970 2 10566734 TGGGCCTGGTGTAACACACTCTATAACATATTCTA[C/T]GGAAGGGGTTCCCAAAACTTGCTCTCAGAAGCTTA Y 2 1 2 1 102000 r 74 goat snp20620-scaffold203-491771 2 125930651 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383972 Affx-122972937 AX-123254330 2 10599262 GAGACTGTGTAAAGATCTTATTCTCAGCATTGGCT[A/G]CACAGTAGAATTATCTATGAAAAAAAATTAATATG R 2 1 2 1 101000 f 74 goat snp20621-scaffold203-524299 2 125894120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792725 Affx-122970223 AX-385279705 2 10633795 GAATATTCACATTTGATTCCACCTGGCTTGGTTCA[C/T]GAAAGATGATGCCATCTTGCTTACAGTTTTCCAGT Y 2 1 2 1 101000 r 74 goat snp20622-scaffold203-558832 2 125859788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380721 Affx-122975147 AX-123251079 2 10665796 ACGGCAGACAAGGATACACAAGAAAAAAAGAACTG[C/T]AGGCAAATATCCTGATGAAAGTGAAAGTCACTCAG Y 2 1 2 1 101000 r 74 goat snp20623-scaffold203-590833 2 125826093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438739 Affx-122930832 AX-123309076 2 10701900 AGAAAAAAGCGAAATTAGGGAATGTGGATAAGATG[A/G]TAGAGAAGGGAGACCCCAGGCTTCCTTCCTTGATC R 2 1 2 1 201000 f 74 goat snp20624-scaffold203-626937 2 125789374 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797997 Affx-122944808 AX-385284933 2 10741595 GCAATGATGGTACACGAGACAAAGAAGTACATACT[A/G]TAAAGGGATCAATCTAACAAAGACATAACAATTAT R 2 1 2 1 101000 f 74 goat snp20625-scaffold203-666632 2 125749572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777144 Affx-122938306 AX-385264267 2 10780857 ACGTGCCCTGGACACATATCAGAGAATCTCAGTTT[A/G]CCATTCTTTAGTTACATATCTTGAATATATTTTGA R 2 1 2 1 101000 f 74 goat snp38134-scaffold477-23223 2 125295495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792514 Affx-122973519 AX-385279495 2 10850108 GGAACATAGAATAGGCAATGAAAGAAGACAGCCAC[A/G]GTTACTCTCCGAAGCCTCAGGAATTGTACGAAGGT R 2 1 2 1 101000 r 74 goat snp38135-scaffold477-92474 2 125226552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403786 Affx-122957980 AX-123274138 2 10881635 CTGTGGCCCATTATCATTAATTTTCTTGGAATTGA[C/T]GAAAATTCTTTCAACTCAATTTCCCAGATACCGAT Y 2 1 2 1 101000 f 74 goat snp38136-scaffold477-124001 2 125194906 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433931 Affx-122934295 AX-123304272 2 10921940 TCTATGGTTCAGTTCCCCAAAGTGCAAAGCAGAGA[C/T]AATAATAACAGCTATTCAATTGTTTTAAGACTTCA Y 2 1 2 1 201000 r 74 goat snp38137-scaffold477-164306 2 125153768 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788387 Affx-122959723 AX-385275405 2 10966886 AAGAACAATTATTGAAAAACAAGTTTGATGTTTGG[C/T]AGATACAAAATTTATGTAATAGAACTTCATCGTTA Y 2 1 2 1 101000 f 74 goat snp38138-scaffold477-209252 2 125108100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431093 Affx-122936616 AX-123301434 2 11007018 ACATGAAAAAGTAGAAACTAAGGTAGAACTGGACA[C/T]GGAACATCAGACTGGTTCCAAATAGGAAAAGGAGT Y 2 1 2 1 103000 f 74 goat snp38139-scaffold477-249384 2 125067794 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787003 Affx-122955229 AX-385274031 2 11038227 GAAATCAAATCCATGGTATGGAGAAAGAGAAACAG[C/T]GACTTGAAGATGTTGTTTCTAACAATAATCATAGT Y 2 1 2 1 101000 f 74 goat snp38140-scaffold477-280593 2 125035805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765652 Affx-122948891 AX-385253119 2 11073581 GTCCATTCTTAGGGCCATTGTACCTAAATTAACAA[C/T]ATTTTCCTGCACATATACTTCCACAGTATTCCTAT Y 2 1 2 1 101000 f 74 goat snp38141-scaffold477-315947 2 125000258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412074 Affx-122951698 AX-123282424 2 11118209 CCTCAAATATACTATTTCCCTGAAGAAATGCACAT[A/G]CATACACATGCACACACCTCCTTTTCCCTTTCTCA R 2 1 2 1 303000 f 74 goat snp38142-scaffold477-360575 2 124955059 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771077 Affx-122925769 AX-385258237 2 11149852 AGAATATAATTAATACCGTCTACTTCCCATGGTAT[C/T]CTCTCAGCATCTTATGGCACTTCCTTCTACCAAAG Y 2 1 2 1 101000 r 74 goat snp38143-scaffold477-392218 2 124923022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407345 Affx-122955286 AX-123277696 2 11194776 AGGTGGAATGTAACAGAATGTTCCCCAATATGCAA[C/T]ACTGGCAGTAGTGAGAGGAGGAGGAAAAATAAAAA Y 2 1 2 1 101000 f 74 goat snp38144-scaffold477-437142 2 124876410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769138 Affx-122970570 AX-385256313 2 11249300 TTTATTAAATCACAGAATCTTTCATAAAAACCTAT[C/T]GACACCTTTAGGGACTAGTAACCAGAGTGATAGGC Y 2 1 2 1 101000 r 74 goat snp38145-scaffold477-491666 2 124821928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783430 Affx-122952996 AX-385270493 2 11284903 GTACACTGTATGGTATCTTAACTTCATTAAGAATA[C/T]GGAGCTGGAAAGGTCCTCATGATAATCTAAGTGAA Y 2 1 2 1 101000 r 74 goat snp38146-scaffold477-527269 2 124785838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771616 Affx-122974213 AX-385258774 2 11313776 ACATATAAGCACAGACCTGATGAAGCTGATAAACT[A/C]TAATTTCATCATTAATTACAGTTTATGTAACTTTT M 2 1 2 1 201000 r 74 goat snp38147-scaffold477-556142 2 124756936 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425368 Affx-122941574 AX-123295714 2 11350192 AAGACTGTCTTCAATGCTTAAAACTCAATATAGAA[C/T]ACATTTCCAAAACTGTATTGAGCCACTTGGATGAC Y 2 1 2 1 103000 r 74 goat snp38148-scaffold477-592558 2 124720482 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439548 Affx-122930102 AX-123309885 2 11400822 AAGGAACATGTGATTTAACTGTACTTTTAAAAGAT[A/G]TCATCCTTATAGTAAGTTTTCTGAGACTTAATCAT R 2 1 2 1 101000 r 74 goat snp38149-scaffold477-643188 2 124669062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447846 Affx-122923898 AX-123318182 2 11485925 CTCCTTACATGGAAATTGCTCTGTACATGTTTATT[A/G]TTGGGTACAGGAAATATTTCAAAATAAATAAACAT R 2 1 2 1 103000 f 74 goat snp38151-scaffold477-728291 2 124583779 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446326 Affx-122925628 AX-123316662 2 11525983 TTTCACAGGCTAAATATAATTTAATTTGTACCCTG[C/T]ATTTCTTACATCTAATTTTTAAAATACTTCTCTTT Y 2 1 2 1 103000 f 74 goat snp38152-scaffold477-768349 2 124545216 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784952 Affx-122933003 AX-385271999 2 11576444 TTTACCAAAAGGAATAACATTAAGATATCTTATTG[C/T]AAGTCAGGGAAAAGATGATCAATTATTACATTCCC Y 2 1 2 1 101000 r 74 goat snp38153-scaffold477-818810 2 124494451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769145 Affx-122946135 AX-385256320 2 11612200 AGCATTTATATGTTCCTGTCAGTTTATAGCTCCAG[A/C]GTTTTTTTTTCTCCAAGTAAGCAGATCTCAGTTGT M 2 1 2 1 101000 r 74 goat snp38154-scaffold477-854566 2 124460462 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789805 Affx-122956218 AX-385276812 2 11619032 AAGTAATTGAATGGAGGTACACATAGTTTTATAGG[C/T]GGATATTTGAGTATGATGATTTTTTATAATAGTAT Y 2 1 2 1 101000 f 74 goat snp35278-scaffold422-2805090 2 124091544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415755 Affx-122948934 AX-123286104 2 11651262 AAAATTCATGTTTAAAATACAGAGCTTTAGTGTTT[C/T]ATAAATAGCCAGTGGTGTACAAGTAAGTTCAATTC Y 2 1 2 1 101000 r 74 goat snp35277-scaffold422-2772860 2 124058527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797128 Affx-122922243 AX-385284068 2 11704450 TACTTTTTGTATAAAAAACTTACCAAGAATTGATA[C/T]ACTTATATTGCATGGCAGCAGCAGCACCCTAAAGT Y 2 1 2 1 102000 r 74 goat snp35276-scaffold422-2719672 2 124005988 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383091 Affx-122973730 AX-123253449 2 11737631 ATTTTTATCAAGTGAAATCTGTGCATGTATGGTTT[A/G]CTACATAATCCTGCATATAAGTACAAAGATCGTAT R 2 1 2 1 102000 r 74 goat snp35275-scaffold422-2686491 2 123971307 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439909 Affx-122930020 AX-123310246 2 11776715 GAAATGTGTAGCCACTGTAGTCAGAATAAGGACCT[C/T]GGGGTTGGGTAAAATGAAGTATTTCCTTATAATAA Y 2 1 2 1 201000 f 74 goat snp35274-scaffold422-2647407 2 123933366 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420288 Affx-122945038 AX-123290636 2 11857269 AAGAATACATAAAAAATTCATTATTTTTTGCTTCC[A/G]TTCAACACAAATGTAATAACTTCTAGGTTATTATT R 2 1 2 1 103000 r 74 goat snp35273-scaffold422-2566853 2 123850676 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779203 Affx-122973986 AX-385266307 2 11915280 GTGTCCTCTTGTGTAGACATTGTGATGGAATACCC[A/G]TATCTTCCTCCAGAAATCAGGCAGTTGTTACTCCA R 2 1 2 1 101000 r 74 goat snp35272-scaffold422-2508842 2 123792265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804435 Affx-986696602 AX-385291017 2 11946563 AGAAGGGAGGGGAAGACAGAGGCCCAGCCAGGGCG[A/G]GAGAAACACTTGTGGTCACACAGCACGTCTCCCGT R 2 1 2 1 600010 r 74 goat 2_11946563 2 11946563 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 320803896 Affx-986696568 AX-385290610 2 11946590 CCAGGGCGGGAGAAACACTTGTGGTCACACAGCAC[A/G]TCTCCCGTCCCAGGGACAGAGTGGGGGTCCAGGGC R 2 1 2 1 600010 f 74 goat 2_11946590 2 11946590 Ancestral_priority_1043 ancestry 0.536 neutral IMAGE 10K 10K ancestral 38388665 Affx-122969101 AX-123259023 2 11951138 TATATTAGTATATATAAAATTGTATGTACATAGCT[A/G]TATTTGCTATTGTCTTAATGCCTGCTGATCTTTTC R 2 1 2 1 101000 r 74 goat snp35271-scaffold422-2472984 2 123756825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410531 Affx-122952164 AX-123280881 2 11983265 TTCAGACCTTCACTAGAGAAATAGTGAAATTAACT[A/G]TCATAAAGACATGACCCAACTTCAACAATTACAAA R 2 1 2 1 101000 r 74 goat snp35270-scaffold422-2440857 2 123724414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801181 Affx-122963816 AX-385288094 2 12016946 CATTCCTTTTATGGTGAATAACCATATTTTAAACA[C/T]AATTTTCATTGCATTGAGTTAAAAGGTCAGGTGAT Y 2 1 2 1 101000 r 74 goat snp35269-scaffold422-2407176 2 123690593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603205 Affx-1002479400 AX-413837390 2 12045678 ATTTCGCCTGGGGCATGTCATGGGGGATTGTTGCC[A/G]TTTGAATGCTGTGGTTCCATCCTTTAGGGCCCTCC R 2 1 2 1 101000 r 74 goat 2_12045678_RH-map 2 12045678 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320786468 Affx-122948896 AX-385273502 2 12059257 ATATTAAAGGGACACTAGAACTTGAGAGAAATACA[A/G]TGACCTTCCCAAAGCCACATGGTTGCCAAATGGTG R 2 1 2 1 102000 r 74 goat snp35268-scaffold422-2364865 2 123649091 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603114 Affx-1002479401 AX-413837309 2 12072547 AATTACTTCTCTGGCACTGGTTGTCGAGAGTGAGC[C/T]GGTCCATTTTTCTCTTTTATTACTACTGAATTTCA Y 2 1 2 1 102000 f 74 goat 2_12072547_RH-map 2 12072547 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603116 Affx-1002479402 AX-413837311 2 12088359 TCGAGGCATTCCACCCAGCTAATTGGCTAAAGAAG[A/T]GGCAGAGGTGGAGGGTTGCAAGAGGGTTCAGAATC W 4 1 2 1 102000 f 74 goat 2_12088359_RH-map 2 12088359 T A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38400907 Affx-122959737 AX-123271260 2 12089124 GTTCACTGCCCCAAATTTCACTGAGCCATGAGTGG[A/G]TGTAGGAGAGGTGCAGAGGATCAAGCAAACCAGTA R 2 1 2 1 201000 r 74 goat snp35267-scaffold422-2334998 2 123619112 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776456 Affx-122953231 AX-385263583 2 12122560 TGCTGAATTGAAGTGACCAGACATAATAGACTATA[C/T]GATAAACAAAAATTTCTAGTATGGAAGAGGCAAAA Y 2 1 2 1 201000 r 74 goat snp35266-scaffold422-2301562 2 123585520 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603118 Affx-1002479403 AX-413837313 2 12136097 GACAGCAGAGACCCTGAAAGGCTTTGAGGACTTTG[C/T]CTGTCAGGGAGAAGCATCCTCAGGAAGTCTGGGCT Y 2 1 2 1 102000 f 74 goat 2_12136097_RH-map 2 12136097 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38449811 Affx-122922409 AX-123320146 2 12152671 GTAGTTGATGTTCTTGGAGTCACTGCTACAGCAAA[G/T]CACTTGATAAGAAAGGAAAGAATTAAACCAAAGCT K 2 1 2 1 101000 f 74 goat snp35265-scaffold422-2271451 2 123554880 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277087 Affx-1111835735 AX-519550594 2 12184609 CCACTCTCAGGGTTAAGAGATGACTGGAGTGGGAT[A/G]CCTTGGTTTCCCCTAGGTAGGTAGATAACGTGTCT R 2 1 2 1 201000 f 74 goat Random2.2K-166 2 12184609 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789560 Affx-122948199 AX-385276569 2 12205856 GAAAAATGGGGTAAAGGGTTAATGATACTGCTCTG[C/T]ATTTGCATGTTATATGAAGACTATACACTGCAGAT Y 2 1 2 1 101000 f 74 goat snp35264-scaffold422-2218266 2 123501327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789589 Affx-122946281 AX-385276598 2 12235357 CCTGAAGTTAAATGTTCAAGTAAATTAACAATCCT[A/G]TTGTTTTTCTCCAAGCAGGCACCTATCTTTCCTAG R 2 1 2 1 101000 r 74 goat snp35263-scaffold422-2188765 2 123471696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603120 Affx-1002479404 AX-413837315 2 12258123 ACTGAAATTTGAATTTCCTATAAAGGTCACATCAT[A/G]AAATAATATTCTCTTAATTATTCTTTCAATCATTT R 2 1 2 1 101000 f 74 goat 2_12258123_RH-map 2 12258123 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416012 Affx-122948382 AX-123286361 2 12269075 AAATTGTTCAAGAAGAGTGAGTGAAGAAAACAACA[C/T]AAATCTGGGAAAACCTGGCATGTTAGAACAGGAAG Y 2 1 2 1 201000 f 74 goat snp35262-scaffold422-2155047 2 123437327 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377640 Affx-122977869 AX-123247999 2 12303237 TCAAGGTAATAACCTATAAATGAGAAAAGGGTTAA[A/C]CATCATATTTGAAGTCAACATGGGGGTCTCTGAGG M 2 1 2 1 201000 f 74 goat snp35261-scaffold422-2120885 2 123403908 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425526 Affx-122941460 AX-123295872 2 12340491 AGAGCAAAATAAAAATAGTTTAAGTTCACTGGAAG[C/T]CCCTCCAGGCAGCTTCCACATCCTTTGGTGACCGC Y 2 1 2 1 303000 f 74 goat snp35260-scaffold422-2083631 2 123366371 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375394 Affx-122979212 AX-123245753 2 12387543 CACTAAATGTTTCTCTGAAATTCAAATTTAACTCC[A/G]TGCCTTCTATTTTATCAGGAAACCCTGGGATTAAA R 2 1 2 1 101000 r 74 goat snp35259-scaffold422-2036579 2 123318510 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789694 Affx-122970479 AX-385276702 2 12423729 TTGTTTCACATACCTAAATATCTTCATCCCTATGA[A/C]TCATGTAGAAGAACACAAGAATACGGAACACACCA M 2 1 2 1 101000 r 74 goat snp35258-scaffold422-2000393 2 123282206 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603122 Affx-1002479405 AX-413837316 2 12437740 CTGGACACAGGCATGAGATTGCAAGTCCTGTCCTC[A/G]GGCACCTGACCCACCTCCAGGGGGTCTCCTCCAAC R 2 1 2 1 102000 f 74 goat 2_12437740_RH-map 2 12437740 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320802116 Affx-122961938 AX-385289020 2 12501855 AAGCTTGTTGGAAGGGTTTATGCATTCAATTGAGT[A/G]TGGTCTGAAGACATTAATTCCAGAAGCTTGGATCA R 2 1 2 1 101000 r 74 goat snp35257-scaffold422-1922267 2 123203232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790687 Affx-122973567 AX-385277689 2 12536781 ACTAATCCTTATAGCCAGAGAAGAAAGAGTCATGG[A/C]GTTTTTTTTGGCCAGACACTTAAGAAAAATCCATG M 2 1 2 1 101000 f 74 goat snp35256-scaffold422-1887341 2 123167289 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603216 Affx-1002479406 AX-413837400 2 12548235 AGAAAACTGAGGTCCCAAGAAGAAAGAGGCTGGAC[C/G]AAAGAAACCCAATAGGATGGTGGCAGAGGAAGGAG S 4 1 2 1 400000 r 74 goat 2_12548235_RH-map 2 12548235 C G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401213 Affx-122959326 AX-123271566 2 12589967 TGCATCCATATAAGAAGGTGAGGCTAAAGAGGCTG[A/G]GAGAGAATATTTGTTGGAGGAAGTTGTCTTGGGTT R 2 1 2 1 101000 f 74 goat snp35255-scaffold422-1834155 2 123113401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603127 Affx-1002479407 AX-413837321 2 12591366 AACTCAGAATCCCTCTCTGCTGCCCAAATGCCATA[C/T]TCCCCAGACCCACCCATCTCAGGCTGTCAGGGCCT Y 2 1 2 1 102000 f 74 goat 2_12591366_RH-map 2 12591366 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404551 Affx-122957385 AX-123274903 2 12627491 GAGCAGACTCCAACTGTAAACATCTGGAACACCTT[A/G]CAGGTAATTTCAGCTGGCTATCATCCCTGTATACC R 2 1 2 1 101000 r 74 goat snp35254-scaffold422-1796631 2 123076849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603129 Affx-1002479408 AX-413837323 2 12676503 TTGGAGGGCCAGATCGCTGATGACTGTGACATCCT[C/T]GTTTACTGATATGGCAAGAGATATTCCATTTCTCA Y 2 1 2 1 103000 f 74 goat 2_12676503_RH-map 2 12676503 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377126 Affx-122978241 AX-123247485 2 12677845 TATCTCTTGTCAATAGAAGATGGTTTCCTGTAGGA[G/T]ATAACTAATAACTTTATAGAATTTGGGGATGTAAT K 2 1 2 1 101000 f 74 goat snp35253-scaffold422-1746277 2 123026128 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452023 Affx-122920906 AX-123322356 2 12707034 GTAACCATTCCATTCTTCAGGGGACCTTCCTGACA[C/T]AAGGATTGAACATGGGTCTGTGATAGTTTAGATGC Y 2 1 2 1 101000 r 74 goat snp35252-scaffold422-1717088 2 122996917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603131 Affx-1002479409 AX-413837325 2 12708429 TCAGAAAAAGAAGGAGACCAGCACTTTACAGGACC[A/G]GATCACCTTTAATGAGGTGAGAAGGGGCCGCGATC R 2 1 2 1 400000 f 74 goat 2_12708429_RH-map 2 12708429 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603590 Affx-1002479410 AX-185150951 2 12722993 TCAATACCACAGTTCAAAAGCATCAATTCTTCAGC[A/G]CTCAGCTTTCTTTATAGTCCAACTCTCACATCCAT R 2 1 2 1 303000 f 74 goat 2_12722993_RH-map 2 12722993 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38419214 Affx-122945694 AX-123289562 2 12738270 AAAAAAGATTCAGTATTGTTAATTATAGTCATCAT[A/G]TTGTATATTACATCTGTTGGGCCTGATTTTGAGTT R 2 1 2 1 101000 r 74 goat snp35251-scaffold422-1685852 2 122965745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422413 Affx-122943373 AX-123292759 2 12771576 GATAGTGTGTGATTAACTGCAAAAACTAATTGATT[A/G]CTGTAAATTATATAATTGAGTTTGTAGTGAGCCTT R 2 1 2 1 101000 f 74 goat snp35250-scaffold422-1652546 2 122932668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449013 Affx-122923093 AX-123319348 2 12845217 TGAGTCATTGTAATACCCTCCTAACAAATCTCCCT[G/T]CTTCCATGTTGCCCCTACTCCTCCTCACAGCCGCC K 2 1 2 1 101000 f 74 goat snp35248-scaffold422-1578905 2 122861067 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770289 Affx-122928981 AX-385257455 2 12877003 ACAAAACTCTCAGTGACATACTGAAGACTGGAAGG[C/T]AGGTCTCCTAACTTCTGGCTTGATACTCTTTACTT Y 2 1 2 1 101000 f 74 goat snp35247-scaffold422-1547119 2 122825920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400354 Affx-122960034 AX-123270709 2 12916721 CATTTAGAAATCAAAAAACTGTGAATAGTACAATG[C/T]AAATAATGAGCATTTTACAATAAACTTCACTGACA Y 2 1 2 1 101000 f 74 goat snp35246-scaffold422-1507401 2 122786230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275456 Affx-1111834909 AX-519549029 2 12927607 ATATTTGTTCTGGAAACTGGAACACACAGATAAGG[A/C]AAGCGCCTGACATTGGAACTGCAGAATAAATTTGC M 2 1 2 1 101000 f 74 goat GoatD01.058445 2 12927607 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350603650 Affx-1002479411 AX-413837788 2 12947664 GACCTCTCAGAGTCTCAGCACTGATCTCAATTAAT[A/G]TATGTCTGGGCATTTTTCTCCTATCTTTCCACTCC R 2 1 2 1 102000 r 74 goat 2_12947664_RH-map 2 12947664 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38436643 Affx-122932486 AX-123306981 2 12969544 AATCAAACTGCTACAAAAGTCCATCCATCAATTTA[G/T]CACAAAGGTAAAAACAAGATTAGAGACAGAAGAGT K 2 1 2 1 101000 f 74 goat snp35245-scaffold422-1454578 2 122733503 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603134 Affx-1002479412 AX-413837328 2 12976611 ATGGAGCACTTACAGTCTAAATGGGAACTGATTCT[C/T]TTTGAAGGACTCAAATGGGGTAAAAATGATACATT Y 2 1 2 1 101000 f 74 goat 2_12976611_RH-map 2 12976611 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320783404 Affx-122961992 AX-385270467 2 13004256 TTTGATAAAATACTTAGCACTCCTTAGTCACTTGA[A/G]TAAATAATATATATGCTAACAGTTATAATGAAGGA R 2 1 2 1 202000 r 74 goat snp35244-scaffold422-1419866 2 122698394 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782923 Affx-122935455 AX-385269993 2 13040923 TGATTCAGATCATCCAAATACTTCTAAGCTTAGAC[A/G]TTTGGTAAATCCTTCATCTCTCTTGATAGACATTC R 2 1 2 1 201000 r 74 goat snp35243-scaffold422-1383199 2 122661413 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272937 Affx-1111833157 AX-519546623 2 13058359 TTGAGGGAGAGATGAGCCTGAGGGTGAAGCTCCGG[A/G]ACCAGGTAGCTTCTCTCCCTGCAGACTTGCTGGGA R 2 1 2 1 202000 f 74 goat 2_13058359_AF-PAKI 2 13058359 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450181 Affx-122922308 AX-123320516 2 13072027 CTCAGCTAACTAGTTACCCCTGTTCAAGGCCACCT[A/G]CCCTCACAGACATTTTACAGACTCTGCAACCCACC R 2 1 2 1 101000 r 74 goat snp35242-scaffold422-1352095 2 122630391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433819 Affx-122935166 AX-123304160 2 13127893 ATTCTGGAGAATCAGAAAACTGAATTCTAACACTC[A/G]CTGTGTAAACTTATGTCTCATCACTTGTCCGTTTC R 2 1 2 1 101000 r 74 goat snp35241-scaffold422-1296229 2 122573997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445740 Affx-122926089 AX-123316077 2 13161369 ATAATAGCTTTTTGTGTTGTTTGTCTCCCCAGGGA[C/T]GCTAACATGATTAGTATTACCCAGTCATGATAGAG Y 2 1 2 1 201000 r 74 goat snp35240-scaffold422-1262753 2 122540040 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442829 Affx-122927701 AX-123313166 2 13191492 TATTTCCAGTTTACATCCGGAGTATTTATTTCTCG[A/C]GACTGACTTTTCAACATAGTATTTTCAGGTATATT M 2 1 2 1 101000 f 74 goat snp35239-scaffold422-1232630 2 122509551 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427579 Affx-122939474 AX-123297922 2 13226022 TGTCTCCTGAACTTCCCTCCTTCCACAGATGCATC[G/T]AATGTAAAGTAATTCAAGTCACCATAGCTGGAATT K 2 1 2 1 101000 r 74 goat snp35238-scaffold422-1198100 2 122475008 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423248 Affx-122942679 AX-123293594 2 13259224 TTTTTTATTGTATGCCTTTTTATTTTACTTTTGAT[A/G]TGGTCTACACATACAACTTTATTTGAAGCAAATCT R 2 1 2 1 101000 r 74 goat snp35237-scaffold422-1164898 2 122442874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448370 Affx-122924107 AX-123318706 2 13302225 ATTATTGAGTTTTAAGAAGTCCTAGTTTCTCAGCT[A/G]TTAAATGAAAGTTAAAATGGCACTTATTTCATTGA R 2 1 2 1 101000 f 74 goat snp35236-scaffold422-1121897 2 122400178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783458 Affx-122970339 AX-385270521 2 13331929 AATAAAGTACAATTGATACATTTATCAAGACAGAC[A/G]TCTCTTCCACACATACTGTTCTCCTTCCCTGGACA R 2 1 2 1 101000 r 74 goat snp35235-scaffold422-1092193 2 122370400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777105 Affx-122965198 AX-385264228 2 13361462 TAAAACATGTAATTTCACTTGAAAAAAATTGGTTT[A/G]TACAAGTTTAACTGAATAAAACAACTTAGAAACTT R 2 1 2 1 202000 f 74 goat snp35234-scaffold422-1062660 2 122339862 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394975 Affx-122964267 AX-123265330 2 13419975 AACTCTACGCAGTAGGTAACTGCCAATTTAACAAG[C/T]GGAAAACACAGCAGCTGCACACAGACTGTTCCGTG Y 2 1 2 1 101000 f 74 goat snp35233-scaffold422-1004147 2 122280511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786561 Affx-122926780 AX-192223468 2 13453075 TGTGCTAATGTCAAATTCTCTTATTAGATTTTAAG[A/C]GCCCCACTTCCTAAGGTTTCAGATTCTTCTTTTTA M 2 1 2 1 101000 r 74 goat snp35232-scaffold422-971047 2 122247122 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772150 Affx-122958675 AX-385259305 2 13511640 CTGCTATACAGATACTTCTAAATTAGCTGTAAAAT[A/G]TACATAGTATAGTACAATAGCCATCAAGTTCAAAT R 2 1 2 1 101000 r 74 goat snp35231-scaffold422-912482 2 122187918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423642 Affx-122942356 AX-123293988 2 13544177 CCAAATAAATAAATATTTAAAAATAAGGCTACAGA[C/T]ATCTCTCCAGTATCATAGAGCATCAGAGCTTCAAG Y 2 1 2 1 101000 r 74 goat snp35230-scaffold422-879945 2 122155160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444482 Affx-122926527 AX-123314819 2 13575248 CACACACACACACAGAGTTCAGAGATGTGTGTTTT[A/G]TTTCAGTCATGCACATGTGTATTTTATAAGGAACT R 2 1 2 1 201000 r 74 goat snp35229-scaffold422-848874 2 122123523 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425043 Affx-122941864 AX-123295389 2 13628520 ACCTGGGAAGCCTCCATATGCTCACTTAGTGCTTT[A/G]TAAACTGTGAAAGACAGCCTCAGTGTACCACTGGA R 2 1 2 1 101000 r 74 goat snp35228-scaffold422-795602 2 122070058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389667 Affx-122968717 AX-123260025 2 13674323 ATAGGGCGCACACATAGCAGACCCACTGAAGGGCC[A/G]TTTAACATTTTACGTCATTCTCTTGGACCTTGGAA R 2 1 2 1 101000 r 74 goat snp35227-scaffold422-749799 2 122024147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437950 Affx-122931621 AX-123308288 2 13714712 CATAGAAAAGACATCACACACATACATGTATTTAT[A/G]CATGTATATTACAGTTGTTAGTGATAAACATCTAT R 2 1 2 1 103000 r 74 goat snp35226-scaffold422-709410 2 121984442 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766019 Affx-122957756 AX-385253438 2 13757148 CATTTGAAAATTAACAGGCTCACACTCGCTCTCCA[C/T]GACCACCAGTTCTCAGTATTACCTATTTGGGACTG Y 2 1 2 1 101000 f 74 goat snp35225-scaffold422-666974 2 121941747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441584 Affx-122928673 AX-123311921 2 13795481 TCATAGACGATAAAAACAATACTTGCAGGGAATAA[C/T]GTAAGGCACATGATCAGCTGGGTATTAGAGACTCC Y 2 1 2 1 201000 f 74 goat snp35224-scaffold422-628641 2 121902761 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383276 Affx-122972726 AX-123253634 2 13828899 CCAAGTTAAATTTAAATTCTACATCTTCCTGACTA[C/T]AAATTCTATTAAAAACATTAACCTCCATGATGAAA Y 2 1 2 1 101000 f 74 goat snp35223-scaffold422-595223 2 121867744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420651 Affx-122944828 AX-123290998 2 13874248 TTTACAACCCTTCAAATGCACACCCATCCCTTTAG[A/G]ACAAGGCACTGGAAATAATTTGCAGGGCTGTTTAT R 2 1 2 1 101000 f 74 goat snp35222-scaffold422-549874 2 121822529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407795 Affx-122954565 AX-123278146 2 13904903 TTCCAGACCCAATTCCAACAGGGGTGTGTTCCTCA[C/T]ACCAACAGGCCAATTCTTCCCCACACCAACAAGCA Y 2 1 2 1 101000 f 74 goat snp35221-scaffold422-519219 2 121791284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793067 Affx-122947817 AX-385280045 2 13933883 ATAAACAGATGTGAATTTTTGTTTCTACGTAATAG[C/T]ATACATGAAGGACATTGTAATCAGCCATTCCAGGA Y 2 1 2 1 101000 r 74 goat snp35220-scaffold422-490239 2 121762401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785771 Affx-122934314 AX-385272811 2 13964453 TCAAAGAAATCAAAGTAAGTCTCTCTACCCAATTC[A/G]CACAAGCCTTCATAATCACGTGTTTCACAGCATGC R 2 1 2 1 101000 r 74 goat snp35219-scaffold422-459669 2 121731857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392240 Affx-122967573 AX-123262597 2 14038058 TATTATAAAGACTAATTAAATATAGAAATGTGATA[C/T]GTAAACATAGGGAAAATATATATTGAGTGAATTAG Y 2 1 2 1 101000 r 74 goat snp35218-scaffold422-386064 2 121657035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419387 Affx-122945613 AX-123289735 2 14119591 GAAAACAGAAGTGCTCGTTGCAAGGGAAGTGAATT[A/G]TGCAGAGGTAGGATTTGAAATGGTTGAAACAGCAG R 2 1 2 1 101000 f 74 goat snp35216-scaffold422-304531 2 121574732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387044 Affx-122969912 AX-123257402 2 14152428 TTGAACTTTCAAAAGTTCTCAGGTATATCCTCTGC[G/T]AGTGAACTATGCAGACTTTGAGTGCAAGCCTCTGC K 2 1 2 1 101000 r 74 goat snp35215-scaffold422-271694 2 121542012 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409464 Affx-122954072 AX-123279815 2 14215380 TTTGTGGACTGACACACACACTGAAATTGAATGGC[A/G]CACTTAGACACTACGCTATTAGGACTCCATCAGTC R 2 1 2 1 201000 r 74 goat snp35214-scaffold422-208742 2 121478323 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421361 Affx-122944053 AX-123291708 2 14264594 ACACCTGTTTCAGCTGGACTGAGAAACAGCACGCT[A/G]TCTAAAGGGGGCTACAATGGGCTGGATAACCGACA R 2 1 2 1 101000 f 74 goat snp35213-scaffold422-159528 2 121428472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391839 Affx-122967003 AX-123262196 2 14299056 AGAGAAGTTTCTTTTAAGTACTTGTCTTCATATAG[C/T]GCCACGTGGCTGTGGTGTACTTAGGAACACCAGGA Y 2 1 2 1 101000 f 74 goat snp35212-scaffold422-125066 2 121393848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790778 Affx-122951696 AX-385277779 2 14360228 AAGCATCTTTAAATAAACCACTGGCATATTAATGG[A/C]AAGACCAAGCAATGGAATAGAACAGAAAGCCCAGA M 2 1 2 1 102000 r 74 goat snp35211-scaffold422-63894 2 121332462 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396010 Affx-122963487 AX-123266365 2 14392269 AAAATATTTACACTCAATCATAGCCAAATTAACCC[A/G]GGGGTAGCTACTAATACTATCAATAAATTTGCAAA R 2 1 2 1 201000 f 74 goat snp35210-scaffold422-31853 2 121300176 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793727 Affx-122937029 AX-385280699 2 14420827 ATAAATTCTTGTTTGGATGTTATTCTTTTCTCAAG[C/T]GTAAGTATGAAATGTACTTTCACCAGTGCTATAAG Y 2 1 2 1 101000 r 74 goat snp35209-scaffold422-3295 2 121271182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796169 Affx-122962559 AX-385283120 2 14466134 GGCAAAATGTCCTGGTTTTACTGAATATGTTTACC[A/G]TGTGAATTATTTCTCCCAAGCAGTCATTTTACAAC R 2 1 2 1 101000 f 74 goat snp38200-scaffold480-41913 2 121225739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786305 Affx-122943522 AX-385273339 2 14496839 CCTGTGTTAGACAATATTTGAAAAGGAACTACTCC[A/G]TTTAGAAAATGATAGTAATATCTTTTTGCCCTCCT R 2 1 2 1 101000 f 74 goat snp38201-scaffold480-72618 2 121194945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797660 Affx-122940835 AX-385284599 2 14528450 AAAAATAGCAGCCAAAACTCAGTTACCCAGAGTAC[G/T]TACTAGTTAGTTAGGAGGTAATGCTATTTTCCCAA K 2 1 2 1 101000 f 74 goat snp38202-scaffold480-104229 2 121163020 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388422 Affx-122969278 AX-123258780 2 14560881 GCTATAATTTAAATTAGTTTAAAATTCTATAAATT[A/C]TCCATCTTCATTTTGGGAAAGCAGTTTATACATAT M 2 1 2 1 103000 r 74 goat snp38203-scaffold480-136660 2 121130831 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775726 Affx-122933615 AX-385262857 2 14680037 GATTTTATTAAAAACACCATTGCACCCATATTTCC[A/G]TCAGCATCTTCAGGTATAATGCTTTAAAAGACTTA R 2 1 2 1 101000 r 74 goat snp38205-scaffold480-255816 2 121009124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420834 Affx-122944661 AX-123291181 2 14730503 GAGCAGTTCCCACCACATTATGAACTTAATGCTAT[G/T]AAATATGCAGTTTTAAAAAATAAGAGCTTCTCTAT K 2 1 2 1 103000 f 74 goat snp38206-scaffold480-306282 2 120958554 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783798 Affx-122966723 AX-385270854 2 14799346 CTGGGAAAAAAATATCTTGACCTCTTTCCACCAAG[C/T]AGTGATACTGAAAGCCACAAGATAATAAACGTTAG Y 2 1 2 1 101000 f 74 goat snp38208-scaffold480-375125 2 120888954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442046 Affx-122928395 AX-123312383 2 14851284 CTGAACAGAATTATGTTCAAAAGACAAAACATTTT[A/C]TTGACTTGGAGAGATTACAAAGCATGCCAAACAGA M 2 1 2 1 101000 r 74 goat snp38209-scaffold480-427063 2 120836881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401037 Affx-122959666 AX-123271390 2 14883818 AATTTGACATGTCTCTCTGCCTTCTTTGCTCCAGT[A/G]CTAATTAAAATAGTCAATAAAACAATGTCACCACT R 2 1 2 1 201000 r 74 goat snp38210-scaffold480-459597 2 120803899 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388571 Affx-122969539 AX-123258929 2 14926744 TAGAAATCTCCTGGAGTAGACCAGATCTTAAAGTT[C/T]ACTTAGTGATAGGAGTAGTACCATTGCTGGTAGTA Y 2 1 2 1 101000 r 74 goat snp38211-scaffold480-502523 2 120760917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440687 Affx-122929916 AX-123311024 2 14963911 CAAAGTTTTCCTATTAAAGACAGAAAGAAATGGAA[A/G]TGGTGCAGACAGCCCAAGGGTTTTTATTTCAAGTT R 2 1 2 1 101000 r 74 goat snp38212-scaffold480-539690 2 120724003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415620 Affx-122948594 AX-123285969 2 15001699 AATATAGGAGGTACGGCAGAACAAGATAGCAAGAA[C/T]AGTTCAGTTTTCTGGATGTACAACTGAGATGCACT Y 2 1 2 1 101000 f 74 goat snp38213-scaffold480-577478 2 120686207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416748 Affx-122948193 AX-123287096 2 15064308 AAGTTTCTGTTTAGACAAGTATTCCAGTAGCTACC[A/G]GCATCACAAAAAGACAACCAGATTTTTAGGTGTTT R 2 1 2 1 101000 f 74 goat snp38214-scaffold480-640087 2 120623377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775405 Affx-122943253 AX-385262536 2 15142350 TTTTCAAAACAGCGGCAGATAAGCAGCAAATTTAA[C/T]GTCAGGAAAAAGGCTGCTAGAGATAGACTTATTAA Y 2 1 2 1 101000 r 74 goat snp38216-scaffold480-718129 2 120544313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277232 Affx-1111835746 AX-519550738 2 15174359 GGCAATGAAGTTGGATGAAGAATGAGGGAGAAGGT[A/G]GAGGAGAAAATAACACTGGTGTTTTGTAACATGGG R 2 1 2 1 101000 r 74 goat Random2.2K-168 2 15174359 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789629 Affx-122921099 AX-385276638 2 15178463 AATAGCTATGAAAAAGTAAAGGGGTCATTTTGAGA[A/G]AATCAGTGATATCCAAAAGATAACATACTAATTTC R 2 1 2 1 101000 f 74 goat snp38217-scaffold480-754242 2 120507788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432310 Affx-122936306 AX-123302651 2 15215485 ACTAGAAACACGAAAATTACAAAGGGAAAAATCTC[A/G]TTGGAAACCGCAAATATACAGTAAAAGCAGTTAAT R 2 1 2 1 202000 r 74 goat snp38218-scaffold480-791264 2 120471386 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382430 Affx-122974240 AX-123252788 2 15251410 AAATACATTCTTTCTCTGATTTGGGGCTCTGCTGC[A/G]CATCTCCACCTTCTCTATTTTTAGCTTTGCTCATA R 2 1 2 1 103000 f 74 goat snp38219-scaffold480-827189 2 120435074 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395940 Affx-122963580 AX-123266295 2 15301931 ATTTGCAAAAATGTGTACAAATAGAGTGAGTAATG[A/C]TGAAAGTTGTGAGTGCTTTGTACAAAAGTCTTTAA M 2 1 2 1 101000 r 74 goat snp38220-scaffold480-877710 2 120382890 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433338 Affx-122935151 AX-123303679 2 15330570 ACAGTCTGCTGTGTATTGAATAGATTATTGTTTGC[A/G]TTTTTTAAAGAATTGATCAGTTTTATCTAAGCTGT R 2 1 2 1 102000 f 74 goat snp38221-scaffold480-906349 2 120353569 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413497 Affx-122950643 AX-123283846 2 15371216 GAAGCTGCCTCAGTAGTTTCTAGCTCCCTTTGAAG[A/C]TTGCAGGAAAGAGGAAAGATGTGGGAGGAAATCAG M 2 1 2 1 101000 f 74 goat snp38222-scaffold480-946995 2 120313096 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383998 Affx-122972918 AX-123254356 2 15449492 TTTGATTAGTGTAAATCAAATTGCTACAAACTGTT[C/T]TCTGAACCAACACTAGGCTGTTTCAGATGTGCATT Y 2 1 2 1 101000 f 74 goat snp38223-scaffold480-1025271 2 120234133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391075 Affx-122966838 AX-123261432 2 15539512 GACTAAGCACTCACTCAAGCGAGTAGAAGTTAAAC[C/T]ACTCTGCATTAGAAGTTATCAAGAATGTAAAGATC Y 2 1 2 1 101000 f 74 goat snp38225-scaffold480-1115291 2 120143928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272556 Affx-1111833161 AX-519546272 2 15558544 CCAGCCTGGTTAGGATTTGGGGAGGTGGGAAGGCC[A/G]ATGGGTAAACACGTTTGGTGCTTGAGTTTCTGTGT R 2 1 2 1 101000 r 74 goat 2_15558544_AF-PAKI 2 15558544 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792487 Affx-122920457 AX-385279468 2 15579213 TTACTTATTATCTTATATGTTATTCAAAATAAAAC[G/T]AATGAAAGTTTTCAGTGAATTAAGAGAGAGTAAGT K 2 1 2 1 202000 f 74 goat snp38226-scaffold480-1154992 2 120103519 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402332 Affx-122959070 AX-123272685 2 15627719 GTGCTCTATTACGTTGGAGTTTTATCTACCCAGTG[A/G]GGTCAGATTCAGATAGCCCAGGGTTACCTGTTTTA R 2 1 2 1 101000 f 74 goat snp38227-scaffold480-1203498 2 120056888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804440 Affx-986696607 AX-385291021 2 15638266 AAGGCCGCCTCCGTCATCTCCTCCAGGGTCGGGTC[C/T]TTGGTGTGGTCTTGCTGAACATTATACTTCATGTC Y 2 1 2 1 600010 r 74 goat 2_15638266 2 15638266 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 38442292 Affx-122928255 AX-123312629 2 15656877 AAGTTAAGAAGAAGCTAGGAGAAGTTAGGTTTTTA[C/T]GTTGAGTTTCTTTCATATACATAGGCCTATTCTTA Y 2 1 2 1 101000 f 74 goat snp38228-scaffold480-1232656 2 120027050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800441 Affx-122920856 AX-385287362 2 15711031 TGTCCTCAATATGTTGTGATATTTTTACACTGTGT[A/G]CTTTCTAATACCAATTATTACCTCTTATAATAATG R 2 1 2 1 101000 f 74 goat snp38229-scaffold480-1286810 2 119971255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404307 Affx-122957024 AX-123274659 2 15769357 CATTTTCATACCTCTCAGTTCTTTAAGGCAGAATC[A/G]TGTAATTTTGATGTTGCCTACAAAATATCAACAGA R 2 1 2 1 201000 r 74 goat snp38230-scaffold480-1345136 2 119911460 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779980 Affx-122921052 AX-385267079 2 15821023 AACAGAAAAACTCTAAAGCCCTTAGTCCATGTTGC[A/G]CAAAGAACTTCAAAGGTTTCAATTAATGGTGTGTA R 2 1 2 1 101000 r 74 goat snp38231-scaffold480-1396802 2 119858895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410453 Affx-122952382 AX-123280803 2 15858625 AGATGGTTCACTGCTGTATTCTCTGTCCCTAGAAC[A/G]TTGCTTGTACATCAGAGGCTCTGTTGTGTCCGACT R 2 1 2 1 201000 r 74 goat snp38232-scaffold480-1434404 2 119820777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435886 Affx-122932782 AX-123306225 2 15914252 TGAGTCCCTGGAGAAAGTTTCATTTATAAACATAC[A/G]TTTTAATCCAAATCAAGCACTAATCATTTACTTTG R 2 1 2 1 201000 r 74 goat snp38233-scaffold480-1490031 2 119765322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794726 Affx-122963871 AX-385281686 2 16004340 TTTGCAAAATCTTTGGGACAATTTACCAAACAATC[A/G]TATTTTATGTTCAACAACTTGGCTTGCCCAATAAA R 2 1 2 1 101000 r 74 goat snp38235-scaffold480-1580119 2 119674072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451072 Affx-122921419 AX-123321406 2 16035023 AATATTAAAACTGGAAAGGATGTCAGAGTTTATCT[A/G]TTTGAACTTTCTCATTTTGATACAGGAAAAGCTTT R 2 1 2 1 101000 f 74 goat snp38236-scaffold480-1610802 2 119642477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383551 Affx-122972611 AX-123253909 2 16088516 GGCTTTAGCCCAGTAAGCATTAGGGTGGTTTGCTA[C/T]ACAGTAATTGATAAACTCTTCCATTGGTTGCTTTT Y 2 1 2 1 101000 f 74 goat snp20673-scaffold2035-483220 2 119587953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422093 Affx-122943580 AX-123292440 2 16125266 AGGGAGGTTATTCCTGTTGACCTTTGACTTGACCC[A/G]TGAGTAAAAAGCCATTAGACCCACAGTGAAAAGAA R 2 1 2 1 201000 r 74 goat snp20672-scaffold2035-446470 2 119551023 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398865 Affx-122961048 AX-123269220 2 16163462 TTATAGCACATTTTGCTTGGTCATTGGCTGAGGCC[A/G]CCCAAAGAAGGGCATGACCTGAGCTCCAAAGCTGA R 2 1 2 1 201000 r 74 goat snp20671-scaffold2035-408274 2 119512977 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425193 Affx-122941038 AX-123295539 2 16240406 CCCTACATGACTTTGGGCAGCTATCCCCTTTCTTC[A/G]TCTACCTGTGTAAAGCTGGCCAAAGGTGAACCAAG R 2 1 2 1 101000 r 74 goat snp20669-scaffold2035-331330 2 119435049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793033 Affx-122954307 AX-385280011 2 16286652 CTAAAGTAAATAAACTTCCACCCACCTAGACAGTA[C/T]GCTTTTTGATTGCTGATGCAAGACAATCTCAGTAA Y 2 1 2 1 101000 r 74 goat snp20668-scaffold2035-285084 2 119388571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409594 Affx-122953564 AX-123279945 2 16333103 AACATGAAAAGATCATCAAGGAGTTTAGCTCAGAT[A/G]TGATGAGAACTCAGGACAGCCTATGGAAAGTCACC R 2 1 2 1 201000 f 74 goat snp20667-scaffold2035-238633 2 119342183 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439210 Affx-122931032 AX-123309547 2 16396894 CCAGTGACACACGCCCCAGGAACTTCCCCTCAAGA[C/T]GCTCCCTGCAAGGTGCCTTACAGGTATATCTGTTG Y 2 1 2 1 101000 r 74 goat snp20666-scaffold2035-174842 2 119278302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776183 Affx-122924015 AX-385263311 2 16440937 ACTTTCTGTAGAAATCTTCACCATGGAAAATAGTA[C/T]ACTTCACATTTTCTTTAGTTATGTCACAGATGAGG Y 2 1 2 1 101000 r 74 goat snp20665-scaffold2035-130799 2 119233059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404362 Affx-122956815 AX-123274714 2 16483515 GCCAATTAGAGCATGGACTAATGAGACTAATATCA[C/T]GGCCTTCCTGTTGTCTAACTGGCTCTAATATAGAT Y 2 1 2 1 101000 f 74 goat snp20664-scaffold2035-88221 2 119190328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434207 Affx-122934856 AX-123304548 2 16515514 ACATTTGGATTTAATCCTAAATTAGGTCACAAGAT[A/G]GAGAACTTCAAGCACAAAATTACGACATGATCAGA R 2 1 2 1 101000 f 74 goat snp20663-scaffold2035-56222 2 119157831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769610 Affx-122966341 AX-385256780 2 16545571 CTTTTACCTGTGATGCTATCAAAGGACATAGATGC[A/G]TACGTGACAAGGTCAAACAAATGCATCATGGTAAA R 2 1 2 1 101000 f 74 goat snp20662-scaffold2035-26165 2 119125743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771711 Affx-122973954 AX-385258868 2 16574820 GTGAAAGGATGGTCCTTGTTTAAATTTTTCAGCAT[A/G]CTTTACATTTTGTATTAGAGTCTCTGACAAGACAG R 2 1 2 1 101000 f 74 goat snp6771-scaffold1245-1331909 2 119096414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438221 Affx-122931445 AX-123308559 2 16632478 ATTTATGGGAAGTCAGGCATGAAGGTGGGATATCA[C/T]GCTCCATTTTTTAACCAGGGTGACAGCTGGTCCCA Y 2 1 2 1 101000 f 74 goat snp6770-scaffold1245-1274251 2 119038965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775836 Affx-122975625 AX-385262967 2 16688259 CAAAACAGTACATACAGCTCAGAGGTGGTTCATTT[A/G]TATCTGAGTATTTTGTCCATGCACTGAACATCTTA R 2 1 2 1 101000 f 74 goat snp6769-scaffold1245-1218470 2 118983524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782303 Affx-122944321 AX-385269381 2 16726644 AGATTGAGTATATATTCATACTTGGTTATATCTGT[A/G]TAAACAAACCCAGGAAAGATAGGCAAGAAATATTA R 2 1 2 1 201000 r 74 goat snp6768-scaffold1245-1180085 2 118945168 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768981 Affx-122942001 AX-385256155 2 16763147 ACACAACATGATCAAATTATGTCTCCAAATGCATC[A/G]TAAAAAATGTTGCCCCAGTTGCTAAAATAGCAGGT R 2 1 2 1 101000 f 74 goat snp6767-scaffold1245-1143582 2 118907890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394268 Affx-122964720 AX-123264623 2 16799114 GTACTAGTTCAAATTAATATACCCCTCAGGATTGA[C/T]CCATTCTGCCACCTCAGAATCAGGGTGGATGATAA Y 2 1 2 1 201000 r 74 goat snp6766-scaffold1245-1107615 2 118872126 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790914 Affx-122966187 AX-385277911 2 16846202 TTCTCCTCCTTTCCTTAGAACATCTAGGTGATCCC[C/T]GGCTTTTGGCTTATCCTAGAAATTTTAATATTTGA Y 2 1 2 1 101000 f 74 goat snp6765-scaffold1245-1060527 2 118823344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415740 Affx-122948499 AX-123286089 2 16883658 ATTACTATGGGGCTACGGACAAAGATTCATCTTCC[A/G]TAATTTCTTCATGCTGACATATGGCGCCATACTCT R 2 1 2 1 101000 f 74 goat snp6764-scaffold1245-1023071 2 118785699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443506 Affx-122927796 AX-123313843 2 16944545 CTGAAACCGCCAGACATGCTCTCCTCTCAGAACCT[C/T]TGTCTTCTTCCTCTACCTGAAACACACCTCAGGCG Y 2 1 2 1 101000 r 74 goat snp6763-scaffold1245-962184 2 118725384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438566 Affx-122931167 AX-123308904 2 16973362 ACAACCAAAATACACACCTCAGTAATCCTACACTG[C/T]AAAGTGAATCTGGCAAACTGCCCTGTCCAAAAATA Y 2 1 2 1 101000 f 74 goat snp6762-scaffold1245-933367 2 118696657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414660 Affx-122949310 AX-123285009 2 17031741 TTCATCAGCTATCTATACAGCCTGGCCTTCACTTC[A/G]CTCATCTCTGGTAAAATGTTATCTTATCATTTTGT R 2 1 2 1 201000 r 74 goat snp6761-scaffold1245-874988 2 118637437 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773435 Affx-122957342 AX-385260577 2 17063411 AACAGGGACATGTAAGTATGAAAATGTGAAGTATA[C/T]TGGCCTACCAGGCTAATTTCTCTTAAACATCAGGA Y 2 1 2 1 101000 r 74 goat snp6760-scaffold1245-843318 2 118605720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277255 Affx-1111835757 AX-519550760 2 17100962 GGACAGGAGTTGAGTCGCAGCGTCATGGAGTTGAC[A/G]TCATCCCCGAGGGTGACTGCAGTGAAGAAAATGCT R 2 1 2 1 101000 r 74 goat Random2.2K-171 2 17100962 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415278 Affx-122948837 AX-123285627 2 17114501 AGGAGGATGCGGGTGAGTAGAGGACTGACTGGAAA[C/T]GGCAACATGGGAATTTTTTAATAGCATTTTACATT Y 2 1 2 1 101000 r 74 goat snp6759-scaffold1245-792228 2 118554621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778275 Affx-122936670 AX-385265390 2 17146719 GGCAAGCGGCCTTGGTAGGAACACTTTGCATTCCA[C/T]GCTTCCAGTGCTTCTAGATGGAATCATTTTGTTCA Y 2 1 2 1 201000 f 74 goat snp6758-scaffold1245-760010 2 118522296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766000 Affx-122947332 AX-385253422 2 17181135 GTGATACTTGAAAAATGCACTCTATCATTTTAAGC[A/G]TAGCTCTGAAATCGCTGGTTTGAAGTGGAGCATAT R 2 1 2 1 101000 f 74 goat snp6757-scaffold1245-725594 2 118487659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779596 Affx-122925039 AX-385266699 2 17239352 TGAGCTAAAGAAATTGTTAAAGGGTGGAGAAAGGG[A/C]GAGGAAAATTGATTTTTAGCCTAATTTTACAAAAA M 2 1 2 1 101000 f 74 goat snp6756-scaffold1245-667377 2 118429137 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402313 Affx-122959085 AX-123272666 2 17268893 TCCAGGTGGAGGGCACAGCTGGAGGCTTTCAGGTG[C/T]GAGTCTTCCTGCTGGGTTGGAGAAACAGCAAGGAG Y 2 1 2 1 201000 r 74 goat snp6755-scaffold1245-637836 2 118398903 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801237 Affx-122958199 AX-385288150 2 17303120 CCTCTCCTCCAGCAAAACTGTACTTATTTCTGGTA[C/T]GGTTTTGCTGCTATTTTGCAGGGCCTCTCATCTCC Y 2 1 2 1 101000 f 74 goat snp6754-scaffold1245-603609 2 118364651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800424 Affx-122952508 AX-385287345 2 17333864 TGAAGGGAATGGGCAAAATGGCAATGAGAACAATA[C/T]GCTATTTACCTGCATTGTGAAACTCATAAATGACA Y 2 1 2 1 101000 f 74 goat snp6753-scaffold1245-572865 2 118333891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767509 Affx-122977075 AX-385254771 2 17366746 TCCTGAAACAGAGCTTTCCTGGAAAAGAATTTGAT[A/G]CTTTATTCATGTTAAGAATAACTTCATGGGATAGC R 2 1 2 1 101000 f 74 goat snp6752-scaffold1245-539983 2 118300553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770251 Affx-122967816 AX-385257417 2 17431727 AAAGACAGCTTCTAATTGACAATAATAATTCCAGG[A/C]ATCAGTCAACTATTTTAAGATGAAATTGTCCATAA M 2 1 2 1 101000 f 74 goat snp6750-scaffold1245-475002 2 118235182 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794747 Affx-122935406 AX-385281707 2 17461494 ACATTTCTTTTTATGGATATGACATTTATGAAACC[A/G]TACCTTCCACATAAAGAGTGGCTGTTGAGGTAGCT R 2 1 2 1 101000 r 74 goat snp6749-scaffold1245-445235 2 118205513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425245 Affx-122940996 AX-123295591 2 17503370 GTGAAATTGTAAAACAAAACAAAAACCAAACACAC[A/G]TCTAAACCCAAGTGTAAGGATTAATATGATCTGCA R 2 1 2 1 101000 r 74 goat snp6748-scaffold1245-403359 2 118163607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779061 Affx-122976430 AX-385266166 2 17563283 TATTTCTGATATTTAAATCCTAGAGGATATCAATT[A/G]TTTCAAATTCCTGTGCTTGTTTTTGGTGGTAAATT R 2 1 2 1 303000 r 74 goat snp6747-scaffold1245-343446 2 118103687 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413500 Affx-122950641 AX-123283849 2 17600289 AAAAGAATTAAAAAATGGGCTTGATTCTTTAAAAA[C/T]AAAACTTTTCCATGCTAGGGCAGGTACTACCCTAG Y 2 1 2 1 102000 r 74 goat snp6746-scaffold1245-306440 2 118068654 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434607 Affx-122934093 AX-123304948 2 17639395 AGTAACATTTAGAGATGCCAAGATTTAAATGTGTC[A/G]TCATAATACTTAAAAAAATAATTACCAATTGGAGT R 2 1 2 1 102000 f 74 goat snp6745-scaffold1245-267334 2 118029550 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405298 Affx-122956846 AX-123275650 2 17675376 TCATTTTCTGCAGAAACACGGAAATAGTATGGAAC[A/G]CCTTCTAGCAGGTCACTGACTCTGAGGATCTGACG R 2 1 2 1 201000 f 74 goat snp6744-scaffold1245-231353 2 117993569 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445229 Affx-122925499 AX-123315566 2 17705903 CATCCTGAGAAAGCCTCGGCATTGCCTCTTTGTGG[C/T]TGGAGATTATAATCACCGGTTGCTCTTCTCTGACC Y 2 1 2 1 101000 r 74 goat snp6743-scaffold1245-200826 2 117963025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770412 Affx-122967346 AX-385257578 2 17746617 CCAGCTATCTTTCTTTGAGGAAATTTATGTTAATT[A/G]TCATCACCATAATAATATATTAGAGCTGTCCTATT R 2 1 2 1 101000 r 74 goat snp6742-scaffold1245-160112 2 117922101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770173 Affx-122963611 AX-385257339 2 17792534 CTCTTTACATGCTGAAAAAATGTGAGGCTTGGATA[C/T]AGGTTTGCATAGTACAAAACAAAGTCACTACACGT Y 2 1 2 1 101000 f 74 goat snp6741-scaffold1245-114195 2 117876444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407850 Affx-122954521 AX-123278201 2 17833841 TTAATTCCTAACTTTAAAATTAGCTGTTAGTTTCC[A/G]TAGAGACCTCAGTTGAGTATATAAATTCCCTGCTA R 2 1 2 1 101000 r 74 goat snp6740-scaffold1245-72888 2 117835976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448244 Affx-122924205 AX-123318580 2 17869603 GAGAGACAGAAATGATTTTGATTATAAAATGAACT[A/C]GTGACTTGAAATTTATTAGAGAAGTGACTGAAACT M 2 1 2 1 101000 r 74 goat snp6739-scaffold1245-37126 2 117800298 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799791 Affx-122973611 AX-385286717 2 17899205 AAGAACGTACCATTCACCTACTTAGGTATCTCATT[A/G]ACATAATGAGTGATTGTGTGTCCTTATGTAACTTC R 2 1 2 1 101000 f 74 goat snp6738-scaffold1245-7524 2 117770942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409357 Affx-122954171 AX-123279708 2 17935302 GGAGCAGACATCAACTGTCTTGCTGTACCAGAACC[G/T]AGTACTCTTTCTCTTCTTCCAGTTTCTGCCTATGT K 2 1 2 1 101000 f 74 goat snp27453-scaffold2926-28474 2 117729264 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440850 Affx-122929258 AX-123311187 2 17997502 GCACATCCAACTGCCACTGCCCCCGCCCCAGCATC[A/G]CCACCTTACATTCCCAGACTAGGGATACCCCAGGT R 2 1 2 1 101000 r 74 goat snp27454-scaffold2926-90674 2 117666477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776425 Affx-122929623 AX-385263553 2 18046932 GAATGTATAGCTGAGGCAGGGGGTGTGGATAATCA[C/T]CCCTGAATAATTGAGGTTTATAGTCCTTTATTCCC Y 2 1 2 1 101000 f 74 goat snp27455-scaffold2926-140104 2 117620627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425945 Affx-122941186 AX-123296291 2 18089670 ACAGGTGGCAGATGGCATGAACATTATTACAGAAG[A/C]TGGAAAAATGGCAACTTGTATTTGGTAACAATGCT M 2 1 2 1 201000 r 74 goat snp27456-scaffold2926-182842 2 117578123 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277195 Affx-1111835789 AX-519550701 2 18104378 TTAAATGCACGTCAGTATAATGCTTTCCGGAACAC[A/G]TCACTTAAAAATGAAGGTCTGGTCCATAGGGGACA R 2 1 2 1 101000 f 74 goat Random2.2K-175 2 18104378 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450400 Affx-122922072 AX-123320735 2 18107006 TTCCTCCTTGCAGAAGGCACTTGTCGATAGGAAGT[A/G]CCCTCGGGCCATTATGAATATCTCAATTTAGAAAT R 2 1 2 1 101000 r 74 goat snp19176-scaffold1928-359491 2 117561261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420566 Affx-122945277 AX-123290913 2 18172327 TCCGAGGAAATGAGGATGCTCAGAGACAGGGGGAT[C/T]ATTTTTCTGGGATGTGACTGTGGATTCTTGGCTCC Y 2 1 2 1 101000 r 74 goat snp19175-scaffold1928-294170 2 117496316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272025 Affx-1111833162 AX-519545791 2 18222596 GAGTAAAAGTGGCTCAGTTGGGTCCAACTCTTTGC[A/G]ACCCCCATGGACTATACAGTTCATGGAATTCTCCA R 2 1 2 1 303000 f 74 goat 2_18222596_AF-PAKI 2 18222596 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399778 Affx-122960299 AX-123270133 2 18257948 TTTGAGAATTCTCAGCTTGTTGCCTCATTCTGGCC[A/G]TGAGACTTTTACACATATCACAATATTTCCCATGA R 2 1 2 1 201000 r 74 goat snp19173-scaffold1928-208549 2 117410718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423234 Affx-122942690 AX-123293580 2 18292712 ACAATTTGGTGGCTGGGCAGGGCTGCTGGATGGAA[G/T]CTGGAGCCTCTCTGTACCTGAAGCTGTGCTGTCTC K 2 1 2 1 201000 r 74 goat snp19172-scaffold1928-173785 2 117378270 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406306 Affx-122955468 AX-123276658 2 18335234 AACATCATCCTAAACTACCCTTCAGCAACCAGTCT[A/G]TATTCCATTATCTCACTTTGTTCTTTTTTTATAGC R 2 1 2 1 101000 f 74 goat snp19171-scaffold1928-131263 2 117335396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383785 Affx-122973200 AX-123254143 2 18368687 CTTAATATGAAACTCACTACCTGCTTACTCTCCCA[C/T]GAGTAAGCAGGCATGTAGTCAGGCTCCAGGACAAT Y 2 1 2 1 102000 r 74 goat snp19170-scaffold1928-97810 2 117301265 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413657 Affx-122950119 AX-123284006 2 18410166 CTGTAGATATTTGTGTTTATTTCTTACTGGAGAGA[C/T]GTTACATATAAACAAAGCAGGACTATCTCGGAGGG Y 2 1 2 1 101000 r 74 goat snp19169-scaffold1928-56331 2 117250799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452039 Affx-122920894 AX-123322372 2 18458997 TGAAATCAGAAGATCAGATACAAAGAAAAGTAAGG[C/T]GGTACCAGCCTAGCATGAACGCTTACTGAAGATTC Y 2 1 2 1 101000 f 74 goat snp19168-scaffold1928-7500 2 117186963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420894 Affx-122944614 AX-123291241 2 18471639 AAAGTGCAGAAACAAAGAGAAAATCCTGTCTTCCC[A/G]TGTGGTTTGCACAGGACCATGTGAAGGGGAAACTG R 2 1 2 1 201000 r 74 goat snp9464-scaffold1341-4775090 2 117174374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803980 Affx-986696611 AX-385290675 2 18519995 ACTTGAGTATAATTAATAAGCATATGCACAAAATG[A/G]ATGGGATATTTTCATCCTGGCCAATTACAAAAGAT R 2 1 2 1 600010 f 74 goat 2_18519995 2 18519995 Ancestral_priority_1043 ancestry 0.762 recommended IMAGE 10K 10K ancestral 38386243 Affx-122970967 AX-123256601 2 18587913 AGCTGTAGGATCTATTCAGCAATAGCGGATTGTCT[A/G]TGTCTGATTTTTGCAAGTGCCAAAAATTACTGTCA R 2 1 2 1 101000 f 74 goat snp9462-scaffold1341-4658816 2 117058374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789954 Affx-122932947 AX-385276960 2 18621912 AACTGATATAAGCCAACAATTCAGAATAAGTTGGA[C/T]AGATAGGTGGAATACAGTACTGGAGGATTATCAAG Y 2 1 2 1 101000 f 74 goat snp9461-scaffold1341-4624817 2 117024160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791063 Affx-122972672 AX-385278058 2 18679157 CTGAAATCAATAAGCAGAGGTGAGTACTTTGAAGG[C/T]GAGTTTAAAAGAAATACATCCTAAAACCAGAGGAC Y 2 1 2 1 101000 r 74 goat snp9460-scaffold1341-4567572 2 116966655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776722 Affx-122936064 AX-385263847 2 18708565 ATTTTACCCAATCATTTTTGGTATTTGAACATTTT[C/T]CTTGTTTTCTAGTTTTATGTTCTCATATTTATTTC Y 2 1 2 1 201000 r 74 goat snp9459-scaffold1341-4538164 2 116937231 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782235 Affx-122962797 AX-385269313 2 18742843 ATTTGTGGTTTTTTATCCAGTTCTGTATGGAAAGG[C/T]GATGTTGTAAAATCATTCCTTTCAGTTCAGTTGCT Y 2 1 2 1 201000 r 74 goat snp9458-scaffold1341-4503886 2 116902752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775886 Affx-122975777 AX-385263017 2 18778999 GTGTGTTAAGTGAATGATTAATCACAGAAAGTGTC[A/G]CAACTATTTATACCTTACTGTATGAACCCTTATAC R 2 1 2 1 101000 f 74 goat snp9457-scaffold1341-4467730 2 116863672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437465 Affx-122932381 AX-123307803 2 18818401 TGAATTTTCTCCAAATAATTAAATGGTTCTTTCGT[A/G]TTGGTCAAATAACTTCTGGAATATTTTAACTCTTT R 2 1 2 1 101000 r 74 goat snp9456-scaffold1341-4428328 2 116826814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398329 Affx-122962130 AX-123268684 2 18865362 GGAATGGTCTGAACCTGGTCAAGGTCATTTTCTAC[A/G]TTTGCAAATGTATTTTCCAGGCCAGGTTCAAGAAT R 2 1 2 1 101000 f 74 goat snp9455-scaffold1341-4381367 2 116780072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391184 Affx-122967428 AX-123261541 2 18910083 TTTGGAGTCAAAATAATACTAAAAAGGGATGTGCC[A/G]CTTAGGAGAAAATTGTATGGTGTTTTACAGTGTAC R 2 1 2 1 101000 r 74 goat snp9454-scaffold1341-4336646 2 116736007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415888 Affx-122948479 AX-123286237 2 18971444 GTGAAGGAGTGTGTCTGCGACGGAGTTCACAGAGA[C/T]GGCTTATCAGTCCACATAAGCAGGACATCCAACCG Y 2 1 2 1 201000 r 74 goat snp9453-scaffold1341-4275285 2 116676692 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801049 Affx-122971387 AX-385287963 2 19000085 TGTTGTGAAGAGAATGTTCCAGAGTGTAGCATTTA[A/G]TATGAAGACTGGTAGCTGTCTAGTCTCTTGAGCCA R 2 1 2 1 101000 r 74 goat snp9452-scaffold1341-4246644 2 116648294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792963 Affx-122943189 AX-385279941 2 19037704 TGACCTTCATCCTACGACATTCCCAGTGTATATTT[C/T]ACATACATTTTGCCTCAGATTTGGTGTTATGTGGA Y 2 1 2 1 101000 f 74 goat snp9451-scaffold1341-4209025 2 116610363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780825 Affx-122941577 AX-385267914 2 19088198 AATCAGGCTATGTGAAGTCTGAAGCACTTTGGTTC[A/G]TTAAATTGTTTATTATGAGCACTAAAACTATGGTG R 2 1 2 1 101000 f 74 goat snp9450-scaffold1341-4158531 2 116559639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802637 Affx-122966374 AX-385289538 2 19120923 TAGTAAGGGCTCCAGACACATCAGTTGTTGTTAGC[A/G]TGAATTGTTAACCTAAAACGATCAGTCTAAACTGA R 2 1 2 1 101000 f 74 goat snp9449-scaffold1341-4125806 2 116526246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427758 Affx-122939244 AX-123298101 2 19150176 TCTTCTCTGCATAAACATGTTCCTGAGAGATTAAA[C/T]ACGTATACTGTTGCTCAAACTCAGTATAATTTCTG Y 2 1 2 1 101000 f 74 goat snp9448-scaffold1341-4096553 2 116497235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795643 Affx-122928304 AX-385282598 2 19207518 TGAAAGCAGAGCATTTAATATTCTAAGGGCAGACA[C/T]TACTCCTTGGTGAGTCTTCAAAAATCTTGTCACCT Y 2 1 2 1 101000 f 74 goat snp9447-scaffold1341-4039211 2 116439301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803511 Affx-986696088 AX-385290330 2 19235203 CGAATGTGCCATCTTAGATAGAGCACCCCATTTGC[G/T]GCCATATGTGCTATCTGAAATAACACATTATGGTA K 2 1 2 1 600010 r 74 goat 2_19235203 2 19235203 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 38441653 Affx-122929197 AX-123311990 2 19247028 AGAAAATGAGTGATTCTGGAGGGGCAAACAGAAGG[C/T]ATTAAGTGCAGGATGTGTCGGGAGGTACTGTGGAG Y 2 1 2 1 201000 r 74 goat snp9446-scaffold1341-3999701 2 116398611 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436714 Affx-122932317 AX-123307052 2 19294426 TGAGTTCCCTCTGCAAGAGACATCTCTGCAGCAAA[C/T]AGCAAGCAGGGCTCCCAAGCCTGCATGGGACTCAG Y 2 1 2 1 202000 r 74 goat snp9445-scaffold1341-3952303 2 116351188 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376214 Affx-122978805 AX-123246573 2 19363701 ATTCCTTCTTTGGGTTATCATATATACATATCTCA[C/T]GAGACCTTACTCTAATCCCCTCCTTTTTTCAAACA Y 2 1 2 1 101000 r 74 goat snp9444-scaffold1341-3883028 2 116280966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394356 Affx-122964652 AX-123264711 2 19402720 TTCTGGGAATAGCCTTGGTTAGCAATTGCTCATAA[C/T]GTCAATGCTTTTGGAAACTTTTTACAGTCATTTTA Y 2 1 2 1 101000 f 74 goat snp9443-scaffold1341-3844009 2 116241683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795615 Affx-122926863 AX-385282570 2 19465202 ATCTGGTCAGTCAACAGTTTATTGGGCCTCTACTG[C/T]GGTCCAGAAAGTATTCTAGGCCCAGAGGACTGTGG Y 2 1 2 1 101000 f 74 goat snp9441-scaffold1341-3781527 2 116177800 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774049 Affx-122950319 AX-385261187 2 19495299 TGCAAAGCTTTGGAAGGGATATATCTGCCCTCAAG[C/T]AGAAACCTTTAGCTTCGGTTACGGTGAATGAGAGA Y 2 1 2 1 101000 f 74 goat snp9440-scaffold1341-3751430 2 116147866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411812 Affx-122951251 AX-123282162 2 19533990 GACTAAATGAGACATTTTATATATATAGTAGCAAA[C/T]AGTCATAGGTACATTTCATTTTGAAAGTCCCATCT Y 2 1 2 1 101000 r 74 goat snp9439-scaffold1341-3712739 2 116109140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387415 Affx-122970405 AX-123257773 2 19597303 GACATGGAGGCACAGAGATGTTATGAGATCTGCCC[A/G]TAGGGAGAGTCATGGAGATTTCTGAGTCCCAGTCT R 2 1 2 1 201000 r 74 goat snp9437-scaffold1341-3649426 2 116047767 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424689 Affx-122941703 AX-123295035 2 19655961 ACCTTGCTTAATCTTACTAAGATTGTCAGATCACT[A/C]TAGTCATTTACTCTTCACCTAGCAACCAAACAGAG M 2 1 2 1 101000 f 74 goat snp9436-scaffold1341-3590768 2 115988958 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452612 Affx-122920484 AX-123322945 2 19699707 TTCAGGCTTCTTTGGGATGGCCCTTTCATAGGCCT[A/C]GTCATAGCAACTAGAGACACGTGATGGAATCAGAG M 2 1 2 1 101000 r 74 goat snp9435-scaffold1341-3547022 2 115945347 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383506 Affx-122972644 AX-123253864 2 19743426 AGTTCCCTCTTATCAAAGCAAATTCACTGTCAGTT[A/G]TTTTGGGGGTTCCCTTCAGCTCTGATGAATTAACA R 2 1 2 1 102000 f 74 goat snp9434-scaffold1341-3503303 2 115901609 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393555 Affx-122965408 AX-123263911 2 19791655 AGTAGTTCATGTTCTACATGTTTATCCCAAATCAA[C/T]GGATGTCTGTATGGGAGAAACCAGGTTGTGGTAGG Y 2 1 2 1 201000 f 74 goat snp9433-scaffold1341-3455074 2 115853237 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787163 Affx-122953772 AX-385274189 2 19841633 CCATTCGCAATGATCATTGGAATCCTTTCATGTGA[C/T]AGTACATTTTTTGGAAGATAGAGATTCTTCTTTAT Y 2 1 2 1 101000 f 74 goat snp9432-scaffold1341-3405096 2 115802847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411544 Affx-122951652 AX-123281894 2 19888749 CCTACTGAACTAGATGCACTGGTATTTGGCCATCT[A/G]TATACCATTCTTACTACACAAATGACCAATGATGA R 2 1 2 1 101000 r 74 goat snp9431-scaffold1341-3357980 2 115755506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769437 Affx-122964537 AX-385256607 2 19926465 TGAGTGCCTGCTACATGCTAATCACTGTGCTAAGC[A/G]TTTAATTCTTAGGAACTCACTTAATCCTTATAATA R 2 1 2 1 102000 f 74 goat snp9430-scaffold1341-3320264 2 115717349 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375434 Affx-122979181 AX-123245793 2 19958674 ATCAGGGCAATGTCTGTTCTGTTCTTTATTTAGAA[G/T]CTCTGTAAACTACATAAAGGATGAAAAAGAAGACT K 2 1 2 1 101000 r 74 goat snp9429-scaffold1341-3288055 2 115685115 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785205 Affx-122968165 AX-385272251 2 20017456 CAAACCTCCCCAGACAAGATTTAATTCTCAAATAC[A/G]TTTAGGTAGGCACTGGATGTATCTACCAGTGCATC R 2 1 2 1 101000 f 74 goat snp9428-scaffold1341-3229273 2 115625877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389538 Affx-122968278 AX-123259896 2 20048676 TTCGCGGAGTATGGAGCCGCCACCCCCTCCAGCGC[G/T]ATCCGCACGAATTTCAGCACCAAGCAACTGACAGA K 2 1 2 1 101000 r 74 goat snp9427-scaffold1341-3198053 2 115594972 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426206 Affx-122940369 AX-123296552 2 20080790 AAATTCTTTGTTTATAAGTCTCAGTTCTCCTTCTC[A/G]GCTTCTAGGGATTCTCTTTTGAAATGTTAATGGGG R 2 1 2 1 101000 r 74 goat snp9426-scaffold1341-3165939 2 115562519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443582 Affx-122927330 AX-123313919 2 20139526 TCCCAAATGCCATGGTTCCTTGTAGATGAAGGAAA[C/T]GCAGCACCAGTTCTGGTCTCTCAAGCCTCCAGGCT Y 2 1 2 1 101000 f 74 goat snp9425-scaffold1341-3107203 2 115502970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409568 Affx-122953587 AX-123279919 2 20180419 TTCTCACTAAGAGAGCCACCATCAATGCCCAAAGA[C/T]ATCCAGCTGGCTCTTTAGATGGATGGGGTTGGGGT Y 2 1 2 1 101000 f 74 goat snp9424-scaffold1341-3066310 2 115461828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804446 Affx-986696613 AX-385291026 2 20214453 AGGCAAAAAAAAATTCCTTAAAAAAAAACAAAAAC[A/C]AAAACAACTAGATCCTATTTACAAAACATGCAAAG M 2 1 2 1 600010 r 74 goat 2_20214453 2 20214453 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38446383 Affx-122925585 AX-123316719 2 20236668 AAAAGTCAACAAAAAGAATATTTTACTTACATTAA[C/T]GGGAAAGCAAAAAATGGAAGTGTCATGGCAAGTCT Y 2 1 2 1 201000 f 74 goat snp9423-scaffold1341-3010061 2 115405486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379732 Affx-122975875 AX-123250090 2 20297198 ATTTTCCTCATCCTCACTCTCATTAAGAAAATAAA[C/T]ACAATCAGAAAACAATTCGAATCACCTACCTATAA Y 2 1 2 1 101000 f 74 goat snp9422-scaffold1341-2949531 2 115344023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408864 Affx-122953997 AX-123279215 2 20328738 TCTCCTCTGGTTCCTCTATGCCAGATGCTTGTTCA[A/G]TCACTGGGTCTGTCTGCTCTGTATCTGGTATTTTG R 2 1 2 1 201000 f 74 goat snp9421-scaffold1341-2917991 2 115311902 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398610 Affx-122961481 AX-123268965 2 20391461 CTGAATTTCCCTCTTTCTTAGATGAAACTCCATCT[A/G]CATGAGTAGACAGATCCAACAGGTACCCGTAGGCC R 2 1 2 1 101000 f 74 goat snp9419-scaffold1341-2855268 2 115248741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425130 Affx-122941213 AX-123295476 2 20445133 TTAATTCTTAACTCACACTAAAATATTTATCTATT[A/G]TGTATGGTGCAGGCTTTGGGACATGATTCTCCTGT R 2 1 2 1 101000 r 74 goat snp9418-scaffold1341-2801596 2 115195002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776776 Affx-122950049 AX-385263900 2 20496916 ACCACTGAGAAAAGGCAATGAAACATGAAGATAAG[C/T]AAACAACTGCCTTCCAGTCTGTAAACCAGTTCCAT Y 2 1 2 1 101000 r 74 goat snp9417-scaffold1341-2749813 2 115143037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769993 Affx-122970423 AX-385257160 2 20556666 TATTGTACCAAGGATATCACAGAAATTATCTCAAA[C/T]GCATAAGGTAGGCATTATTTTTATCCTAAATTAGA Y 2 1 2 1 101000 r 74 goat snp9415-scaffold1341-2690063 2 115082740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783953 Affx-122929724 AX-385271007 2 20589364 CAGGCGTGCACTATCTTTGCAAATAAAAAGCTCAC[A/G]TACACAGACTATACACTGCATCCTGCTTTCCCTCA R 2 1 2 1 101000 f 74 goat snp9414-scaffold1341-2657365 2 115050192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379990 Affx-122975615 AX-123250348 2 20622014 GAGAGATGCTAGGACCCTCCATAAAATGATCAAAT[A/C]AGGCCTATTCAATCAATGTCTCTAGAGCTAAAGAA M 2 1 2 1 101000 f 74 goat snp9413-scaffold1341-2624715 2 115017403 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770270 Affx-122954636 AX-385257436 2 20651655 GTAGCATTTTCTTCTGCTAGAAATGTCAGAAAAAT[A/C]TTCCTAGAAAAGGAGACCCTCAAGGTGAGTCAGAA M 2 1 2 1 101000 r 74 goat snp9412-scaffold1341-2595074 2 114987844 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795993 Affx-122967324 AX-385282945 2 20717799 GAACAAAAATGTCGATGCATAGTAACGACTATTTT[C/T]GGCATATGCAGAATGGAAGGTGCTTAGGAAGATGG Y 2 1 2 1 101000 r 74 goat snp9411-scaffold1341-2528930 2 114921116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464112246 Affx-1110321707 AX-515588223 2 20778482 AATAGTGTGTTAGTTTCTGGTGTACAACAAAGTGA[C/T]TCATAGATATATTCTTTTTCATATTTTTTTCCATT Y 2 1 2 1 103000 f 74 goat 2_20778482_AF-PAKI 2 20778482 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449244 Affx-122923477 AX-123319579 2 20789696 AAAGGGGAAGATCCACAATATCAATAGGTGGCAGG[C/T]GCCAAGTGTGTTGCTGGTAGATACAGTGGAGTATC Y 2 1 2 1 101000 f 74 goat snp9409-scaffold1341-2457033 2 114847930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426781 Affx-122940550 AX-123297127 2 20821438 CAAATCGATTTGAACCACACTAAATCCTAGACCCA[C/T]ACTGAAACAAAACTGGTGTGTGACAAGCAATTGTT Y 2 1 2 1 101000 r 74 goat snp9408-scaffold1341-2425291 2 114816028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793565 Affx-122962331 AX-385280540 2 20876780 GATAATAATGAGTGCATGTGTCTCCAACAGCTTTT[A/C]GGAAAAGGTACAATGTTCTATATGTAAACTAGTGG M 2 1 2 1 101000 f 74 goat snp9407-scaffold1341-2369949 2 114760586 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391519 Affx-122966661 AX-123261876 2 20910714 GCAGAGTAATCATATTGTGAGAAACACCAGGCTTA[C/T]GTAGTAACAGCTGTTGCAGTTATCCATGCCGACTT Y 2 1 2 1 101000 f 74 goat snp9406-scaffold1341-2336015 2 114726573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375395 Affx-122979211 AX-123245754 2 20969690 ATCCCAAGGATTCTCTATCCTCCTTTTCCTTTGTA[A/G]TAATGGAGCTGTGGCCAGGATGAGACTTCCCCCTT R 2 1 2 1 101000 f 74 goat snp9405-scaffold1341-2277039 2 114667500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444801 Affx-122926337 AX-123315138 2 21013309 AGCCCTATCCAATATATTTCAAATTATATTCAAAC[G/T]CTAATCTATTCATGGTAAGGCTATTCCTGTTTTAA K 2 1 2 1 101000 r 74 goat snp9404-scaffold1341-2233420 2 114623860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770485 Affx-122975931 AX-385257651 2 21062750 TTGTTAGCCTTTCATAAATATGTAACCTTCAAAAA[C/T]GTTTCAGAAAAAGCCCTTCACAAACAGAGATGACA Y 2 1 2 1 101000 r 74 goat snp9403-scaffold1341-2183979 2 114574536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769030 Affx-122919968 AX-385256205 2 21114637 AGTGTAAATCACAAACAATAGAAAGACACAAGAGA[C/T]CTTATTACTCTAAGAGCCATTTTTAGCACTGCTTA Y 2 1 2 1 101000 f 74 goat snp9402-scaffold1341-2132092 2 114522555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771427 Affx-122947383 AX-385258585 2 21143621 ACAGAGAAGGGACACTGCCCGGCTCATTGGTACAT[A/C]TAGTGAAGCAAGCAATCATAGCCTGCTAGTTTTTC M 2 1 2 1 101000 f 74 goat snp9401-scaffold1341-2103108 2 114493366 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432469 Affx-122935606 AX-123302810 2 21191530 GAATGAATGTTTGATTGGTATTCTTATTTACTTGA[C/T]ATGCAAAAAAAAAAAAAAAGCCCCACCCCCTACCT Y 2 1 2 1 201000 f 74 goat snp9400-scaffold1341-2055199 2 114445522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781415 Affx-122922143 AX-385268500 2 21225157 TCCTACTTTACAGATTACTGAAAGGATTAAATACT[A/G]TATGTAAAAGACTTAAAACGGTCTCCAGCATATGA R 2 1 2 1 201000 r 74 goat snp9399-scaffold1341-2021572 2 114411359 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798582 Affx-122962009 AX-385285515 2 21355434 AGACTTTCTGAACAAGATGACTTCCCTCTTTTTAA[C/T]GGACCAGACTGCTGCTCATTAAGTACAGGAAGGTT Y 2 1 2 1 101000 r 74 goat snp9397-scaffold1341-1891295 2 114281189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794358 Affx-122956693 AX-385281322 2 21402215 GACTACAAAACCTTTTTTCGATGTCACCACTGCCA[A/G]TTAGCAGCAGTGAACCCCAGTGAATGCTGGGAACC R 2 1 2 1 201000 r 74 goat snp9396-scaffold1341-1844514 2 114234150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389859 Affx-122968154 AX-123260216 2 21452954 TTTTTGAGTTATATGCAGAAAGAACCTGAAATAGC[A/G]TCTCCACTGCAATCTGTTTTCAATTAGCTCTGTTG R 2 1 2 1 101000 f 74 goat snp9395-scaffold1341-1793775 2 114184193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275289 Affx-1111834817 AX-519548864 2 21534277 CTTCTCATCTGGGCAAACTTATAGGTTTGGATTCA[A/G]CACTGCAGTGTGGTTCAAACCTGCAGTGATCGAGT R 2 1 2 1 101000 f 74 goat GoatD01.054658 2 21534277 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435544 Affx-122933393 AX-123305884 2 21548148 TTTAAAAATAATCTCAGAAACAGAGAAATTGAGAA[C/T]TAACATCACACTATTCTATGTCCTGCTAATATAAA Y 2 1 2 1 101000 r 74 goat snp9393-scaffold1341-1698581 2 114089174 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415996 Affx-122948395 AX-123286345 2 21577895 TGAGGTGGAAGTAAGCTTAAGTTAAAAAACCAAGG[C/T]TCATATGCCAGGGACACAGTGAGCACAGAGGAGAA Y 2 1 2 1 101000 f 74 goat snp9392-scaffold1341-1668834 2 114059505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451988 Affx-122920931 AX-123322321 2 21623112 CGGGGACACCTATATAGATGGAGTTAAGTAAAGGA[C/T]ACTATAGAAAGGGAAAATGAAGGCATTTCCATACA Y 2 1 2 1 101000 f 74 goat snp9391-scaffold1341-1623617 2 114014282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799945 Affx-122974621 AX-385286871 2 21657592 GTAAGAAATTTGAAAGTTAATGGCAAATTTCAATC[A/G]TTCATTTCATTAAGTTTCATTTAGTTTCTCACCAG R 2 1 2 1 101000 r 74 goat snp9390-scaffold1341-1589137 2 113979647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396003 Affx-122963493 AX-123266358 2 21694759 CACATGGCAATAATTTTGTTGGCAAATTTAAATGC[A/G]TCTGTTCAAATTATTATTTTTAGTACCAAAGTTAA R 2 1 2 1 101000 f 74 goat snp9389-scaffold1341-1551970 2 113946180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772088 Affx-122955085 AX-385259243 2 21751380 ACAAACAAAAAGGTTAAGTAAGAGACATACAGATA[C/T]ATGTGACCATTCACTCTATTAAAGCCAAAATAAAC Y 2 1 2 1 101000 r 74 goat snp9388-scaffold1341-1495349 2 113889645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423896 Affx-122942288 AX-123294242 2 21781949 TATGACTGAAATCCATCGCGGGGGTCGCTTCTGCT[A/C]GGATTCTTGTCTTCGTGTGTGTGTATGTAAACATT M 2 1 2 1 201000 f 74 goat snp9387-scaffold1341-1464780 2 113859367 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432560 Affx-122935536 AX-123302901 2 21839525 GGGATGCAGGTGGCTAGAGCAAAGCAAGGAGTTTA[C/T]GGTGGCAATGGAAAGAGACCCAATCCTAAAGGAAT Y 2 1 2 1 101000 f 74 goat snp9386-scaffold1341-1407204 2 113801692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413718 Affx-122950072 AX-123284067 2 21888833 TTACCTATATGATGGGTAAAGTATCTAGAGGTCTG[A/G]TGAAACAGTGGGGTCTTCTTTAGTTCCCAACAGGA R 2 1 2 1 101000 f 74 goat snp9385-scaffold1341-1357896 2 113752088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382171 Affx-122974026 AX-123252529 2 21940595 CCTCTTCTCTCCTGCTACCTAGGAAATGATCTAAT[A/C]TTTCTCACTTCACAGAGAAAATGTAAGTCATCTTG M 2 1 2 1 101000 f 74 goat snp9384-scaffold1341-1306134 2 113700309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770211 Affx-122945518 AX-385257378 2 21998988 AAGAAAAACAGATTTGAAGTGAACCAGCAGGAAGT[A/G]TATTTCACTTTGCTATAATTTCTAAACCAATATTA R 2 1 2 1 101000 f 74 goat snp9383-scaffold1341-1247741 2 113640964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437641 Affx-122931804 AX-123307979 2 22043100 ACCTATATTTTTAAGTTTCTCCTTCACTCTTTTCC[A/G]CTCTCCATATAAACATATAACTAGTGCCGAAAACA R 2 1 2 1 101000 r 74 goat snp9382-scaffold1341-1203629 2 113596387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773138 Affx-122936645 AX-385260281 2 22088868 AAGAAACTGAGAATTATGGGTTGAATAAATTTGCT[A/G]TCTAACTAATGATAACAATTCACATTTAAGTGCAT R 2 1 2 1 101000 f 74 goat snp9381-scaffold1341-1157861 2 113550311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412191 Affx-122951055 AX-123282541 2 22143982 ATTTAACAGCTTATCCTGCCTTTCTTGTACAAACC[A/G]TGCTTTGGGGGTAACCAAACAGCTAACAAGAGAAG R 2 1 2 1 101000 r 74 goat snp9380-scaffold1341-1102747 2 113495459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796683 Affx-122964454 AX-385283628 2 22182319 TAAAGATACAGCCCTTTGATAGGAGTCCTCAGATT[A/G]CAGATGGACTCCTAGGCCTTTTCATCCGTTCTCCT R 2 1 2 1 101000 r 74 goat snp9379-scaffold1341-1064410 2 113457148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774301 Affx-122934500 AX-385261437 2 22280188 GTAAGCAATCATACTCTGAAAGGTCCCTGGTTTTC[A/G]TCTCTTACAGGTCTGCAAATTTCTCAGAAGCTAAA R 2 1 2 1 101000 f 74 goat snp9377-scaffold1341-966541 2 113358912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381060 Affx-122974620 AX-123251418 2 22309389 GTTCTCTAAATCATGAGAGCCTGGGCAAAAAAGGA[A/G]CACAAACCAGTCAAAAGGGGAGAATTTTTCTCTGT R 2 1 2 1 101000 f 74 goat snp9376-scaffold1341-937340 2 113323200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419397 Affx-122945605 AX-123289745 2 22347876 ACACAGTGACAGCATTTTCTGCAGGACGGTGGCAC[G/T]AGAACTGGTGACAGAGAGGGGAAGAGTTCGAGGAC K 2 1 2 1 201000 f 74 goat snp9375-scaffold1341-898853 2 113284441 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438158 Affx-122931461 AX-123308496 2 22393150 AATGGAAGCATGGTGCTTTAGGCACAGGATCACCA[C/T]GGAAGTCTCTCTTTTGTCTTTTGACTTTGCTTATT Y 2 1 2 1 303000 f 74 goat snp9374-scaffold1341-853579 2 113239463 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431268 Affx-122937111 AX-123301609 2 22430265 ACTGAAGAACGGAAACAGGGCTCATTTTCTCTTCT[C/T]GCCTTTCCCCCCTTCTCTCTCCTCATCTTCCTCTT Y 2 1 2 1 101000 f 74 goat snp9373-scaffold1341-816464 2 113202022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798018 Affx-122938301 AX-385284954 2 22467769 AGCCATACAGCTGTGGGTGAAGCAGCTGTATGATA[C/T]CCTGCCTTCCACATCGTCAACCAAATTGTCTGTTC Y 2 1 2 1 101000 f 74 goat snp9372-scaffold1341-778960 2 113163921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419816 Affx-122945832 AX-123290164 2 22525683 GCAAGCTACCAATGTGATGTAACTGAAAGTAGAGA[C/T]AGGAAGAGATATACAGTAGGGAGTCATCAGATAGC Y 2 1 2 1 101000 f 74 goat snp9371-scaffold1341-721046 2 113105599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789872 Affx-122936206 AX-385276879 2 22572067 ACAATAGAGGAGGATGAGGCAAAGGGAGTTAAGAA[C/T]GTTTGAAAATGGAATGAAACGTGGAGTTGAGGGTA Y 2 1 2 1 101000 f 74 goat snp9370-scaffold1341-674662 2 113058875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425763 Affx-122940729 AX-123296109 2 22668308 CGTTTGGCTTTGCATCTGCAGCCTGTAGCTATGCC[A/G]TTCAGTTCAGTGTTTGGTGCATAATTGGACCTTGA R 2 1 2 1 201000 r 74 goat snp9367-scaffold1341-578421 2 112962549 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383890 Affx-122973121 AX-123254248 2 22722562 CTTATTCATCTCAAGTGCACAGAACTTAGATCCCT[A/C]GTTACTTGTAACTGAATTAAAAAAAAGAAAAAAAG M 2 1 2 1 103000 f 74 goat snp9366-scaffold1341-524167 2 112908119 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399971 Affx-122960828 AX-123270326 2 22778039 TTTAAGTGGACACTGAGACACGCAGCAGAGAAGGA[A/G]GCAGCGGCTCATAGGAGGGTTTTGCGGACTTGCAA R 2 1 2 1 201000 r 74 goat snp9365-scaffold1341-468690 2 112852824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411322 Affx-122952278 AX-123281672 2 22821640 AAAATCAGTGGCTCCAAGGAAGATACTTTTGTCCC[A/G]TTTTGTGACACTGTAATTGACCAGCTTGCTCAATA R 2 1 2 1 201000 r 74 goat snp9364-scaffold1341-425089 2 112808948 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442037 Affx-122928400 AX-123312374 2 22855529 GCCCTGTGCAATGGGCTTTGCATTTCTTTTCACTG[C/T]GGCTATTTAGGAGATATAATGAAATCATCAATAAG Y 2 1 2 1 303000 r 74 goat snp9363-scaffold1341-391200 2 112774990 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404330 Affx-122957005 AX-123274682 2 22892354 CATTGCATTTAGTCATGTTTCTTGAAGTCTTCCAT[A/G]TACTAGAAGCTTCTCTGCCTTTTAAATCATGACTT R 2 1 2 1 101000 f 74 goat snp9362-scaffold1341-354375 2 112738399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429296 Affx-122938610 AX-123299638 2 22921789 TCACACAGCTCGTAAGAAGCAGACCTCAGTCAAGG[C/T]CTATCCAACCCAAAGCCCATGTTCTTAGTCCCTAT Y 2 1 2 1 201000 f 74 goat snp9361-scaffold1341-324940 2 112708489 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421623 Affx-122944472 AX-123291970 2 22952405 TCTGAAGAACTGTCCTAAAAGAACTAAACATGTTT[A/G]TTGTTGCTTAAGAGCTTCAGAGATAGGATGCTAGG R 2 1 2 1 101000 r 74 goat snp9360-scaffold1341-294324 2 112678034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420987 Affx-122944568 AX-123291334 2 22981313 ATGTTTTCTTTATTTCTTGACTCTGCTTCTCAGAC[A/G]TGTGTCCTCTGAGTTGCAGACATTCATCTGTCATC R 2 1 2 1 101000 r 74 goat snp9359-scaffold1341-265416 2 112649225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395492 Affx-122963892 AX-123265847 2 23037427 GCCATTCTCTCTCGAGCACCTCACATGATAAGAGA[C/T]AGAAAATACCACCTAAAGACATACAGGTATGTGTG Y 2 1 2 1 102000 f 74 goat snp9358-scaffold1341-209302 2 112593115 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277209 Affx-1111835796 AX-519550715 2 23053013 CAGTTAGCTTCATCCAATGGGAGGTTACCAGCCAG[A/C]AGTCTAGAGGAAGGAGAAGAAGAGTAAGGCTGGGG M 2 1 2 1 202000 f 74 goat Random2.2K-177 2 23053013 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446043 Affx-122925841 AX-123316380 2 23081441 CCCTTTATGTTTCTCTAATAGCAATAATATGCCTG[C/T]AGACTGAAACAAAAGCACTTAGGCTATTGTCTCAG Y 2 1 2 1 201000 f 74 goat snp9357-scaffold1341-165288 2 112548991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379011 Affx-122976373 AX-123249370 2 23121853 TTAAGTAAATCTAGTATTTTTCTTCTAAATGTATA[C/T]TAAATTTCTCAAATTAGATTTATTGGATTGATTTC Y 2 1 2 1 202000 f 74 goat snp9356-scaffold1341-124876 2 112508579 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424251 Affx-122942464 AX-123294597 2 23154612 CAGGAAGGCTGGGTAACAAGAGCTAGTATCCCAAG[A/G]GAGCCAGGCAGAAGTGCTTTCAGTTTGATGACCTA R 2 1 2 1 201000 f 74 goat snp9355-scaffold1341-92117 2 112475925 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273724 Affx-1111833763 AX-519547336 2 23194919 GTGAGAATATGCAGCCCTTCACCTGAAAGCTGCAG[A/G]CAGATTTACTTGAATTCCGGAAATATGGTGGTTAA R 2 1 2 1 201000 r 74 goat GoatD01.003848 2 23194919 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386854 Affx-122970073 AX-123257212 2 23203793 ACCCCGCATGGAGGGTCATACTTACTTCTCATTGG[C/T]GATACCCTCTGAGCAGAGTAGTATTAACTCTCATC Y 2 1 2 1 201000 r 74 goat snp9354-scaffold1341-42936 2 112426682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451819 Affx-122921477 AX-123322152 2 23240701 TAAGATATAAAAAGGTTTGAGTTCGTTTGTATCTC[C/T]ACAAAGATAAACCCTTTCTCTGAAACAAACATGTA Y 2 1 2 1 101000 f 74 goat snp9353-scaffold1341-6028 2 112389314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443714 Affx-122927150 AX-123314051 2 23256815 ACTCTTTAAACAGCTTTGAGATATAGGAAAGTTCT[A/G]TCTCTAGTGTCCCTCGCCACTCTTGTCGCTCCTCC R 2 1 2 1 201000 f 74 goat snp26534-scaffold2760-100572 2 112372574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769875 Affx-122925112 AX-385257044 2 23309379 ATACATTGACTGTGGTCCATTTTGACTTAGCAGTT[A/C]TAATTATCTGACAGCAGATAATTGAGAGGTTATTG M 2 1 2 1 101000 f 74 goat snp26533-scaffold2760-48008 2 112319729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804448 Affx-986696615 AX-385291027 2 23313711 AAGCAGCTTCTAAAAAGCCCTTCTGCCTTCTAGGA[A/G]TACATTATATTCAGGGGATATCTGGGATCTCTAGC R 2 1 2 1 600010 r 74 goat 2_23313711 2 23313711 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 468272026 Affx-1111833163 AX-519545793 2 23328927 CTGGAATGCCATCACCTCTACTAGCTTTGTTCATA[A/G]TGATGCTTCCTAAGGCTCACTTGACTTCACATCCC R 2 1 2 1 103000 f 74 goat 2_23328927_AF-PAKI 2 23328927 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776007 Affx-122938640 AX-385263137 2 23354524 CTTAGCAATGGTTTAAATTCATGATTAACAAGTCC[A/G]TAATAGTTAAATCCTGAGTAGAAGATACTTCACAC R 2 1 2 1 101000 f 74 goat snp26532-scaffold2760-2863 2 112274662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389271 Affx-122969016 AX-123259629 2 23358490 ACGTTTCTTAGTGCAGGCTTTCTAATCGCTAACAC[A/G]CAGGTTACTGTCTGTCTGCTAGCAACAAAGTACAC R 2 1 2 1 101000 f 74 goat snp29696-scaffold3212-1004 2 112270835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397533 Affx-122962040 AX-123267888 2 23535963 CTCTACTAAGCACCCAAACTGTGTGCTTTCTTAAA[C/T]GTAAGAAAAGCAAGAAGCCGTGCAGAATCTAGGAT Y 2 1 2 1 102000 r 74 goat snp29700-scaffold3212-178477 2 112093291 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414696 Affx-122949283 AX-123285045 2 23568400 GACATCCTTGCCTCATTACCTACCATGCCCACCCC[A/G]CACTCTAGCCAAATTTCTGTTGTTTTCCAAACACA R 2 1 2 1 101000 r 74 goat snp29701-scaffold3212-210914 2 112060340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390902 Affx-122967099 AX-123261259 2 23607634 AAGAAAAAGGCAATCGGAGAAAGATGGAAGGAGAA[C/T]GGAAAAAGGAGAACAGTGAGTGGAGATGGGCCATT Y 2 1 2 1 101000 f 74 goat snp29702-scaffold3212-250148 2 112020942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447333 Affx-122924890 AX-123317669 2 23700090 ATACTTTAGACTTCCATTTTCAGTTTGTCAGTTCC[G/T]ACCAAAAAAATCTGGGGAGAAATGACATCTTAACA K 2 1 2 1 101000 f 74 goat snp29704-scaffold3212-342604 2 111929443 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418005 Affx-122946662 AX-123288353 2 23786385 CATGAAAAAGTCTGGTGGGAACAAAGGAACAGAGA[A/G]AGTCAAGACTATGGAAACTGGATCTTTTATGTTTC R 2 1 2 1 101000 f 74 goat snp57704-scaffold928-51669 2 111842521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376420 Affx-122978078 AX-123246779 2 24090600 TAATTCCTGTTACAAAGTTACTTCATGGTCCTTTT[A/G]TGCCTGTGCCACTGTATGCAAGCTTATCTGAATGA R 2 1 2 1 101000 r 74 goat snp57710-scaffold928-355884 2 111537915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774115 Affx-122925350 AX-385261253 2 24125480 AGCAGAGTGCTTACTACATATCAGGTATCGTGTAA[A/G]ACACTTACACTATCTCTAATCCTCTTACCAAAACC R 2 1 2 1 101000 f 74 goat snp18657-scaffold1882-999231 2 111503287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774263 Affx-122959271 AX-385261399 2 24187269 TTAACTCTCGCTTCCAAAATTTTGTGGGATGAAGA[G/T]TAGGGATGATGTCCACTGAAAATCTCAATTTAAAT K 2 1 2 1 101000 f 74 goat snp18656-scaffold1882-937442 2 111441636 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799936 Affx-122953595 AX-385286862 2 24227815 TGGTAATCTTTTTCACTGTACAGTGCCGACTCTGA[C/T]TACTCCCTGTGGATATTTCTTAGCTAAAAATTAAT Y 2 1 2 1 101000 f 74 goat snp18655-scaffold1882-896896 2 111400608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393629 Affx-122965307 AX-123263984 2 24257222 AATTTTGTGGCTGTTAGCTGCAAATTAGAGTTCAC[A/G]TATGGCACATTGTTGCCAACATGCATCCTCTTCAG R 2 1 2 1 101000 f 74 goat snp18654-scaffold1882-867489 2 111371307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802615 Affx-122972463 AX-180660645 2 24297182 ATGCATGATCATATAGTTCTGATCAAATTAGTATA[A/G]TCTTTTATGAAGTAAGTTAGCAATTTGTTTTTTTT R 2 1 2 1 201000 r 74 goat snp18653-scaffold1882-827529 2 111334490 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452168 Affx-122921241 AX-123322501 2 24389923 TTATGGCCTGTCTAAGCTGGTAGTACAGAAAGCAG[C/T]GGTGATTTAGGATGTGGAATTGAGGGAGACTATAA Y 2 1 2 1 101000 f 74 goat snp18651-scaffold1882-734788 2 111246283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476164 Affx-1251763667 AX-586011592 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 4 1 4 1 20000 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 539476419 Affx-1251763667 AX-586011821 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 4 1 4 1 20000 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165680 Affx-1251763667 AX-606941089 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165712 Affx-1251763667 AX-606941121 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165724 Affx-1251763667 AX-606941133 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165838 Affx-1251763667 AX-606941247 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165951 Affx-1251763667 AX-606941360 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562166377 Affx-1251763667 AX-606941785 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 320780846 Affx-122946609 AX-385267934 2 24424909 TTGTGTTTTCCTATCTTGCTTGAAATGCCACCTTT[A/G]CCTATCTCCCAGAGAAAGCAATAATATGACTATCA R 2 1 2 1 101000 r 74 goat snp18650-scaffold1882-699802 2 111211281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274738 Affx-1111834467 AX-519548324 2 24468858 CTTCCACAGCTTCAGAGAAAACCTCAGGCAAAGAC[A/G]TGTAGACAGGGAGCGATGGAAGGTG R 2 1 2 1 101000 f 74 goat GoatD01.036983 2 24468858 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393935 Affx-122965074 AX-123264290 2 24483094 TAAAGTTCCTTTTAAGGAGATAAAGAGAAGGAAAG[C/T]GATGATTTCTGCAGTGTGATTTTGTGATGGTCTGT Y 2 1 2 1 101000 r 74 goat snp18649-scaffold1882-641617 2 111152051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772379 Affx-122962182 AX-385259533 2 24550719 CTAGGAGAAACAGGGTAACAAGGGCCATGTTTTCC[A/G]TATAAAAATCTCTTCACTAGAATATGAGGACTTCA R 2 1 2 1 101000 f 74 goat snp18647-scaffold1882-573992 2 111087165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788897 Affx-122935805 AX-385275912 2 24585412 CATGACAAGAGTTATCAGCGTTAACAGTTTTTATA[A/G]GAACTGTGCCAGTGCCATGAGTTGAAGTGTAAGAA R 2 1 2 1 101000 r 74 goat snp18646-scaffold1882-539299 2 111052769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775771 Affx-122950946 AX-385262902 2 24617359 CTTGCAACAGAGAGGTAACACACAAATATGCAGGA[G/T]GTGATGGCGAAGCAAAGTTGCAACCATCTGCGTGG K 2 1 2 1 101000 f 74 goat snp18645-scaffold1882-507352 2 111022333 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438293 Affx-122931393 AX-123308631 2 24675161 ATTGAGGCAACGTGCTGCAACTATCGAAGTCCGCA[C/T]GCCTAGAGCCCGTGCTCCACAAGAGCAATCACTGC Y 2 1 2 1 101000 f 74 goat snp18644-scaffold1882-449550 2 110963992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411366 Affx-122952245 AX-123281716 2 24865131 ACTTAGTTGTAATGATTAACTGTCTGCTATGTCAT[A/G]TGCTAAATGCTGGGAGGATTGTCTCCTCCCACCCC R 2 1 2 1 201000 f 74 goat snp18641-scaffold1882-259580 2 110773087 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785671 Affx-122948273 AX-385272712 2 24898294 AAAATCTGATCTGTGGTCTAGATCAGATAGATCAC[A/G]TCTGATCAGTGGTCTACTTTTTCACTGAAGACAAT R 2 1 2 1 201000 r 74 goat snp18640-scaffold1882-226417 2 110739735 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409560 Affx-122953593 AX-123279911 2 24941452 TAACCAAACAATGCTTCCATATTATTATTACATCA[A/G]TACACTTAGAACAGCACAGGTTCTAAAAGGTAGTA R 2 1 2 1 103000 r 74 goat snp18639-scaffold1882-183259 2 110696724 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803995 Affx-986696619 AX-385290688 2 24970721 CCCGGGTATTAATAATTGTGGGGGGGCCAGTCCAT[C/T]GATTTCCTTTTAGATACTGGGGCAACTTACTCTGT Y 2 1 2 1 600010 f 74 goat 2_24970721 2 24970721 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 320791431 Affx-122976227 AX-385278423 2 24974323 GGCTGTTTTCTGTGTCCAAACTTGGTTCTCCCTGG[C/T]CAACGCTGTATTTGTCAGTTACTTCCACAGAAATG Y 2 1 2 1 101000 r 74 goat snp18638-scaffold1882-150388 2 110665073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443471 Affx-122927823 AX-123313808 2 25003729 CTCTGCATTGGCAGTACGGAATCTTAACCACTGAA[C/T]AGCCAGGGAAGTTCCCCCGATAATTTTTATGATCT Y 2 1 2 1 103000 r 74 goat snp18637-scaffold1882-120982 2 110635585 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408303 Affx-122953777 AX-123278654 2 25045382 CAGAGATGAGTCTTTGAGTCTTAAGGTCCTTTAAA[A/G]GCCTATTATCTATTGGTCTGAAATGGTTCATGAGG R 2 1 2 1 101000 r 74 goat snp18636-scaffold1882-79329 2 110593841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777792 Affx-122919981 AX-385264910 2 25091626 AATGCTCTCTATGACATCATTTTTCTTTCTAAGCA[A/G]TCTCCTGAGATAGGTAACTGTAACATTCCTAGCAA R 2 1 2 1 201000 f 74 goat snp18635-scaffold1882-33085 2 110547883 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451661 Affx-122921593 AX-123321994 2 25135148 AGGCATTCCTGAAAAAGGAACCCAGTGAGCTCCAT[A/G]TTGGGTGCCGGTTTGGAGTGTCAATGCTGGTAATT R 2 1 2 1 101000 f 74 goat snp33253-scaffold39-1061865 2 110504424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448404 Affx-122923677 AX-123318740 2 25167125 TAAACAATACTTGTTTGGGGTAGTCTCTAGGGTTC[A/G]TTACGAAGAAGCAGGAGGCACCTGTGCCCTCCCCC R 2 1 2 1 101000 f 74 goat snp33252-scaffold39-1029888 2 110472431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434543 Affx-122934143 AX-123304884 2 25223409 CTTTTTTTATAAAAAGCCTTTTTTTTTTTTAGTAT[A/G]ATAAAGCCTGTACTTTTTCTAAAGAAATCTCAACC R 2 1 2 1 101000 r 74 goat snp33251-scaffold39-973604 2 110415651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390125 Affx-122968003 AX-123260482 2 25273333 GACCCAGAGGAAATAAACATCCTTATCAATGAAGA[C/T]GAAGGGACACAGAGCAGAATCTGAACAGACAGGCC Y 2 1 2 1 201000 f 74 goat snp33250-scaffold39-923680 2 110364556 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396167 Affx-122963779 AX-123266522 2 25313919 GATAGGTATCAACTGTCTAGGTTCCAGCACTTTTG[C/T]GAACACATGTCATGTCACTTGGCAGTCATGGTATT Y 2 1 2 1 101000 f 74 goat snp33249-scaffold39-883094 2 110323206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449823 Affx-122922400 AX-123320158 2 25360592 GTTTATTGAATATTATGATGAATAGCTGAGAAAAG[C/T]GATGGAATCTATTTAAAATTCTTTCTAAACTCTAG Y 2 1 2 1 101000 f 74 goat snp33248-scaffold39-836421 2 110276338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410897 Affx-122952071 AX-123281247 2 25417261 AGGAGCTCAGCCTAATCCAGAATAAGCAAATGGCA[C/T]AGTAAAGTAGGTGCCCCAGACTCCTGTCAGCATAT Y 2 1 2 1 101000 r 74 goat snp33247-scaffold39-779752 2 110219595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797614 Affx-122920506 AX-385284553 2 25461019 TGTGTGTATATTTGTGTAACTGTATTTCTGTGAGA[C/T]AGATAATAGAAAGTGGAGCCTGTGACTCAAAAGAT Y 2 1 2 1 101000 f 74 goat snp33246-scaffold39-735994 2 110175934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447075 Affx-122924501 AX-123317411 2 25510613 TCAGCATTTCCTTTCCTAAAGCTAATGGCAAGTAA[C/T]GACAAAAATCCTTTGAATCTATTTGGTTTCAGAAT Y 2 1 2 1 101000 f 74 goat snp33245-scaffold39-686400 2 110125645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445607 Affx-122925111 AX-123315944 2 25565983 TGATGCAAGTGCAGAGGGGACTCACATGAATTAGA[C/T]GGTCCCTGTCTATAAGAAGACTGAGATCCTGATGG Y 2 1 2 1 101000 f 74 goat snp33244-scaffold39-631030 2 110070349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402365 Affx-122959042 AX-123272718 2 25607905 TAGTCTTTTATTAGAATATTGTAGACAAGAGCCCA[G/T]AAGGGGTTGTCTGTATGGAAAAATGAATCTGGCAT K 2 1 2 1 101000 f 74 goat snp33243-scaffold39-589108 2 110028734 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800799 Affx-122923337 AX-385287715 2 25643693 AGCCGTCAGGGAAGCCTAGCAAAGAGCAGTATGCA[C/T]AATTTATAACCCAACTATACCAACCCTGGATGTTT Y 2 1 2 1 101000 f 74 goat snp33242-scaffold39-553320 NW_017213515.1 3838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404004 Affx-122957196 AX-123274356 2 25702056 TACTGTATTCAAATTTTAATGTATTTCTAAGAAGC[A/G]TTTTGTTACAGTTACCAGTCATTCAGATGGATTAT R 2 1 2 1 101000 r 74 goat snp33241-scaffold39-494957 2 109933805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409284 Affx-122953113 AX-123279635 2 25739445 TCTAATCCAACACCATAGTATTTATTCATCTTTTC[A/G]CTCTTTTCAAATTATAATCTCTAGTCCCACAGTGA R 2 1 2 1 101000 r 74 goat snp33240-scaffold39-457568 2 109896294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432377 Affx-122935860 AX-123302718 2 25771696 TTAAAACACTTTTAAGGCAGCCTGATTTAAAGGAG[C/T]GGTACTTTATTATGAGTACAGAGAGATCGTTCAGG Y 2 1 2 1 101000 r 74 goat snp33239-scaffold39-425317 2 109864045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791732 Affx-122969600 AX-385278723 2 25804305 TTTTTATTATAAGATACAGTGCTTGTATTTCTTTT[C/T]GAACAGTTAACTCTCTAAGATACGGAATTGCTTGA Y 2 1 2 1 202000 f 74 goat snp33238-scaffold39-392708 2 109831402 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377633 Affx-122977874 AX-123247992 2 25870395 TTTCTCAATGACTTTGGTAATATGTTTATTAAATA[C/T]AATGGTTTTTCCTGTGTTCTTTTACTTCCAGCACC Y 2 1 2 1 201000 f 74 goat snp33237-scaffold39-326618 2 109764483 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272029 Affx-1111833164 AX-519545795 2 25876254 AAATGAAGTCTTTAATTTATTTATAATATATTTCT[A/G]GAATTTTGGCCCTATTTACTTATTTTTTTGGTTAC R 2 1 2 1 303000 f 74 goat 2_25876254_AF-PAKI 2 25876254 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440806 Affx-122929827 AX-123311143 2 25924958 CCCAAAGTTTCTGCAGTAGTTGGCAGCATGGGAGA[C/T]GTGGCTTCAAGCTCAGTGCTGTTGCTGCTCTGGTT Y 2 1 2 1 201000 f 74 goat snp33236-scaffold39-272055 2 109709093 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413691 Affx-122950094 AX-123284040 2 25988237 AGTAGCTTGTTTCTTATTTTTCCTGTTTTATCAAC[C/T]GTCTATAGATATAGTTGAGTATTTTTTTCAGCTGA Y 2 1 2 1 101000 r 74 goat snp33235-scaffold39-208776 2 109645287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447286 Affx-122924928 AX-123317622 2 26095191 AAAGATGTCCCCATATGCAAGGCTCTTCTGATGTA[C/T]AGAGACTTAAATCTCTCGTTCTGATAACTTTATTT Y 2 1 2 1 201000 r 74 goat snp33233-scaffold39-101822 2 109538325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453386 Affx-122919924 AX-123323719 2 26145829 TCCTTCCTTAGAAAGCTAATAAGAATTCAGAAAAA[C/T]AACCAAATGAATCAAGAAAAAGAAAATTTGTGGAT Y 2 1 2 1 303000 f 74 goat snp33232-scaffold39-51184 2 109486693 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788412 Affx-122935638 AX-385275430 2 26192385 AAACTTTGCATCAAGTCAGAAATTCCACAAGGACA[A/G]TTCCTCTCTTGTCTCCCAGGATTTGCTCCTACTAT R 2 1 2 1 101000 r 74 goat snp33231-scaffold39-4628 2 109439511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424274 Affx-122941992 AX-123294620 2 26222010 TATTCCCGCTTTTAGGAGCTCACACTTTAGAATAA[C/T]GTGCTGTTCTTGATAGAATCATAATAAATTCCTAT Y 2 1 2 1 101000 r 74 goat snp28227-scaffold301-24898 2 109409326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425839 Affx-122940672 AX-123296185 2 26252553 AACTGCGTCGGTAAGTGACAGTCTTTCATCACAGT[A/G]CTTACAGCGCTGCGGGCACTCCCTTTAACATCAAG R 2 1 2 1 101000 f 74 goat snp28228-scaffold301-55441 2 109378804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438992 Affx-122930374 AX-123309329 2 26287493 GGAGACATGAGCGATGAGAAGGACTGCCCTACTCA[A/G]CCCTTTCAGTGTCCCAGTTGGCAGTGGCAATGCCC R 2 1 2 1 101000 f 74 goat snp28229-scaffold301-90381 2 109343874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778124 Affx-122954794 AX-385265239 2 26319244 CTTCTTGTTCTTAGATTATTTCCCGCTAGAAATAT[A/G]CAGTCATTTGTTACTATTTCCAAATGTTGGAAATT R 2 1 2 1 101000 r 74 goat snp28230-scaffold301-122132 2 109312198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779214 Affx-122920812 AX-385266318 2 26363717 GCAAGGTCAGGCTAGTCAAGTCATCCTGAGCTAGG[C/T]AAGCCTTAGCTTAAAGCTTGAAGGATGCCTTTTTA Y 2 1 2 1 201000 f 74 goat snp28231-scaffold301-166605 2 109267092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410310 Affx-122952488 AX-123280660 2 26404366 ATCAACTACAAAAAAGAAAGAAGAAAGAACAAAAT[A/G]CAGTTAGATAGAAGATTTCAAGCACCTGAGGAATG R 2 1 2 1 101000 r 74 goat snp28232-scaffold301-207254 2 109226837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434589 Affx-122934109 AX-123304930 2 26434990 CATATCCTGAAATGCAGTGGGAAGTGCTGAGGCTG[C/T]AGGCGCTAATATGTACCACCACCTCCTCTCCCCTG Y 2 1 2 1 201000 r 74 goat snp28233-scaffold301-237878 2 109196137 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777736 Affx-122921005 AX-385264854 2 26477425 CTCATTGCTTTGGAACGGATGGTCTGTAAATCCTC[A/G]TGTTTTTCTCCTCAGGTTACAAGATGAGAAGAAAG R 2 1 2 1 101000 f 74 goat snp28234-scaffold301-280313 2 109153361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382997 Affx-122973334 AX-123253355 2 26523499 TTTAGTTACAGAGCTGCACATGGTAGGACATCAAG[C/T]GATTTTTAAAACTAGGATGAAAAATTAACTTTTTA Y 2 1 2 1 101000 f 74 goat snp28235-scaffold301-326387 2 109107749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383586 Affx-122972584 AX-123253944 2 26552508 CTTATATTGTCCAATAGCTTTACATAGGAAACCCC[A/G]TTTCATAACCCATGGAGTCTCAAAATTGAGCAATT R 2 1 2 1 202000 r 74 goat snp28236-scaffold301-355396 2 109078871 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394209 Affx-122964903 AX-123264564 2 26680865 TCTAAATGAAAGGGGAAAATACGCAAAAGCCTTGC[A/G]CCCGACTTAATTCCTAAAGCCCCAAACTGGCTGCA R 2 1 2 1 101000 f 74 goat snp28239-scaffold301-483753 2 108949553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781548 Affx-122952879 AX-385268633 2 26750049 AAGAGTTGGCAAACTTGTTCTGTAAAGGATTTTTA[C/T]GATTAGCAGGTCATATGCTCTTTCCCAACCACTTA Y 2 1 2 1 101000 r 74 goat snp28241-scaffold301-552937 2 108879578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452220 Affx-122920801 AX-123322553 2 26778595 AAGAAAAATACAATCTGTATTCTTCTGCCTTAAGC[A/G]GGCCATTTCGACACATGCTACAACATGGACGAACC R 2 1 2 1 201000 f 74 goat snp28242-scaffold301-581483 2 108851469 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390156 Affx-122967981 AX-123260513 2 26820799 CAATTGCCTTAAGGACTGAGCATAAACTAAGACGT[A/C]GTGAAAGCAGTGCAATGAGAATAATTCCCAATTTG M 2 1 2 1 101000 f 74 goat snp28243-scaffold301-623687 2 108809347 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400681 Affx-122959947 AX-123271036 2 26899897 CTAGCAAGGCAAAGAAGGTTTTTCACAGCCAGGAG[C/T]TAACACTTAGCTAATACCTCTGGCCATAAAGGAAC Y 2 1 2 1 201000 r 74 goat snp28244-scaffold301-702785 2 108730242 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376090 Affx-122978902 AX-123246449 2 26960357 AGCTGTGCATTTTAATTCCCTTAAATACCTACATC[C/T]ACAAAGGGTCCTTATTTGGGACTCGGACGGTAGAA Y 2 1 2 1 201000 f 74 goat snp28245-scaffold301-763245 2 108668880 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393348 Affx-122965932 AX-123263704 2 26991603 ATGTCCTTATATACCCCACACACCATAAATAAAAT[A/G]TATTCTTTTAAAAGTTGAAATTTTAAAAATTTTAA R 2 1 2 1 103000 f 74 goat snp28246-scaffold301-794491 2 108637631 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439818 Affx-122930475 AX-123310155 2 27056082 GGCTCTGGGCAGCAGGTGAGAAGTGCCCAAATATT[A/G]CAGATAATGAGGGTTTCCTGGCCAAAGGAGAAGGG R 2 1 2 1 201000 f 74 goat snp28247-scaffold301-858970 2 108572819 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426972 Affx-122940398 AX-123297317 2 27088641 TCTTGACCTTGCAAAAGGCCAAGACTGAAGAATGG[C/T]GTTATGCTTTCATTCTCTCTCTCTCTTATTACTTA Y 2 1 2 1 101000 f 74 goat snp28248-scaffold301-891529 2 108539916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776772 Affx-122963271 AX-385263896 2 27119802 CCTCTTTTAAGAACTTGGAAGTTCACTCTGAATTG[C/T]GTGAGGTTTCCTTTTTAGCATTTCCAGTAAATTGT Y 2 1 2 1 101000 r 74 goat snp28249-scaffold301-922690 2 108508756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431717 Affx-122936758 AX-123302058 2 27188817 TTGATCTTATTCTTAGGAAATAGTCACATATTTTT[A/G]CCCCAATAGGGGGTATTAATCCTTCTTATGATTTT R 2 1 2 1 201000 f 74 goat snp28251-scaffold301-991705 2 108439393 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382435 Affx-122974236 AX-123252793 2 27237315 GGAACTTAGAAAGTCTCCAGGAGAAAACAGGGAAC[C/T]GATTACATCCCAGTGAGGTCATTCTCTAGCGGAGC Y 2 1 2 1 101000 f 74 goat snp28252-scaffold301-1040203 2 108390615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386369 Affx-122970851 AX-123256727 2 27269489 GCTGCTTCCTGCAGTTACTGTGTCCCTGATGCCTG[C/T]GGAACCAGTTCTTTATACTAGATGATATCTGTTAC Y 2 1 2 1 101000 r 74 goat snp28253-scaffold301-1072377 2 108358429 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769980 Affx-122934984 AX-385257147 2 27305188 TATATAGTGAAGAAATATCAACTATTATAATTAGT[A/G]TTTGTAATCAGTATTTCCCCAGAGAAGAGACTGAC R 2 1 2 1 102000 r 74 goat snp28254-scaffold301-1108076 2 108321831 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425113 Affx-122941225 AX-123295459 2 27342106 TCACTTAAAAAAATTAAATCTAGGTTATTTTGTAC[A/G]TGTCTTGGTTTTTGAAATTTGGTTTCATAGCGTCA R 2 1 2 1 101000 r 74 goat snp28255-scaffold301-1144994 2 108285024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793516 Affx-122929510 AX-385280493 2 27395248 TTTGTTTAATCACTGTTTATTGCTTAAAGGCCAAC[A/G]CCACCATTTCTTTCAATATCCGAGGCTATAATTCT R 2 1 2 1 101000 r 74 goat snp28256-scaffold301-1198136 2 108231591 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445898 Affx-122925948 AX-123316235 2 27454522 TGAACAGTTGCTGGCATAGGCTGAGAGACATTACC[A/G]TGCAGCCGAGGGATGCATATAGTCCTGAGCTGGCC R 2 1 2 1 101000 f 74 goat snp28257-scaffold301-1257410 2 108172539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789906 Affx-122969776 AX-385276912 2 27486005 TTGTTATTAATATTTCAGATATCCAGAGAAGTCTG[C/T]AAAGTACCATAGACCCACAGGCTCATCACTGAGAT Y 2 1 2 1 101000 r 74 goat snp28258-scaffold301-1288893 2 108140602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399933 Affx-122961262 AX-123270288 2 27535246 TGAAGAGTGCTTTGCCATGGAGGATAGCGCCAACC[C/T]GGACCCAGCACTGTACCTGAACAGGGAGAGGGTGA Y 2 1 2 1 101000 f 74 goat snp28259-scaffold301-1338134 2 108090986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410597 Affx-122952113 AX-123280947 2 27606970 ATCTCCATAACAAACTCCCGGGATTTGTGTTTTAC[A/G]TCTCAGGCAGAACTTCTCTATGATTAAATCCTTCA R 2 1 2 1 101000 f 74 goat snp28261-scaffold301-1409858 2 108019331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414891 Affx-122949127 AX-123285240 2 27676938 AGGCGAACTCCTGCGTCACTGATCTCTCCTCTTGC[A/G]CTTTCTCCTGCCAGCAAGGCTTAGCAATTTCACAG R 2 1 2 1 101000 r 74 goat snp28263-scaffold301-1479826 2 107949432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796217 Affx-122975115 AX-385283167 2 27707065 TATATTCAGATCCAATTTTGACTATGTAATCTAGC[C/T]AAGCATTGTGGACCAGGAATGCCACCTGTCACTTC Y 2 1 2 1 101000 r 74 goat snp28264-scaffold301-1509953 2 107918889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449282 Affx-122923022 AX-123319617 2 27749738 ATATCACTACCCACATTCATTACAGGCCTACTTGA[C/T]AGCTGAGAATGGAGGGAAAGAAGAAAGTGAAAAGG Y 2 1 2 1 201000 f 74 goat snp28265-scaffold301-1552626 2 107876198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776705 Affx-122942655 AX-385263831 2 27780804 TCCTCCATCATTCTCCTTAACATGCGTCACCACCT[A/G]CGCATTCAACAAGTATATTCCCTATTGATTCTTAT R 2 1 2 1 101000 f 74 goat snp28266-scaffold301-1583692 2 107844502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797613 Affx-122920578 AX-385284552 2 27815996 CAACATTTTTTAATCTCCTAGTAAAAGATATTAAC[A/G]CTTTCTCCTTCAAAGTATTAATATTTATATAACCC R 2 1 2 1 101000 r 74 goat snp28267-scaffold301-1618884 2 107809338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399865 Affx-122960233 AX-123270220 2 27851203 CTCTATCTGCTACAGTAGAGAGAAGAGACCTGAAG[C/T]AGCAAGGCGGAAGCAAGGAGGCTAATAAATGGGCT Y 2 1 2 1 101000 f 74 goat snp28268-scaffold301-1654091 2 107774475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277358 Affx-1111835808 AX-519550862 2 27860194 CACAATGCGGCACGGTCCTCATGGCCTTAGGGGCC[A/G]AGTACCACCCAGGAGGGCTGAAATGAAGCTCTTGA R 2 1 2 1 102000 r 74 goat Random2.2K-179 2 27860194 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388095 Affx-122969502 AX-123258453 2 27882439 GATGGCTTTATAGATAGGTTGGAGAAGGCAATAGA[A/G]CTTGAAGAGATAGGAAAGTTAAGCATAATATCACC R 2 1 2 1 201000 r 74 goat snp28269-scaffold301-1685327 2 107742417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397216 Affx-122962386 AX-123267571 2 27928562 GCTCACTTTGAGCAAGTCATCACTCTCTCAGCCTC[A/G]TTCTTCTCATTTGTTAAAAAAGAAACAAAATCAAA R 2 1 2 1 103000 f 74 goat snp28270-scaffold301-1731450 2 107696322 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418020 Affx-122946651 AX-123288368 2 27972191 TCTCTTTGTCTCCTATTATGCTGCCAGGGAAGCCC[A/G]TTCTTAACTGCAGTTTTATAAAATTTTAAGTCTCT R 2 1 2 1 202000 r 74 goat snp28271-scaffold301-1775079 2 107652040 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802799 Affx-122951237 AX-385289698 2 28010061 CGGCCCATCTCTCCACTGCATATGGTATTTTGCAG[C/T]ATGCTATTTCTTTCCTAACCTTATAGCTGATTTAA Y 2 1 2 1 101000 f 74 goat snp28272-scaffold301-1812949 2 107614319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417646 Affx-122946846 AX-123287994 2 28098982 TTTAAAGCTCAGTCCAGAGGGCTTACTGCTCATAC[A/G]CAGACATCCATGTGTAAGAGCAGTGGGGCCACTGA R 2 1 2 1 101000 f 74 goat snp28274-scaffold301-1901870 2 107525609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272394 Affx-1111834090 AX-519546122 2 28127682 GCCACAAGGACAGTCCCAGCGCTCCTGCTGGTGCT[A/G]TGAGGCTGGCGATATAGCGCGTGATGGCAAACACG R 2 1 2 1 201000 r 74 goat GoatD01.017662 2 28127682 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388815 Affx-122968903 AX-123259173 2 28164414 TCATTTACTAATAATCAATGCAAAACTTATCAAAT[C/T]GAAAATATGAATGAAAAGCTACAGAATTTAGAGAA Y 2 1 2 1 101000 f 74 goat snp28275-scaffold301-1967302 2 107460103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387843 Affx-122969654 AX-123258201 2 28197923 AAAGCATCATGGTTGCTTCCAAGTTTTGGCAGTTT[A/G]TGAACCAACTTGCTATAAACTTTGGTACGCAGGTT R 2 1 2 1 303000 r 74 goat snp28276-scaffold301-2000811 2 107427013 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783795 Affx-122954819 AX-385270851 2 28240937 AAGCTATGCACGCAATAAAATGATGTATGTAACTA[C/T]AGAATATCTCTCCTCTCATCCAGGTCAGTGAGCAA Y 2 1 2 1 102000 r 74 goat snp28277-scaffold301-2043825 2 107383516 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408688 Affx-122953443 AX-123279039 2 28278008 GGAGATATGTGTCTTCATTACAAATAAATTTAAGA[C/T]GCCATTTCACTTTTCTTTTTTTCTGGGAAACCTTT Y 2 1 2 1 201000 f 74 goat snp28278-scaffold301-2080896 2 107346689 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394319 Affx-122964681 AX-123264674 2 28322657 GTGAGTTGTTCAGACTGGACTTCCACTCTGGGAAA[C/T]GGAGGCTTGGCTGTAAATTCACAGCTCGGAGCATC Y 2 1 2 1 201000 r 74 goat snp28279-scaffold301-2125545 2 107301198 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436003 Affx-122933496 AX-123306342 2 28351527 TCATAACCCTTCTAAATCATTCTGGCCCCCAGGAC[A/G]TGGAAATTTCTATAGAGGCATGGCCAGAGAGTAGC R 2 1 2 1 101000 r 74 goat snp28280-scaffold301-2154415 2 107272277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784052 Affx-122939390 AX-385271105 2 28397373 GAACATATTACAGATATGGAAGTAGACATTTATCA[A/G]TGACAACGTAACACATACCTTCTGTAATATTTAGA R 2 1 2 1 101000 r 74 goat snp28281-scaffold301-2200261 2 107226601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377038 Affx-122977704 AX-123247397 2 28426584 GTGTATTCTGGATAAGTCTTCAATAATGCCCCAAC[G/T]AAAACATAATGCTCACCTTTTAGGCTGTGCAATTT K 2 1 2 1 101000 f 74 goat snp28282-scaffold301-2229472 2 107197498 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433034 Affx-122935768 AX-123303375 2 28457576 TGTACATAAGTGCTCATAACAGCTTTGTTTATAAT[A/C]GCCCCAAGCTGCAATTGACACATGTCCTTCAGTGG M 2 1 2 1 201000 f 74 goat snp28283-scaffold301-2260464 2 107166216 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772090 Affx-122924348 AX-385259246 2 28487431 TGAAAGTGTACAGTGAACAGAAGATTTAAAACATG[A/C]TAAGCTACACTATCAAAAAACTAACCTTACTTTGA M 2 1 2 1 101000 f 74 goat snp28284-scaffold301-2290319 2 107135993 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412659 Affx-122950783 AX-123283008 2 28533364 ATGGTGTTGTATATTATATATAATATGTTATATGC[A/G]TAATACTGTATGTAATATGCTCTACACATACACAT R 2 1 2 1 103000 r 74 goat snp28285-scaffold301-2336252 2 107088777 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277375 Affx-1111835817 AX-519550879 2 28605200 TGGGTCCAAAAGTCACCTCATTAACATAGCAAGAC[A/G]CCTTGACCACTCTCAACACTTAGGGAATTCTCAGG R 2 1 2 1 101000 r 74 goat Random2.2K-180 2 28605200 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795149 Affx-122935692 AX-385282107 2 28640418 AGAATCTAGTATAATACCTCTGAAATTATACTCTA[A/G]GGAACTTGGACCCGAGGGAAAATCCATATCAATGG R 2 1 2 1 101000 r 74 goat snp28287-scaffold301-2443306 2 106982245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769131 Affx-122929740 AX-385256306 2 28736535 CTTTAAATCAGCACATTATCATAGGAAATAGTTTC[A/G]TTATGTCTTTCAAACATGAGTAGCCAAATGTTTTG R 2 1 2 1 101000 r 74 goat snp28289-scaffold301-2539423 2 106883985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404007 Affx-122957193 AX-123274359 2 28821420 GGAAGAAATTCCAGGCCTAAGAGGTAATGTGAGTC[A/G]TCCATGGCTACTTAAGAGGCAGTCAGTGGTAAATC R 2 1 2 1 101000 f 74 goat snp28290-scaffold301-2624308 2 106796556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448250 Affx-122924201 AX-123318586 2 28883680 CTTCATTTTTTGCTAGAGAATAATGGGTTTAGAGG[C/T]GATTTTATATGTAAATAGCAATTACACTATTTTTC Y 2 1 2 1 101000 f 74 goat snp28291-scaffold301-2686568 2 106733947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771925 Affx-122936466 AX-385259081 2 28918563 TATCACTGATCTCTCATTTAGCTAGGTTCTGAATC[G/T]AAGATTTGTCAGTGATTTTTTCACTTTCTCTTTCC K 2 1 2 1 101000 f 74 goat snp28292-scaffold301-2721451 2 106698779 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796790 Affx-122947148 AX-385283733 2 28951977 AATGCTTTGCCCATTAGAGTTACTGTTTGTTTGTA[C/T]GGTTTCAGACTAAAATTTGCACAGGAAAACTTAAA Y 2 1 2 1 101000 f 74 goat snp28293-scaffold301-2754865 2 106663852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790725 Affx-122953503 AX-385277726 2 29000164 CCATCTCATTTACAATTCCATCTCCAAATAGATTT[A/G]TTCTCCTTAGGTACTATCTTAATTTCTTTCTTGCC R 2 1 2 1 101000 r 74 goat snp28294-scaffold301-2803052 2 106616920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418067 Affx-122946615 AX-123288415 2 29042056 TACTTGAAACAAATGTTCAATAAACGATAGCTATC[A/G]TCATGTTTTTGTTGGTGATACAGTGACACCATCTC R 2 1 2 1 101000 r 74 goat snp28295-scaffold301-2844944 2 106582843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800559 Affx-122932701 AX-385287478 2 29076720 ATTTTCCATTTTTTTCATTAGTGTAATTACGCTAC[A/G]CTGTCTTTTAAAATCCAGGTAGTATACACATTGTG R 2 1 2 1 101000 r 74 goat snp28296-scaffold301-2879608 2 106547508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381157 Affx-122974550 AX-123251515 2 29119743 TTACTTCGAGGACTAAAACTTGTTAATCACACATC[A/G]TTTAAGAGGCACAGTCACAAGCTGATTTGGAATTA R 2 1 2 1 101000 r 74 goat snp28297-scaffold301-2922631 2 106504205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779749 Affx-122936309 AX-385266849 2 29162313 ATCCTTACAAAATTGTGTGCCTTGGATAACAATTC[A/G]TATTTAAACACTTGAATATTCTCAAGATATGCTTT R 2 1 2 1 201000 r 74 goat snp28298-scaffold301-2965201 2 106461674 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407783 Affx-122954958 AX-123278134 2 29192831 TGCCATCTATATCAAAAAGCATTCTTCACAGAAAT[A/G]TTGCACCTTCAATTTCAGAACAAATTCAACTTCAG R 2 1 2 1 101000 f 74 goat snp28299-scaffold301-2995719 2 106431151 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439727 Affx-122930546 AX-123310064 2 29227530 ATTCTATTCAACTTTTTATTTATATATATCCAGGT[A/G]TTCTGTCTTAGTTTAATAGGCAAGTCTCGGGAAGA R 2 1 2 1 103000 r 74 goat snp28300-scaffold301-3030418 2 106396459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439120 Affx-122931097 AX-123309457 2 29287557 TATTTTTAAGTGATAAATGCAAAACATGAAGTGGT[A/G]TGTATATAGAATATTATTAATGTGAAAAAAATTAA R 2 1 2 1 101000 f 74 goat snp28301-scaffold301-3090445 2 106335919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776125 Affx-122974264 AX-385263255 2 29366924 TTCTGAGTTGGTCTTCTCTCCAAAATTTCTTACAC[A/G]TATTCCAAGGCAGGATGTTTAAACTTGTGCCCTGA R 2 1 2 1 101000 r 74 goat snp28303-scaffold301-3169812 2 106256975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803028 Affx-122921162 AX-385289904 2 29414684 TCATGGGTGAAGGAAAATGTAGTAAATATTGTGTT[A/G]TTTATGCTTACATTCTGAACACAGGTGTTTATTTT R 2 1 2 1 201000 r 74 goat snp28304-scaffold301-3217572 2 106209711 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775344 Affx-122932708 AX-385262475 2 29475382 CAAAATCATAAAGTCATGGGGCTGGAACAGATATT[A/G]CACTTAATTTGTATGTCTTTAGAATTCATACTGAA R 2 1 2 1 101000 f 74 goat snp28305-scaffold301-3278270 2 106149352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420594 Affx-122945255 AX-123290941 2 29511984 ATAAAAAGAACATTTTTTTTTGCCTTTTTCACTGT[A/G]TTGATTATTGCACTTAGGGTCAAAAGCAATTAAAA R 2 1 2 1 101000 r 74 goat snp28306-scaffold301-3314872 2 106112393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776904 Affx-122964095 AX-385264028 2 29559883 AGTAAACTTTCACTAATACTTCTGGATTTTCTTCT[A/G]TCAGTAGAGATAGTTGAACATTTACTAGTTTTCAG R 2 1 2 1 201000 f 74 goat snp28307-scaffold301-3362771 2 106064276 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801187 Affx-122932087 AX-385288100 2 29638690 AATTAAGCAGATTTCTTAACCTCTCCTAATCTTAA[C/T]ACATTCTCATGCATTTTGGGCCTCTCAGAGTAGTG Y 2 1 2 1 101000 r 74 goat snp28309-scaffold301-3441578 2 105985158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402890 Affx-122958216 AX-123273243 2 29669421 ATCTTGTAAACAGATCTAACAACTAGATACTTTCT[G/T]CAAGGGACTGTATGAGATAAAGCAAGGGGTTCTCA K 2 1 2 1 201000 f 74 goat snp28310-scaffold301-3472309 2 105954585 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451992 Affx-122920928 AX-123322325 2 29698435 TCTTTCTTGGACCTTGATTTTTAATAACTTTGGAT[A/G]CATCATCACAGAATGCCTAGTCATTTTGAAAGTTG R 2 1 2 1 101000 r 74 goat snp28311-scaffold301-3501323 2 105925075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425678 Affx-122940864 AX-123296024 2 29749143 CAAGACATTATGTGCTCCTGAATGAAGAACACACT[A/C]TCAGACAGTCAGACTGGGGGTGAGACAAGTGAAAC M 2 1 2 1 101000 f 74 goat snp28312-scaffold301-3552031 2 105874461 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774541 Affx-122964347 AX-385261675 2 29789318 TGAAGTAACTTAGCAAACAAGGATAGCATATTCAT[A/G]TTTCTAATACAAAATGATAGAAGTGAAATAGGACA R 2 1 2 1 201000 r 74 goat snp20364-scaffold202-12575 2 105834834 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375387 Affx-122979216 AX-123245746 2 29834873 CTGCCTGCATCGTGGTATCCTGTCAACAGACAAGT[A/C]GGGCTGAAATTCACCCGGGGCTCCCTTTAGCTACC M 2 1 2 1 102000 f 74 goat snp20365-scaffold202-58130 2 105789735 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416933 Affx-122948039 AX-123287281 2 29884743 AAAACTTGACTTTTTCTACTAAAACATTGTTATTG[C/T]TAGGATATTATTAGGAAATATTGTTAGGAGTAAGC Y 2 1 2 1 101000 r 74 goat snp20366-scaffold202-108000 2 105726840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382579 Affx-122973755 AX-123252937 2 29971596 ACTGCCTGGTAAACACCCGGTGGGCAAGGAGGTAA[C/T]TTTGCTCCCTAAAGAGCCCTCAGGGGACAGCACAC Y 2 1 2 1 101000 f 74 goat snp20368-scaffold202-194853 2 105640228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429703 Affx-122937626 AX-123300044 2 30003699 GTCTCCTTCCTCTTGAAAACTATGTTCTGCTCATG[C/T]AGTTTTCCAGAATAAGTATTAATAAAATTTGTGTT Y 2 1 2 1 101000 f 74 goat snp20369-scaffold202-226956 2 105608109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407801 Affx-122954560 AX-123278152 2 30032239 TCAGAAAGCAGGAAATTAATTTTTGAAAAATCCTT[A/C]AAGATTTCTTTGAAGTCTGATATAACACCACCTCT M 2 1 2 1 101000 r 74 goat snp20370-scaffold202-255496 2 105579556 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396211 Affx-122963357 AX-123266566 2 30083794 TGTTATTTCTAGATGCATAAATTATACAAATTATC[C/T]AGCAACTGTGTTAAAGATAAATACAGAATGACTAC Y 2 1 2 1 101000 r 74 goat snp20371-scaffold202-307051 2 105530523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377289 Affx-122978118 AX-123247648 2 30112887 ATAGAAGGAAGGAAGGGAGTGAGGAAGGAAGGAAA[C/T]TGAGAAGGAAGGTAACATACTCCAGGCTTCCTCCC Y 2 1 2 1 303000 r 74 goat snp20372-scaffold202-336144 2 105501498 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409777 Affx-122952983 AX-123280128 2 30142673 ACAATATAAATGCTGTGATGGAATTTTTATATAGA[C/T]ATATTTGATTAATAAAACTACCAATGAAACTTTTC Y 2 1 2 1 101000 f 74 goat snp20373-scaffold202-365930 2 105471694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800087 Affx-122919822 AX-385287010 2 30241667 TAGTTATTTATACTGATGGCTAATGTAATGTTGAT[A/G]TAAGTTGTAACATCACAGTGAAAAAGGAAAAGAAG R 2 1 2 1 101000 r 74 goat snp20375-scaffold202-464924 2 105372893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787992 Affx-122939617 AX-385275013 2 30276961 TTCAGTCAATCCTATCTAGAGCTTCAAACTGAAAC[A/G]TATTAGTCCTTGATTTACTCACATCTTATTAGATC R 2 1 2 1 101000 f 74 goat snp20376-scaffold202-500218 2 105337093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277400 Affx-1111835830 AX-519550904 2 30299373 CTGGTGGTCGCAAAGAGTTGGACACGACTGAAGCG[A/G]CTTAGCACTCACTGATGGCAAACAAGGAGATATGG R 2 1 2 1 101000 r 74 goat Random2.2K-182 2 30299373 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772603 Affx-122970125 AX-385259751 2 30317420 TTTACATTAGTTGTATGGTCATCCCTTTCTTTCCC[A/G]TTACTCCTGGTCAGTGAATGTGTCATAGGATATTT R 2 1 2 1 101000 f 74 goat snp20377-scaffold202-540677 2 105296587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435751 Affx-122933276 AX-123306090 2 30352453 TTGTGACACCAGAATAGTATTGCAATCTACACTTT[A/G]TTACTTCCTCCAGATATTTGGTCAATTTACTTTTT R 2 1 2 1 102000 f 74 goat snp20378-scaffold202-575710 2 105260699 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430155 Affx-122937379 AX-123300496 2 30381311 GATTTATATTTCAGAAAAGGTAGATGACTAAACAA[C/T]GACATCACTTCAAGAGAAAACTAGAAGTCCTCCCA Y 2 1 2 1 201000 f 74 goat snp20379-scaffold202-604568 2 105231638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418077 Affx-122946607 AX-123288425 2 30423898 CTCAAAGGATGCAGGTTACATATGAAGTAAGCACC[A/G]CCATCTTGAAGTGATGCAAGTTGTACCTCAAGCTC R 2 1 2 1 101000 f 74 goat snp20380-scaffold202-647155 2 105190080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771783 Affx-122960661 AX-385258940 2 30475419 ATTCCTGTGACTATTTCTAACCAAATCCAAAGGAA[C/T]AGCACATTTCTCAATGAATAGTATCTTTCCAGAAT Y 2 1 2 1 101000 r 74 goat snp20381-scaffold202-698676 2 105138526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772194 Affx-122968437 AX-385259349 2 30515869 TTATTTTTCTGTTCAATATTAACAATAAGGGGATA[A/G]TGGCTCCATCTGCCTTAAAGTCTCAGTTCTGGTTT R 2 1 2 1 101000 r 74 goat snp20382-scaffold202-739126 2 105098059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797958 Affx-122935634 AX-385284894 2 30549993 TTTAGCCTCAGAAGTAAGTATGAAAGTACTTACCT[A/G]TTAAAATATCTAATACTTACCAGAAGTAAGTATTA R 2 1 2 1 101000 f 74 goat snp20383-scaffold202-773250 2 105064044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444900 Affx-122926256 AX-123315237 2 30591074 ACTTAGTGAATTATAAACACTGTTGAAGATTTTCA[C/T]GCAAAGAGTCATAGTGTTTTTATTTTTTATAGTAG Y 2 1 2 1 201000 f 74 goat snp20384-scaffold202-814331 2 105023660 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453848 Affx-122919538 AX-123324181 2 30627300 AGGGAAATAGATCTTTTAACTAGGGTATGGAAAAA[C/T]GAACAAACAAACAAATGCAGTTTTCCCTCTAGCTG Y 2 1 2 1 303000 f 74 goat snp20385-scaffold202-850557 2 104987617 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800086 Affx-122950218 AX-385287009 2 30656798 GTTGTGATAGTACCAGAAGCATCATTTAACTTTAG[C/T]ATTTGATAAAATGCAAGAACGATTACATTACAATA Y 2 1 2 1 101000 f 74 goat snp20386-scaffold202-880055 2 104958327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782160 Affx-122921051 AX-385269238 2 30725442 GTAATGTGAATGCAACTAAACAAGTCAAAGACAGT[A/G]CCAAGATTTTTACACTGTTTCTTATTTAAATATTA R 2 1 2 1 101000 f 74 goat snp20387-scaffold202-948699 2 104888421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425554 Affx-122941440 AX-123295900 2 30787968 TTGACTTCCGTTCCTATTCTTTACCCACTTTTTTC[A/G]TTATTTAGATATGATCATATATATTATCACCTTAG R 2 1 2 1 201000 r 74 goat snp20389-scaffold202-1011225 2 104825666 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441350 Affx-122928877 AX-123311687 2 30828999 GCACTGAAGACATCACTGTCTGTGGGTCAGAGACT[A/G]TATGTGTGGTGCTGAAGTTATGCTGTGGGAAGAGA R 2 1 2 1 101000 f 74 goat snp20390-scaffold202-1052256 2 104784167 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802831 Affx-122974367 AX-385289730 2 30875155 ACTTTTAAAATTTGTTATCTTCACTGAGACTAAGA[A/C]CTTCTTGATTTACACAAACTTGATTGACCTAAATA M 2 1 2 1 101000 r 74 goat snp20391-scaffold202-1098412 2 104738420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415597 Affx-122948615 AX-123285946 2 30907194 AGGTAGGTACATTTGTTTTGTTTGTATTTTTAAGA[C/T]GGGGAAGGGGACCATCCATTTTTCCTCTTAACTAG Y 2 1 2 1 102000 r 74 goat snp20392-scaffold202-1130451 2 104706077 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796729 Affx-122936983 AX-385283674 2 30935873 AGGATTATATCTTCATTTCTTTGTAGCTGGAATAA[A/G]CTCTGATTATAGCCTTGAAGAGATAGATGAAAAGG R 2 1 2 1 101000 r 74 goat snp20393-scaffold202-1159130 2 104677398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788354 Affx-122978348 AX-385275372 2 30984112 GAATCCTCTATATTTGGCATATGGTGCTCTTCTAT[A/G]CACCAGTGTGCTTGCCTATCAGTGTATTTTATGCT R 2 1 2 1 101000 r 74 goat snp20394-scaffold202-1207369 2 104629496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430953 Affx-122936828 AX-123301294 2 31042640 AGCTTTGGACTCCACAGGTTTTCTTTCATTTCAGC[G/T]AATTCCTCAGTTTGGAAGCTTCTGACTGCAGAAGA K 2 1 2 1 201000 r 74 goat snp20395-scaffold202-1265897 2 104570837 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445622 Affx-122925098 AX-123315959 2 31080893 TCACAGTCTTTTCTTTAGCTAAGAGAACATTGTGC[A/G]TTTCATTATTTTCTCTCTTCTGTTTTTCCCTTCTG R 2 1 2 1 303000 f 74 goat snp20396-scaffold202-1304150 2 104532616 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272939 Affx-1111833166 AX-519546625 2 31149945 CCAATTCCACACGGTCATTCAAGCTCCAGTGTGGC[A/G]CGTGATGCTGGCCCAGGAACTGCGCTCTGGTTATT R 2 1 2 1 102000 f 74 goat 2_31149945_AF-PAKI 2 31149945 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771468 Affx-122948473 AX-385258626 2 31153427 AAAGCCAGGGGCACTGGGGACAGAACGTCTTTGAA[G/T]AAAACAATCTTATTAGTAGATGGCAGACTTTTCAC K 2 1 2 1 102000 f 74 goat snp20398-scaffold202-1376684 2 104460619 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784046 Affx-122956137 AX-385271099 2 31198489 TGGATTCTGGTCTCTGGATCCATCTTTAATAAATG[C/T]GTTGACAAGGTATTAAAACAAGATGTATATGTTTT Y 2 1 2 1 101000 f 74 goat snp20399-scaffold202-1421746 2 104415201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790294 Affx-122949539 AX-385277297 2 31233071 TTGAAAGAGGAGACTAAATAGGAAGTCAGCTCATC[A/G]TTTGACTTTGAACTTAATTTCTGATTATGAGCCTC R 2 1 2 1 101000 f 74 goat snp20400-scaffold202-1456328 2 104380558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425638 Affx-122940893 AX-123295984 2 31281996 TTAGCTCAAATAATGAATATAATTCTCTCCCAGAG[C/T]ACTGAAGAATATATTTTATTCCATTGTACATATAA Y 2 1 2 1 101000 f 74 goat snp20401-scaffold202-1505253 2 104330959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407937 Affx-122954366 AX-123278288 2 31313241 GATCACTGACAGCCATCTGTGCCTGGCCCCAGGCA[C/T]GGGCTCTCCTAGGATATGTCTACACTCACCTGTTG Y 2 1 2 1 102000 r 74 goat snp20402-scaffold202-1536498 NW_017205466.1 9452 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422048 Affx-122943612 AX-123292395 2 31350756 ATGATGCTAGACGAGAGGCTTAGAACTTCCCTAGC[A/G]TCTTCAGAGGGAGCATGGCCCTGTGGCACCTTGCC R 2 1 2 1 103000 f 74 goat snp20403-scaffold202-1574013 2 104261755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431822 Affx-122936102 AX-123302163 2 31383002 ATATATTGACTCATTTTAGGTATAGACACATGCAT[A/G]TGCATGTACAAACACACACGCAAAGAAAATTTATG R 2 1 2 1 201000 f 74 goat snp20404-scaffold202-1606259 2 104229987 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406399 Affx-122955227 AX-123276751 2 31419671 TAGTGAATGACCCAGTGTTTTACCTGTCAGTCACC[A/G]TGAACTACTTTACAAAACAGGCTTAACAGCTCATA R 2 1 2 1 101000 f 74 goat snp20405-scaffold202-1642928 2 104192169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399978 Affx-122960824 AX-123270333 2 31486141 ACACATTCTTTCTGACTATCCCCATCAAACTCTGG[C/T]GTACATATTACTTTGTTCACTTTGTGTACATCTGT Y 2 1 2 1 201000 r 74 goat snp20406-scaffold202-1709398 2 104124026 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277413 Affx-1111835836 AX-519550917 2 31542578 GGAAGCTGGCCAGATGTGTCCCCAAGGAGTGGAGC[A/G]GAGACCCATCTTAGTATTCCTTGCTGTTGGGGCCC R 2 1 2 1 201000 r 74 goat Random2.2K-184 2 31542578 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793364 Affx-122937955 AX-385280342 2 31544059 AATGATAATACCATATTCCTGTAAAACACTGCCAC[A/G]TCTAACAAAAATGTTTGCTTGTTCCGAATTCCCAG R 2 1 2 1 201000 f 74 goat snp20407-scaffold202-1767316 2 104065937 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453951 Affx-122919474 AX-123324284 2 31594197 CTGAATTCTAAATAATGTTTAATTTAACTTTAATC[A/G]ATTCAGGAAAGATATGTTAGGTGTTTCCCTGTTCC R 2 1 2 1 101000 r 74 goat snp20408-scaffold202-1817454 2 104015122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423048 Affx-122942964 AX-123293394 2 31637569 TCTTTAAAGTTTCTAGATTTTTCCTTCTGCCTCTT[C/T]ATTCATAAATTGTGTCTAGAGAGCTAAGTTTTTGA Y 2 1 2 1 201000 r 74 goat snp20409-scaffold202-1860826 2 103970833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416545 Affx-122947751 AX-123286893 2 31666728 ATAAGTGACTACATGTGAACTTGGTATCTAAGACT[A/C]GAGTTTCTTAATCTTGGTACTATTGACATTCTCAG M 2 1 2 1 101000 f 74 goat snp20410-scaffold202-1889985 2 103941658 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430009 Affx-122938029 AX-123300350 2 31706593 ACTTGAGAGATAAAAATCAGCAGAATTGTTGAGTT[A/G]CATATTGTGGAATTGTGTCTATTCCATCTTGGGCA R 2 1 2 1 101000 r 74 goat snp20411-scaffold202-1929850 2 103901999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446305 Affx-122925645 AX-123316641 2 31821130 AAATTATCTGCAAATCACAACTCTTTTATATATTC[A/G]CAAAGCCACATGCACTCCATTTTACAGATAATTAA R 2 1 2 1 201000 f 74 goat snp20413-scaffold202-2044387 2 103787285 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443420 Affx-122927374 AX-123313757 2 31867325 TTGCTTAGTGAAAGCATTGATTCAATAATATGAAT[A/G]TTTTAGAAGTTGCAGTAAGAAAGATAATTTTGGTT R 2 1 2 1 101000 r 74 goat snp20414-scaffold202-2090582 2 103740766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277300 Affx-1111835842 AX-519550804 2 31886910 AGTTGATCACAGTAGAAAGTTACGCTGATCAACTG[A/G]GGCAAAATGTTAGCTTACTGGAAGGATTACTGCTG R 2 1 2 1 101000 f 74 goat Random2.2K-185 2 31886910 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406127 Affx-122956199 AX-123276479 2 31901285 AACTAGACTCACTGTCTGGTCATATTATACCCCCA[A/G]ACATTTCAGACTCAACTCCTCCTTCTTTCCTTTTT R 2 1 2 1 202000 r 74 goat snp20415-scaffold202-2124542 2 103706954 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781401 Affx-122967844 AX-385268486 2 31933165 ATGCAGCTGGCTTCAAGTGCTATAGAGTATTTCCT[A/G]CCTTTCTTTTCTAGTGAAATTTTGTTCTGAAACTA R 2 1 2 1 101000 f 74 goat snp20416-scaffold202-2156422 NW_017193395.1 9921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443713 Affx-122927151 AX-123314050 2 31994759 TAAAGGAAGTGAAAGTTATTTCCCTTGAGAAACTT[A/G]AGGAAAGTCAAAACAACTGATGACTAGTAAACAAG R 2 1 2 1 101000 r 74 goat snp20417-scaffold202-2218016 2 103608433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439846 Affx-122930457 AX-123310183 2 32030485 AGCACTTAAAAAAAAAAATCTCCTTTCAGTGATTC[A/G]CCATGTTTCTTCCTCTGTAGATTGCTGTGCATTTG R 2 1 2 1 101000 r 74 goat snp20418-scaffold202-2253742 2 103572499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423783 Affx-122942828 AX-123294129 2 32072413 AACCCAGTTTGAGATCCACGTCCCCATATCTATTC[A/G]TAGTACCATATTGGATTTATAAACTGGAATGCTAT R 2 1 2 1 201000 r 74 goat snp20419-scaffold202-2295670 2 103530507 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426539 Affx-122940189 AX-123296885 2 32164663 CTTGTGCACAACTAACAAAGTATGCTGGCCTAAGG[C/T]AAAATTGGTTTGATACCCACAACCATATCTTTAAA Y 2 1 2 1 101000 f 74 goat snp20421-scaffold202-2387920 2 103437938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447982 Affx-122923751 AX-123318318 2 32199276 TATCATCTGTTTTTCCTTTTAAGAGCAATCTGGAA[C/T]GAGGAATCCTTGTTAAATAGAAAATCTTTCTCAAC Y 2 1 2 1 101000 r 74 goat snp20422-scaffold202-2422533 2 103402209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774546 Affx-122959037 AX-385261680 2 32232271 AATAGAGATCTCTGAGGCCTAGAACTGCAGTGATA[C/T]GGAGTTTGTCCTGATACATAGTTTGTTTGCAATTC Y 2 1 2 1 101000 f 74 goat snp20423-scaffold202-2455528 2 103369518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412969 Affx-122951039 AX-123283318 2 32261918 CTTCCAACTTCATCCCTTCCCCCATCACCTGAAAG[G/T]CAACCAGAAATTAAGTGAGAGAGAAAAATATATCA K 2 1 2 1 303000 r 74 goat snp20424-scaffold202-2485175 2 103339913 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802534 Affx-122978533 AX-385289438 2 32347509 ATTAAAAATATGTAGATTAGAAAGCATCAGAGTGC[A/G]TCACACAGAGTAATGGCAAAAACTGTTCTGTGAAA R 2 1 2 1 101000 r 74 goat snp20426-scaffold202-2570766 2 103253948 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408924 Affx-122953951 AX-123279275 2 32435308 GCAGCCTCGCTGTTTGCAGAGCTTGCCTTCTCTTT[A/G]CCTCTTAAGTGCCCCTGGTAGGTTTCTAACACACA R 2 1 2 1 201000 r 74 goat snp20428-scaffold202-2658565 2 103165917 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449177 Affx-122923530 AX-123319512 2 32479052 GGGGAAAATGACAGGTCATTGTATTCAGACCTCTG[C/T]ACCTAATGCATGCTATTGCCAGACAGTTTTATTAT Y 2 1 2 1 101000 r 74 goat snp20429-scaffold202-2702309 2 103122276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413893 Affx-122949839 AX-123284242 2 32514108 TTCTAAATCAGCAGGAAGGATTTCTGGAGGAGATA[C/T]GCTTTCAGTCCTCATTAATTGGAAATTGCTATTTT Y 2 1 2 1 101000 r 74 goat snp20430-scaffold202-2737365 2 103087153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421102 Affx-122944218 AX-123291449 2 32577071 GAAAGTTTGATTGCAACGGCAAGCTAGAACACTTT[A/G]GATGTGCAGGGTATTGATTTCTCTCCTGTATTTAT R 2 1 2 1 201000 f 74 goat snp20431-scaffold202-2800328 2 103023823 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416334 Affx-122947902 AX-123286683 2 32650568 CCTTCTGAAATTCTTTCTAGGTCCCCACAGGGAAG[A/C]GTAGCCTCAAGCTTTTAGGTCTCAAGGAAACCTAA M 2 1 2 1 201000 r 74 goat snp20432-scaffold202-2873825 2 102949909 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798527 Affx-122937384 AX-385285460 2 32712944 AGAGAAAACTTGGCATTATATAACACTTAATCTCA[C/T]TAAGAAAATCCTTGAACTTGATTTAATGACTTCCT Y 2 1 2 1 201000 f 74 goat snp20433-scaffold202-2936201 2 102885234 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768287 Affx-122955097 AX-385255468 2 32751804 TAATTCCAGACTTCCATTTTAGTAAAAAATATCAA[C/T]AAATATCTCTGCAAAGGTAAGCTGACAATTAGAAA Y 2 1 2 1 201000 f 74 goat snp20434-scaffold202-2975061 2 102845972 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443002 Affx-122928180 AX-123313339 2 32794454 CTCAGTCCTGAGCAGAATCTCAGTTTGGGTCTCTT[C/T]ACCCAGCTTTCCCAGAGGTGGGTACTTGAGATGGG Y 2 1 2 1 101000 f 74 goat snp20435-scaffold202-3017711 2 102802805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414602 Affx-122949356 AX-123284951 2 32840232 TTAAAACATCATAATACTCTGTGTTAGTAAAGGTA[C/T]GAGCTAATGATGTCCTATACTACTGGTATGAACAT Y 2 1 2 1 101000 r 74 goat snp20436-scaffold202-3063489 2 102756860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275313 Affx-1111834721 AX-519548888 2 32846783 CGAATTAAGGACAGA[A/G]CAACAAAAGGGAATGATATTATTTCCTCTGGCATC R 2 1 2 1 102000 r 74 goat GoatD01.048752 2 32846783 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392511 Affx-122966121 AX-123262868 2 32890637 ATGCTGGCTCATCCAAAGTGGAGAAATGTCACAAA[A/G]TACAGTGGACATTCAAATAAGACCCTAGAAAGAAT R 2 1 2 1 101000 f 74 goat snp20437-scaffold202-3113894 2 102701624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783197 Affx-122954325 AX-385270264 2 32946608 CCCTCAGCTTCTCACCCTGAAGAAACCATTATCAT[A/C]TTTCCAAAGGCAGATCAAAACAAGTCTTCTGATGC M 2 1 2 1 101000 f 74 goat snp20438-scaffold202-3169865 2 102645060 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439504 Affx-122930140 AX-123309841 2 33005151 CAATCCAATTTTTATCCTCCTCATTCTCTTCTGCC[A/G]CATTTAGTTGCTCCCATTTTCCTAGTCATGAGCAT R 2 1 2 1 101000 r 74 goat snp20439-scaffold202-3228408 2 102586512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387449 Affx-122970376 AX-123257807 2 33036845 GCTTATCCACACCTCAACCTCTCAGTGATTAAAAT[A/G]CACTGTTTTATTTTTCATCATTTTCTCCTCATCAT R 2 1 2 1 101000 f 74 goat snp20440-scaffold202-3260102 2 102555274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395767 Affx-122963675 AX-123266122 2 33078729 TCTGTGATTCTCAAAATCTGCTTTTGTTTCCCTGA[C/T]GTTAAAATTGTTCACTTTGTTTTTTAAATTCTAAA Y 2 1 2 1 101000 f 74 goat snp20441-scaffold202-3301986 2 102512882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451721 Affx-122921549 AX-123322054 2 33107752 TTACAAAAACAATTAATGTCTCTTTATTAAGACTG[A/C]AAATTACAGAAAGAACAGAGTAAAATCATATATGA M 2 1 2 1 101000 f 74 goat snp20442-scaffold202-3331009 2 102483886 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386704 Affx-122970167 AX-123257062 2 33154775 TTAGCTCACTGTTTTGTTGAGAAAGAATTTTAGAT[A/G]TATTTTCATAGAAATCAAGGGAACTTTCTGGCTGA R 2 1 2 1 101000 f 74 goat snp20443-scaffold202-3378032 2 102436136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419321 Affx-122945660 AX-123289669 2 33184314 ATGAGAAATGGCAAGAGGAAACTACCCTTTAAGAG[C/T]AATTTTATCTTTTGGTATTTTGATAGCATTTCTCA Y 2 1 2 1 201000 r 74 goat snp20444-scaffold202-3407571 2 102406685 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795537 Affx-122942642 AX-385282492 2 33256929 AAAATAACCTGTATAAGTGTTTCTTTAAATTTACC[A/G]CAAAGGGTCTTCCCAAGGTTTTTCAAGAAAAGCAG R 2 1 2 1 101000 r 74 goat snp20445-scaffold202-3480186 2 102333094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407854 Affx-122954518 AX-123278205 2 33310736 AGCAGAAAAGTTTAGGACAGACAAATTATATTTGG[C/T]AGCTTCTGATACTATCCAAGTTCTACTTTATATCA Y 2 1 2 1 101000 r 74 goat snp20446-scaffold202-3533993 2 102278806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387959 Affx-122969608 AX-123258317 2 33340585 ACTATAGCCCACCAGGCTCCTCTGTCCTTGGGATT[C/T]TCGAGGCAAGAATACTAACAAGGTGGAGATCAAAT Y 2 1 2 1 103000 r 74 goat snp20447-scaffold202-3563842 2 102249009 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409075 Affx-122953341 AX-123279426 2 33391710 CAGAAGGAAATCTTTTGAGGACAGTTTTCCAGCAG[A/G]CTACAGTCCATAAGATTGCAAAGAGTCCAGCACAA R 2 1 2 1 101000 f 74 goat snp20448-scaffold202-3614967 2 102197905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778965 Affx-122942470 AX-385266072 2 33421587 AGCCATGCTAAATCATTTTCCTCACTCTCCTGGCC[A/G]TCTTCTTAACTCAGAATGCTCGACAATTCACACAG R 2 1 2 1 101000 f 74 goat snp20449-scaffold202-3644844 2 102167399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407797 Affx-122954564 AX-123278148 2 33467023 GATACATTGTACAGAACGAGCCTGCTAAACTCTAG[C/T]GTGGAATAGGAGTGATGGCTAGAGGCTCAGTGTGG Y 2 1 2 1 101000 f 74 goat snp20450-scaffold202-3690280 2 102121974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376374 Affx-122978111 AX-123246733 2 33495634 CTTCAGTCTACTGACATCACAGCTGAAAGAGCAAC[A/G]CTTTAAGAAAATAAGTTACATCATGTCCAGCTAAG R 2 1 2 1 101000 f 74 goat snp20451-scaffold202-3718891 2 102093838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275433 Affx-1111834893 AX-519549006 2 33498633 TGATACTATAAGGGAATGGGGACATATGATGAATA[A/G]TCTGGAATAGACCTAACTGCAGTGTAACAGTAAAC R 2 1 2 1 101000 f 74 goat GoatD01.057667 2 33498633 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424446 Affx-122941788 AX-123294792 2 33534104 GTGTTTGGGATGAACTTACATTTATGCAGAGTTCC[A/G]CAGATAATCCCCCAAACTTCTTTTACCATTCTTTG R 2 1 2 1 101000 r 74 goat snp20452-scaffold202-3757361 2 102056875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391245 Affx-122967381 AX-123261602 2 33575666 GAATTACCAATCACATTTCCTGATCTTAACTATTC[A/G]GAATATTGTTTGTTTAGTGATGAGGACTGACGTTT R 2 1 2 1 101000 r 74 goat snp20453-scaffold202-3798923 2 102014915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418870 Affx-122946120 AX-123289218 2 33616977 TGGGCAGGGCTTCCAGTGCCTGCAGTAAAAGGAGC[A/G]CCACCTTTAGCTAGCGTAGGTTCAGATCTCCTTGA R 2 1 2 1 101000 r 74 goat snp20454-scaffold202-3840234 2 101972863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403902 Affx-122957486 AX-123274254 2 33661557 CTCGTCTGCTATGGTAGGTAACGGACCTAACACAG[A/G]CTCTACCCTTCTCTGCCTCTTTCCTTGTCCTTGTC R 2 1 2 1 201000 f 74 goat snp20455-scaffold202-3884814 2 101928187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397026 Affx-122963119 AX-123267381 2 33751806 AAGACCCTCAGCCAATAGCCACGTCGACCACCTGA[C/T]AGGTGAGTAAAGGAACATTCAGACAACTCCAGCCA Y 2 1 2 1 101000 r 74 goat snp20457-scaffold202-3975063 2 101837681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272941 Affx-1111833167 AX-519546627 2 33769581 TTGTAGGTTTGATCCCTGGGCTGGGAATATTCCCC[A/G]GAGAGGGGAATGGCAACCCACTCCAGTATTCTGGC R 2 1 2 1 103000 f 74 goat 2_33769581_AF-PAKI 2 33769581 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781826 Affx-122976288 AX-385268907 2 33826497 AAAACCATATGGGAAAGTATCATTTTCTACTTAAG[A/G]GTGCAAAAGGAGATAAGACAGAAAGAAACCTTAGT R 2 1 2 1 101000 r 74 goat snp20458-scaffold202-4049754 2 101762205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774310 Affx-122930860 AX-385261446 2 33857071 TGCACATTTATTACAAAAGGAGCCTGGGAGGTCAT[C/T]GGGATAGAAGCTCTTACCAGTGATTATCTGTAAGT Y 2 1 2 1 101000 f 74 goat snp20459-scaffold202-4080328 2 101731485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375522 Affx-122979115 AX-123245881 2 33885702 AACTGCCTTGTAAACATGGAGAGGGTTCAGCTTTT[A/G]TAAGAAACAGATACAAAGAAATGTGCTAAATTAAG R 2 1 2 1 101000 f 74 goat snp20460-scaffold202-4108959 2 101703006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415972 Affx-122948415 AX-123286321 2 33957354 GTCTTCCAAACGTTATCAGGAGCTTAAACTTACCA[C/T]ACCACATAATAAGATTTGAAGATTTACTGAGGCAA Y 2 1 2 1 101000 f 74 goat snp20461-scaffold202-4180611 2 101631420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277453 Affx-1111835857 AX-519550957 2 33993750 ATTAGCCAGGCCATTTCCCAATTACCTCCCAAATG[A/G]AAATTCTTAAGATCAGCTGATGGCCTTTAAGAAAA R 2 1 2 1 201000 r 74 goat Random2.2K-188 2 33993750 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778962 Affx-122954192 AX-385266069 2 34009670 CTTCAATAATTATGAAATAACTTCAGGATAGAAAT[A/G]TAGAAATGAGCCATCAGAATAGTTTCCTTCAATTA R 2 1 2 1 101000 r 74 goat snp20462-scaffold202-4232927 2 101578608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376903 Affx-122977805 AX-123247262 2 34056139 TGTGTAGAGTTCCAAGAAAGATAAAGAAACTCTGG[A/C]TCTGTTCTTAGTGTTCAAGGACCAAAATGTCAGGA M 2 1 2 1 201000 r 74 goat snp20463-scaffold202-4279396 2 101531982 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412470 Affx-122951394 AX-123282819 2 34138308 TGATTTTTACTCCTTAATTTTAATCTCTAACTAGT[A/G]CTTTAAAAAAAGACCTGATATTGCTGTTAAGCTTT R 2 1 2 1 101000 r 74 goat snp20465-scaffold202-4361565 2 101449954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408700 Affx-122953437 AX-123279051 2 34179885 AACAAACTTGCATTTTGAGGGAAAATATGAGCATC[G/T]AGCTTCATATGTATAATATTTCCTCTCTATAAACA K 2 1 2 1 201000 r 74 goat snp20466-scaffold202-4403142 2 101407580 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442470 Affx-122927939 AX-123312807 2 34235387 AAAAATCACTATTGTATTTATGCCCACTGTACTTA[C/T]AAAAGAAGCAGTACAAACATAACAATAATCAAATA Y 2 1 2 1 101000 f 74 goat snp20467-scaffold202-4458644 2 101354401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426116 Affx-122940631 AX-123296462 2 34267256 TGAATGTAGAGCCATCAGACTTTGGTTAAGGATGG[A/C]ATGCAGAATGTAGGAGAAAAAAGAATTGAGGATGA M 2 1 2 1 101000 r 74 goat snp20468-scaffold202-4490513 2 101322139 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433539 Affx-122934998 AX-123303880 2 34298010 CCCTTCTGTAAAGAAAAAGGGAAAATAATCAAGAA[C/T]AGGTTGCAGGGAGGTAAATCATCTTTGGTCACTTT Y 2 1 2 1 103000 r 74 goat snp20469-scaffold202-4521267 2 101289991 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413832 Affx-122949882 AX-123284181 2 34346143 GGGAAAGTAAATCTGAACAGTACTATGGGTGAATT[A/G]TTGACAATATAGGCCTCCACATGGGATAAGACTTT R 2 1 2 1 101000 r 74 goat snp20470-scaffold202-4569400 2 101241639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794559 Affx-122950542 AX-385281521 2 34377872 TATCTAGAATATTTCAGGTTATACAGAGTCCTCTG[C/T]TCACTGTCACTAACTACCATAAAAATTTAAAGTAT Y 2 1 2 1 101000 f 74 goat snp20471-scaffold202-4601129 2 101209900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771806 Affx-122976409 AX-385258963 2 34434249 CACTAATGAGCAATGGGTGCAGAAGGTGTTAATTA[C/T]GCCACACTAAGATTCAAGAAAAAGCCCTAGTGAGC Y 2 1 2 1 101000 r 74 goat snp20472-scaffold202-4657506 2 101153073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447363 Affx-122924866 AX-123317699 2 34462993 TTAAAAACCCTAGGCAGGGGGTACCTGAACAGAAA[C/T]GAAGAAAATTTAAACATATACAAATAACTACCACT Y 2 1 2 1 103000 f 74 goat snp20473-scaffold202-4686250 2 101124263 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435964 Affx-122933523 AX-123306303 2 34494905 TAAGGTTTCAAGACAGGATGGGATCAGAGAATAAG[C/T]GAAAGGATTAGCCATGGAAAAGAGAAATGTCATTT Y 2 1 2 1 101000 f 74 goat snp20474-scaffold202-4718162 2 101092154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797928 Affx-122943282 AX-385284866 2 34523534 GGATAAACTCCAAATAAACACAAGAAGTTTTCTTG[C/T]GCACTTGACAATTGCATAAGAAAAAGATACCTTTG Y 2 1 2 1 201000 f 74 goat snp20475-scaffold202-4746791 2 101063498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429883 Affx-122938130 AX-123300224 2 34583522 GACTATTCCAGTTTTCAAAGTATACTGATTCAGAC[A/C]TAAAGTAGGAATGATTACTTCTGAAACTAAAGCCT M 2 1 2 1 101000 r 74 goat snp20476-scaffold202-4806779 2 101002974 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783183 Affx-122954992 AX-385270251 2 34629474 TACCTGGATATATCTGAAGGCTAGAGTTTGGAAAG[C/T]AGAATGCTCACATCTAATATTTATGAGGTTTAGCA Y 2 1 2 1 101000 r 74 goat snp20477-scaffold202-4852731 2 100955498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429086 Affx-122938274 AX-123299428 2 34688003 TGTTGTAAGGAGAACCCAGGGTTCCTGAGCTATGC[A/G]GCAATGTTACAGACAACAATTCTGTTGGCTTTCTT R 2 1 2 1 101000 r 74 goat snp20478-scaffold202-4911260 2 100896884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444185 Affx-122927268 AX-123314522 2 34727610 TAAAAGGTTGGAAATTGCCTAAATGTCCACAGAAG[A/C]CAGGATTGCTTGGTAAGATACTGTTTCCATCATAT M 2 1 2 1 101000 r 74 goat snp20479-scaffold202-4950867 NW_017189798.1 8887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446437 Affx-122925973 AX-123316773 2 34761336 CAAGTGTCCTAACATCCTCAGGGGGAGTTCCCAGG[A/C]GTTAGGGCTTTATCTGGAGCCTGAGGCAGAAGCTG M 2 1 2 1 101000 r 74 goat snp20480-scaffold202-4984593 2 100822989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793471 Affx-122934519 AX-385280448 2 34819703 CTTTACTTTCATTTTTTCAGATGATTTTGGCTATC[A/G]TAATTCTATATGCATTTTGAGGTCAACTTTTTTAC R 2 1 2 1 101000 f 74 goat snp20481-scaffold202-5042960 2 100763616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791806 Affx-122932213 AX-385278796 2 34857281 AATAGGGTCTGTGAAGGAGGAATTCTGAAATTATA[C/T]GGTATGCTATTTGAGTATAGATTTGCTCTGTCCAA Y 2 1 2 1 201000 f 74 goat snp20482-scaffold202-5080538 2 100725382 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437866 Affx-122932070 AX-123308204 2 34904461 CTCACTGTTTATCTGTGATCTCACTGCCATGTCTC[A/C]CACTTCTCACTATCTGCTCTGGTCCTGGATTGCCT M 2 1 2 1 101000 f 74 goat snp20483-scaffold202-5127718 2 100677900 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776956 Affx-122919296 AX-385264080 2 34944422 GAGTGCATCAAGGCATCAAGGGAGTGCCATGAACA[C/T]GCACTTGAAATTCTGTGGTGCTCCTTGGTACCTAT Y 2 1 2 1 101000 r 74 goat snp20484-scaffold202-5167679 2 100637722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790643 Affx-122923223 AX-385277645 2 35005799 GCCTCTCATTGGAGCACAAAATAGCAGGGCAAAAT[A/C]TTGCCTTTGTGCTCAATTCTAGGCTGCTCTGGGTC M 2 1 2 1 201000 r 74 goat snp20485-scaffold202-5229056 2 100576372 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275410 Affx-1111834881 AX-519548983 2 35032693 AAAAGTGGTCTAATTAATGTGAGGCTTATTATATC[A/G]CTTTTGTTAACGGATATTTTTTTTAACTGCAGTTG R 2 1 2 1 101000 f 74 goat GoatD01.057374 2 35032693 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435602 Affx-122933793 AX-123305942 2 35059794 ATCTTAGTAATGCCAGGGTGTTCCTGAGTCACTGC[C/T]GATGCAGCACTGGAACCCAGTTCCCCAGTATCCCC Y 2 1 2 1 101000 f 74 goat snp20486-scaffold202-5283051 2 100522464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424100 Affx-122942031 AX-123294446 2 35101095 GGCTACTTATTTCCACATAGCAAATCTCTCAAGTT[A/G]CTTACTTTGAAACACGTTTTGCAAAATATTTGTTT R 2 1 2 1 101000 f 74 goat snp20487-scaffold202-5324352 2 100480795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793272 Affx-122943174 AX-385280250 2 35180973 CCCTCAAAAACCACCCTGAGGAAATCAGCCCAGAA[C/T]TACTCTGAGAAATTTAATATGCCTAGTGATGACAC Y 2 1 2 1 101000 f 74 goat snp20488-scaffold202-5404230 2 100400834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384327 Affx-122972263 AX-123254685 2 35215758 ATGGAAATCAATTTCACACTACTCAGTTTACACCC[G/T]GTAGCTGTTATTTTCATCTGCCCATGATCCATACT K 2 1 2 1 101000 f 74 goat snp20489-scaffold202-5439015 2 100365286 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777084 Affx-122944466 AX-385264207 2 35248799 TCAAAGACAGGTTTAATTATGGTTACAGAAGATAA[C/T]GAAAATAAACAGTCTGATGAAAAGACGAAGAAATG Y 2 1 2 1 101000 r 74 goat snp20490-scaffold202-5472056 2 100332038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417043 Affx-122947527 AX-123287391 2 35282403 CTGCTAGGCTCTTAATGCTGGTTAGTTCATGGCCA[G/T]TCCCTTATCAAATACATTAAAAGGTCCCACATTGA K 2 1 2 1 101000 r 74 goat snp20491-scaffold202-5505660 2 100297701 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790740 Affx-122957346 AX-385277741 2 35319957 CAACTGAAACGACCTGCTCAATCTGGCAAGTGACC[A/G]TGGCTAATATGTTCTTTATCTTTTGCCCAAATTCT R 2 1 2 1 101000 f 74 goat snp20492-scaffold202-5543214 2 100259785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802561 Affx-122957167 AX-385289463 2 35350185 TTTTAATTTGTATCTATGCATAATAACCATCAGAT[A/G]TATTATTAGTAGTTATGCTAGTTGAAGGGGAAAAT R 2 1 2 1 102000 r 74 goat snp20493-scaffold202-5573442 2 100229661 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789815 Affx-122940134 AX-385276822 2 35394123 TCTTGTTTCAGCTACGAAAAGGCTATGATGGATGC[A/G]TTTTGTCCCAGATGTCAAACTCCTTTCTCAGACAG R 2 1 2 1 101000 f 74 goat snp20494-scaffold202-5617380 2 100185685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793133 Affx-122975766 AX-385280111 2 35437282 TTAGAATTTATGCTCAGATTATAATGTTATTCATA[G/T]TGAAAATAAACTTATTTCAGTAGACTACAGTGAGA K 2 1 2 1 101000 r 74 goat snp20495-scaffold202-5660539 2 100142592 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439060 Affx-122930321 AX-123309397 2 35466386 CTTGGTAATAAAATATGTATGAGCGTGAGAGATAC[A/G]TGTGTGCCTGCATACATCTTCATAGTGGGTTGCAT R 2 1 2 1 101000 f 74 goat snp20496-scaffold202-5689643 2 100114020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404463 Affx-122956736 AX-123274815 2 35496099 ATAGTAAATTTCTTGAGGGTGGGGCCCATGTCTTA[C/T]TGCCTTTACCTCTTTGGTGCTTGATACTCAAATAC Y 2 1 2 1 201000 r 74 goat snp20497-scaffold202-5719356 2 100084334 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379980 Affx-122975623 AX-123250338 2 35526186 GATGCTTCATCCTTCTTCACAAGAGCTGTATGGCT[A/G]TGTTTGAACTCTTTTGTGCCCAACCAGAATAAATC R 2 1 2 1 101000 f 74 goat snp20498-scaffold202-5749443 2 100054123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395705 Affx-122963725 AX-123266060 2 35578590 GATAAAATAGTTACTACTTCAAAGGGGAACTGTGA[A/G]AATGAAATAGGACAATACTAATAAAATATTGAACA R 2 1 2 1 101000 f 74 goat snp20499-scaffold202-5801847 2 100001684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422693 Affx-122943659 AX-123293039 2 35613199 CCATTCCTAGCTATCAGGCCAGGAGAGGAGCAGCC[A/G]TTTCCCACAGTAAACGACTTTGAAAGTCACTGAAC R 2 1 2 1 101000 r 74 goat snp20500-scaffold202-5836456 2 99966960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401693 Affx-122959551 AX-123272046 2 35655662 AAATCAGCTTCTTTGAAACGCATACATATTGTCTA[C/T]GGCCATACCACCCTGAACACACCCGATCTCGTGTG Y 2 1 2 1 201000 f 74 goat snp20501-scaffold202-5878919 2 99923715 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428992 Affx-122938852 AX-123299334 2 35696001 GATGCAACTTGATTTCGTGACTGGAGGATCAGGAG[A/G]CCAGCCTCTTGCTCTCTTCAACTCCCCCTTTTCTA R 2 1 2 1 201000 f 74 goat snp20502-scaffold202-5919258 2 99883303 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446912 Affx-122924699 AX-123317248 2 35740004 AAGAGGAAATGGAGTTGGGCTTTGGAAAATTCGTG[A/C]AGAAGGGTGTCCGGGGTTGAACATGAAGTTCAGCT M 2 1 2 1 101000 f 74 goat snp20503-scaffold202-5963261 2 99838931 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796779 Affx-122929492 AX-385283722 2 35773283 AAGTAATAGAAATATGCAGTAAAGTAGTAAATAAA[C/T]AGGGAAAAGATGTTCCCAAATTCCTTACCAACTCA Y 2 1 2 1 101000 r 74 goat snp20504-scaffold202-5996540 2 99805583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379330 Affx-122976179 AX-123249689 2 35841742 ATTTAAACCATTTCCAAGTAATGTGTGTGTTAGTC[A/G]TTCAATTCTGTCCGATTCTTTGTGACCCTCCATGG R 2 1 2 1 303000 f 74 goat snp20505-scaffold202-6064999 2 99737387 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412762 Affx-122950513 AX-123283111 2 35905794 GCATGATATTAGGTGCAGTCGGAGGTTAAAAGTAC[A/G]CTCGTGGTCCAGCCCTCAAGCAACCTAACTTACAC R 2 1 2 1 201000 f 74 goat snp20506-scaffold202-6129051 2 99676334 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789491 Affx-122920577 AX-385276500 2 35940001 ATCGTAAAGCGTGATGGATTTCCGCTATGGGTTGG[A/G]CTCTCAAGTCACGATGTAAGTCTTGTTTTGTTTTC R 2 1 2 1 101000 f 74 goat snp20507-scaffold202-6163258 2 99641830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388495 Affx-122969225 AX-123258853 2 35969172 CCGGGGTCTCCTGCATTGCAGGCAGATTCTTAACC[A/G]TCTGAGCCACCAGCGGAGCAAGCTACTTTTTTCTT R 2 1 2 1 103000 r 74 goat snp20508-scaffold202-6192429 2 99614930 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425143 Affx-122941203 AX-123295489 2 35999709 TCACACATGAAAATTTCTTAACCCATCCCCTCCAT[C/T]AGCTAAAGACCCTTATTAAGAAAACAGAGGCAATT Y 2 1 2 1 201000 r 74 goat snp20509-scaffold202-6222966 2 99584398 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796708 Affx-122977673 AX-385283653 2 36052714 AATATTGTCAGAAAGTCAGTTTTTTCCAACTTGAT[A/C]TATTAATACAATACTATCCCAGTTAAAATCACAGC M 2 1 2 1 103000 f 74 goat snp20510-scaffold202-6275971 2 99533154 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380409 Affx-122975316 AX-123250767 2 36108592 TTAGTGATCCTGATATATACTATGTGTTTGCTTGT[A/G]TGTTTATTGCCTGTCTCTCCCCACTAGAAAGTAAG R 2 1 2 1 103000 r 74 goat snp20511-scaffold202-6331849 2 99477456 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409070 Affx-122953345 AX-123279421 2 36139983 ACAACATACTGATTCAGTATTTGTATAAATGATAT[C/T]CCGTCTAAAGTTATTATAAAATAAAGGCCGTATTT Y 2 1 2 1 101000 r 74 goat snp20512-scaffold202-6363240 2 99445837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452648 Affx-122920341 AX-123322981 2 36186025 AAGTGATACAAAATAACTATACATGTTAATAAACA[C/T]GTTATTTACTTCCTTTTTATTTGGTTTTCACTCCT Y 2 1 2 1 103000 r 74 goat snp20513-scaffold202-6409282 2 99399864 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382751 Affx-122973596 AX-123253109 2 36226056 TTTGTTGCCTCTGTTTGTAAACTGTTGCTTCTCAG[C/T]AAACTGGTGAACCCACAGTGTTCAACAGTGTCTAT Y 2 1 2 1 101000 f 74 goat snp20514-scaffold202-6449313 2 99359602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776409 Affx-122931333 AX-385263536 2 36290778 ATTTACTAGAAATGAATACTCTAAAAATACCTTTT[A/G]CTGCCACACATACTCATAGATAATTATATGCACAT R 2 1 2 1 101000 r 74 goat snp20515-scaffold202-6514035 2 99294795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272994 Affx-1111833168 AX-519546675 2 36305963 AATAATAATGGCTGGAATCATCATTGCTTTCAAAG[A/G]CTTGTTTTTATATACTATTCCTATGAAACTTATTC R 2 1 2 1 101000 r 74 goat 2_36305963_AF-PAKI 2 36305963 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431102 Affx-122936610 AX-123301443 2 36339205 TAAAGTTTATCATTGCCTTTAGTTCTTCGTTTTGC[A/G]CAAGAATAGAAAGGAGATAGAGAAACATTTTTAAA R 2 1 2 1 101000 r 74 goat snp20516-scaffold202-6562462 2 99245758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780314 Affx-122928009 AX-385267409 2 36380990 GGCCTTCCCAGAACACTTAATTTTGCCTTTTCTTA[C/T]ACCTAACCTCTAGAACTCTATCCCATTATCTTATT Y 2 1 2 1 101000 f 74 goat snp20517-scaffold202-6604247 2 99203996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420896 Affx-122944612 AX-123291243 2 36426211 TGTAATTTGATTTGATATTTTGTGTTTTATTCAGA[C/T]GAGAAATTTATGCTCTAACATTATCCTGTGATATT Y 2 1 2 1 103000 r 74 goat snp20518-scaffold202-6649468 2 99159260 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402503 Affx-122958575 AX-123272856 2 36458471 ATATGACGAAACCAAGGCTTAGAAATGTTTGGTTA[C/T]ACAGCTAATTAGTTGTCAGAACTAGAATTCAAACT Y 2 1 2 1 201000 r 74 goat snp20519-scaffold202-6681728 2 99126765 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399673 Affx-122960504 AX-123270028 2 36506892 TCAGTGAATTCCATAGGAAGGACGTCCCTTAAGAT[A/G]CAGGCAGTTGTGGGGTTGACTTCCCACACTTTCAT R 2 1 2 1 202000 f 74 goat snp20520-scaffold202-6730149 2 99079439 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443222 Affx-122927571 AX-123313559 2 36540529 CCAGGATTTCTGGAACAGACGTTTAGAAGGCTCCT[A/C]ATGCATGCTCATTTCAGGCAAAAAGACTAATTTTG M 2 1 2 1 101000 f 74 goat snp20521-scaffold202-6763786 2 99045881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421945 Affx-122943822 AX-123292292 2 36574598 ATCTACTCGGCACGCTCCATTTCCCATCTGGCCTA[C/T]GGCACAAGACACTGGTTCTAAGACACAGAAGTTCA Y 2 1 2 1 101000 r 74 goat snp20522-scaffold202-6797855 2 99012202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437781 Affx-122931698 AX-123308119 2 36605069 AAGTAGTTCTTAAGTGACCTGCTACTCAAAAATAC[C/T]TATTCTTCCAGGCTAACAGGAATATACTCCTGATT Y 2 1 2 1 102000 f 74 goat snp20523-scaffold202-6828326 2 98981872 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392953 Affx-122965690 AX-123263310 2 36636654 AAAGTCAATAAAACTGCAGTCAGTAGCCACACAAG[C/T]GTAAGGACTTACATACATTAATTCATCCAGTCCTA Y 2 1 2 1 101000 f 74 goat snp20524-scaffold202-6859911 2 98950015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431342 Affx-122937057 AX-123301683 2 36676832 GAGGAATTAAAAACATTTCACTGCAACAACCAGTA[C/T]GGCAGGCACATTTCTTTTTAGCCTTGAAAAGATGT Y 2 1 2 1 201000 f 74 goat snp20525-scaffold202-6900089 2 98909716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376532 Affx-122978000 AX-123246891 2 36765061 CTTCGGCCAGCATTCCAGGCCTACCAACACCTTCA[C/T]AGATACCAGGATTCGGGGTTCCTTTCCCTGTTTCA Y 2 1 2 1 201000 r 74 goat snp20527-scaffold202-6988318 2 98820992 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780697 Affx-122958644 AX-385267787 2 36809018 TTTGCTGCCCTCTCCTGTGAGAGAGTTATTCTTCC[C/T]TTCTCCTCCTCTGACATCAGCTTTGGCCATGTGAT Y 2 1 2 1 101000 f 74 goat snp20528-scaffold202-7032275 2 98776658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412018 Affx-122951743 AX-123282368 2 36845781 ATGCCCACTTCGATCTGTAAAAGCCACTCTAGAAA[C/T]GCACAAAGGCTGACACCTTGTACAGAAACTCAAAG Y 2 1 2 1 101000 f 74 goat snp20529-scaffold202-7069038 2 98739480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791975 Affx-122971352 AX-385278963 2 36881880 ATATTAACAATTATCCTGGTATCACTACGCATATA[C/T]GAAACACAATATGCTAAGAAGGCCATGGGCACATT Y 2 1 2 1 101000 r 74 goat snp20530-scaffold202-7105137 2 98703367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435083 Affx-122933722 AX-123305423 2 36929680 CAAGGGCCCAGTGGCAGCTTCCACCGTCAGATCAC[C/T]TCTGCACTGTGATTTCGGATCTTGCCCAGATGCCT Y 2 1 2 1 101000 r 74 goat snp20531-scaffold202-7152937 2 98655675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434908 Affx-122934325 AX-123305248 2 36963788 CCAATAAATGATACACCATTTCCTGGTGCCATTTA[C/T]AGATGCTTCTTGCCTCTTTCTGTTCTTTGGGATGA Y 2 1 2 1 202000 f 74 goat snp20532-scaffold202-7187045 2 98621593 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769466 Affx-122921333 AX-385256636 2 37000211 CCTTATTATAGGCAGAAGTCTGCTGTGGGGAAAAC[A/G]GCTAACAGGCATGGAACACTAGGTATCAAGCATTG R 2 1 2 1 101000 f 74 goat snp20533-scaffold202-7223468 2 98584491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410242 Affx-122952544 AX-123280592 2 37037705 GGGTACCAGATGCTATGGAGGAGGCTGGGCCACTT[C/T]TGTGTACCCTAGTTGGTGTAAACTTGCATAAACCT Y 2 1 2 1 101000 r 74 goat snp20534-scaffold202-7260962 2 98546727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415607 Affx-122948605 AX-123285956 2 37072481 CTCCCCAATCCCTTTTTCTCCACCTGAACCCTGTA[C/T]ACGTAATCAACTATCCTGAATCTTTTATCATTTTA Y 2 1 2 1 201000 r 74 goat snp20535-scaffold202-7295738 2 98511498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435653 Affx-122933347 AX-123305993 2 37127885 AGTCTGCCTCGTTCACAGATACACGTACAGAACCC[A/G]CAGCAGCTTGTGGCACACGGCTGTCACTCAAAACA R 2 1 2 1 201000 f 74 goat snp20536-scaffold202-7351142 2 98455805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451208 Affx-122921319 AX-123321542 2 37180259 ACTCTCCTCGAAACTAAACCTAAATGATCACTTTA[A/C]ATACACACCTGTGACACTTACCTTTTAAAATAAAC M 2 1 2 1 101000 f 74 goat snp20537-scaffold202-7403516 2 98403545 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387586 Affx-122970263 AX-123257944 2 37223899 GACAGGTTCTCTGAATCTTGAGGCGGAGACTAAGA[C/T]ATGAGGACATCTATGTTCTGAACTGACGTGAATGC Y 2 1 2 1 101000 r 74 goat snp20538-scaffold202-7447156 2 98359931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434488 Affx-122934623 AX-123304829 2 37258712 TCTAGACACTCATGCCCTTTTCAAGACCGATTAAA[C/T]AGATGTTTAAAACCATCCCCTGCACTGACTCTGAA Y 2 1 2 1 201000 f 74 goat snp20539-scaffold202-7481969 2 98325130 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784629 Affx-122959583 AX-385271677 2 37302617 AACATGATTGAAAATCTTCCAAATGCATTTCAGTG[A/G]ATTTAGACCCAATATGTTAAATGTTAAATAAAAAA R 2 1 2 1 101000 f 74 goat snp20540-scaffold202-7525874 2 98281341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454314 Affx-122919248 AX-123324647 2 37349805 TGAATACTGTTTCCTTCCTTTATCATTGATTACCC[A/G]TATTTATGATCATTAAAAATAATTACTTTCATTAA R 2 1 2 1 103000 f 74 goat snp20541-scaffold202-7573062 2 98233660 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443665 Affx-122927189 AX-123314002 2 37404070 TAATTTTAATCTTCAATACACCTCATTTTAAAAGC[A/G]TTATTTTACTGATTTATTTTACAGTTGTAGCTATA R 2 1 2 1 303000 f 74 goat snp20542-scaffold202-7627327 2 98179812 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773648 Affx-122970940 AX-385260788 2 37434134 CACATATGGTTTTACAAAGAAAAGCTGATAGTCTA[G/T]AAAACTGAGGTGTATTTCAGACATGGACCATGTTA K 2 1 2 1 101000 r 74 goat snp20543-scaffold202-7657391 2 98149684 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398951 Affx-122960982 AX-123269306 2 37482462 CCAAAGAATAAGGTAAATATGGCCAAGATTATCAG[C/T]AGTTGGGGAAACCTACTGCTTATTTAACTTCTATG Y 2 1 2 1 201000 f 74 goat snp20544-scaffold202-7705719 2 98100277 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453986 Affx-122919447 AX-123324319 2 37523201 AGAGGATAAAAATATTCTTGAGTAACAGGTAGATC[A/G]TATACTTTAGAGACAATAATATGCTTTTGTTGTGG R 2 1 2 1 101000 r 74 goat snp20545-scaffold202-7746458 2 98059129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436537 Affx-122932928 AX-123306875 2 37580290 AAACATTGGCATCTCTAAGAATGAAGACTTTGACT[A/C]TGTCTCCTTAAAATTTCCCATGGCCAATCTTCACA M 2 1 2 1 101000 r 74 goat snp20546-scaffold202-7803547 2 98001738 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429807 Affx-122938192 AX-123300148 2 37636633 GGAATAATTTCACCCAAAATAAAAATGCATGCCAC[A/G]TCCATATTTGGCTTCATAATACCATTCTCCACCCA R 2 1 2 1 101000 r 74 goat snp20547-scaffold202-7859890 2 97944603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383981 Affx-122972932 AX-123254339 2 37683010 ACTCTTTGCAGCCCATCCCTGGGTCAGAACCACTG[A/G]TGGGTGGTGCTGGATAGTGAACATTTCATAGATAC R 2 1 2 1 101000 r 74 goat snp20548-scaffold202-7906267 2 97898190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401178 Affx-122959351 AX-123271531 2 37727792 TTTTTTCTCAGCATTTCAGATCTTCCCCTAGCAGG[C/T]ATCGAGCCAGTGCCCCCTGCATTTAACCACTGGAC Y 2 1 2 1 101000 f 74 goat snp20549-scaffold202-7951049 2 97853236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395334 Affx-122964041 AX-123265689 2 37785781 ATAACATTTCAGCTTAGTCTTGAAGGAGGGTCCAT[A/G]TTTGTCAAATGAAGAGAAATGAACAGAAGTTCTAG R 2 1 2 1 201000 f 74 goat snp20550-scaffold202-8009038 2 97794532 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403252 Affx-122957879 AX-123273605 2 37825614 CTAATCATTGTCTAGACTTTGCAGTCCTTTGCTTT[A/C]TGCTACCCAGACCAGAAAGACATTGGAGGTGGCAA M 2 1 2 1 101000 f 74 goat snp20551-scaffold202-8048871 2 97754701 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382313 Affx-122973905 AX-123252671 2 37854250 TGAGTCACAACGAGACTGAGATGCAAGCAAAGAAT[G/T]AGATAAGACTCTGAGATCTCTGAGAAATTCTCTTT K 2 1 2 1 101000 f 74 goat snp20552-scaffold202-8077507 2 97725984 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421774 Affx-122944349 AX-123292121 2 37897703 ATGTTTTCTGGGTTTAATGGTGCCAGTTTTTCCCT[A/G]TTAGTTTGTACACTAGAGATGTCCTAACTACTAAT R 2 1 2 1 201000 r 74 goat snp35725-scaffold430-16360 2 97680926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435613 Affx-122933785 AX-123305953 2 37932531 GTACAAAGGAGTTGAAAATTACTTTTAAAAGCAGT[A/G]TTTTCTTCTTAGCATATTTTAAACTTAGATGCCTG R 2 1 2 1 101000 r 74 goat snp35726-scaffold430-51188 2 97646041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445371 Affx-122925410 AX-123315708 2 38021900 GTCCTCTTTAAACCTCTAATTTCTAATAATTCCAC[C/T]CTCTCTTCTTTATTGTTTAACCCTTAGGTGTATAG Y 2 1 2 1 101000 f 74 goat snp35728-scaffold430-140557 2 97555856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394137 Affx-122965322 AX-123264492 2 38115717 AGCCACTCACCAATATCCTTAGATTGCTCTCCCAC[A/G]TGAAACAAAAACCTTATAATTAAATACATCTTTTG R 2 1 2 1 201000 r 74 goat snp35729-scaffold430-234374 2 97462217 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425254 Affx-122940988 AX-123295600 2 38145018 CTTTATTATTTATAGCAAGTAAGGTGAACACAAGG[C/T]ATCTTTCAGAAAGCAGTGTCTGAATTCCATAAATT Y 2 1 2 1 101000 f 74 goat snp35730-scaffold430-263675 2 97432386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387930 Affx-122970436 AX-123258288 2 38195434 CTGACCTTTTGTGATTTCAGGAACCATGTTTTATC[G/T]CCTGATAAACTAAGCACTTAACTACCAAGGACTAG K 2 1 2 1 101000 f 74 goat snp35731-scaffold430-314091 2 97381681 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795726 Affx-122954253 AX-385282679 2 38240297 CCCTGATCTCCTTCTCCTATTAATTTACTATTTCT[A/G]TATCAGAGCTTAGCATCAATTCCTGTGTTTGTGAT R 2 1 2 1 101000 f 74 goat snp35732-scaffold430-358954 2 97336286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400506 Affx-122961277 AX-123270861 2 38282415 GAGTGTAGCGCAAATAAAGACACTGGAACAATTAA[C/T]GCTTTTGGCTAACACTTTCAGAGCATTGGAATTGA Y 2 1 2 1 101000 f 74 goat snp35733-scaffold430-401072 2 97293948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426334 Affx-122940272 AX-123296680 2 38321789 TGCTCTCTGAACTTTCTAATCTACTCTTACTTAAA[C/T]ACTCTATATTTTTCTGCTATTACTTTGAATATTTA Y 2 1 2 1 101000 f 74 goat snp35734-scaffold430-440446 2 97253762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431607 Affx-122936162 AX-123301948 2 38355908 GAAATAAAGTAGGTTTTGTTAACAAAAAAGAACGC[A/G]TTATAACTGGTCACTACAGGGCTGACCCTACTCAA R 2 1 2 1 101000 f 74 goat snp35735-scaffold430-474565 2 97220885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791184 Affx-122940416 AX-385278179 2 38396717 TAGGTTCTTAATCTCACTTTTTATTAAATTATGTC[A/G]TTATATCAATCAGAGTTTAATTGGGAAAATAGAAA R 2 1 2 1 101000 f 74 goat snp35736-scaffold430-515374 2 97173553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397100 Affx-122962702 AX-123267455 2 38447279 TCACAGTGTCTAGTGGGTTTACTAGATAAAAATAT[C/T]ACTTCCTCTTCAGTCTTCATAATAGTTTTCAAATT Y 2 1 2 1 101000 f 74 goat snp35737-scaffold430-565936 2 97122218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777487 Affx-122969985 AX-385264607 2 38480056 ACCAAGCTTCAATATGAGTAGGAACTGCAAGGATT[A/G]TCTTTTTATAAAGAAAGGGTTAAATATGGAAATGT R 2 1 2 1 101000 f 74 goat snp35738-scaffold430-598713 2 97089483 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792761 Affx-122953052 AX-385279740 2 38510335 CCAAAATTTGTTTTTTTGCAAAGACTAAGATAAAC[A/G]TTTGGTAAGAATGATGAAAAAAAAGTAAAAAGGCA R 2 1 2 1 201000 r 74 goat snp35739-scaffold430-628992 2 97059349 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389065 Affx-122968602 AX-123259423 2 38539242 TCGTCTGATGACTGGGTGACTATCACCATCTTGAG[C/T]ACATTATTTCCTGAATTCTTTACTCCTATGAGAGA Y 2 1 2 1 101000 r 74 goat snp35740-scaffold430-657899 2 97030383 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798465 Affx-122954641 AX-385285398 2 38586943 ACAAACAAATGTGGTTCTTTGCAATTGAGCTGATA[A/G]TCTTTTCTTTTTTGTCCAAGTTTCAAAATTTTCTT R 2 1 2 1 201000 r 74 goat snp35741-scaffold430-705600 2 96981949 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439751 Affx-122930528 AX-123310088 2 38637710 CTTTTGATTTTCTAAACTACGTGCAGTTTTCTGAC[A/G]TCTGGGGTCCCAACCATTAATCTGGTACATAGTAG R 2 1 2 1 201000 f 74 goat snp35742-scaffold430-756367 2 96931211 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772339 Affx-122948814 AX-385259492 2 38671739 GAAATCTGTTTTTCTTCCATAGGAATGAGCCTACC[A/G]TCATAAGAAGCTTTAAAGCATTACAATAAAGAGGG R 2 1 2 1 101000 f 74 goat snp35743-scaffold430-790396 2 96897229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791428 Affx-122954335 AX-385278420 2 38704613 AGAAACACTCTGACAAAGGGTCTCAGCATAAATAG[C/T]AGCTCCACGTTTCAACTTACATATGGAGTGTTTTC Y 2 1 2 1 101000 f 74 goat snp35744-scaffold430-823270 2 96864003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785269 Affx-122937242 AX-385272314 2 38735494 TATATTTTCTTAATCCTAATTGCCAAAATGTATGT[A/G]TTATTCACTGTTGTTTTCAAGGGTTTTCACCAAAA R 2 1 2 1 101000 r 74 goat snp35745-scaffold430-854151 2 96832550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781920 Affx-122961701 AX-385269001 2 38764334 ACAGATGGGAACTACCTCTCCAACTTCAGGTCTAT[A/G]TTTATTTCACAATTAGATTTTCTCTTGAAGAAACT R 2 1 2 1 101000 f 74 goat snp35746-scaffold430-882991 2 96803667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782985 Affx-122946212 AX-385270054 2 38794674 AGCGCTGTTGGAAGTAAAGAGTTTGAATGTGGAAT[A/G]TTCTGATTATAACAAGAAGCTCTCTCCCAGCCTCT R 2 1 2 1 201000 r 74 goat snp35747-scaffold430-913331 2 96773222 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272033 Affx-1111833169 AX-519545798 2 38859332 AAGTTTTGTATTTTTCCATAAGACCCTGTGGAAAA[A/G]CCCAAATGAACTTTTGGCCAATCCATAATTCAGGG R 2 1 2 1 202000 f 74 goat 2_38859332_AF-PAKI 2 38859332 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395660 Affx-122963761 AX-123266015 2 38873291 AAAAGAAAAAATAATCATGATGGTTCAGATGTTTC[A/G]TTACCCAATATCTGTACACACTTTTTTAACATCAA R 2 1 2 1 101000 r 74 goat snp35749-scaffold430-991948 2 96694209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787623 Affx-122962369 AX-385274646 2 38917780 CGACTGGAAAGGTGTTGAGTCTTCAATCTTTAAGG[A/C]TGAATTAGTCTAATGGTTTTCAACTTTTAACCAAT M 2 1 2 1 101000 f 74 goat snp35750-scaffold430-1036437 2 96648888 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381414 Affx-122974364 AX-123251772 2 38969800 CCTCATCTACAGCCTTATTCATTTAAAGTCCCTGA[C/T]ACCCTAAACAAAGGGTTAGCCACTGTCTGTCTGCT Y 2 1 2 1 101000 f 74 goat snp35751-scaffold430-1088457 2 96597292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438795 Affx-122930806 AX-123309132 2 39025170 AAATCCCAAAAGGGATATTGTGCCATTGATAAGTT[A/G]AGCAAGATTATCACTCTAAAAGTGGCAATTGGAAA R 2 1 2 1 101000 f 74 goat snp35752-scaffold430-1143827 2 96541734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398514 Affx-122961549 AX-123268869 2 39055396 AAGTGACATTTAGGCAAAAGATAATATTTCATCCC[A/G]TCTTTAAATATTCTTTAAAATTTACATGAAACCCC R 2 1 2 1 101000 f 74 goat snp35753-scaffold430-1174053 2 96510054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386543 Affx-122970723 AX-123256901 2 39099584 CCCAGAGGCTCACAGTGTATGCTTCCTGTGATATG[C/T]GGTATATGTTCATTATTCTTAACTAAATCCCCCCA Y 2 1 2 1 201000 r 74 goat snp35754-scaffold430-1218241 2 96465873 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403591 Affx-122957567 AX-123273944 2 39149920 AAATTTCTTGCAGCAGTACCCAGCCCAACGTGCTG[C/T]ATCTAAGAACACCACAGAGGATGATTTCTCCAGGA Y 2 1 2 1 101000 r 74 goat snp35755-scaffold430-1268577 2 96414918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400056 Affx-122960769 AX-123270411 2 39195020 TTGTAAACACCCTGACACAGACTTCTACAGGTCTG[C/T]ACTAAGCCAGTGACAACAGAGCGGAGAGCAGAGTC Y 2 1 2 1 101000 r 74 goat snp35756-scaffold430-1313677 2 96369193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428123 Affx-122939069 AX-123298466 2 39231241 GTCCTTATCTTATAAGTTTATTTTAAATAAGGAAA[C/T]GTTTGGTTTTAACCAAAGAAGAGAGGCAGACAGAC Y 2 1 2 1 103000 r 74 goat snp35757-scaffold430-1349898 2 96332945 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776088 Affx-122969130 AX-385263218 2 39262825 TCTTGATTTACCTTGTTTTGGTTAGATAAAGGCAA[C/T]GATACAGCTATTGCATAGAAACTTGTGCTTATAAA Y 2 1 2 1 101000 r 74 goat snp35758-scaffold430-1381482 2 96301415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392370 Affx-122966241 AX-123262727 2 39292529 GGTAAATGAGTAGCCCTTATATAGAATGTGTGATG[C/T]AATTGTCCTGACAGGTATCACATGCTACTTTTCTT Y 2 1 2 1 101000 r 74 goat snp35759-scaffold430-1411186 2 96271372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783936 Affx-122952752 AX-385270990 2 39323575 ATGTGCCTGGGCCACATGTGTGGAAACATCAAAAA[C/T]GTTTGACAGATTGGTGACTTATTTTTAATATATTG Y 2 1 2 1 101000 f 74 goat snp35760-scaffold430-1442232 2 96240392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410332 Affx-122952471 AX-123280682 2 39352989 TTATCAAAATGCCTTGTAGGCAAAAGAGTTTGTGG[C/T]AAGCAGTTATCCTTCAACGTTCTGAGTAAGTGTGA Y 2 1 2 1 201000 f 74 goat snp35761-scaffold430-1471646 2 96210916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446491 Affx-122925049 AX-123316827 2 39389197 TTTAAATGATAGGTTTATAGGATATCATATCATTT[A/G]CTCATTATAGACATTGGTTCATCTCAGACTGCCTG R 2 1 2 1 101000 r 74 goat snp35762-scaffold430-1507854 2 96174706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425484 Affx-122941489 AX-123295830 2 39445008 AAGCACTGTCTATTTCATCCAGCTGACATTGAAAA[C/T]AAGAATTTCAGTTGGTGGATACTAATTAGTGCTTT Y 2 1 2 1 101000 f 74 goat snp35763-scaffold430-1563665 2 96116792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406415 Affx-122955213 AX-123276767 2 39476023 TCTTTGTGTGAGAAGTTGCTGCATGCTGCAGAAAT[A/C]TGTGGCTGGGCTCTCAAGATGGCCTATTTAAGGCC M 2 1 2 1 101000 f 74 goat snp35764-scaffold430-1594680 2 96085310 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397069 Affx-122962725 AX-123267424 2 39507406 TATGCACATTTTTATATAAGTATCCTGCTAATTTG[C/T]GTAGATTTTCTTAGTCTAGTTGTACATACATTTTT Y 2 1 2 1 101000 f 74 goat snp35765-scaffold430-1626063 2 96053874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400402 Affx-122959996 AX-123270757 2 39548324 TTGTCTTTGGACTTCTTATAAATGGAATAATATAG[C/T]GTGTATATGTTCTACTTTGTATTTAGCTCCTCTTA Y 2 1 2 1 201000 r 74 goat snp35766-scaffold430-1666981 2 96012797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389421 Affx-122968367 AX-123259779 2 39583290 CTCAGTGAAACATCTAGCATGTGGTAGATTCCTTA[C/T]AATTGTTAGTTCCTCTTGCCTCCTCCTGTTCATCC Y 2 1 2 1 101000 f 74 goat snp35767-scaffold430-1701947 2 95977318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441770 Affx-122929106 AX-123312107 2 39618406 AAGGAATACCTAATATATTGGTAAAATTGAGAAGA[C/T]CTTGATATTTACTGACAAAGTTTTGCTTTTCTGCT Y 2 1 2 1 101000 r 74 goat snp35768-scaffold430-1737063 2 95941703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796523 Affx-122951386 AX-385283470 2 39652066 GTAATACAAATGTTATCAGTAATACAAATAAAAAT[A/G]TTTCAAGCTCTACAGAAGTCATCAGGAATCATACC R 2 1 2 1 201000 f 74 goat snp35769-scaffold430-1770723 2 95908294 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384413 Affx-122972196 AX-123254771 2 39685127 GCTGTTGGCACAGAGCAGTGGTTGCTTCATTCAGA[C/T]GCCTTGTTTGCCACTGGAAATATCCCAAGTCTCTA Y 2 1 2 1 201000 r 74 goat snp35770-scaffold430-1803784 2 95875195 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801752 Affx-122948973 AX-385288660 2 39736166 GAACATAGTTTATATGTACAAGGAGCCCATGAAAA[C/T]GGCTTCAGTGTTGATCCTCACATTAATCCTGTTTT Y 2 1 2 1 101000 r 74 goat snp35771-scaffold430-1854823 2 95824151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442440 Affx-122927964 AX-123312777 2 39779458 CTGCAGATGCTTTCATTTCATACATCATTCACACA[C/T]GCAGCAATTACAAATTGGTAAATGACCTCATGTTA Y 2 1 2 1 101000 f 74 goat snp35772-scaffold430-1898115 2 95780890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429205 Affx-122937940 AX-123299547 2 39813896 TCCCTTCTCTGTCTATATGTCACTGTGTCTAATAC[C/T]AGTAACAACTGGAGTGTGGGGAACAAAGTCAGAAT Y 2 1 2 1 101000 f 74 goat snp35773-scaffold430-1932553 2 95746474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783174 Affx-122926772 AX-385270241 2 39846258 TTTGACAGTAGTAACTCTTCCCTAATTGAATCAAT[A/G]CATATTCCAGAAATACATGAAAGATATTTTATAGT R 2 1 2 1 201000 r 74 goat snp35774-scaffold430-1964915 2 95714105 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804023 Affx-986696633 AX-385290707 2 39897741 GGTCTATAAAGATACAAGATATCCTCCTGAAGTCT[C/T]TGTGCAATTTGAAGCTCTGATACTTGTAGAAGTAT Y 2 1 2 1 600010 f 74 goat 2_39897741 2 39897741 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320804468 Affx-986696635 AX-385291038 2 39897774 CTCTGTGCAATTTGAAGCTCTGATACTTGTAGAAG[A/T]ATAAATGCTACAAACTTATAAAACATCACCTGAGA W 4 1 2 1 600010 r 74 goat 2_39897774 2 39897774 Ancestral_priority_1043 ancestry 0.736 recommended IMAGE 10K 10K ancestral 320804032 Affx-986696637 AX-385290716 2 39897803 TAGAAGTATAAATGCTACAAACTTATAAAACATCA[C/T]CTGAGAGTTTACTTGAATTTCTTCTAAATTCATTA Y 2 1 2 1 600010 f 74 goat 2_39897803 2 39897803 Ancestral_priority_1043 ancestry 0.744 recommended IMAGE 10K 10K ancestral 320803964 Affx-986696603 AX-385290663 2 39897825 TTATAAAACATCACCTGAGAGTTTACTTGAATTTC[C/T]TCTAAATTCATTAAGTTTTGTAAATTTTAAACATT Y 2 1 2 1 600010 f 74 goat 2_39897825 2 39897825 Ancestral_priority_1043 ancestry 0.668 neutral IMAGE 10K 10K ancestral 320804441 Affx-986696608 AX-385291022 2 39897832 ACATCACCTGAGAGTTTACTTGAATTTCTTCTAAA[C/T]TCATTAAGTTTTGTAAATTTTAAACATTAAGCTCA Y 2 1 2 1 600010 r 74 goat 2_39897832 2 39897832 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 38385483 Affx-122971282 AX-123255841 2 39920056 TGTCAGGACTGCCTCACCAGCCAGTCACAAATGCC[A/C]TTTGTAGTAGTTAGTAATTTAATTCACCCCTTTAT M 2 1 2 1 201000 r 74 goat snp35775-scaffold430-2038713 2 95639510 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277461 Affx-1111835862 AX-519550965 2 39971726 TAGAGAACCATGTTATTTTGAGTCAAAATTTGAAT[A/C]ATGTTGAGACCATGGTATGCCTGACAGAGTCCCTC M 2 1 2 1 101000 r 74 goat Random2.2K-189 2 39971726 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772996 Affx-122960006 AX-385260140 2 39992525 TCAGCTTTATATTTGGTTGGGGCAATTCTAGAACA[C/T]GCTATGTTTTAAACTAGAATAGAACTTGTATAATT Y 2 1 2 1 201000 r 74 goat snp35776-scaffold430-2111182 2 95566849 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446751 Affx-122925331 AX-123317087 2 40026991 GACAGGTCCTCCAAAGGCAGTGTCCTGCCTACTTC[C/T]CATGTCTGATTTCTGTTACTCTCTTCATGAATACT Y 2 1 2 1 201000 r 74 goat snp35777-scaffold430-2145648 2 95531913 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419152 Affx-122945743 AX-123289500 2 40077889 AAAATTCTTCTAAGAATGTTCTGCATATTTGGGAA[A/G]TAAAGGGAAGAAACAAAAGAAGGAAAGAAGGAAGG R 2 1 2 1 201000 f 74 goat snp35778-scaffold430-2196546 2 95481091 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438728 Affx-122930839 AX-123309065 2 40112579 TTAACCATGTCAAAACTTAGATTAGATTTAGAATG[C/T]ATATGCCAATGTTATTATTATTGTTACTGTGTTAG Y 2 1 2 1 101000 f 74 goat snp35779-scaffold430-2231236 2 95446389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415352 Affx-122948781 AX-123285701 2 40157121 TATCACTCAGCTACAAGAGTTATCTGCTTAAAAAG[C/T]AAGCATTTTAGCACATTTCAAAATACACTGTAAAA Y 2 1 2 1 101000 f 74 goat snp35780-scaffold430-2275778 2 95402215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404191 Affx-122957679 AX-123274543 2 40208540 AATTGGATGGTTTTTAAGAGAACAATTTGTTTGAC[A/G]TTAAGGAGAGTACTATTCAAATACAGCCTATTGTC R 2 1 2 1 101000 r 74 goat snp35781-scaffold430-2327197 2 95350707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449952 Affx-122922897 AX-123320287 2 40237572 CTCATCCACCACTCCCCACAACCCTTGATATCTTG[C/T]ACCTGCCTACCTTCAGTAAGAGTCCCTTCCCTCTC Y 2 1 2 1 201000 r 74 goat snp35782-scaffold430-2356229 2 95321043 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441153 Affx-122929565 AX-123311490 2 40274436 TCTACAGGCAGCCTAATTTGGGCAAACTAGCCATG[C/T]ACATGAATCAGCACAAAGAGCAAACCAAGCAAAGG Y 2 1 2 1 201000 f 74 goat snp35783-scaffold430-2393093 2 95283743 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776432 Affx-122937244 AX-385263559 2 40332616 TAAGTAAGCAACATGCTTCCCTAAGTACTCACTGT[A/G]CTATATACTGCCATTATATTCTAGCAATCTTGTTT R 2 1 2 1 101000 f 74 goat snp35784-scaffold430-2451273 2 95224366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777297 Affx-122968395 AX-385264419 2 40366938 GCCAGACACCTGGCACATCAAGGTGTAATTGATTT[C/T]GCAGAAACATATCACTATTTTTATAGTAAATATTT Y 2 1 2 1 201000 r 74 goat snp35785-scaffold430-2485595 2 95188716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796909 Affx-122965811 AX-385283851 2 40407850 GGGACTCTAGTAACCCAATAGATTATAACAAATAA[C/T]AACTCCATCAAATTTCAATTTACTGTTGCATAACA Y 2 1 2 1 201000 r 74 goat snp35786-scaffold430-2526507 2 95147540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796730 Affx-122944333 AX-385283675 2 40447630 ATCATTATACTTCCTGAACTAGTAGCAAGAAATTG[C/T]GGTTATTATGCTGTTAATGTGTATTGTTATTATAT Y 2 1 2 1 101000 f 74 goat snp35787-scaffold430-2566287 2 95107414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445452 Affx-122925346 AX-123315789 2 40521144 CTTCCTTGACTTGGGTTTTAGTAAAATAACCAGCT[A/G]CTGTCTATCTCCATTTATTTTTGTTCTCAAGCCAG R 2 1 2 1 101000 f 74 goat snp35789-scaffold430-2639801 2 95033026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775894 Affx-122968743 AX-385263025 2 40564292 TGCTGTTTCCATAAACTTTGATGCCTGAAGCACTT[A/C]TTAGTAAATATCTCACACTAAATACTTTCCAAAGA M 2 1 2 1 101000 f 74 goat snp35790-scaffold430-2682949 2 95014476 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792775 Affx-122942227 AX-385279754 2 40593417 ACAGCTGAAGTAAATTCATATCATGAACTCTGTTC[A/G]ATTATTTCTAACAATAGAGTACATACTGAAACAAA R 2 1 2 1 101000 f 74 goat snp35791-scaffold430-2712074 2 94984853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787724 Affx-122925206 AX-385274747 2 40629104 TGCAGTGTTTGGTGTACTTCTGCTGCCAGACAGAC[A/G]TACACTTATTTGAAAAAATTAGTGCCTTCTCTTTT R 2 1 2 1 201000 r 74 goat snp35792-scaffold430-2747761 2 94947889 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800224 Affx-122933417 AX-385287147 2 40658477 CTTTGTATTGTATATCCTGAGTGCCATTCCTAAAA[C/T]GAGTCTCTTTTTGTAAATCTTCTACCTTAAAGATA Y 2 1 2 1 201000 r 74 goat snp35793-scaffold430-2777134 2 94918739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764740 Affx-122954077 AX-385252356 2 40744737 TTTTAGCCTGGCTAACTCCCTTACCATTTCTAAGC[A/G]TAGGTTGTAGCTTTGAGACATCTCCTACTAACTAT R 2 1 2 1 101000 f 74 goat snp35795-scaffold430-2863394 2 94831940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793935 Affx-122952056 AX-385280904 2 40785387 AGCAGCAGGTGACATAATTTTGACTGAACCAATTT[C/T]ATGATCTCTGAGCATGTCTCAAGGTTGTCTGGCAC Y 2 1 2 1 101000 r 74 goat snp35796-scaffold430-2904044 2 94790995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378765 Affx-122977012 AX-123249124 2 40817723 CTCTGGAAAAGAACATTTAGAAATGTGCATTTTTC[A/G]TGAAACATGACAAGAAGCTTAAATCATTCAGTTGG R 2 1 2 1 101000 r 74 goat snp35797-scaffold430-2936380 2 94758625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800552 Affx-122956906 AX-385287471 2 40891946 TAATGTTTCACCTGTTCCTGGATGAATATAACTTC[A/G]TAGGAATTTATAAAGAAATCTATAATAAAAGAAAT R 2 1 2 1 202000 r 74 goat snp35799-scaffold430-3010603 2 94683791 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445154 Affx-122925557 AX-123315491 2 40930787 AATATCTTTAATTAATAATATAGCATCCCTTGTGG[C/T]CATAAAATAATAGAGGGTTTCCAGGCTTTAGATGT Y 2 1 2 1 101000 r 74 goat snp35800-scaffold430-3049444 2 94644751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405472 Affx-122956027 AX-123275824 2 40999463 ACATGTTTGTTGGATGTCACTTGGTGCCCAGCACT[A/G]TAATCGACTGGGGAGTTACTGTTGAGTAGAGAAAA R 2 1 2 1 201000 f 74 goat snp35801-scaffold430-3118120 2 94574689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413774 Affx-122949927 AX-123284123 2 41075092 CATATTTCATTTCCATAAGGCAGGGTATTTGTTCA[C/T]AGAAAACAAAATATAGTCCTTACATGAATATGAAG Y 2 1 2 1 101000 f 74 goat snp35803-scaffold430-3193749 2 94487562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426357 Affx-122940256 AX-123296703 2 41106568 GAAGCCTTTTAGACTCACCCCTGTCCTTATCAGAT[A/C]TTTTTTTCTCTGAATGCCTTCTGTATAATAGTACA M 2 1 2 1 202000 r 74 goat snp35804-scaffold430-3225225 2 94455800 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406704 Affx-122955769 AX-106754664 2 41136969 GAAAATATTTATTAAAAAAGATAATATTTTGAGAA[A/C]GTATGGAACAGATCAGGGGTTCTCCATGTGTCCAA M 2 1 2 1 103000 r 74 goat snp35805-scaffold430-3255626 2 94424997 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442540 Affx-122928532 AX-123312877 2 41182351 CTCCATTTGAACTCTCATCTAAAGTATCACCAGCT[A/G]CCTGCCTTAGCGCTGCTGTGAAGGGAGGGGAAGGG R 2 1 2 1 101000 f 74 goat snp35806-scaffold430-3301008 2 94379580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434722 Affx-122933930 AX-123305063 2 41234887 AATCAGAAGTCTGTGACTATTGACTATGCAAACTG[C/T]ACTTCTAATTTAAAATATTTCTACCACTAACCATT Y 2 1 2 1 101000 f 74 goat snp35807-scaffold430-3353544 2 94326419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443259 Affx-122927495 AX-123313596 2 41274752 TTCACGTGTAAAAGAAGAGGAATAGAGGTTGATAA[C/T]GACTAAGTTTTCTTTTGGAGTTATAGGATTCAGAC Y 2 1 2 1 101000 f 74 goat snp35808-scaffold430-3393409 2 94286616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779578 Affx-122979224 AX-385266681 2 41315838 CAGGTGATTCAGATGCTGTTGATCCCTGGAATACA[C/T]GGTTAAGTAAAAGCCTGCATCATAATTGTTATTAA Y 2 1 2 1 101000 f 74 goat snp35809-scaffold430-3434495 2 94245581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424221 Affx-122942488 AX-123294567 2 41360219 TTCTGTAAGTGAAAAGCAAAGAATTCTCGAGTACA[G/T]ATGCTTATGGCAAAAAGCCGTTTAGTATTGACTCC K 2 1 2 1 101000 r 74 goat snp35810-scaffold430-3478876 2 94200904 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272034 Affx-1111833170 AX-519545799 2 41375513 GTCTATGGGGTCGCACAGAGTCGGACACATCTGAA[A/G]GGACTTAGCAGCAGCATCAGCAGGAGTGGGGGGAG R 2 1 2 1 303000 f 74 goat 2_41375513_AF-PAKI 2 41375513 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396755 Affx-122962780 AX-123267110 2 41413058 ATGTTTCCTTAGTGCTGTTCACATTCTGAGCTGCT[A/G]TTCCAGTTCACCTTCCGGGGGATTGCCATCTAGAC R 2 1 2 1 101000 f 74 goat snp35811-scaffold430-3531715 2 94147104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429277 Affx-122937882 AX-123299619 2 41481929 CTCCTGTAACAGAAAGAAGAGAGGCATCCTTATCA[C/T]GAGAGATAGGGAATTTAGGGGCAAGGAGGCTACAC Y 2 1 2 1 101000 f 74 goat snp35812-scaffold430-3600586 2 94077731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786180 Affx-122930848 AX-385273216 2 41516404 ATAAATCATGGGAACAAAGCTTATTTAACACATAT[A/G]TTTTCTCCATAAGGCATATCACACCTCTTTGCACA R 2 1 2 1 201000 f 74 goat snp35813-scaffold430-3635061 2 94043301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769948 Affx-122931252 AX-385257117 2 41597384 AAGCTCTGCTTTTGTTTTCTAGTCTAGTAACTATC[A/G]CTTACAAATTAGCAATTACCTGGAAAATAACTCTA R 2 1 2 1 101000 f 74 goat snp35815-scaffold430-3716041 2 93964958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410797 Affx-122952658 AX-123281147 2 41627393 TCTTGCTTATCCTCAATTTCTAACTATCTCAAAGC[G/T]AGGCACATTTCTATTCTTAAATCCTTGTCTCTCAA K 2 1 2 1 101000 f 74 goat snp35816-scaffold430-3746050 2 93934492 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386646 Affx-122970211 AX-123257004 2 41676881 GAAGCAAACAGAATACTGCATGATGCAAATCTCAG[C/T]GAACTCAGCTAACATGGTTTCAATGTGCTGAAAAT Y 2 1 2 1 101000 f 74 goat snp35817-scaffold430-3795538 2 93884687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440580 Affx-122929296 AX-123310917 2 41742638 GGATTATCTAAGCCTGCTTTTTCCTTCTTTTTTAA[C/T]CTTCCTTTTAACTATTGAGTTTTTTGCTATCAGTG Y 2 1 2 1 303000 r 74 goat snp35818-scaffold430-3861295 2 93818985 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419266 Affx-122946256 AX-123289614 2 41771612 AGCTGAAATTCTTTTGTCCTTTACCTTTGTCTTTA[C/T]GCACTGACCTGTTTTAGAGGAGAGCTTCTAAGCAG Y 2 1 2 1 101000 r 74 goat snp35819-scaffold430-3890269 2 93789542 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423274 Affx-122942659 AX-123293620 2 41804405 CTCAGAAATAACTCAGAAAATATATGTCACCTATA[C/T]GTTCTGCTTTATCTCTAATTATTTTACTCTGATCT Y 2 1 2 1 101000 f 74 goat snp35820-scaffold430-3923062 2 93756828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433609 Affx-122934949 AX-123303950 2 41853235 GAAATCAGAGTACTGTTTACCCATGACCAAGTTAA[C/T]ATTGGCAATGGAGCAGGATTTAACAAAGTGCAAAA Y 2 1 2 1 101000 f 74 goat snp35821-scaffold430-3971892 2 93706738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383930 Affx-122972969 AX-123254288 2 41927941 AAGTGTAAGACCACCACCTAATATATTTTCAGTAA[C/T]GGATACTATCAACCTAGTGGCATTTGTCTATTCTG Y 2 1 2 1 101000 r 74 goat snp35822-scaffold430-4046598 2 93631361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443120 Affx-122928089 AX-123313457 2 41975791 ATGAATTTCGAGGAAACACAAACACTCAGACCACA[G/T]CAACTTCCGTAAATTAAATCTCTCTACTATGGATA K 2 1 2 1 201000 r 74 goat snp35823-scaffold430-4094448 2 93582986 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376794 Affx-122977947 AX-123247153 2 42030189 CAAATTGCAAACTGCAAGGCCATCAGTAGAATGTT[A/G]GAAGAAAATATGAGAATTTCTATCAATGGTATTTT R 2 1 2 1 101000 f 74 goat snp35824-scaffold430-4148846 2 93528909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408090 Affx-122954718 AX-123278441 2 42075063 GTGACTTTTATTGTCTCCTTCCACTGTGCGTACAC[A/G]TTTGCAGAAGACATAAATCTTGTAAGTTCAAATAC R 2 1 2 1 101000 f 74 goat snp35825-scaffold430-4193720 2 93483750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789236 Affx-122936217 AX-385276247 2 42115165 TGATTTTTTTAAGACACAATTACTTCTCAGATCCA[C/T]GGTTTTCTCATATTAACAGTGTAAAATTCTACCCT Y 2 1 2 1 101000 r 74 goat snp35826-scaffold430-4233822 2 93443554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277471 Affx-1111835867 AX-519550975 2 42115997 TTTTCTGCTGCCTGACAGTGGGGCATGTTTCACTC[A/G]TTAATGTTGGTGATACGTTACATTGTTAGTGAAAG R 2 1 2 1 201000 r 74 goat Random2.2K-190 2 42115997 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441506 Affx-122928727 AX-123311843 2 42157210 GCTCTGCATTAACTCATAGAGTCCTGCACCTTGTC[A/G]TTAATAAAATATTGATAAAATATATGAAGTCTCCT R 2 1 2 1 103000 f 74 goat snp35827-scaffold430-4275867 2 93401647 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387553 Affx-122970290 AX-123257911 2 42199576 AAACTGTAAACCTTTTGATCCAGCAATCTAACTTA[A/G]GATAAATATACTAGAGTGCTACTTATATGTGTGCA R 2 1 2 1 101000 r 74 goat snp35828-scaffold430-4318233 2 93359280 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38421494 Affx-122943909 AX-123291841 2 42267863 CAAGAGGTGGAGGTTAATAAGAGGCTGAGAGTAAG[C/T]GGAAGTAGGGGACATGAGGTCTTTTTTAAACCCCT Y 2 1 2 1 201000 f 74 goat snp35829-scaffold430-4386520 2 93291212 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441654 Affx-122929196 AX-123311991 2 42298529 ATGGAAGGGAGGACTAATATCATTGCCCTTAGCAT[A/G]CTGGTGAAAACCTTTTCTGTCTGGGGAAGAAAATA R 2 1 2 1 101000 f 74 goat snp35830-scaffold430-4417186 2 93259671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797477 Affx-122978571 AX-385284416 2 42394814 GTGACTACCTGAATCCATGACAGTCAAAATGGCTG[A/C]TTTGATTAAATGTTCAGCATTTTCTCCTATCATTC M 2 1 2 1 103000 f 74 goat snp35832-scaffold430-4513471 2 93162614 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774239 Affx-122947440 AX-385261375 2 42426853 CTGTGCCACTGACAAAGAGTTTCCTAGATAAAGGA[C/T]GCCTGTGTTTCAAGTAAGAATCCCATATTTAACTG Y 2 1 2 1 201000 r 74 goat snp35833-scaffold430-4545510 2 93130554 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446522 Affx-122925025 AX-123316858 2 42467079 AGATCTTGTATGTAGCAGAGAGTTGTATTTTACTC[A/G]TTTAGATAATTTGAAATATATTGGTTTTAACTTTA R 2 1 2 1 101000 f 74 goat snp35834-scaffold430-4585736 2 93089728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277479 Affx-1111835871 AX-519550982 2 42469391 CACAAGATTCCTTTTTCTGTGCTGTTTAAACATGT[A/G]TATTCAGAAAATGCTTCTTTTTTCTAGCCTCCAGA R 2 1 2 1 101000 r 74 goat Random2.2K-191 2 42469391 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418930 Affx-122946510 AX-123289278 2 42514382 CCTGAGATTTTATGTAGTCAGGGAGATGGAAAACT[A/G]TCTTTGGCAGTACTTTTCATATCTGTTGTTCATGC R 2 1 2 1 101000 f 74 goat snp35835-scaffold430-4633039 2 93047095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780207 Affx-122935409 AX-385267303 2 42548057 TTAATGCCCATTTTGAGGAACACTTAGAACCTAGG[C/T]AAAATGCACATTTGCACTGGAAAAATTGTTTTTAT Y 2 1 2 1 202000 f 74 goat snp35836-scaffold430-4666714 2 93013306 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437173 Affx-122932127 AX-123307511 2 42608189 ACTAACTTTGAGAGGATACACAACCTAAAAACGTG[C/T]AGAGGCAGAGCCCAAACTCAAATGTAGCCTAGGTC Y 2 1 2 1 101000 f 74 goat snp35838-scaffold430-4726846 2 92952278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799333 Affx-122953758 AX-385286263 2 42639424 AGGAAAATTCACTTTCCTCTCAGGAAATGACATTG[C/T]ATTTTCCACTATTTTGAAAGTAACTCTCAAGAGAT Y 2 1 2 1 101000 f 74 goat snp35839-scaffold430-4758081 2 92919766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445151 Affx-122925559 AX-123315488 2 42707073 ACGTGAAAACCCTACATGGAAGACAGTTATGAATC[A/G]TCCCCAGCCCAGAGCTGTTTGTCACATGGGCACTG R 2 1 2 1 101000 f 74 goat snp35841-scaffold430-4825730 2 92853420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446825 Affx-122925278 AX-123317161 2 42740982 ACTTTGCCAGTGTAATGCCAAGAAAACTAAAGAAA[C/T]GTGATTCCTGTATTTCTAAACTATATGAGAATATA Y 2 1 2 1 101000 f 74 goat snp35842-scaffold430-4859639 2 92818792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452907 Affx-122920206 AX-123323240 2 42774065 GGGACTTGAACCTTAGAAGAAGGCTCCACTTGCAA[C/T]CTGGCCCTAAGCAAATGTTGGAGACCTCTAAATCA Y 2 1 2 1 101000 r 74 goat snp35843-scaffold430-4892722 2 92785254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794160 Affx-122969725 AX-385281126 2 42805234 AATAGGAATCATTAATGATTCTGATTTACAAAATA[C/T]ACTTCTGATTCATTTTAATTGTAGACTTCTACATG Y 2 1 2 1 101000 r 74 goat snp35844-scaffold430-4923891 2 92753669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794341 Affx-122943591 AX-385281305 2 42836231 ATTTCATTGAACATCTCATCTAAAATTTACTATTA[G/T]AACAATACAGATTATTATTTTCTCCCCTCAAGGAG K 2 1 2 1 101000 r 74 goat snp35845-scaffold430-4954888 2 92722472 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769350 Affx-122975534 AX-385256521 2 42902914 CTTTTCGGCCAACCCAGTAAAGGAGAGTAAAAGCC[A/G]TACAGTTTTAGCATAATGGTTTTCAAACCTGAATT R 2 1 2 1 101000 f 74 goat snp35846-scaffold430-5021571 2 92655987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787773 Affx-122941790 AX-385274796 2 42953791 GAACTGACAGGAAATACGCTCTCATTTGCCAACAG[C/T]GCAGGTGTTCTAAAGGGCTTAACACCATTTATAAT Y 2 1 2 1 101000 r 74 goat snp35847-scaffold430-5072448 2 92605285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778189 Affx-122935277 AX-385265304 2 42990505 GGGTGATTGATTAGAGCCACACACCTCTACCAAGC[A/G]TATGAGTCACACGGATTCACTTAGGTAGGGCTGGA R 2 1 2 1 101000 f 74 goat snp35848-scaffold430-5109162 2 92568784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397951 Affx-122961914 AX-123268306 2 43020751 CGCTTTGCAACTGCAGGATTAACTGAGACACAACT[A/C]AACAGACTTCACCGCGTGTTCTGTTCTCTGGGGGA M 2 1 2 1 101000 f 74 goat snp35849-scaffold430-5139408 2 92538509 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406079 Affx-122956236 AX-123276431 2 43112527 GCTCCTCAGAACCCAGGCAAGAGAAGCTGAGGCCA[C/T]GAGAGTGCAGAGGAAAGCTCACGAATGGTGGAGAA Y 2 1 2 1 202000 f 74 goat snp35851-scaffold430-5231184 2 92446759 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434483 Affx-122934626 AX-123304824 2 43148641 CAATGCTAACAGCTCTATGAGGTAAGGTCTGCTAG[A/C]ACACAGCAGAGGCAGAACCCAAACCCAAGTCTGCC M 2 1 2 1 102000 f 74 goat snp35852-scaffold430-5267298 2 92410652 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394084 Affx-122964960 AX-123264439 2 43182645 ACTGAAAATGAACACGGTAAAACTCTCTTACATTC[A/G]TTTGATTTTTACAACTCTGTTAGCTAGAGATTCGT R 2 1 2 1 101000 f 74 goat snp35853-scaffold430-5301302 2 92377332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394335 Affx-122964670 AX-123264690 2 43231632 AGACATGCACGGTCAGTGACCTTTATCATTACTAC[A/G]GATGTTCACGTATCCAACCCATATTCAACTTGAGG R 2 1 2 1 101000 r 74 goat snp35854-scaffold430-5350289 2 92328726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398764 Affx-122961441 AX-123269119 2 43281163 ATGCCTCCACCTTTCTAATAGCTTAAACACGTTTC[A/G]TAAGGCTCCCAAAAGCTCCTGTGAGATTGGGCATC R 2 1 2 1 101000 f 74 goat snp35855-scaffold430-5399820 2 92278252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406918 Affx-122955612 AX-123277269 2 43322140 AATATGTCAAACACATATTACAAAGCTTAGGTAGA[C/T]GTGACATATAAGATATTTTAAGAAGTTTGTTTTAA Y 2 1 2 1 101000 f 74 goat snp35856-scaffold430-5440797 2 92237240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444891 Affx-122926263 AX-123315228 2 43371038 CGTCTGGCCTGCTTCTTAACGTGTATCATGCACAA[C/T]GCAGTCAGGTTAGTATCTGGGAACTTTTTGTGTAC Y 2 1 2 1 101000 r 74 goat snp35857-scaffold430-5489695 2 92188113 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385225 Affx-122971698 AX-123255583 2 43425016 CAATTACTATTCGCTCTTCTAGTGGGTATTGAACA[A/G]AAGGAGAAATGTTCAAGGCAAGCAGAGGGACAGAA R 2 1 2 1 101000 f 74 goat snp35858-scaffold430-5543673 2 92133390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418447 Affx-122946477 AX-123288795 2 43471344 ACTTTTTAGGAGCCATGTAAGATAATCTCAGAACT[A/G]TCTGCTTGGGAAGACAGATGTGTCCATTGGCTTCT R 2 1 2 1 101000 f 74 goat snp35859-scaffold430-5590001 2 92086984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396343 Affx-122963060 AX-123266698 2 43535923 AGACAGGAGACCACGGGCAGAGAGAGAGGAAGAGG[C/T]GGTGCTGGGCCTCAGACACCAGGCCCCACCATCAT Y 2 1 2 1 201000 r 74 goat snp35860-scaffold430-5654580 2 92021930 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430845 Affx-122937430 AX-123301186 2 43572735 TCTGTCATAGAGCTTTTGGAGAAGGAACCTTAACC[G/T]CTTTTAAGATGAAGATACCCAAGAGGGTTGAAAAG K 2 1 2 1 101000 f 74 goat snp35861-scaffold430-5691392 2 91978396 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385341 Affx-122971654 AX-123255699 2 43609395 TCTCCCTAGCTTTCTTTCATTTTTACCTTCTCCAG[C/T]ATTAACGTCAGTCTTAGTAACCTAGTGTCTGTCTT Y 2 1 2 1 201000 r 74 goat snp35862-scaffold430-5728052 2 91941739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445142 Affx-122926168 AX-123315479 2 43641007 AAGCCTCAAGCCTTGGTGACCTCTCATCTAGCAGC[A/G]CCTGCCAACGCCTCTACTGGGCTTGGTGATTAGCT R 2 1 2 1 101000 f 74 goat snp35863-scaffold430-5759664 2 91909947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390483 Affx-122967595 AX-123260840 2 43678657 TGTCCACACCTTTTTTGTTTTCAGAACACATGAAG[C/T]AGTTTTCATTTCCTGATTTTTGTTTGTGTGTTATT Y 2 1 2 1 101000 r 74 goat snp35864-scaffold430-5797314 2 91872039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776201 Affx-122974889 AX-385263329 2 43708849 CCCCTAAATAATGAAAGATCCAGATATCTAATGAG[C/T]ATTCCCATTTTTATGTCATTGTCCCAATTTGTACA Y 2 1 2 1 101000 r 74 goat snp35865-scaffold430-5827506 2 91841263 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798678 Affx-122929386 AX-385285610 2 43747822 ATAGGATTATTATGCTCAACTTTGAAAAGAACAAA[A/G]CTCCATACCTCTGCTCATGCAACTGGATTTAAATA R 2 1 2 1 101000 r 74 goat snp35866-scaffold430-5866479 2 91802567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783669 Affx-122941590 AX-385270728 2 43816831 CCTTGGAACTCCAGGAGCCTGTGCCTTTGTGTGGG[C/T]AAAGAGGATCTTGGAGGAGTTTTGCTGTGATTCTG Y 2 1 2 1 202000 f 74 goat snp35867-scaffold430-5935488 2 91733250 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408084 Affx-122954723 AX-123278435 2 43847021 AGAGTCATGTAACGATACCTCCACCAGAAAAAGAG[C/T]GATAAGTAGAAAACAAAGGAGGGAAGAAATTATGT Y 2 1 2 1 101000 f 74 goat snp35868-scaffold430-5965678 2 91703092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375560 Affx-122978754 AX-123245919 2 43878223 CCTTAGGAGTCCTTGGCAACTATATCACTGCTGGT[A/G]CATATGGGACTGGGGGTCAACCAAAACTCTAACAC R 2 1 2 1 101000 f 74 goat snp35869-scaffold430-5996880 2 91672001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464125649 Affx-1110328481 AX-515601526 2 43981903 TTGGGGTAGTGACTACATGAGGCCTAGAAACACTG[A/G]ATGATCTACCTAATATCACTGAGCAGATGGTGAGC R 2 1 2 1 101000 f 74 goat 2_43981903_AF-PAKI 2 43981903 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413851 Affx-122949869 AX-123284200 2 43983251 CTAACCCTGCCTTTGAGAAAAGGCCTATATATGTA[C/T]GGGGACTGGCCAAAAAGTTCATTTGGGTTTTTTGG Y 2 1 2 1 303000 f 74 goat snp35871-scaffold430-6101908 2 91567259 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408346 Affx-122953746 AX-123278697 2 44077559 TAAATATCTAAAAATTTAAAAAACACAATAGAGGT[A/G]CCAAATTGCCTCTATGAGAAAGCAGTTAAGAGGCT R 2 1 2 1 101000 r 74 goat snp35872-scaffold430-6196216 2 91472555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776993 Affx-122928509 AX-385264117 2 44116718 GGTTCAAATCCTACCTGTGTTGTAAATCCCTGCTA[C/T]GCTGCCCTTACTTATACTGACCTGAAACTCTTTTA Y 2 1 2 1 101000 f 74 goat snp35873-scaffold430-6235375 2 91433082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412225 Affx-122950920 AX-123282575 2 44156829 GCAATACCCAAGACAGATTGCTGGAGAGAAGTTGC[A/G]TGTTTCACTCATTGCACAGGGATTGCCGTAAGTCA R 2 1 2 1 101000 r 74 goat snp35874-scaffold430-6275486 2 91394032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274711 Affx-1111834378 AX-519548297 2 44159602 CTAAAATGACCCCACCCATTGTTGGCAAGGATGAA[A/G]AGAAACATGCTCTCATATCCTGCAGGTGGGAATAT R 2 1 2 1 201000 r 74 goat GoatD01.032694 2 44159602 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446124 Affx-122925780 AX-123316461 2 44218475 AATGTATCTGCAACCCCCATTCCTGAACTTGAGTG[C/T]AAGCTCACAAAGTTTGAGTGGCCCTATAGGCCTGT Y 2 1 2 1 201000 r 74 goat snp35875-scaffold430-6337132 2 91331837 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379899 Affx-122975767 AX-123250257 2 44278025 AAAGAAACTTAGAATCCCCATACCTCCCCAGTCAT[A/C]TCCTGGGCCTTAGGATTTAATGCTGCTAGGGCTGT M 2 1 2 1 101000 r 74 goat snp35876-scaffold430-6396682 2 91271860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418889 Affx-122946106 AX-123289237 2 44322480 CTAATCCTTTCTTCCCCCAACCTCCTCACCTCTGA[C/T]GACTATCTGTTCTCTGTATTTATGACTCTGTTTCT Y 2 1 2 1 201000 r 74 goat snp35877-scaffold430-6441137 2 91226656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421778 Affx-122944346 AX-123292125 2 44352486 GGAGGTTCCTGTGCACCAAAAGATCTTTGTTGTCT[A/G]TGCAAAACTTTTCCTTAATAAAATGGGTCTGTCGA R 2 1 2 1 101000 f 74 goat snp35878-scaffold430-6471143 2 91198462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407887 Affx-122954494 AX-123278238 2 44408766 GGCCTGAAGACAGCACATCAGCCTTCACAGGGACG[G/T]TCTCAGTTTGGCTGTGCAGCTTCTCTCGTCTGTTC K 2 1 2 1 101000 r 74 goat snp35879-scaffold430-6527423 2 91141638 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388962 Affx-122968803 AX-123259320 2 44458924 AGATGATAATAATTATTATGCAGTTTCTTCAGTGA[C/T]GCCAAGAGATGGGGCTTAGAGCAGTGCTTGTCTCT Y 2 1 2 1 201000 f 74 goat snp35880-scaffold430-6577581 2 91090041 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429410 Affx-122938523 AX-123299752 2 44511635 CTCAACTCTGAAGAAGTCTTTCAGGCTCATTTGCT[A/G]CCAGACTCCGAGGTGAGAGCTTGCACCTTCTGGTT R 2 1 2 1 101000 f 74 goat snp35881-scaffold430-6630292 2 91037521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423185 Affx-122942728 AX-123293531 2 44578450 CTTATAATGGAGAACAAAACAAACACAACAGAGGA[C/T]GGGAATCTGAACCACACATGACAGAGAGAATACTA Y 2 1 2 1 101000 r 74 goat snp35882-scaffold430-6697107 2 90970031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790788 Affx-122930591 AX-385277788 2 44611261 GCTTTTCAATTTGTTGGTATCTCAAAATGTAGTTT[A/G]TGGATTTATTCTGACATATAATTATATCTTATGGT R 2 1 2 1 201000 r 74 goat snp35883-scaffold430-6729918 2 90936555 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767301 Affx-122956501 AX-385254582 2 44645817 GGGGTATGTCTTGGTGCAAAATTTGAGCATTTCTT[C/T]AGTTGGTTTTTGTGTTTACTTTGAGCCCTTGTTCT Y 2 1 2 1 101000 f 74 goat snp35884-scaffold430-6764474 2 90901562 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443348 Affx-122927427 AX-123313685 2 44696134 TGAAAGCTATCATATTTATTATTCATTGTATAGTG[C/T]AACTATCAGAGCTAATATAATATAGCAAGTTGCTT Y 2 1 2 1 201000 f 74 goat snp35885-scaffold430-6814791 2 90850726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768616 Affx-122951266 AX-385255796 2 44726153 ATCTGTGAAAGTCCCTTTGCCATTTTATTAGAGTT[A/G]TTCAGAAATGAATAGGATACTGAATCCAAACATGG R 2 1 2 1 101000 f 74 goat snp35886-scaffold430-6844810 2 90820760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439512 Affx-122930132 AX-123309849 2 44760631 TTAGATCACTTCCAGCTTCAGTATTCACTAACACT[A/G]CTGTGCTGGTTCAGTGTTCATGGGGCGTTCCCACT R 2 1 2 1 101000 f 74 goat snp35887-scaffold430-6879288 2 90786563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771827 Affx-122978739 AX-385258984 2 44822496 CTTTAACATCGCAAGAAATCAGATGGCTCTCAGAG[A/C]AAACTGGGCCAAATGTATGAAACGGCAAACTTTTC M 2 1 2 1 101000 f 74 goat snp35888-scaffold430-6941153 2 90725269 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389641 Affx-122968737 AX-123259999 2 44859339 TAACACTCAATATTCAAAAAACACCAGATCTATCC[C/T]GGAACATGCTGGACTTTAAAAAATTTCACCCAATC Y 2 1 2 1 101000 r 74 goat snp35889-scaffold430-6977996 2 90687996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449847 Affx-122922380 AX-123320182 2 44898230 AGGAAAACTGCAGTGAAGGGCTTGAGCTTTCCATC[A/G]TGTCACCGGGAGCTTGAATGGTTGCGAGGCTGACA R 2 1 2 1 101000 f 74 goat snp35890-scaffold430-7016887 2 90648886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433613 Affx-122934946 AX-123303954 2 44942512 ATGCATACCAAAAATAGAAACCTGCTGGCTTAAGC[A/G]GTGGAATTTCTGTTGTTTGCAGGATGCTCCTGTAA R 2 1 2 1 102000 r 74 goat snp35891-scaffold430-7061169 2 90604757 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385646 Affx-122971167 AX-123256004 2 44974092 CACTGTGATGGCTTCTCTCATTGCGGAGCACAGGC[A/G]CTATGTGCGTAGACTGCAGTGTTGTGACTTATGGG R 2 1 2 1 101000 r 74 goat snp35892-scaffold430-7092749 2 90572822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443638 Affx-122927285 AX-123313975 2 45019575 GATAAAGCTTCATTTTTGAAGTGTTGAAGCTGTGC[C/T]CCCATTCAGTTGTGGCAGGAGAGGAGATTAAGGTA Y 2 1 2 1 201000 f 74 goat snp35893-scaffold430-7138232 2 90526947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792567 Affx-122934585 AX-385279548 2 45063618 TATATTTTGAAAAACTGCCACAAACAAGTCTGCAC[A/G]ACTGAATCCATAACATATGAAACTGTGCTGTGACT R 2 1 2 1 101000 f 74 goat snp35894-scaffold430-7182275 2 90484832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448412 Affx-122923673 AX-123318748 2 45100582 CACCTCAAAATTCAAAGCCCAGCCCTCCTACAAGC[C/T]GTAGGATCACTGCCCAAATCATCATCCTTAAATAC Y 2 1 2 1 101000 r 74 goat snp35895-scaffold430-7219239 2 90447878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775697 Affx-122954979 AX-385262828 2 45132670 GCGAGTTTCTCAAGAAGATAAGAGTCTCCGGATGA[C/T]AGCACAGTGGTCATGCCTCAGATGGCAAGTTTATG Y 2 1 2 1 101000 r 74 goat snp35896-scaffold430-7251327 2 90415243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425912 Affx-122941615 AX-123296258 2 45177365 CAGAGTCTGCCACATTTTTGCTCATCACTTCAGGT[A/G]ATGTGACCCTTCCAGGAGAAGCACACCGGTGGATG R 2 1 2 1 101000 f 74 goat snp35897-scaffold430-7296022 2 90370453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414725 Affx-122949263 AX-123285074 2 45218300 TTGTGGCCTGGACTGAAGGGGTGCCACACATTGCT[C/T]CTGGACATATTTTTTCTTTCATTCTCTCCTGTGAG Y 2 1 2 1 201000 f 74 goat snp35898-scaffold430-7336957 2 90329083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385213 Affx-122971709 AX-123255571 2 45271308 GCCACAGTCGGACATGACTAAGCAACTGAACTGAA[C/T]TGAACTGAATCCTCAAATAAGAGAACCCCAAAGAA Y 2 1 2 1 103000 r 74 goat snp35899-scaffold430-7389965 2 90275805 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450768 Affx-122921838 AX-123321102 2 45330956 TTTATAGCAAAAGGATCACCTAGATGTACTATGCT[A/C]TCCTTCACTTTTTTCACTTACATTATGAGATATTT M 2 1 2 1 101000 f 74 goat snp35901-scaffold430-7449613 2 90215983 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401575 Affx-122958885 AX-123271928 2 45364005 TTCAAGGCGAAAAATGCTTAGACGGATAATTTAGA[G/T]TCATGTAACAAAAAACTGAGAAAAGAAATAAACTG K 2 1 2 1 201000 f 74 goat snp35902-scaffold430-7482662 2 90182903 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768213 Affx-122947030 AX-385255399 2 45421072 TTCTCACACATACACTCACCTTCTGTTCAGAAACC[A/G]TCTACATGCCTAAACCATTTTGTTCCTAAGAGACG R 2 1 2 1 101000 f 74 goat snp35903-scaffold430-7539729 2 90125741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422284 Affx-122943488 AX-123292630 2 45453744 TCTAGAGAGCCTGCCCATAAAAAAATCAGACATGT[C/T]AAGTAGGATAAACTCTTAAGACTGGTGAAGATATG Y 2 1 2 1 102000 r 74 goat snp35904-scaffold430-7572401 2 90093207 A G 1 parentage parentage neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402544 Affx-122958467 AX-123272897 2 45487167 TGGCACTGGGTGCTCGAAGTAATTCACATTCCTTA[C/T]GACAGTACAGTACTGAATATTCATTGGAAGGACTG Y 2 1 2 1 101000 f 74 goat snp35905-scaffold430-7605824 2 90059650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401059 Affx-122959648 AX-123271412 2 45530706 GCGACTAATATATTGATTTTTCCTATGTGCCCAGT[A/G]CTATGCTTAACATCTTACATGGCTACTTTATTTAA R 2 1 2 1 101000 r 74 goat snp35906-scaffold430-7649363 2 90016630 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412416 Affx-122951432 AX-123282765 2 45575595 TTTCACTTCACTTTAATTTTCTAAGCATAGTTGCT[A/G]CAAGGTTGGTAGTTTATTTATTGGTTGGTAGTTTT R 2 1 2 1 101000 r 74 goat snp35907-scaffold430-7694252 2 89971659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386438 Affx-122970796 AX-123256796 2 45610184 TTTGATTAAGAAACTTTCTCAGTCTTCCCACACAG[C/T]AGACACTGAACTACTGAAATGTGTTGTGGCTAGAA Y 2 1 2 1 101000 r 74 goat snp44980-scaffold614-16023 2 89934967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793235 Affx-122977078 AX-385280213 2 45666342 GTTATAATGCTAGCCTCACAAGACATCATCAAAAT[A/G]CTGATTCATACTTGACTAAATAAGCCACATATTAA R 2 1 2 1 101000 f 74 goat snp44981-scaffold614-72181 2 89877592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391476 Affx-122966718 AX-123261833 2 45714248 GAACATTCAGAGCCGGGTATGTTCCTTACAGACTC[A/G]CACTGGGGGCAGGCCTGAAGCAGCACAGTCTCCAT R 2 1 2 1 101000 f 74 goat snp44982-scaffold614-120087 2 89829393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796832 Affx-122959038 AX-385283775 2 45744376 CAAAATGTCTTGCTCAAAAACGTGATGTGATGAAT[A/G]TAATGAATACCTACAGTGAACAGGTAATATATACT R 2 1 2 1 101000 f 74 goat snp44983-scaffold614-150215 NW_017216733.1 8797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788191 Affx-122938397 AX-385275210 2 45786268 ATTTATTTCAATGACTCCAGGGAAAGAAGTTAGAG[A/G]AATAGCCCAAGATGTATATCTTTGGTGTATTTTTT R 2 1 2 1 201000 f 74 goat snp44984-scaffold614-192107 2 89755211 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397655 Affx-122962605 AX-123268010 2 45852501 TCTCATCAGAAACTAATGTGTAACTACTGAGAAGG[C/T]GATTAAAGGGAAATCCATTTCACAGCCTTAGGAGA Y 2 1 2 1 101000 f 74 goat snp44985-scaffold614-258340 2 89688135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795011 Affx-122932766 AX-385281970 2 45901099 AGCTGAATTATTTAAGGTGTACCCTAATCAGGAAC[A/G]TTCACATGCTCTCCTCTGGTGTCCAGGCATCTGAT R 2 1 2 1 101000 r 74 goat snp44986-scaffold614-306938 2 89639217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438454 Affx-122931249 AX-123308792 2 45942450 GATGAGGTAGGCAAGGAGAATCAAATAAATGGGAT[A/C]GGAACCTCTGAAAGAATTTGGGCCATAGAAACTGG M 2 1 2 1 101000 f 74 goat snp44987-scaffold614-348289 2 89597429 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405708 Affx-122956536 AX-123276060 2 45978331 TCCACCCTTGGTCTCCACAGTCTCTTCTCAGTAGG[C/T]AGTGGTTCTTTAAAAGACACCAGTTAACATCCTCC Y 2 1 2 1 101000 r 74 goat snp44988-scaffold614-384170 2 89560917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766891 Affx-122948301 AX-385254209 2 46029607 TATGCAAAGCTTGAGAGATTTGGGCTCAAAAAACC[A/G]TCCTATTTCCAGATGTATCGCTAAAAGTAATTTTC R 2 1 2 1 101000 f 74 goat snp44989-scaffold614-435446 2 89509394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408390 Affx-122954490 AX-123278741 2 46072979 CTCACTATTCCCCAGTACAAACCCACATTCATATC[A/G]TGTCAGTTATTTCACTGGGCTCCATGTGAGCTCCA R 2 1 2 1 201000 r 74 goat snp44990-scaffold614-478818 NW_017210027.1 15005 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773201 Affx-122971350 AX-385260344 2 46116901 CAATGTAGCAATACATACCCAGAGCCCTTTTGAAA[C/T]GAGATTATCACACTCAAATGTAATTTGTAAGTGTA Y 2 1 2 1 101000 f 74 goat snp44991-scaffold614-522740 2 89423023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798517 Affx-122976095 AX-385285450 2 46149879 GGATTAATTCATTTCAGTAGTAGTGTCCTCCAGTC[A/G]TGAACATAGAATGTTATTCCAGTTATTTAGGTCTT R 2 1 2 1 101000 f 74 goat snp44992-scaffold614-555718 2 89389007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795213 Affx-122966093 AX-385282171 2 46191290 ACTAGTGCATCGTTTACTGCTCTAAGGTCTGTGCC[A/G]TTCCATAGTCCCCATTTGGCGTAACAACTGGCAGA R 2 1 2 1 101000 f 74 goat snp44993-scaffold614-597129 2 89347568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786760 Affx-122959819 AX-385273791 2 46241550 TCTGTAAAGTGGTTCAATAACACCCAGCCTGCCCA[C/T]ACCCTGGGTCATTGTGACCATCCAATAGAGGCTTG Y 2 1 2 1 102000 f 74 goat snp44994-scaffold614-647389 2 89297235 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420209 Affx-122945544 AX-123290557 2 46271377 CTGTGATGACCACTACAGGGTTGAAATGGAGTTAT[A/G]CTTTATATTTAAGAAAAGTCTTTGACCTGAAGAAC R 2 1 2 1 101000 f 74 goat snp44995-scaffold614-677216 2 89267646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424120 Affx-122942017 AX-123294466 2 46328925 CAAGTCATTACTATTTTCTCTTCCTCCAGAAGCTA[G/T]AATTCACTGTGCATGTCTGGAGCAGCTGAAATGTG K 2 1 2 1 101000 f 74 goat snp44996-scaffold614-734764 2 89209005 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436892 Affx-122933223 AX-123307230 2 46375179 CCTAAACTCACTTTTTGTCCTTGTCAGTAAAAGCC[C/T]TACCCCAAGAGTGGAGAAGGCTCCCAGATGCATGT Y 2 1 2 1 101000 f 74 goat snp44997-scaffold614-781018 2 89162749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421307 Affx-122944094 AX-123291654 2 46434995 ACGACTGAGCAAGTGAACAAGAACTCCTCCATTTA[C/T]AGTTTCCTCCCTTCTTTCCTCCCCAAGAGAAGGTT Y 2 1 2 1 101000 f 74 goat snp44998-scaffold614-840834 2 89102570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379153 Affx-122976720 AX-123249512 2 46475441 CAGATAAGCCTGAAGGTACCAGTGCTTTTTATCAC[A/G]CCATACGAAGAAGCAGTCAACATAGGGGGGAAAGA R 2 1 2 1 201000 f 74 goat snp44999-scaffold614-881280 2 89062338 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422133 Affx-122943549 AX-123292480 2 46506807 CTTGAGCTCTCTGAAGGCCTCCTTCAGAGAGGACA[C/T]GTTGTCCACAGCAGCACAAGGTTTGGAGTGTAGCC Y 2 1 2 1 201000 r 74 goat snp45000-scaffold614-912646 2 89030877 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800103 Affx-122927950 AX-385287026 2 46541845 GAGCGAGGGCAAGCATTAGGAAACCTGACATAAAC[A/G]TCAGTCTTCAGTCTTACATCAGGTTGCATGGGGCT R 2 1 2 1 101000 f 74 goat snp45001-scaffold614-947684 2 88995710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796302 Affx-122950376 AX-385283252 2 46591587 TGGGTTAGATGAAAGTATTACTAAGGAATGCTGAG[C/T]GGTAAGAACAACTCACTAACCAGCAAGGTAATGTG Y 2 1 2 1 101000 r 74 goat snp45002-scaffold614-997426 2 88947298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272037 Affx-1111833171 AX-519545801 2 46612012 GAGGTCTCAGAGAGCCCACTGCTAGCTCTCTCAGA[A/G]AAGGAGAAAATCCATCCAGGACCTGTTCCTGGAGC R 2 1 2 1 201000 f 74 goat 2_46612012_AF-PAKI 2 46612012 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447530 Affx-122924057 AX-123317866 2 46631049 TGGCTCATGCTCTCCTTTCACCTTCAAAGCAGCCA[C/T]GACCAGCTGAGTCCACTCCAGTCTCTCTCAAGATG Y 2 1 2 1 101000 r 74 goat snp45003-scaffold614-1036888 2 88907329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443296 Affx-122927466 AX-123313633 2 46663587 ACTTTGGAAACAGACCTTTCACTCAAAGAGCTTCA[A/G]TCTAATCGGGAGACAAGATATACAGAGATTAAAAG R 2 1 2 1 101000 f 74 goat snp45004-scaffold614-1069426 2 88877558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385656 Affx-122971158 AX-123256014 2 46700296 ATAGGCAAGAATAGAGGTGGGAAGAAGTGCTGCTG[C/T]GGTGCAGAGAGGAACAGATGACTCAATATACATTT Y 2 1 2 1 201000 r 74 goat snp45005-scaffold614-1106135 2 88840531 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434489 Affx-122934622 AX-123304830 2 46747780 GAAATAACACAAGTCTGATCAAGCCTAGGATTGCT[A/C]GGAAAATTTGCATATAAAGAAGAAAAACTGAAACT M 2 1 2 1 101000 f 74 goat snp45006-scaffold614-1153619 2 88792846 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802508 Affx-122935417 AX-385289412 2 46786734 AAGCCCAAGAGGGAGCAAGACGGAACACAAGAACT[A/C]GCATCACCAGACGATCTGATACTGCTTCAGGCAAT M 2 1 2 1 202000 r 74 goat snp45007-scaffold614-1192573 2 88753035 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782942 Affx-122961030 AX-385270012 2 46819899 CCAAGATAATCAGACTCAACTCTAGATCCCTATTA[C/T]GTTAATAAAGAATGCAAATTAAAAATTGTTTTAAT Y 2 1 2 1 201000 r 74 goat snp45008-scaffold614-1225738 2 88719911 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430133 Affx-122937398 AX-123300474 2 46866127 TTGAGTCCAGGCTTCCCTTCTGTGAAATGTAACAA[C/T]GATATCTACTTTGCAAGTGCTAGAGTAAAGGAGAC Y 2 1 2 1 101000 f 74 goat snp45009-scaffold614-1271966 2 88673028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801885 Affx-122974937 AX-385288792 2 46895698 GTGGGGTGGTGAGAAGGAAAGTAACTAAAAGATGG[C/T]ACCACTTTTACTTTTATCTCACTCATTATAAAAAT Y 2 1 2 1 101000 f 74 goat snp45010-scaffold614-1301537 2 88643657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395747 Affx-122963692 AX-123266102 2 46931197 CAGCCTGGACTCTAGCAGGACCAGGGACCAATGGA[C/T]AAGGGAAAACCACTCCATCTCTGTAAAGCCCCCTC Y 2 1 2 1 101000 r 74 goat snp45011-scaffold614-1337036 2 88609588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451104 Affx-122921395 AX-123321438 2 46969465 CATGCAGCCTTTTCACAGGTCACGTACTTTCCCAA[C/T]AATTTCAGGTGGGGATAAGGAGAGAGCTTATCAGT Y 2 1 2 1 201000 f 74 goat snp45012-scaffold614-1375304 2 88570994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412046 Affx-122951720 AX-123282396 2 47005652 CTCAGAAAAAAAAGAATTTCATTTTTTTTGATTAT[C/T]ATTTGAGTCAACACTTTTAGGCTAGATCAAAGATG Y 2 1 2 1 101000 r 74 goat snp45013-scaffold614-1411491 2 88534802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438514 Affx-122931206 AX-123308852 2 47037815 TAATGAAAATTATTCTAATTCTATGACAGCCAAGA[C/T]AAATACATGGAAAAGTATAGTATCTGATAATGTTC Y 2 1 2 1 101000 f 74 goat snp45014-scaffold614-1443654 2 88502642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796828 Affx-122977808 AX-385283771 2 47074706 TTGCCTTGGGTGAGTTTCCAGTCTGTGTGCAAAGA[C/T]GGTGAACCCAGTTAGAGCCCAGCAGACTAAGTTGA Y 2 1 2 1 101000 f 74 goat snp45015-scaffold614-1480545 2 88465944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416531 Affx-122947761 AX-123286879 2 47108500 ACATGTGCATGAATTATACTCAACGAATGAATGAA[C/T]GCCAAAGCAGCTTTTCCAACTGTGCATTCAATCAC Y 2 1 2 1 201000 f 74 goat snp45016-scaffold614-1514339 2 88431526 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795751 Affx-122959060 AX-385282703 2 47150216 AGAGCAAATATAAGCTAGTGGAAGAGAGAATTATG[C/T]ACAATATTCAGTACAACATTCCACTTCCATTCTAG Y 2 1 2 1 101000 f 74 goat snp45017-scaffold614-1556055 2 88389725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787484 Affx-122932249 AX-385274509 2 47289469 TTGCAGTGATTTTTCTGCATAAATAAGCATATATA[A/C]ATGAATATTCTGTTCCCCTATTATACTATATGTAC M 2 1 2 1 201000 f 74 goat snp45019-scaffold614-1695308 2 88316891 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402406 Affx-122959011 AX-123272759 2 47323586 ATGAAAAACAGAAGGAAGAAATCAAAGCCTACCTT[A/C]TCCTAAGGGTCAGCACTTTGCAGAAAAACATCTAT M 2 1 2 1 101000 r 74 goat snp45020-scaffold614-1729425 2 88282576 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426380 Affx-122940239 AX-123296726 2 47364272 TCTTTCTCCCCAAATCAGGGATGTCTTGCCACTTG[C/T]ATTCAATGTGGTACTACAATTTCTGTGTTTGTGTG Y 2 1 2 1 201000 r 74 goat snp45021-scaffold614-1770111 2 88241914 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391235 Affx-122967390 AX-123261592 2 47424580 CATTCAACTTTGAGAAACTTCATATTTTAATTCAT[A/G]CTGTGATATCCCCTATATTAATTTCCTTCCCTAAG R 2 1 2 1 101000 r 74 goat snp45022-scaffold614-1830419 2 88180760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798296 Affx-122926196 AX-385285231 2 47485233 AAGAGTGGTAATATTTAAACTCATATATAGGAACC[A/G]CTTAAACTTGGGTTAGTGAGTTTTTGTTGTTTCTT R 2 1 2 1 201000 f 74 goat snp45023-scaffold614-1891072 2 88119907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446670 Affx-122924761 AX-123317006 2 47529255 TGAATTTCTTTTTTGATTTTCATTTCAAGGTAACA[C/T]GCAAAGTAGTTCACAGTATTTCACAGAAATTAATG Y 2 1 2 1 101000 r 74 goat snp45024-scaffold614-1935094 2 88075674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387325 Affx-122970501 AX-123257683 2 47575459 GTACAATGACCAAGTCCTATCCACCACAGGGACAA[C/T]AGGAAGGAATTCTCCCCATAAAGCCATTTTATAAA Y 2 1 2 1 101000 r 74 goat snp45025-scaffold614-1981298 2 88029308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447486 Affx-122924090 AX-123317822 2 47680897 GATTATACTAAGTCCCTGTTTCTGCAGCATGCTCT[A/G]CTCAAATGTAGAATGATTGACTACCATCGATGGTT R 2 1 2 1 201000 r 74 goat snp45027-scaffold614-2086736 2 87925046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277389 Affx-1111835887 AX-519550893 2 47687080 ACTTGCCCTGAGCAGCTGTTAAAAAAATGTTGATC[A/G]TATTGCGCACTGGCCCTGTGTCCTTTATTGCAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-195 2 47687080 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424724 Affx-122941673 AX-123295070 2 47719790 TAAGAGACTTGAGGAACTGGTAGGATTTAGACAGG[C/T]AAAGACGATAGGCAGAAAAAGAGCATAAGCAAACA Y 2 1 2 1 101000 f 74 goat snp45028-scaffold614-2125629 2 87885647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410211 Affx-122952567 AX-123280561 2 47769871 AAAAGAGAAAGAAAAAGCAAGCTGGGAAGAGGTGG[C/T]GAGACTGAGAAGAAGGCAGGATTGCGGACAGCAGT Y 2 1 2 1 101000 f 74 goat snp45029-scaffold614-2175710 2 87836299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435872 Affx-122932794 AX-123306211 2 47818057 TTCTCCTTTACCATTTGTAGCTGTGTGACCTTATG[A/G]TCTTGTGCTGTTTATTATTTCTTTAAACTGTATGA R 2 1 2 1 101000 f 74 goat snp45030-scaffold614-2223896 2 87787710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433379 Affx-122935120 AX-123303720 2 47857010 AATAGGAGAAGACCTAGTTTGGGGCACGGCTGAAA[G/T]AGGACCTTGGCCCAGCAATCAGGGTAGCAGATAGG K 2 1 2 1 101000 f 74 goat snp45031-scaffold614-2262849 2 87748256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769395 Affx-122972365 AX-385256566 2 47885761 TTGCAATCATAAATACAACTGCAATGAACATCCTT[A/G]TATGTGTGGCCTCATGTACTGGTACTTTAATTTCT R 2 1 2 1 101000 r 74 goat snp45032-scaffold614-2291600 2 87719396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771385 Affx-122928744 AX-385258543 2 47929683 AATTGACTCAAATGAATCTCCTTTTTTTGTGATGT[A/G]TCTGAAGAACATCTTATTCTTAAGTCATCTTCGTC R 2 1 2 1 101000 f 74 goat snp45033-scaffold614-2335522 2 87675465 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396057 Affx-122963451 AX-123266412 2 48014756 GCTGGCTGAGACAGAGGATGTCTTAGCATCAACCA[C/T]GTTGGACCGATGGTCAGTGACCACAAGGTACTTCA Y 2 1 2 1 101000 f 74 goat snp45034-scaffold614-2420595 2 87591464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427239 Affx-122939564 AX-123297582 2 48061965 TAGTGATGGCGGAAGTGATGGAACTAAGAGGGAAG[A/G]ACATGGCCTCTCTATATCTTGAGGCTGCTGAACAT R 2 1 2 1 101000 f 74 goat snp45035-scaffold614-2467804 2 87546146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784966 Affx-122951533 AX-385272013 2 48115375 ATTTATTCTTTTTCCACATTGATAACTTTATATGC[A/G]TTTGGAATGCCAAAGATGCCCTTGTTATTTGAGTG R 2 1 2 1 101000 r 74 goat snp45036-scaffold614-2521214 2 87492171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783445 Affx-122925318 AX-385270508 2 48149912 GTCCCCTGGAGTATTCAGTGGAAAAGTATCTAGAG[C/T]GGTCTTCATTAAGGAACACAACTAATTTCTCTTAG Y 2 1 2 1 101000 f 74 goat snp45037-scaffold614-2555751 2 87457291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796324 Affx-122975795 AX-385283274 2 48209052 CTGTCACTGTGTTTCCAAGCAGACCATATTCTCTA[G/T]GAGAGTAGGGACTGTGTCAGCTGTTTTAACTTTAG K 2 1 2 1 101000 f 74 goat snp45038-scaffold614-2614891 2 87397241 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406619 Affx-122955834 AX-123276971 2 48266328 AATTAAAAAATAGAGTTCATTTACAAAAGTCATAC[A/G]CCCATAATTTAAAGTAGGAGACTAATAGTCTATTG R 2 1 2 1 101000 r 74 goat snp45039-scaffold614-2672167 2 87340876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443872 Affx-122927507 AX-123314209 2 48322309 GTATTCCAATTATAGGTGAGTTCCAAGTTTGGTGG[C/T]ACTTTTTCTGGGTTTTACTTTTCCTGAATATATTG Y 2 1 2 1 101000 f 74 goat snp45040-scaffold614-2728148 2 87285131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453119 Affx-122920016 AX-123323452 2 48413882 TTTCTTGCTGAACTCTCATTACATCCTACTGAGGT[C/T]GCTTCTGTGTAAGTGTGTAACCATCACTAGACTGC Y 2 1 2 1 201000 f 74 goat snp45041-scaffold614-2819721 2 87193106 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394656 Affx-122964380 AX-123265011 2 48445858 CCTATGAACTGGGAAGGGGGCACACATTGCAGCTT[A/G]TAACATCAGATGAGTCTAAGAGGGATCTCCAAGAA R 2 1 2 1 101000 r 74 goat snp45042-scaffold614-2851697 2 87160376 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423696 Affx-122942893 AX-123294042 2 48496589 GAGCCATTAATAATGTCACACCTGTAGCCAATGAC[A/G]CCATGCAATCAACAGATATTTGTGCTGTCACCTGT R 2 1 2 1 101000 f 74 goat snp45043-scaffold614-2902428 2 87109034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384074 Affx-122972861 AX-123254432 2 48525554 GAATATTCATATATTTCATCACATTTTCAAAAGGA[G/T]CAGACCCAAAAGTGTTAAGTACTGATATGAACCAA K 2 1 2 1 101000 r 74 goat snp45044-scaffold614-2931393 2 87080026 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401352 Affx-122959251 AX-123271705 2 48583647 GAGAGTTGCATTCCATATCTCCCTCAGTATTAGGT[A/G]TAAGACTTGATCTTTTAAAATTTCCACATGAGGAA R 2 1 2 1 101000 f 74 goat snp45045-scaffold614-2989486 2 87021794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395775 Affx-122963670 AX-123266130 2 48659112 AAATTGTTTCATGGAAAAAAAGACAGAAATCAGAT[A/C]TTTACTAATATTTTCTACACTAGTGAATGACTTCA M 2 1 2 1 303000 r 74 goat snp45046-scaffold614-3064951 2 86944782 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779746 Affx-122950759 AX-385266846 2 48700248 TCTGGGAGCGACAGATGTGTACTTTTATAGCAGCT[A/G]TTACAACAGGTACTAAGAAAAACTATATACTACAT R 2 1 2 1 101000 f 74 goat snp45047-scaffold614-3106087 2 86903671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449490 Affx-122922633 AX-123319825 2 48763309 TTTTAAAAGAAAAAGGGGACCTTGACTACCAACAG[A/C]GTTCTGGATATTTGGAGGGGTTTCCTAGAGATATT M 2 1 2 1 101000 f 74 goat snp45048-scaffold614-3169148 2 86840346 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376788 Affx-122977952 AX-123247147 2 48799099 CACCTTCCCACTTGCAAAAGCTAACAGACAACCTC[A/G]AGTTTAATAGTGCTAATCTTTCTCCTGTGTTAATC R 2 1 2 1 201000 r 74 goat snp45049-scaffold614-3204938 2 86804591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802978 Affx-122929955 AX-385289863 2 48837285 ACCTTATAAAAAAGAAGCCTAATATGAGCTTCAAA[C/T]GTTTTGCCTCTAAGGCATCATGCTGTGCAATGAGC Y 2 1 2 1 101000 r 74 goat snp45050-scaffold614-3243124 2 86765750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767407 Affx-122924416 AX-385254680 2 48867411 TATGCCTGATTCATACTGTATAGGTTTGCATAGAG[C/T]ATATGTCTATTTGTGTTTAGGTCTAGGTTATTTTC Y 2 1 2 1 101000 f 74 goat snp45051-scaffold614-3273250 2 86736774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389396 Affx-122968382 AX-123259754 2 48900174 ATCCTTTCTAAGAGAAATAAAAACATAAGACATTG[C/T]ATTTTGCTTCTAATACCATTTCCAGTGACTTCTTC Y 2 1 2 1 101000 r 74 goat snp45052-scaffold614-3306013 2 86703349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385257 Affx-122972082 AX-123255615 2 48931964 AATCAGAGGCTCCCTTTTACTAATTCTGTAAAAAA[C/T]AAGTTTCATGGAAAATTGGAAGGACATGTACTATA Y 2 1 2 1 102000 f 74 goat snp45053-scaffold614-3337803 2 86670706 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794799 Affx-122958252 AX-385281759 2 48961191 GGAACTGGAACTTCGTCTGTGAAAGCCTCATCAAG[A/G]CTATTTCCTAATCACTGGGCTGTGCCGTAGTTCTG R 2 1 2 1 101000 r 74 goat snp45054-scaffold614-3367030 2 86639686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404471 Affx-122956731 AX-123274823 2 48992986 TATATGTTCTTAAAAATCTGTGTAGAGACTTCCCC[A/G]TCTCAAAGTGATAAATTAGGTAAAAACGGAGCAGC R 2 1 2 1 201000 r 74 goat snp45055-scaffold614-3398825 2 86607808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379102 Affx-122976759 AX-123249461 2 49025350 GCTCAGGGGAGGGCACTGGAAGGAAAAGGAGCAAG[C/T]AAAGTTAAAAAGAGAACATTAGATATTGTCAGTTT Y 2 1 2 1 101000 f 74 goat snp45056-scaffold614-3431189 2 86575378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789743 Affx-122961669 AX-385276751 2 49054573 ATTTGTTTCTCTTCACCACCAAACTCACACTTTAC[A/G]TCTCTTTTTGTATGATTCCCCCCCCCTCCTAATTT R 2 1 2 1 101000 r 74 goat snp45057-scaffold614-3460412 2 86546161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391941 Affx-122966925 AX-123262298 2 49095874 TCTATTCAATCCACCACACAACCCTATTCAATCTC[C/T]ACAATATTTCTAAATTCCAGCACTTTTCCTCGTTT Y 2 1 2 1 101000 f 74 goat snp45058-scaffold614-3501713 2 86505299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802321 Affx-122944059 AX-385289225 2 49143218 TTATGCCCTGTGTAAGATACTGAAGGAAGTATTTG[C/T]GCATTTAGTACTCATTTCAGATGTTGTTGTTGTTT Y 2 1 2 1 101000 f 74 goat snp45059-scaffold614-3549057 2 86457569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429290 Affx-122938615 AX-123299632 2 49173461 ATACATATATCCTTATCTCTGGAGTCTGTGAATAC[A/G]TCCCCTACAAAAAGGATTTTACAGATGTGACAATG R 2 1 2 1 101000 f 74 goat snp45060-scaffold614-3579300 2 86426484 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274707 Affx-1111834375 AX-519548293 2 49218335 CTGCTCCACCATCTTGGCCCATCTCCCTGTATGCC[A/G]GCAGTCTTTGTACTCAAAGGCACATGTAGTAAGAA R 2 1 2 1 101000 r 74 goat GoatD01.032527 2 49218335 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776641 Affx-122960154 AX-385263768 2 49218485 TTATGTGAAAGACTACACTTCGATATGAAAAGGAT[A/G]GCACCAAAGCTCTAACTCTTGGTAAGCTCCCTTAC R 2 1 2 1 101000 r 74 goat snp45061-scaffold614-3624324 2 86382766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787258 Affx-122926878 AX-385274284 2 49289159 GGGACTCTTTCCATACAATGCCATAGTGATTATCC[A/G]CTGCAAATGAAACGTAAGTTGCTGCTGAGCCTAAA R 2 1 2 1 101000 r 74 goat snp45063-scaffold614-3694998 2 86311180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423342 Affx-122943163 AX-123293688 2 49345370 ATGGATGAGTTGCAAATGTGTGCCTTAAGGTTTGA[C/T]AAAATTTAACATTTTATAATATATTTGTGTCTATT Y 2 1 2 1 103000 f 74 goat snp45064-scaffold614-3751209 2 86255319 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426722 Affx-122939882 AX-123297068 2 49418638 ACCAAGAGACCCATGAGCAGGCACAAAGCACTTCC[C/T]GCACTGGTTCAACAGTGTGTGGGCCACAGCTGCCC Y 2 1 2 1 101000 f 74 goat snp45066-scaffold614-3824477 2 86180485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382879 Affx-122973423 AX-123253237 2 49501153 ATAGCATCAGGACTATAGAGGTATAGTCTATATAC[G/T]CTTCTGTACACAGAATTTAAAGCGATTCCTCTACT K 2 1 2 1 101000 r 74 goat snp45068-scaffold614-3906992 2 86097707 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401366 Affx-122959240 AX-123271719 2 49583222 CATATCAAGTACTTGTTTTCCTGCCATTTTCAGTG[C/T]CTAGAAAGGGCATATTTTTGTCTTATCATTGATGC Y 2 1 2 1 201000 r 74 goat snp45070-scaffold614-3989061 2 86014728 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405927 Affx-122955568 AX-123276279 2 49622498 GAGGAGTATAAATGCCTGTGTGATTAAACAGAAAG[C/T]AATATATATGGTAAAGGAAGAGAATGGGGCTTGCT Y 2 1 2 1 101000 f 74 goat snp45071-scaffold614-4028337 2 85975024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777217 Affx-122964394 AX-385264340 2 49657617 ACTTATGGAGTTAAACTAGCATCATACACCTCATC[A/G]TCACAGACCACTGTCCAGTACAAAAACGCACTGGT R 2 1 2 1 101000 r 74 goat snp45072-scaffold614-4063456 2 85939487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785062 Affx-122977739 AX-385272109 2 49700254 AGTTACAGATGGTTCCTAGTGCTACTAGCACCTTT[A/G]TCTTCAGTCATGTTAAGTATCATTTTGTTAACATT R 2 1 2 1 101000 f 74 goat snp45073-scaffold614-4106093 2 85897114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407730 Affx-122954998 AX-123278081 2 49761085 AGGATAAATTCAAAATAACCACTGAAGAAATGGCA[C/T]GAAGATGTAATTCTTTCCCAAGGGAAATTGTAAAG Y 2 1 2 1 101000 f 74 goat snp45074-scaffold614-4166924 2 85836653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442843 Affx-122927690 AX-123313180 2 49823620 CTTAGGAGAATGAGGGTGCCTAACAATATCAAGTA[C/T]GGAAACATACTTAAAATGAGTCAAAATACATTGCT Y 2 1 2 1 101000 f 74 goat snp45075-scaffold614-4229459 2 85773923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437358 Affx-122931934 AX-123307696 2 49870863 AAGGTTCCTGCATAGGGTACTTACTGTATTGGAAA[G/T]AGTGAACTGAATCTCTGTCTGTTTGTTCAACATTG K 2 1 2 1 101000 f 74 goat snp45076-scaffold614-4276702 2 85730023 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774194 Affx-122940305 AX-385261331 2 49921754 GCCTTAGTCTTGTCTTAATCATTATATTTAATCTG[C/T]AGAGTTAACTACTTATAGGCCATGATAACCATTTT Y 2 1 2 1 101000 r 74 goat snp45077-scaffold614-4327593 2 85678679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400100 Affx-122960735 AX-123270455 2 49959567 ATATAGAAGAAGAAAAAAAAAAGGTAAGAAAATCT[A/G]CTACATAAGGGGAAAGCCACTGACACTGTTTGTGG R 2 1 2 1 101000 r 74 goat snp45078-scaffold614-4365406 2 85640919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774992 Affx-122946470 AX-385262124 2 49993846 TGAGAGAAATCTGACAAGCAATGTCTTAATTCAGC[A/G]TTTCTCAAGCTATACTTGGTGGACCACCTGCATCA R 2 1 2 1 101000 r 74 goat snp45079-scaffold614-4399685 2 85606559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400795 Affx-122959823 AX-123271150 2 50044163 AAAAGAAAGAAAGAAATCGTATCTTCTGTCCTATT[A/G]TGATGATTTTCTAACAAATTTTATGTCGTTTGTCA R 2 1 2 1 101000 r 74 goat snp45080-scaffold614-4450002 2 85556239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798585 Affx-122948556 AX-385285518 2 50076965 AGGGGGCCAGATTCTATGGTGTTTCAAGGATGGAA[C/T]ACCATCCTTGAGAGCAGTGTATTGTTATTTGTCTA Y 2 1 2 1 101000 f 74 goat snp45081-scaffold614-4482804 2 85523522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393646 Affx-122965293 AX-123264001 2 50112086 TTGATTTTTGCAAAGTTTGGACTCATACTTCATTT[A/C]GAATCAAAATATCTAGAAATAAAGGATGGCAATGG M 2 1 2 1 101000 f 74 goat snp45082-scaffold614-4517925 2 85488590 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801350 Affx-122943310 AX-385288262 2 50173875 ACTTTTTTCCTAACCTTAACATGTTTACTTGGGAA[C/T]GCAATTTTCCTTTTTGTTCCTCTGTCCCTCATCTC Y 2 1 2 1 101000 r 74 goat snp45084-scaffold614-4579714 2 85427224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767159 Affx-122932971 AX-385254444 2 50277879 ATTTTTCAAAAATTTGAGGGCTTAAACCAATAAGC[A/G]TTTTTAAGCAAGTGACTTTAGTTATTAAGTTGTAT R 2 1 2 1 102000 f 74 goat snp45086-scaffold614-4683718 2 85323011 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391753 Affx-122967477 AX-123262110 2 50319514 ACATTTTAATATTAAAGCTTCCATCTTAAAAAAAA[G/T]CTTCTTTCAAACTACTTAACTCTGTTGTTAATTCA K 2 1 2 1 201000 f 74 goat snp45087-scaffold614-4725353 2 85280615 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436552 Affx-122932917 AX-123306890 2 50369754 AACAACATCCAAATAAATATAAAATATCCAAATAA[A/G]ATATCAAACTGTGAAACCATCAATAATGTGCTTTT R 2 1 2 1 101000 r 74 goat snp45088-scaffold614-4775593 2 85230072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799988 Affx-122960722 AX-385286912 2 50453234 AAATGTCTAAGAGTTGGTGGTTGTACCATGTCTGA[C/T]GGCTAGGCATTTATAAAGTGTGAATAATATCACCT Y 2 1 2 1 101000 f 74 goat snp45090-scaffold614-4859073 2 85146308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397439 Affx-122962115 AX-123267794 2 50489402 CCTCTAAATCCTCTAAATGTTACTCAAGATTAAGG[C/T]AAACCAGCAGAGAGTTATATCCTTAAATAATAGTC Y 2 1 2 1 201000 f 74 goat snp45091-scaffold614-4895241 2 85110014 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778172 Affx-122967540 AX-385265287 2 50538568 TTCCAATGTTAGCATAAAATCCATGAGCTATAAGA[C/T]CCAAGAGTTCAGGATCATGTTTATGATCCTAGTTT Y 2 1 2 1 101000 r 74 goat snp45092-scaffold614-4944407 2 85060101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797979 Affx-122946233 AX-385284915 2 50568810 TTAAAGAAGTTAGTTTATTGACATTCAAAGTAATT[A/G]TTGATAGGTCTGCCTTTTTTGTCATTTTATTCTTT R 2 1 2 1 101000 r 74 goat snp45093-scaffold614-4974649 2 85030894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443596 Affx-122927318 AX-123313933 2 50597421 GAAAGAACAACTTAAACAAGTAGCATTGTCAATCA[C/T]GGCAGCTGACAGAAAAGGCCCTTGCATTCAAGATC Y 2 1 2 1 101000 f 74 goat snp45094-scaffold614-5003260 2 85001970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388431 Affx-122969271 AX-123258789 2 50641010 GTACCAGAGGTCAAATGTTAAAATCCTTTTCTTAG[C/T]AAGAGGCACTATAGCATCACCTGCAACAGTCAACA Y 2 1 2 1 101000 f 74 goat snp45095-scaffold614-5046849 2 84958168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778616 Affx-122933960 AX-385265727 2 50683519 TAGGTTTTGAACATAATTTAAAAGCCTATACTTGA[A/G]CACAGTTTATCTCAGATATGTATTAGGCTTGTCTC R 2 1 2 1 201000 f 74 goat snp45096-scaffold614-5089358 2 84915910 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774331 Affx-122941936 AX-385261467 2 50733875 AAATACACTGGGTCCTAAACTATAGTAAAATGAAA[C/T]GTTTGGAGACTGACTTCTCTTTACTTCTTGTCCTC Y 2 1 2 1 101000 r 74 goat snp45097-scaffold614-5139714 2 84865134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775074 Affx-122924274 AX-385262206 2 50762417 TGAAAATATCTCCATTATTTTGCAACTCTGAGACA[C/T]CGCCAGTATCATTGCAAGATTTGGCTTGTGTACAC Y 2 1 2 1 101000 r 74 goat snp45098-scaffold614-5168256 2 84836372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420059 Affx-122945127 AX-123290407 2 50793280 ACTCATTCTGAGTCCCCTATTTTTCTCTTCCTCAT[A/C]TTTTCTGTTCTCTGCTCCCGTGTATTTTGCAGCTA M 2 1 2 1 201000 r 74 goat snp45099-scaffold614-5199119 2 84805046 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437560 Affx-122931890 AX-123307898 2 50828279 ATTAATAGATAGTTTGAGACAAGAGGCTACTTAGA[C/T]TCCTTTGATGAGAAGATGCATCAGCTTACATCTAA Y 2 1 2 1 201000 f 74 goat snp45100-scaffold614-5234118 2 84769148 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405564 Affx-122955953 AX-123275916 2 50880997 ATCCTCCTATTCTATCATGGGCCCATGACAATGCT[A/G]TTGGAAAATTACATATTAGAAATATGTTATGGCAA R 2 1 2 1 101000 f 74 goat snp45101-scaffold614-5286836 2 84716395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768147 Affx-122966524 AX-385255346 2 50924812 CCTCGGCTATTTCCTGTCCTCAAGAAGCCAGTAAT[A/G]TGTATAAGAATCATTTGACTTATCAGAAAGGAAAA R 2 1 2 1 101000 f 74 goat snp45102-scaffold614-5330651 2 84672572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798961 Affx-122919551 AX-385285891 2 50965438 GGCTGGATCTAAGTACATATGGGCTTATGTAAAAA[G/T]ATAAGCCCATTTTTCTAGCCTCAGATTCATTGTTC K 2 1 2 1 202000 r 74 goat snp45103-scaffold614-5371277 2 84631388 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382229 Affx-122973967 AX-123252587 2 50997520 TTGACTTTCTGCTGCATTTTACAACTACTCCCCAA[C/T]GTGCTATCCTCAGAGGTGATAAAGGAGAGCTGTTT Y 2 1 2 1 101000 r 74 goat snp45104-scaffold614-5403359 2 84599266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376931 Affx-122977782 AX-123247290 2 51028229 TTAAATAACACAATAAATAAGATCTATTTCTCTTT[A/C]GTTTTCTCACCAATCACTTCCAAGCCCCCTTTGTT M 2 1 2 1 101000 r 74 goat snp45105-scaffold614-5434068 2 84567954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418148 Affx-122947102 AX-123288496 2 51122889 CAGATAATTCTTGTGATTGGAGAGAGAGACATAAT[A/G]CTTGGGATCCTGGCATAGCCAATTCTGGAACTACA R 2 1 2 1 101000 r 74 goat snp45107-scaffold614-5528728 2 84471749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776216 Affx-122946722 AX-385263344 2 51166566 ATGTATAATTCTTACCCTTAGTAACAAAAACATAA[C/T]GTCTGGCATAATACATGTATTACAGAAATCCCTGT Y 2 1 2 1 101000 r 74 goat snp45108-scaffold614-5572405 2 84427386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444573 Affx-122926970 AX-123314910 2 51242109 CAGATCTACCCCTTCTAAGGACAATATTGTGCATC[A/G]TTGTGGATTTGGGGTTTTTAGAATATTCATGCTAA R 2 1 2 1 202000 r 74 goat snp45109-scaffold614-5647948 2 84351553 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409378 Affx-122954155 AX-123279729 2 51299755 CTTCCTCCCCTCGCCTCTCTTTCTCCCTCTCTGTC[C/T]CTCTCTTTCACTCTCTCTCTTCAACTTCCTCCCAC Y 2 1 2 1 103000 r 74 goat snp45110-scaffold614-5705594 2 84293840 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432156 Affx-122936420 AX-123302497 2 51328455 ACACAGTTAGTATGTTCGGTTGCCATAAGACAAAT[A/G]GCCGTAAGATTTTAAAATATCAAAGTGATAAGCTA R 2 1 2 1 101000 f 74 goat snp45111-scaffold614-5734294 2 84265213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379499 Affx-122976465 AX-123249857 2 51397404 TATAAAAGAAGGAAGTCAATGGCCATGTTGACTTA[C/T]GTAACAGACACCTTTATCCATCGTTAACAGGAAGT Y 2 1 2 1 101000 r 74 goat snp45112-scaffold614-5803243 2 84197477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476167 Affx-1251763670 AX-586011594 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20000 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 539476422 Affx-1251763670 AX-586011823 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 4 1 4 1 20000 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165407 Affx-1251763670 AX-606940818 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165673 Affx-1251763670 AX-606941082 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165897 Affx-1251763670 AX-606941306 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165961 Affx-1251763670 AX-606941370 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562166363 Affx-1251763670 AX-606941771 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562166514 Affx-1251763670 AX-606941923 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 320774689 Affx-122923819 AX-385261823 2 51450299 TTTCATTTCTTGATTGTTTCAAGGTGTCTTGGGGA[C/T]GACTTGCCCTTAAATAACTAATTATCAGCAAAGGA Y 2 1 2 1 101000 f 74 goat snp45113-scaffold614-5856138 2 84146457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401325 Affx-122959275 AX-123271678 2 51497393 CGCTCATATTGCTGAGATTTTCCAACTTCCAGTAC[A/G]AGGTTGTTTCCTCTTTCTTCACTTCCTTTTTGGAA R 2 1 2 1 101000 f 74 goat snp45114-scaffold614-5903232 2 84099434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444479 Affx-122926530 AX-123314816 2 51554046 TCTAGAATCCATCTTCCCTATCTAACTCTGCACCA[A/C]CCTGGCTCTGTGAATGAATTACCACTGTCAGAATC M 2 1 2 1 101000 r 74 goat snp45115-scaffold614-5959885 2 84042705 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413328 Affx-122950175 AX-123283677 2 51605907 GTGTCTTGGCACCTGTGGCTTATTTAATATCAGCC[A/G]TGGAATGTGACACCTTCTCTACCCAAGTACAGATC R 2 1 2 1 101000 r 74 goat snp45116-scaffold614-6011746 2 83990661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429680 Affx-122937646 AX-123300021 2 51636892 CTATTTTATTACCTGATTTTCTTCCCATTAACACT[A/G]TAGAGCAACCCTTTTTTTTTCTTGTTAATACTTCG R 2 1 2 1 201000 f 74 goat snp45117-scaffold614-6042731 2 83959937 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271873 Affx-1111833172 AX-519545656 2 51694566 AAATTCTCTCTTCTTTAGCCTCTTCACTAATACTT[A/C]TCTTTATTCTCTTCCTGAATAGCACTCTTTTCCAG M 2 1 2 1 101000 r 74 goat 2_51694566_AF-PAKI 2 51694566 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401725 Affx-122959526 AX-123272078 2 51720295 ATTAGGTCATCTTGGTGTCCCTACCTGTAGCATAG[C/T]ACCTAGATAGACCCTCAATTAAACACTTGTTGAAT Y 2 1 2 1 101000 f 74 goat snp45119-scaffold614-6126134 2 83875630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413686 Affx-122950097 AX-123284035 2 51764849 ATTGTTAAAGAAAACCCTGAATAGCTTTCATTTCA[A/G]TTCAATATACAATTGACTCTTAAACAACTTATGGT R 2 1 2 1 101000 r 74 goat snp45120-scaffold614-6170688 2 83831049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783616 Affx-122939905 AX-385270675 2 51808420 ATCTAATTTATCTCGTCAAGGAGTATATACTCTTA[A/G]TGGGAGGAAGCAAGATACCGTATGAAATATGGCAG R 2 1 2 1 101000 r 74 goat snp45121-scaffold614-6214259 2 83786519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421480 Affx-122943919 AX-123291827 2 51897206 GAGTAGAAGTGAAGGGCCAACCTGATTGCTTTTTC[A/G]TGCTGATTTCTTTCTCCCAACTTTCTTTAACCCAG R 2 1 2 1 101000 f 74 goat snp45123-scaffold614-6303045 2 83696977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450762 Affx-122921844 AX-123321096 2 51930790 TTCTCCATTTGGCATTAATCCTCCGGAGCTACTCC[A/G]TCCCACGTTGTTCCTTCCCGTCTCTGAATTCCTAT R 2 1 2 1 101000 r 74 goat snp45124-scaffold614-6336629 2 83663025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381820 Affx-122974269 AX-123252178 2 51973442 AGAAAAGGAACATTTTTTTTCACAAGAAAGTTCAC[A/G]CATTTTCTTCTTTTCATCCCCTAGATTCTCTTGTC R 2 1 2 1 102000 r 74 goat snp45125-scaffold614-6379281 2 83621089 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789171 Affx-122969982 AX-385276183 2 52003993 TTGATTATCTCTCTGTGATTCAGTGTATATTTTCA[A/C]CTCCTCCTCCTCCAAAGTGTTTTCCTGTTATATAA M 2 1 2 1 101000 r 74 goat snp45126-scaffold614-6409832 2 83590083 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452717 Affx-122920293 AX-123323050 2 52042080 CTAGCACCACATGGTGAATACCAAGAACAGAAGAT[A/G]TCATGGCTCCAAAATCTTCATGTCTAGGAGACAAA R 2 1 2 1 101000 f 74 goat snp45127-scaffold614-6447919 2 83551158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397211 Affx-122962390 AX-123267566 2 52118426 AAATAGCTTATATTTAATGTGTCTGCTCTACTGAG[C/T]TTGGAGTGGCGATCAGAGGGACTGAATTGTGAAGG Y 2 1 2 1 201000 f 74 goat snp45128-scaffold614-6524265 2 83474726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780874 Affx-122978974 AX-385267961 2 52188063 TAATCTTATATCAGATAGATATAAATAATGAAGCT[A/G]CTTTGATACAAATGAATTCAAGAGACCTCCAATGC R 2 1 2 1 101000 r 74 goat snp45130-scaffold614-6593902 2 83404148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448285 Affx-122924175 AX-123318621 2 52249005 CTGAAGCTGAAAGAGCAATGTGACCAATCAATAAT[A/G]TCTACATGGGATTTGGATGAGAAATGGTGGTGTAT R 2 1 2 1 101000 f 74 goat snp45131-scaffold614-6654844 2 83343747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376521 Affx-122978008 AX-123246880 2 52310902 TGTTCATTTCCACAGTCTTATGTGAAAAATTCTTG[C/T]AGGTAAAATTGTCCTGTTGCCTCAAAGCTGCATTT Y 2 1 2 1 101000 f 74 goat snp45132-scaffold614-6716741 2 83281592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785848 Affx-122957568 AX-385272885 2 52374939 ATATCATTAATACAGTGACAAGAACCTATTACATC[A/G]TGAAACTCTCATAAAGGATATGGTATCTGCTTCCA R 2 1 2 1 101000 r 74 goat snp45133-scaffold614-6780778 2 83217087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393048 Affx-122965624 AX-123263405 2 52408988 CTATTTCTAAATATAAGAATTGCTAGTTTATCCTT[A/G]CTCACAAGAGGTCTTCCAGTCTGAGCTTTAACTTG R 2 1 2 1 101000 r 74 goat snp45134-scaffold614-6814827 2 83183043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778293 Affx-122931505 AX-385265408 2 52441508 GGCTATTAACAAATGCATTAATTGGTGTGAGTTTT[A/G]TAGTTCTAGAATAGTCTAACAATAAATTAGCAAAC R 2 1 2 1 201000 f 74 goat snp45135-scaffold614-6847347 2 83150403 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403461 Affx-122957719 AX-123273814 2 52513109 TGGGTCCTCCAGTTTTCAAACCTGTTAAGTTTTCA[C/T]GACACTAGTTTATCTTAGACTTTCTTCCTAGCCCT Y 2 1 2 1 101000 r 74 goat snp45136-scaffold614-6918948 2 83078328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397366 Affx-122962284 AX-123267721 2 52545755 TCCATGGGCAGAGGAGGCTGGCAGGTTACAGTCCA[C/T]GGGGTCATGCAGAACTGGGCATGACTGAGCACAGG Y 2 1 2 1 103000 f 74 goat snp45137-scaffold614-6951594 2 83045579 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444501 Affx-122926512 AX-123314838 2 52581798 AGATCAAACTAATATGCATGGAGGGTGTTATATTC[A/G]CAGCTTTGGGGACCAGTAAAGCTCCCTTTATTTAA R 2 1 2 1 101000 f 74 goat snp45138-scaffold614-6987637 2 83009690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384929 Affx-122972331 AX-123255287 2 52612547 GCCTCACTTTATATTTAATTATTATTCTTGTGTCT[A/G]TTTTGAGTTCATTTCAACTGCATGAATGTCCACCT R 2 1 2 1 101000 r 74 goat snp45139-scaffold614-7018386 2 82978940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438873 Affx-122930747 AX-123309210 2 52673629 GAAGGACTCACCATCAAGAGATTTTGAACAAAATA[A/G]CTAGTAATCATTTATCTATAATATATCTTTCTACA R 2 1 2 1 101000 f 74 goat snp45140-scaffold614-7079468 2 82917773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792538 Affx-122962281 AX-385279519 2 52709609 GAGTAGGAAGGAATAAGGTTGATTCCATAGGAATA[C/T]GTTTATTAGATTTAGTTAGCTAAGCAAATCTTCTT Y 2 1 2 1 201000 r 74 goat snp45141-scaffold614-7115448 2 82881682 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397910 Affx-122961943 AX-123268265 2 52739097 TTTTCCCAGATAGGACAAGCAATTGTCCTCTCTCT[A/G]CTCCAGACAGAAACTATCCCATTTTCCCCAACACT R 2 1 2 1 101000 r 74 goat snp45142-scaffold614-7144936 2 82851762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408862 Affx-122953999 AX-123279213 2 52775088 ACCACTGCCCAGAGTTTTCTCCTGCTCAGTGGCTT[A/C]TGGTATATAAATGCTGTGAATATATATTCTCTTGC M 2 1 2 1 101000 r 74 goat snp45143-scaffold614-7180927 2 82816920 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795440 Affx-122962234 AX-385282396 2 52808940 ACTGGAATTGGTTAGAAATGAAATTGCATGAAATT[A/C]GATTATCTCATGGTTCTCAGAACTTTGAGCTGCTG M 2 1 2 1 101000 r 74 goat snp45144-scaffold614-7214779 2 82783113 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775022 Affx-122971695 AX-385262154 2 52846967 GAAATATGCTATTATGCCAAATCAGATTATGCTGA[C/T]GGAGACTTATGATTTAGGAAATTCTTGATCCAAAA Y 2 1 2 1 101000 r 74 goat snp45145-scaffold614-7252806 2 82744833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439950 Affx-122929990 AX-123310287 2 52912903 GTGTGTGGAAACTCCACAGACAGATACTGTATTTG[C/T]GAGAAACTCATTTCCGTCCCCTGGAAAGATCTTCT Y 2 1 2 1 201000 r 74 goat snp45146-scaffold614-7318742 2 82677792 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418730 Affx-122946272 AX-123289078 2 52959294 GCAAAGTGAGGAAAATGTTGAAAATTATCTTCATT[A/G]CTTCCAGTCTAATGCCTTTCAGTCTCATTTACTGA R 2 1 2 1 101000 r 74 goat snp45147-scaffold614-7365133 2 82631223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382065 Affx-122974922 AX-123252423 2 52999372 AATTGCTGTCTGTAATAATACTTTTCCATTGACAC[A/G]CACTTACTAAATAATATGTAAAATACTGACACCTA R 2 1 2 1 101000 f 74 goat snp45148-scaffold614-7405211 2 82590752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428646 Affx-122938662 AX-123298988 2 53040419 TCTGTGGAATTCTCCAGGCAAGAAAGTGGGTTGCG[A/G]TTTCTTTCTTCACCTGTATAAGATAACCGCAAGTG R 2 1 2 1 103000 r 74 goat snp45149-scaffold614-7446258 2 82549904 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778930 Affx-122954544 AX-385266037 2 53096066 CTATTTCTAGCACCCTGATAATGTGACATTAATTA[C/T]AAGGGAAAGTTATTCCATGTTTTGCAGTTCTACCT Y 2 1 2 1 101000 r 74 goat snp45150-scaffold614-7501905 2 82493860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383132 Affx-122973255 AX-123253490 2 53149428 AGTAGACGCAAAACAAACTGATAAAGGTGAAAGTT[A/G]TGTTTATTTTTAGAATGTTAATTTTTTACGTTTTC R 2 1 2 1 201000 r 74 goat snp45151-scaffold614-7555267 2 82439765 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396926 Affx-122963198 AX-123267281 2 53183441 TAGGAAATCCATGAGGGTAATCTTGGGCTAGTGGG[C/T]TTGGAAATGAACCACATGAATTAGCACTTGTAAAT Y 2 1 2 1 201000 r 74 goat snp45152-scaffold614-7589280 2 82404191 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427110 Affx-122939667 AX-123297453 2 53213961 CTTGAAGACAGATGTCAGAACTATAGGATGCTAAA[C/T]GAACATAAACTTCAAATGAAGAACAATTATTTTCA Y 2 1 2 1 101000 f 74 goat snp45153-scaffold614-7619800 2 82373282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785157 Affx-122951689 AX-385272203 2 53277046 GGAACAGTTGTGCAGCTGTTAAAATAGTTTTCTTT[A/G]CTCCTCACCCTCCTGGATCACTTGATTTTAAATCC R 2 1 2 1 101000 r 74 goat snp45154-scaffold614-7682885 2 82310056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799906 Affx-122936130 AX-385286832 2 53335134 TTTTTCTCTCTTTTCTACCAGACTTGAGCTGGTGC[A/G]TGTAGGCCTAGAGCCATATTGTGATCATAAGAACA R 2 1 2 1 101000 f 74 goat snp45155-scaffold614-7740973 2 82251613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412474 Affx-122951391 AX-123282823 2 53423416 TTTCATATACTTGATTTTTGTTTTTTCTCATTCAT[A/G]GTATTGATCTCCTTCTGATGTTTGCTGATCATTAG R 2 1 2 1 101000 r 74 goat snp6936-scaffold1252-1139021 2 82163173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389649 Affx-122968731 AX-123260007 2 53472858 CCTCTCACCTTCCTCTCTCCCTCATCCCTCTATTT[C/T]TTATCCTCCTCTTCTTAAACCCTGAACCCATAGAA Y 2 1 2 1 101000 r 74 goat snp6935-scaffold1252-1089579 2 82112356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795837 Affx-122960573 AX-385282790 2 53516747 AGCATGCATATATGCATACAAGGCGCTGCTGGTTA[C/T]AGATGCTTTAATTTTGATGGATCAGTCAGTGCAGA Y 2 1 2 1 101000 f 74 goat snp6934-scaffold1252-1045690 2 82069126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392161 Affx-122966313 AX-123262518 2 53549737 ATGTCTTATTCACATTTCTGACACCAAATTAAGCT[A/G]TTATTTGCTTGGTAAATGTAAATTATTATCTGTAT R 2 1 2 1 101000 f 74 goat snp6933-scaffold1252-1012700 2 82035483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802865 Affx-122939344 AX-385289763 2 53623212 TAATGCATTAATATGTTCTTTCAAAAAAAGAGATA[C/T]AAATCCTTTCAGTAATTTTCAATCTCATCCATTCC Y 2 1 2 1 201000 f 74 goat snp6932-scaffold1252-939225 NW_017189834.1 21377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429123 Affx-122938009 AX-123299465 2 53661960 GAATACAGATAAAATGACTTAGCTTGAAAGCAACT[A/G]CAGTGGTTCAGAGGACCGTGAAACCAGCCTGATCT R 2 1 2 1 201000 f 74 goat snp6931-scaffold1252-900477 2 81934232 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782561 Affx-122971533 AX-385269635 2 53696969 CCTTACCACTATACCACCTAGAAAGCACCTATTGT[C/T]GTAATGTCCTAATTTAAGAATTGTTCCAAACATGT Y 2 1 2 1 101000 f 74 goat snp6930-scaffold1252-865468 2 81897944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792482 Affx-122940710 AX-385279463 2 53761441 CATGTCACATAATTACACAATGTGATTATATGTAA[C/T]GGAATACTAAAAGTATGCATATGCCTTGCAACTTT Y 2 1 2 1 201000 f 74 goat snp6929-scaffold1252-800996 2 81833717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415368 Affx-122948768 AX-123285717 2 53795934 ATAGGCTCATACCCAAAGCAGGCAAAAACCTCTAG[C/T]AGTTCTTAGGCAGAACTGTCAGCTCCTCCCTGTTT Y 2 1 2 1 101000 f 74 goat snp6928-scaffold1252-766503 2 81799511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454292 Affx-122919267 AX-123324625 2 53836098 GTTGGTTAGTGTTTGTCTTTGAAATCAATATGAAC[A/G]TTAACCCATATACTAAACTGCAGTATTTTCAGCTT R 2 1 2 1 101000 r 74 goat snp6927-scaffold1252-726339 2 81758826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799968 Affx-122933719 AX-385286894 2 53875171 TTTTCTTTCTATGAAAAAAATGTCCAAGTATAAAA[C/T]GAAGATTATAGATTCCCCTTGTTTGCTACACAGAA Y 2 1 2 1 201000 f 74 goat snp6926-scaffold1252-687266 2 81719281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802010 Affx-122957096 AX-385288914 2 53921424 GAAATATAGTAAGTAATCCACTTGGAATTCTCACC[A/G]AATTTCCCACCTTCCCAAGTAGTTGTTTCTCAGGC R 2 1 2 1 202000 f 74 goat snp6925-scaffold1252-641013 2 81672794 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795497 Affx-122939471 AX-385282452 2 53963404 TCTTGGATGGACAATATTTAAATCATAGGGAATTG[C/T]GCATGAACATCAAAACTCCTGGTCTCTCCTGAATT Y 2 1 2 1 101000 r 74 goat snp6924-scaffold1252-599033 2 81630726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789679 Affx-122931080 AX-385276687 2 53997579 CTACTCTTGTTCACACTCTTCAAGGTGATCTCATA[C/T]ATACTAAGGATTTTACCTCTGAATTGATGAACCTG Y 2 1 2 1 101000 f 74 goat snp6923-scaffold1252-564858 2 81596581 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789385 Affx-122976672 AX-385276395 2 54039764 TTTGTTAGAGGTTTGTTAGTAACAAAATCAATGCT[A/C]GTTTAATATAAAAGTAATAACATTGGGTGGGGGAA M 2 1 2 1 101000 r 74 goat snp6922-scaffold1252-522673 2 81554327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378363 Affx-122976823 AX-123248722 2 54071466 TAGTACCTTTGAAATAAATAGCAAGAATCACAACA[C/T]GTCTTTCATGCATTTTTGCTGTACTTTTGCTCCTT Y 2 1 2 1 101000 r 74 goat snp6921-scaffold1252-490971 2 81522614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277580 Affx-1111835920 AX-519551079 2 54111276 GATATTTACAATATTTCTCTTTAATAAGGCCCAGA[C/G]TCCCTGAACAGAAGGCAATTCCTATTCCTGGGATA S 4 1 2 1 101000 r 74 goat Random2.2K-200 2 54111276 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418022 Affx-122946649 AX-123288370 2 54128337 ATTATAAAGCAAGGGTCTAGAAGAATCCACAAGTG[A/C]CCAATAAACTTGGATATGGTACAACATCTCAAATA M 2 1 2 1 101000 f 74 goat snp6920-scaffold1252-434100 2 81464961 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392534 Affx-122966104 AX-123262891 2 54159875 TTGCATCTCTCTCGCTTTTTCAACGTATAAAAAAG[C/T]GACAATAAGTAGTATTCAAAGTAGAGAATAATGCC Y 2 1 2 1 101000 r 74 goat snp6919-scaffold1252-402562 2 81433336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786775 Affx-122925333 AX-385273806 2 54207692 AAAAAGTAAACATGAGACTCAGGAGTGAGAATAAG[A/G]ACACAGTTCCTCTAACAATGTATACTTACAATGTT R 2 1 2 1 101000 r 74 goat snp6918-scaffold1252-354745 2 81384918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445981 Affx-122925885 AX-123316318 2 54241618 GAGAAGGATAAGAAAATATGGCTCATTTGTATATC[C/T]CAGGCTTTGCCAATAAAACAAACAGCAGCTAATTT Y 2 1 2 1 201000 f 74 goat snp6917-scaffold1252-320819 2 81351117 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421883 Affx-122944269 AX-123292230 2 54283483 GTGTATTTTTATCATGTTAAAATATATATTATATG[A/G]CTAAAAACTGGTAGGTAGTGTTATATATGTGTATA R 2 1 2 1 103000 r 74 goat snp6916-scaffold1252-278954 2 81309204 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436335 Affx-122933244 AX-123306674 2 54322409 CTGCCACAGGTGGTACCAAGCTTTCATTTCTCAAA[C/T]AACATTTCCACTATTCACTTTAATTCTCATCATAC Y 2 1 2 1 101000 f 74 goat snp6915-scaffold1252-240028 2 81270118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794828 Affx-122967126 AX-385281788 2 54402235 TAATTGAAAAGATATGAACTATTAATAAAATTATT[A/G]TGATTATCTCTGGGTAAGAGGTGATTTGCTTTTAA R 2 1 2 1 202000 f 74 goat snp6913-scaffold1252-160202 2 81189709 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783691 Affx-122967770 AX-385270749 2 54433732 AACCTGATATGATATCAACATCTGCAATATTATTG[C/T]AACTTTCAACTCAAACCCTTTGCAAAGTCTGGTAT Y 2 1 2 1 201000 f 74 goat snp6912-scaffold1252-128705 2 81159155 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783350 Affx-122951052 AX-385270414 2 54488939 GTTTTATATAACGAGATAGCTTGCCATTTCACACT[G/T]TATTTCTCGGTTTTGAATTTGCTTAGAGCAATGAG K 2 1 2 1 101000 r 74 goat snp6911-scaffold1252-73498 2 81102675 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416038 Affx-122948362 AX-123286387 2 54554491 AAAAGTCAAGTAGGTAGAAGGTAGAGGGGGGAGCC[G/T]AAACAGTCATCAACTCCCCAATAACCCTTCCTTCT K 2 1 2 1 201000 r 74 goat snp6909-scaffold1252-7946 2 81037069 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791808 Affx-122969392 AX-385278798 2 54587667 CATAATTGGATATATGTGTTGGAGGGAAGTTAAAG[C/T]AGGTTTTAAGTAAGCCTGGATATTAGATGATTTCT Y 2 1 2 1 101000 f 74 goat snp57652-scaffold923-1754168 2 81004029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779944 Affx-122977590 AX-385267043 2 54621724 TTTCTGTGACCTATAGTCCTTCCTCAACTGGGTCT[A/G]CATTTTCTAATACACATCTCTGGAAGCAATCTTTT R 2 1 2 1 101000 f 74 goat snp57651-scaffold923-1720111 2 80969983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413717 Affx-122950073 AX-123284066 2 54677744 CAGATTCTCCCTGGGAAGCCCTGTAGGGGATCCTG[C/T]AGGCCCTTTTGGTGTTCTAACTGTTCTGTTTTGCT Y 2 1 2 1 101000 r 74 goat snp57650-scaffold923-1664091 2 80913718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794263 Affx-122923805 AX-385281228 2 54728485 TGTATTTTCCCAATTTTTCCAAGATAAATCTGAAA[C/T]AATTAGGAGAGAGACATTGAAAGAATGCACTATGT Y 2 1 2 1 101000 r 74 goat snp57649-scaffold923-1613350 2 80860914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442703 Affx-122927871 AX-123313040 2 54839809 TGGGGAAACTCTAGTGTTTTAGCTTCCCAGACTCC[A/C]AGAGCTCTCTCACACTCAAGGAGACAGCTGGAGTC M 2 1 2 1 102000 f 74 goat snp57646-scaffold923-1502026 2 80748288 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447603 Affx-122924003 AX-123317939 2 54883820 ATCTGGGAATCATTCTTGTTAAAAGGGAGATAGCT[A/G]TTGTGGAGAAGGAGGTTTTTATACAGTGTGGGAGA R 2 1 2 1 101000 f 74 goat snp57645-scaffold923-1458015 2 80706117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772058 Affx-122942458 AX-385259213 2 54917783 TTTTTAATAGGACAAAAACTATAACTTTCAATTTG[C/T]ATGAGAATATCTCCTAAGGATTTACTCTTCTTTCA Y 2 1 2 1 101000 r 74 goat snp57644-scaffold923-1424052 2 80671961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401485 Affx-122958952 AX-123271838 2 54996585 AAGACCCTTAAGGATGTAGAAATCACAAGACAGAA[A/G]GACTCTCCATCTTAGCATTATTAACACCTGGAGAA R 2 1 2 1 101000 f 74 goat snp57642-scaffold923-1345250 2 80592997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393593 Affx-122965378 AX-123263949 2 55028971 TACCTTCTTTTTCTAATACAGAACACTTATGTAAT[A/G]CTATGAAAAATAAATGTACCTAGTCAGTGTGTGGG R 2 1 2 1 201000 f 74 goat snp57641-scaffold923-1312864 2 80560144 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427913 Affx-122939674 AX-123298256 2 55103172 AACATTTATATTCAAAAGACTGCATTTTCTGGCTA[C/T]ATGCAATAAAACTAAAGTCAAATAATATATTAAAC Y 2 1 2 1 101000 f 74 goat snp57639-scaffold923-1238663 2 80485095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800495 Affx-122963114 AX-385287415 2 55133367 AGAGGAAATGGGGAACAAGATTATTGAAGATAAAT[A/C]TGCATCATAACTTATGAAGAAATACTCAGAGATGA M 2 1 2 1 101000 r 74 goat snp57638-scaffold923-1208468 2 80455012 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271877 Affx-1111833174 AX-519545660 2 55186669 TTACATAAAGCATTTCTCTTAATCCTCATAGGTTT[A/G]TAGACTACATGCAACTGAAAAACAGTTTATAGAAA R 2 1 2 1 201000 r 74 goat 2_55186669_AF-PAKI 2 55186669 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445781 Affx-122926058 AX-123316118 2 55248555 ATATGAAAGTTGATTCCCTTAAGCCAGTAGTTCCT[A/C]AAGTGTGGTCCCTGGAATGACCTACAGGATCAGAG M 2 1 2 1 101000 f 74 goat snp57635-scaffold923-1093280 2 80340205 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450993 Affx-122921726 AX-123321327 2 55282545 GAGATGAGTGAACATTAATCTCAGAGATGACCAGA[C/T]ATTAACACTTTTCCCATATATAAATCATACTAATG Y 2 1 2 1 101000 f 74 goat snp57634-scaffold923-1059290 2 80305901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393066 Affx-122965612 AX-123263423 2 55337590 ATAACAGGAATCTTCTGTTCTGAGTGACTCACTGA[C/T]GAAAAAATAATCAGTTCAGTTGTGGAAACAACATT Y 2 1 2 1 101000 f 74 goat snp57633-scaffold923-1004245 2 80249583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453802 Affx-122919572 AX-123324135 2 55382454 TTTTTTTTAACTTTTTTTAATTGAAAATGTTGTTT[A/G]TAGTTAAATATACTAATAGCTCCAAGTGGAATCCC R 2 1 2 1 101000 r 74 goat snp57632-scaffold923-959381 2 80203102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801905 Affx-122975853 AX-385288810 2 55420189 ATCTTCTTATATTATCTTTATACTGTCTTGAAATA[A/G]TACTCATTAATGGTATGTGTTTTTATTGTTGTTTA R 2 1 2 1 201000 f 74 goat snp57631-scaffold923-921646 2 80165005 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776650 Affx-122947987 AX-385263777 2 55465221 TATATTAAAAGGTTCCAATATTTCAAAAATTACTT[C/T]AAATGGCTGTTCTATCCTGGATAATTTATGGCTCT Y 2 1 2 1 201000 f 74 goat snp57630-scaffold923-876614 2 80118803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382501 Affx-122973815 AX-123252859 2 55497500 GTTTCATCAAGTACTGCCAATAATGGTCTAAGTAA[G/T]ATTGTGTTTAAAACATTAGAAATGCAAGATGGCAT K 2 1 2 1 101000 f 74 goat snp57629-scaffold923-844335 2 80086225 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778559 Affx-122971076 AX-385265671 2 55541797 TATAATTTGTTAATATGCCTCTCTCTGAGTCATGT[A/G]TTAATAGAAAAAGGTGGATGTGATTTGGGGAATTA R 2 1 2 1 102000 r 74 goat snp57628-scaffold923-800038 2 80042086 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438574 Affx-122931161 AX-123308912 2 55609153 AGTGAAAAGCTGCATGGAAGAGCTAGAATATCTAG[C/T]CTTTGACAAGTCTTTTAGAATTATATGACTCTTTA Y 2 1 2 1 201000 r 74 goat snp57627-scaffold923-732682 2 79973792 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772063 Affx-122926147 AX-385259218 2 55699944 TTCAGAGAGATACATGTGCTCTTTTGAATAAGCTT[A/G]CATCACCACATTCACTTCAGTTACAAAGGCATTCA R 2 1 2 1 101000 r 74 goat snp57625-scaffold923-641891 2 79883160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425408 Affx-122941545 AX-123295754 2 55734512 AATAAACAAACAAACAAAAACTCTAGACAAACTTT[A/C]TAAAAGAATGTCAAAAAGTAAGAAACATCAGCAAT M 2 1 2 1 201000 r 74 goat snp57624-scaffold923-607323 2 79848729 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785425 Affx-122960644 AX-385272470 2 55778124 AAAAGGAAATAACAAAATCTGTAGAACTCATTGAT[A/C]TGTTCATTATCTTGATGTGATGATGACTCACAGAT M 2 1 2 1 101000 r 74 goat snp57623-scaffold923-563711 2 79804576 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423817 Affx-122942801 AX-123294163 2 55815455 TCCTTCTTCTCCTTCACTAGTTCCTCTTCATGCAA[C/T]ACATATGTTCAAGTCTCTTCCAGTCCAATAATAAT Y 2 1 2 1 101000 f 74 goat snp57622-scaffold923-526380 2 79767454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396898 Affx-122963220 AX-123267253 2 55850195 ATAGAATAATCCACACAAGAATTAGGGAAAGATTC[A/G]TGGGACTAAGACTACACTTAAATGTTCCCAGGATA R 2 1 2 1 101000 f 74 goat snp57621-scaffold923-491640 2 79732325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430832 Affx-122937440 AX-123301173 2 55889891 AGTTTGTTATAGTAGAATAACTCATCAGGTAGCAG[A/C]GACCAAAAGGAGTCCCAGAGAATATGAGGATTAGA M 2 1 2 1 101000 f 74 goat snp57620-scaffold923-451944 2 79692151 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437698 Affx-122931760 AX-123308036 2 55918982 TTGGCCACTTTCTTTTTGACAAATGAATTTGAAAT[A/G]CATTTTAAAATGTATGCCAAAATAAAGACGGAAAT R 2 1 2 1 201000 r 74 goat snp57619-scaffold923-422853 2 79663793 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421855 Affx-122944287 AX-123292202 2 55958727 CATATTGTCTTTACAGAATATTGAGAATAAGATGA[C/T]AGAATAAAGTTTCCTTTTTAAAAAGAAAAAATACT Y 2 1 2 1 103000 f 74 goat snp57618-scaffold923-383108 2 79623520 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38446454 Affx-122925075 AX-123316790 2 55998172 TGTACTAAAATTCTTCTCAGAGTACCATCCATGGC[C/T]GCCTCTTCTATGTGGGAGTGGTCCCCAACAACAGT Y 2 1 2 1 101000 f 74 goat snp57617-scaffold923-343663 2 79584150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798709 Affx-122972514 AX-385285640 2 56051910 TCATAAAATGTAAGAAGTGCTATGACTGCTAATAG[C/T]GATAATAAAACTCTAATGCTGCCTTTTATAACACA Y 2 1 2 1 101000 r 74 goat snp57616-scaffold923-289925 2 79530542 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391385 Affx-122967270 AX-123261742 2 56123310 ATGGTTTAAAAGAGATAAAGTAGGAAAACAGAAGA[G/T]AAATATAACTCCCTAACAGATAGCACACATTCCCT K 2 1 2 1 101000 r 74 goat snp57615-scaffold923-218525 2 79458037 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437078 Affx-122932668 AX-123307416 2 56161659 TATGTATCTCACTCCCAGAAGACAGAATGAGAGAA[C/T]TGAGCTTTTAAAACTCATTTCCATAGTGTCTTGCT Y 2 1 2 1 202000 f 74 goat snp57614-scaffold923-180176 2 79419831 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442492 Affx-122927922 AX-123312829 2 56229103 CAAACAGTTCAAACAGTTACTAATCAGGGCCTGGA[C/T]GGAATGCAGAAACAAAGGAAAGTCAGTCAAGAAAC Y 2 1 2 1 101000 f 74 goat snp57612-scaffold923-112732 2 79352699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794823 Affx-122960781 AX-385281783 2 56264972 AATAATTTTTACTTTGATTCCTGACTTAACATAAA[C/T]GTGTCTTTCTGACTTAAAATTCTCTTAACTGTGTA Y 2 1 2 1 101000 r 74 goat snp57611-scaffold923-76863 2 79316404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384197 Affx-122972400 AX-123254555 2 56305844 CAAAATTATTAAAAAGAAGAAACTTGTTTCAGACT[A/G]TACAACAGTTAATAAGACAGAATCTGACCCAGGAA R 2 1 2 1 101000 r 74 goat snp57610-scaffold923-35991 2 79275525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777649 Affx-122931615 AX-385264768 2 56335824 TGAGGAATCCAAGAAAAATGTTACCATCCATGTTA[A/C]CAAAATTCAAGTGCTTTGAAGAGCCAACTGGAGGC M 2 1 2 1 101000 r 74 goat snp57609-scaffold923-6011 2 79244950 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797577 Affx-122924777 AX-385284517 2 56527900 ATCAATATCAACACAGGTTGAAGTTTCAAAGCAAT[A/G]CTATAAGTAGCACTAGTTCTAGAAAGATACTCTAA R 2 1 2 1 101000 f 74 goat snp51422-scaffold752-1500030 2 79055047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385903 Affx-122971581 AX-123256261 2 56581717 TTACAGTATTTTACATATAATAAATGTTCTATGCC[A/G]CTAAATTTTGACTTAGGTTAGCAAAAACATGATGC R 2 1 2 1 101000 r 74 goat snp51421-scaffold752-1446213 2 79001194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452940 Affx-122920182 AX-123323273 2 56647888 TAAATATTTGTTATTATTGCTGTAAGATTAATGTA[C/T]AGCTAATCAGCACTATAAGATATAAGCCACATAGA Y 2 1 2 1 101000 r 74 goat snp51419-scaffold752-1380042 2 78934409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375905 Affx-122978482 AX-123246264 2 56865047 TCTTAATGTCTAGACCTCAGTTTCTTAATCACCAA[C/T]GGGGAGGGTGTTCTCTCAGTTAATGAGTGCTTCAA Y 2 1 2 1 201000 f 74 goat snp51414-scaffold752-1162883 2 78714809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376657 Affx-122979013 AX-123247016 2 56903205 GTTCCATTAAGATGTCCAAAACCATACCACAACTT[A/G]CATGCTAAATACACAGTAATTTAATTCCTTACATT R 2 1 2 1 101000 f 74 goat snp51413-scaffold752-1124725 2 78676239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794796 Affx-122961915 AX-385281756 2 56999432 ATTTTCCTTTATGAAACTAAAAGGTGGGAACTTAT[A/G]CCTTGGCATTAGAGGAAGGAAAATAGAGGGAAAAT R 2 1 2 1 201000 f 74 goat snp51411-scaffold752-1028498 2 78579104 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780181 Affx-122935413 AX-385267278 2 57041573 TGCTGAGAAAGTTGTAATTTAAAACTCTTGAAGTG[C/T]ATTTCTCCCAGTATTGTGAGAATTTTCTCATACTG Y 2 1 2 1 201000 f 74 goat snp51410-scaffold752-986357 2 78536483 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450961 Affx-122921750 AX-123321295 2 57148434 AAATTTTTCTTTGTCTAATTCCTTCATTTTAACAA[C/T]GAGAAGGAAGTAGAAAGGAAATTTGAGAGTTCAAT Y 2 1 2 1 303000 f 74 goat snp51408-scaffold752-879496 2 78429748 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383779 Affx-122973204 AX-123254137 2 57181104 ATAGACTAGACCAAAAAAGAGCAGAAGTGAAGTGG[C/T]GTAGGAATAACAAGAATCAGACAGAAGTAAGTCAG Y 2 1 2 1 101000 f 74 goat snp51407-scaffold752-846826 2 78396746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765401 Affx-122937518 AX-385252908 2 57250321 TCACCTTAGCCACAAATAAGGCATTGGAAAGGAAG[A/C]ACATTAACAGAGTTGATGTGTTTCATAACGTTGGC M 2 1 2 1 101000 f 74 goat snp51406-scaffold752-777609 2 78325684 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783435 Affx-122925420 AX-385270498 2 57281550 TGACTAACATGGCAGAGCTCTAAGGGACAGGGTCA[G/T]CACTTAAAATTCCCCTTCTTAATCATGTCTGTATC K 2 1 2 1 101000 f 74 goat snp51405-scaffold752-746380 2 78294380 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769839 Affx-122971817 AX-385257009 2 57313136 TGTGAGTTCCTGTAGAATTACATCCAAAATATTTG[C/T]AAAGTTTGCTGTGAGCTCAGGAAGCATTTCTCATT Y 2 1 2 1 101000 r 74 goat snp51404-scaffold752-714794 2 78262680 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448451 Affx-122923643 AX-123318787 2 57360631 TGTGTTTTGGAATTTATGAGTGCAACCTGTGTGTC[A/G]TAACAGCAAGCAGCTGAGGCCTTGAGTCCCTCACT R 2 1 2 1 201000 f 74 goat snp51403-scaffold752-667299 2 78214820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795574 Affx-122921825 AX-385282529 2 57405723 CATCCATGTTGCAGCATTTAATATTAGCACAGTCT[A/G]CAGAGGCAAAATATTATGATTATAAGATTACTGGT R 2 1 2 1 201000 r 74 goat snp51402-scaffold752-622207 2 78169517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409214 Affx-122953165 AX-123279565 2 57453196 TTAATCTAATATTGTGGAGAGAACCATGTGTGTGG[A/G]TTGTCATAGAGCAGACTCGCGTCATTTTGTGTATG R 2 1 2 1 101000 f 74 goat snp51401-scaffold752-574734 2 78121068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401489 Affx-122958949 AX-123271842 2 57558876 GCAATTATCCTATTTTGAGTGTGCTATCTGTTTCC[C/T]GTTGGGACTCTGACTGATACACGTATTGCTCAAAA Y 2 1 2 1 102000 r 74 goat snp51398-scaffold752-469054 2 78014805 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379921 Affx-122975750 AX-123250279 2 57605771 GTTCTAATTTAGAAAAAAATCATTCACAAATTAAT[A/G]TATTTTATTAACAAATTCTCTAGGACACACAGATT R 2 1 2 1 101000 r 74 goat snp51397-scaffold752-422159 2 77968109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395067 Affx-122964187 AX-123265422 2 57637509 AATGGCAGAGAAATATTATAAAGGGATATATGAAC[A/G]TGGGCAAAATAAATGTTTTTTACAGATGTAAATAA R 2 1 2 1 101000 f 74 goat snp51396-scaffold752-390421 2 77936563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436160 Affx-122932623 AX-123306499 2 57672496 TGCTCACTATGCTGAGCACACAATAGGTTCTCCCT[A/G]TTGTGGGAAGTACATCCTTCAGGGCCAGAAATTTT R 2 1 2 1 202000 r 74 goat snp51395-scaffold752-355434 2 77901048 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779035 Affx-122928530 AX-385266142 2 57701497 TGAACCAGTATTTTTGATTCTAGGAATTCATTTTA[C/T]AAACATACTCACAAATGTACTGAAGAAATTCAAGG Y 2 1 2 1 201000 r 74 goat snp51394-scaffold752-326433 2 77872012 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802343 Affx-122941775 AX-385289247 2 57845095 TTATAGTGGCATATTCATGGGTTCTTGAAATGGAA[C/T]ATTACACTATGGAGACTGTGAAGACATCAAATGCA Y 2 1 2 1 101000 r 74 goat snp51391-scaffold752-182835 2 77729937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385887 Affx-122971593 AX-123256245 2 57884885 TCTTTATAAGCCTTAGTAAATATAGGGGAGATTTT[A/G]CAATTCTAACACTAATAGTTACAGAGAGTCTAAGA R 2 1 2 1 101000 r 74 goat snp51390-scaffold752-143045 2 77689851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451568 Affx-122921694 AX-123321901 2 57932132 TAATTTCATGAGACTTGCTTTGTGATAAGTGCTTT[A/G]TTGTGGTGGTGTGGAACTAAATCCTTAATATCTTG R 2 1 2 1 201000 f 74 goat snp51389-scaffold752-95798 2 77642573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433968 Affx-122934264 AX-123304309 2 57979492 CAGAGACTAGGGTTCAGGAGAGAGCAGTGGAAGCA[A/G]AGACTTGGTAGGAGCTTAGGTCTCCAATCCAGGTG R 2 1 2 1 101000 f 74 goat snp51388-scaffold752-48438 2 77595035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423553 Affx-122942425 AX-123293899 2 58013150 CCAGCATTTAGATGTGGGATTCATTCCAACTTTCT[A/G]CGTTTCACAATGATGTACAAACATTTCACATTCAT R 2 1 2 1 101000 f 74 goat snp51387-scaffold752-14780 2 77561293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452764 Affx-122920258 AX-123323097 2 58033267 TAATTAATGGTACTAGAAAACAGGTTGTGGTTATC[A/G]TTTTCAGGGGATACTGACTGGGAGAGGGGAGCATC R 2 1 2 1 101000 f 74 goat snp29136-scaffold312-7998425 2 77527360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782959 Affx-122934080 AX-385270028 2 58062303 CAACCATAGACTTTCTAGTCCCACATCAAACTTCT[C/T]AAAACCTCACATTTCCTTTGCATTTGATTCATCTT Y 2 1 2 1 201000 r 74 goat snp29135-scaffold312-7969389 2 77498468 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793193 Affx-122955520 AX-385280171 2 58096165 AGAACTTTACTGTGAACACACGAGCAGTCTGTAAC[A/G]TAATAAAAGATTAACTCTACATGAAGAAATTTAAT R 2 1 2 1 201000 r 74 goat snp29134-scaffold312-7935527 2 77464180 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794816 Affx-122971736 AX-385281776 2 58135484 GTTTTTATGACCATAGAATCCTTTTTTGAAGTATA[C/T]GTTATGACTAGGATCCAACAGAACATATTTAAGAA Y 2 1 2 1 101000 r 74 goat snp29133-scaffold312-7896208 2 77423976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429484 Affx-122937876 AX-123299826 2 58176416 GCTCCACTAGGGCATCAGTCTGTCATGGAGTCTGA[A/G]CTTCCTTGCTGTTTCCCCCCAGGAAAAGCAGTGGA R 2 1 2 1 101000 f 74 goat snp29132-scaffold312-7855276 2 77381573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397894 Affx-122961955 AX-123268249 2 58223741 TTCCAGATATATTTAACATAGAAGCTAAAAGGTTT[A/G]CCTATGGAGTGTTTAATGGATAGGAAAGTGCCATA R 2 1 2 1 201000 f 74 goat snp29131-scaffold312-7807951 2 77334304 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397496 Affx-122962069 AX-123267851 2 58264847 TACAGGCCCTGGACAACACATTCCTTCCCAAGTCA[C/T]GCAATTGTACCTCATTTCCCAAACAGAGCTGTGAA Y 2 1 2 1 201000 r 74 goat snp29130-scaffold312-7766845 2 77293465 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389305 Affx-122968505 AX-123259663 2 58302257 CATAGCATCTCAGGAACCAAGACTCTCAGCTGTAG[C/T]GAACTGGGATGGAACAGAGCTAGAAGGGGTTGCAC Y 2 1 2 1 101000 f 74 goat snp29129-scaffold312-7729435 2 77255473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772035 Affx-122935727 AX-385259190 2 58345058 TGGATATAGCCAAAATGATTCCATAAGCTTGGTTT[C/T]CCCTTTAATGACATAAAAATATACAATTTTAAATT Y 2 1 2 1 201000 r 74 goat snp29128-scaffold312-7686634 2 77212026 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380872 Affx-122975055 AX-123251230 2 58376723 TTGTAATGAAGACTGCTTAAATGCCTTTTGAAATC[A/G]TTTATTTCTAGACTTTGCAATATGTTCTCCCCATT R 2 1 2 1 101000 r 74 goat snp29127-scaffold312-7654969 2 77180581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765490 Affx-122951954 AX-385252980 2 58407176 TCCTGGTTATATGCCCACAGGCATGTCAGCAGTAA[C/T]TAATATAATTATAGATGATAAAGGAACTTGTTCTC Y 2 1 2 1 101000 f 74 goat snp29126-scaffold312-7624516 2 77149729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423694 Affx-122942895 AX-123294040 2 58442591 ATCTGGACCCTTTGAGAATAGGAAGCCTGGACAAT[A/G]TGCATGAGACTCAGTACCAAGGCTTAAGCTGTTGG R 2 1 2 1 101000 r 74 goat snp29125-scaffold312-7589101 2 77114472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375599 Affx-122978724 AX-123245958 2 58474309 GTATATGCCTACTGATACATTAGACATTAAGAAAG[C/T]GTATGTTTATTGACTTTCCCCTTTTGTAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp29124-scaffold312-7557383 2 77082457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443362 Affx-122927417 AX-123313699 2 58503496 AGTCCTAGAGATTGGGGGTCAAAACCCAGGGTCTT[C/T]GAGGCTTTGTCTCTATTAACAATAGCAAACTGATA Y 2 1 2 1 101000 r 74 goat snp29123-scaffold312-7528196 2 77051734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423549 Affx-122942428 AX-123293895 2 58542113 TGTTATGTTTCACAGAAAGGTAAATATAATTTTAG[C/T]GGGAATAAGGAATTTGCCTGTGGTGACACAGCTAA Y 2 1 2 1 101000 r 74 goat snp29122-scaffold312-7489579 2 77012676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426547 Affx-122940183 AX-123296893 2 58586417 CATGACATGTTCTGGGCTCATCTTATGGTTTCCCT[A/G]CCTGGTCCAGGAATTACCATTTTTCAGATAAGGAC R 2 1 2 1 101000 f 74 goat snp29121-scaffold312-7445275 2 76968211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436177 Affx-122932612 AX-123306516 2 58656910 CAGCCATATGATACTATATCAATATATTGGGTTGG[C/T]CAAAAAGTCCATTTGGGTTTTTATGGAAAACCCAA Y 2 1 2 1 103000 f 74 goat snp29119-scaffold312-7374782 2 76900055 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378340 Affx-122976839 AX-123248699 2 58720656 CACATCACTCCAGTTGGTTTCTCCCACTCTATTCA[A/G]AGAATCACACTTCCTTAATCTACTTTCCGAAATAG R 2 1 2 1 101000 r 74 goat snp29117-scaffold312-7311036 2 76836735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799745 Affx-122936511 AX-385286672 2 58773322 ATGGTAGCATGTCCTACCCATCACCTCTGTAAGAA[C/T]AGAGCGTAACAGCCTGCAACCCAACAAGCTTAAGC Y 2 1 2 1 101000 f 74 goat snp29116-scaffold312-7258370 2 76784357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783341 Affx-122975983 AX-385270405 2 58815990 CTTCATGTATTTGGAACAACAGTATACTATTACTA[C/T]CTTGTCACTGAGTTATACTAACCTTCCTAATCTCC Y 2 1 2 1 101000 r 74 goat snp29115-scaffold312-7215702 2 76741631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799635 Affx-122965334 AX-385286564 2 58866098 CTGCAAAAGTAATAGTGCCTCAACTTCGTTTGGAC[A/G]TGGAGTCAAGAATTATTAGGTCTGCCGTTTTGCTT R 2 1 2 1 101000 f 74 goat snp29114-scaffold312-7165594 2 76691062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798428 Affx-122972992 AX-385285362 2 58899670 GGAATGTGTACCCCTAAGAAAGGGGCACAAAATCA[G/T]GCAGTCTGTACACCAAAGATTAAAGGGAGCTCTTG K 2 1 2 1 102000 f 74 goat snp29113-scaffold312-7132022 2 76657142 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379292 Affx-122976210 AX-123249651 2 58991053 CTTTGAGAAATGACTGACTAGCCTAGCTTATCAGG[C/T]AGTACGTGTAAATGAGCTGTGGCATCTCTCACTCT Y 2 1 2 1 101000 f 74 goat snp29111-scaffold312-7040639 2 76565702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396546 Affx-122962940 AX-123266901 2 59025325 GGACTTCTCAGCCTTAAGTATCAATTGCTTAAACC[A/G]TTTGGGCTTGAGTTTTTGCCAGTTGCAATAAGGAT R 2 1 2 1 101000 f 74 goat snp29110-scaffold312-7006367 2 76534098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418538 Affx-122946408 AX-123288886 2 59053954 TTACTTGCTTGGTGCATCATTTTCATTCAGGTTGC[A/G]TAACCTCTATGAACTCTGGTTCTCTCCCCTGTAAG R 2 1 2 1 101000 r 74 goat snp29109-scaffold312-6977738 2 76506885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787854 Affx-122922317 AX-385274877 2 59089532 TTTGATTTGCTCTAATTAGTTAACCTCTCTTCAGC[A/G]TCTTAGGACACAGCTAAAAGGGCCTGGGCATTGGA R 2 1 2 1 101000 r 74 goat snp29108-scaffold312-6942160 2 76471665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797540 Affx-122964644 AX-385284479 2 59150553 ATCTAGAGGAAGTGTGTTAGTAGCAAAGTTGCGTC[A/G]TTACAGAGTGTCTTAGAATCCATTAAACATAATTA R 2 1 2 1 101000 f 74 goat snp29106-scaffold312-6881139 2 76410390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773511 Affx-122925533 AX-385260652 2 59183719 GTTTGTTTTGTTACCAAGTGTCTATGCTAATCTTA[C/T]GAGTTTTCAATAGAACCATGAACTGTAATGTACCC Y 2 1 2 1 101000 r 74 goat snp29105-scaffold312-6847973 2 76377069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776681 Affx-122927635 AX-385263807 2 59214448 TATTTACAAAAGGAAGTACTATTTAATAGCCTGCT[A/G]TGTTCCAAGGTACCAGGGATAAAATGGAGAACAGA R 2 1 2 1 101000 r 74 goat snp29104-scaffold312-6817244 2 76345944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422573 Affx-122943754 AX-123292919 2 59243578 TCCAAGCGAGTTGTTCTAGCAGCCTTGGATCACTT[A/G]TCACTGCTTTTGTTTTATGAGAGAATGAAATTGGA R 2 1 2 1 101000 f 74 goat snp29103-scaffold312-6788114 2 76315899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383812 Affx-122973180 AX-123254170 2 59308395 GTCCTACTTTAATACAAAACTGCTAGCCTCATGCT[A/G]CCTTCAAAATTCATGCATGAGAAGAGGATTGGCTG R 2 1 2 1 101000 r 74 goat snp29102-scaffold312-6723297 2 76251140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378434 Affx-122976770 AX-123248793 2 59342752 GAAGGCAGTAAAAATTAGTATCTATATAATGTGCG[C/T]GCGCACACACACGCACACACACACACACACACACA Y 2 1 2 1 303000 f 74 goat snp29101-scaffold312-6688940 2 76216437 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764873 Affx-122942764 AX-385252470 2 59373805 AGGTAAACCCACTGCTTTCGCAAGCAAACTGACAC[A/G]TCAGATGAGGCCTTGCATATCTTTACATAAATGCT R 2 1 2 1 101000 f 74 goat snp29100-scaffold312-6657887 2 76184991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403360 Affx-122957798 AX-123273713 2 59443457 TTTTGACTTATGGAGTGAAGCGATCCACAGAATAG[A/G]AGGAGATTAGAAAGTGGATTCAGGATTCAGCAGTG R 2 1 2 1 101000 f 74 goat snp29098-scaffold312-6588235 2 76114582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392513 Affx-122966120 AX-123262870 2 59499927 TTCCATTTGGTGGGGCTTTTGGCATCTGTAAGACA[A/G]CTCAGGAAATATGCATCAGATACAGCTATTCTAGG R 2 1 2 1 101000 f 74 goat snp29097-scaffold312-6531765 2 76058179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435305 Affx-122934024 AX-123305645 2 59586689 ATCCCAAATGTTTTTATTTATGTATGAAGATTTTC[A/G]TCTTATTTAATGTTTCAGAAAATAAAAATGTTTTG R 2 1 2 1 303000 r 74 goat snp29095-scaffold312-6445003 2 75971172 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426007 Affx-122941135 AX-123296353 2 59620378 TTGTTGATTTTCACAGCTTTCTGTACGTTAGCATG[C/T]GGATGAGAGATTGTGGACTTACAGTAGGTATCCCC Y 2 1 2 1 201000 f 74 goat snp29094-scaffold312-6411314 2 75936797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386254 Affx-122970957 AX-123256612 2 59696364 GTTCCTTCCCCTGTCAATTCCATGATACATATATT[A/G]CAGAGTTAGTTTGGAGTGCTTCTGTGCTTGAAATA R 2 1 2 1 201000 r 74 goat snp29092-scaffold312-6335328 2 75862260 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393498 Affx-122965816 AX-123263854 2 59807554 TGGAGTTGGTGGGCTTTAAAAATGATATCTTTTAC[A/G]TATACGTCTTATTTCAGTTGGTATATTCTCTGGTG R 2 1 2 1 101000 r 74 goat snp29090-scaffold312-6224138 2 75750874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798590 Affx-122967257 AX-385285523 2 59839804 TATGGGAGAGATTATTATATTGATGCAGGTGGATA[C/T]GGGAATTTGAGAAGCTTGGAAGGTATCTTTTTATA Y 2 1 2 1 101000 r 74 goat snp29089-scaffold312-6191888 2 75718572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274356 Affx-1111834153 AX-519547951 2 59851009 GTTTTTAGGATCTGCCGGGGTACCCATGCTA[A/G]TGTCACAGCTGCAGAGAGTCTTGGTAGATGTGCCT R 2 1 2 1 101000 r 74 goat GoatD01.022037 2 59851009 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414509 Affx-122949530 AX-123284858 2 59934396 TTAAGTCCAGGGTGTAGGAGGGAGGGGCTGGGATT[A/G]TGAACTACAGAGGGAGGGAAACCCCTATGAAGTGA R 2 1 2 1 101000 r 74 goat snp29087-scaffold312-6097296 2 75623436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770300 Affx-122944471 AX-385257466 2 59967721 TAAATTGTAGTTTTTTGATTCCCTTCACTAGAAAG[A/G]TGGGAGCTGTCCAAGGTCTGTGTCTAACAGCTTCC R 2 1 2 1 101000 r 74 goat snp29086-scaffold312-6063971 2 75590291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799934 Affx-122968672 AX-385286860 2 60010451 CATTCATCTAGATGTCTGTAGTAGCCTATCACTGG[A/G]TCTTGCTGCCTTTGATCTCATACTTCTATTACAGA R 2 1 2 1 101000 f 74 goat snp29085-scaffold312-6021241 2 75547552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400477 Affx-122961298 AX-123270832 2 60052187 CCAGTACAAGCTACTCCATCACTTCTCCTGGACCA[C/T]AGCACCAGGCTGCAAATGTTCTACTGCCTTCTAAA Y 2 1 2 1 101000 r 74 goat snp29084-scaffold312-5979505 2 75506956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431492 Affx-122936247 AX-123301833 2 60183033 AATGTACAGAGTCAGGCAGTAGAGGGCTTCCTGGG[C/T]AGTGCTATGATAAAGAATCTGCCTGCCCGTGCAGA Y 2 1 2 1 101000 r 74 goat snp29081-scaffold312-5848659 2 75374015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393436 Affx-122965863 AX-123263792 2 60253866 GAAAGCTGGACAGTTTTCATAAACAAGGGGAAAAC[C/T]ATAAGCAGAGTAACACTTCTGTTCCAGAGATTCCT Y 2 1 2 1 201000 f 74 goat snp29079-scaffold312-5777826 2 75302263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388543 Affx-122969190 AX-123258901 2 60283115 TGTATTTAATATACATCATTGAGGAAGTCTATCAG[C/T]GGGAAAGCAAAGCTGACATCTGTCCCTTGCTCACA Y 2 1 2 1 201000 f 74 goat snp29078-scaffold312-5748577 2 75272920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790197 Affx-122948789 AX-385277201 2 60314015 ATCACTAATCGTAGTCTCTTCCAAAAGGCCTAGAA[C/T]AGTTTTCTAATGGTTTATTAAGATGTAATTCACAT Y 2 1 2 1 101000 f 74 goat snp29077-scaffold312-5717677 2 75242067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272044 Affx-1111833175 AX-519545808 2 60383582 GAGAGTCCCTTGGACTTGAAGGAGATCCAACCAGT[A/C]CATCCTAAAGAAGATGAGTCCTGGGTGTTCATTGG M 2 1 2 1 303000 f 74 goat 2_60383582_AF-PAKI 2 60383582 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395696 Affx-122963733 AX-123266051 2 60560139 ATGCATTTAGCCTCCCTGACCACCCAGAGTCTGGC[C/T]TTATCTGACTTACCCAACAGCACCTTCCTGGTCCT Y 2 1 2 1 101000 r 74 goat snp29071-scaffold312-5471553 2 74997841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795158 Affx-122929331 AX-385282116 2 60601796 CTATTAGCTTGTTTGGGATATGGAATAAATGTAAC[A/G]TGGTTTCCACCCTTAAGAGTCAGGAAAAAGAGCAC R 2 1 2 1 101000 r 74 goat snp29070-scaffold312-5429896 2 74955919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393844 Affx-122965155 AX-123264199 2 60701500 GGATTCATCTTTTCATATCTGCAAAATTGGTTAGC[A/G]CTGGTTTGTCTGCTCTCCAGCTCCTCGAATTTTGT R 2 1 2 1 201000 f 74 goat snp29068-scaffold312-5330192 2 74855875 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440499 Affx-122929359 AX-123310836 2 60738400 GTGTGGCAGTGCTGCTGCTAAGTGAAGTGAAAGTC[A/G]CTCAGTTGTGTCCGACTCTTTGCGACTCCATGGAC R 2 1 2 1 103000 f 74 goat snp29067-scaffold312-5293292 2 74820096 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769792 Affx-122966139 AX-385256962 2 60778590 GATAGTGTTAAGATTTGCCAAAGCTTGGTAGCAAG[C/T]GCAGGGATGTCCTTTTTTATTATGCTCTAATCTGG Y 2 1 2 1 101000 r 74 goat snp29066-scaffold312-5253102 2 74779956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425235 Affx-122941003 AX-123295581 2 60819618 GGCAGAAACGTTTCACCTGGTTGGTTAGGTGGGTG[C/T]GTGCACGTTCCCTTGATTTAAGTTTTAAACAGCTG Y 2 1 2 1 101000 f 74 goat snp29065-scaffold312-5212074 2 74739088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798513 Affx-122924301 AX-385285446 2 60848954 CTCACAAGATGTTATGCTTAAATGTTTACCATAAT[A/G]TCATATTTCCATCCCTTTTCTATATTCATGAATAA R 2 1 2 1 101000 r 74 goat snp29064-scaffold312-5182738 2 74709928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410846 Affx-122952617 AX-123281196 2 60885744 GGGCGCCGTGAGAAACTGGGCAAGGGTGGGGTGTG[C/T]GGAGCATAACAAGTCTACATTTAAATCGACTCTGT Y 2 1 2 1 101000 r 74 goat snp29063-scaffold312-5145948 2 74673435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411397 Affx-122951853 AX-123281747 2 60989657 TTCTCTGTTTAATGTGGGGAAAGGCTTCTGTAATA[C/T]GTAACTTTATAGTCTTAAAAGAGTTTTATTAATTG Y 2 1 2 1 101000 f 74 goat snp29061-scaffold312-5042035 2 74569557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771735 Affx-122944088 AX-385258892 2 61018642 TCAGCGCTTAGTTATAGTTAGAAGCTGTGGTTTCT[C/T]ACTTAGGATTAGTTAACATTGATTGCATTTTTAGC Y 2 1 2 1 101000 f 74 goat snp29060-scaffold312-5013050 2 74540558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427970 Affx-122939189 AX-123298313 2 61064660 AACCCAGCATTAGACCAAGCTTCGCAGGTTAAGGG[C/T]ATAGTCCTCTGTAAGTCTGCCCTCACTTCTAATCA Y 2 1 2 1 101000 r 74 goat snp29059-scaffold312-4967032 2 74494366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787711 Affx-122974684 AX-385274735 2 61096167 ATCTTTATATTTCTTTATCTCTATAGGAATGAGCT[A/G]GTGATTGGTGACAAGGAAGATCTTATGGTACATTT R 2 1 2 1 101000 r 74 goat snp29058-scaffold312-4935525 2 74463016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781238 Affx-122934693 AX-385268323 2 61130879 CTCTGAAAAGACACAGTAGAATAAGTAGTTACAAA[C/T]AGAAATAAAAGCATTCAGAAGTCATCAGATCCTAC Y 2 1 2 1 101000 r 74 goat snp29057-scaffold312-4900813 2 74428149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408488 Affx-122954414 AX-123278839 2 61199421 AGTTTGGGTACAGAATTCTAGGTTAATATTCCTTT[C/T]TCCTCAAAACGTTGGTAAAACAGTCCCGTTCTCTT Y 2 1 2 1 101000 r 74 goat snp29055-scaffold312-4832271 2 74358892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277604 Affx-1111835932 AX-519551103 2 61213938 TTATCATCTGGGGATTTTCTCTTTTACATGGTTCT[A/G]CATGTGAATAGGAGCAGTTTCAAAACTCATCTTCA R 2 1 2 1 101000 r 74 goat Random2.2K-202 2 61213938 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443325 Affx-122927446 AX-123313662 2 61255148 CATAACTAATTTCATGAGACAAGTATTATCTTCAA[C/T]TGTACCCAAAGAAACTGAGGCTCAGAGAGGTTAAC Y 2 1 2 1 201000 f 74 goat snp29054-scaffold312-4776544 2 74303103 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277617 Affx-1111835939 AX-519551116 2 61258502 TTTGCTGGAAAAAAGTAATCAGCAGATTCATATGT[C/G]TCATTGCCCTACTATTAATTGCGTCAATCTATCAG S 4 1 2 1 101000 r 74 goat Random2.2K-203 2 61258502 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446834 Affx-122925272 AX-123317170 2 61318340 AGACAGCTAAAGCACCAGTTATCATCCCTATTTTA[C/T]GAATGAGGAAACAGATGCAAAGAGAGGTTGAGGAA Y 2 1 2 1 201000 f 74 goat snp29053-scaffold312-4713352 2 74237990 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380235 Affx-122975469 AX-123250593 2 61349804 TAATGTAACACCTGATGATCAATAAAGGCTACTGT[C/T]TCCAGTTTCCTTTGAAGTCAGTTGTGGCTCTGGGA Y 2 1 2 1 201000 f 74 goat snp29052-scaffold312-4681888 2 74206337 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401303 Affx-122959855 AX-123271656 2 61381640 TAGAGGAATTTTTATGATTTGTCATGGGAGAAACA[C/T]GGCACAATAAATATTTCAGTAGGCGAAGAAGCTGC Y 2 1 2 1 101000 f 74 goat snp29051-scaffold312-4650052 2 74174246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442465 Affx-122927944 AX-123312802 2 61425189 ATTTTCTCTTTGGCTGGGGCTGACCCCTTTACCTC[A/G]GAAGCTGGCTGGACCTCCTGCCTGCCTAATGCTAC R 2 1 2 1 201000 r 74 goat snp29050-scaffold312-4606503 2 74130609 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399195 Affx-122960618 AX-123269550 2 61523111 TTCTTCAATTTGTTTACAGTATGAATTGCTCCGCA[C/T]GTTGCTGTGTTCTGTGGGAAGGTGAGCTCAGTAGT Y 2 1 2 1 201000 f 74 goat snp29047-scaffold312-4508581 2 74031915 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441583 Affx-122928674 AX-123311920 2 61609408 AAAAGCCCAAGTTCGTATTGAAGAGTTCCTGGGAA[C/T]GTTCCTCTTTCTTTGCAAGTAAAGGCTCCGTGGTC Y 2 1 2 1 101000 f 74 goat snp29045-scaffold312-4422284 2 73944892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379637 Affx-122975953 AX-123249995 2 61640178 TTTTTGTTCTTGGTAATTTAGATGTGAAACCTCTA[C/T]GGAGCTATCATGTGAAATGATACTGGGTGGTTGTG Y 2 1 2 1 101000 f 74 goat snp29044-scaffold312-4391514 2 73914081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453786 Affx-122919583 AX-123324119 2 61685422 TTTGAAATACCGAGCAGACTGTGTAAAGCAAGCTG[C/T]GGAGGTTGAGCAGGGCAATACCAGGGTAGACTGTT Y 2 1 2 1 202000 r 74 goat snp29043-scaffold312-4346270 2 73868842 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386689 Affx-122970179 AX-123257047 2 61727979 ACAGTGAGGGAGGGGAGAGCAGAAGGAAGTTGGGA[C/T]GGAGACTTGCTAGGCTCCAAGGCCCTGGGAAATGC Y 2 1 2 1 201000 r 74 goat snp29042-scaffold312-4303713 2 73826139 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781739 Affx-122952424 AX-385268821 2 61756885 CACTGAAGTCAGTACCACTGACCCAACCTTATCCC[A/G]TTTGATTCTGCTTCCTTCCATTATCTGGCTCTCTG R 2 1 2 1 101000 f 74 goat snp29041-scaffold312-4274807 2 73797458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401735 Affx-122959518 AX-123272088 2 61805160 ATGGATGCAAAGGTCCAGAGGTGGAAACAAGTTGT[A/G]TGTGGTTACAGCAAGCTCAGTATGTTTGAGGGACA R 2 1 2 1 101000 r 74 goat snp29040-scaffold312-4226532 2 73749070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405128 Affx-122956967 AX-123275480 2 61838305 AACCAAAAATATTATGCAGGTCCCACTGACTCCCT[A/G]TAATTTATTTCCCTTTTCCCAGATGACACAGAAAT R 2 1 2 1 201000 r 74 goat snp29039-scaffold312-4193387 2 73715670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782329 Affx-122962774 AX-385269406 2 61871285 GTCCTTTTCAGAGAAATGACTGTCACAGGTCCTAG[C/T]ATCATGCCCACCATTGAGCATGAGGAAAGGAATAC Y 2 1 2 1 101000 f 74 goat snp29038-scaffold312-4160407 2 73682816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798889 Affx-122933635 AX-385285819 2 61918897 CAATAAAAAGATGGAATAGAACCAAACCAGGCACA[C/T]GTTCTTAAACTTCTAACTCTAGCAGCTAAGTTTAG Y 2 1 2 1 101000 f 74 goat snp29037-scaffold312-4112795 2 73635031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800788 Affx-122963322 AX-385287704 2 62011645 ATGTTATAAGCAACCAACTACTGACTTGATTTTTA[C/T]AGATAATTGGGACACGTGATTAGCAAGTGTTCTAG Y 2 1 2 1 201000 r 74 goat snp29035-scaffold312-4020047 2 73544201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410426 Affx-122952406 AX-123280776 2 62050252 TTGGCTACAGGAACTGGAAGAGAAATAAAGCCTTC[A/G]CCACAGCCCTGGGCCCTAGCAGAGCCCACAAGACT R 2 1 2 1 101000 f 74 goat snp29034-scaffold312-3981440 2 73505509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388377 Affx-122969325 AX-123258735 2 62084085 ACTCCTGGAAATGGCGTGAAAGGCCTGAGACTAAG[A/C]GCAGGAGGATTCACTGACTAGGTCCTTCAGAGGCC M 2 1 2 1 101000 f 74 goat snp29033-scaffold312-3947607 2 73471510 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402822 Affx-122958269 AX-123273175 2 62116396 CACCATGCCCAGGAAACCATCTGATTGCTCTCCAG[C/T]GGGAAACTAAGGTCATATAACAGAGATCCCTCTAA Y 2 1 2 1 101000 r 74 goat snp29032-scaffold312-3915296 2 73439252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441854 Affx-122929039 AX-123312191 2 62162547 TTGGCCTGGCGTGAAATTGGGGTGAGAGAGGTGCA[C/T]GAGGGAGGCTTCTCCAAGGAGGAGCACCTGAACTG Y 2 1 2 1 102000 f 74 goat snp29031-scaffold312-3869145 2 73392957 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413356 Affx-122950150 AX-123283705 2 62204980 CCTACTTGAATATCAGGACTTGCAAAGGCATATCC[A/G]CCTTAACAGAGCTTGGTGAGACAGATACTGACCTA R 2 1 2 1 101000 f 74 goat snp29030-scaffold312-3826712 2 73350236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800120 Affx-122930730 AX-385287043 2 62241434 ACACTCAGAGTGCAGATTTCTGTTTTCCTAAATTC[C/T]TGGAGTAATTTTAATCCAGAGCTTTCCATCCTAGA Y 2 1 2 1 101000 f 74 goat snp29029-scaffold312-3790258 2 73313928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801134 Affx-122948641 AX-385288048 2 62304449 GAACATCATTTCTGTTTGTAGTAAGTCATGTCTCT[C/T]ATTTTTTTCCAGCCCTAAGAATGATCAGATAATTG Y 2 1 2 1 101000 r 74 goat snp29027-scaffold312-3727243 2 73251606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431314 Affx-122937078 AX-123301655 2 62338280 AAGGATTAGGTGCTTTGAGTGAATGGCTGTGAATG[A/C]GTTGTCTATACTCCTGGTGGGTGGTATACAAGCTC M 2 1 2 1 101000 f 74 goat snp29026-scaffold312-3693412 2 73217728 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274396 Affx-1111834175 AX-519547989 2 62367870 GAGGTGAGGGCAGGC[A/G]GATGGATGAGAGAGTGAAGCCCTTGCTGCAGGTGG R 2 1 2 1 102000 r 74 goat GoatD01.023402 2 62367870 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444938 Affx-122926695 AX-123315275 2 62433293 GACCCATGGGTGGTAGAAAGAAGAACCGTAGTAAA[A/G]CATGCTGTAGGAAAGCAGGCAGATGTGACTTTAAC R 2 1 2 1 101000 f 74 goat snp29024-scaffold312-3598399 2 73125173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438167 Affx-122931841 AX-123308505 2 62462003 GAAGATTCCGAAGCTGAGTGAAATAATTTCCCCAA[G/T]GTCCTACAGCTGGGATCTGAGCTGAGTTGGGATCT K 2 1 2 1 101000 f 74 goat snp29023-scaffold312-3569689 2 73096413 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409314 Affx-122953090 AX-123279665 2 62497324 ATTTAAGATTGGAATCGAATAGTTTCAAATGTTGC[G/T]CCTTCACAAAGGCATGTTATAGCTGGGGCATAGCA K 2 1 2 1 201000 f 74 goat snp29022-scaffold312-3534368 2 73060217 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777714 Affx-122967903 AX-385264833 2 62556317 GCCAACCTGAGGACATCCGTCACTCTTAATGACCT[A/G]CACTTAGATCCTTTGTCTTATTTGGCCTCACCTGA R 2 1 2 1 101000 r 74 goat snp29021-scaffold312-3475375 2 73001391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413233 Affx-122950244 AX-123283582 2 62589986 CTAACTGTTTTGACCTGGAAGCCTTCCCTTAACCC[A/G]TAAAACTGCTCCAAAATGAAACGTTTATAGTAAGT R 2 1 2 1 201000 r 74 goat snp29020-scaffold312-3441706 2 72967159 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385090 Affx-122971800 AX-123255448 2 62627330 CCACCAGGGAAGCCTATGGTCATCCTTAGGGGACC[A/G]TTATTCAGCCTACCACAAGGCCTCACAAGTGTATC R 2 1 2 1 101000 r 74 goat snp29019-scaffold312-3404362 2 72929660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393135 Affx-122965554 AX-123263492 2 62693027 CTGTCAGTCTCTCTGCATCTGGCTTAGCTGGGCTC[A/G]TTGTATGTTTATGTTTAGTCTTTTCAAAGACATCT R 2 1 2 1 101000 f 74 goat snp29018-scaffold312-3338665 2 72862670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793343 Affx-122979120 AX-385280321 2 62727765 AGTTAATCCTTTGTGTCTGTTTCCCATCAGTGAAA[C/T]GACTAATAGCTAATCCTAAAATTATAAGAGTTACT Y 2 1 2 1 102000 f 74 goat snp29017-scaffold312-3303927 2 72828002 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416655 Affx-122947600 AX-123287003 2 62764321 CCCCATGCTGATGGATGAGATCGTATTGTAACTAT[G/T]TCAAGTTTAAATGGGCCTCTTCTAGTGCGGTCTAG K 2 1 2 1 101000 f 74 goat snp29016-scaffold312-3267371 2 72791269 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382415 Affx-122974250 AX-123252773 2 62899824 GTCTCTGCACACTGGTGTCTGGGGCCAGGTTCTTG[A/G]TCCTCCAGTGGACAAGGCCATGTCCAAGGATGGCT R 2 1 2 1 101000 f 74 goat snp29013-scaffold312-3131868 2 72654293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272046 Affx-1111833176 AX-519545810 2 62903668 GTCTCTGTGTCACTTTTCCATTGCTAGTACTATTT[A/G]TTATGGTGATCTGTCATCAGTGATCATTAAAGTCA R 2 1 2 1 101000 f 74 goat 2_62903668_AF-PAKI 2 62903668 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390265 Affx-122967749 AX-123260622 2 62941697 GGCCTCTAGCAGTCCCCACACACTTACCTTTAAGA[C/T]GGTTTTCTCATATATCCTCATGCAGAACAACTCAT Y 2 1 2 1 201000 r 74 goat snp29012-scaffold312-3089995 2 72612512 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801508 Affx-122945842 AX-385288417 2 62973288 ATCTACAGGATTAGAAATGTGTATCCATTGTACCA[C/T]ACAGGTGTGCAGATGCAGTCTCATTATGTTAATTT Y 2 1 2 1 101000 f 74 goat snp29011-scaffold312-3058404 2 72580063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424803 Affx-122941383 AX-123295149 2 63016835 TTTTGTCCTAAGTGCAACTTTTCATATCTTGATCA[C/T]TACTTATTTAGTTCTCTCCTACCTACTTTTATATC Y 2 1 2 1 101000 r 74 goat snp29010-scaffold312-3014857 2 72536075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429249 Affx-122937905 AX-123299591 2 63060593 AAACTGGAGCCATGAAAGTCACTGACCAAGCAAGG[C/T]AGTCAAGGAATGAAAGTTTTCAAGCAGGCAGCTCT Y 2 1 2 1 101000 r 74 goat snp29009-scaffold312-2971099 2 72492168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274432 Affx-1111834193 AX-519548024 2 63066909 AAATATGGATGGGTCTACTTCTGGGCTCTCTGTTT[A/G]TTTTCATCATACAGTTGCAGTTTGTCTATTACTGC R 2 1 2 1 201000 r 74 goat GoatD01.024847 2 63066909 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410456 Affx-122952379 AX-123280806 2 63114624 CCCATTTTCAAACTTGTGGGTATCATTTAGGTACC[A/G]TTCTATCCCTATCTTGATTCCACCATAAAAATGCA R 2 1 2 1 101000 r 74 goat snp29008-scaffold312-2917068 2 72437966 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775465 Affx-122953289 AX-385262596 2 63152315 TTTCCTGACTGTATATATAATATGTGGACTGGAAA[G/T]AGAAAAAGCATCATCAGGTATCTTTAATACCTGGG K 2 1 2 1 201000 f 74 goat snp29007-scaffold312-2879377 2 72400241 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428708 Affx-122938468 AX-123299050 2 63221579 CCCCAAATTTCCCAATCTTCTTTCTCATAATAGCC[A/G]TCTTCTCTGCATTCCCACTGCCATGACCCTAGCTC R 2 1 2 1 101000 f 74 goat snp29005-scaffold312-2810113 2 72330619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791210 Affx-122934323 AX-385278204 2 63272054 ATTGACTTGGGAGGAACAAATTTAATCCATTCTGC[A/G]TAGAATCATGTCAAGCAATCCAATTGTTTATCCTG R 2 1 2 1 101000 f 74 goat snp29004-scaffold312-2759638 2 72279617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273859 Affx-1111833860 AX-519547469 2 63305057 GACACCTGCAGAGCCCACACCTAGGGCGCTGCTAA[A/C]CACACAAAAGCTCCATCGGCATGCCCTCTGGCATT M 2 1 2 1 202000 r 74 goat GoatD01.007953 2 63305057 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427865 Affx-122939711 AX-123298208 2 63313199 TATTAGAGTTGGAATATTATAGCATACAAACCATA[G/T]AGTGAAGAGAAAGTATGATTTTTTTTACATATTTT K 2 1 2 1 101000 f 74 goat snp29003-scaffold312-2718493 2 72238502 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443431 Affx-122927365 AX-123313768 2 63360750 GACAAAAAGAGTGTTTCCAGCCCCAGTGTGCTTAC[A/G]ATGCTTATTGACCTGAAAGTAACAAATGGGATTCA R 2 1 2 1 201000 r 74 goat snp29002-scaffold312-2670942 2 72190846 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277531 Affx-1111835959 AX-519551032 2 63370656 TCTTCCTCCTTACCATCTCCCACTTCCTCTTCCTC[A/G]GCCAGTCAGTAACTCTTCTTGCCTGTTCACCTGAT R 2 1 2 1 103000 f 74 goat Random2.2K-206 2 63370656 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407597 Affx-122954652 AX-123277948 2 63389280 AGGAAGTTGGGGATGGGTCAGGAAGAAAAAGTCAG[C/T]ACAGGGACCTAAGGCAGGAAATATCTTTTCTCTCT Y 2 1 2 1 201000 r 74 goat snp29001-scaffold312-2642412 2 72161945 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430374 Affx-122937782 AX-123300715 2 63419343 GAGTTTTCCTCCCTGTCCTTCACTGGAGAAGCTTA[A/G]GAAAGCAAAGACCACATGGAGACCAGGCTGAGAAA R 2 1 2 1 201000 r 74 goat snp29000-scaffold312-2612349 2 72131584 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395535 Affx-122963860 AX-123265890 2 63451720 GTTCTACTTTAATTAAAGGAATGGAACTCTTTAGG[C/T]AGCCTCTGCTGATTTTTGCCCCCAAAGGTGCTTTT Y 2 1 2 1 201000 f 74 goat snp28999-scaffold312-2579972 2 72099365 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801312 Affx-122970407 AX-385288224 2 63498901 TTCCCACGTCTGCTACACTGATTTCCTTCACTAAA[C/T]GTTTTTGTTATCTTACAGGTATATTTCTTATTCCA Y 2 1 2 1 101000 f 74 goat snp28998-scaffold312-2532791 2 72052215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436585 Affx-122932891 AX-123306923 2 63535592 ACTTTGGCAATGAAATGTTGAGTAGAAGGAACATG[C/T]GTAACTTTGGGGCAGAAACTTGTAGAGCTAGGACA Y 2 1 2 1 101000 f 74 goat snp28997-scaffold312-2496100 2 72017171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771219 Affx-122948741 AX-385258377 2 63565353 GAAAAGTATGACATTGATGTATTTCTGCAATAAGT[A/G]TATTATAAATTTTATGAAAGCAAGTACTTCATTTT R 2 1 2 1 201000 r 74 goat snp28996-scaffold312-2466339 2 71986939 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397334 Affx-122963295 AX-123267689 2 63594428 GCGCCATATCTTTGCCGTCATTAAGAATAATTCCC[A/G]TGTGGATCATTTCTAAACTGCATGGTGAATGATGC R 2 1 2 1 101000 f 74 goat snp28995-scaffold312-2437264 2 71957937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397895 Affx-122961954 AX-123268250 2 63655062 ACTGCCTCCAATTGTTACAGATCTGTGGGACTTCA[C/T]AATGCAAGCCCCTCTGGCTACCAGAGCCAGGCAAT Y 2 1 2 1 101000 f 74 goat snp28994-scaffold312-2376630 2 71898393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379862 Affx-122975794 AX-123250220 2 63697834 TGGCTTTTGAATCAGTTACTAACATCCTCAATAGC[A/G]TGTCAGCCAGGCTCCTCAAAGCACATCCAGATTGT R 2 1 2 1 201000 f 74 goat snp28993-scaffold312-2333858 2 71856532 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383917 Affx-122972979 AX-123254275 2 63735710 CTAACAAACTTGTAACTAGCAAAGTGAGGCATCAT[A/G]TATTAACTTAAAAGCTCGTTAGGGAGGAATCTAAA R 2 1 2 1 101000 f 74 goat snp28992-scaffold312-2295982 2 71818689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435816 Affx-122932838 AX-123306155 2 63766999 TCTCTGTAGGAGGGAAAAAACTAAGTTTTTCCTTT[A/G]CATAAGGTGATATTCACAAGTTCCGGATATAGGAC R 2 1 2 1 101000 r 74 goat snp28991-scaffold312-2264693 2 71787806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768513 Affx-122965054 AX-385255693 2 63807004 GACTAAATCTATGTCATCAATAACTAAAGACAGCA[C/T]GGAAACTGAAATTTACTCTGGTTAAATGTGGGAGA Y 2 1 2 1 101000 r 74 goat snp28990-scaffold312-2224688 2 71747890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793932 Affx-122959775 AX-385280901 2 63842790 AGTGGACTAATGAGACCATTCCACAGGTCAAGGAA[C/T]GTTGGCTTTACTCTAAGGGCAATAAGAAGCCATGG Y 2 1 2 1 101000 f 74 goat snp28989-scaffold312-2188902 2 71711943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432073 Affx-122935882 AX-123302414 2 63887192 TTGTCATGAAGCAGCAGCTGGCCTGCAACTGCTCT[A/G]TCTTCCTCTGGATTCTTCTTCACTTCTTCCGACTC R 2 1 2 1 103000 r 74 goat snp28988-scaffold312-2144500 2 71667364 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402875 Affx-122958228 AX-123273228 2 63924393 TTAAGGGACGACCCCTAGACTGTATGAAGTGCTCC[A/G]TTTCACAGACAAAAACTTGAAAAATCATCCATATA R 2 1 2 1 101000 f 74 goat snp28987-scaffold312-2107299 2 71630166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791348 Affx-122921622 AX-385278341 2 63958833 CATAAAACTCTGCCTTGCTCATCATGGAGTGCAAA[C/T]GTACTAATACTGGTTCCCAAAGCCATCAATTATTT Y 2 1 2 1 101000 f 74 goat snp28986-scaffold312-2072859 2 71596022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776816 Affx-122941158 AX-385263940 2 64019032 TCAGATTACTTGCCAGCCACAAAAGGATGGAAGAA[G/T]CTACTTAACCTACCTCTCAGGTAGGGAAAGGTACT K 2 1 2 1 101000 f 74 goat snp28985-scaffold312-2012660 2 71536261 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449135 Affx-122923564 AX-123319470 2 64071361 TCTTTTTCAAATTCTTTTTTCACATCTACCTTCTG[C/T]ATGCTATCAAACTATACCCGCAGGCTTTCTGGTCT Y 2 1 2 1 101000 r 74 goat snp28984-scaffold312-1960331 2 71483844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378763 Affx-122977014 AX-123249122 2 64106561 CAGACAGAAGCACAGAACAGGCTCCACAGGCCAGC[A/G]TGAGAGGCCCAGACAGGAGCACAAATGTCCCTTCT R 2 1 2 1 101000 r 74 goat snp28983-scaffold312-1925131 2 71448503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401700 Affx-122959546 AX-123272053 2 64177372 TTTCTGGGCCAGCCTTCAGAGGCAGCTATGGAGAG[C/T]GAATGAAGCAACTCCTGGTGAGAATTCCTGTAGGT Y 2 1 2 1 101000 r 74 goat snp28981-scaffold312-1854320 2 71377086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453133 Affx-122920005 AX-123323466 2 64219527 CAGCAGTTCCTCTGCAAGAGCTAACATGGTTTTCT[C/T]AAGCACTTTTCACAGCGAGGCCAAGCCCGAGTCTA Y 2 1 2 1 201000 f 74 goat snp28980-scaffold312-1812165 2 71334920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795123 Affx-122924260 AX-385282081 2 64255830 CTTCAGAAAATTTCATTGATCTCTCTGAGATCAGA[C/T]GGAGAAAGTGGAAATTGCCTGTCATCTGAGGTCAT Y 2 1 2 1 101000 r 74 goat snp28979-scaffold312-1775862 2 71298789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411740 Affx-122951513 AX-123282090 2 64288024 ATTGGTGCTAAAGAGGAAATTAAAACATGGGAATG[C/T]GATTTTAAATAGGGTGATCAGCTAGGGTTCACTTA Y 2 1 2 1 201000 r 74 goat snp28978-scaffold312-1743668 2 71269051 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409120 Affx-122953309 AX-123279471 2 64368256 TCAAAGATATGGCCAATGGTCTTGGAGGAAAACTG[C/T]GCAAATATAAACCAAATAGGTCTATGATCCAAGAT Y 2 1 2 1 101000 f 74 goat snp28976-scaffold312-1663436 2 71188590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401077 Affx-122959636 AX-123271430 2 64423893 AGCAGAAGCTAATACAGCACTGTAAAGCAACTATA[C/T]GCCAATGAAAGTTGAAAATAAAAAGGCTCTATAGT Y 2 1 2 1 201000 r 74 goat snp28975-scaffold312-1607799 2 71132300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412004 Affx-122951753 AX-123282354 2 64454675 GCTGAGGAATTCCACCTGTTTCTTAAGCTTCTTAC[A/G]CCTCCTTCCCTAGCACACCCACTGTCGGGTTTTTC R 2 1 2 1 101000 f 74 goat snp28974-scaffold312-1577017 2 71101173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802318 Affx-122944404 AX-385289222 2 64505087 CTTTGCAACAATGGGAAACATATTTATTGTTGGAA[C/T]ATAGTCATCAGAAGGACTCAAGAGAGAGTTTTTTC Y 2 1 2 1 101000 r 74 goat snp28973-scaffold312-1526605 2 71050922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452013 Affx-122920913 AX-123322346 2 64534003 TATTTTTGAAGAGGATTAGACCGTAGAGGAAAGTT[A/G]CGTAGATCCACATGCCATGCCCCACCACCATGGCT R 2 1 2 1 101000 f 74 goat snp28972-scaffold312-1497689 2 71022241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769403 Affx-122921551 AX-385256574 2 64566787 TTCAAGATTATTGCAATGGAGTTCAACTCTGTTGC[A/G]ATGGAAAAGAAAGACTGAGTTCAAGTTCAAACACA R 2 1 2 1 101000 r 74 goat snp28971-scaffold312-1464905 2 70989341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406892 Affx-122955633 AX-123277243 2 64609700 AGCTTAGCGACTAGACAACAACAACAACAATTACA[C/T]GGCTGCCCTAATGTACTCTGTTTCCTGACAAGTAG Y 2 1 2 1 101000 r 74 goat snp28970-scaffold312-1421992 2 70945992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774978 Affx-122968740 AX-385262110 2 64643424 CCCTGTGATTTATTAGTTATGAATTTATTGACTTT[C/T]GGCTAGTTTAAGCATTTCTATTTTTTCTGTCTTCT Y 2 1 2 1 101000 r 74 goat snp28969-scaffold312-1388268 2 70912285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778816 Affx-122977641 AX-385265925 2 64686168 CAGGTATTGAGGGTATAGAAATCTTTGAAGAAATA[C/T]AGAGTATTTAGAAATGCCATGACAGAAAAAAATTA Y 2 1 2 1 101000 f 74 goat snp28968-scaffold312-1345524 2 70869028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793899 Affx-122965273 AX-385280868 2 64719752 TTCACTTTCTCGAAGACTTTACTCCCACAAATAGA[C/T]GTCTCTCTCCTGAATTATCAGTTTCCCTCTTTCTA Y 2 1 2 1 201000 r 74 goat snp28967-scaffold312-1311940 2 70835426 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401224 Affx-122959318 AX-123271577 2 64835485 TGGGTCTCCTGCACTTCAAGCAGATTCTTTACCAC[G/T]GAGCCACCAGGAAAGCCTCCTGCTAAGTATATAGT K 2 1 2 1 103000 f 74 goat snp28964-scaffold312-1196207 2 70718428 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770128 Affx-122941016 AX-385257295 2 64869482 ACACCGTCTCCACTGTCTATTACCGTACCGGTCAA[C/T]GTCCGTTCTCCTACTTGTCTGGAGGTCCAAGATGC Y 2 1 2 1 201000 r 74 goat snp28963-scaffold312-1162210 2 70684097 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405491 Affx-122956011 AX-123275843 2 64920230 GCTCTCTCCCTTTTTCTTCTTACAAGGCCACTTAA[C/T]GCCATCATGACAACCCCACCCACAAGGGCCCCATC Y 2 1 2 1 101000 f 74 goat snp28962-scaffold312-1111462 2 70633353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410410 Affx-122952419 AX-123280760 2 64962732 TAAAACCTCAGTTGTGCCTGGAGTTGTGTCCAAAT[A/G]CTTGGGGGTAACAGTACTTGAATGACAATTTCCCT R 2 1 2 1 201000 f 74 goat snp28961-scaffold312-1068960 2 70576844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398410 Affx-122961632 AX-123268765 2 65006561 TTGTTCCAGTGGTCAGTAAATAGCATAAGATTTGC[A/G]CAGTTCATTGGCTCCAACTCAATTTGAGTGGTGTC R 2 1 2 1 101000 f 74 goat snp28960-scaffold312-1025131 2 70532761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403259 Affx-122957874 AX-123273612 2 65035464 ATAAGACAGCCACCAATTGCTTCGTTTTGCAGTGG[C/T]AACCCCCAAGCTCCAGCTCAAAGATCATGATTAAA Y 2 1 2 1 101000 f 74 goat snp28959-scaffold312-996228 2 70503828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403774 Affx-122957989 AX-123274126 2 65069570 GCTTTGCATAACTGCCTGCAATGCTCACAGTGCCG[A/G]GTCCAATGCACCAGCAGACCCTTGATGAGATTGTC R 2 1 2 1 101000 r 74 goat snp28958-scaffold312-962122 2 70469582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791872 Affx-122921814 AX-385278862 2 65105361 GAGCCATGTGACTTCCTTTGAGCCATGGGATTTTC[A/G]TGGATGAAGAACACATCTTAGGGATGCTAATTAAT R 2 1 2 1 101000 f 74 goat snp28957-scaffold312-926331 2 70433740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449798 Affx-122922419 AX-123320133 2 65136116 AGCTAATACTTCTGAAAGTGGTGGTGGGGGAGAAA[C/T]AAGAGGCTTCCTTCAGGAATGCTTTTTTCCATATT Y 2 1 2 1 101000 f 74 goat snp28956-scaffold312-895576 2 70403144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790514 Affx-122924969 AX-385277517 2 65165444 CCTCTAAAAGAGCAATTTGTATTCTGGGGTCGTTC[A/G]TAGACCTAGAAATCCTGCATTAGTGCCTTGACGTT R 2 1 2 1 101000 f 74 goat snp28955-scaffold312-866248 2 70373403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417312 Affx-122948160 AX-123287660 2 65198383 AGCTACCAACTTCCCCAATTTTGGAAACACATAGG[A/C]GGGACATTTCTGGAAGTAAATGGAGGAAATTTGAG M 2 1 2 1 201000 r 74 goat snp28954-scaffold312-833309 2 70340297 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779543 Affx-122973477 AX-385266646 2 65237763 ACAAAATGAAATGTATATGACCTTAACAATAAAAG[C/T]ATGTACTTAGCACAACCAATGACATAGATCTAAGA Y 2 1 2 1 101000 r 74 goat snp28953-scaffold312-793929 2 70300716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446729 Affx-122924715 AX-123317065 2 65294014 GCCTTGAACACATTTCATGGACTAGAAATCACAGT[A/G]ATTCTGTATGTACTGGCTTCTCATATGGGTAGTTA R 2 1 2 1 101000 f 74 goat snp28952-scaffold312-737678 2 70243743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415458 Affx-122949170 AX-123285807 2 65391758 CCAGTCAATCCTTACCTAAATTCCTTGTATTACAT[A/G]CATCACAGGAAATGCCACAACCTTAAATAATCATA R 2 1 2 1 101000 f 74 goat snp28950-scaffold312-639934 2 70144175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277660 Affx-1111835962 AX-519551159 2 65408928 ATTGAATCTCTAAGGCGCAAACCTAGACTTTCAAT[A/G]GACTTGTCTATTCCTATGTTGCCAAGAGAAAGACA R 2 1 2 1 101000 r 74 goat Random2.2K-207 2 65408928 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779756 Affx-122923221 AX-385266856 2 65471262 ATACTTTAACATGGATAAAAACCAACCTATTAATA[C/T]CAAGATCCTGTTTCTGTTGTGCCTAACCTTGTGAG Y 2 1 2 1 101000 r 74 goat snp28948-scaffold312-560430 2 70064421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769338 Affx-122945476 AX-385256509 2 65513840 GATATAGTTTGTAGACATCTAAAACAAATCCTTCC[A/G]TTACCTGCGTTCTTTGGAGGAAATATGGCAAGAAA R 2 1 2 1 101000 r 74 goat snp28947-scaffold312-517852 2 70021550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272945 Affx-1111833177 AX-519546631 2 65546821 CTGGAGAGTTACAGTCCATGGGGTAGCAAAGAGCT[A/G]GACAAGACTAAGCAACTAAGCAACAACAACCACCA R 2 1 2 1 303000 f 74 goat 2_65546821_AF-PAKI 2 65546821 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433452 Affx-122935062 AX-123303793 2 65550249 TGCAAGCCATGCCAAGCCATGGATACTTCTCAAGG[C/T]AGAATTTCATTTGGAGTTTTTCATACATAACACAA Y 2 1 2 1 201000 r 74 goat snp28946-scaffold312-481443 2 69985860 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381922 Affx-122974138 AX-123252280 2 65639215 TGCATGATCCCCCACCCTAAGATTCTTTAGTCTGA[G/T]CCCCATGCAGAGTGACTGCAATTAGAAACTGAAGA K 2 1 2 1 202000 f 74 goat snp28944-scaffold312-392477 2 69904026 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415033 Affx-122949016 AX-123285382 2 65673171 GACTCCAGAGATTTGGGGTCTGTTTCCAGCTTCAC[A/G]CTCACAAATGGTGGTGTTTACAACAAAGCAGTGAT R 2 1 2 1 600000 r 74 goat snp28943-scaffold312-358521 2 65673171 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797266 Affx-122949016 AX-385284205 2 65673171 GACTCCAGAGATTTGGGGTCTGTTTCCAGCTTCAC[A/G]CTCACAAATGGTGGTGTTTACAACAAAGCAGTGAT R 2 1 2 1 101000 f 74 goat snp28943-scaffold312-358521 2 69872867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432741 Affx-122935454 AX-123303082 2 65717949 ACATATACCCTGGAGCTAAACATAACATTCACTGC[A/G]TCAGAAAAATAAACAGTAAAAAAATTGAAAATAAA R 2 1 2 1 101000 f 74 goat snp28942-scaffold312-313743 2 69827755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781598 Affx-122977820 AX-385268683 2 65762790 GCACTACAAATTGGATAAAGTTCAGGGAACAAAAA[C/T]ACAGTACATGGTTCTTACCTGTACTCAAGTAACTT Y 2 1 2 1 101000 r 74 goat snp28941-scaffold312-268902 2 69783060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785651 Affx-122945718 AX-385272693 2 65803156 GACAACCATTTATCAGATGTCAACAAAGGATTAAG[C/T]TACTTTGATATTTTAATCATGCTGACACATTGAGA Y 2 1 2 1 101000 r 74 goat snp28940-scaffold312-228536 2 69709286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390958 Affx-122967054 AX-123261315 2 65834158 TAGATCACAAGTACTTGCATTTCTGTTTATGATGT[A/G]AAGGTTTATTTAATTAATGCTATTTGTCCCCAGAA R 2 1 2 1 101000 f 74 goat snp28939-scaffold312-197534 2 69678133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277669 Affx-1111835966 AX-519551168 2 65870239 GCTTTTAAAGTATGCAAATACATATAGTATTGCAT[A/G]TAGTCTGGTGGTAGTGCATTCATAATCACTGCTGA R 2 1 2 1 101000 r 74 goat Random2.2K-208 2 65870239 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386863 Affx-122970066 AX-123257221 2 65876782 ATAAGTAGAGTTGGTGGCTGGCATACCATGTGCTA[C/T]GCTTGAAATGGACATGAGTTTGAGCAAGCTCCAGG Y 2 1 2 1 101000 f 74 goat snp28938-scaffold312-154910 2 69637271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381736 Affx-122974329 AX-123252094 2 65919343 TCTTTTAAAGAAATTTGGTACAAAATATGCAAAAC[A/G]TACTTTCAAGTATTAAGGAAAGACATTGACATAAT R 2 1 2 1 101000 f 74 goat snp28937-scaffold312-112349 2 69594632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799581 Affx-122931327 AX-385286511 2 65953131 GAGATTACAATACTTGAAGAAAAAGCATTGAAGAG[C/T]GGAGATATGATTGAAGCTTTTAAGATGTTAAAAAG Y 2 1 2 1 101000 f 74 goat snp28936-scaffold312-78561 2 69560363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801817 Affx-122929945 AX-385288724 2 65984375 AGAAATGTTCTCTAAAAATTAGGGCAAGAGTTCAC[A/G]TATAGGAAAACAAATTTAGAGACCTGCCTTTTAAT R 2 1 2 1 101000 f 74 goat snp28935-scaffold312-47317 2 69528597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392925 Affx-122965708 AX-123263282 2 66024363 AAAGAAGAAAGATCTTTTCAGTTTCTCAGTACATC[A/G]TTACAGAAGGAAATGCTTTAATATAAAAGAGTAAC R 2 1 2 1 101000 f 74 goat snp28934-scaffold312-7329 2 69487994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386583 Affx-122970695 AX-123256941 2 66051262 TTAAAGGTCAGATCTGTTTTCTTCTCAGCAGCTGC[A/G]TGGGAATTGCTCATCTTGCAGTTCTTGTATGGGGT R 2 1 2 1 101000 r 74 goat snp4619-scaffold1148-19471 2 69460254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394728 Affx-122964329 AX-123265083 2 66080483 TGGGTTAGTGTACAAGATTGTTCAAGAACACTCAG[G/T]TAACTCACAGGTAACTCATGGTGCATACACAAAAA K 2 1 2 1 101000 r 74 goat snp4620-scaffold1148-48692 2 69431025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401692 Affx-122959552 AX-123272045 2 66135910 CTGGGTACCACCAACCACACTCATTCCCATCCTTT[A/G]TTCTGATCCTTTTTGAAGATGGTTCATTTTAGACC R 2 1 2 1 201000 r 74 goat snp33515-scaffold393-1569489 2 69380444 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398403 Affx-122961637 AX-123268758 2 66189431 CCACATTGCACACATAGGTAAGTATGATGATATTA[C/T]GGTAAAAAAATACAAATATATTTGTTATTCAGCAT Y 2 1 2 1 102000 f 74 goat snp33514-scaffold393-1515968 2 69326768 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429426 Affx-122938513 AX-123299768 2 66258183 TAATATAAATGTGTGCAGGAGGGGAGACTGGTGAG[A/G]TGTTGAAGATGCAGTCTTTCATGCAGACACTGCTA R 2 1 2 1 201000 r 74 goat snp33512-scaffold393-1447216 2 69256077 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411477 Affx-122951797 AX-123281827 2 66297978 GTCCTTATTTTGTCTAAGCTAAGAGGATTATTTTA[C/T]AGCTGTTGGGATCTAAGTTAAGGGCATTAATTAAA Y 2 1 2 1 101000 f 74 goat snp33511-scaffold393-1407421 2 69216272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790281 Affx-122953020 AX-385277285 2 66338397 TGTGTGTATCTGGTACCCCAAGCATATAAAGAGCA[C/T]TCTATTTTCTCCACATAGAAAAATATCCATGTAAA Y 2 1 2 1 101000 f 74 goat snp33510-scaffold393-1367002 2 69175497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790027 Affx-122971401 AX-385277033 2 66391499 CAGCTTATATATCTCTTTCATTATGATGCCATAAT[C/T]AAAGAATTCCCAGCACAAACATCACTAAGACCAGT Y 2 1 2 1 101000 r 74 goat snp33509-scaffold393-1313900 2 69122162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452802 Affx-122920230 AX-123323135 2 66469526 ATTACCACTGAGAGTAGTACACTTAAAAATTCTAG[C/T]GGTACACTTAAAAATTATGTTTATGTTATGCATAT Y 2 1 2 1 103000 f 74 goat snp33508-scaffold393-1235873 2 69043186 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779394 Affx-122927974 AX-385266497 2 66527722 ACACAATTTGCAAACATAAATGTACTTAATTAGGA[C/T]ATTAGAGAAGAAAGGATGGACTGTGAGACAGTACT Y 2 1 2 1 101000 r 74 goat snp33507-scaffold393-1177677 2 68983592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775523 Affx-122975414 AX-385262654 2 66559149 AAATACACCTTGTACAGTGTGTGAAATTTTAGCAC[A/G]TCAATTATCCTATAAAGTTATTGGAAGGAAAAATG R 2 1 2 1 102000 f 74 goat snp33506-scaffold393-1146250 2 68949902 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784556 Affx-122941941 AX-385271605 2 66609319 AACATTAAATAATCGAGCCAAAATATAATTAAACT[A/G]TATTAGGTATGAGGCCAGAGGTTAACTAGAAAACA R 2 1 2 1 101000 r 74 goat snp33505-scaffold393-1096080 2 68899004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784811 Affx-122931186 AX-385271858 2 66658443 AGGCAATACCTAGTCTATGTACTAAAGATACAAAA[C/T]ATCCTCACTCATTTAGTTCAGAATTCAGTGGGGGA Y 2 1 2 1 101000 r 74 goat snp33504-scaffold393-1046956 2 68849941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385118 Affx-122971779 AX-123255476 2 66728262 TCTAGCTTCTATTCTCTCTGACAGCCCTTCAACAC[A/C]CAAGATGCATATTATTCTCCCTGTATTTTGCCAGG M 2 1 2 1 201000 r 74 goat snp33503-scaffold393-977137 2 68780003 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774489 Affx-122922519 AX-385261624 2 66768518 ATGTCCATATGATAAAATTTGAGTGAAAAATTATT[A/C]AAGATCTCTTTTAAACAGACTTACCCTGTCCAAGG M 2 1 2 1 201000 f 74 goat snp33502-scaffold393-936881 2 68741278 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451708 Affx-122921560 AX-123322041 2 66823703 TGACAGTTTTTATAAATTTCAGTACCTGCTAATTT[A/C]TTTTCAATGTTAATTTTCTTTCTTTTCACAGACAA M 2 1 2 1 103000 f 74 goat snp33501-scaffold393-881696 2 68685595 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423239 Affx-122942687 AX-123293585 2 66872937 AAACACTTAAAATCCTTGGATACTTCTCTGTATAG[C/T]AGACATATAAACAATTACCTTATAATTATTATATT Y 2 1 2 1 101000 f 74 goat snp33500-scaffold393-832462 2 68636115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376665 Affx-122979006 AX-123247024 2 66921383 TTACCTACTCAGCTATGGAAAGCCCAATTGAGGAA[C/T]AGGGAGGTCAGAAAAGGCTTCAGATGATGCATGAC Y 2 1 2 1 101000 f 74 goat snp33499-scaffold393-784016 2 68587464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412846 Affx-122950453 AX-123283195 2 66960317 CATTTTAGCATGGAGAAAAATGATAATGGATACTA[C/T]AATCAATCAGGAAAAAATGCTGAATTGAGATAATA Y 2 1 2 1 101000 f 74 goat snp33498-scaffold393-745082 2 68548056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277680 Affx-1111835971 AX-519551179 2 66977348 TATATAATAAATAAAAAAAAACTAATTTATTCAAT[A/G]ACATCAATTTGTGGGACTGGATTCCCTGTAACCCA R 2 1 2 1 101000 r 74 goat Random2.2K-209 2 66977348 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420909 Affx-122944603 AX-123291256 2 66995227 TTAAGTTTGATCTCTACTCTGGGTAAATAATCCCA[G/T]TACCAATCACAATATGGTAGATGCCCATACAGTAA K 2 1 2 1 101000 f 74 goat snp33497-scaffold393-710172 2 68513464 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449360 Affx-122922732 AX-123319695 2 67039545 CAGAAATCCCCAGGGACTCATACAAAGAATAGCAC[A/G]TCAAGGTTGAGAATAGAGACACACATTTTTGTTGA R 2 1 2 1 201000 r 74 goat snp33496-scaffold393-665854 2 68469281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776594 Affx-122946488 AX-385263721 2 67099305 TGTTTTCTCCTCAGAGACTCTATATATAAACTACA[C/T]GCCCTGTTGCTATGAGCTGATCTTCTAAAACTGAT Y 2 1 2 1 101000 r 74 goat snp33495-scaffold393-606094 2 68409822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777179 Affx-122964731 AX-385264302 2 67142738 TGTTATACGCTGGCTGCTATCAAGGAAAGTCTTTT[A/G]CAAGATTGGATGTAGAAGAGAGCAACATGAAGTAA R 2 1 2 1 101000 f 74 goat snp33494-scaffold393-562661 2 68366283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277569 Affx-1111835978 AX-519551068 2 67171584 ATGCCATGATCTTCATTTTCTGAATATTGAGCTTT[A/C]GGCCAACTTTTTCACTAAACTGGCTGACCCACAAA M 2 1 2 1 303000 f 74 goat Random2.2K-210 2 67171584 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400536 Affx-122960442 AX-123270891 2 67202240 ATAAACATTAAACCTGAGATTCCAGAGAGATGATG[A/C]GTCCTTTGTAGTTAAACCTCATTCCCTTCTCAGAA M 2 1 2 1 101000 r 74 goat snp33493-scaffold393-503159 2 68306047 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407207 Affx-122955801 AX-123277558 2 67240896 ATCATAAGTATTTTATAAATTAATGAACAAATGAA[C/T]TGTTCTCAAATCAGGTAGTAGTAAGATGCTCCAAA Y 2 1 2 1 103000 r 74 goat snp33492-scaffold393-464503 2 68272364 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775497 Affx-122964660 AX-385262628 2 67272667 GTGATACATAGATAAATCATTTTTCATACGACTTG[C/T]CTCATGTTTAAATAGGAATAAATTCCCAGTTCAGT Y 2 1 2 1 101000 r 74 goat snp33491-scaffold393-432732 2 68240615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424421 Affx-122941805 AX-123294767 2 67312516 GTGAGTGTGAGGCTACCCTGAGGCCTCAGGAATTG[A/C]TTTTCTCTTTTCTACTTCATTTTTCGATAACTATC M 2 1 2 1 303000 r 74 goat snp33490-scaffold393-392883 2 68200223 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408196 Affx-122954190 AX-123278547 2 67352833 AGATCAAACAAAGATATGATAAGAAGAGGAAATTA[C/T]AGAGGAACCTCCATCATCAACACAATTATAAAAGT Y 2 1 2 1 101000 r 74 goat snp33489-scaffold393-352566 2 68160558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277583 Affx-1111835985 AX-519551082 2 67368096 TGATTTTCACCAAGAGTTATCTCATTATTTAAAAC[A/G]ATGAATTGATTTGAAATAATAAGTACTAGTTGAAG R 2 1 2 1 101000 f 74 goat Random2.2K-211 2 67368096 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418171 Affx-122947084 AX-123288519 2 67399880 AAAATCTTCAGTTTAATTTCTGTATTGGGCTTTCC[C/T]AAGCTATTCAGTTTGAAACATGATTTTTATACTCA Y 2 1 2 1 101000 r 74 goat snp33488-scaffold393-305519 2 68115265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414719 Affx-122949267 AX-123285068 2 67445881 GTATGAAGATTTTGAGGCAAGTGCTTAGAAAGTTC[A/G]TATAAATAAAGGAAAATGTTTATAGCTGGACAAGA R 2 1 2 1 103000 f 74 goat snp33487-scaffold393-259518 2 68068705 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780998 Affx-122965277 AX-385268085 2 67516860 TATTGTTCTTACTTAGAAAACAGGGACACAAAATG[C/T]ATTGTTGGATGTAGTTGACAAGAAGAAAAATTTAT Y 2 1 2 1 101000 f 74 goat snp33485-scaffold393-188539 2 67994515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393645 Affx-122965294 AX-123264000 2 67547728 CAATCCTAGATGATATTATCTTAAGAAAACAAATT[A/C]TTTGTCCCCAAATCAAAATGGGATAAACATGTATA M 2 1 2 1 101000 r 74 goat snp33484-scaffold393-157671 2 67963376 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397903 Affx-122961949 AX-123268258 2 67584099 AAATTTTATCTAGAGAAAAGGAAAACAAATATATA[C/T]GATGGGAGAGGAATGCCCAGAACTGGTTTTAACAA Y 2 1 2 1 103000 r 74 goat snp33483-scaffold393-121300 NW_017211749.1 6609 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783670 Affx-122965683 AX-385270729 2 67646005 GATACTCTTAGTTAAAATCTGATGTTGAATATTCC[A/G]TTCATTAATACCAATAAAGTATTCTTTCTTTTTTG R 2 1 2 1 201000 r 74 goat snp33482-scaffold393-59394 2 67865613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797386 Affx-122979061 AX-385284325 2 67679646 GACTTATTGTCTCCATGAGCTTCATGATATTTGAG[A/C]AGCATGGGTTGAAAGTGATACTCTCCCTAGGAAGC M 2 1 2 1 101000 r 74 goat snp33481-scaffold393-25753 2 67830853 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448165 Affx-122924265 AX-123318501 2 67732659 TAACTGAGCAGGAACCCTATGGGGCCTTCCCAAGA[C/T]AGATGCCTCCTTTATATCCACTACTGTAGCTCCTC Y 2 1 2 1 201000 r 74 goat snp5762-scaffold1203-27161 2 67654392 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427893 Affx-122939690 AX-123298236 2 67824766 CTGATACTTCATCAAACCAGTTCATGCTAACAGCC[A/G]CCTGGTCTCCTGCATAAGAACAGCAGACCTCCAAT R 2 1 2 1 101000 f 74 goat snp5764-scaffold1203-119268 2 67561016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445990 Affx-122925878 AX-123316327 2 67863884 GCCCAGATACCCTCATACTCCCACTATGTTTCTGA[C/T]GATAAGATATAGGGAAAAGAGAAAGAAAATTTCAG Y 2 1 2 1 103000 f 74 goat snp5765-scaffold1203-158386 2 67522364 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417358 Affx-122947718 AX-123287706 2 67901509 AACACTCAAAATGGAAGTTCAGAGAGATGAACCTT[A/G]CATCATCAGTTCCACTCCAACCCAGGCAGGGAGAC R 2 1 2 1 101000 f 74 goat snp5766-scaffold1203-196011 2 67484141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773471 Affx-122967526 AX-385260613 2 67967266 ATTTATGATATGTACCATTAATATGGGTACATATG[C/T]ATTGGGAACAGCACCTTATCTCTGTGATCCAATTA Y 2 1 2 1 101000 r 74 goat snp5768-scaffold1203-261768 2 67417205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390461 Affx-122967611 AX-123260818 2 68004298 AATCTCCACACTGCATCCTCTGTCTTGCTAGAAAC[A/G]TAAGAGGGCAAGGTGCAGAGAATCACGCCAGTGGA R 2 1 2 1 101000 f 74 goat snp5769-scaffold1203-298800 2 67379951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476169 Affx-1251763672 AX-586011596 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 4 1 4 1 20000 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 539476424 Affx-1251763672 AX-586011825 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 4 1 4 1 20000 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165303 Affx-1251763672 AX-606940714 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165597 Affx-1251763672 AX-606941008 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165872 Affx-1251763672 AX-606941281 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165907 Affx-1251763672 AX-606941316 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562166089 Affx-1251763672 AX-606941498 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562166365 Affx-1251763672 AX-606941773 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 320771716 Affx-122925526 AX-385258873 2 68067133 GGTGCTCACATTGCCTTTTAAGTTGACTTTTAAGT[A/G]TATGTCTAGGCCTGTCTCATTTCATCATCTGTTTG R 2 1 2 1 101000 r 74 goat snp5770-scaffold1203-361635 2 67316229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416044 Affx-122948357 AX-123286393 2 68104760 TGCTGTCTTCTGGTCCAGCTGATTGAATTGCTACC[A/G]TAACTCTTACAACTTTTTCCTCCTCTTTTTACCTT R 2 1 2 1 101000 f 74 goat snp5771-scaffold1203-399262 2 67278490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272947 Affx-1111833178 AX-519546633 2 68106110 CAGGAAAAAATGATGGAAATAAAGAAAGGCAGTAA[A/C]GACAAAACAAATTGGAATATCAGTACTAACCAGAA M 2 1 2 1 101000 f 74 goat 2_68106110_AF-PAKI 2 68106110 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764763 Affx-122931851 AX-385252376 2 68193798 TGACAGAAAAGGTGGCTTACACTCTGCTTTCTACA[C/T]TGGATTCTATGAAGGCACTTTATCTCAGAGATAAC Y 2 1 2 1 101000 f 74 goat snp5772-scaffold1203-488300 2 67188121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277723 Affx-1111835990 AX-519551222 2 68270375 CTGATTTTAGTACTCTGAAAAATAAATGTATTTGA[A/G]TATATGGAATGAGTATACCTTTATCATAATAGCAA R 2 1 2 1 101000 r 74 goat Random2.2K-212 2 68270375 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381447 Affx-122974339 AX-123251805 2 68290722 ACCTTCTGAATAGAGAAAACATGGATTTGCTGATC[A/G]TAGTTCAGTGAACTGTATGTTGGCCCTCACACCTC R 2 1 2 1 101000 r 74 goat snp5774-scaffold1203-585224 2 67092459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435908 Affx-122932767 AX-123306247 2 68325531 AAGGGTAAGGCCTCAGAAGGCTCCAGAAAGGAAAA[C/T]AACCTTTACCTTGAATTTTGCAGGGTTGATTCTGA Y 2 1 2 1 101000 f 74 goat snp5775-scaffold1203-620033 2 67057322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440650 Affx-122929941 AX-123310987 2 68354969 CCTTGGCAGGGCTGTTTCTCTGCAACTGCTCTTCA[C/T]GGTGAAGCCATTTCTGAAAATGGCTCGGTTTAGCA Y 2 1 2 1 201000 f 74 goat snp5776-scaffold1203-649471 2 67027055 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399988 Affx-122960815 AX-123270343 2 68392864 TCTGGGGCCAGAAAGCATTACCTTTGGCACTACCC[A/G]CTACCTTGGTGCGCTGCTGCACCTGATGGACTTCC R 2 1 2 1 101000 f 74 goat snp5777-scaffold1203-687366 2 66989113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398268 Affx-122962178 AX-123268623 2 68493471 GACATTTCTGCCTCAGTTTCCCCATCTTGCAAAGA[C/T]GAGTAAATGATCACACCCTTATTGTGAGAATTGGG Y 2 1 2 1 201000 r 74 goat snp5780-scaffold1203-787973 2 66889063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774559 Affx-122946885 AX-385261693 2 68547846 TCAATTAAGCTTTCTGTCTGCACTTTCTACTTCTT[A/G]TCAGTAACCTGACTGACTCTCTTCCTTGCCCCTTT R 2 1 2 1 202000 f 74 goat snp5781-scaffold1203-842348 2 66835438 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383286 Affx-122972719 AX-123253644 2 68571803 TATGTGACCGAAATATCTAATCCCTAAGGGAAATA[C/T]AAGAATTAAAATATGTAAAGCAATTTTTGAAAGGG Y 2 1 2 1 101000 f 74 goat snp2208-scaffold1067-793682 2 66812408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381119 Affx-122974578 AX-123251477 2 68610098 CCACAGTAGAATTCACTTCCCTGTTACTTCCTGTT[A/C]GTCATGGACAAGTGACTTGCTTTAGCCCACCAAGA M 2 1 2 1 101000 f 74 goat snp2207-scaffold1067-755387 2 66773833 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435994 Affx-122933502 AX-123306333 2 68645434 AATGAAAGATTTGAGGAAACTAGGGAGTGACATCA[C/T]AGCATAAAATAGAATGAATCATCAAGGATAGGCTG Y 2 1 2 1 101000 f 74 goat snp2206-scaffold1067-720051 2 66738708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441151 Affx-122929567 AX-123311488 2 68679509 TTGATTTATTTGATTCATAGTCGTTTTCATCTGGC[A/G]TCCAAGGTCTGTAAATCACCACCAGGGGGCCCCGA R 2 1 2 1 101000 f 74 goat snp2205-scaffold1067-685976 2 66704034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426434 Affx-122940818 AX-123296780 2 68731290 AGGTCTGAAGCCCAGCACATGTCCAGCAAGGGGGA[C/T]GGTGGTCAAGCCCAGATGTGGGATAGTATCTTTCT Y 2 1 2 1 101000 r 74 goat snp2204-scaffold1067-634195 2 66651654 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407098 Affx-122954891 AX-123277449 2 68760463 TGAAACTGGGTTAAACCATTAGTCTGGGGATTCTG[C/T]GTTACTCAGTGTATCTTAGCTTATCCTGACAAATA Y 2 1 2 1 201000 r 74 goat snp2203-scaffold1067-605022 2 66622515 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406855 Affx-122955658 AX-123277206 2 68801803 GGGAGAGTCACATGGTGCCTTAACCTCTGCGATGA[C/T]GCACAATGTAAGTACCTGCCCATTCTCAGGACCAG Y 2 1 2 1 101000 r 74 goat snp2202-scaffold1067-563682 2 66580532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785408 Affx-122942358 AX-385272453 2 68840006 CTGGGAACACACCCATAGTTAGACAAGTTGGGCTT[A/G]TTACTGGTTGTAGTGAAGGAGACCACACAGCAGTG R 2 1 2 1 101000 r 74 goat snp2201-scaffold1067-525479 2 66542383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453233 Affx-122920422 AX-123323566 2 68878365 AATACATAGTATATACCCCTTAATCTACTAAGCTA[C/T]AACATCTAAAGAATTGTGAGTTCTGAAGCACATCT Y 2 1 2 1 101000 r 74 goat snp2200-scaffold1067-487120 2 66503797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769051 Affx-122938437 AX-385256226 2 68919385 TAAGCCAGATGATAGAATGGCGTTTTGACGTGGGA[A/G]TTGTGGAATGACTGACAATGTCTTTTGGTAACTGC R 2 1 2 1 101000 f 74 goat snp2199-scaffold1067-446100 2 66463045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777373 Affx-122929592 AX-385264495 2 68961673 AGTATAAAAGTCTGAATAATAAGCATCAGAGTTCT[C/T]ATTTGCTCACAGGAAACACATTTTCATAGAAAAAT Y 2 1 2 1 101000 r 74 goat snp2198-scaffold1067-403812 2 66420680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387933 Affx-122970027 AX-123258291 2 68999875 CAGAAAAGATGTTTGTTTTGCATTTTTAAATCAGA[C/T]ATTCACTTCATAGACACAGACACAGTCTAGTTACT Y 2 1 2 1 201000 f 74 goat snp2197-scaffold1067-365610 2 66382460 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785493 Affx-122961505 AX-385272538 2 69039446 TGAAAAAGAGGAATGAAGCATAAATTCAGGAGGTA[C/T]AATAGCCAATTAAGAAAAGTTACAAAAATGTAAGG Y 2 1 2 1 101000 r 74 goat snp2196-scaffold1067-326039 2 66343010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406351 Affx-122955433 AX-123276703 2 69093966 ATATAGATGTAATCACAGTGGACCAAGAGGACAAG[C/T]ACACGTTTTAGAAATGGTGGAGAAGTGAACAGAAA Y 2 1 2 1 101000 f 74 goat snp2195-scaffold1067-271519 2 66288260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381619 Affx-122974775 AX-123251977 2 69136095 ATATTTCACATGGCAAGACTGTGGAAGGCCACAAA[G/T]ATCGTGGAAAGCCACACAGGCCAGAAGTGTCCTTT K 2 1 2 1 101000 f 74 goat snp2194-scaffold1067-229390 2 66245314 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405559 Affx-122955958 AX-123275911 2 69167683 CTCTCAAGAGTTTTCTCCAACACTACAGTTCAAAA[G/T]CATCAGTTCTTCATATAACAGGATGTAAATATAAA K 2 1 2 1 303000 r 74 goat snp2193-scaffold1067-197802 4 82560227 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442399 Affx-122927999 AX-123312736 2 69198245 ATCATTCGTAAGCACTTTCTTTCCTTCATTTTTCT[A/G]CAAGAGCAAATGAACTTCACACACAGAAGAAGGGC R 2 1 2 1 103000 r 74 goat snp2192-scaffold1067-167240 2 66182991 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389572 Affx-122968791 AX-123259930 2 69234218 GTTTTTGCTAAGGCTCTCACCCTCTGTTCCCATTC[A/G]TCCTCCACACAGACCTACTTCAGCACACCTTGCAT R 2 1 2 1 201000 r 74 goat snp2191-scaffold1067-131267 2 66146801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793468 Affx-122938031 AX-385280445 2 69269215 AACCCATGGACAAAGCACTTAGCACGTAATAATAA[C/T]TACAGAAAAGAATATCAATGCCAAAACCTTGATAC Y 2 1 2 1 201000 r 74 goat snp2190-scaffold1067-96270 2 66111043 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277730 Affx-1111835993 AX-519551229 2 69300503 ATGGGCATCAAAAAATATCCCTCAATCAATTACAA[A/G]TCACAGTGGTCCTTGAATTCAAGCATGCATCAGAA R 2 1 2 1 101000 r 74 goat Random2.2K-213 2 69300503 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432641 Affx-122935474 AX-123302982 2 69303854 TGATCTTTCCTGGTACCCAGGAGAAGCTCAGTAAA[C/T]AAATGAATGAGGCTTGACATCACCTGACAGTTCTA Y 2 1 2 1 101000 f 74 goat snp2189-scaffold1067-61631 2 66075722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773723 Affx-122974716 AX-385260863 2 69360775 GCTAGGAGATGCACCATCCACAAAAATTTATGTAG[C/T]ATTTCTCACAGGTGGTGCCAATGCTCCAGCCTCAT Y 2 1 2 1 101000 r 74 goat snp2188-scaffold1067-4710 2 66019056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406377 Affx-122955409 AX-123276729 2 69387190 CCTAGATTGCTACATACCCCTGGACCAAATCCCCC[A/G]TGCAGCAGGACATCAACAATTAATAAGTTTTAAAA R 2 1 2 1 201000 r 74 goat snp7023-scaffold1259-670446 2 65983307 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418686 Affx-122946305 AX-123289034 2 69430770 ATCCAGGTATTTGCTCTTAGTTTTGTTTTTCCTCT[A/G]CAGGTATAGATGCATCTTTCTTGGTCACAGATTTG R 2 1 2 1 101000 r 74 goat snp7022-scaffold1259-626866 2 65939605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425355 Affx-122941583 AX-123295701 2 69490482 TTTTAACAAGGAGACAGTGAACTCTAGGCTCAGAA[C/T]CTTCAGCAGGAAATGTCAATACTAATGGTTAACTG Y 2 1 2 1 101000 r 74 goat snp7021-scaffold1259-567154 2 65879215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402945 Affx-122958175 AX-123273298 2 69575303 GGAAAATAGAGGCTGCCTTTTGCTGGGCGGAACAC[A/G]CTGCACATACAAGAATGGCAAGATTGCTGGTGACC R 2 1 2 1 101000 r 74 goat snp7019-scaffold1259-482333 2 65793662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412444 Affx-122951413 AX-123282793 2 69604325 CCAGATTCACTCAGGCGGAGGCCTCGGTGATTTCC[A/G]CTTCTACTTTGGTGTTCCTGCTTTTTCTTGAACGT R 2 1 2 1 101000 r 74 goat snp7018-scaffold1259-453311 2 65764664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377096 Affx-122978266 AX-123247455 2 69639845 CCACTCCCACCACAGAATGGAGAGAAAAACAGGGA[C/T]GGATGGAGAAGGTTCTATGACTCAGTGTTCTTGAT Y 2 1 2 1 101000 r 74 goat snp7017-scaffold1259-417791 2 65728563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277743 Affx-1111836000 AX-519551242 2 69661318 TATTACACCTAGCTTTTTAAAAGTTATGTGAAATC[A/T]GATCTTTAAAGACTCTTTTTGGCTACCTCAATGTC W 4 1 2 1 201000 r 74 goat Random2.2K-214 2 69661318 T A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785733 Affx-122926046 AX-385272774 2 69679386 TTTTGAAACTTTCTGTTAGACACTAGACATTGTTA[A/G]TTGCCTATTAAATGACCATCAGCTTTTTTCCTCTT R 2 1 2 1 101000 r 74 goat snp7016-scaffold1259-378250 2 65688851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384531 Affx-122973033 AX-123254889 2 69713409 CTGAGTCTGGAATCTGTTCTGATAAAATCTGTTAC[A/G]AAATCAGGACATTCTGCTTTGGAGTTTTCCAAAAT R 2 1 2 1 101000 f 74 goat snp7015-scaffold1259-344227 2 65654524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800643 Affx-122923844 AX-385287562 2 69751256 GAATCACTGGAAAGCGTTAAAAAAGAACATAAAGC[A/G]TATATTGGAAGGGCCAGTAGAGGCCTGTAATTAAC R 2 1 2 1 101000 r 74 goat snp7014-scaffold1259-306380 2 65616915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411091 Affx-122951925 AX-123281441 2 69799239 GAGGAGTTTTTGATCTCAGAAAATGTCATTTGAGG[A/C]TGTGAATTAGGGCAGGAGGGAGAAAAGGGGCTTCT M 2 1 2 1 201000 f 74 goat snp7013-scaffold1259-258397 2 65568639 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453904 Affx-122919497 AX-123324237 2 69862032 ACCACATTGTTAACAAACTATACTCCAGTATAAAG[C/T]AAAAATTTTAAAGAAGGATTAATACCAAGTATAGG Y 2 1 2 1 103000 f 74 goat snp7012-scaffold1259-195604 2 65507038 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780500 Affx-122952111 AX-385267591 2 69904771 AGCAAAAAATAAACTTTGGTTGGGTTAAGGCATAG[C/T]GATTTCACTATCAGTTTTTTACTGTATGACCTGGC Y 2 1 2 1 101000 r 74 goat snp7011-scaffold1259-152865 2 65463691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272452 Affx-1111834269 AX-519546178 2 69924229 ATAAAACTGCAGCTGTAGTGTGTAACAGATGAAAT[A/G]AGGTCTGTATTTCTCAGATGTAACAGAGCCAAGAG R 2 1 2 1 101000 r 74 goat GoatD01.028299 2 69924229 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320773136 Affx-122949083 AX-385260279 2 69955025 ATCTTGTACAGTTTTTTCCTAAGTCCCACTCAGAC[A/G]CTTTTATCTCCAGAACACAGATCTGGCTGTTACTT R 2 1 2 1 101000 f 74 goat snp7010-scaffold1259-102611 2 65412105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405129 Affx-122956966 AX-123275481 2 69989844 GTTCAGGAAGTCACTTTGAGATTCAGATGGGAGAG[A/G]TGACCCCTCCTCTCTGTTTCAGGTTGGACCTGCTC R 2 1 2 1 101000 f 74 goat snp7009-scaffold1259-67792 2 65377471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394134 Affx-122965325 AX-123264489 2 70035830 CTGAGTTCTGTACTTCCTCCAGAGCCCATATTTCC[G/T]CTTTCTCATACGTACTGGTCTGGAGTATCCTTTGA K 2 1 2 1 101000 r 74 goat snp7008-scaffold1259-21806 2 65331443 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433259 Affx-122935233 AX-123303600 2 70075677 ACTGTGTAAGGGCAGCACAAGCATAGTAAATGTGC[A/G]TTATGGGGAAGGGAAGGTGAGCCTTGAAAAATGAA R 2 1 2 1 201000 f 74 goat snp50895-scaffold739-17942 2 65291372 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432910 Affx-122935319 AX-123303251 2 70107799 GGTACCCCTCTCTACTCACATGCCAATGTAACAAG[C/T]GCTACTTGAGCACCTGCTGTCTGCACAGGCCTGCC Y 2 1 2 1 101000 f 74 goat snp50896-scaffold739-50064 2 65259090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424424 Affx-122941803 AX-123294770 2 70165000 TCAGACATCTTAGACTTGGGCTTCCCTCATGGCTC[A/G]GTGAAAAAGAATCCGCCTGCCAATGCAGGAGACAC R 2 1 2 1 103000 f 74 goat snp50897-scaffold739-107265 2 65201626 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392477 Affx-122966148 AX-123262834 2 70266783 CGTTTAAAATCTATGCTATTGAAACTGCGTGTTTT[A/G]TTTTTACCTTGAGGAGCTTGTCTGAGAAGCAGCAA R 2 1 2 1 201000 r 74 goat snp50900-scaffold739-209048 2 65085810 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275074 Affx-1111834582 AX-519548655 2 70298542 ATTTTTTAAAAATTCTGTTTCACTGCAGGTATC[A/G]AGGAAAATCCCTTCCTATAAGGGACTGCATTCCAG R 2 1 2 1 101000 r 74 goat GoatD01.042215 2 70298542 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447115 Affx-122924472 AX-123317451 2 70322777 TTCATATCAAAGCTGTGTGCAGCACAGCAATTGTC[A/G]TCCAAGAAAAGAGGCTGAGAAATGTGTCCTGACTG R 2 1 2 1 202000 r 74 goat snp50901-scaffold739-265042 2 65029503 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375415 Affx-122979196 AX-123245774 2 70390078 TGGAGGCCCTGACAACCTATGTGTTCCGAACCAAG[C/T]GAGTCCCAGTTGCAAACTGTAAAGAAATTTTTTTC Y 2 1 2 1 101000 r 74 goat snp50902-scaffold739-332343 2 64961307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433409 Affx-122935096 AX-123303750 2 70438795 GGTCATTTACAGGAGAAGTTTGAGAATCACATGAA[C/T]AGCCAGGAAATATATCAGAGTTGGAAAATGCTGCG Y 2 1 2 1 101000 f 74 goat snp50903-scaffold739-381060 2 64911682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277628 Affx-1111836007 AX-519551127 2 70454143 GGGGCTGGAATCCTGTCTCGCTCGTGGAATCCCCA[A/G]CATGTGGCCCGTGGCCTGCTGGCATATAGTAGGCT R 2 1 2 1 202000 f 74 goat Random2.2K-215 2 70454143 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785041 Affx-122973833 AX-385272088 2 70492831 GTCATCCATTATACATGTGATCCTTCTGAATCTTA[C/T]GGACTTTACAAATGTGATCCATATAAGCCTCCTGT Y 2 1 2 1 101000 f 74 goat snp50904-scaffold739-435096 2 64857563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428829 Affx-122938373 AX-123299171 2 70526170 ATGCAGGGCCTGGTGAGACTGATGCGAGTAGGGAA[C/T]GGGTGAGAGCCAGGGTGCTGCAGGCTGAGGAACGG Y 2 1 2 1 101000 f 74 goat snp50905-scaffold739-468435 2 64824467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425420 Affx-122941535 AX-123295766 2 70575971 AGACTTGATGCTTTTGACTTAATGGCTTTTCCCCA[A/G]CTTTTAATGACACAAGCTGCCCACACTGTGTTCAG R 2 1 2 1 201000 r 74 goat snp50906-scaffold739-518236 2 64775729 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764374 Affx-986696789 AX-385252086 2 70651049 TGTAATGCACTTGAATCATCCTGAAAGCAAACCAC[C/T]CCCCACCCCGAGTCCATAGAAAAACTGTCTTCCAT Y 2 1 2 1 600010 r 74 goat 2_70651049 2 70651049 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 38413858 Affx-122949863 AX-123284207 2 70674112 CCAGCAACATCCAGGCTCCACATCAGCCACTCCTC[G/T]ACCCAGGTGCAGAACCCTCCTTCCTGAGTCCCACC K 2 1 2 1 201000 r 74 goat snp50908-scaffold739-616377 2 64676775 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272949 Affx-1111833179 AX-519546635 2 70741104 GCTGATTGCTGCCAACTTCATTTCTTAGACTCACT[A/G]GCCCATGCCAAAAAAGAATTAGGATAATGAAAGAT R 2 1 2 1 101000 f 74 goat 2_70741104_AF-PAKI 2 70741104 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419822 Affx-122945827 AX-123290170 2 70885459 GCTCTAAGATAGTACCCAACTCCCAACCACATTCT[A/G]TCCTTTGTTCCTTCTCTTATGACAAATATCTGGAG R 2 1 2 1 101000 f 74 goat snp50911-scaffold739-827724 2 64464441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417480 Affx-122947174 AX-123287828 2 70914765 ATTTCTTTTACCTTATTTACTTGTTTGTTTTCACA[C/T]AGTAGTGCAGAGCTATAAAGATAACCATGTGGCCT Y 2 1 2 1 101000 r 74 goat snp50912-scaffold739-857030 2 64435110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397795 Affx-122962500 AX-123268150 2 70949333 GACAGATAGTTTGTTTTTTATTCTCAATATTTTGG[A/G]CAGGTAAAACCACTGAGCCCTACTCTGACCTATAG R 2 1 2 1 101000 r 74 goat snp50913-scaffold739-891598 2 64402682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421514 Affx-122943892 AX-123291861 2 71032432 GCTTTATGTATTAACTAACCCCTAGTTTAAATCCA[C/T]GTAGTAGGAGTTTTAAGTAGTCTTTATCCAGCAGC Y 2 1 2 1 101000 r 74 goat snp50914-scaffold739-974697 2 64319017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277654 Affx-1111836019 AX-519551153 2 71181491 AAAATGGCTTGGCTTGAAATAAATGCTTAGATATT[A/G]ATACATCTTTTTACTTCACAATTGGGGTGAATTAT R 2 1 2 1 101000 f 74 goat Random2.2K-217 2 71181491 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424687 Affx-122941705 AX-123295033 2 71196688 CACCCAACCACTGAGGCTACAGTTTTTTTGTTTAC[A/G]TGTAGACTTGGCAAATAAATAAACTTACTTTACCT R 2 1 2 1 101000 r 74 goat snp50916-scaffold739-1138953 2 64156446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396774 Affx-122962767 AX-123267129 2 71301416 CGAACCCTTCCTCTAGACCTGGTCTTACTCCCTGG[A/G]AGGAAATGAGGCCCCTGAACAATCACTTCATGGCT R 2 1 2 1 201000 r 74 goat snp50918-scaffold739-1243681 2 64051966 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798739 Affx-122958102 AX-385285670 2 71341027 GTAGGTTTAAGGGGACCTTTCCCACGAATAGTATA[A/G]TATAAACTTTCCCCTATGCAGCTGAATATTCTGTC R 2 1 2 1 101000 f 74 goat snp50919-scaffold739-1283292 2 64011775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790553 Affx-122979165 AX-385277556 2 71369877 TGGCCCCAAGAAGGATGTGAGGAAGGTTATCTGAA[C/T]GGGAACTCACCCATTGCTGGGCAATTCAACAAGTC Y 2 1 2 1 101000 r 74 goat snp50920-scaffold739-1312142 2 63983334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438707 Affx-122930855 AX-123309044 2 71401866 CTACCCTGTTCTTTCTGTGTCCTGACCAGAAGCAG[C/T]GCTCCTGGGATACAAGGTGCCCACTGCCTTGGGAT Y 2 1 2 1 101000 f 74 goat snp50921-scaffold739-1344131 2 63951421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410858 Affx-122952610 AX-123281208 2 71444302 GGTTGTTATCTCTGGGAAAGAACTTGCACTCCCCC[A/G]CTTCCTAGATGCGAGTCCTTGGGAGGCTACTAGGC R 2 1 2 1 201000 r 74 goat snp50922-scaffold739-1386567 2 63909121 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426444 Affx-122940810 AX-123296790 2 71515777 CTGTAAGGCTAAACTCGCCATCACCTTGGTTGCCT[A/G]CTGGAACCACTGGATCCCAGAGGCTGTGAGCTGGC R 2 1 2 1 101000 f 74 goat snp50923-scaffold739-1458042 2 63842159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443620 Affx-122927300 AX-123313957 2 71554889 AGAGATAAAGATACCGAAGGGAAGGGGGTCAGGAT[A/G]GGGAAGATGAACTATCTATAGGCTGTGAAAATGAC R 2 1 2 1 101000 r 74 goat snp50924-scaffold739-1497154 2 63802470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408177 Affx-122954202 AX-123278528 2 71613938 AGGAGACATTAGCATCTTCATCTTAGAGATAAGGA[C/T]ATTGAGGTTCAGAGAAGTTAAGTACATTGCCCAAA Y 2 1 2 1 201000 f 74 goat snp50925-scaffold739-1556203 2 63742595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783461 Affx-122973085 AX-385270524 2 71647037 GTAGAAACAATGGCTAAAAGCATACATATGTGCAC[A/G]TGCACACACATGGGCACTCGCAACAGCAGAAGGCA R 2 1 2 1 102000 r 74 goat snp50926-scaffold739-1589302 2 63709602 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398505 Affx-122961556 AX-123268860 2 71680370 AGAAGACCCTGGTTCAATTCCTGGGTCTGAAAGAC[A/C]CAGGTAGGTTTTGTTATTAGGTACATAGTTGTTAC M 2 1 2 1 201000 r 74 goat snp50927-scaffold739-1622635 2 63676472 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432089 Affx-122936485 AX-123302430 2 71709679 ATACATCCAACAGTCAAAATGAGTCTAGTGATCAC[A/C]CATAAGTTTCTTTATGTTTCTTTGTTATCCATTCC M 2 1 2 1 101000 r 74 goat snp50928-scaffold739-1651944 2 63647095 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420385 Affx-122944937 AX-123290732 2 71787531 CGCGGTAGCTGCCCAAGGAGGTACTTGCTGTTCAA[C/T]GCACTTGGCAGGGGAGGGGGGTGTTTTTCATGAGT Y 2 1 2 1 201000 f 74 goat snp50929-scaffold739-1729796 2 63569262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420371 Affx-122944947 AX-123290718 2 71836233 CGCTTCTGGGCCGATGTGGCTTGTTTCACCACTAA[C/T]GAACTGGGAGCTTCTGTTTCCTGATTTGAGTTATG Y 2 1 2 1 201000 f 74 goat snp50930-scaffold739-1778498 2 63520783 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400281 Affx-122960118 AX-123270636 2 71869010 CATCTAGGAAAAATTATTTGGGTAGGGATGGCTAC[A/G]TGAAAGTGTTGACTGAGCCTGAGTCCCTGATGGGA R 2 1 2 1 201000 f 74 goat snp50931-scaffold739-1811275 2 63488287 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435731 Affx-122933292 AX-123306070 2 71916786 ATAGCCGAGGTCTCTTTTCTTGGTTTTAATGACTC[C/T]AAGACCTGAGCCCTTGCTACCGTGTCCCTTTTGCT Y 2 1 2 1 101000 f 74 goat snp50932-scaffold739-1859051 2 63440697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394051 Affx-122964986 AX-123264406 2 71959246 TGAATGAATGAGTAACTGAATGACCCAGAGAGGGC[A/G]CATTGTGAGTTCAAGGAGGGCTGGAGCTGTGTCCC R 2 1 2 1 201000 r 74 goat snp50933-scaffold739-1901511 2 63398419 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387893 Affx-122969618 AX-123258251 2 72001345 TGTTTAGATTACTGGTACAGGGTGACCCTGAAAAG[C/T]GGAGCAACTCAATCTGTTTTATCATTGTTTTTATA Y 2 1 2 1 101000 r 74 goat snp50934-scaffold739-1943610 2 63359612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419464 Affx-122945485 AX-123289812 2 72032730 AGCCAAGAGTCTGCCCTCCCCTGGGGGCTCCACTG[C/T]ATGGCTGTGTGGAGGCTCCTGACAGTGTTCTCCCA Y 2 1 2 1 103000 r 74 goat snp50935-scaffold739-1974995 2 63328166 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401342 Affx-122959261 AX-123271695 2 72061814 CCAGGAGCCAGCGCACTTATATCCCCCAGATGTGA[C/T]CTCTGGAATTTCTGTGATTTATCACCGACCAGGAA Y 2 1 2 1 101000 r 74 goat snp50936-scaffold739-2004079 2 63299561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382859 Affx-122973527 AX-123253217 2 72094564 CTTGTGGCTTCACATTTATCATCTAACCCCTCGAA[G/T]CCTCTCAAAAATCCTGCAAAGCAGAAATGGTCATC K 2 1 2 1 201000 r 74 goat snp50937-scaffold739-2036829 2 63267006 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387628 Affx-122969861 AX-123257986 2 72125759 AAATGACCAATAGCATCCAAAGCCTGGTCTGGGAG[A/G]TGACATGGATAATCAATCAGAGCTTGCTATTTTTT R 2 1 2 1 201000 r 74 goat snp50938-scaffold739-2068024 2 63235752 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411438 Affx-122951823 AX-123281788 2 72158779 AACTGGATGGGGTCTACTTCTGTGTAGGAGGAAGC[A/G]TAAGGAGGCAACTGGACCTCCAGTGGCCCACAGTC R 2 1 2 1 101000 f 74 goat snp50939-scaffold739-2101044 2 63202379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277681 Affx-1111836033 AX-519551180 2 72222414 TCATTCCTTGAGCTGATTTTTAAGAAGTCAGGGAA[A/G]GCAGGTTTGGAAACCACAAGTAGATTAGAGTAGTG R 2 1 2 1 201000 f 74 goat Random2.2K-219 2 72222414 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404402 Affx-122956784 AX-123274754 2 72233077 TGTCTGTAAAATCCTCTGCTTGCTACACGGTATGA[C/T]AGTAAAGCCTGTTCTAATTTCAGAATTGTGAAATG Y 2 1 2 1 101000 f 74 goat snp50940-scaffold739-2175342 2 63127711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419972 Affx-122945191 AX-123290320 2 72275030 CTGTGAGTCCTCTGTGGATCCTATTTGAGCTGGGG[A/G]GCTGAAATGTATACTCACACTGATCAGTCATGGAG R 2 1 2 1 101000 r 74 goat snp50941-scaffold739-2217295 2 63085795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449461 Affx-122922656 AX-123319796 2 72354575 TCTGTATCAGTGAGGAGTTAGAATACCAGAATACT[C/T]AGGCAAGGATAAAAACTGGGTTATATTTATCATCA Y 2 1 2 1 101000 r 74 goat snp50943-scaffold739-2296840 2 63005515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405352 Affx-122956323 AX-123275704 2 72383398 TTTTCTGATTAACGTTCCTACCCCCAAAGTGAACA[A/C]GTTTACCTTTCTAAATGTTATCATGATTTTACTTT M 2 1 2 1 201000 r 74 goat snp50944-scaffold739-2325663 2 62976401 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775317 Affx-122935459 AX-385262448 2 72433384 TCAGAGTCTGTCCTCAAACAGCTTGTAGTTTTAAC[A/G]GCTCATCACAAATTGTTCACACTCATTGCAGACGT R 2 1 2 1 101000 f 74 goat snp50945-scaffold739-2375649 2 62927005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378806 Affx-122976560 AX-123249165 2 72473660 CCTGTGTATCTCAATATTCTGCCCCAGATGGAGAT[A/G]CCCAATACTCTGCAAGCTCATCTGTGGAATGGATA R 2 1 2 1 101000 r 74 goat snp50946-scaffold739-2415925 2 62886830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429220 Affx-122937928 AX-123299562 2 72504593 TCCAAGTGGCAGACAGAGCATAAATAGGCTTTGGA[A/G]TCAGACAAAACTGGGTTCAAAACATGGCACCACCG R 2 1 2 1 201000 f 74 goat snp50947-scaffold739-2446858 2 62855907 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444951 Affx-122926684 AX-123315288 2 72552910 ATCTCACTCCCCTTTGAGTCTGGATTAAATTCCAC[A/G]TGGGCGTTAATAGCATGGCACTACCCTCCACTGTC R 2 1 2 1 201000 r 74 goat snp50948-scaffold739-2495175 2 62805125 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447439 Affx-122924378 AX-123317775 2 72614430 CAGTTTCTAGACACATGGAGCCTCTGGGATGATCA[C/T]TGAGCAGCTACCTCCACGCTCTGCACAAGGGACTT Y 2 1 2 1 201000 r 74 goat snp50949-scaffold739-2556695 2 62743242 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384044 Affx-122972883 AX-123254402 2 72662391 TTCATCTGACTGCCTTGTCGGCAGACTTGTGTCTT[A/G]CTCATCACTCAATGCCAGCCTCTTGCACTAGTGCC R 2 1 2 1 201000 f 74 goat snp50950-scaffold739-2604656 2 62695143 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383232 Affx-122972760 AX-123253590 2 72691503 AGCGTCGATGAAATCAATACAGAAAAAGTGCTCTC[A/G]TTATCCAGACCTTCTTGCTGTCCAACCTAGAGACT R 2 1 2 1 201000 r 74 goat snp50951-scaffold739-2633768 2 62665972 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399829 Affx-122960261 AX-123270184 2 72723206 GATAGTAACAATTTTAGGCTTTGCAGGTCAGGAGA[C/T]GAAATCAAGCAAGCCTAAAGATTTTAAACCCCCAA Y 2 1 2 1 201000 r 74 goat snp50952-scaffold739-2665471 2 62634414 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764386 Affx-986696795 AX-385252095 2 72762561 CCGAGGGGGCGGGGACTCGTCTGACTACGGGAGCC[A/G]AGAGGCCCCTTCGTCTACTGTTCGAGCGTTTCCTT R 2 1 2 1 600010 r 74 goat 2_72762561 2 72762561 Ancestral_priority_1043 ancestry 0.5 neutral IMAGE 10K 10K ancestral 320764389 Affx-986696797 AX-385252098 2 72765215 GGATCCAGTAGCTGCGGGATGGCCACCCTGTCTCC[A/G]TATCATCGCGGCCATTGCTCTCCTTGTCCATGATG R 2 1 2 1 600010 r 74 goat 2_72765215 2 72765215 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 38404973 Affx-122956408 AX-123275325 2 72767314 TGCCTGATCCTCCAATTATGCTGTTTTTGACATAT[A/C]CTTTCCTAATATTCCTGAGAACATCAGACTTAAGA M 2 1 2 1 201000 f 74 goat snp50953-scaffold739-2709579 2 62590230 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423099 Affx-122942922 AX-123293445 2 72813170 CTTTAGGATGGGGAAGATGGAGGGAAGGTGGAAGA[C/T]GAGGTTATGGGGCAACAGGGAGACAGGAAGGGGTC Y 2 1 2 1 103000 f 74 goat snp50954-scaffold739-2755435 2 62543550 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377928 Affx-122977223 AX-123248287 2 72860745 CACGGGAATTCCTAGGATATATTTTGAATCATAAA[C/T]GATACAGTTTTGGGGACAGACTGGATGGGAGTGTG Y 2 1 2 1 201000 f 74 goat snp50955-scaffold739-2803010 2 62495384 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419091 Affx-122945788 AX-123289439 2 72893150 TCAGTGATATTCATTGAACACACACTGTGGTGCTC[A/G]GCTGTGCGCAAGGCTTCAGGGTCTCCACTGGGTGT R 2 1 2 1 202000 r 74 goat snp50956-scaffold739-2835415 2 62462627 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442073 Affx-122928377 AX-123312410 2 72939737 AGCTCTCTGGGAGAGCATACTGATCTTATCTCAGC[A/G]CTGCTCTTTGTCCACCTGGACCTCTCGATTTCCCA R 2 1 2 1 101000 f 74 goat snp50957-scaffold739-2882002 2 62415399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428938 Affx-122938895 AX-123299280 2 72979788 TAGGAGATCCTTTAAGTGAAGTAAGGGAAGAGATA[G/T]ACTGGATTATATTGTACCCTCTTCAACAGATGTTG K 2 1 2 1 101000 f 74 goat snp50958-scaffold739-2922053 2 62372366 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451555 Affx-122921705 AX-123321888 2 73040794 GCAGTCATGGCCAAAGACTCTTCCTGATCACTCCT[C/T]CATCTCAGGGACATGAAATGCAGAAGAATGAGTGC Y 2 1 2 1 201000 r 74 goat snp50959-scaffold739-2983059 2 62311273 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434620 Affx-122934008 AX-123304961 2 73095009 TCTCTAATAAATAATAAAAGAAAAGGGCTTGTGCT[A/G]TTCATCAGGTTTGGCCTCTGGCTTTTTGTCCCTTA R 2 1 2 1 101000 r 74 goat snp50960-scaffold739-3037274 2 62257081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773162 Affx-122961382 AX-385260305 2 73139265 TTTATACATGTATTCACTCCAGTGATAAATACTTT[C/T]AGGGCTTACTCCACTGCACTTTTATACAGTGGTTT Y 2 1 2 1 101000 r 74 goat snp50961-scaffold739-3081530 2 62214684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380376 Affx-122975340 AX-123250734 2 73194831 GTATGGTCGTGGAGATATGAGCTCTCTGGAAAAGA[C/T]GAAGGATTTCATGTTTGAAATATGTGTAGTTTCTT Y 2 1 2 1 101000 f 74 goat snp50962-scaffold739-3137096 2 62161334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450077 Affx-122922799 AX-123320412 2 73224983 TGATTTGATTCTTCTACTGTCTGGTGGCTGTAATC[G/T]AGGAGAAAGATCCTTGCATGCCCCTGGGAGGACAG K 2 1 2 1 101000 f 74 goat snp50963-scaffold739-3167248 2 62131096 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426044 Affx-122941108 AX-123296390 2 73254115 AAAGGGCAACATCCCTAATTAAGAATAATGTGCAT[A/G]TGGGTTGGGGGAGGAGAAAATCCTGGGTAGGAGAG R 2 1 2 1 201000 f 74 goat snp50964-scaffold739-3196380 2 62101714 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395096 Affx-122964166 AX-123265451 2 73307257 ATTGATTGAGCATGTACTAAGTGCCAGAAACTCTC[A/G]TGAAACTTGCATTTATGTCAGACAGTGATAGGATG R 2 1 2 1 202000 f 74 goat snp50965-scaffold739-3249522 2 62048346 G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427743 Affx-122939256 AX-123298086 2 73338241 GTGGCTAAACAACAACAAGAAATGTAGGTCTCACC[A/G]TTGTAGTATCTCAGGCCACTTACTGAATGCTAGTG R 2 1 2 1 201000 r 74 goat snp50966-scaffold739-3280506 2 62016888 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396812 Affx-122963285 AX-123267167 2 73370160 TTAAAAAGCACAGAACTAGATTCCAGTTTATGGAA[G/T]CCTTGTTTCCTGTGCTGTGCTTTGCTTAATGTGCA K 2 1 2 1 303000 f 74 goat snp50967-scaffold739-3312425 2 61985992 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442290 Affx-122928256 AX-123312627 2 73417551 ACTGGTGGCCAGCATATTTGCAGCATCTGGGCTTG[C/T]ACATTTCTCACCAAAAAGACTTATTCTGAAAATTT Y 2 1 2 1 101000 f 74 goat snp50968-scaffold739-3359816 2 61937811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464149787 Affx-1110336939 AX-515625459 2 73434957 CCCTGAGTGTCTCCCTGTCTGACAGGAAGTCTGGC[A/G]TCACTAGGGACAGACTGCTAGCCGTCCACACCCAA R 2 1 2 1 202000 r 74 goat 2_73434957_AF-PAKI 2 73434957 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782184 Affx-122930990 AX-385269262 2 73448426 GCTGATTCTATGAATCTCAAATGCTCTTTCATCAA[C/T]GTACTTTCTTTAAAAGTCTGGTCAAAAAAATATTG Y 2 1 2 1 101000 f 74 goat snp50969-scaffold739-3390691 2 61906773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441062 Affx-122928916 AX-123311399 2 73481464 TCAGAGACAGAAAAACTCAAATAACATCCAATACA[C/T]AGATCCAACTAGGAGGAAACAGAGTGTCCCTTAGG Y 2 1 2 1 201000 f 74 goat snp50970-scaffold739-3423729 2 61873515 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390101 Affx-122968019 AX-123260458 2 73525128 GATGGTGATGCTGGCAGAACAACCAGTTGGTGCCA[C/T]GAATATTTTTGAAAATGTTATTTTTAAGGCAATAT Y 2 1 2 1 101000 f 74 goat snp50971-scaffold739-3467393 2 61829352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385846 Affx-122971001 AX-123256204 2 73559972 TCAGTTTCATCAGCTGTCCAGTCGAGAGCTTATAA[C/T]GAGCTATTTGGAGACAATTCTCATCGGATTTCTCA Y 2 1 2 1 101000 r 74 goat snp50972-scaffold739-3502237 2 61793750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405624 Affx-122956600 AX-123275976 2 73589011 CAGATTTTGAGGGCAGAACATGAGGGCTGGTTGCA[A/G]TTTTAAAATATAACAGTGAAGCTATATCTCATGGA R 2 1 2 1 303000 r 74 goat snp50973-scaffold739-3531276 2 61764236 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405422 Affx-122956274 AX-123275774 2 73637216 GCTGAGGAAGGTGGCCAGGGGCAAGTGAAAACACC[A/G]CACAACTTTCCTATTATTTTTAATTTTTCTTCTTG R 2 1 2 1 103000 f 74 goat snp50974-scaffold739-3579481 2 61715599 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385611 Affx-122971193 AX-123255969 2 73666511 TAAAATCTTGCTAAAATATTTAAATCAAGCCTCCA[G/T]AACTCCACTGCCCTGCCTTATGGAGAAATGAAACA K 2 1 2 1 201000 f 74 goat snp50975-scaffold739-3608776 2 61686696 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789460 Affx-122923482 AX-385276470 2 73699729 AGGCCCATCTGATGATATTCAAGGTTATCAGAGTT[A/G]TCAAATCTGACAGGCTAGAATCAGATTCTACTTCT R 2 1 2 1 101000 f 74 goat snp50976-scaffold739-3641994 2 61653519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444689 Affx-122926439 AX-123315026 2 73735978 TTCTTGTACTCTTTACTATAACAACAATGGAGTAT[A/G]CATTATTTTATAAATGAGGAATTCACACATTCCTG R 2 1 2 1 101000 f 74 goat snp50977-scaffold739-3678243 2 61616437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395386 Affx-122963969 AX-123265741 2 73784262 TGAAGTTTTTTTAAAAGGGAAAAGGAAAACCTGAA[C/T]TTTGGCTACTGGACACGATTTTAAATAGTGGAGGG Y 2 1 2 1 101000 r 74 goat snp50978-scaffold739-3726527 2 61568062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779376 Affx-122925229 AX-385266480 2 73824119 ATAGCACTGAAGAAGACAAACAACAGCATTATACA[A/C]AGTCTCCATAGCACAATACCATTTATATAACCTAA M 2 1 2 1 201000 r 74 goat snp50979-scaffold739-3766384 2 61530481 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415980 Affx-122948409 AX-123286329 2 73854331 AGAGTCTTCATGCATGTTTGTGTTGGCTGGAAAGG[C/T]AAAAGAAAGTTCTGGGGAGCAATGACAAGTGTTAG Y 2 1 2 1 101000 f 74 goat snp50980-scaffold739-3796596 2 61500541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442886 Affx-122927655 AX-123313223 2 73908515 TGAGATGGCCATTCCCCAAAACAGAAATAACATCT[A/G]CTAAATTCATGGGTTACAAGTGTGAGAGGACTGAC R 2 1 2 1 101000 r 74 goat snp50981-scaffold739-3850780 2 61446673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782646 Affx-122929483 AX-385269718 2 73945811 AAAAGAGATGTGTGAGTCAGCTCATATACAAACAC[C/T]ATTGCCTTGACCTTGATTTAGACTTCACTACTGTT Y 2 1 2 1 101000 f 74 goat snp50982-scaffold739-3888076 2 61409473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794981 Affx-122920156 AX-385281941 2 73975159 TTATCTCTTATCACAACTTTTAGACTCTGTATATC[A/G]TACTTCTTATAGGTAGGACCCTTTGTTTCAGCTGC R 2 1 2 1 101000 r 74 goat snp50983-scaffold739-3917424 2 61381941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422481 Affx-122943319 AX-123292827 2 74028245 ATAAAACAATTATGAAAGATAGAATGGATTGGTTT[G/T]CCAACAAGCAATGTCTCTTTTAGTTTGGTTTAACT K 2 1 2 1 101000 r 74 goat snp50984-scaffold739-3970510 2 61330100 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779227 Affx-122976522 AX-385266331 2 74079151 TTTTTGTTAGTATGTTCACCCTTTTATTAGAGATT[A/C]TCTGTTACTCTGTTCATGCATTTCTTGGGTATCAA M 2 1 2 1 101000 r 74 goat snp50985-scaffold739-4021416 2 61278699 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418085 Affx-122946602 AX-123288433 2 74193632 GCATTGCTTCCTTCATTCATTCACTCAGAAATATT[A/G]CTTGAGTGACAATTACATGGCAACCATTATGTTAG R 2 1 2 1 101000 r 74 goat snp50987-scaffold739-4135897 2 61162780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434839 Affx-122934381 AX-123305180 2 74222312 TTCAAAATTTGCCCAATTCTCTTTTCAAATCTCAC[A/G]TTAACTACAGAAACTATTAAAAAAAATGTGGCTCC R 2 1 2 1 201000 f 74 goat snp50988-scaffold739-4164577 2 61132999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421142 Affx-122944191 AX-123291489 2 74255050 AGGCTATAGTCCACGGGGTCACAAAGAATTGGACA[C/T]GACTCAGTGACTAAGCACCCACAGAAATACTTTAA Y 2 1 2 1 103000 r 74 goat snp50989-scaffold739-4197315 2 61100116 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378560 Affx-122976606 AX-123248919 2 74300904 TAAACCCAAAATGGTTTTCACTGAACATCCAGCAC[A/G]TTCACTGCCTACTGCTGTGTGTGTGAGAAACACCA R 2 1 2 1 101000 f 74 goat snp50990-scaffold739-4243169 2 61054036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448878 Affx-122923267 AX-123319213 2 74353178 CATTCTATATTGAGCACCTACTATGTGATCTCACT[A/G]TGATAGCTGCTAGTATGATGTGAAGAATAAAAAAT R 2 1 2 1 101000 r 74 goat snp50991-scaffold739-4295443 2 61002127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784155 Affx-122926693 AX-385271207 2 74381812 AAATGTTTCTTTCTCACAAGGACTAAAGAAAAAAT[A/G]TTCAACTGTTTCATAAGAATTCTATAAGAGATATA R 2 1 2 1 101000 f 74 goat snp50992-scaffold739-4324077 2 60972832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438736 Affx-122930834 AX-123309073 2 74447312 AAATACCAAATTTAAAGAGTGCATGAATTTGCCTC[C/T]ATTGGCAGCAGATACTTCTCTTCATATTCTAGATT Y 2 1 2 1 101000 r 74 goat snp50993-scaffold739-4389577 2 60906345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421760 Affx-122944361 AX-123292107 2 74559084 TGTCTCCTTCACTGGACTCCCATGAGCCCTGGCCC[A/G]CTCGGTTCCTCACTGTCTTACCTAAGATCCTGCAA R 2 1 2 1 101000 r 74 goat snp5724-scaffold1200-98182 2 60785935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435527 Affx-122933406 AX-123305867 2 74610006 CAAACATGTCCTGTTCTCATCTTACCCCTTCTAGT[C/T]CTCTGTAAAACTCACTCTTGCCCAAAATGCCTAAG Y 2 1 2 1 201000 r 74 goat snp5725-scaffold1200-149104 2 60734487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449990 Affx-122922871 AX-123320325 2 74639062 GTTCCAGTTTATTCCCATTTATGCCAGTGGGAAAT[A/G]CAGACTTTTTTGTTTTGTTTTAATCTTTGTGCAAA R 2 1 2 1 101000 f 74 goat snp5726-scaffold1200-178160 2 60706615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421090 Affx-122944227 AX-123291437 2 74694355 GAAAATATTAAACTTTATCCAGGAACATAAAGAAC[A/G]TTGGAATATCTATGTCCTTGGATTCTCTCCCAAAT R 2 1 2 1 101000 f 74 goat snp5727-scaffold1200-233453 2 60652583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795890 Affx-122963530 AX-385282842 2 74724702 TTGTCCTAGATGATAGAGTTGGCCTGAAACTCTTT[A/C]TAGTGAATACTTTTCATGGGATCTTGATAAGTAAA M 2 1 2 1 201000 r 74 goat snp5728-scaffold1200-263800 2 60622450 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403097 Affx-122958497 AX-123273450 2 74755422 TTAGTTTCATCACATTCATGTTTTTCAGTAAGAAC[A/G]ATTGAGGAAGTGCAGAACAAAATAGATAAGAGCCA R 2 1 2 1 101000 r 74 goat snp5729-scaffold1200-294520 2 60590806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383620 Affx-122972550 AX-123253978 2 74865907 TTCAGCAAATCTTCAATAAGTAAATCCTTTAAGCC[A/G]TGCATGGACTACAGCCTTGTCTAACTCAAAGAAAC R 2 1 2 1 201000 f 74 goat snp5732-scaffold1200-405005 2 60481669 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390580 Affx-122967198 AX-123260937 2 74909377 TCATTCCCTTCTAAGCACATGGTAAGATTACACTC[C/T]CACTATTGTCTAAAAGCTTTGTCCAGAGTGTGCAA Y 2 1 2 1 101000 r 74 goat snp5733-scaffold1200-448475 2 60437925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431039 Affx-122936655 AX-123301380 2 74956006 GAGAGCTGATTCAGCAACCCAGGATATATGCAAAT[A/G]GCCAGGAACACAGGAAGTTGAGTGAATCAGTAGCG R 2 1 2 1 101000 f 74 goat snp5734-scaffold1200-495104 2 60390982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801206 Affx-122938059 AX-385288119 2 75040487 GTAAACCAACTTTACTTGACGGTTTTATGTAAACT[A/G]TACACTAGGACATCTTTTATAATTGTTGCTTCTCC R 2 1 2 1 101000 r 74 goat snp5736-scaffold1200-579585 2 60307101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277820 Affx-1111836039 AX-519551317 2 75103598 ATGTTCGTGCAACACACACACACACACATACACAC[A/G]CAGTAGTATATTTACATAAGAACATTAGTTATACC R 2 1 2 1 201000 r 74 goat Random2.2K-220 2 75103598 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433531 Affx-122935005 AX-123303872 2 75161006 TTGTTTTAATAGAATAGTCCACTCTTCTGCAAAAG[C/T]GGAATTCTGCATTCATTACCCCAAGATTTGACTTT Y 2 1 2 1 101000 r 74 goat snp5739-scaffold1200-700104 2 60184268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783274 Affx-122940544 AX-385270339 2 75194523 TCATCTGCAAAATAGCGATTAAAATATTCACTTTA[C/T]AGAGCTGTTGTAAAAGTCAAGTGTAACATCCAGTT Y 2 1 2 1 101000 r 74 goat snp5740-scaffold1200-733621 2 60150769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435471 Affx-122933452 AX-123305811 2 75249617 TCTGATGGTGATTTCTGTAGGATTGACATTGCCCA[C/T]GGATAAGATGGCAGCATCACCGAACATCAGCGTGA Y 2 1 2 1 101000 f 74 goat snp5741-scaffold1200-788715 2 60095964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416429 Affx-122947835 AX-123286778 2 75284673 TTTATCCTTGAAAATCCTCCCTCATCCCTGCAAGG[A/G]GAACCATGCCAGAGCTCCATCCAGCTATATTTAGA R 2 1 2 1 101000 r 74 goat snp5742-scaffold1200-823771 2 60061820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785413 Affx-122929479 AX-385272458 2 75352845 CACACTGGCTCCACACAACACTTATTGGGTCAAGG[A/C]TCTTAATCTTAAAAATCCAGACATATCCCAGACTT M 2 1 2 1 101000 f 74 goat snp5744-scaffold1200-891943 2 59993893 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442347 Affx-122928036 AX-123312684 2 75386956 AACAGAAAAACACAGAGGGCCCTGCTTAGTGTGTC[A/G]CAAGTTTTTTAATAAATAAACTATAAGTACAGAAA R 2 1 2 1 101000 f 74 goat snp5745-scaffold1200-926054 2 59957813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447196 Affx-122924994 AX-123317532 2 75419507 ACACTGTATAAAGTGTATAGGAGAGTCCCAGTAGA[A/G]ACCTGTGTATAACATTTTGTGCTCATTTCCAATGT R 2 1 2 1 101000 f 74 goat snp5746-scaffold1200-958605 2 59925675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415855 Affx-122948860 AX-123286204 2 75478034 GATCATTTGGCTTTGTTTGGAAAAGTCACGAATTC[A/G]TTGCATGACTCTGGTAAAGAATATCTCTAAGCATC R 2 1 2 1 201000 f 74 goat snp5747-scaffold1200-1017132 2 59866883 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417909 Affx-122946735 AX-123288257 2 75527198 ATGAAATCAACAGAAGGCTGGCTCCACAAGACAGG[C/T]GTTCTTTTCTATTCCACAGATTTATCCCAAGTTCC Y 2 1 2 1 201000 r 74 goat snp5748-scaffold1200-1066296 2 59817204 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445688 Affx-122926126 AX-123316025 2 75564972 TCATATCAGGGAGTGGTCACCCACAATAGTGAAAG[A/C]TACAGAGAGGGTTGGAAATAAGAGTAGTCATAGAA M 2 1 2 1 101000 f 74 goat snp5749-scaffold1200-1104070 2 59779036 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799845 Affx-122933709 AX-385286771 2 75611747 TGCTAGACATCACTTCAAAGAACTGTGGGTTCTGG[C/T]ACAATTCTGTGTTGCCCAGTAGAAATGTTACATTT Y 2 1 2 1 201000 f 74 goat snp5750-scaffold1200-1150845 2 59732329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414099 Affx-122949742 AX-123284448 2 75632484 AGGCCAAATAAACAGAAACATCAGAGTTTGGAAGA[A/G]AGAAATATTTATTGCAGGGACAAGCAAGAGAACTG R 2 1 2 1 201000 r 74 goat snp12713-scaffold1489-7310 2 59709393 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441098 Affx-122928892 AX-123311435 2 75669154 TTACACAAGGGCAAGATAACATTGTGTTCATGGCT[A/G]TAGTTCTGGAAACTAGGAGAACACCTACCTGCAGT R 2 1 2 1 101000 f 74 goat snp12714-scaffold1489-43980 2 59672826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788349 Affx-122947385 AX-385275367 2 75707810 CAGGAGACTCAGGGAATCAACAAATCAGGCAACAG[A/G]TTTAAGGTAATGCCCATCAGTTACAAAAGGTAATT R 2 1 2 1 101000 f 74 goat snp12715-scaffold1489-82636 2 59634164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794114 Affx-122930190 AX-385281080 2 75753111 AGAATCCCTAGGCCAAAAGACACATGATGAGCAAA[G/T]ATCCGGAAATCAAACAGATGCTACAAAAATGCTTT K 2 1 2 1 101000 r 74 goat snp12716-scaffold1489-127937 2 59588829 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388608 Affx-122969144 AX-123258966 2 75790087 TGCATTTTATTCTCACTTGAGTCACCTAAGTTTAG[C/T]GGAATTTAGTGATGGGCGAGGTGCCTTGCTAGGTT Y 2 1 2 1 201000 f 74 goat snp12717-scaffold1489-164913 2 59551834 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386516 Affx-122970744 AX-123256874 2 75819978 AAATTATTGCATCCCATTCCCTCCCATTTTTTCCC[C/T]GTTTCCAAGCCATGGCTGGATACTATGGAGTTATC Y 2 1 2 1 201000 r 74 goat snp12718-scaffold1489-194804 2 59521345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437583 Affx-122931872 AX-123307921 2 75852885 ATTTAGTAGTATTTCCATTTGTGTTATCTTTTGGC[C/T]ACTTTCCCTTTGATTTTCTCCTTACATGACATTTT Y 2 1 2 1 101000 r 74 goat snp12719-scaffold1489-227711 2 59488128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398795 Affx-122961417 AX-123269150 2 75886910 GTTTGCATTATCTTCTGGCCAAGAGGCCTGTTAAC[A/G]TTTTTATGGCTCTCTTCCTAGATAAATGTCTATCA R 2 1 2 1 303000 f 74 goat snp12720-scaffold1489-261736 2 59454223 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377538 Affx-122977463 AX-123247897 2 75922769 CTTCTGTCTGCTCTTGCCTCTGGCTCTGGTTCTGT[G/T]CTTCTAGTGGCAATGGAAGCAGAAAGAGGAGAAAG K 2 1 2 1 101000 r 74 goat snp12721-scaffold1489-297595 2 59418283 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398297 Affx-122962154 AX-123268652 2 75953962 GACCCACTGTCATAGTTTAGAATCTGGGTTGGGGA[A/G]AGGAAGTGAAAGCTAAATGTGTAAACAGACGCTCC R 2 1 2 1 101000 f 74 goat snp12722-scaffold1489-328788 2 59386836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789963 Affx-122971791 AX-385276969 2 75984810 TCCTTGAAATTATATCAAATTCAGAAGAATGATCC[C/T]CTTCTGTGCGTCTATTAGCAATGCCTTCTCTTTTG Y 2 1 2 1 101000 r 74 goat snp12723-scaffold1489-359636 2 59355109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389783 Affx-122968223 AX-123260140 2 76066973 TGGTATTGCTGTTGTGTCCATGATAGCTTCCTAAG[C/T]ACCAGATTGAATTTTATAAAATGGATGCACCTCTT Y 2 1 2 1 101000 f 74 goat snp12724-scaffold1489-441799 2 59272708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770066 Affx-122933256 AX-385257233 2 76106617 GTATGAGCTGCATAGACTGTAAAGCACAAAACACC[A/G]TGTATTTTCTTACTCATGATTACAAAATAATATGA R 2 1 2 1 101000 f 74 goat snp12725-scaffold1489-481443 2 59233125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427700 Affx-122939290 AX-123298043 2 76152899 TAATGGTCTTCTTTTTCTGGGTCACATGCTAGGCT[A/G]TGTGCATCTCGGGAGAAAGGCTGAATCTTTCTTCT R 2 1 2 1 101000 f 74 goat snp12726-scaffold1489-527725 2 59187081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771276 Affx-122966690 AX-385258434 2 76186963 AGGATGAAAATTTAAAGTGAGTTACTAAATTACTG[C/T]ACCTTGTACTAAATTATCTTGCTGGGTGGCTCAGT Y 2 1 2 1 101000 r 74 goat snp12727-scaffold1489-561789 2 59152756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385444 Affx-122971314 AX-123255802 2 76199285 AAAGTGGTAGCTGTGTAGTCATTGCAGAGGGAAAT[G/T]AAACCATTCTGATCAAGCCTGGGCCCATGTTTACC K 2 1 2 1 101000 f 74 goat snp10170-scaffold1365-163 2 59141544 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408983 Affx-122953905 AX-123279334 2 76243808 AGCAAACATATATTGTAAACAAATTTACATCCATA[A/G]TGTATGTACTGGGAAGTGATATACTTAAGTATTCT R 2 1 2 1 101000 r 74 goat snp10171-scaffold1365-44686 2 59097291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390290 Affx-122967729 AX-123260647 2 76291876 GAGGCAATATATCATATTTTATTTGTGTGTTGTTT[C/T]AGAATTTTTCTGTCTCATTTGAATATCCAAATTAG Y 2 1 2 1 303000 r 74 goat snp10172-scaffold1365-92754 2 59049081 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393656 Affx-122965286 AX-123264011 2 76321425 CTGACAGTAAGGAAGTATAAAATAACAAATATAAT[A/G]TTGTTTATATTTAGAATAAATATGTTTCATTTTCT R 2 1 2 1 303000 r 74 goat snp10173-scaffold1365-122303 2 59019692 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400091 Affx-122960742 AX-123270446 2 76352711 TATAACCAACTTCATAATGAATAGTTAATATACCT[A/G]TGATTATTATGGTGTGGCATTTAGGTCAGATGTAC R 2 1 2 1 101000 r 74 goat snp10174-scaffold1365-153589 2 58988406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412541 Affx-122951337 AX-123282890 2 76429319 TCTAAAAGTTGTTTAATTCTTGAAGTATCCACTTC[C/T]ATTTATAAAAAGGAGATAAAACCACAAACTTCAGA Y 2 1 2 1 103000 r 74 goat snp10175-scaffold1365-230197 2 58910051 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454049 Affx-122919400 AX-123324382 2 76472987 TTTTTAACTTGATCAAATGTCTATCTCAGAAAGCC[A/G]CCGAAATCATTGTATTAGTCATGACACTTTAAAAT R 2 1 2 1 101000 f 74 goat snp10176-scaffold1365-273865 2 58866517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421558 Affx-122943858 AX-123291905 2 76544072 CCTTGCTGCTCCTGACCTGCATTTCTTGCAGCTTA[C/T]TCCAACAGTAAGCACTTTTCTAAGACTTTTATGCT Y 2 1 2 1 201000 r 74 goat snp10177-scaffold1365-344950 2 58792202 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453883 Affx-122919511 AX-123324216 2 76573965 GATCAAATTTTAATGAAACAATTCAGAGGAAAACC[A/G]TCATCTTACTTCAAAAATTGTTTTCACTGAAAATA R 2 1 2 1 101000 f 74 goat snp10178-scaffold1365-374843 2 58762094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403212 Affx-122957907 AX-123273565 2 76605098 ATATTGTGCATTTATTTTTTCCAGTGGGCACATCA[G/T]CCAAGGAAAATGGGGAAAGATAAACTGTTCTTTCC K 2 1 2 1 201000 f 74 goat snp10179-scaffold1365-405976 2 58730558 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778085 Affx-122925721 AX-385265201 2 76638010 ATTTCATATTTTCTTTTGTAACACTGTAGTTGATA[C/T]AGCTACAAGTATCTGGATGGTTTGAATTTTATTTG Y 2 1 2 1 101000 r 74 goat snp10180-scaffold1365-438888 2 58697080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787086 Affx-122971616 AX-385274113 2 76702890 ATAAAGAAGTCTTCAGAAACTGATAGTTACAAAGA[A/C]AAAAAGCTTAAAATATAATCCTCAGAACAGGCTTT M 2 1 2 1 202000 r 74 goat snp10182-scaffold1365-503768 2 58631403 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384869 Affx-122971942 AX-123255227 2 76742544 CCAACACAGTTTGATGGGGTCTGAAACAAATCTGG[A/C]GGGTGGTTGAAATGCTTCAAGGACAGAGATCTTAT M 2 1 2 1 101000 f 74 goat snp10183-scaffold1365-543422 2 58591736 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789357 Affx-122952368 AX-385276367 2 76789177 GTTTGTTTTTCTTCCCAATAAACACCTCCAAATGA[C/T]AAGCTTATTAAGTGAAAAGTTGTCTTTTTCCAATG Y 2 1 2 1 201000 r 74 goat snp10184-scaffold1365-590055 2 58543572 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399624 Affx-122961079 AX-123269979 2 76820044 TATTTCTTAGACAATAAAGCTTAATAGCTAAGATG[A/G]GACTATACTTTTTTTCCAACCCTCAACAAAAGGAT R 2 1 2 1 101000 f 74 goat snp10185-scaffold1365-620922 2 58512757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772782 Affx-122950260 AX-385259927 2 76857184 GAAGTGTTTAGTACTGATATAACTAATCTTGTGTT[A/C]TGCAGTTAGTTAGCTGAAGAGCATGTGGATGATTC M 2 1 2 1 101000 r 74 goat snp10186-scaffold1365-658062 2 58475967 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409590 Affx-122953567 AX-123279941 2 76898018 AAAAGTATTGGCAAAGCAAAGTATCTCAGGAGTTT[G/T]CTCAAACTCATGTCCATTGATTCTAGGATGCCATC K 2 1 2 1 303000 f 74 goat snp10187-scaffold1365-698896 2 58435561 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784223 Affx-122977347 AX-385271274 2 76928993 AAAGTCAGCACCATCCTCATTTTTTAAGCACCTGC[A/G]GTTCATTTGTAGTCTAGTCTTTATAGTGTAAGCTC R 2 1 2 1 101000 f 74 goat snp53913-scaffold82-9558262 2 58396183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793639 Affx-122955667 AX-385280612 2 77011194 CTCTTGTTCATCTTTTTGTCTAATTAATCTTCACA[C/T]GGGCACAAAGTATCAGGAAAAGTCACTATTGATTG Y 2 1 2 1 101000 r 74 goat snp53911-scaffold82-9476061 2 58313482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386926 Affx-122970002 AX-123257284 2 77062774 GAAAAGTAATGGTTCAGAGGCATTGAGAACAAGAT[C/T]TGAGAAGGGCAAGAAAGCAAAGATGAAAACAGAAA Y 2 1 2 1 101000 f 74 goat snp53910-scaffold82-9424481 2 58261366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766596 Affx-122940589 AX-385253951 2 77091627 ACCTGTATAGAAATCAGAATTTTGGCAGCTGAATT[C/T]TTTTAAAGATAATGTAAGAGGAAAGGAGTTGCTTT Y 2 1 2 1 202000 f 74 goat snp53909-scaffold82-9395628 2 58231626 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795976 Affx-122964953 AX-385282928 2 77129133 ATGTAGGGTAAACAGGACTGCTTAGCAGCCCAGAT[A/G]TAAGAGCAAAAGGGTGAAGCTAAAAGAAAAATCTA R 2 1 2 1 101000 f 74 goat snp53908-scaffold82-9358122 2 58193182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797257 Affx-122944734 AX-385284196 2 77177078 TCTTTGTAGTACTATTTGGAAAGTGTTTGGATATT[A/C]TTTACCCCTCAACTGTGAGGTGAGATAATCAGACT M 2 1 2 1 101000 r 74 goat snp53907-scaffold82-9310177 2 58144736 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782630 Affx-122919393 AX-385269703 2 77213792 TAATAATTGCCATGAACTTGCTCTAATGTGCACTT[A/G]AGTTTATTAAATCATGACTATGACACTATTGTCTG R 2 1 2 1 201000 f 74 goat snp53906-scaffold82-9273463 2 58106672 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419377 Affx-122945621 AX-123289725 2 77296037 CTCCACATCAGTCACCCCAGCCAGAAAGCCTGGAC[C/T]AGGAAGACAAGCTCCCAGACTGTCTGGCATTTAAG Y 2 1 2 1 101000 r 74 goat snp53905-scaffold82-9191218 2 58022967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438340 Affx-122931337 AX-123308678 2 77331140 AATGTCATGTTCATTGAGAAATGCCTGGCAAATAG[C/T]AGGTGCTCAATGCATATTTTTGCATAAATAAAAAT Y 2 1 2 1 101000 f 74 goat snp53904-scaffold82-9156115 2 57987640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379698 Affx-122975903 AX-123250056 2 77369556 CCTAGTTGAGATTAGTAAAAGGCCTACACACATCA[C/T]GACATACTTGATATGAGATACACATAGAACAATGA Y 2 1 2 1 101000 f 74 goat snp53903-scaffold82-9117699 2 57949384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413508 Affx-122950634 AX-123283857 2 77414372 GAAAGACTAGTTTAGGATACATTGAAATACGACAT[A/G]TTAAGGGGGAATGAGGTGGCATCCCCCTTTACTAG R 2 1 2 1 201000 f 74 goat snp53902-scaffold82-9072883 2 57903331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412795 Affx-122950492 AX-123283144 2 77463420 GAGCATAACTGGTAAAAAATATTTAAAAACCAATC[A/G]CTTGGTCTCTAAAGGGAATTTCCTGATGGTACAGT R 2 1 2 1 101000 r 74 goat snp53901-scaffold82-9023835 2 57853837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399111 Affx-122960861 AX-123269466 2 77492357 CCCTTGGCAGTGATTTAGGACAGCCTGGGTGACCA[C/T]TTGCTAGGTGCACTTCAGGAGTTATGTTGTAAGCA Y 2 1 2 1 201000 r 74 goat snp53900-scaffold82-8994898 2 57824899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789149 Affx-122972536 AX-385276161 2 77526531 CCTGCTTTTTGATTACATTGCTTAAGTAATTCATC[A/G]TCAATGTTTAATTGATACGATTTGATTTATTCCTG R 2 1 2 1 202000 r 74 goat snp53899-scaffold82-8960724 2 57790959 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375828 Affx-122978548 AX-123246187 2 77677829 CAATGTAAGTCATCCCCATTTTCTGTATTTTCTCA[C/T]TGATGATACTTTTGCAAACTGCATTTCCTTGTCTT Y 2 1 2 1 101000 r 74 goat snp53896-scaffold82-8809426 2 57634828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423232 Affx-122942691 AX-123293578 2 77710833 ATTTCTCTACCTTAAACTGTGACAAATGATTTCCA[C/T]GGCATTTGGTGAGGATTAAGTAAGAAAAATTTTTC Y 2 1 2 1 101000 f 74 goat snp53895-scaffold82-8776422 2 57601453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776933 Affx-122928032 AX-385264057 2 77751123 AAAACCAACTTTGTGAATGGGGAATATCCAGAAAG[A/G]TTAAATAACAGTTTTCTGGGAATTAAACCCTTTGG R 2 1 2 1 101000 f 74 goat snp53894-scaffold82-8736132 2 57560650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780823 Affx-122973130 AX-385267912 2 77783786 AGCCCAAAGGAGGAAAAGCTTCCCAGAATGTAAAC[G/T]ACTGGATGTCGAAGACTCAAGCTGTCTTTCTCTGA K 2 1 2 1 101000 f 74 goat snp53893-scaffold82-8703469 2 57527247 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779573 Affx-122963087 AX-385266676 2 77819577 TAACCTCAAAAATATCACAAATGTCTGTCATCTAG[A/C]TTAATATCTATGTTGCTCCTCAAATCGTGGTCTTA M 2 1 2 1 101000 f 74 goat snp53892-scaffold82-8667678 2 57491653 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453982 Affx-122919450 AX-123324315 2 77859599 AGCCTGATTCTCCTACCTGACTGCTGAGTATCACT[A/G]GTAAACTTTCTGGCTGCTACCGGATCAAGTAGTTT R 2 1 2 1 101000 r 74 goat snp53891-scaffold82-8627656 2 57451936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802475 Affx-122974601 AX-385289379 2 77890254 CTCCTAAGTGACCAAGTCAGTTGTGTGCCAGACAT[A/G]CCAACTTGGGCCTAAACTCAGCAGCTATTATTGAG R 2 1 2 1 101000 f 74 goat snp53890-scaffold82-8597001 2 57420976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436329 Affx-122933250 AX-123306668 2 77928954 TTTTCCCAGTGAGAGGAACTCTCTCAGGCCAGAAA[G/T]TTCCCTCTTGGCTCTAAACAGAGTCATCTTGGGAG K 2 1 2 1 201000 r 74 goat snp53889-scaffold82-8558301 2 57382166 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435741 Affx-122933285 AX-123306080 2 78000720 TTGTATTTGAGGAGTGCATTCTCACTGCCTCTCTC[A/G]TTGCTCAATTAAAAGCGTGTCACTGACACTTCAAA R 2 1 2 1 201000 r 74 goat snp53887-scaffold82-8486535 2 57310071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435679 Affx-122933330 AX-123306018 2 78079128 ACCATCCCCAGGGCTGGAGATATAGAGACACAGGG[A/G]CTTCAGCTTTCTTTACATGGAGTTCAGCGCTTCGG R 2 1 2 1 101000 f 74 goat snp53885-scaffold82-8408127 2 57231905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443693 Affx-122927167 AX-123314030 2 78138114 AGTTTTGAGAGCTGTTATGTATTCTGCATATAAGT[A/G]CTTTATTAGATATGGGATTTGCAAATATTTTCTAG R 2 1 2 1 303000 r 74 goat snp53883-scaffold82-8349141 2 57172530 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428910 Affx-122938918 AX-123299252 2 78168315 GTGGTCAGCTCTCTTTTCTCTGTTCACTAGCTGTG[C/T]ACCCCAAGCATGTTTCTTACCTTCTCTGTGGCTGG Y 2 1 2 1 101000 r 74 goat snp53882-scaffold82-8318940 2 57142128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795171 Affx-122925613 AX-385282129 2 78198827 TAGAGCTGCCTGTTTGACACAGTGGAAAGTATTTC[G/T]AATTCTCTTTTGTTAGATAATGTTTATAGCTGCTA K 2 1 2 1 101000 f 74 goat snp53881-scaffold82-8288428 2 57110982 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434055 Affx-122934195 AX-123304396 2 78229602 ATAAGTTCCTATACTGGTGCAATTTCTCAGGAGAA[C/T]GAATTGGATGCAATAATGCCCATCACTTAACAGTG Y 2 1 2 1 101000 r 74 goat snp53880-scaffold82-8257653 2 57080219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381191 Affx-122974540 AX-123251549 2 78262221 TGGACTTCAAGGCTATTAGTGAGTTTTCTTCTCAC[A/C]TTTTCCAGGACTCTGGGAATATCAGACCCACTTAT M 2 1 2 1 201000 r 74 goat snp53879-scaffold82-8225034 2 57047510 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379915 Affx-122975754 AX-123250273 2 78317594 CCCTGATTAGCAGCTTTCAGACTCAAGGAAGTTCA[C/T]GGAGGCTGGAGTCTGTTCCTTAACAAATAAGAAAC Y 2 1 2 1 101000 f 74 goat snp53878-scaffold82-8169661 2 56991086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384736 Affx-122972044 AX-123255094 2 78363113 GTACATAATTTTTGCATGAAGTGTTCTACATCTAG[C/T]GTGCATTTTAAACTCACAGTACACCTCAGTTCAGG Y 2 1 2 1 101000 r 74 goat snp53877-scaffold82-8124142 2 56945164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793873 Affx-122944961 AX-385280842 2 78408332 CAAAGGACATGGGCTTTAGACTCATGCTGGCTTCA[C/T]TGACAATTCCAACTTCTCCTGTGCTGGGTACATGA Y 2 1 2 1 101000 r 74 goat snp53876-scaffold82-8078923 2 56899901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380980 Affx-122974683 AX-123251338 2 78474361 GAACAGTCGGGGTCTCAAGGGGAGACAGAGCCAAC[A/G]TGAGAGGTTTGGTGAGGATTCAGTGAGGGTCTGAT R 2 1 2 1 202000 f 74 goat snp53875-scaffold82-8012894 2 56832967 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431333 Affx-122937064 AX-123301674 2 78503105 GTCACTCCTCAGCTGATAAGCTTTCCCTCTTCCAC[A/G]TTGTGCTTCCAACCAATTTGAGTTCCTCAAGCTGA R 2 1 2 1 101000 r 74 goat snp53874-scaffold82-7984150 2 56804227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450894 Affx-122922203 AX-123321228 2 78554510 TTTCTTTCTTGTTAGCAAACATTTGCTTCCCTAAA[C/T]GTGTGCCCACCCATCCTGCTGCTGTTGCTAAGTCG Y 2 1 2 1 101000 f 74 goat snp53873-scaffold82-7932745 2 56752608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437467 Affx-122932379 AX-123307805 2 78585480 GGGCCAGTAGGTGGCTGAAATTTGAGAGGTCAGGC[A/G]CCAGAGAAAAGGGAACCATCAAGGAAAAGCCCCAC R 2 1 2 1 201000 f 74 goat snp53872-scaffold82-7901775 2 56726811 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797166 Affx-122954322 AX-385284106 2 78681084 CAGATATTTGTGAAAATACTGATATAGCTATACAC[A/G]TATTATCATAGATACAAATGCACCAAACACAATCA R 2 1 2 1 101000 f 74 goat snp53870-scaffold82-7806171 2 56629384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795474 Affx-122960288 AX-385282429 2 78765117 TAGCCCTTATATTATGTAGAGGATTTTAAAAACTG[C/T]AAACATTTTATTTAACATTTGAGGATATCATACCT Y 2 1 2 1 103000 r 74 goat snp53869-scaffold82-7722138 2 56544211 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272359 Affx-1111833959 AX-515629181 2 78807129 TATTCTCCTCACCCAGCAATCAACCAGAAAGCCAA[A/G]TGTCCTCCCACCCTCTTAATCACAGATCT R 2 1 2 1 101000 f 74 goat GoatD01.011623 2 78807129 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778699 Affx-122953740 AX-385265810 2 78811930 TAGCAGAAACACCTGGGGTGCTTAATAAAAATGCA[C/T]ATTTTAAAAGCAATCTTCGGTGTTGGACTTTAGGA Y 2 1 2 1 201000 r 74 goat snp53868-scaffold82-7675325 2 56497170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767416 Affx-122926486 AX-385254689 2 78844910 ATGTATTTTTGAAGCATATGTTGAGCACAGCCTCC[A/G]TTACTGCAAGGCTGAGATAGTCCTGACCAAGACAG R 2 1 2 1 101000 f 74 goat snp53867-scaffold82-7642345 2 56464269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423255 Affx-122942673 AX-123293601 2 78879754 CTGTATGTACAAGGACCAAGAACGCCTGGTTCACA[A/G]TTATTTCCCTAAAATCTACCACAGTGTGCCTCTTA R 2 1 2 1 201000 r 74 goat snp53866-scaffold82-7607501 2 56429505 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419148 Affx-122945746 AX-123289496 2 78916756 GTAGTGCATATATCCCGTTTTCCCTTGAGACACCC[G/T]TATGTGATATATTCAGTCTAAGATGTTCTCTGGGG K 2 1 2 1 101000 r 74 goat snp53865-scaffold82-7570499 2 56391639 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433234 Affx-122935251 AX-123303575 2 78954290 GATTGAGACAATGAAAAACAGAATTATACTTTGAA[C/T]ATTTCTGCTTAACCTGGGTAAGTGGCTAAGCCATA Y 2 1 2 1 101000 r 74 goat snp53864-scaffold82-7532965 2 56353830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403576 Affx-122957577 AX-123273929 2 79042768 CCTTTCTCTAGTAGGGCAGGGGACACAGATTAATT[A/G]CCCTAGTCATCAGGTGGGGCCAGGTAGAAGACAGG R 2 1 2 1 101000 f 74 goat snp53862-scaffold82-7444487 2 56264300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379432 Affx-122976105 AX-123249790 2 79086341 TGTTTTTACTAAAGAGAAAGAAAAATAGATGGTTG[A/C]TTTTTTTCCTCACCTCCCACCTCCATACTTAAATG M 2 1 2 1 103000 r 74 goat snp53861-scaffold82-7400914 2 56220815 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441095 Affx-122928894 AX-123311432 2 79128300 GGATGGCCCTCTAACTTTGGGCATTTACTGTGTTA[C/T]GGGCATCAGCTGATGTATTTTACAAAGGAAAAGAG Y 2 1 2 1 101000 f 74 goat snp53860-scaffold82-7358955 2 56178372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385871 Affx-122971606 AX-123256229 2 79174353 TGGTACTCCCACCCCTAGACAGGCCTCCTGTGTTC[A/G]TGTCACCATCTCCAACACCATTTATTTCCTTCTCT R 2 1 2 1 101000 r 74 goat snp53859-scaffold82-7312902 2 56132365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784706 Affx-122931938 AX-385271754 2 79228831 ATATCTACTCAAATCAAATGAATGATTATGTGTTG[C/T]GACCACCTCAGAATCAAAGACTGATCATTATTATT Y 2 1 2 1 101000 r 74 goat snp53858-scaffold82-7258424 2 56077674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385267 Affx-122972076 AX-123255625 2 79370528 ATCACTTCCAGCCTGTGGGGTTTTCACCCTGTTAC[A/G]TGGGGATGATGACACATGGTCTGCAGAGCATCATA R 2 1 2 1 201000 f 74 goat snp53855-scaffold82-7116727 2 55935305 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433640 Affx-122934581 AX-123303981 2 79407462 CACACTACTCTAGAGACTAGAAATGACATTGTTAA[A/C]AGGCCCAAGTCTTATGTATGCCTGCTTCTTGGACA M 2 1 2 1 101000 f 74 goat snp53854-scaffold82-7079793 2 55898047 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410064 Affx-122953220 AX-123280414 2 79455249 GAATGAAAGTTTTCGGTCTTTCCTCCCATATCATC[A/G]CTTCCAGCTAGAATGATAGAATGTATCAGATAGAA R 2 1 2 1 101000 f 74 goat snp53853-scaffold82-7032006 2 55850416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416946 Affx-122948029 AX-123287294 2 79486248 CCTAATTTTTATTGGTGGTCCTCATCCTTTCCTCC[A/G]CTTCCTGGGAACTACAGATCCTCTCACTTTTAAGT R 2 1 2 1 101000 f 74 goat snp53852-scaffold82-7001007 2 55819134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376963 Affx-122977760 AX-123247322 2 79546300 AAATGAGTTGAGAACAATACCAGAAAGTTGAGACA[C/T]GCATGCCAGGCAGTTTTCTGGCCTTGTTCATCAGC Y 2 1 2 1 101000 f 74 goat snp53851-scaffold82-6940955 2 55759905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385578 Affx-122971839 AX-123255936 2 79580931 AAGGCTTTGTGAATTGTGTTCAGAAATTTTGACAA[C/T]AAACACACATACACAGTCCCTTCAAATAAGAAAGA Y 2 1 2 1 201000 f 74 goat snp53850-scaffold82-6906324 2 55725024 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431246 Affx-122937131 AX-123301587 2 79700884 ATGACCTTGGGCAAGTTACTTAACCTCACTGTGCC[G/T]CATTTGTCTCATCCATAAAGTTGGGAGACAGTAAT K 2 1 2 1 201000 r 74 goat snp53848-scaffold82-6786371 2 55603686 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389503 Affx-122968305 AX-123259861 2 79732255 TAAATCTATGAGCTTAAAAAAAAAATGTATCTCCA[C/T]CTTCATAGTTTTAGGTTAACCTCTAAAACTTTTCC Y 2 1 2 1 103000 r 74 goat snp53847-scaffold82-6755000 2 55572148 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787830 Affx-122957655 AX-385274853 2 79762925 AGACTATTATAGTTTAAAGACAGTTATATCAGAGA[A/G]CAGATTTCCTACCTTAAGTATATACCACTCACTAT R 2 1 2 1 101000 r 74 goat snp53846-scaffold82-6724330 2 55541474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428480 Affx-122938787 AX-123298823 2 79828627 AAGTAAGCATGCATGATGCTTGAGCAAGCGATAGT[A/G]AGAGCCTGTCAAATTGGAGACATCTTTGATAATGT R 2 1 2 1 101000 f 74 goat snp53844-scaffold82-6658628 2 55474924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791935 Affx-122935069 AX-385278925 2 79861381 CAAATAACCTTTCTAATTCTGCATACATTCCTGTG[G/T]CTGTACATTTACATTACTGGAGTCTCCGGTGCCAC K 2 1 2 1 101000 r 74 goat snp53843-scaffold82-6625874 2 55446489 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787938 Affx-122951971 AX-385274960 2 79895602 AGTCATGATCTCAAAATGCAAATCCTACTTTGACC[A/G]CAAATTTGGGATGGAACTATGAGCAAGTCATCTCA R 2 1 2 1 101000 f 74 goat snp53842-scaffold82-6591653 2 55412218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390922 Affx-122967085 AX-123261279 2 79945380 ATGGGTTGTAGCTTATTCCCTCCAGTTGATCATTT[A/G]TAAGACGCTCAGACTTTTAGTTTGAACTCAAATGG R 2 1 2 1 101000 f 74 goat snp53841-scaffold82-6541875 2 55362547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793453 Affx-122947476 AX-385280430 2 79977499 GAAACGCTGACGTTGATACCATGGTCAGTGAAAGC[A/G]TTTCTGAAAAGGTCATATTTGACTCATGTAAATAT R 2 1 2 1 101000 f 74 goat snp53840-scaffold82-6509756 2 55329383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379689 Affx-122975910 AX-123250047 2 80115168 ATAATTTCATTTCACAACCTCCTTCTTCAGAGCCC[A/G]CATTTCATTTCAATGGTACTAAGTTTTATTCCTGG R 2 1 2 1 201000 r 74 goat snp53837-scaffold82-6372087 2 55191223 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803340 Affx-122944728 AX-385290176 2 80148673 CTGCTTTCAAATTGGGCAATTATAGAAACACTGAT[A/G]GAGACACATCTCTGCTAATTTACATATGCATGGCA R 2 1 2 1 101000 r 74 goat snp53836-scaffold82-6338582 2 55157767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423175 Affx-122942736 AX-123293521 2 80200334 ATTATGCCACCTGCAAATGTCAGTCATCTAAAGAG[C/T]ATAGACTCTCCTTTTCATCCTTTATCATTTGCCAT Y 2 1 2 1 101000 f 74 goat snp53835-scaffold82-6286921 2 55105932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436717 Affx-122932315 AX-123307055 2 80234085 AACTAAGAAAAGCATTTCATCCCATCACTTCAGGG[C/T]AAATAGAAGGAGAAAAAGAGGAAGCAGGGATAGAT Y 2 1 2 1 103000 f 74 goat snp53834-scaffold82-6253170 2 55072012 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769828 Affx-122920141 AX-385256998 2 80262853 AAAGCAAGCAAATTCCAGGTGAATACAATTTAATT[A/G]CTATTTATTCTTTATTGTAAACTATGAAGTAATCA R 2 1 2 1 201000 r 74 goat snp53833-scaffold82-6224402 2 55043068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406353 Affx-122955431 AX-123276705 2 80294106 TGGGATTCTCCAGGCAAGAATACTGGAGTAGGTTG[C/T]CATTTCCTTCACCATCTAGAGCAAAGGTCTATTTT Y 2 1 2 1 303000 r 74 goat snp53832-scaffold82-6193149 2 55008222 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390186 Affx-122967804 AX-123260543 2 80331509 GATTTGTGAAGAGTAAAAACAAAAGGAATTATGTT[A/G]TGTTAGCATCTCTATCCCCTTCAGTATCATTGCCA R 2 1 2 1 101000 r 74 goat snp53831-scaffold82-6155746 2 54970376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445525 Affx-122925173 AX-123315862 2 80381700 AAAATGTTAAACAAAATGTCCAACAAGTGAGTTAT[A/G]GTTAAATAAAACATGGTTTACCTTAGCAATAAAAA R 2 1 2 1 101000 r 74 goat snp53830-scaffold82-6105555 2 54919053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777286 Affx-122948270 AX-385264408 2 80414439 AGATGCATCTCAGATTTAAGCTGAATAACCAAGCC[A/G]TGTAAAATACCTCAACTATTTGCTAGTATTCAGAA R 2 1 2 1 101000 f 74 goat snp53829-scaffold82-6072816 2 54885900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791231 Affx-122938961 AX-385278225 2 80505441 AAGTCTGGTGGGCATCAATACACATCTAGTTATTT[A/G]TATAGCATCTGTAGAGATGGAAATTTACCATGTTC R 2 1 2 1 201000 r 74 goat snp53827-scaffold82-5981814 2 54793987 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779442 Affx-122923671 AX-385266545 2 80578936 AAATGACAGTGCAAATGGTATTTCCATACAGTAGA[C/T]GTTTTTGACCAATGTCCACATTATTTAACTGAATT Y 2 1 2 1 101000 f 74 goat snp53825-scaffold82-5908319 2 54720521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277724 Affx-1111836057 AX-519551223 2 80584628 TTAGAAAATCTCACTTAGAGATACTGGTTAGTTAT[A/T]AACTGCTATACAGAAGGAATTCAATTAAAGAGGAT W 4 1 2 1 101000 f 74 goat Random2.2K-223 2 80584628 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277738 Affx-1111836064 AX-519551237 2 80611131 GTCTTGGATGTTGTTATTTTTGTTAGAAAGAATGG[A/C]CAGGAGATGACAGAGATTTTGAACTTCTCTCCACC M 2 1 2 1 101000 f 74 goat Random2.2K-224 2 80611131 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442867 Affx-122927670 AX-123313204 2 80868153 GGACAATTTATGAAAGCATACCTTTTTCTTGAGTA[C/T]AACAGAGGGTTAACACTGCACATCAACTAGGTGAA Y 2 1 2 1 201000 f 74 goat snp53820-scaffold82-5619102 2 54423577 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783940 Affx-122945753 AX-385270994 2 80972831 CTGAATTTAATCATGCTACAACTGATAGATATAAG[A/G]AAAGCTGACAAATAGTAAGGACCAGTCAAGTGCTT R 2 1 2 1 101000 r 74 goat snp53818-scaffold82-5514424 2 54319222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464147516 Affx-1110339546 AX-515623200 2 80985878 CTCAGAATTAGCTAATTCTTCAATTGAGGCAAGGT[A/G]TACAGTAATGGAGTCCTATCCCATTCTCTTTATAC R 2 1 2 1 101000 f 74 goat Random2.2K-226 2 80985878 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798455 Affx-122969835 AX-385285388 2 81006441 GCTGCGAAAATGCACTTTATTGCTAAACAAAAGTG[A/G]TGTAAATTAACATCCTGGATTGGTCTACAGTCATC R 2 1 2 1 101000 r 74 goat snp53817-scaffold82-5480814 2 54285519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786054 Affx-122945935 AX-385273090 2 81042782 AAGAAAAGAAAGATAATAATCATTTCTAACTGTGG[A/C]TTATAATGTTTTACAGGACAGTATTTTCATTTTGA M 2 1 2 1 101000 f 74 goat snp53816-scaffold82-5444473 2 54249419 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785871 Affx-122946065 AX-385272908 2 81080576 CCTATCAAATATCTCTTGGAAAGTTTGAAACACAT[A/G]AGGAATATGTATTTCACATTGCCTCACTACTTAAG R 2 1 2 1 101000 r 74 goat snp53815-scaffold82-5406679 2 54210954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402324 Affx-122959076 AX-123272677 2 81115463 AAATGAGACTATAGATAGGATTTAGGGTTGCAGTC[A/G]CAAGAATGAGAAAGAATTGTGACGATACATAGAAA R 2 1 2 1 101000 f 74 goat snp53814-scaffold82-5371792 2 54175531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796616 Affx-122959906 AX-385283562 2 81146786 TATGAGGAACCTAGTTCTCTCTGGTCTAGTTAACA[G/T]CTAGCTTTGCCTGGATTCATTAGTTTTTTTCAATT K 2 1 2 1 101000 f 74 goat snp53813-scaffold82-5340469 2 54146205 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438400 Affx-122931291 AX-123308738 2 81204062 CATCAGAGGGAAAGTACCCTTACTAAGGTCACATG[C/T]GAGAAAGAAGGAAGGGTAGTAGGGAAAGCCCTCCA Y 2 1 2 1 101000 f 74 goat snp53812-scaffold82-5283193 2 54088309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427194 Affx-122939599 AX-123297537 2 81256073 TTTTTATTCTTTCTGTTCTTCACAGCTCCTTTGCC[A/G]TTTGACACCATTTGGGTGTTTACTGTCTTCTTACC R 2 1 2 1 201000 r 74 goat snp53811-scaffold82-5231182 2 54034947 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779333 Affx-122921860 AX-385266437 2 81312552 TACCACTTAAGCAAATTATAAAAGATTGCTTTACT[A/G]TACAGCCCTGAAATTTCTTGTTTAAAAATGGAAAA R 2 1 2 1 201000 r 74 goat snp53810-scaffold82-5174703 2 53978071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767858 Affx-122936786 AX-385255078 2 81361639 ATCACATCTTCAAATAGCCTAATTTCATATAAATT[A/G]CATTTAATCTGTGTCAGGGTACTTTGTGCTAGGAC R 2 1 2 1 202000 f 74 goat snp53809-scaffold82-5125616 2 53929225 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400577 Affx-122960410 AX-123270932 2 81416370 ATAGACTTAATGTCCTAAATCCAACACACATAAGA[C/T]GAGGAAAAATAACAAATTACTAATAGATAACTGTT Y 2 1 2 1 101000 f 74 goat snp53808-scaffold82-5070885 2 53873960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789125 Affx-122938225 AX-385276138 2 81456453 GAGTAGCTATCAGGTCAGCCAGATGTCTTTGTAAC[C/T]TGACTGAGTATTCAAATATATTAAGGGAAAGGACC Y 2 1 2 1 101000 f 74 goat snp53807-scaffold82-5030802 2 53833344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449362 Affx-122922730 AX-123319697 2 81502186 AGTTTTACTCTCAACTTTTCTTCAAAAATTATCCC[A/G]CAAAGATCATGATGAATCTAAAGATATCTAGCTTC R 2 1 2 1 101000 f 74 goat snp53806-scaffold82-4985069 2 53787625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273003 Affx-1111833181 AX-519546684 2 81545553 TCTCGAAAGGATCTCACTGGACTGTGTCCACTGCC[A/G]TTTTCAACCACTTTCCATAGCAGTGTGTCCTAGAC R 2 1 2 1 101000 r 74 goat 2_81545553_AF-PAKI 2 81545553 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380705 Affx-122975159 AX-123251063 2 81607276 AAAGGGACTAATGAAAGAGTTATGAGACAGATGTG[A/C]ATAGCTCTGATATTTTAAACATTATGACACTGCAT M 2 1 2 1 101000 f 74 goat snp53804-scaffold82-4879979 2 53678844 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766969 Affx-122952465 AX-385254268 2 81645592 TTTTAAATATGATATTGATTTTCAAAAATGTGTAT[A/G]CATTTTGTAATGTATGATGGTACATTTTTTCTTGG R 2 1 2 1 303000 f 74 goat snp53803-scaffold82-4841663 2 53641244 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449833 Affx-122922391 AX-123320168 2 81680302 AACCTTAGTAGTAAATAAAATATTTCACGAATATC[A/C]CCTATTTTTTAGTTCCAATTCACTTCATTTCCAGG M 2 1 2 1 101000 r 74 goat snp53802-scaffold82-4806953 2 53606043 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416440 Affx-122947827 AX-123286789 2 81787463 TTTCTTCACCCCAGCCTTTACTGAGTTCCTTCCAG[C/T]TCTCTTTATTCAACTTTAGTGCTTTGATCAGTTCA Y 2 1 2 1 201000 r 74 goat snp53800-scaffold82-4699792 2 53497947 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382226 Affx-122973969 AX-123252584 2 81856799 AAAGCAACGACAACCACAAAAAGACTATATACGGC[A/G]TTTGCTTTAAAAATAGGGTCCTTTTTTTTTGAAAA R 2 1 2 1 303000 r 74 goat snp53798-scaffold82-4630456 2 53428311 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440223 Affx-122930683 AX-123310560 2 81908735 CATAAATTTGAGAATTATGATAATTAATTAGTCAC[G/T]AGTTTTCAACAGTGCAGCACCTGGAAAGGAGAAGG K 2 1 2 1 202000 f 74 goat snp53797-scaffold82-4578520 2 53375946 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273559 Affx-1111833690 AX-519547173 2 81953220 ATACCTGACACTTCAAATACAAGATTATATGCTTG[A/G]CACTAAAGGTACAG R 2 1 2 1 101000 f 74 goat GoatD01.001658 2 81953220 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802168 Affx-122966174 AX-385289072 2 81983795 GCCAATCAACATGAAACAAAACTTCAGCTTTGGAA[C/T]AATTTTTCTTATCCACACATATGCCTATTATAAGT Y 2 1 2 1 101000 f 74 goat snp53795-scaffold82-4503460 2 53299302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277774 Affx-1111836082 AX-519551273 2 82025322 CATGACCATGAAAAAATGGTGCCTTAGTAATCTTA[A/C]TAAAATAAACATTTAATAATGATGCTCCACTACTT M 2 1 2 1 101000 f 74 goat Random2.2K-227 2 82025322 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376671 Affx-122979001 AX-123247030 2 82147574 ACAGAGAGGGATTTAGCCATATATATATTAATGGA[C/T]AAAGAATGAATCTCAAAAATACACAAGCAACTCTT Y 2 1 2 1 303000 r 74 goat snp53792-scaffold82-4339681 2 53135416 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768301 Affx-122941592 AX-385255481 2 82176664 GTTAAACAAACATTTCTGAGGGTAAGGGAAGAGAA[A/C]TCTTATATGCAGCATTTGCTAAACTTTCTTCACCA M 2 1 2 1 101000 f 74 goat snp53791-scaffold82-4310591 2 53105683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766622 Affx-122976050 AX-385253973 2 82230748 CATTCACATTAATAGTGTGTGGCTTGCAATTGATC[A/G]CTTTATAAGCTGAAAATTTGAACAATTTATGAAGT R 2 1 2 1 101000 f 74 goat snp53790-scaffold82-4256507 2 53051414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788409 Affx-122929072 AX-385275427 2 82281432 CATTTTTTTAAGACCCTTTAAAAGCTTTCATTGCT[A/G]TTTTTTCATCCTTGGCATCTTGTCTTCATTCCCGA R 2 1 2 1 202000 f 74 goat snp53789-scaffold82-4205823 2 53000462 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379069 Affx-122976329 AX-123249428 2 82382033 CCCATAATTACTCTGAATGAATAAAAATAGTGGCA[C/T]GCTCTTGAAAATGTCAACACTCTTAACACTTAAAT Y 2 1 2 1 101000 r 74 goat snp53787-scaffold82-4105222 2 52896278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277802 Affx-1111836096 AX-519551300 2 82464505 ACCTTGTAGAATTATGGAAGGATACAATAAAAGGA[C/G]GGCTTCCCAGCTGGCTCAGTGGTAAAGAATCTGCC S 4 1 2 1 101000 f 74 goat Random2.2K-230 2 82464505 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438474 Affx-122931234 AX-123308812 2 82476534 ATTTGTTCTAATTTAGGGGTGGGAAAGGCAGCAAG[G/T]TTCCGTGGAAATCTGAAATACTGAGTCAAGCAATG K 2 1 2 1 101000 r 74 goat snp53784-scaffold82-4010721 2 52797791 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446905 Affx-122924704 AX-123317241 2 82523695 GGAAAACATCAAATAAATAGCCCTTCACAAGAAGA[C/T]ATGCTCTTTCTTTATTAAATCCACAGTCATAAGCA Y 2 1 2 1 101000 r 74 goat snp53783-scaffold82-3963560 2 52750593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441760 Affx-122929115 AX-123312097 2 82559467 CATGCATTAGCAGGCAGATTCTTTACCACTAGCGC[A/G]GTTGCCTGTAAATCATGAAACCCTTTACCATTTCT R 2 1 2 1 201000 r 74 goat snp53782-scaffold82-3927788 2 52713419 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420709 Affx-122944784 AX-123291056 2 82647596 GATAAAGAATTCTGTGAACAAAGCTAAGGTCAAAC[A/G]CAAACTCTGTGCACAAATACTCTCTATAGATCTTT R 2 1 2 1 101000 r 74 goat snp53780-scaffold82-3839659 2 52624330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777959 Affx-122954990 AX-385265075 2 82701760 GTTCTGTTTAATTAGAGGCTATAAACACTACATTG[C/T]ATGGCCAATGAGAACCAAAACCTATCCCATAAAAA Y 2 1 2 1 101000 r 74 goat snp53779-scaffold82-3785495 2 52569307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399985 Affx-122960817 AX-123270340 2 82740545 TATGCCATATTGTGTTTTAAAATTCTGCTATAAAA[C/T]GCTTTCTTATTTGAAGGATTTAAAGTGACTAGAAC Y 2 1 2 1 201000 f 74 goat snp53778-scaffold82-3746710 2 52528717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795791 Affx-122968761 AX-385282744 2 82776004 GTTGGCAGGGGAGAAGTTAGGATGTGAAGTAATTT[A/G]TTTGGTACAAAATGTGAATAACTAATTTAGTAAGT R 2 1 2 1 201000 r 74 goat snp53777-scaffold82-3711251 2 52492623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437952 Affx-122931619 AX-123308290 2 82815190 AAGGAACATATATGTAAACCACTGATTCTCTAAAC[A/G]TGCAGCATTTAGTAGTATGCTTATAAGGCATAGGA R 2 1 2 1 101000 r 74 goat snp53776-scaffold82-3672065 2 52452934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420459 Affx-122944883 AX-123290806 2 82894667 AGATGTTGACCTTGTCCTACAAAAATTTTTGGATT[A/G]TAGTGCAACTATTTTGTTTTTTAAGAGTAGAAGTT R 2 1 2 1 103000 f 74 goat snp53774-scaffold82-3592588 2 52372711 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414198 Affx-122949658 AX-123284547 2 82934971 TGCAGGCTTTACCATCTGAGCCACGAGGGAATCCC[A/G]TCAGATGCCAACACTCAGCTATTTTGGTATCACAA R 2 1 2 1 101000 r 74 goat snp53773-scaffold82-3552284 2 52331939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402932 Affx-122958185 AX-123273285 2 82988735 TCTGCATTCTCCTCAGCTCCAGGCAAGCCTAGCTG[C/T]AATCTTCCTTTCTTAACTGTGACTATGGAAAATTT Y 2 1 2 1 101000 r 74 goat snp53772-scaffold82-3498520 2 52277252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782854 Affx-122964577 AX-385269924 2 83030853 AATAGTGGATGGTTGTTTACAACCAGTCACCATCA[C/T]TGAACATTCTCCTTTATCTTGTTACTCTCCTATGT Y 2 1 2 1 101000 r 74 goat snp53771-scaffold82-3456402 2 52234338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769878 Affx-122926387 AX-385257047 2 83118030 GCTTTTGGCTGAAGAAGAAGTTAAAAGATAAGGTT[A/C]GGGGCTGCTTTTAGGGCAGATCATGAAGATCAGGT M 2 1 2 1 101000 r 74 goat snp53770-scaffold82-3369225 2 52147226 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277952 Affx-1111836100 AX-519551447 2 83126326 TTGATATAAACCCTCTAATTCACATCATTGACTTT[A/G]TTCTTATTTCTGCCCAGGTCATTCTTCTCAATGCT R 2 1 2 1 101000 r 74 goat Random2.2K-231 2 83126326 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435573 Affx-122933371 AX-123305913 2 83296024 ATGTTAAATGTTCAATAAATACTGTAAACTGGTGG[C/T]GTGCATTTTTTCTTTTTGCTATCCATTATCAAATG Y 2 1 2 1 103000 f 74 goat snp53766-scaffold82-3191231 2 51966551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780745 Affx-122948153 AX-385267835 2 83324851 TTTAAATACTGGAGAACCACAAACATGCTATACCA[A/G]AAAAGTATAGAAAATGCATTTAAGATGAAAAAAGG R 2 1 2 1 201000 r 74 goat snp53765-scaffold82-3162404 2 51937773 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451313 Affx-122921282 AX-123321646 2 83361523 CTCATTCTGGTGTTTTGCATTTTCCTGATTATTAA[C/T]GACATTGAGCATCTTTGCTTGTCCTATTGACAATT Y 2 1 2 1 303000 f 74 goat snp53764-scaffold82-3125732 2 51900162 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434659 Affx-122933980 AX-123305000 2 83395760 AGTCAACTTTCTTCATTTTACTTCATTTGAATTTT[A/G]CTGCTTCTCATATGGGAAAAATGCCATGAATCAAG R 2 1 2 1 101000 r 74 goat snp53763-scaffold82-3091495 2 51866025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453079 Affx-122920049 AX-123323412 2 83431583 ATTTCTCTTTCATGTAATTCAGGAACTTGATTAGG[C/T]GAGCTGAGAAATATCATGATGGCTTTATTTCTACT Y 2 1 2 1 101000 f 74 goat snp53762-scaffold82-3055672 2 51830355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784005 Affx-122919397 AX-385271059 2 83483666 GGAAACAGATCCAATGTCTCAAACCAAACAAAAAT[A/G]TCCCAAACACCAAAATAACCAAAATGTATACAGGC R 2 1 2 1 201000 r 74 goat snp53761-scaffold82-3003589 2 51779754 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425772 Affx-122940721 AX-123296118 2 83519956 CATTATCTGGAACAATACAACCTCATTGAATTTGG[C/T]AGAACCGAAACTTTGAAACCTTGTAAATATCCATC Y 2 1 2 1 101000 r 74 goat snp53760-scaffold82-2967299 2 51742981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774242 Affx-122953918 AX-385261378 2 83553505 CAGACCCTCTCTCTGGAGAATTGGATCAAGTGATA[C/T]AGGGATGTTTCAAAGCATCTGTAAATAAAAATTGT Y 2 1 2 1 101000 f 74 goat snp53759-scaffold82-2933750 2 51709385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439092 Affx-122931121 AX-123309429 2 83592836 TCGGATACACAGACTGGGGTAGATTTTGTGATATA[C/T]AGACATTTAGAAAAAGAAAAAATAAGAAAATTATT Y 2 1 2 1 101000 f 74 goat snp53758-scaffold82-2894419 2 51670082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415775 Affx-122948920 AX-123286124 2 83683286 TGATATTATTCCAAGGCCTGATACTGCCTTCACAA[C/T]AGTCATGAGCGTTCTGTCATCCTCTATCCTCCTAG Y 2 1 2 1 101000 f 74 goat snp53756-scaffold82-2803969 2 51579633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434040 Affx-122934206 AX-123304381 2 83741640 GAAAGAAAGTTTCCAAATGTTCTAAACAACCATAC[A/G]TCAATCATTATTTCAGGAACTTTGCAGAGCAACTT R 2 1 2 1 101000 f 74 goat snp53755-scaffold82-2745615 2 51521378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791927 Affx-122970999 AX-385278917 2 83794987 ATTGAACTGTGTTTACAGTTTGAAATTTAGATTGT[A/G]TCTAGTTTTCCTTCTTTATAGATAATACTGCAACG R 2 1 2 1 101000 r 74 goat snp53754-scaffold82-2692268 2 51467330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451067 Affx-122921424 AX-123321401 2 83824310 CTCTTCCTGTTTTTCAGGCCAAAAGCAGAAGAGTC[A/G]TTGTTTTTCTTTTTCCTTTTACTGTCATAAATATC R 2 1 2 1 103000 f 74 goat snp53753-scaffold82-2662945 2 51437701 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795936 Affx-122971699 AX-385282888 2 83971566 CTTCCAGCCAAGTAAACCCTTAGTGTGTAAAGAGA[C/T]GTTTTACTGTTGCACATGGGTTAGTTTCTGCATTT Y 2 1 2 1 101000 f 74 goat snp53749-scaffold82-2515689 2 51284288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396858 Affx-122963249 AX-123267213 2 84030527 CCAGGTAAAGTAGAAAGCATTTCTTTACTGTCACT[A/G]CAGTGCTCTAGGGGGGGAACTTTAGCTTAAGTGTG R 2 1 2 1 201000 f 74 goat snp53748-scaffold82-2456728 2 51225625 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438775 Affx-122931381 AX-123309112 2 84060189 TTTCTAGGAATTTAAATGCAAGAACACCTCATTTA[G/T]CTGATATTGTTGGAGATGAGCTCACTTATGTGAAT K 2 1 2 1 101000 r 74 goat snp53747-scaffold82-2427066 2 51196000 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801088 Affx-122974310 AX-385288002 2 84090440 ATATTTTCTTTCAACTCCTCTGCCTCAGAATTTTA[A/G]TTATTTTCATGGTCTAGTAATAAGGATGCTAAGGT R 2 1 2 1 102000 r 74 goat snp53746-scaffold82-2396815 2 51165564 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415580 Affx-122948629 AX-123285929 2 84122854 AGTGTGACAAAGCCATGGCTAGATACAGGCTTTCT[A/G]TTTACTAATCTAGTTCAACACATGCGTGTGCACAC R 2 1 2 1 201000 r 74 goat snp53745-scaffold82-2364401 2 51133391 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273005 Affx-1111833182 AX-519546686 2 84157714 TCTCTGAATGTAGTGGAGAGCTTTCACTGTTTTTT[A/G]ATTTATATCGTATTGATACTGTTTTGTATATCTGA R 2 1 2 1 201000 r 74 goat 2_84157714_AF-PAKI 2 84157714 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375930 Affx-122978464 AX-123246289 2 84223200 TCTGCAATAGAATTCTTAAATATTGAAGCCAATTA[C/T]ATTTTTTAAATATGGCATGATCATGTCAACCACCC Y 2 1 2 1 101000 r 74 goat snp53743-scaffold82-2264055 2 51032777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380537 Affx-122975674 AX-123250895 2 84264521 AAGCTTACCTTCTTGTGGGGGAAAATACACAAGAA[C/T]GAAATAAGTGCATGGTACTCTGTGGTACATCAGAT Y 2 1 2 1 101000 r 74 goat snp53742-scaffold82-2222734 2 50991635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448377 Affx-122924102 AX-123318713 2 84322756 AGTTATGGGACCAAGGCTCTTGTGTGCCTGTGATG[A/G]TCTGTACTGGCCCTGTTAATATCTCTTTACTGATG R 2 1 2 1 101000 r 74 goat snp53741-scaffold82-2164499 2 50932050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440421 Affx-122929604 AX-123310758 2 84365569 TAGCTTTCTTTTTCAGGCTCTTCAATTGTGATCTT[A/G]TAGAAAATGTTTACTGGTTTAGTTTTATAGTTTGT R 2 1 2 1 101000 f 74 goat snp53740-scaffold82-2121686 2 50888737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396496 Affx-122963534 AX-123266851 2 84402781 TGGCCAGACCTAAGACATGTGCCCACCCAGCCATC[C/T]AAACCTTAGATTCTCTTAATAGGAATGAAGTGTTC Y 2 1 2 1 101000 r 74 goat snp53739-scaffold82-2084474 2 50851918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407415 Affx-122955236 AX-123277766 2 84436175 ACAATTTTTTTTTGCCAGTGTTCTCATTGTTTTTA[C/T]GGAGGATTAGGTTTTTGGAGGTCCTTACTTAGCCA Y 2 1 2 1 303000 f 74 goat snp53738-scaffold82-2051080 2 50818489 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796743 Affx-122925211 AX-385283687 2 84524509 TGTGGATATCTGGGGACAGAAAAGTCCAGAAAAAA[C/T]GAATATAGTGCAAAGACCTTAAGTCAGAATGTCTG Y 2 1 2 1 101000 f 74 goat snp53736-scaffold82-1962746 2 50730732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771278 Affx-122932424 AX-385258436 2 84572535 ACCTTGTCAAACAGCTTTAAGAAATCTAACTTACT[A/G]CTGATTTCCCAACAGATAGAACTGTCAGGGGAAAA R 2 1 2 1 201000 r 74 goat snp53735-scaffold82-1914720 2 50682994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415705 Affx-122948526 AX-123286054 2 84610459 CAGTGACTGTAGGGCACAAAGAGGGAGATGGTTGG[C/T]GAACCTGCCCAAGTTTGGGATTTGACATGAATGGT Y 2 1 2 1 201000 r 74 goat snp53734-scaffold82-1876796 2 50644673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426756 Affx-122939856 AX-123297102 2 84666330 AAATCCTTTGTTTAGTAAACATTTGAATGCCTTGT[A/G]CGTGCACATTCCCATGTCTGACCTCAGTCATGGAA R 2 1 2 1 201000 f 74 goat snp53733-scaffold82-1820925 2 50587642 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415097 Affx-122949449 AX-123285446 2 84713509 TCCTGTCTCACTTCCCATTTATCCTGCATATTCCC[A/G]TTATCCTTTTTAAAACAGCAATTTAGCATAATTAT R 2 1 2 1 101000 f 74 goat snp53732-scaffold82-1773746 2 50541377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393647 Affx-122965292 AX-123264002 2 84745367 CTTCTTGTCAGTTATTTATTGCCTTGTGAATAGAT[A/G]CTCTAAGACAGAAGTTGTAAGCATTTCTGTAAAGG R 2 1 2 1 101000 f 74 goat snp53731-scaffold82-1741888 2 50509206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777338 Affx-122939736 AX-385264460 2 84774247 TCTTCATAAATATGCCTTTGCTCGGCTTAGCTACT[A/G]TTGCTCTTCCTTAGATTGCTATTCATTAAGTAAAT R 2 1 2 1 101000 f 74 goat snp53730-scaffold82-1713008 2 50480326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793221 Affx-122944449 AX-385280199 2 84833313 TGCCCTTGGAAATTGCCACATATTCTCCCTGACAA[C/T]ATGATTTCTCAGTAATTTAGGATTGAATCCTTTTC Y 2 1 2 1 101000 f 74 goat snp53729-scaffold82-1653942 2 50420213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421607 Affx-122944483 AX-123291954 2 84883896 TGTCCTAGCAAATAAGGTGCTATATGTGCAGTCCT[A/G]CCTGATACACAGCAAGTGCTCCATGAAATTAGCTG R 2 1 2 1 101000 f 74 goat snp53728-scaffold82-1603359 2 50369633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421845 Affx-122944296 AX-123292192 2 84930611 TAAAATTTATTATTTATCATTTTACTCTAGTCTGT[A/G]TTCCTAGTGGTACAGTGTCAGCCTCTTTCTTCAGA R 2 1 2 1 101000 r 74 goat snp53727-scaffold82-1556644 2 50323989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792415 Affx-122935336 AX-385279396 2 84973754 AATTTACTGTTGGCTAAAGGGGCAAACATCAATGC[A/G]TTTGACAAGAAGGATCGACGTGCTCTGCACTGGGC R 2 1 2 1 101000 f 74 goat snp53726-scaffold82-1513501 2 50281528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798156 Affx-122943430 AX-385285091 2 85006571 ACCATAGGGATATCATTGGCCAATGACCTATTTTT[A/G]CTAGTATTAGTATTAGCATTTTCTTTTCCCCTTGG R 2 1 2 1 101000 r 74 goat snp53725-scaffold82-1480684 2 50248184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383075 Affx-122973742 AX-123253433 2 85038731 GTGGGTAGACTGCAGGCCCCTTCACAGCTCTGGGA[C/T]GGGTGTTTTTGTCCTGAGGGTAGGTGCTCACCTCT Y 2 1 2 1 101000 r 74 goat snp53724-scaffold82-1448524 2 50216323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427223 Affx-122939576 AX-123297566 2 85104816 TAGATCTGTCAAGTTTTCTTTCAAGGAACAAAAGG[A/G]TATATCATAAGGAGCTTGTTTCCTGGACTGGGGAC R 2 1 2 1 101000 r 74 goat snp53723-scaffold82-1382439 2 50150342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381653 Affx-122974752 AX-123252011 2 85203721 TCCCCATGGCTCTGGGCTCCACAGAGGGAGATGGC[A/G]TGGAGGGACCTCTCTGTGAAGTTGCTGGGAGCAAT R 2 1 2 1 102000 r 74 goat snp53721-scaffold82-1283534 2 50051321 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448356 Affx-122924119 AX-123318692 2 85234005 TCCTGGACATTTTCCACAGGTGAGTTGGGATGGAT[A/G]AGTGTCAGTCACTGTTGTTCTTGGAGTGGGGCACT R 2 1 2 1 101000 f 74 goat snp53720-scaffold82-1253250 2 50020983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277824 Affx-1111836107 AX-519551321 2 85287737 TACTCAATTATTTCTGGTATCTTGCTGTTGCTGCT[A/G]CTGCTAAGTCGCTTCAGTCGTGTCCGACTCTGTGT R 2 1 2 1 102000 f 74 goat Random2.2K-232 2 85287737 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449052 Affx-122923061 AX-123319387 2 85375465 ACAGAGATCCCAGCAATAAACCCACACTTACATGG[C/T]CAGTTGTCCATAACAAAAGAGGCAATATATACACT Y 2 1 2 1 201000 r 74 goat snp53717-scaffold82-1111790 2 49883481 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791119 Affx-122974875 AX-385278114 2 85412248 ACTGTTCTCTCTGGAAGATGTTCTTGATTCTAAGA[C/T]ATTTTCCTCCCACTCAACCCTACCCCACATTTCAT Y 2 1 2 1 101000 r 74 goat snp53716-scaffold82-1075007 2 49846445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409077 Affx-122953340 AX-123279428 2 85462071 TAATCTACAGGGTCTAGGGATTTGAGGTCTAGAGT[G/T]TGAGTTAAGGGCCTCTGATCTAGAATTCTACAGAC K 2 1 2 1 101000 f 74 goat snp53715-scaffold82-1025184 2 49795662 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400384 Affx-122960011 AX-123270739 2 85498564 TCTTTGCTCTTTTTTTCACCTTCCTGTCTTCTGTT[A/G]TATTGAGTTCTTTAACATTTCATCTGGCTAAGAAG R 2 1 2 1 201000 r 74 goat snp53714-scaffold82-988691 2 49758283 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420643 Affx-122944834 AX-123290990 2 85548976 TGTCTAATATATAAATTAATTGAATGGGTTGGTTT[A/G]TATTTTAAGTGTTTTTTCCTCTAAAATTAGAAAAC R 2 1 2 1 103000 r 74 goat snp53713-scaffold82-938279 2 49707566 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437397 Affx-122932430 AX-123307735 2 85581732 AATGTCTCCCTGTTTAACCTCAGCTGGGACCACAT[A/G]TGTAACACAACTCAAATTGCCAAATGAGGAATTAG R 2 1 2 1 201000 r 74 goat snp53712-scaffold82-905523 2 49674400 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385811 Affx-122971030 AX-123256169 2 85636938 GCCAAGGTGGAGGCTATGGAAGCTTTTCCTAAAAC[G/T]CAATCAACTTGAAGCAAGAAAAAAGTTCATTAATA K 2 1 2 1 101000 f 74 goat snp53711-scaffold82-850317 2 49618813 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778233 Affx-122977667 AX-385265348 2 85668217 TTTTCCAAAACAGCCACTTGTTTTCACTGTGCTTA[C/T]GTTTAAAAGCATATAGAGATTTAAACTATTACAGT Y 2 1 2 1 102000 f 74 goat snp53710-scaffold82-819038 2 49587445 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387828 Affx-122969668 AX-123258186 2 85707883 AGAACACTACCCACAACAGAACCACCTGAGGCCTC[A/G]TCCTTGACCCGCTGAATCATATTCTCTAGGGAACA R 2 1 2 1 101000 r 74 goat snp53709-scaffold82-779372 2 49547565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390656 Affx-122967136 AX-123261013 2 85771307 GTTTCTGGATAAGCCTTGTAGAATATTAAATATTT[A/G]TCAGAAGATAATTAGTCACTCAGTCAATAGGATTT R 2 1 2 1 201000 f 74 goat snp53708-scaffold82-715948 2 49483714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378354 Affx-122976830 AX-123248713 2 85800307 GCACAACCTCTTACAAACCATATGGAAGGACTTAC[A/G]TGTCATTTCCTAGCATTTTTCAGAGCCTGGATTTC R 2 1 2 1 101000 f 74 goat snp53707-scaffold82-686948 2 49454586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402801 Affx-122958285 AX-123273154 2 85839919 CTGCCAAAGCAATTTAGATCCCACACAGAATGCAA[C/T]GCTCAACCATGCTGCAAGAAAAAGACAATTTCTAA Y 2 1 2 1 101000 f 74 goat snp53706-scaffold82-647336 2 49414873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435874 Affx-122932793 AX-123306213 2 85869473 TGAAGACACGAGCTTGTTTCTGTCCCTCAGAGACC[A/G]TTTTCCATAATGTCCCAACACAGTGAGGAAGTGGA R 2 1 2 1 101000 r 74 goat snp53705-scaffold82-617782 2 49384851 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772759 Affx-122939595 AX-385259904 2 85900066 AAATCAGAAGTTCTTGACTCAATCTAGGATGACTC[A/G]TAGGTTTCTGGCTTGAATGAAAGGTGAATGGAAAT R 2 1 2 1 101000 f 74 goat snp53704-scaffold82-587189 2 49354050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394355 Affx-122964653 AX-123264710 2 85955490 GACATGACTGAGCGACTTTCACTTTCATAGCTTGC[A/G]CTTTTTAGCATTTGCATCAACGATGAGAACGCACA R 2 1 2 1 201000 r 74 goat snp53703-scaffold82-531765 2 49298424 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453323 Affx-122919974 AX-123323656 2 86009871 GCTTGAACCCCAGTAGATGCCATTCTCCTTTGTTA[C/T]AAACTTAAATACACTCTGACTCCCTCTCCTGCCTT Y 2 1 2 1 201000 r 74 goat snp53702-scaffold82-477384 2 49242718 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382371 Affx-122973859 AX-123252729 2 86040675 ATTAACTGTATATTTCTGCCTCATTCTTTCTCAGG[C/T]TCAGAAACCTTGTCAGAGACTATTGATGTTTACCG Y 2 1 2 1 201000 r 74 goat snp53701-scaffold82-446580 2 49211808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424690 Affx-122941702 AX-123295036 2 86074192 AATCCTAGGCAAGGAAGATAGGCATAATCATAGGC[A/G]CACACTGGAACATGGGCAGGATAGGGTTCCCCTTG R 2 1 2 1 101000 f 74 goat snp53700-scaffold82-413063 2 49178247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378720 Affx-122977046 AX-123249079 2 86129436 ACTTGAAAAGTCAAGGCTTAGGATTTTAAATGATC[A/G]TCAAGTGCTAGTAACACTAAGCCACAAATATGACT R 2 1 2 1 101000 f 74 goat snp53699-scaffold82-357819 2 49124528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427128 Affx-122939654 AX-123297471 2 86173736 GTGGAGCTTCTGATCAGCCAAAAATTGAAAGATAC[A/G]TAGATAAGAAAAGGTCTAGATTTAGTTTAAGGAAA R 2 1 2 1 101000 f 74 goat snp53698-scaffold82-313519 2 49080451 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397130 Affx-122962677 AX-123267485 2 86218377 AACACAAATAATTTAAAATGCATTAAGTAGGAACT[A/G]CCCCCTTGGACTTAAACTAACTTATAAACTTTACC R 2 1 2 1 101000 r 74 goat snp53697-scaffold82-268878 2 49035761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769961 Affx-122943179 AX-385257130 2 86247887 GAGAATAGTTCAGGTATTTCAACATTCCAAAAAGC[C/T]TTACTGAGTAAGTTTCTTAATTAGCTATTTCTTGA Y 2 1 2 1 101000 f 74 goat snp53696-scaffold82-239368 2 49005956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417579 Affx-122946897 AX-123287927 2 86291250 TTTGTCATCGAGGAAGGCCATCAGTAGGGTTTATG[A/C]TTTTGGGGATGAGTCTGGAAGTGTTCTAGAAGCTA M 2 1 2 1 101000 f 74 goat snp53695-scaffold82-196005 2 48962165 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802671 Affx-122959601 AX-385289570 2 86343095 TTTGATATAAGGACCACTTCTGTGGATTAAAGTAG[C/T]ATTTTCCAAATAGTGTTTTGCTGCAGGCTGTTCCC Y 2 1 2 1 101000 r 74 goat snp53694-scaffold82-144160 2 48909742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386676 Affx-122970187 AX-123257034 2 86383519 ACGTGACACCCATCCTAACAAGCACAATCAGCGTG[C/T]ATGAACGAAGTAGCTACTATGTACCTTAGTAGGCA Y 2 1 2 1 101000 r 74 goat snp53693-scaffold82-103736 2 48868443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394732 Affx-122964868 AX-123265087 2 86434485 AAGAACTTATCAAAGCTAGCCTCACTCTTCATGAG[A/G]CATCATACCATTAAGTGCTATAGGGGATGTAAAAG R 2 1 2 1 101000 f 74 goat snp53692-scaffold82-52770 2 48816564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437555 Affx-122931895 AX-123307893 2 86496223 TATTCTAAGAATTTAATGAGATAGGCTATGTAAAG[C/T]ATTTAGCATAGTGCATGGCTCAGATGAAGTGTTCA Y 2 1 2 1 101000 f 74 goat snp40299-scaffold515-8869 2 48753642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797161 Affx-122967104 AX-385284101 2 86534788 TGAACTCTAAATAGCTAATTGGGGCCCAAACACAT[C/T]ACCTAGCAAATGATAAAGTGACGACAGAACAACAA Y 2 1 2 1 101000 f 74 goat snp40300-scaffold515-47434 2 48714578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376777 Affx-122977960 AX-123247136 2 86643951 CCTATCATCACTCCTCCCTGGCATGTGTGTATACA[C/T]GCTCTTCTGAAAGTCTTTGCTTGAACCTGACCTCA Y 2 1 2 1 101000 r 74 goat snp40302-scaffold515-156597 2 48599600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789393 Affx-122974195 AX-385276403 2 86701489 GGCTTATAAACCCACACTGGATTGCTAGTTTCAGA[C/T]AGTGTCTCTGGGAGTCAGGCTTTTTGAATACACAT Y 2 1 2 1 101000 f 74 goat snp40303-scaffold515-214135 2 48542876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272956 Affx-1111833183 AX-519546642 2 86720368 TACCATCCGTCAATAGGACATAAGAGGGCATGGCA[A/G]CCCACTCCAGTATTCTTGCATGGAGAATCCCCATG R 2 1 2 1 102000 f 74 goat 2_86720368_AF-PAKI 2 86720368 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384255 Affx-122972354 AX-123254613 2 86743215 TAACTTTACCTGCCATATATTTGTATACTCCTTCA[C/T]TTCTTGCTTTCAGAATTTTAAAGATGCTATCTGGC Y 2 1 2 1 101000 f 74 goat snp40304-scaffold515-255861 2 48501026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783029 Affx-122948736 AX-385270097 2 86788978 CCTGCCTTTGTTTATGCCATTGCTTCTATCTGTAA[C/T]AATCTCTTCTACTCTGTAAAACCCTACCACCCATC Y 2 1 2 1 101000 f 74 goat snp40305-scaffold515-301624 2 48454182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448768 Affx-122923313 AX-123319104 2 86821973 TGAAGTCCTTCAGCCATCTCAGCCTCCATCATTCA[A/G]TATTGATTTCTTCATATCTACTTCTGGAAACAAAA R 2 1 2 1 201000 r 74 goat snp40306-scaffold515-334619 2 48420403 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401095 Affx-122959416 AX-123271448 2 86857555 AATCTGTTAGAACAAGTTCAGCAACATTACAGGTA[C/T]ATGAATGTACAAAAATCAATTGTATTTTTACATCT Y 2 1 2 1 103000 f 74 goat snp40307-scaffold515-370201 2 48384610 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779219 Affx-122951306 AX-385266323 2 86890641 GAGAATTTCTAAACTTTTCTGGTTCAAAGCAAAGA[C/T]TCATGGACAGAGATGAAAACTGTCTAAAAGAATGA Y 2 1 2 1 101000 r 74 goat snp40308-scaffold515-403287 2 48351477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274923 Affx-1111834578 AX-519548505 2 86906803 TAACATGCTTATAATGAACATCAAATCTTCCTTGC[A/G]CAGGAAAAAAGCTTGCTTTCCTAGCTGCCCTCAAT R 2 1 2 1 201000 f 74 goat GoatD01.042123 2 86906803 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429275 Affx-122937884 AX-123299617 2 86929525 AACTTTTATTATAAGAACTCAAAAACATATATCTG[C/T]GATTTGATTCAGTACCACAGCAAATGTATTGCTTT Y 2 1 2 1 101000 r 74 goat snp40309-scaffold515-442171 2 48313080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803016 Affx-122947898 AX-385289893 2 87018695 ATCTCGATCTACTATGGGGGTAGATCAGATTCTAA[G/T]CTGGTCCTACTCCTATCTGTTCTTGCCTCCAATGT K 2 1 2 1 303000 r 74 goat snp40311-scaffold515-531341 2 48223232 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801419 Affx-122959357 AX-385288328 2 87083089 TTTTCTATAACATTCACTCTGATCCCTTGGATGCA[C/T]GAAGTAGCAGCTACTAAAAATGAGAGATGATCCAA Y 2 1 2 1 101000 f 74 goat snp40312-scaffold515-595735 2 48158615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424645 Affx-122942167 AX-123294991 2 87120714 AAGAGGGTAGAAACCTACTTCCTTTTAAATGCTGT[G/T]TTTGCATTCTTAAAACAAGAAGCAGAGAAACTTTG K 2 1 2 1 101000 f 74 goat snp40313-scaffold515-633360 2 48121013 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770380 Affx-122959841 AX-385257545 2 87152712 TAGTCAAGAAATCTCTGACTTTGTATTATTGGAAA[C/T]AAAAGTTGTTAGCACAGACCCCCTTCTAAAAGACA Y 2 1 2 1 101000 r 74 goat snp40314-scaffold515-665358 2 48088038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783355 Affx-122970658 AX-385270419 2 87195086 TTACAGTTCAAGGTTAATTACTGTATACCTTGAAT[A/G]TAATAAGTAAAAATGATCTGCTGCTTTTTTTATTC R 2 1 2 1 101000 f 74 goat snp40315-scaffold515-707732 2 48045652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448072 Affx-122924338 AX-123318408 2 87228879 ATAAAAACAAGGAATGGTAATCACAAAATTCAAGA[G/T]CAGGGTTACATCTGGGGAAAGTCAATGGAAAAGAG K 2 1 2 1 201000 f 74 goat snp40316-scaffold515-741525 2 48011875 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427009 Affx-122939847 AX-123297354 2 87314015 CAGACATGACTGAAGTGACTTAGCACAGACACATG[C/T]AAATACTTCTCTCGATCCAAGGGCTACCAACATAA Y 2 1 2 1 101000 r 74 goat snp40317-scaffold515-826661 2 47926410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424398 Affx-122941821 AX-123294744 2 87343304 AAGCAATCAGTTTTTCCTTTTCATATATGCATATA[C/T]AAATAACTGGAACAAGCACAATAAAAATAAACAAT Y 2 1 2 1 103000 r 74 goat snp40318-scaffold515-855950 2 47897143 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787511 Affx-122975164 AX-385274536 2 87374883 CTCAAAATATAATTATCAATGGATTACCTATTATG[C/T]ATTCAGAATTATGCCAGAGGGTGAGAGGAAAGCAA Y 2 1 2 1 101000 r 74 goat snp40319-scaffold515-887529 2 47866299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800170 Affx-122943468 AX-385287093 2 87430542 GTCAGCCATGACTCTGATTTAAGGAGACATGCATT[A/G]CAGAGGTTTCCTTTTATTGTGGTTTATTTCTAGCA R 2 1 2 1 101000 f 74 goat snp40320-scaffold515-943188 2 47810857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420445 Affx-122944895 AX-123290792 2 87460411 TCTCATGGTGCTTTAGCTTACTATTTTAGGAGTCA[C/T]GTTCAATTTTCTTAAAATTGTTATTTTATGAAAGA Y 2 1 2 1 101000 f 74 goat snp40321-scaffold515-973057 2 47780742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783384 Affx-122945358 AX-385270448 2 87520254 TCAAACCTGAGAAGGGGTTGTGAGAACTCTGATGT[A/G]TCATCAATCAACCAGAAGTTCACCTGGACTTACAG R 2 1 2 1 101000 r 74 goat snp40322-scaffold515-1032900 2 47720658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784519 Affx-122921896 AX-385271568 2 87551902 TAACTAGTCTACCTGTGTCCCTGCCATGGTTTCAT[A/G]CAATGATGAATCCTTTTTCTAGATATCTGTATTAT R 2 1 2 1 101000 f 74 goat snp40323-scaffold515-1064548 2 47688513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443147 Affx-122928067 AX-123313484 2 87689572 TTACTGAACCTTACAGCAAAGCTCAATTAACTGAA[C/T]GAAACAGGGAGAGAAAAGCTCCAATCTGGTACCCG Y 2 1 2 1 201000 f 74 goat snp40326-scaffold515-1202218 2 47550145 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274185 Affx-1111834093 AX-519547786 2 87715701 CCCAGGTGGGGCATGTCTTCAGACGCTGGAAGAGG[A/G]TCGCTGGAGGCCCTCCAGGTGGCTGCAGCGATTCC R 2 1 2 1 202000 f 74 goat GoatD01.017843 2 87715701 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392532 Affx-122966106 AX-123262889 2 87731825 ATTTATCTTTGGTTCCAATTAGGTGAATTCATTGC[A/G]CTCTTGAAGGATCCAGGATAATCAAAATCACCAAG R 2 1 2 1 101000 f 74 goat snp40327-scaffold515-1244471 2 47507659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769174 Affx-122935139 AX-385256349 2 87861362 ATTCCTAGAGAATAGATGATGGAGAATAATAAGCT[A/G]TGTTGAGTTGGCAATTTTTGTACTTCTGTGTGTAC R 2 1 2 1 101000 r 74 goat snp40329-scaffold515-1374008 2 47376193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787248 Affx-122927062 AX-385274274 2 87911848 AGGTAGCCCAAATTAATCGCCGTTGTGCCTTTGCG[C/T]ACCCCTAAGACACCATTTGGAGACAAACGTCGAGT Y 2 1 2 1 101000 r 74 goat snp40330-scaffold515-1424494 2 47325778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382361 Affx-122973868 AX-123252719 2 87949534 AGAAGAGGAGGTGCCTACCCCAAGGAGGAAGGAGG[A/G]CTGTGAGGGATAGCAGGGACCCCAACTCAGAATTC R 2 1 2 1 101000 r 74 goat snp40331-scaffold515-1462180 2 47289117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410176 Affx-122952593 AX-123280526 2 87981570 TGCTTCAGTTGCTTACAGGTATCGGACACTAACAT[A/C]AAGATTTGGGACAAGCTTTTATGTGTTTTACCATC M 2 1 2 1 101000 f 74 goat snp40332-scaffold515-1494216 2 47256764 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428913 Affx-122938915 AX-123299255 2 88019313 ACTCTTCACACGAATGTCATAGCCTTCTCTGTACA[G/T]GGCTTGTTCCTCATCTAGGATGCAGACTATTGGAG K 2 1 2 1 101000 r 74 goat snp40333-scaffold515-1531959 2 47219005 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770881 Affx-122923991 AX-385258044 2 88075911 ATTCAAGAAGGAGTCTCTTAGAGGATGTTCAGCCC[A/G]TATGAACTCAGTCTCCAAAATGGAAACGTTGTAGA R 2 1 2 1 101000 r 74 goat snp40334-scaffold515-1588557 2 47162616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413650 Affx-122950535 AX-123283999 2 88105132 GCCCAGGTATGTGGTCAAATGTTATTCTGGATGCT[G/T]CTGTGAAATATTTTTGCAGCAGTGGACTTTGTATA K 2 1 2 1 101000 r 74 goat snp40335-scaffold515-1617778 2 47133149 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430694 Affx-122936916 AX-123301035 2 88136799 GGGCTTGAGAGTCATAAGGAACTCTGGCCTGCGTA[C/T]GTCTGAGTTTTGACAGCCAAGGAGCCGCTGAGAAA Y 2 1 2 1 201000 f 74 goat snp40336-scaffold515-1649445 2 47101160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776557 Affx-122944951 AX-385263684 2 88169278 TCTGAAAAGAGAGCTTGAAGAGCCAATTAAGAAGT[A/G]TGCGCTGCTCACCTAGAGTAACAAAGAGTTAGGGA R 2 1 2 1 101000 r 74 goat snp40337-scaffold515-1681924 2 47068691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798452 Affx-122930788 AX-385285385 2 88222598 TTTCTGTGCTCCGTGGAATTCCTCCCTGATTCTTA[C/T]GTAGATTACAACACTCCAGCTTTAGAAAACGCTGC Y 2 1 2 1 101000 f 74 goat snp40338-scaffold515-1735244 2 47014933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393828 Affx-122965166 AX-123264183 2 88286330 TTTTTATCAACCACAAACATGCATTTATGCCAAAG[A/G]GAAAAACTTGGCCTCTATTCAAAATAAGTATGCTG R 2 1 2 1 101000 r 74 goat snp40339-scaffold515-1798976 2 46951347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379852 Affx-122975803 AX-123250210 2 88329053 TGCACATTCAAAATGCTATTTAAATAAAAATTCCT[A/G]TATGAACGATTTCTCAGGGAAGGCCAAATATGCTT R 2 1 2 1 101000 r 74 goat snp40340-scaffold515-1841699 2 46908778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449959 Affx-122922892 AX-123320294 2 88377461 CCAGTGCCTACCTTAGCTCCTGGCAGGCAGGCATA[A/G]TGATACAGGTTTGAGTGAAAAAACAAAGTCATTTA R 2 1 2 1 101000 r 74 goat snp40341-scaffold515-1890107 2 46860385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392551 Affx-122966089 AX-123262908 2 88470401 AAAGCAATCTATCCAGTCTCAGTGCTCTAGTGTGA[C/T]AGGTCTGAAAGACAAATTTTCACAGTTCAGAAATC Y 2 1 2 1 101000 f 74 goat snp40343-scaffold515-1983047 2 46767949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797079 Affx-122939893 AX-385284019 2 88550183 GCTATATTCGTTGTAGTTTTTGCCTGGGCAAAACC[A/G]AAATGATCATCCAGTGAACCGTGAGTGTGCTAACT R 2 1 2 1 201000 r 74 goat snp40345-scaffold515-2062829 2 46688231 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796476 Affx-122958026 AX-385283426 2 88583586 AGACCTAGAGCCCAGGATTATAACAATAGAGGTAC[A/G]CAGGCCATTCCATGTCTTCTAGAATGACTAGGGTG R 2 1 2 1 101000 r 74 goat snp40346-scaffold515-2096232 2 46654836 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414122 Affx-122949713 AX-123284471 2 88617508 TTATTAATTCTGGGCAAACCTGCTAGTGCTTGTCA[C/T]GCATAGAAACTTACCTTTACTATTGCTTAACTGTA Y 2 1 2 1 101000 f 74 goat snp40347-scaffold515-2130154 2 46621273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381106 Affx-122974585 AX-123251464 2 88647204 GACTTTGCCTTCAAGGTGCACAGCAACCCCTTTAA[C/T]GAAAGGAATTTTATTTTACTCCTTCTCTCATCCAG Y 2 1 2 1 101000 f 74 goat snp40348-scaffold515-2159850 2 46591510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789610 Affx-122963092 AX-385276619 2 88683770 AAGGTATTCACACCAAAATGCTACAGGTGAGGGAA[A/G]TAAAATTCATCTCTCTATACACTGTTGACATGACT R 2 1 2 1 101000 f 74 goat snp40349-scaffold515-2196416 2 46554551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421208 Affx-122944142 AX-123291555 2 88716965 AATAGGTGTAGAGAACTGATGGAGAATTTCACTTT[A/C]ACACTTCCTATAACAAGTTACCAAGTGCTAAGAAT M 2 1 2 1 101000 r 74 goat snp40350-scaffold515-2229611 2 46521803 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379517 Affx-122976076 AX-123249875 2 88774320 GGGTCGATACAAGTTGCATACAGATTTCTCTCATC[A/G]GCCCATCTAACTCATGTGACCTTTTTTGTGTGTGT R 2 1 2 1 201000 r 74 goat snp40351-scaffold515-2286966 2 46463937 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438088 Affx-122931517 AX-123308426 2 88843534 AGGAACTGAAGGAACAGATTTACATTTCCCCAATA[A/G]CACACACTGGAACACTGTTCACTGAGGAAAAAAGT R 2 1 2 1 201000 r 74 goat snp40352-scaffold515-2356180 2 46394892 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452092 Affx-122920855 AX-123322425 2 88942310 TACTCTGTTTAATCTTTATAATAACACTATAAGAT[G/T]GATGGTAATCATTGCTGAGTAGAAGAAACAGGCCC K 2 1 2 1 101000 r 74 goat snp40353-scaffold515-2454956 2 46295556 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441944 Affx-122928577 AX-123312281 2 88975434 GCAAAGTTGATGAGAACTGGGACTTTCTGTGCTGT[A/C]GTGTGTGTCTCCGCAGAGCGACTGCTAGGACGGGA M 2 1 2 1 201000 r 74 goat snp40354-scaffold515-2488080 2 46262345 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436261 Affx-122932547 AX-123306600 2 89010456 GATCCAGAGGCCTATATCAGTATCTGCAAAATAGC[C/T]GAAAGATATTGTCTGTTGATGGGTACACAGGACTT Y 2 1 2 1 201000 r 74 goat snp40355-scaffold515-2523102 2 46227038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436903 Affx-122933212 AX-123307241 2 89055111 ATCTAAAGATGGGCTTTTAATTGATCTAGACAGAG[C/T]AACGGGCATTTTGGCTTTCCCTGCTCTGAGAACAA Y 2 1 2 1 201000 f 74 goat snp40356-scaffold515-2567757 2 46182401 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779973 Affx-122978915 AX-385267072 2 89120226 GAACCTCTTGAACTTGTAGTTGATGTCAGAAGTGA[C/T]GATGGTTTGTAGACTGTTCTCTAACTCTGTTGTGT Y 2 1 2 1 101000 f 74 goat snp40357-scaffold515-2632872 2 46115411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788566 Affx-122977630 AX-385275583 2 89158591 TTTTAAGGGAAATGATGTTAATATTAACTCGTTTT[A/G]TACTTCCAGTACATCTTTTCCTAAGCTATCGTTTA R 2 1 2 1 201000 f 74 goat snp40358-scaffold515-2671237 2 46076686 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415213 Affx-122948977 AX-123285562 2 89208794 GCATCCGACATCAGAGGAGTGAGCCACTGAACACC[A/G]AGAGCTCTGGTTCCAGATGTCAAGAGTCAATGTTT R 2 1 2 1 201000 r 74 goat snp40359-scaffold515-2721440 2 46025751 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407050 Affx-122954930 AX-123277401 2 89248860 ATTGTAAAAGTCAACAAGATACTCATGATCTTTAG[G/T]TCAATGGATAAATTCAAATACTCACTCATATAACG K 2 1 2 1 101000 r 74 goat snp40360-scaffold515-2761506 2 45985196 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271884 Affx-1111833184 AX-519545667 2 89279385 TAAATCTGGTCCCTAAGAAAAGTAACAATAATCAC[A/G]CTGTGGGAAAGTAAATAGTAATAACATAAAAGCTG R 2 1 2 1 101000 r 74 goat 2_89279385_AF-PAKI 2 89279385 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773277 Affx-122957171 AX-385260420 2 89285652 CACACCAGGAAATTCCCAAACCAATGACTTTGTTC[A/G]TGCTATGTCTTCTTTAACGTCCTCTCCCCATTCTA R 2 1 2 1 101000 f 74 goat snp40361-scaffold515-2798298 2 45947717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375756 Affx-122978603 AX-123246115 2 89360334 TGGGCTTTGGTCAGCTTCTTTAATCCATAGGTTTA[C/T]GTTTTCCACAAATGCTGGGGTGTTTTCAGCCAATA Y 2 1 2 1 101000 f 74 goat snp40363-scaffold515-2872980 2 45872586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447039 Affx-122924531 AX-123317375 2 89390361 AGTCCATGGGGCTGCAAAGAGTTGGACATGACTGC[A/G]CAACTGAACAACAACAACTACAGTGGCATCCCTAG R 2 1 2 1 303000 f 74 goat snp40364-scaffold515-2903007 2 45841987 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799411 Affx-122930372 AX-385286341 2 89426439 ATTAAACTTCCCACTCTTTTCCTTATAACGCCTTC[A/G]TTCCCAGTTTTCAGTAGAATCCACCTAAATAAAAT R 2 1 2 1 101000 r 74 goat snp40365-scaffold515-2939085 2 45805950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417549 Affx-122946920 AX-123287897 2 89462711 TGAAGAACCTGCTCCTCAATTCCTTCTGCCCTAGA[A/G]GTAAAGAAATACTCATCAGAAATGTCTTCATTGTG R 2 1 2 1 201000 r 74 goat snp40366-scaffold515-2975357 2 45759214 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424970 Affx-122941920 AX-123295316 2 89495458 AATGGGATGTTATTTCTTCCCTTATGAAATGGTTC[A/G]TTCTGTAGAAAATTAGTATTTGCTTAATAGATGCA R 2 1 2 1 201000 r 74 goat snp40367-scaffold515-3008104 2 45726362 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412760 Affx-122950515 AX-123283109 2 89541763 CTGTGCTGGCGCCGGTTGGTGGTCAGGGCCACAGC[A/G]ATATTGTCCCACGCTTTCCAAACTTCCCCTTGGCC R 2 1 2 1 101000 r 74 goat snp40368-scaffold515-3054409 2 45680250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409341 Affx-122954182 AX-123279692 2 89633305 TCTTTGCTATATATCTTTTCAGTTGTAATCGAGCA[G/T]ATGGTTCAGGTTGTAAGCAGTGTTATAATGAAGGT K 2 1 2 1 101000 r 74 goat snp40370-scaffold515-3145951 2 45588278 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394723 Affx-122964334 AX-123265078 2 89676227 TCTGACTATGTCTTTGTGTGTTTGCTGTGAACACA[G/T]CCTAAGCTGTGTGCATCGCATCCACTCGATTCAGT K 2 1 2 1 101000 r 74 goat snp40371-scaffold515-3188873 2 45544997 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406634 Affx-122955823 AX-123276986 2 89714710 ATGTACCTATCAAATCTGTAGAACACACAACTCTC[A/G]AAGAAGCAGCTGATGTTTAGCATTGGATCATGATT R 2 1 2 1 101000 f 74 goat snp40372-scaffold515-3227356 2 45506182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424462 Affx-122941774 AX-123294808 2 89751880 TGGTCTTAACACAAAGGACTTACTTTCTGATCTTA[C/T]GCTGAGGGAATTACAATAACCCTCTAGGTGATTGC Y 2 1 2 1 101000 r 74 goat snp40373-scaffold515-3264526 2 45468678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792224 Affx-122956567 AX-385279208 2 89848019 TAAACATTAGCTGTTAATAAACATAGTAACGATAC[A/G]ACTAATACCAGACACTGGAGTCTGTCAGTTGGCTT R 2 1 2 1 101000 r 74 goat snp40375-scaffold515-3360665 2 45372685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410207 Affx-122952571 AX-123280557 2 89880101 CCAAACCCCCCCATGGAAATGAGTGATTTGAGAAA[C/T]AATGACAGGTTCCCTAAGGAGTTTGGGGGTTGTTT Y 2 1 2 1 102000 r 74 goat snp40376-scaffold515-3392747 2 45340052 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435636 Affx-122933769 AX-123305976 2 89909698 AGATTCACACCAAGACTGTCTACCTCTCCATGCTT[C/T]GCACTTCACCCTGTTGTCTGTGGACTGTGGGGGGG Y 2 1 2 1 101000 f 74 goat snp40377-scaffold515-3422344 2 45310168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426668 Affx-122939923 AX-123297014 2 89986086 TGCTTAAACTTGACATTGACATCAAAGGGTATGTA[C/T]GTTATGCCCAGAAGATATGAAGAATGAGAAATAAG Y 2 1 2 1 201000 f 74 goat snp40379-scaffold515-3498732 2 45233753 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774929 Affx-122966728 AX-385262062 2 90026166 CATCCCCTGTTAGGAAGAAACACTATATTGTCCCA[A/G]TCCTTGGAGAAAGGCGAAAACTGACATAGCCATGG R 2 1 2 1 101000 r 74 goat snp40380-scaffold515-3538812 2 45193248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414274 Affx-122949605 AX-123284623 2 90054824 GTTCCCTGAACACGTCTATAAACTTCCTTCCATCT[C/T]CAGCCCTCTACTGTTCTCGTTTCCTTTACCTGTAA Y 2 1 2 1 101000 f 74 goat snp40381-scaffold515-3567470 2 45164557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797171 Affx-122950831 AX-385284111 2 90095157 GTTTCTTTTATTGGTGTATACCTTGGAAGCAGTCT[A/G]CTACCTCTTCTCCTAAATGTGTGGCATTTGCAAAA R 2 1 2 1 101000 f 74 goat snp40382-scaffold515-3607803 2 45124216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788487 Affx-122922364 AX-385275504 2 90130307 GAGACACTAAAGTCAGATTACACAGTTATACTGTG[C/T]AGTCCAAACACCTGAGGGCTGATTTTCTTCCCACC Y 2 1 2 1 101000 r 74 goat snp40383-scaffold515-3642953 2 45089031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390300 Affx-122967722 AX-123260657 2 90193016 GAGGATTAATGTGGTGTTGAGTATTTTTTCGTGTT[A/C]TTTTTGGCCATCAGCATTTCCTTCTTGGATACCTG M 2 1 2 1 101000 r 74 goat snp40385-scaffold515-3705662 2 45026087 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381561 Affx-122974822 AX-123251919 2 90238066 TTGGACACTTTTTGCTTAAATTGCTTGACAACACA[C/T]GGCCAGTTCTATGTAGTGATACTTTCTGCTGAAAG Y 2 1 2 1 201000 f 74 goat snp40386-scaffold515-3750712 2 44980690 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386972 Affx-122969966 AX-123257330 2 90287285 ATGAAATATAACAAATAATCATTAAGTAAATGGTG[G/T]TAAATTCCTAAGCTTTTTTCAGTAAAAAGGCAGAG K 2 1 2 1 101000 r 74 goat snp40387-scaffold515-3799931 2 44931357 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383250 Affx-122972746 AX-123253608 2 90388801 TGAGAAAAGAAAGGATAAAAAACAGTAAAAGCATT[A/G]CCGCTGAGATTTGCTCTAAGGTTCTATTTGGGCTG R 2 1 2 1 101000 r 74 goat snp40389-scaffold515-3901447 2 44829494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397112 Affx-122962692 AX-123267467 2 90437405 CAATTTAAATTTTTTTTAAATTTTGAATAAATTTA[C/T]TTCCATTGCGGTAAAAGAAACAGGTGGCTTGTATA Y 2 1 2 1 103000 r 74 goat snp40390-scaffold515-3950051 2 44780581 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438726 Affx-122930841 AX-123309063 2 90496716 CTAATCTGAAGCAGGTTCGGTTTTGGCAAATTGAG[C/T]AGGTTCTGAAGAACAATTCCAATAATTAATCACTA Y 2 1 2 1 101000 f 74 goat snp40392-scaffold515-4009362 2 44720288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391807 Affx-122967029 AX-123262164 2 90552515 GTCCCTAAAACTACTTATCTTGACATACTACTTTC[A/G]TTATCTTTTCTTACTGCCCAGTAAGCTCAGTGTTA R 2 1 2 1 201000 r 74 goat snp40393-scaffold515-4065161 2 44664609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412230 Affx-122950917 AX-123282580 2 90582403 TTGTACATTCTGAAATATTTCAGATAAGCAACACC[C/T]AGCTGTGCAGCTAAGTCAGAGCCATCATTTAAAAT Y 2 1 2 1 201000 r 74 goat snp40394-scaffold515-4095049 2 44634668 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405997 Affx-122955513 AX-123276349 2 90668969 CTGATATAGCCTCTTGTCAGAATGTTTTCACATGC[C/T]TGAAAGAAAATACACACCGTCACAAAGGAAACTAT Y 2 1 2 1 101000 f 74 goat snp40396-scaffold515-4181615 2 44549056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800419 Affx-122926358 AX-385287340 2 90712130 GCTACTTGTTTAATTTCACTCTCTCAGGCTAAAAG[C/T]GGATTTCCCTGAGGTTGTGCATGTTAAAAAATTGG Y 2 1 2 1 101000 r 74 goat snp40397-scaffold515-4224776 2 44505892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445442 Affx-122925355 AX-123315779 2 90820636 TGGATGCCTCATCGCCCATCCCTTGTGGAAACTCC[A/G]GAGAGTAATTTGTGTCAGCGCCTTGAGATGATCCT R 2 1 2 1 101000 r 74 goat snp40400-scaffold515-4333282 2 44396985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773587 Affx-122940468 AX-385260727 2 90856509 CCAGGGATTAGGACGTGATCATGTGTGAAAGGGCC[A/G]CTATTCAGCCTACCGCAGTATTTGAACATAGCTTC R 2 1 2 1 101000 f 74 goat snp40401-scaffold515-4369155 2 44360725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418320 Affx-122946971 AX-123288668 2 90899457 GTGAAATGTTACCCCCCTCTTCATTCTCCAGAGAC[A/G]TATTGATATTTCTAGCAGGAAAATTTGAAATTGAA R 2 1 2 1 201000 r 74 goat snp40402-scaffold515-4412103 2 44318131 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383671 Affx-122972506 AX-123254029 2 91011936 GCTCTTAAAGAGATTGGGTTTTTATAGTTCACTTG[C/T]ATTAATACTATTTCTAAGGTTTTTATTTAGTGTTG Y 2 1 2 1 101000 f 74 goat snp40404-scaffold515-4524582 2 44205582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781274 Affx-122933826 AX-385268359 2 91047329 CACAGACTCTGGGACATATAAAATCTCATGACTGC[A/G]CTTGGTTCTGAAGTAGTTGAATGTGAGCATTCGTA R 2 1 2 1 101000 r 74 goat snp46058-scaffold631-3250221 2 44168275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427084 Affx-122939794 AX-123297427 2 91077507 AGCAGGAAAAGAGTCAAATTAGCTAATTACAACTA[A/C]TCAGTAACAATGTAACTTGTACCCTTTCATGTCTT M 2 1 2 1 101000 f 74 goat snp46057-scaffold631-3220043 2 44137739 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424350 Affx-122941932 AX-123294696 2 91109753 GGAATCTTCCATGCTTTCCTGTTCCCTTAAGAGGA[C/T]GCTATATTTTCCTGCTGACCATTCATGAGTCCTCC Y 2 1 2 1 101000 r 74 goat snp46056-scaffold631-3187797 2 44105437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378302 Affx-122976853 AX-123248661 2 91139544 TCTTCCCAAGTCACCTTTCCCACTCACCTCAAGAT[A/G]TTCTATAATAAAGAACTTTTCTCATCCAAATACCC R 2 1 2 1 201000 r 74 goat snp46055-scaffold631-3158006 2 44075243 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431898 Affx-122936007 AX-123302239 2 91168562 CGTGGTTTATGATTGAGGTCTTACCTCCCCGTACA[C/T]GGAAACAGAGATCCCCTGGAGAAGGAAATGGTAAT Y 2 1 2 1 101000 f 74 goat snp46054-scaffold631-3128988 2 44046373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451532 Affx-122921095 AX-123321865 2 91238976 TTGCTCATACTCAGAGATGGCTGATGATCGGAGCC[C/T]GGGTGACCAGAAGGATAGTGTTTCATCCACAGGTA Y 2 1 2 1 101000 r 74 goat snp46052-scaffold631-3058574 2 43975116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382460 Affx-122974216 AX-123252818 2 91288695 TGATTTTCTAATTAGTTACGTGCATGTAAGAGACA[C/T]GGATGAGAGAGCATCCAGTTTTCCATACACGATGA Y 2 1 2 1 101000 f 74 goat snp46051-scaffold631-3008855 2 43923808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275306 Affx-1111834826 AX-519548882 2 91345014 AGCACACATCTAGATACAACCTAACCACTGAGCAC[A/G]TGCCATTGCAGACCATGGAACCCTGGACACAGGAT R 2 1 2 1 201000 f 74 goat GoatD01.055199 2 91345014 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320772623 Affx-122923694 AX-385259771 2 91346507 GAGAAAACAACAGGAAAGATGTCATGAGCGATACT[G/T]ATGCAGCCAGGTATTGATATACCCATACATGGTAC K 2 1 2 1 101000 f 74 goat snp46050-scaffold631-2951043 2 43865712 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779924 Affx-122972838 AX-385267023 2 91397801 CTTCTGAATCCGAGAACACAATGGTGATTCACTGT[A/G]CGCAGTCTAAGTCCTCAGATGACATCTTCCACTCC R 2 1 2 1 101000 r 74 goat snp46049-scaffold631-2899749 2 43814628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278008 Affx-1111836128 AX-519551500 2 91458020 TTAAAGGGCTGTCGAATCAGTATGAAAGGGGACAC[A/G]TTGGAGAGATAGTAGGTTGTGATCTGAGAATGAGA R 2 1 2 1 201000 r 74 goat Random2.2K-237 2 91458020 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398490 Affx-122961570 AX-123268845 2 91497700 GAAAGTATTCACAATTGTGATTCTCAGATGAAGTC[A/G]TTTGTAGATTTCTTCCATTAAGTGGCAGGATGAAC R 2 1 2 1 101000 f 74 goat snp46047-scaffold631-2799850 2 43714325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792728 Affx-122958414 AX-385279708 2 91527465 GATTGTATTCTGAGACAGAAATGTAAAGGAACCAC[C/T]GTTAGTACATGTCTTTCTACCCAGTTCCATCTGAT Y 2 1 2 1 101000 f 74 goat snp46046-scaffold631-2770085 2 43684204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431097 Affx-122936613 AX-123301438 2 91647172 AGAACCACTACAGAATAATTATACATTGAAGTTTT[A/G]ATAAAGTTTACCAGAGCACACACAGGTTTTCACAA R 2 1 2 1 101000 r 74 goat snp46044-scaffold631-2650378 2 43563981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772312 Affx-122937292 AX-385259466 2 91686390 ATTTTTATATATAGTTTTACAAGGAGAAAATAATT[A/C]TGATAGAAGTACCAAAAATGAGGTTCAAAATAATA M 2 1 2 1 201000 f 74 goat snp46043-scaffold631-2611160 2 43524628 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419178 Affx-122945723 AX-123289526 2 91774725 TCTGCTGAGAGTTAGGAGATATGGATTTTTGTCCA[G/T]CGGATGTGCGTAAGCAGTGGAATGACTTCAATTCA K 2 1 2 1 101000 f 74 goat snp46041-scaffold631-2522825 2 43435892 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272050 Affx-1111833185 AX-519545814 2 91794233 CTTACATGTGGCATGTTAGATGTTTCTAACACTGC[A/G]TAAGTTATTTGCTTATAAGTCTTCCCCATGAGATT R 2 1 2 1 101000 f 74 goat 2_91794233_AF-PAKI 2 91794233 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424407 Affx-122941814 AX-123294753 2 91804109 GTCCGTTCTGAACCCAGACTCCAGAATGGATTGGT[A/G]CTCACAGGCCTTTCAAGACTCCTGCCTGGAATTTC R 2 1 2 1 201000 f 74 goat snp46040-scaffold631-2493441 2 43406152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277865 Affx-1111836129 AX-519551361 2 91810949 ACTACTGGGCCTCAGTGTTATAATCCATAAAAGAC[A/G]AGGTTAATTGATCTGTGCAAGTTAACAACTCAACT R 2 1 2 1 101000 f 74 goat Random2.2K-238 2 91810949 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452198 Affx-122920819 AX-123322531 2 91847573 GCATGTTGTAACGTGAGCCATTTTCCAGATCCTGC[A/C]CTGGGGTCTCTTGGGCGATTTTCCCTAGCTGCCTT M 2 1 2 1 101000 f 74 goat snp46039-scaffold631-2449977 2 43362855 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277867 Affx-1111836130 AX-519551363 2 91872886 ATACTCTATCCTTACCACATCCAATATGTAACCCT[A/G]TTAGTATATTAATTAAAAAAAAAACTCTTATTCTT R 2 1 2 1 101000 f 74 goat Random2.2K-239 2 91872886 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403619 Affx-122957548 AX-123273971 2 91909920 GGGAGGGGTGCAGGAGAGCTGTCTCTGTGTACTGT[A/G]TTAGTGGCTGAATTGATATAGGAATAAAATAGAAT R 2 1 2 1 201000 r 74 goat snp46038-scaffold631-2387630 2 43300143 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792989 Affx-122965244 AX-385279967 2 91947048 TCTTCGGCTTTTCTTGTTTAGGTAAATCACTCTCA[A/C]CTGTGATCTTATGTTTGCTTGATGGCTGTGGAGGT M 2 1 2 1 101000 r 74 goat snp46037-scaffold631-2350502 2 43263135 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423046 Affx-122942965 AX-123293392 2 91996682 TTGCAAGCAACCAACTTTCCTTCTATCTCTGACTT[G/T]TCACACCATGTGAATTCAGAACACAGCTCTTGTTT K 2 1 2 1 101000 f 74 goat snp46036-scaffold631-2300868 2 43213335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416452 Affx-122947821 AX-123286801 2 92034027 AAGAATAGAAACATGTGACTACCATCACCAGGCCC[A/G]TTCCCTAAGCCCAGGAGATAACCTGGATTCCTATT R 2 1 2 1 101000 r 74 goat snp46035-scaffold631-2263523 2 43175543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798194 Affx-122960223 AX-385285130 2 92064323 AACAAAGTGGGTACTGATCTGAAAAGAGAGAACTT[A/G]GTAAATTATTGACAGCCATTTGCAAAACTCATTCA R 2 1 2 1 101000 f 74 goat snp46034-scaffold631-2233227 2 43145422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447368 Affx-122924863 AX-123317704 2 92161766 GAAGAAAAGTATGGGCCAGAAAGCCCTCTCTGAAG[A/G]CCACTCTGCTCTGATTTCAGAAATACTCCGCTAGT R 2 1 2 1 201000 r 74 goat snp46032-scaffold631-2135784 2 43048552 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416148 Affx-122948280 AX-123286497 2 92190954 CATCCTAAACAGATTTTTGCTGTTCAGCTTCCCCA[A/G]TCCTGACCCTGAGACCTGGTTCCCGAAGGCTCCCT R 2 1 2 1 101000 f 74 goat snp46031-scaffold631-2106596 2 43019352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408309 Affx-122953771 AX-123278660 2 92253405 TGACCATTTCTTTCCAACTCCCAGTGAAACCTTTG[C/T]ATCACAGATGTGCACAAGCATGCTCAGGGCAAGTA Y 2 1 2 1 101000 f 74 goat snp46030-scaffold631-2044145 2 42956774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441337 Affx-122929427 AX-123311674 2 92339955 TATCTCAAAGACAAAGGGAAAGTCACAGCTGTGAC[A/G]TACTAGAGAACCCAGAAGATTCTTAGATAATTAGG R 2 1 2 1 101000 r 74 goat snp46028-scaffold631-1957595 2 42869977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384136 Affx-122972812 AX-123254494 2 92374806 ACTCCTAATTTCACTATTAAATATGGCAAAGTTCA[C/T]GTAAAAGTTTTAAATCACAAAGCATCTAAGGAAAT Y 2 1 2 1 101000 f 74 goat snp46027-scaffold631-1922744 2 42834912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414294 Affx-122949592 AX-123284643 2 92411522 CTTTAGCGATAACTTATGAGTGAGTTATTCTTTTA[A/G]CATTTTAAAGATGGGTGGGGAGAAAGAAAATTATT R 2 1 2 1 201000 f 74 goat snp46026-scaffold631-1886028 2 42797612 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770403 Affx-122978381 AX-385257569 2 92450284 GTCATCTTTTAAATAGTTATCCAATGAATTTAATG[C/T]ATGTCTAATGTACACAAATTTTGGCCAAAGCTTAC Y 2 1 2 1 101000 r 74 goat snp46025-scaffold631-1847266 2 42758737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400584 Affx-122960405 AX-123270939 2 92487592 AGTGAGGATTGATACTGTTGAATAACTGTTTTTCA[C/T]AAAGATTTTTAAAAGATATTTAAGAGGGAGTTGAA Y 2 1 2 1 102000 f 74 goat snp46024-scaffold631-1809958 2 42721435 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785861 Affx-122964053 AX-385272898 2 92535778 TACATATTAACAATTCTATACCTGTTTGCCTAGTG[A/G]GACCACAGATAAGAGATTTTGTTTCCCAAAGTGAC R 2 1 2 1 101000 r 74 goat snp46023-scaffold631-1761772 2 42673305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423753 Affx-122942850 AX-123294099 2 92566857 ATACTGACAATTGAGTGTATGAAGGAAAACTGCAA[C/T]CCTAACTTACACCATTTGTAAAACGTATTTATACC Y 2 1 2 1 101000 f 74 goat snp46022-scaffold631-1730693 2 42642387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421499 Affx-122943905 AX-123291846 2 92643867 GGTTATTCTGTTCAACACAATCAGATCTAAGATTA[A/G]TTCCTCAGCCAAACAGGAACAGAAGAATGTGCACA R 2 1 2 1 101000 f 74 goat snp46020-scaffold631-1653683 2 42561298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782242 Affx-122943027 AX-385269320 2 92688735 ACACTGTATAACAAATGTCACCTGAAATCCTCATG[A/C]AGCTAACATGGCTCCCATCATACAAAGTTGGAAGA M 2 1 2 1 101000 f 74 goat snp46019-scaffold631-1608815 2 42515808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439581 Affx-122930074 AX-123309918 2 92772610 TAGCTACATTCCGAGTCTCAAGCATACATAGCTAC[A/G]TTAAAGTAGACCGTGTTTGCTGTATGCAAGTCCAA R 2 1 2 1 101000 r 74 goat snp46017-scaffold631-1524940 2 42431441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418989 Affx-122946062 AX-123289337 2 92840450 AGGACTCATCGGCCTTCTTCAGCACTGCATCATCT[C/T]AAAGAGCTGGGTCAGCAAGGATCTCTGCAGACAGT Y 2 1 2 1 201000 f 74 goat snp46015-scaffold631-1457100 2 42362687 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433286 Affx-122935211 AX-123303627 2 92902449 AACATAAAGTAACTACTTCAATGCCTAGTATATAG[C/T]AAAGCTCAGGAAACAGCTCTATCATTTCTTATTAT Y 2 1 2 1 201000 f 74 goat snp46014-scaffold631-1395101 2 42301458 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406514 Affx-122955141 AX-123276866 2 92931549 ACTGGGATTATACTTTTTTTTTTCAATTTTCCTCC[A/G]TAAAATAATATCCTTTCTCTTTTCTTATGATTGAA R 2 1 2 1 201000 r 74 goat snp46013-scaffold631-1366001 2 42272358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393873 Affx-122965133 AX-123264228 2 92971317 ACCTCTTTTGATAACCATTCCAGGCTTTAAGAGTC[A/G]TATTGTCAGAAAATTCTCTCTTTTATCTAGCTTAA R 2 1 2 1 101000 f 74 goat snp46012-scaffold631-1326233 2 42232375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796782 Affx-122968768 AX-385283725 2 93003720 AATTTATGTAGGTATCAGTGACCACTCTTCTTTCT[C/T]TTGGCACAGACTATATGAAAACAATTCTGAGCAAT Y 2 1 2 1 101000 f 74 goat snp46011-scaffold631-1293830 2 42200002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409792 Affx-122952973 AX-123280143 2 93058861 TGTCTGCCATCAAACTGGCAGAGCTATTTCCTCCA[A/G]ATACAGATCTATCAGCTCATTCTCCAGTTATGGCA R 2 1 2 1 201000 r 74 goat snp46010-scaffold631-1238689 2 42144369 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391086 Affx-122966830 AX-123261443 2 93136268 CCTGATATAGAATGCACCACCAGGGATAAGGTGAC[A/G]CAGCCGGGGCAATGGAGGAAGGCCTCACAAGAGTT R 2 1 2 1 101000 f 74 goat snp46009-scaffold631-1161282 2 42066373 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431068 Affx-122936635 AX-123301409 2 93196856 TCAGAGATGCTGCGCCTTATACTTGAGAAAAGATC[G/T]AAATTTATTACGTTTAATGTTTAATATAAATCACC K 2 1 2 1 202000 r 74 goat snp46008-scaffold631-1100694 2 42003466 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782731 Affx-122932887 AX-385269803 2 93276246 TATGTTTGGAAACACCTGCAGGTACAATTCGTGAC[C/T]AGATGGTAAATGAGCTTGTTCTTAGTTGATCATGA Y 2 1 2 1 101000 f 74 goat snp46006-scaffold631-1021304 2 41924277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379835 Affx-122975816 AX-123250193 2 93350711 CAGACCTTCTGGAAAATCCCTCCTTGTTATTTCCA[C/T]ACCAAGATAAGCACCGCTGGACGGTCACTCAGCTG Y 2 1 2 1 201000 f 74 goat snp46004-scaffold631-946839 2 41849106 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385588 Affx-122971211 AX-123255946 2 93397645 GCAAGAGAACTGACGTGAGTTGAGCACCTCGAGGT[A/G]CCAGACATCACGCTGGGGGCTTCATCGCCTTCCGT R 2 1 2 1 103000 r 74 goat snp46003-scaffold631-899905 2 41802155 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428725 Affx-122938455 AX-123299067 2 93432452 GAAGGCCAGTTGTGCAGCTTTGCCCATAAAAGGAA[C/T]GTTAGACCAGGCTTTGCAGGGGGAGTCTGCATTCA Y 2 1 2 1 101000 f 74 goat snp46002-scaffold631-865098 2 41767343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781328 Affx-122919965 AX-385268413 2 93501373 TCCAGGTGTTCTGGATCTCCAGGTGTACGAGTTAC[A/G]TCTTCTGGTTACAAATGACAGAAACCAACTCTGAG R 2 1 2 1 101000 r 74 goat snp46000-scaffold631-796177 2 41698550 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436958 Affx-122933170 AX-123307296 2 93600894 TTGGTTACCAGTCAGGCTCATCCAACCAAGCAATG[C/T]AAGAGCCTGTAAGCCTTAGAGAAGATTCTCCACAA Y 2 1 2 1 201000 r 74 goat snp45998-scaffold631-696656 2 41598002 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386026 Affx-122971489 AX-123256384 2 93641723 TTTTTTACTGAGGTAAAAGTGGTACATACACATTG[A/G]CTTTCTTATCAGCCCTTCTTTGACAGTGAAGGGAA R 2 1 2 1 101000 f 74 goat snp45997-scaffold631-655827 2 41557749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401620 Affx-122959602 AX-123271973 2 93686489 TACTCCTTTTCCACACAGCTGCTGTTTTCTGATGA[C/T]AGGAGGGCAGTTGCAGCTAGCTGTTTCCTTCCAGT Y 2 1 2 1 101000 f 74 goat snp45996-scaffold631-611061 2 41513049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413561 Affx-122950595 AX-123283910 2 93719529 CTACTTTTACCAAGGATTTGGACAAATGTGCAAAA[C/T]ATACTGCAGTTTTTTAAAAAGTGACTTATGGGGCT Y 2 1 2 1 101000 f 74 goat snp45995-scaffold631-578021 2 41479909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441880 Affx-122928627 AX-123312217 2 93774178 TTAACATTTTGGTCAAGCTACTTGGTACTCAAGCT[A/C]TCTGGTGCTCAAGTGACTGTGAATTATTTTTGGCT M 2 1 2 1 101000 r 74 goat snp45994-scaffold631-523372 2 41425178 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776888 Affx-122953942 AX-385264012 2 93822320 GAAATATAATTTGTATGTGAAATTAGATCATTAGA[C/T]CTAGTAGAAAGTGCTTATAGATATGACATCCTTAA Y 2 1 2 1 101000 f 74 goat snp45993-scaffold631-475230 2 41377173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437604 Affx-122931857 AX-123307942 2 93899772 ATATTGACATCACATGACTTTTGTTCTAATACACT[A/G]AGAAGTCCACAGATTTTCTGCCCCACCCCACCGCC R 2 1 2 1 201000 f 74 goat snp45991-scaffold631-397778 2 41298683 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439743 Affx-122930534 AX-123310080 2 93950220 TAGAGCATCTCTGTCCAGGAAGAGCTCTCTTTGAT[C/T]ACCCCAACTCCATAGGAAACTTGTTTTCCTAAAAA Y 2 1 2 1 101000 f 74 goat snp45990-scaffold631-347330 2 41247854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399180 Affx-122960628 AX-123269535 2 94026224 TACCATGTTTCAACCTGAAGCTCCAGTTTCCTTGC[A/G]TTTATATTTTAGAATGTGTTGAGGGGCAACGGGGA R 2 1 2 1 102000 f 74 goat snp45988-scaffold631-271326 2 41173494 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428360 Affx-122938976 AX-123298703 2 94055097 ATTGTTTGGGACTAGATTTCTGCAAAAAATAGGAG[C/T]AGTGAAAGTAAAGCAAAAATGTAAAAGGCAAGTAG Y 2 1 2 1 101000 f 74 goat snp45987-scaffold631-242453 2 41146618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404658 Affx-122957299 AX-123275010 2 94098226 CACTGTTAGGTGGGCAATTATAAATCCTAAGAAAT[A/G]TCATGACCCTTGGGCAGTAGTTAGTTCAGGCTACC R 2 1 2 1 101000 f 74 goat snp45986-scaffold631-199324 2 41103320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378339 Affx-122976840 AX-123248698 2 94188695 TAAGCTTAGCACTCGAAGCACCACCAAAAGGAAGT[A/C]GCTTCAGGCAGGCTTCCTTTGACCCCCTGTGGCTT M 2 1 2 1 101000 f 74 goat snp45984-scaffold631-108855 2 41013140 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447918 Affx-122923798 AX-123318254 2 94243087 CATGATACCTGTTCTCTGGATATACCACGATACAT[A/G]CAATATGTGCTAACCTTTAATGCTTCTCAGTTGCA R 2 1 2 1 101000 r 74 goat snp45983-scaffold631-54463 2 40958782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766084 Affx-122935350 AX-385253500 2 94278541 AAGGTATATTAATAATTCTTTTCTGACTATAAAAG[C/T]AACATGTGCTCTTCACCAAAAATTTAGGTAATATT Y 2 1 2 1 202000 f 74 goat snp45982-scaffold631-19009 2 40923045 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432468 Affx-122935607 AX-123302809 2 94308188 TTTCTCCATGTTATTAAAACTGTCCGATAAAGGCA[C/T]GAGGGAAGAATATTCAGTCGGAATTTTAGAATATG Y 2 1 2 1 101000 r 74 goat snp30957-scaffold341-3069205 2 40893203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443056 Affx-122928138 AX-123313393 2 94354968 TGGCCTGGATAATTCGCTGTTGCAGTGCTGACTCG[C/T]GCACAGTAGGGCACTGGCAGCATCCCCAGCCTCCA Y 2 1 2 1 101000 f 74 goat snp30956-scaffold341-3022425 2 40846902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384954 Affx-122971915 AX-123255312 2 94387324 CCTAAACCATCCCAAGCTGATGAGACCTCCAGAGA[C/T]GTAGCTGCACCATCTCCTTGGTCACAGTGTTCCAG Y 2 1 2 1 101000 f 74 goat snp30955-scaffold341-2990069 2 40814521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450315 Affx-122922140 AX-123320650 2 94474101 GAGCTTTCTCAGGGGCTCATGGGTGGCAGGGCTAG[A/C]GAACTCTTAGTGTGGAATGTCTGCAAGAAAGACAT M 2 1 2 1 101000 r 74 goat snp30953-scaffold341-2903292 2 40728614 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397105 Affx-122962697 AX-123267460 2 94513392 AAAACCCAGGGCTCCTCCCTATAGCCGCTGTGTCC[A/G]TAACGGTGGGAGCCCCAGCTGGAGCTTGGTAATAA R 2 1 2 1 303000 f 74 goat snp30952-scaffold341-2864001 2 40689314 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464154871 Affx-1110343241 AX-515630492 2 94536131 GACTTTTTACAACCTGTGAATTGTTTACAGACCCC[C/T]CAACCAGGAGAGGCACAAAGCTTAAAGCATCTTAA Y 2 1 2 1 303000 f 74 goat 2_94536131_AF-PAKI 2 94536131 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797314 Affx-122978914 AX-385284253 2 94594383 TAGTTTAGATGCTTTGTTCTGCCTTGTGATTTATG[C/T]ATTTAAACTTCCATTTAAGAAGTTATTCTTCTTTT Y 2 1 2 1 201000 f 74 goat snp30951-scaffold341-2783010 2 40607741 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770901 Affx-122928082 AX-385258064 2 94672352 TTTACTTCCCTCTTCTATTTATTCTACCTGCCAAA[G/T]AATTAACCAAATAAATCATTAGAACTGGCAGGGCC K 2 1 2 1 101000 r 74 goat snp30949-scaffold341-2705041 2 40529671 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377304 Affx-122977692 AX-123247663 2 94738446 GTGATGTTGGGGTCCAATCCATTTAAAGGGCAGAG[C/T]AGAAGATGCACTGTGACACCTCACCCTGAAATGAT Y 2 1 2 1 101000 r 74 goat snp30948-scaffold341-2638947 2 40463650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272261 Affx-1111833646 AX-519546000 2 94760522 TCCATCAACTTCTAAACAATCATTATATGAATGCT[A/G]TTTCTGCAGATATTATCTTCTCAACTTTTCCACTA R 2 1 2 1 201000 r 74 goat GoatD01.000345 2 94760522 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320790956 Affx-122928519 AX-385277953 2 94767347 TGGCAGCGAAGGAAACACCTAAGCTAGAGTTAAAA[C/T]GCAGAGAGCCTGCATGTTAGATTGATTCATGCAGT Y 2 1 2 1 101000 r 74 goat snp30947-scaffold341-2610046 2 40435000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419020 Affx-122946042 AX-123289368 2 94802243 GTAAGAAAGCATTGTGTTGCAATGTATTGGCATCA[A/C]TTTTTTGTCTTAGCGGCACATAAAATAATGGTATA M 2 1 2 1 101000 r 74 goat snp30946-scaffold341-2575150 2 40400640 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780553 Affx-122937601 AX-385267644 2 94838399 CAATGTTTAGTTCTGAGTCAATTAAAGAAGATACT[A/C]TTTTTGACCTAATCTTTGTGATAGCTGGAGAAATT M 2 1 2 1 101000 f 74 goat snp30945-scaffold341-2538994 2 40364170 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415702 Affx-122948529 AX-123286051 2 94888037 TCTGGCTAAGGTTAGCTTTTTAGTTGTTACTGCAC[A/G]TCTCCCGTGTTCACCTGGAGAGCTCTACCTCGAGA R 2 1 2 1 201000 f 74 goat snp30944-scaffold341-2489356 2 40313878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780813 Affx-122958658 AX-385267902 2 94916727 TCTGAACTAATATCAGCATCAAATAGCATCTGTTC[A/G]CTGTGAGGAGAGAAAATGCACTTTAATTGTAGCAG R 2 1 2 1 101000 r 74 goat snp30943-scaffold341-2460666 2 40285259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435275 Affx-122934049 AX-123305615 2 94973370 CCCCCAGTGTGATGGTATTAGGATGTGGGGCTTTT[A/G]ACAGGCAATTAGGTCTTGGGTGTGGAGCTTTCAGG R 2 1 2 1 101000 r 74 goat snp30942-scaffold341-2404023 2 40228827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452542 Affx-122920534 AX-123322875 2 95011960 GAGAGGCGTCTCTGCTGAATAAAACAGTGGTAACT[A/G]CTTGGATTGACTGGTTGCTACTCACATGAGCTAAA R 2 1 2 1 101000 f 74 goat snp30941-scaffold341-2365433 2 40190142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433816 Affx-122935169 AX-123304157 2 95046104 CTGAGGGTAAGCCACTGACTCCAAGTCTGAGAGAA[C/T]GTAAGTGGCAAAACTGAAGGTATAATTTAGTTCTA Y 2 1 2 1 201000 r 74 goat snp30940-scaffold341-2331289 2 40156073 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783993 Affx-122949978 AX-385271047 2 95137116 TCCATTTCTCAAGATCCATTCTTGCTCATGACTCT[A/C]TTTGGAGAGCTTTTAAACTCTCTGGGAAGCAGAAG M 2 1 2 1 101000 r 74 goat snp30938-scaffold341-2240277 2 40064762 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787559 Affx-122967349 AX-385274583 2 95178937 CAAACCACCTCCAAATATGAAGAAAACTATACTTA[A/G]TAAGTTTCCACTTTTCAGTATCTATCCTGGAGATA R 2 1 2 1 101000 f 74 goat snp30937-scaffold341-2198456 2 40022638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801212 Affx-122944727 AX-385288125 2 95225640 AAACAGATTAAGTATGTACAACTAAACATACTTGA[G/T]AGCTCTGTACAGCTAAACTCTAGTTTATATCATAT K 2 1 2 1 201000 r 74 goat snp30936-scaffold341-2151753 2 39975657 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385890 Affx-122971591 AX-123256248 2 95273606 TTTTTGTTCAAACCACTGTTGGCTCTCAGCTGAGC[A/G]CTGCACCAGCCTCCTAGTTGGTCTCCCTGCTTCAT R 2 1 2 1 101000 f 74 goat snp30935-scaffold341-2103787 2 39927821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453116 Affx-122920019 AX-123323449 2 95333768 ACAACAAGCACTTTCTACTTCAGCTCCAGCATCTG[C/T]AGTTTATGTGAAGTTTCATTAGGCAGACTTGCTGA Y 2 1 2 1 201000 r 74 goat snp30934-scaffold341-2043625 2 39867478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446684 Affx-122924750 AX-123317020 2 95371343 CAGATAGATGTCATTTTCCCTCATTTCTGTTCATG[A/C]TGTACAGAACTGTCTAAAACTTGGGGCTTGGGCTA M 2 1 2 1 101000 f 74 goat snp30933-scaffold341-2006050 2 39829778 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452819 Affx-122920745 AX-123323152 2 95420864 CTAACTCTTAGTGGGTCATTCCCATGCATGATCAG[A/G]TAACATTGCTTCAATTTCTCCTCTATTTCTCTACT R 2 1 2 1 101000 f 74 goat snp30932-scaffold341-1956529 2 39779968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464155209 Affx-1110343409 AX-515630829 2 95465983 TGAGGGAGTCCCTATGACTGGGTCTCCCTAAGACT[C/T]GTCTACCTGGAGGTTTTTATAAAGTTGTCCACCCT Y 2 1 2 1 101000 f 74 goat Random2.2K-242 2 95465983 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449766 Affx-122922444 AX-123320101 2 95470222 AGAGAAAAAGAAAGGTAAAAATTGAATAAACATGA[C/T]AAAAAGGGGATTTATAAGTATATATTAAAAAATCT Y 2 1 2 1 101000 f 74 goat snp30931-scaffold341-1907171 2 39733627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437104 Affx-122932177 AX-123307442 2 95507495 AGTGTGGTTGTGGCTATACAAGCACATCAAAAAGC[A/G]CAATAGTTTAAGGAGGCATGTGCTGTATGCAAATG R 2 1 2 1 101000 f 74 goat snp30930-scaffold341-1869898 2 39696384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403726 Affx-122958025 AX-123274078 2 95560745 TCCAGTCACAGAATTCCTAGTCTCTTTTGCTTACT[A/C]TTTTAGGTCAGTATCAACAGAGATTTGCCAGGGCA M 2 1 2 1 101000 r 74 goat snp30929-scaffold341-1816648 2 39643309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385619 Affx-122971187 AX-123255977 2 95606054 TTCCCTAGAAACTTCATCAGTCAGATTTTTGCTTA[C/T]ATCTCATTGGCCAGAACTTGTTATCTTAACTGCAA Y 2 1 2 1 101000 f 74 goat snp30928-scaffold341-1771339 2 39597309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386073 Affx-122971455 AX-123256431 2 95635448 ATCCATCCACCCTCAAGCAGGAAATGGGATACACA[C/T]ACATACACATTCACACAAAAAAGAAGCATATAGGT Y 2 1 2 1 101000 f 74 goat snp30927-scaffold341-1741945 2 39567926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445694 Affx-122926122 AX-123316031 2 95686081 CACTATGACTAATACCAAACAGTTATTCAGTGCTC[A/G]TTTGTGCCATGTACATGCCCAACACATTAAACACA R 2 1 2 1 101000 r 74 goat snp30926-scaffold341-1691312 2 39518077 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799693 Affx-122954708 AX-385286621 2 95722475 TGACAGAAAGCCATCAAGGACCCAGAATTGTTCAA[C/T]TCTATTAATGCAATACAAACTTCTAGTTCTACTCC Y 2 1 2 1 101000 f 74 goat snp30925-scaffold341-1654918 2 39482012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776246 Affx-122927984 AX-385263374 2 95814604 TTTCTTCACCTATACTCAATGTCTTCTGTCATGCT[A/G]TATTGTATACATCTTGAAGACTGCCCTAAATCCTT R 2 1 2 1 101000 f 74 goat snp30923-scaffold341-1562789 2 39388192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422550 Affx-122943772 AX-123292896 2 95875735 TCCAGTGAAGACTGAAAACTACAGGGAACTAAATA[C/T]AAGGAAGAAGAGCAGTTAATTTTTAAGTTAAAACA Y 2 1 2 1 101000 f 74 goat snp30922-scaffold341-1501658 2 39326410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383971 Affx-122972938 AX-123254329 2 95931569 AATGACCCATCTATTCTGGGAATGGTGGAAATCCC[A/G]TAAGGAGGAGAAAAAATCTATACCCTCTGCTCCTC R 2 1 2 1 303000 r 74 goat snp30921-scaffold341-1445824 2 39270289 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801376 Affx-122923112 AX-385288287 2 95965775 TTTCAGGTTTGAGCATACCCTACTTTTGAGCATTC[A/G]TTGACAATTTTATTGCTCAATGACAGCGTACCTCG R 2 1 2 1 101000 f 74 goat snp30920-scaffold341-1411618 2 39235925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794694 Affx-122936844 AX-385281654 2 96010422 CTATACTTATTTTCTGCTTCCTGCTCGCTCCAACT[A/G]GAATTTAAGTTTAGATAGGCAGGGATTGCTGTTGT R 2 1 2 1 101000 f 74 goat snp30919-scaffold341-1366971 2 39191162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415877 Affx-122948487 AX-123286226 2 96072112 CAATATTTGAAACTGTCATGATTCCTCATCATTTT[A/G]CCTTCAAATATTATTTTTTTCATAGTTACAACATT R 2 1 2 1 103000 f 74 goat snp30918-scaffold341-1305281 2 39128624 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447357 Affx-122924871 AX-123317693 2 96106921 AGAGTAGTAACTTCCTTTTTTTATTCTTTGTCATA[C/T]CCCCAACATCTAAAACAGTGCCTGACATATAGTAG Y 2 1 2 1 101000 r 74 goat snp30917-scaffold341-1270472 2 39093594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795085 Affx-122940714 AX-385282044 2 96175663 GAGTCAAGAGGTCAATTGCAAATATTAGAAAAGCT[A/C]GATGGCACTTTCATGTGCTATCTTCTTGCTATTTG M 2 1 2 1 101000 r 74 goat snp30916-scaffold341-1201730 2 39023691 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432423 Affx-122935828 AX-123302764 2 96350523 CAAATAAGCTGCTTAATTCTTAGGGGGAATGCTTC[A/G]CTGTGAATAAATAAATGATACATTTCTGTGCAAAT R 2 1 2 1 101000 f 74 goat snp30912-scaffold341-1026870 2 38848358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440013 Affx-122929779 AX-123310350 2 96385521 TACCTTCCCCAACCCTGAGCAAGCCTAAGTTGCTC[A/G]TTAGTTAAGTCTCTGATTCCAGGAACTGGAATCAG R 2 1 2 1 101000 r 74 goat snp30911-scaffold341-991872 2 38812821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790683 Affx-122970095 AX-385277685 2 96426756 GATTTGACTGCAGGAAGTTTATTGGGGGGTGAATG[G/T]TCTTGAGATCAACATTCCCATGGAAAGTAAAGGAA K 2 1 2 1 201000 f 74 goat snp30910-scaffold341-950637 2 38771044 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398650 Affx-122961896 AX-123269005 2 96491145 ATAAGGCTAATAAAGCAAGTAATTCTAAGTGGTAC[C/T]GTATGAGAGAAAGAGATAAAAACTTCTCTAAACTG Y 2 1 2 1 101000 f 74 goat snp30908-scaffold341-886248 2 38705748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437476 Affx-122932373 AX-123307814 2 96523318 GGGAGAGAAGCAGAATGGAATGAGGCTAGATAGCT[A/G]CAGTGTGCTGTGAAGAACATTATCCCATTGCTGGG R 2 1 2 1 101000 r 74 goat snp30907-scaffold341-854075 2 38673431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768043 Affx-122979002 AX-385255255 2 96559308 TTTCAATTAATTTGGAACTTATGGGTCCTAACAGT[A/G]TTTGAATTTGTCTTAAGTAGGCCACTATTTCTAAC R 2 1 2 1 101000 f 74 goat snp30906-scaffold341-818085 2 38637182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437053 Affx-122933097 AX-123307391 2 96605667 CTATTAATATATTTAGTATTTAATTTGAGGAACTG[C/T]TAGTCTGGGAGATAGAAATATCATTCTAGCTAACT Y 2 1 2 1 101000 r 74 goat snp30905-scaffold341-771726 2 38590648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447430 Affx-122924384 AX-123317766 2 96634795 ACTCATGTAGCAATTTATGACGTGAGATAAACGAG[A/G]TGGCATATAGAATAGTGTACAATTATTCACACACA R 2 1 2 1 101000 f 74 goat snp30904-scaffold341-742598 2 38561526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768510 Affx-122947811 AX-385255690 2 96685393 TGATTAGCAGGGTGAGAGCTTTTGAAGAATAAGGT[C/T]TATATAATCATGCCATGATATCCTTTCTAAGGATA Y 2 1 2 1 101000 f 74 goat snp30903-scaffold341-692000 2 38510758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394911 Affx-122964320 AX-123265266 2 96728443 AAGAAATACCGACCACAGAAGACTAAAAAAACAAA[C/T]GCTAGTTTTCACCAAATGCAAAGGTATTTTGTCTC Y 2 1 2 1 101000 r 74 goat snp30902-scaffold341-648950 2 38469587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436364 Affx-122933059 AX-123306703 2 96766335 TAAGCAGAAAAAAATGATAATAGCCATGCCAGATT[A/G]TACTTCCGTATCGTACGATAGCTTAAATAAATAAA R 2 1 2 1 101000 r 74 goat snp30901-scaffold341-611058 2 38429666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777265 Affx-122931559 AX-385264387 2 96814045 ATGTGGCACTGAATGTACTGTGTTCTGTATTTGAA[G/T]TAGCTGTACCCACAGGTCTCATGTGTGCTACTAGA K 2 1 2 1 101000 r 74 goat snp30900-scaffold341-563348 2 38381953 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801569 Affx-122967693 AX-385288478 2 96867463 TCTTTCCCTCCCTTTCGGCTAAATAAACTTCTTGC[A/G]CAGCATTCTTTCAAATCTTTTCAATAGCAGTACAA R 2 1 2 1 202000 r 74 goat snp30899-scaffold341-509930 2 38328251 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277869 Affx-1111836131 AX-519551365 2 96924675 ATTGTCCAAAAGCCCACTGAAATGAACAATCATCA[A/G]TGAAATAAGCTAAACAGGTTCAAAACTCATTTAGA R 2 1 2 1 101000 f 74 goat Random2.2K-244 2 96924675 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395163 Affx-122964114 AX-123265518 2 96939361 TGAAAGTCTCTGCCAGGAAGCACATTCTCTGCTTC[A/G]TCATTACACCACTCTGAGTGTCTGAGACGTTTAAA R 2 1 2 1 101000 r 74 goat snp30897-scaffold341-438032 2 38256534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398936 Affx-122960994 AX-123269291 2 96968765 AAGATGGACAAGCCCTTCAGAGGGATGTGACAGAC[A/G]TCCCAGAAGTCTCCTGTAGGTCAACGCTCTTATGA R 2 1 2 1 101000 r 74 goat snp30896-scaffold341-408628 2 38227108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444112 Affx-122926820 AX-123314449 2 97015451 GTATATTGAATGTTTCCTTTATGAAGGTAAAGCAG[A/G]GAACTAGAATACTAATTCAAACAGCTGTGTTTTAT R 2 1 2 1 101000 r 74 goat snp30895-scaffold341-361942 2 38180319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272052 Affx-1111833186 AX-519545816 2 97036634 AATTTACATATTAACTGGATATTTGACAACGTTGA[A/G]AACTTTTTCGTGATAATCACATTGTGATTAGAGGT R 2 1 2 1 101000 f 74 goat 2_97036634_AF-PAKI 2 97036634 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419071 Affx-122945802 AX-123289419 2 97051649 ATATATTCTGCCATAAAAACTGATTAAAAAGGAAA[C/T]GAGAATGAAATACCGATTGCTCTAAGTCTCGATTT Y 2 1 2 1 101000 r 74 goat snp30894-scaffold341-325744 2 38144188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408441 Affx-122954450 AX-123278792 2 97093843 ACGACAGGACTAAATTCTTGGAACTCTGCTTAGGA[C/T]GAACCCTGGTGTCAACTGACCTTTCCATTCCCAAA Y 2 1 2 1 101000 f 74 goat snp30893-scaffold341-283550 2 38102159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409876 Affx-122952911 AX-123280227 2 97164633 CATGAAATATCAGCTGCACTATAAAGAAAGCACAG[A/G]TTTCCAATGATATTGGACATCTAAAAACATCCCTT R 2 1 2 1 103000 r 74 goat snp30891-scaffold341-212760 2 38031197 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424650 Affx-122942163 AX-123294996 2 97207031 TCAGTAAACAAAGGAGAAACAAGTCTAATATTCTC[A/G]TTACTAATAGGCCATATAATTTATCATATTCCACT R 2 1 2 1 101000 r 74 goat snp30890-scaffold341-170362 2 37988136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767806 Affx-122941665 AX-385255030 2 97235796 CCATAAGAGTCAGATTATGTTTATTTTATGGAAAA[C/T]GTCATTATAATTATGCCATCAAAATACATATTTCT Y 2 1 2 1 101000 f 74 goat snp30889-scaffold341-141597 2 37959157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451456 Affx-122921151 AX-123321789 2 97294465 GTGTGAGATAAATCAGCAAGGGTTAAAAAATGATA[C/T]TGTACTTGCCTGTAGACAGTCTGTAATGGAAATCT Y 2 1 2 1 101000 r 74 goat snp30888-scaffold341-82928 2 37902089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783063 Affx-122977356 AX-385270130 2 97326964 CACTTTCCCAGATGTATCCAAAGTGGAATAGTATC[A/G]TTTACTTCTCAAAGTCAACCACTGCCCCTTTCACA R 2 1 2 1 101000 f 74 goat snp30887-scaffold341-50429 2 37869849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795913 Affx-122965416 AX-385282865 2 97401699 GAAATTCGAGTTGGTCTCTAGAGACTCCCTGTGGT[A/G]CAGCAAGAGAGCAGAGCTCAATGTGCAGAAGATTG R 2 1 2 1 102000 r 74 goat snp37775-scaffold464-5300048 2 37788459 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440088 Affx-122929721 AX-123310425 2 97448971 TTCTGTAACTCTGTCTAAAATTATATTTTAAATAA[C/T]ATTTAACTAGATAATGTCTTTGCAAAGTAAAGGCA Y 2 1 2 1 103000 r 74 goat snp37774-scaffold464-5252776 2 37740491 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792558 Affx-122958640 AX-385279539 2 97483470 GGTCTTAATAATTTCAAAGAGACCCTCAGATCTTT[A/G]CAAACATTTGTCATTAAATTTAGTTATTAAAAGCA R 2 1 2 1 201000 r 74 goat snp37773-scaffold464-5218277 2 37705885 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399766 Affx-122960310 AX-123270121 2 97518065 TCCTCCCGTGTGTGTCTGTGAATGTCACATCCATT[A/G]TTTACATCAATCCTATTGATCTGTGGTCCCATCAA R 2 1 2 1 201000 r 74 goat snp37772-scaffold464-5183682 2 37671329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394353 Affx-122964655 AX-123264708 2 97620016 TTTTTGATAACTCTGAAATGAACCTGTTCCCAAGG[C/T]GCTTATTAATGATCATTTGATTGATTTCCCCCTTG Y 2 1 2 1 101000 r 74 goat snp37770-scaffold464-5081731 2 37568963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793664 Affx-122919438 AX-385280637 2 97674222 GAATTTTGCAGAAACATCTTTCCCATATTATTTTC[A/G]CATATTTTTGCCATAGCAAATTCAAGTGAAAGGTC R 2 1 2 1 201000 f 74 goat snp37769-scaffold464-5027525 2 37514357 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430800 Affx-122937463 AX-123301141 2 97719479 TCTTTCCATGGAATAATAGATTGCTATGCATTTTT[A/G]GTCTACAATTTAAAATAATAACAGGCATAACACTG R 2 1 2 1 103000 f 74 goat snp37768-scaffold464-4982268 2 37469503 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441346 Affx-122928881 AX-123311683 2 97751681 CATGTTACCAAGAAGAATTTTCAGTATAGATGGAA[C/T]GCTGAGAAAGAAAAGGTGTATTTTAAATGAAAAAG Y 2 1 2 1 101000 f 74 goat snp37767-scaffold464-4950066 2 37437223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792955 Affx-122923360 AX-385279933 2 97795034 CCTGAGTATGGCAGATGCTGTTTAAAAATGGCAAT[A/C]GTGTCTGTAAAGGATATATAGAAAGAGTTCAGAAG M 2 1 2 1 101000 f 74 goat snp37766-scaffold464-4906713 2 37395189 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275203 Affx-1111834651 AX-519548782 2 97843654 CAGGTTTTGAGTTAGTGC[A/G]ACACAGACTGCATTCATTGTGCTGCAGAAAGAGGA R 2 1 2 1 101000 r 74 goat GoatD01.044464 2 97843654 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448097 Affx-122924320 AX-123318433 2 97844906 CAGGTGGCTATGATTCACTCTAAAACCTGAGAAAT[A/G]TACTTCCTGATTATGAGATAAGAAATGCCGGGCTG R 2 1 2 1 101000 f 74 goat snp37765-scaffold464-4856841 2 37345046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376541 Affx-122977992 AX-123246900 2 97886862 CAGCAAACAATTAAAACATCATTGGACTCCCAAGC[A/G]CATGTGTTTTCTTTCCCTATTTTTATATATGTTAT R 2 1 2 1 101000 f 74 goat snp37764-scaffold464-4814885 2 37303032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422549 Affx-122943263 AX-123292895 2 97922285 ACCAGCTGTTCCTACCGTCTGGAATTCTCTTTCCC[A/G]TATATTTGTATGGCTAGTTCTCTTTTTAAAATATA R 2 1 2 1 201000 r 74 goat snp37763-scaffold464-4779462 2 37267468 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444162 Affx-122926783 AX-123314499 2 97954685 TGTCATCAAGGTGGGTACAGTCTCAATAGTATTCC[A/G]AAATTAGATATGCTAAATTCCTGATGCATCTTCTG R 2 1 2 1 101000 r 74 goat snp37762-scaffold464-4747062 2 37236248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420505 Affx-122944850 AX-123290852 2 98002883 TGAAAAGGAAAAATATAACTTTGTAATGGAAAATC[A/G]TATCAATCATGATCTAATCAAAGTCAACACCACCA R 2 1 2 1 101000 r 74 goat snp37761-scaffold464-4698864 2 37189532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799548 Affx-122976006 AX-385286478 2 98031783 AGTCTGTAAGAGAGTGTAAACAATTCCCTTTTTTG[C/T]AGCTATATTTGCAGTGTACATTTGACTGTTCTCTA Y 2 1 2 1 101000 f 74 goat snp37760-scaffold464-4669964 2 37160636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764798 Affx-122923036 AX-385252406 2 98082533 GCTCATATTTATATAAAATTCATAAGTGGTGCACA[C/T]ATATGCAAAACACAATCTAGATGTATTGATGTGTT Y 2 1 2 1 101000 f 74 goat snp37759-scaffold464-4619214 2 37109772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429787 Affx-122938207 AX-123300128 2 98137566 AAATACTTAGTGAATAATAGTAGTAACTGCCACAT[A/G]TGCTTTCTCCAAAAGTTTCTCCCAGTTTGAGAAAA R 2 1 2 1 101000 f 74 goat snp37758-scaffold464-4564181 2 37054277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454091 Affx-122919369 AX-123324424 2 98178696 ATAACAGTTGAAATAAATTGGTTAAGAGAGAATTT[C/T]GCCCTACTCTCTAAGACTCTGATAAATTCATTGCT Y 2 1 2 1 101000 r 74 goat snp37757-scaffold464-4523051 2 37013178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424982 Affx-122941909 AX-123295328 2 98271718 AGTTGAGGTAAGTAGAGTAGGTAAGCCTGCCTGGT[G/T]GCTGCTGTTGTTCAGTTGCACAGTCATGTCTGATA K 2 1 2 1 201000 f 74 goat snp37755-scaffold464-4430029 2 36920022 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425018 Affx-122941882 AX-123295364 2 98354546 TTCAACAGGCCCCCTGCCCTCCACCCACTAGATGA[C/T]ATTAACATCTACTCCTCCACTTGATACAGCTAAAT Y 2 1 2 1 201000 r 74 goat snp37754-scaffold464-4347201 2 36837313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394549 Affx-122964463 AX-123264904 2 98426564 TTTTTACCATTAAAAACAGAACTTTGGATAACTAG[C/T]ATTTTTCATATTAAACTGAAATTTCTTTATTTGGT Y 2 1 2 1 103000 f 74 goat snp37753-scaffold464-4275183 2 36765133 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802863 Affx-122923375 AX-385289761 2 98474007 ATAGGTACTAGTTTTTCTGATCTGGAAAGGAGAAG[A/C]TGTGTTGGTTCTTTGGAAATACGATGATATTCTAA M 2 1 2 1 101000 f 74 goat snp37752-scaffold464-4227740 2 36717032 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782834 Affx-122940572 AX-385269905 2 98522549 TAGTAGGGTTGCTTTTTAGTATGGGAGACTGCTTT[A/G]CTTTGCAAAATCCGTAGGACCAGGGAAGGTTTTAG R 2 1 2 1 101000 f 74 goat snp37751-scaffold464-4179198 2 36667262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775033 Affx-122938841 AX-385262165 2 98552056 TACATAACAGGTACTAATAACTGGAGATAGATGCA[C/T]GTATAATCCAAAATGACCTAAAATGCCTCACAAGA Y 2 1 2 1 201000 r 74 goat snp37750-scaffold464-4149691 2 36637395 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403115 Affx-122958124 AX-123273468 2 98585730 AAACACTGGATCATTTACTAGCATTAATTCCTTTC[A/G]CTTTATTTTGCCCTCATCTATTGAGAGTATGCCTT R 2 1 2 1 101000 r 74 goat snp37749-scaffold464-4116017 2 36603593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772735 Affx-122961151 AX-385259880 2 98623491 CAAAAAATTAGGACGCATATTCTAAAGAGAACACC[A/G]CTGGCATATCAATCGATAACAAGTTTATGATATCA R 2 1 2 1 101000 f 74 goat snp37748-scaffold464-4078256 2 36566102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437709 Affx-122931751 AX-123308047 2 98655115 CTCAGGGGGAAATTTTTAGCCTACCAAATCATACT[A/G]TAGGAAATAATAAATGTTCCTATTATTATTATTGT R 2 1 2 1 101000 f 74 goat snp37747-scaffold464-4046632 2 36534608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394815 Affx-122964801 AX-123265170 2 98689678 TATTTCTCATCCCTTTATTACTTATGTTGTATTCA[A/G]TCACTCATAGCAAGTTCTATCTTTCCTTAAACTAA R 2 1 2 1 101000 r 74 goat snp37746-scaffold464-4012069 2 36499638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781245 Affx-122954254 AX-385268330 2 98730933 TCTTGAATATAAATATATTAGTAAGATGAATTTAT[A/G]TAGCAAAAGTTTCACAGTATCCAATTAAATATGGG R 2 1 2 1 202000 f 74 goat snp37745-scaffold464-3970814 2 36458709 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437027 Affx-122933118 AX-123307365 2 98790928 AATAGTAAGAGAGTTCTGAAGAATAAGTGTACTTT[A/C]TAAGGTCAATGGGAACTTTGATTTCCCCTAGCAAA M 2 1 2 1 101000 r 74 goat snp37744-scaffold464-3910819 2 36398671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404314 Affx-122957018 AX-123274666 2 98850163 GGTGGTTAGTAATGGAAAATACAATTAATCTGCAG[C/T]GTGAGAAATGTGGATTCTGTAAAGAATGTTCAGAA Y 2 1 2 1 101000 r 74 goat snp37743-scaffold464-3851584 2 36339334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801155 Affx-122944013 AX-385288069 2 98900554 ACAAAAGGGATTTCTATTGACTTGACCCTTGAAAA[C/T]GTGTAAGCATTAGATAGGCAGAAAAGGAGTTTAAA Y 2 1 2 1 101000 f 74 goat snp37742-scaffold464-3801193 2 36288785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400778 Affx-122959837 AX-123271133 2 98929089 CCTAAATAGACTACACTCTATCTAGGATGGAGGAT[A/G]CTCTGGGGATGTTCCTGGTCGCCCTGGCTGGTTCA R 2 1 2 1 101000 f 74 goat snp37741-scaffold464-3772658 2 36259855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444401 Affx-122926586 AX-123314738 2 98977623 CTTTTTTTAGAGCAGGAGAAAAAACAATGGACAAA[C/T]AAAATTTCATCTACACTCCGCCCCTGGCTGAAAAT Y 2 1 2 1 201000 f 74 goat snp37740-scaffold464-3724124 2 36210952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414286 Affx-122949597 AX-123284635 2 99039624 CTACACGGTGTTCTATGACTTCAAAACAAGATGCT[A/G]TCATTCTTTAAAGAAAGATGTTAAGGATAAAGTTA R 2 1 2 1 101000 f 74 goat snp37739-scaffold464-3662123 2 36149238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794675 Affx-122978923 AX-385281636 2 99071315 CTCTTGAATATTATATTCTAGCAGAGGCAGATGGA[C/T]AGTAAATAATAAAGACAGTAAAATATATTAATATC Y 2 1 2 1 202000 r 74 goat snp37738-scaffold464-3630432 2 36116543 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409661 Affx-122953515 AX-123280012 2 99117704 CAGTTGTGGCACCTTGACTATTGTAAACTGAAGGC[A/G]TTGGAGAAAACAGAAATCGAGAGGTCACTCTTGCT R 2 1 2 1 201000 r 74 goat snp37737-scaffold464-3584043 2 36069966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799700 Affx-122978427 AX-385286628 2 99148263 TTTCTTCTTTATTAGTTGGAATAGTTTACAAATGC[A/G]TGCCTTTGATCTAGTATTCAGTTACTCAGTGTTAT R 2 1 2 1 101000 r 74 goat snp37736-scaffold464-3553484 2 36039342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416279 Affx-122947947 AX-123286628 2 99193718 ATCAGAAAGTCAGTATTTCTGCATAATTATAAGGT[A/G]TAATTTTTTTCAGTTTATTATATTTGTTTATTTCA R 2 1 2 1 103000 f 74 goat snp37735-scaffold464-3508029 2 35993312 A G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320799540 Affx-122922957 AX-385286470 2 99268980 TGGTTCCAAAGCCAATGTCCAACTAAAACATTTCC[A/G]TTATATCTTTTTTATCAACCTAAGCTCTGATGCTT R 2 1 2 1 101000 f 74 goat snp37733-scaffold464-3432767 2 35917588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796746 Affx-122948785 AX-385283690 2 99300718 GCTAAGGAATCTAGTATTGAAGTGTAGAACTGTTT[A/G]CTCATTCAGAAATTTCTTAGAAGGTATTACTCAGC R 2 1 2 1 201000 r 74 goat snp37732-scaffold464-3401029 2 35885743 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278017 Affx-1111836132 AX-519551509 2 99307917 ATGTAGAAAACAGGGTGTCCTACAATAGTTTGAAA[A/G]TCACTAGCTATGTAGACCAGAGCTACAAGCTCTTC R 2 1 2 1 101000 r 74 goat Random2.2K-247 2 99307917 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785559 Affx-122957081 AX-385272603 2 99340721 AGATTTGTAGATTTAGTTAGAAATGCCAAGAAACT[A/C]AATGATATTATAGAAAAGGAAAACTAAGAGATGAA M 2 1 2 1 201000 r 74 goat snp37731-scaffold464-3361026 2 35845542 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779128 Affx-122943610 AX-385266233 2 99371410 ATATTAAAAATAGGACTTGTGAAACACCTTCAGAG[A/G]CATATACTATTGCGCTGCTGTTTCTGTCTTGCTAT R 2 1 2 1 101000 r 74 goat snp37730-scaffold464-3330337 2 35814819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441894 Affx-122928617 AX-123312231 2 99402220 ATCAAACAGTACGTTCCTATTCATAGGCTGAACTT[A/C]TTAGGACAGCAAAAATCTGTATTTGAAAAAAAAAA M 2 1 2 1 101000 f 74 goat snp37729-scaffold464-3299527 2 35783785 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789951 Affx-122972915 AX-385276957 2 99435353 AAACAATATGTAAGAACTAGCTGTGAAAACAGAAG[C/T]ATAGGAATGTTACAGCAACTTGTTGAAAATTGTGC Y 2 1 2 1 101000 r 74 goat snp37728-scaffold464-3266394 2 35750575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435876 Affx-122932791 AX-123306215 2 99477190 ATGACACCTCTATCTTATGAGAATATCTATATTCT[C/T]ACATTAACTTGAAGCTACTTGAAGACAGTAATTCT Y 2 1 2 1 101000 r 74 goat snp37727-scaffold464-3224557 2 35708398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803360 Affx-122925895 AX-385290195 2 99536268 TATGTACAAACTTGTATTTATGCAAGAATGCATAT[A/G]CATACATATGACTTGTGCCTTTAAAAATGCAAATA R 2 1 2 1 101000 r 74 goat snp37726-scaffold464-3165479 2 35649222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272054 Affx-1111833187 AX-519545817 2 99577748 TCTCTGATTACTCATCAACCATAACTATGCTTAAA[A/G]AAAAAAAAAGTACTGGCCGGGAACTCCTAGTCAGA R 2 1 2 1 201000 f 74 goat 2_99577748_AF-PAKI 2 99577748 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448654 Affx-122923347 AX-123318990 2 99589616 CTGCTTGGTTTAGTCTGAGACATCATCACCAAGCA[C/T]ATAATATCTGAACTGAGGATGTGTAAAGATGTGTT Y 2 1 2 1 101000 r 74 goat snp37725-scaffold464-3112131 2 35595729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393901 Affx-122965110 AX-123264256 2 99632728 TTCAAGTCTCCCACATGGTGCAGGGCAGCACACTG[C/T]ACTTTTGATAGAAAGCTACATTTCTGCACTATTTA Y 2 1 2 1 201000 r 74 goat snp37724-scaffold464-3069019 2 35552713 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768487 Affx-122924840 AX-385255667 2 99664005 GCATAAAAGTGTAATCTTCCAGTTATTCTACAAAC[A/G]CTGCTGAATTTTTCTGTCATAAACATGAAGATTGC R 2 1 2 1 101000 r 74 goat snp37723-scaffold464-3037742 2 35520826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407626 Affx-122954629 AX-123277977 2 99694412 AAGATCAGAAGTAGGATAGATAGAAACTGATCAAG[C/T]GTATTCACTTAGGGCTTCATCCTTTTTGTGTTGTG Y 2 1 2 1 101000 f 74 goat snp37722-scaffold464-3007335 2 35490029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775089 Affx-122933627 AX-385262221 2 99723793 CTTGATATTAAGTAGAAATGTGACAGAAAACAAAG[C/T]AGTTCTCCAAAAGGTCTTTCTGTAAATTATTGAAT Y 2 1 2 1 101000 f 74 goat snp37721-scaffold464-2977954 2 35460234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398583 Affx-122961498 AX-123268938 2 99763887 GGTTGCATAATGAATACATACTTTTATGGATATGC[A/G]TTTTATAATGTATTATACCTATTATTAAACTCGCA R 2 1 2 1 102000 f 74 goat snp37720-scaffold464-2937860 2 35420144 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411846 Affx-122951225 AX-123282196 2 99796554 TTCACTCAAGTTCTTTTTTAAATCTCCAGCTATCC[C/T]CTGAATATCTCTAGTTAAGTGTTCCCCATTCATGT Y 2 1 2 1 101000 r 74 goat snp37719-scaffold464-2905193 2 35387494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781765 Affx-122929733 AX-385268847 2 99830473 TGTCCTTATTGGGTCCTCGTCTTTTTTCAGGCCCT[A/G]CTAGGATCACAGTTATTCTTTGCACAAGTGCATCT R 2 1 2 1 101000 f 74 goat snp37718-scaffold464-2871274 2 35353087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389091 Affx-122968583 AX-123259449 2 99860027 CAGCAGGATCAACATATTAAGTGTGTGCCCATGGA[C/T]GAGGGGTCCCTCCTGATTGCCAATACAAGCTCATT Y 2 1 2 1 101000 f 74 goat snp37717-scaffold464-2841720 2 35323509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790697 Affx-122956993 AX-385277698 2 99896166 ACAGATATGAAGAGAATGCCTGGCTCAGCATAAAG[A/G]GAGAATCTGTAAAGTTCATGGTCATTTTGGGAGAT R 2 1 2 1 101000 f 74 goat snp37716-scaffold464-2805581 2 35287425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450119 Affx-122922768 AX-123320454 2 99995104 TGCTGAGTCCTGAGCAAGATGTTTTATATGAGTTA[G/T]CCACATTATCAGGAAACATTAACAGTATTAACCTG K 2 1 2 1 101000 f 74 goat snp37714-scaffold464-2706643 2 35186614 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412728 Affx-122950731 AX-123283077 2 100024624 TGGGGAGATCACCTCATCTCTCATGCTGCCATTAA[C/T]GACTTGCATTCCTGAGAGATGGAATAAGCCATTTC Y 2 1 2 1 101000 r 74 goat snp37713-scaffold464-2677123 2 35157157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784758 Affx-122935442 AX-385271806 2 100054061 TGTACTTCACCAATAACACACAGAAGAATCAGCAG[C/T]TGGGCAATTCGATTGTGTTTATTAATAAATAGATC Y 2 1 2 1 101000 f 74 goat snp37712-scaffold464-2647686 2 35128090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772498 Affx-122949094 AX-385259649 2 100112130 GATATGGAGTTACAAAATACATGTGTGAGTTGGAA[C/T]GAATTAGATTCCAGCTATATCACTCATTCTCCATA Y 2 1 2 1 101000 f 74 goat snp37711-scaffold464-2589617 2 35069131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278019 Affx-1111836133 AX-519551511 2 100123406 TTTTATAGGGGAAAATATGAAAACAAAGATTCTTT[A/G]GGTTTTATCAGCTTCAAAGTAAGAAGACTTAGACT R 2 1 2 1 101000 r 74 goat Random2.2K-249 2 100123406 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411743 Affx-122951511 AX-123282093 2 100153493 CAGGAAATATTCCATTTCTTACTTTGGATACAATT[A/G]TTTAAGCCTATTATCAATCCACATAATTATCTTTA R 2 1 2 1 101000 r 74 goat snp37710-scaffold464-2548254 2 35028221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429171 Affx-122937970 AX-123299513 2 100192855 TTCTCATGCCCAGCATGGTCCAGGAGCTAGGGAAC[G/T]CACACTGAGGCAGGACACACACACATACACACACA K 2 1 2 1 101000 r 74 goat snp37709-scaffold464-2508892 2 34988805 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386250 Affx-122970961 AX-123256608 2 100221477 AATTGATAGGATAGTCCTCCTCCTCGCCTTCCCCA[G/T]AGGGAACTGAGAACACGTACCAGCATGAATATTCA K 2 1 2 1 201000 r 74 goat snp37708-scaffold464-2480270 2 34959833 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784211 Affx-122977937 AX-385271262 2 100263772 AGCATGGAGGTGGTAATTCCAAGGAAACCAAGTTG[C/T]AAGCCTTTTGAAATCAAGAGCTGTGGTTTTCCAGT Y 2 1 2 1 101000 r 74 goat snp37707-scaffold464-2437975 2 34917099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433206 Affx-122935631 AX-123303547 2 100302724 TAGATTATCTTGAGTAGAAACTGCCCTCTAACACA[G/T]ATCTTAGGCTCTCTCCATAGTGCAAATGCATGGAT K 2 1 2 1 101000 r 74 goat snp37706-scaffold464-2399023 2 34878018 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785587 Affx-122943340 AX-385272631 2 100332845 TGCCTTTTTTTAATTTGTGCCAGTTCCTTCTATAA[C/T]ACTGACTTTTCAACGTGCAAATTAGACCTCTTTTT Y 2 1 2 1 101000 r 74 goat snp37705-scaffold464-2368902 2 34847941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383731 Affx-122972457 AX-123254089 2 100364524 TGGGTGAAGGCACAGTGGGACTGTTGGTCTAAGTG[C/T]CCTGCCCTCTTCTGGGGAATGTGGACATGTGACCT Y 2 1 2 1 201000 f 74 goat snp37704-scaffold464-2337223 2 34816296 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443030 Affx-122928159 AX-123313367 2 100413581 CGGAGCGATTATATTGAGGGAGATAACACACTTGG[A/G]GATGTCTCCGTCTCACATCTAGCAATGTAGAAACT R 2 1 2 1 101000 f 74 goat snp37703-scaffold464-2288166 2 34767039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435902 Affx-122932771 AX-123306241 2 100456116 AAAGTCCATCTCTTTTGGAGATCTTGACACCTATC[A/G]TTAACAAGGTGCAACCTCCTTCGGGATAATTGAGA R 2 1 2 1 101000 f 74 goat snp37702-scaffold464-2245631 2 34724423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380851 Affx-122975444 AX-123251209 2 100512072 TGAATGTCGATAAATAAACTGCTTCTCACCTCTTA[C/T]GCCTGAGAATTCTTCAAAAGTGTATAAATCTAAAG Y 2 1 2 1 101000 r 74 goat snp37701-scaffold464-2189675 2 34668549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788252 Affx-122933497 AX-385275271 2 100579319 AATGCTTTTAAAGGGATTCTGCATTCTAAATAACA[C/T]GTTACGTGTATTAAATGAGTATAGTAATAATCAGA Y 2 1 2 1 201000 r 74 goat snp37700-scaffold464-2122428 2 34600804 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387244 Affx-122970569 AX-123257602 2 100621022 TTCAGGAAATTTATTCTCTTGTGGTTCAGTGAGCC[A/G]TGACGGAGGTGGACTAAACAGATTGAGAATAAATC R 2 1 2 1 201000 r 74 goat snp37699-scaffold464-2080725 2 34558987 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418379 Affx-122946567 AX-123288727 2 100739526 AGCTTCCCAGCAACCTGGCTGGAGGTGGGAGAGTC[A/C]CCTTTCTCTTGAGTTGGTTAGTTCTCTATTTCCTT M 2 1 2 1 101000 r 74 goat snp37697-scaffold464-1962221 2 34438649 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381700 Affx-122974714 AX-123252058 2 100772460 AAAAAGATAGGAAACCACTAAAAGTTTTCAACTGA[A/G]ACATGTAATGGATAGATTTATGTTTTAGGAGGATC R 2 1 2 1 101000 f 74 goat snp37696-scaffold464-1929287 2 34405551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411158 Affx-122951875 AX-123281508 2 100804087 TGGGAATTTGGTACAGACTCAGTGCACAATGGAAG[A/G]GGACAGAACTCCTTACTAGCACATATCTGAAAATA R 2 1 2 1 101000 r 74 goat snp37695-scaffold464-1897660 2 34373809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450797 Affx-122921815 AX-123321131 2 100857557 TTTGGGAAACTAGGAGGCCCACATCTTTTCTCAGG[A/C]ACCAATTACTTTCTTCTGATAAAACACTCTGGACA M 2 1 2 1 101000 f 74 goat snp37694-scaffold464-1844190 2 34319474 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425600 Affx-122940923 AX-123295946 2 100909155 TTTATTTTTCTCCAAGTAATAATCAACCCACTATG[C/T]TTATGACCCTCCATATCCTAATACTTCATTATGTT Y 2 1 2 1 101000 r 74 goat snp37693-scaffold464-1792592 2 34267492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795632 Affx-122933598 AX-385282587 2 100946891 TTAATGGAAGTAACCACATGATATTAAATTTTTCA[C/T]CACAACATCTCAGTGAGTTTGATTTAATTGCATGA Y 2 1 2 1 101000 r 74 goat snp37692-scaffold464-1754856 2 34231878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412104 Affx-122951115 AX-123282454 2 100978803 GCCTCAATTAAATTTTGAGATCTTTTTGTAAATTC[A/C]TATTTGTTTAAATTACCCAGAGCCCCCAGTACAGA M 2 1 2 1 101000 r 74 goat snp37691-scaffold464-1722944 2 34199463 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391938 Affx-122966927 AX-123262295 2 101034410 TTTATTGAAAATGGTGTTCCTTTAGGGTCACTGGG[C/T]TGGGTATAGGGGGGTATAGGGGGGCTTGGCAGGAA Y 2 1 2 1 101000 f 74 goat snp37690-scaffold464-1667337 2 34143535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395783 Affx-122963665 AX-123266138 2 101068291 TGAGTTCTTGGGGACATCAGGAGAAAAAGTGCAGT[A/G]TTTTGAGAATATTCTGCTGCACTCTCTGAGGCAAA R 2 1 2 1 102000 f 74 goat snp37689-scaffold464-1633456 2 34109047 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451484 Affx-122921131 AX-123321817 2 101128870 CTTAGAGCTCTGAGAATGTTGAAGAGGGTGGAATA[C/T]AGCCCTCCTGTGACTGCCTAGGGAAGACCCTGAAG Y 2 1 2 1 101000 f 74 goat snp37688-scaffold464-1572877 2 34048245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771491 Affx-122943606 AX-385258649 2 101185219 CTCATACTTAATGATGGCACATGCTCACACATCAC[A/G]TATGCTTTTATCCAGCTTACCAGGACAAACATACA R 2 1 2 1 101000 f 74 goat snp37687-scaffold464-1516528 2 33991834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406262 Affx-122956096 AX-123276614 2 101305007 CCAGCATTTCAACAAAGAAGCACACAGTAGTTTTT[A/G]TTTTTGTTTTTAACTGTATTTTATCTTTAGATTCA R 2 1 2 1 103000 f 74 goat snp37685-scaffold464-1396740 2 33871234 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412108 Affx-122951113 AX-123282458 2 101341296 TATAGGTTTCCCCTCAAAAGAGAATATTTCTTGAA[C/T]GCCAGGTAGTCAAATAAACAACAAGTAGCCATTTC Y 2 1 2 1 201000 r 74 goat snp37684-scaffold464-1360451 2 33835179 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427032 Affx-122939830 AX-123297377 2 101414148 CACATTGTGATTTTCTTTCTGTTCATTTCCCTCAT[A/G]TCTTAGCTCTTTTGTAGCAAATATCATGTTCTCTT R 2 1 2 1 201000 r 74 goat snp37682-scaffold464-1287599 2 33760715 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797863 Affx-122955898 AX-385284801 2 101475572 TGAAGACAGTTGCAAAAGTGGAGCCTTATAGTTTG[C/T]ACAATGATGTCATTAGATTAAGTACACACCCTTTC Y 2 1 2 1 101000 f 74 goat snp37680-scaffold464-1226175 2 33698972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788394 Affx-122955099 AX-385275412 2 101539657 TGCGAGATGAAAATCTGTGCTGGGTGGAATTCTAG[A/C]TCACAGTGCTCTAGGCCCGGATTTCTGATTTCTCA M 2 1 2 1 101000 f 74 goat snp37679-scaffold464-1162090 2 33647333 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388224 Affx-122969403 AX-123258582 2 101619982 TCTCTCTAGAATTGTATTCTGTGAACACGACTGAG[C/T]GACAGAACTGAACTGAACTGGTATCCACAAGTTCT Y 2 1 2 1 201000 f 74 goat snp37678-scaffold464-1081765 2 33570051 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784180 Affx-122955032 AX-385271231 2 101663625 TAGTAGTTTTGAAAAAAATCCCACTATCCCTGCCA[C/T]GAGTCATGTTCCTTTTGAAGAAATAGATTTTTAAT Y 2 1 2 1 101000 f 74 goat snp37677-scaffold464-1038122 2 33526002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453190 Affx-122920456 AX-123323523 2 101736145 TGGTTCTGCAGTCAGGCTCTGAACTACAGGCCCTG[A/C]TGCCCATCCGAAACAATGAAAGCTACGAGACAGGG M 2 1 2 1 101000 r 74 goat snp37675-scaffold464-965602 2 33452302 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411721 Affx-122951527 AX-123282071 2 101850008 TCTGCTGGGCACTGGAGAGAAAAAGATAAAAGAGA[C/T]ATGCTTGTTATTTGTCTTCAAGGAGAAGAAACATG Y 2 1 2 1 201000 r 74 goat snp37673-scaffold464-851739 2 33337846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779171 Affx-122978954 AX-385266275 2 101880096 AAACTCTGGACTTTGGCCCAGGATTAGAAATCAGG[G/T]GTACAAAGTTAAAGCTTGGTTCTATCACTGATTTC K 2 1 2 1 101000 f 74 goat snp37672-scaffold464-821651 2 33307434 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415929 Affx-122948447 AX-123286278 2 101916414 AAGGCTATGAAGCTCACTCCTACTCGTGGTGATCA[C/T]GGGGATTTACAGAAGGCACTGCTGGTGTCTAAGAA Y 2 1 2 1 201000 f 74 goat snp37671-scaffold464-785333 2 33271101 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391197 Affx-122967417 AX-123261554 2 101961129 TGTTTTGAAGATGTGCTGTGTGGAAGCCATGGCCT[C/T]GTCTCCTAAGAGCTCGTCGTCGGGTGGGAATCGCC Y 2 1 2 1 101000 f 74 goat snp37670-scaffold464-740618 2 33225990 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38389263 Affx-122969023 AX-123259621 2 102030898 CTAGTCTCATCTGACCATGTCTGACTGGCAGAACC[C/T]AAGTCTCATCTGGAGCCCTCGCTGCAAATGAAGCT Y 2 1 2 1 201000 r 74 goat snp37668-scaffold464-670849 2 33156454 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443707 Affx-122927156 AX-123314044 2 102062761 AGGAGACAGGGAAAGGTGGAAAAGAGCTGCTGAGG[A/C]GCTGAGAGGGTGAAGAGCAGTGTGTGATCACTGAA M 2 1 2 1 201000 f 74 goat snp37667-scaffold464-638986 2 33125668 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797534 Affx-122958541 AX-385284473 2 102116195 ATAATTAAACAAATTTAAGTAAATTAACAAAAATA[G/T]AAAACAGTCTGGATTCCTTGGATCCAAATTTAACT K 2 1 2 1 303000 f 74 goat snp37666-scaffold464-585552 2 33072275 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431192 Affx-122937173 AX-123301533 2 102157371 GAAAAAAGCCCAGGGGAATACTAAGGCAGGAAAAT[A/G]CGGTGGCATGATGCTGTCTTGGTGAATTTTCTCCA R 2 1 2 1 101000 r 74 goat snp37665-scaffold464-544376 2 33031096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403500 Affx-122957638 AX-123273853 2 102189975 TGATTTTATTTTTCTAAATTATCTCTGGTCATTTT[A/G]TTAATAGTAAAGGTGATTGACATTGTTTTGAAGTT R 2 1 2 1 101000 r 74 goat snp37664-scaffold464-511772 2 32998465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278023 Affx-1111836135 AX-519551515 2 102199348 TCTTGCCCTCAAGCCCTAATAGGTCAGGAGCAACC[A/G]TCTACAGAGGGTGTTTGTTTATGATATTTGATCTC R 2 1 2 1 201000 r 74 goat Random2.2K-250 2 102199348 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796762 Affx-122923631 AX-385283706 2 102232264 ATTTTCTGGGGAACATACAGAACTCAGTTTTTGTC[A/G]GCCTACTACATATCCCTGAGAGGCTTTCAAGTAAC R 2 1 2 1 101000 f 74 goat snp37663-scaffold464-469483 2 32955586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275383 Affx-1111834766 AX-519548957 2 102250740 ACCAAGCTCAT[A/G]AACACTTTGCAAAGATCAAGCTTGTCTGCCCACAG R 2 1 2 1 101000 r 74 goat GoatD01.052093 2 102250740 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451972 Affx-122920944 AX-123322305 2 102288703 ATTGCTGTCAATGAACTTACTCCAGTAGCACTTCA[C/T]ATCCCTGATCCCACCAATCAACCAAGACACTTAAA Y 2 1 2 1 101000 f 74 goat snp37662-scaffold464-413044 2 32898616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789042 Affx-122950932 AX-385276055 2 102328243 GAGGGAGCATGTGGGAAAGATCTTGCGAGTATATC[A/G]TACTCTTTCTCATGTATTTCTTTTCCTCCCTCTGC R 2 1 2 1 101000 r 74 goat snp37661-scaffold464-373504 2 32858581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781313 Affx-122923287 AX-385268398 2 102363761 GGTTTACTTCCTTTCCAAGGAAAAGCCTAATGATA[C/T]GGTAAGGTCCTTTATTAGTCTGCTAAACTTCAGTG Y 2 1 2 1 101000 f 74 goat snp37660-scaffold464-337986 2 32822864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402340 Affx-122959063 AX-123272693 2 102413018 ATGGAAATAGAGGCTAAAAGACTCTACAAAAGCAA[C/T]GAACTCTTTGGAAGTAAGTGTTATTCTACTAGAAT Y 2 1 2 1 101000 f 74 goat snp37659-scaffold464-288729 2 32774094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767862 Affx-122932990 AX-385255082 2 102462767 TTTCTGCAACCCTTGCAAGAATAAGTAGAGAAATC[A/G]TTTTGGAGTGAATTTATACGTAACGTTCGGAAAGA R 2 1 2 1 101000 f 74 goat snp37658-scaffold464-238980 2 32724392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278025 Affx-1111836136 AX-519551517 2 102489877 TCAAGGCAGCGGGTGATATGCCCATTTTATAGATA[A/C]GAAAATCAAGACTCAAAAGTTACACTGCTATTAAG M 2 1 2 1 201000 r 74 goat Random2.2K-251 2 102489877 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424738 Affx-122941662 AX-123295084 2 102499862 ACTCATTTTGTTGACTTGAATGACATAAAACAACA[C/T]GGATAATGATCAGGAAAAACTAATGTTGAACTGGA Y 2 1 2 1 101000 r 74 goat snp37657-scaffold464-201885 2 32687006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425039 Affx-122941866 AX-123295385 2 102536887 TTGACTTACAGAAAAATGTTCTGTGTGGTTTGGTT[C/T]GAGTACTCTAACTGCTTGCATATCACAGTTAATGT Y 2 1 2 1 102000 f 74 goat snp37656-scaffold464-164860 2 32649270 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410218 Affx-122952561 AX-123280568 2 102572190 AAATTTAATCCAAAATTCTCCTTTCAGACCAGTGG[A/C]TGTTACAAACTTTCAGGACAAATGACTTCATCAAG M 2 1 2 1 101000 r 74 goat snp37655-scaffold464-129557 2 32613597 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407010 Affx-122955024 AX-123277361 2 102640143 AATGTGCATCTGTGACCAAAATTTGAAGCATGTCT[A/G]TAAGAAGAGTATATATTTTAGCAAATGCTCTTAAC R 2 1 2 1 101000 f 74 goat snp37654-scaffold464-61604 2 32544900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444357 Affx-122926711 AX-123314694 2 102669474 ACCTTCTTTCCAGGTGGCTGGCCTCCTGAATAAAG[A/C]AACATTTTCTTTTCCAACCAACACTTGAGTATTGG M 2 1 2 1 202000 r 74 goat snp37653-scaffold464-32273 2 32515348 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774891 Affx-122922075 AX-385262025 2 102699572 GTAATGATCAAGCAGAAATATCAAGTATTAACGTC[A/G]TTTTTAAAAAAGACTGTTTGAAGCACCTCCTGGTT R 2 1 2 1 303000 r 74 goat snp37652-scaffold464-2175 2 32486845 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453912 Affx-122919909 AX-123324245 2 102721476 GTATACCCCAGAGAAGTTAAAGTGCTTATTCGGGT[A/G]TCAGATTTGATAGGAAGATAATTAATTTGCTAAGT R 2 1 2 1 201000 r 74 goat snp33261-scaffold390-334393 2 32464463 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771959 Affx-122959578 AX-385259115 2 102772796 CTCCTTTTTTGAAGTGTCAAACTATAAAGTTTGTG[A/G]AAGCAATACAGCTATCAACTATCAGTGTTATATGT R 2 1 2 1 201000 r 74 goat snp33260-scaffold390-283073 2 32413152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417626 Affx-122946861 AX-123287974 2 102833860 GCCCTAATGCTCTCCTTAAGTATTTTCTTTAAAAG[C/T]GGCAATTTTTCCACACTCAACAGTTGCACTGTCCA Y 2 1 2 1 103000 r 74 goat snp33259-scaffold390-222009 2 32351650 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426087 Affx-122941075 AX-123296433 2 102874651 ATTTTGCCCATGACCCCTGAAGCATCTGTGTAGTT[C/T]GAAGACCCTGAAGGCCTATCAAGCTTTAGAAACAG Y 2 1 2 1 102000 f 74 goat snp33258-scaffold390-181218 2 32310926 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381926 Affx-122974135 AX-123252284 2 102908817 TTTATCCTTGAAAGAACCTGTTTCACCACTTGCCC[G/T]ATGACGTTATCCCTGTGGTGGTCTTCAATTTCATC K 2 1 2 1 201000 r 74 goat snp33257-scaffold390-147052 2 32276615 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417701 Affx-122947456 AX-123288049 2 102951483 CTATTTGAAAGGGCTCTCACCCTGCCATTTTCCCC[A/G]TCTCTTTCATAGTATCCCCAGTAGGTAAACTTTCC R 2 1 2 1 201000 r 74 goat snp33256-scaffold390-104386 2 32232890 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452107 Affx-122920841 AX-123322440 2 102983353 TTGACTTTAGTGTCTTCTAGTGAAAACCACTAGAT[G/T]AAAGATATCTGAAAGTAGAGACTCATGTCGAAACT K 2 1 2 1 101000 r 74 goat snp33255-scaffold390-72516 2 32200687 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772184 Affx-122940310 AX-385259338 2 103013913 TCCTTCTACTAAGGTTTTGCTTTCCTAACTCACTT[A/G]ATCATAAAAATGCATGGTCATTGTCCTCAAGATTG R 2 1 2 1 101000 f 74 goat snp33254-scaffold390-41956 2 32168959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767530 Affx-122943627 AX-385254787 2 103074084 CACCCTTCATCAAAATCGAGAACTCTGACTCACCC[C/T]GATAGTCATACACAGGATTTAGCCAACCTTCTGAG Y 2 1 2 1 101000 f 74 goat snp16996-scaffold1772-450201 2 32096145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444498 Affx-122926514 AX-123314835 2 103117116 TCAAGGCAAGTTAGCAATGGAGAGGGTGACAGCCA[A/G]CCTGAAGCAGGCTTTGTCCCCCTTCCTCTGATCTC R 2 1 2 1 101000 f 74 goat snp16995-scaffold1772-407169 2 32052934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419610 Affx-122945989 AX-123289958 2 103162957 CGTCATTAATTCCTCCTACATATTGGGAGGGGGTG[C/T]TTTTGACCTTATATGGCTCACCTGGGGCTGTAATA Y 2 1 2 1 202000 r 74 goat snp16994-scaffold1772-361328 2 32007086 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795538 Affx-122930019 AX-385282493 2 103204257 AGAATGTTGGCTCTTCCCAATTAAACATCGTCATC[A/G]TTGTATCCACAGTAAATGTATGAAAAACCATGGAT R 2 1 2 1 101000 f 74 goat snp16993-scaffold1772-320028 2 31964421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441659 Affx-122929192 AX-123311996 2 103246504 ATAGACAGTGGTGGGGACTGGTGGGTAACATGAGA[A/G]CTCAAAAAGGGCACAGGTAGCAGCTGCTTGGGAAA R 2 1 2 1 101000 r 74 goat snp16992-scaffold1772-277781 2 31921770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387256 Affx-122970558 AX-123257614 2 103280315 AGTGGTAGATCCTTGTTTGATCCAGGGCACGTGAT[A/G]CCACCTGGTCTTTTAAACAACTGGCCAGTCTCTAC R 2 1 2 1 101000 f 74 goat snp16991-scaffold1772-243970 2 31887770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442678 Affx-122927891 AX-123313015 2 103318888 TAGTCTGCCCGCTTTGGGATGGAAATATCCATCCC[C/T]TCTGCTGCTGGCAGTGTCTGAGATATTGGTGTCTG Y 2 1 2 1 102000 r 74 goat snp16990-scaffold1772-205397 2 31848774 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790693 Affx-122969679 AX-385277694 2 103357228 TGTTTCATGGTGCAGTTGAACGCACCTTAGTCTCT[C/T]GGAGTTTACTTTTTACTCTTACTTGTTTTTGCCAG Y 2 1 2 1 101000 f 74 goat snp16989-scaffold1772-167057 2 31810109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432074 Affx-122935881 AX-123302415 2 103389189 AGTGGGGTACCTGTTATTAGGTTCCAGGACTGCTG[C/T]GACAAGTTGCCACAAACTTGATAGCTGTATATTAA Y 2 1 2 1 101000 f 74 goat snp16988-scaffold1772-135096 2 31777930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434288 Affx-122934769 AX-123304629 2 103418198 TGATCAATATTTTTCCAAATTTTTATTTCTCTCCT[A/G]CTTGATTTTTAAGAATTTTAGGGCAAATTCCAAAT R 2 1 2 1 101000 r 74 goat snp16987-scaffold1772-106087 2 31750361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392746 Affx-122966010 AX-123263103 2 103451148 GCACAGTTTCAGGGAAGAGTCAGGACACTATTTAA[G/T]AGGATTGTCTTTCTGTCTCCTGCAGTTTACAACTC K 2 1 2 1 101000 f 74 goat snp16986-scaffold1772-73137 2 31717890 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414960 Affx-122949074 AX-123285309 2 103483689 ACCAATAGCTCTAAAGCAGTCAATAAACAACCAAA[G/T]ACTCACAAGACCACAAAATGAACTTATCTACCCAG K 2 1 2 1 201000 f 74 goat snp16985-scaffold1772-40596 2 31685772 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431991 Affx-122935939 AX-123302332 2 103520010 TATTTTAATTCTCACTTGAGTTCTTCTAGAGCCAA[C/T]AAGAATCTCTTCATCCCTGAAAAGCCTGAAAAGAT Y 2 1 2 1 101000 r 74 goat snp16984-scaffold1772-4275 2 31649210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446367 Affx-122925596 AX-123316703 2 103544832 ATGGAAAGCCAGGAGAGCAAAGGTTTTTAATCAAG[C/T]ATCCAAGAAGGACATCAAGGAATTTGTGACCACCC Y 2 1 2 1 101000 f 74 goat snp10730-scaffold138-2121247 2 31624004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277879 Affx-1111836137 AX-519551375 2 103567956 GATGACAACCTCATGTTGATTTCATTTGGATGTAA[C/G]AGTGTCAGGATTACAGATATAAGAATATATTATAT S 4 1 2 1 101000 f 74 goat Random2.2K-253 2 103567956 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448635 Affx-122923365 AX-123318971 2 103601413 CAGGGACAAGAGTCCACAGATCCATTTTAATAACC[A/G]TAAGTCTTGCTGCTTAAGAGAACAAGGTTCCTTTG R 2 1 2 1 101000 f 74 goat snp10729-scaffold138-2064666 2 31578519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390019 Affx-122968449 AX-123260376 2 103652910 CAGACAAGTTAATTACTGAGGCTAGGACACAGGGT[A/G]AGCACACAAAATGACTGAATCAGAGTAAGCTCCGG R 2 1 2 1 101000 f 74 goat snp10728-scaffold138-2013169 2 31527626 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388401 Affx-122969294 AX-123258759 2 103716461 CCTCCTCAAGGAAAATTATGACTTAGTAGTAAATG[A/G]TTTTGTTTTCTTCAGGATATCTCCTGACAAGAAGT R 2 1 2 1 102000 f 74 goat snp10727-scaffold138-1949618 2 31463392 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417372 Affx-122947708 AX-123287720 2 103751319 AGGGCATTGCTGGATTCAATGGAAACTGGGAACCC[A/G]CAGATGCAAGAAGAACTCTGGGAACAGAGATCAAA R 2 1 2 1 201000 f 74 goat snp10726-scaffold138-1914760 2 31428802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423998 Affx-122942109 AX-123294344 2 103803766 CACCACTCAGTGTTCACATCTGCTTTGTCAACAGC[A/G]CCACTGATTGAGTACTGTTATATGCAAGGCTTCTT R 2 1 2 1 201000 r 74 goat snp10725-scaffold138-1862313 2 31375952 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409279 Affx-122953116 AX-123279630 2 103836599 GAATCCAGCATTGGAAGAGGAAGCATGGGAGACTG[C/T]AGCAGCTCTGAACTTTTTCCAGGATGGATTTCTGA Y 2 1 2 1 101000 f 74 goat snp10724-scaffold138-1829480 2 31343054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393484 Affx-122965827 AX-123263840 2 103895990 GTGTGTCCTCCTGCCTGAAGCCTCAGGCTGATGCA[C/T]GAATGCACAGAGTGGACAGGACCCTTGTTTGCACC Y 2 1 2 1 101000 r 74 goat snp10723-scaffold138-1770089 2 31283704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393241 Affx-122965475 AX-123263598 2 103926941 GATAGTCCTGAGAAGGACTTAAGAGCAGCTCTGGA[C/T]GCCATTATGAGAAAAGAAACAGTACAATCCTGGAA Y 2 1 2 1 101000 r 74 goat snp10722-scaffold138-1739138 2 31252832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440280 Affx-122930638 AX-123310617 2 103965264 CAAACACTTAGAAGTAATCTCTCTTGCCTTACTAG[C/T]TTGCCAAGTAACAAATCTCTGATGGCCTGAGCTAT Y 2 1 2 1 101000 r 74 goat snp10721-scaffold138-1700815 2 31214452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443452 Affx-122927834 AX-123313789 2 104042175 TCTCCACCCATTCTTTCTCTGGATCTTCAGCAGTC[A/G]TCTAAACTGGGACTGCCACGTGGATACTGGGGTGC R 2 1 2 1 101000 f 74 goat snp10719-scaffold138-1623904 2 31138798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419713 Affx-122945911 AX-123290061 2 104100113 CCAAGAGGTGATTTTATGTCAGTAAGAAACTAGAA[C/T]GATTTGCCTTTGGAATTACTGCTTTGGACAAGAAA Y 2 1 2 1 101000 f 74 goat snp10718-scaffold138-1565966 2 31080674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446667 Affx-122924763 AX-123317003 2 104132764 CCAGTCCCCCAGGGTGACATCTTGTAGACCTGTAG[C/T]GCAATATCACAGCTAGCATGCTGCTGTTTATACAG Y 2 1 2 1 101000 r 74 goat snp10717-scaffold138-1533315 2 31048264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762263 Affx-986696794 AX-385250455 2 104154096 CCAACTATTTTTATTGGAATGGGCTATTAGGAAAT[C/T]TTCTAGCTATAAAATTTATTTTTAATATAAATTTA Y 2 1 2 1 600010 f 74 goat 2_104154096 2 104154096 Ancestral_priority_1043 ancestry 0.808 recommended IMAGE 10K 10K ancestral 320799847 Affx-122926313 AX-385286773 2 104207828 AGCCAAATTCTGTTTGTATAGCCCGTGAGCTGAGC[A/G]TGTTCATTGCAGTTTTTAGTGGTTAAAAAAAAAAT R 2 1 2 1 101000 f 74 goat snp10716-scaffold138-1458251 2 30972743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768978 Affx-122950945 AX-385256153 2 104238885 GCAGGTATGAAACCTATGAAACTATTAAATAAACC[A/G]TTAAATGTGATTTGTATGATATCAGTGTAATTTGT R 2 1 2 1 101000 f 74 goat snp10715-scaffold138-1427194 2 30941461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776011 Affx-122959016 AX-385263141 2 104283680 GAGCAAATTAAATCCCTTCTTGGCTTGCTCTCCTC[A/G]TCTGTAAAATGAGCCTGTTGGATTCCGTGATCTCT R 2 1 2 1 101000 f 74 goat snp10714-scaffold138-1382399 2 30896276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393156 Affx-122965539 AX-123263513 2 104313537 TGATTTTGGAACCCAAGAAGATAAAATTTGTCACT[A/G]TTCACTTCTGAATTAGAACCTCCTCAACCTGCTTA R 2 1 2 1 101000 r 74 goat snp10713-scaffold138-1352542 2 30867737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416450 Affx-122947822 AX-123286799 2 104344625 GGTTTCATTTTAGAGGAAAAGTAAATTCTGCTCTT[A/G]TTTGTAGTTTCCTTTGACAACTGCTTTGCATCTTC R 2 1 2 1 101000 r 74 goat snp10712-scaffold138-1321454 2 30836354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393591 Affx-122965379 AX-123263947 2 104375919 GATTCAAAATGTAAGAGGAAAAGAAAGAAATGGTT[A/G]TGGGGGAGGAAAGAGGAAAGGAAAAGAAAAGGAGA R 2 1 2 1 101000 f 74 goat snp10711-scaffold138-1290160 2 30804985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400403 Affx-122959995 AX-123270758 2 104404575 TGAAATGCCTGAGAAAGATTTCCTAAGGACACAAC[A/G]TGCTTAGCTGCTCAGTCGTGTCTGCCTCTTTGCGA R 2 1 2 1 101000 f 74 goat snp10710-scaffold138-1261504 2 30775849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391555 Affx-122966631 AX-123261912 2 104434968 ATTTCATGGTGACCACTCAGTTGAGACCCTCTCCC[A/G]CTGACCTTCATCTGGATTATTGGAATATCCTCCTC R 2 1 2 1 201000 r 74 goat snp10709-scaffold138-1231111 2 30744625 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398388 Affx-122961647 AX-123268743 2 104464233 CCTGTGTTTCACTTCTGCCATCCTGTTCTCCAATT[A/C]TCCAGGATAACACTCTCAAGGAAACTCCCTGTACT M 2 1 2 1 201000 r 74 goat snp10708-scaffold138-1201846 2 30715364 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769284 Affx-122936455 AX-385256456 2 104507156 TTACAGGATTCTTTTGGTGACATTGGGGGAAAGAA[C/T]GGGTCTTAAGACAATCCTAAATTACTGATTTTTGA Y 2 1 2 1 201000 f 74 goat snp10707-scaffold138-1158923 2 30672472 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375812 Affx-122978559 AX-123246171 2 104545362 GCCAAATACAAGTCAGCTGTAAGCTATTGTAATCA[C/T]ATCAAGCAGGCAGAGTATTAATGACAAAAAACAGA Y 2 1 2 1 101000 f 74 goat snp10706-scaffold138-1120717 2 30634092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388561 Affx-122969177 AX-123258919 2 104606295 TGAATGTTTGAGCCTATCATTCTGTTACATAAAAT[A/G]TGCACAATTTTTTGTATATCAGTTACACTTCAAAC R 2 1 2 1 101000 f 74 goat snp10705-scaffold138-1059784 2 30572637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771287 Affx-122947348 AX-385258445 2 104649735 CCGAACCAAGTCTGAGTTCATTTTGCAGATCTTAC[A/G]TATGTTCAGTCATCCCATGCACATTGCCCACCGGA R 2 1 2 1 101000 f 74 goat snp10704-scaffold138-1016344 2 30528841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781795 Affx-122931967 AX-385268877 2 104682190 GGAGAGTGCAGTTCACTAGAGTTTAGGGTTTCATC[A/G]CCTGTTATTTAGTGTTTACTGGGAATATATTCCCA R 2 1 2 1 101000 f 74 goat snp10703-scaffold138-983889 2 30496426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426755 Affx-122939857 AX-123297101 2 104725034 GTTGCTTTAAAAAAAAAAAAAGATTCAAGCTACCT[A/G]TGGAATTTATGCAAACTTTCATCTCTTCTGTGCAT R 2 1 2 1 101000 r 74 goat snp10702-scaffold138-941045 2 30453742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783332 Affx-122940117 AX-385270397 2 104756508 TAGGCTTGCCCAAGGACAATTACAGGCAAATTAAA[G/T]AATAATTCTGTAGATGATTGACATCAAGAGAATAT K 2 1 2 1 201000 r 74 goat snp10701-scaffold138-909571 2 30422289 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441643 Affx-122929203 AX-123311980 2 104789717 GTAAACAAAGAGTGAGCAATTGCTCTGTGACTTCT[A/G]TGCTTGAATAGATTAGTAACACCTGCTTTGTCTCC R 2 1 2 1 201000 r 74 goat snp10700-scaffold138-876362 2 30388933 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427180 Affx-122939610 AX-123297523 2 104820135 AGTGTCACTCCCTCAGTGGCCAGGATCAGGGGTAG[C/T]TTTCAGCACATAGGATGGAGCAAAGTTGAGCAGGC Y 2 1 2 1 101000 r 74 goat snp10699-scaffold138-845944 2 30358678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393350 Affx-122965931 AX-123263706 2 104884230 AATGCTTCATGAAGATTCACAGAGTATATATTTTA[C/T]GTGCTCATATTTGAGGGGTGCTCTAATGCTGACAG Y 2 1 2 1 201000 f 74 goat snp10698-scaffold138-781849 2 30294377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786238 Affx-122940657 AX-385273273 2 104933092 TCTATCCTACACTCAGTCTGCTATAGGCAAATCCC[A/G]TTTCATTTGTTCCATGGGCATGGCACAAAGATGGA R 2 1 2 1 201000 f 74 goat snp10697-scaffold138-732987 2 30245936 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440366 Affx-122929646 AX-123310703 2 104968473 TGAGAAATATGGGATTACAGAACTGAATCTCATCT[A/G]TGCAGCTGGAGAGAAAAATTAAGGCCTTTAATGTA R 2 1 2 1 101000 f 74 goat snp10696-scaffold138-697606 2 30210498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399602 Affx-122961096 AX-123269957 2 105001596 CTCTGCAACTTCAGCCTTCCATTCCCCTGCTGCAT[A/G]GGCTATTTCCAGTCTAAATTTATGTAGGCATAATC R 2 1 2 1 201000 r 74 goat snp10695-scaffold138-664483 2 30176189 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790939 Affx-122965011 AX-385277936 2 105092219 CCAAATTTTGATATGTAAAATTAACTGTCACAAGT[A/G]TGGATAGTTTATGTGAGAAAATGGACCCAAAGATG R 2 1 2 1 201000 f 74 goat snp10693-scaffold138-573860 2 30084701 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272927 Affx-1111833148 AX-519546614 2 105105678 ATTATGTCTTAGACTAATGTGGTTAACACTTACTG[A/G]TGAACTGGATATAAAGAATGAAGAAAAAGATTCAA R 2 1 2 1 101000 f 74 goat 2_105105678_AF-PAKI 2 105105678 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426554 Affx-122940178 AX-123296900 2 105126434 AGTTGGGGCTCTTTCCTGGCCCTTGAGCCTGGGGT[A/G]CTGTGGCTAAAATTTCTATCCAGACACCACATCTT R 2 1 2 1 101000 r 74 goat snp10692-scaffold138-539645 2 30050446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423940 Affx-122942252 AX-123294286 2 105170901 GTATGCTCAAGTAACAAAACAGGCTTTGAACTCTT[A/G]TGGGTAGGATGAGGAGGGGGATTTGTGTTGTTCCT R 2 1 2 1 101000 f 74 goat snp10691-scaffold138-495178 2 30005866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407054 Affx-122954927 AX-123277405 2 105201067 TCATGCAGGTCTCACGGTGCAGCACCAGTGCAAGT[C/T]TGCAGGTGCTGCGGCATGGAAGCAGGAGCAGGTCA Y 2 1 2 1 101000 r 74 goat snp10690-scaffold138-465012 2 29975669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397618 Affx-122962632 AX-123267973 2 105245026 TTGAGCCTAGGATGCTTGTCATGAAACACATCTTA[G/T]CACCCTGGGACAGAGCTTGAGCAACTGTGGGCAGG K 2 1 2 1 101000 f 74 goat snp10689-scaffold138-421053 2 29930706 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379958 Affx-122975639 AX-123250316 2 105288353 ACCCTGGCTGCTGACCCCACACCAGCTGCCACCAT[C/T]GTTCACTTCAAAGTTTCTGCCCAGGGAATTACACT Y 2 1 2 1 101000 r 74 goat snp10688-scaffold138-377726 2 29887096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422212 Affx-122944440 AX-123292558 2 105334712 TTCCTGGTTGGCCTGTCTGCCCTGACATCTAAACA[A/G]ATGACCTCTCCCCACTGACATTAGTGAGAGAAGCG R 2 1 2 1 101000 f 74 goat snp10687-scaffold138-331367 2 29840892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434281 Affx-122934774 AX-123304622 2 105368824 AAGAGGAGCATGATGTTTATGATGGTACAATGTGG[C/T]GTGGAGAGTGTGGGCAGGGCAGTCATCTCTGCAGT Y 2 1 2 1 101000 f 74 goat snp10686-scaffold138-297255 2 29806853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762265 Affx-986696796 AX-385250457 2 105409398 AGTGTCCTCTAGAGGGCAGGCCAATGGGGATCCTG[A/G]TGGCACCCACCACGTGGCTGATGCTGTATGGATTA R 2 1 2 1 600010 f 74 goat 2_105409398 2 105409398 Ancestral_priority_1043 ancestry 0.436 neutral IMAGE 10K 10K ancestral 38409997 Affx-122953272 AX-123280347 2 105436138 AACAGGCAGCTGGAGATCTGCCAGGGTAGGGTGCT[C/T]GAGCCAAGACTCACAGCCTGAACACAATGTTCCTA Y 2 1 2 1 101000 r 74 goat snp10684-scaffold138-229941 2 29740361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414216 Affx-122949647 AX-123284565 2 105475080 TAACAGATTATGGCTGAAGGAGGTGGGGTGGGAGA[C/T]GAGGTCGGGAAGAGAGTCAGGGAACCCGGGCTCTA Y 2 1 2 1 201000 r 74 goat snp10683-scaffold138-190999 2 29701505 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400576 Affx-122960411 AX-123270931 2 105528493 GACTTCAGAGAGGAGTGGGGCTCTCTCCAAGTGCC[A/G]TCCCAGGGCTCTCTCTGGACACACTCACCCTTCAG R 2 1 2 1 201000 r 74 goat snp10682-scaffold138-137586 2 29647881 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418400 Affx-122946551 AX-123288748 2 105560614 GGTCAAGACCAAGTTTTCTCAGAAGCCCAGAGTAA[C/T]GAAATCACAAGATAGGTCACTTCTGGGAGCTGATG Y 2 1 2 1 101000 r 74 goat snp10681-scaffold138-105465 2 29615314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407147 Affx-122954853 AX-123277498 2 105598322 GGTTCTATTATAGATACCTTGTCACAGCATTAATT[A/G]TAGCTATACCTTATCATGTTTAGTGGAAACAGCGT R 2 1 2 1 101000 f 74 goat snp10680-scaffold138-67757 2 29577460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403318 Affx-122957830 AX-123273671 2 105640392 TTTGAGAACTAAATCTGTTTTTGTTTTCACTTGTT[A/C]GAGAACATCTTTATTTCTTCAGCTTAAAAAGCAGT M 2 1 2 1 101000 r 74 goat snp10679-scaffold138-25687 2 29535303 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389617 Affx-122968755 AX-123259975 2 105682934 ACCTGTGGCCTCAATCCCCAAGCCTCTGGAACACT[A/C]TCTCAACAGTCTCAGGGATCTCTCAGCCAAAACTC M 2 1 2 1 101000 r 74 goat snp11350-scaffold1410-16756 2 29492752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376688 Affx-122978989 AX-123247047 2 105714981 AATCATGCAATTCATACCAATGTATGAATACTCAA[C/T]GTATGAAGCTTTTGACTGTGTGGATCACAACAAAC Y 2 1 2 1 303000 f 74 goat snp11351-scaffold1410-48803 2 29460570 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411374 Affx-122952239 AX-123281724 2 105751449 TCTCTGATGGGTGAGCTACTGTCGGTGAGGCCAAG[A/G]GGGCAGTACTGAGCACAAACATGGGAGCTCAACCA R 2 1 2 1 201000 r 74 goat snp11352-scaffold1410-85271 2 29423755 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783362 Affx-122943213 AX-385270426 2 105792641 AGTGTCCAAGAATAAGGAACTAGTTAAATAAATGT[C/T]GCTGTATCTATACCAGAGAATATAGTGATGAAAAA Y 2 1 2 1 101000 r 74 goat snp11353-scaffold1410-126463 2 29387240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767576 Affx-122943764 AX-385254828 2 105828819 CACAATATAACTATAGATCTATATGAACAGATAAC[A/G]TTAATGGTTAAGTACGAAAAAACAGAATGAATTTA R 2 1 2 1 101000 f 74 goat snp11354-scaffold1410-162641 2 29350964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781492 Affx-122927291 AX-385268577 2 105860026 CCTAAGAAGGTATAATATCCTTAATCAGATCAAAC[C/T]ATTTCTTGCTACAATAATAGGTTAGTAACACTGTG Y 2 1 2 1 101000 f 74 goat snp11355-scaffold1410-193848 2 29318975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381738 Affx-122974328 AX-123252096 2 105941487 GCTCTTCCCTTCTTCACTTTCCTAAACTTAAAACA[A/G]GCGTCTTAATTCACCAGACTGTCCTGGAAGGATAT R 2 1 2 1 101000 r 74 goat snp11356-scaffold1410-275309 2 29237671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430238 Affx-122937317 AX-123300579 2 105971929 GAACATGACTGGGGCACTGGCTTGGCTTTCCCACT[A/C]TAAGCCTGAAAACTCAAAAGTCCCAGAAGGACCTG M 2 1 2 1 201000 r 74 goat snp11357-scaffold1410-305751 2 29208638 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378156 Affx-122976970 AX-123248515 2 106098084 GCCCCAGCAGATGGGCCCTGGGCAGGAGGGAACCC[C/T]TAGATTAGCTCCTGCTGTGTGAGGACCCTGTCCTG Y 2 1 2 1 101000 r 74 goat snp11359-scaffold1410-431906 2 29105738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454191 Affx-122919299 AX-123324524 2 106132077 GAAACTGTCTAGGGATCCACCATGAATAACAAAGA[C/T]GCTCCTATCACTGACAAAATTCCAACAATTAAAAG Y 2 1 2 1 201000 r 74 goat snp11360-scaffold1410-465899 2 29071340 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277881 Affx-1111836138 AX-313920127 2 106183966 TAATATCTTCTGTTTCTGTTAGGTCCATACCATTT[A/C]TGTCCTTTATTTTGCCGGTCTTCACAAGAAATGTT M 2 1 2 1 303000 f 74 goat Random2.2K-254 2 106183966 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413222 Affx-122950252 AX-123283571 2 106213716 AATGCAGGGCAGGAATAGGAAAGATGCTCTTGGAT[A/G]CTGTCGGTTTGGTCTCTCATTGCAATTAGCCCAGA R 2 1 2 1 101000 r 74 goat snp11362-scaffold1410-547538 2 28989349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386486 Affx-122970759 AX-123256844 2 106272304 TTGTGTGCTTTTCTGTATCTTATTTCAATAACAAG[C/T]TCACACACACACCTACCCCTCTTTCTGTGGAAGAT Y 2 1 2 1 201000 f 74 goat snp11363-scaffold1410-606126 2 28931845 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382888 Affx-122973416 AX-123253246 2 106309507 CAAGAGAAGTGAGACCCCCATCTATCCCAGCAGGC[A/G]TGGGTGTGTGTACATGCACAACACACGTGTAGCAC R 2 1 2 1 303000 f 74 goat snp11364-scaffold1410-643329 2 28894733 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426524 Affx-122940200 AX-123296870 2 106356855 ATTGTAATAAAAAATGAAGGAGTAACTGTGTCCAC[A/G]TGTCTCTGCCTTGTACCAGTGCTGAGAGTGGAAGC R 2 1 2 1 101000 f 74 goat snp11365-scaffold1410-690677 2 28847082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416293 Affx-122947937 AX-123286642 2 106394518 CTCTTTTAGAACAGAAGGTCTAGGGACACCAAATG[A/G]CTCTGTGTCTACAGGACAAGTGTCCCCAGGCCCCA R 2 1 2 1 101000 f 74 goat snp11366-scaffold1410-728340 2 28809348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794208 Affx-122960629 AX-385281174 2 106410342 GCCAAGTACCAACTCAAAATTGGCTACTTCACAAG[C/T]TGGGTGTCCTAGAACCTACAAGAGGAACGTCCTCT Y 2 1 2 1 101000 f 74 goat snp31725-scaffold3533-12077 2 28793258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432163 Affx-122936415 AX-123302504 2 106440546 TGATGTACACGAACCCACTATAGCAGATGCTGATC[A/G]TATCAAAGCCTCTGAGGAGGAGGGAAACATGCCTG R 2 1 2 1 101000 f 74 goat snp31726-scaffold3533-42281 2 28763060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405356 Affx-122956320 AX-123275708 2 106496795 AAAATAACTACTACTGCTAACTGAGCAGCGTCACC[A/G]TCTATTTGGTAGCAGCACTCTAATAGAAACTCCTA R 2 1 2 1 101000 f 74 goat snp31727-scaffold3533-98530 2 28707008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421738 Affx-122944378 AX-123292085 2 106525864 ATGAAACCTGGGGTGGTGGGTCGGGTCAGTAGTTA[A/C]TGCACTTAAGTCACTGTAGCCCGTGGAACCTCCAC M 2 1 2 1 201000 r 74 goat snp31728-scaffold3533-127599 2 28678150 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398885 Affx-122961032 AX-123269240 2 106598658 TGCTCAACCCACATCACACATTTATGTTAGCCTGG[A/C]TCCTGCAGCAATGAGTTCACAGCCCTAAGCAGGCT M 2 1 2 1 201000 r 74 goat "2_28604766_AF-PAKI;snp31729-scaffold3533-200393" 2 28604766 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434853 Affx-122934371 AX-123305194 2 106643386 GAACATCTTCCCCACAATTCTCCCCTTTTTCTTGT[A/G]TCATCATTTTCTCCTGTTGTTTACTGAATTATTCC R 2 1 2 1 201000 r 74 goat snp31730-scaffold3533-245121 2 28560445 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409737 Affx-122953021 AX-123280088 2 106674609 CCACACCACAGAGGAGAGCAAGGGGGAGGCTGAAT[A/G]CAAGGGGCTCTGGGTACTTCTCTCCCATCTAAGGA R 2 1 2 1 101000 r 74 goat snp31731-scaffold3533-276344 2 28529243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414768 Affx-122949244 AX-123285117 2 106738373 GGGGGGATGTGCAGCCCTCAGACAGATTGGAACAC[G/T]GATTGTGGCTCCACCAGGCTCCCTGTGCTTCAGGC K 2 1 2 1 201000 f 74 goat snp31732-scaffold3533-340108 2 28466179 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405528 Affx-122955985 AX-123275880 2 106775939 AACTAGTGCTCAAACCCTGAGCAGATGCTCATCAA[G/T]TGCCATCCTGACTTCCCTCTCCATCTCCATGTCAG K 2 1 2 1 101000 f 74 goat snp31733-scaffold3533-377674 2 28428620 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396389 Affx-122963023 AX-123266744 2 106818470 CGATAGCATGGAGTTGTATTCCGGAAACACTGGGA[A/G]GTGGAGAGGAGAAAGTCATGTAGTTCAGACTTACC R 2 1 2 1 201000 f 74 goat snp31734-scaffold3533-420205 2 28385735 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435422 Affx-122933544 AX-123305762 2 106846311 TATGTGTATGACCACAGGTGTGCATGCGTCTACCC[A/G]CGTGAGGGTACCTGGTATGTATTTGGGATTTTGTG R 2 1 2 1 101000 r 74 goat snp7379-scaffold127-22944 2 28358081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375951 Affx-122978449 AX-123246310 2 106905708 TTTGCTGTTCATGATGTGCTTCCTCTTAGTCTGTT[C/T]CACTTGTTTTAGGCTCTGGGTTCAACTCACATATG Y 2 1 2 1 101000 r 74 goat snp7380-scaffold127-82341 2 28300047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445529 Affx-122925169 AX-123315866 2 106949928 ACCCGAGCTGGAGTGCCTCGACCCTACCTTCACCA[A/C]TTCCTCGGGGGCTGGCCCAACTTCTTCCTTGTTCT M 2 1 2 1 201000 f 74 goat snp7381-scaffold127-126561 2 28255010 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389944 Affx-122968089 AX-123260301 2 106989311 TGCCGCTCTGTTGTCACCTACCTGCAAAGGATGGC[C/T]GGCCTTTCTGAATTGGTTTCCCTCTCTTCCATCAG Y 2 1 2 1 101000 r 74 goat snp7382-scaffold127-165944 2 28215205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386826 Affx-122970096 AX-123257184 2 107021275 TGATCTTACTGGGATGGCCATGTGTCAGGCTAAAA[C/T]GGAGGGCTCTTTCATTAAGGAGAAGAGGGAGAAGG Y 2 1 2 1 101000 f 74 goat snp7383-scaffold127-197908 2 28183236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453788 Affx-122919582 AX-123324121 2 107081626 TTGTCTTGGCCCCACGGCGTATTGTCTGCCCTGAG[C/T]GCTGTTTGGCCTGGCACCAGCCTGGATTTCCCCAT Y 2 1 2 1 101000 r 74 goat snp7384-scaffold127-258259 2 28122485 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399581 Affx-122961112 AX-123269936 2 107187782 TGGGGAGCTCCTTCTTAACTTGCCTCAAACATACT[A/G]TCTCTGGACACTGTAATCAACAGTGTCTGCTTGTA R 2 1 2 1 101000 f 74 goat snp7386-scaffold127-364415 2 28015754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801404 Affx-122969735 AX-385288314 2 107242525 CAGCAACACTTATTAAAATCTATATTCCTGGGCTG[C/T]ACCTCAGACCTCCTATAAAGACTCTTCGCCAGAGT Y 2 1 2 1 101000 f 74 goat snp7387-scaffold127-419158 2 27960765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385827 Affx-122971017 AX-123256185 2 107281090 ACCACCATGTGTTTGTGGTGATTTATTGCAGCAGC[A/G]TGGGAAGCTCTTACAGGGAGCAAGGATGGGGCTTT R 2 1 2 1 101000 f 74 goat snp7388-scaffold127-457723 2 27922076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446941 Affx-122924678 AX-123317277 2 107316606 CATCCAGAGCCCTAGGAATTAATCATACCATATAC[A/G]CTAATGGAGAAAACCTAGGTTGTTTAGGGGAAAAA R 2 1 2 1 101000 f 74 goat snp7389-scaffold127-493239 2 27886907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274028 Affx-1111833995 AX-519547633 2 107345224 AGTCTGCTTCTTGCTGGTTCAAGTTCAGAAACATG[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.013249 2 107345224 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432387 Affx-122935854 AX-123302728 2 107383231 GGCCACTGGAAAGGCCTGCCATCCACTGAGTGAGG[C/T]CTCTGTTCCAGACCTCTATCTTTCTCAGCTTCAAG Y 2 1 2 1 101000 r 74 goat snp7390-scaffold127-559864 2 27821153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408538 Affx-122953690 AX-123278889 2 107420335 AACAGACATGACTGGGAGCTGGGAGAGTGGAAGAC[A/G]CGGGCGATCATATCCCCAGACCTTTCTGCTGAGAA R 2 1 2 1 201000 r 74 goat snp7391-scaffold127-596968 2 27784092 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391865 Affx-122966984 AX-123262222 2 107453287 AGTGGAGAAGTGACTAACTTTCTCCCAAAGCACTT[A/G]TTGAATCATAGGGGAATAAGTAAATCAACAAATGA R 2 1 2 1 201000 r 74 goat snp7392-scaffold127-629920 2 27751137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417426 Affx-122947216 AX-123287774 2 107488861 AAGCTGGCACTATTGTTTAGAAAGAGGGTGGTGGG[A/C]TAATGGACTAGCTGTGTTTTCTCCTGTACGTGGGT M 2 1 2 1 101000 r 74 goat snp7393-scaffold127-665494 2 27715286 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430730 Affx-122936889 AX-123301071 2 107518928 AGAGATAACATTTTCTTTTCTGTCCGTTTTCTACT[A/G]TCTTACCATTCTTTTTATTCTAAACTTTTTTCTTG R 2 1 2 1 101000 f 74 goat snp7394-scaffold127-695561 2 27684644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378080 Affx-122977169 AX-123248439 2 107559379 GCCCGTTCTTCCCAGTTGGGGTTCTTTTTTGCAGC[A/G]TGAGGGGCAGTGAAGCAGGGGGAGGCTAAGCACCC R 2 1 2 1 101000 f 74 goat snp7395-scaffold127-736012 2 27643520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793583 Affx-122922268 AX-385280558 2 107609221 AGCAGCTAAATAAGCTCACACCTAAGAAATTAATG[C/T]CCTCACCAAAAATACCCTTTCAAAGTTAAAGCTAA Y 2 1 2 1 101000 r 74 goat snp7396-scaffold127-785854 2 27593050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272978 Affx-1111833149 AX-519546661 2 107624429 GTTATGATGTTCTCAATTAAGGACTGCAAATACTT[A/G]ACCCCTTACAGAGGATTACAGATCTACCAATGAGT R 2 1 2 1 101000 r 74 goat 2_107624429_AF-PAKI 2 107624429 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773409 Affx-122948092 AX-385260551 2 107645594 GCAAGAATGTAGAAGCTCACAGGATTTGCTGAGTG[A/C]TGAGACCTTCTCTAGCTCAGAGAAAAGTGAAAAGC M 2 1 2 1 101000 r 74 goat snp7397-scaffold127-822227 2 27556862 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277883 Affx-1111836139 AX-519551378 2 107647683 ATTGAATTTTACTTTATCCTAGACACACGGTAGAA[C/G]AGAAACAACAGGGGCCCTGCCATTCTTTCTCAGCT S 4 1 2 1 101000 f 74 goat Random2.2K-257 2 107647683 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787765 Affx-122953432 AX-385274788 2 107707017 CTTACAGGAAACTAAGGCTTTGAATTACTCTCCTC[A/G]TTTTACACATGTGGTAGCTGAGGCTTCATGAAGCT R 2 1 2 1 102000 f 74 goat snp7398-scaffold127-883650 2 27494061 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410525 Affx-122952169 AX-123280875 2 107765472 CAAGAGCTTTTATTTAGCTGGGTAATTGTGTTTGT[A/G]GAAGTTAGGAATGTTTTTGTTCCAAGCACAGGAGG R 2 1 2 1 201000 r 74 goat snp7399-scaffold127-942105 2 27435626 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381555 Affx-122974828 AX-123251913 2 107810813 GCTTCTGATGCAACATCCTTAGGGGACAAGTAAGC[A/G]TGTGAATACAGCCATTAGAATAAGATGGAATAACA R 2 1 2 1 101000 f 74 goat snp7400-scaffold127-987446 2 27390312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796205 Affx-122919507 AX-385283156 2 107845502 CAGAGTCTGCTACCGGTGCCTGCATCATCTTTAGC[A/G]TATCATTAACTCCTCAAGTACTCAGGTCATTCACA R 2 1 2 1 202000 f 74 goat snp7401-scaffold127-1022135 2 27354656 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437287 Affx-122931987 AX-123307625 2 107877611 CTTGGTCACTAGACCAGAGTTTATGGTGGGTCACT[A/G]TGCACTGGGGTTACTGAAGAGCTATCACAATGCAG R 2 1 2 1 101000 f 74 goat snp7402-scaffold127-1054244 2 27322496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785949 Affx-122965387 AX-385272986 2 107915146 TTTATCCTGGGTACTCTTCTGCAAAACCAAACTTC[A/G]TATCTATTGTGGATTCTGGCTATATCAAAGAATCA R 2 1 2 1 101000 f 74 goat snp7403-scaffold127-1091779 2 27284774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415325 Affx-122948800 AX-123285674 2 107950930 GGATGATCCTAATTTCTACCTCACAAGTGAGAAAA[A/G]CACCAAGCAATGCACTTGGGAAATAATAAGTGCTC R 2 1 2 1 101000 f 74 goat snp7404-scaffold127-1127563 2 27248666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794504 Affx-122975566 AX-385281467 2 107985294 CACCACATTCCAATCCAGTCTCATTTCCTACACTG[A/C]TTGTAATAAATCTAAGTGTAGACCTTGCTCAGGAT M 2 1 2 1 102000 f 74 goat snp7405-scaffold127-1161927 2 27214021 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272384 Affx-1111833875 AX-519546113 2 108014406 GAC[A/G]GCCAGCACAGCTGATGCAGATGCCCCTGCAGCTTT R 2 1 2 1 102000 r 74 goat GoatD01.008780 2 108014406 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802509 Affx-122926681 AX-385289413 2 108030624 TGGAGCACCCCCTGCCAAAATTAGGAATAATTATG[C/T]AATTATCAATCAAAGGAACTCAAAGCTCTTTAAGG Y 2 1 2 1 102000 f 74 goat snp7406-scaffold127-1207257 2 27168418 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798150 Affx-122945529 AX-385285085 2 108059831 AATCAGCAACTATTAACTGGGACATGTTGTTTTCC[A/G]TTAAGCAATATACAAATATTGTTGATCCTGTATAT R 2 1 2 1 101000 f 74 goat snp7407-scaffold127-1236464 2 27138680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436405 Affx-122933026 AX-123306744 2 108096257 AAAGTCTGAGGAGGAGCTCCTGACACATAGCAAGT[A/G]CTTTGTGAGTGTCTGTCATTCTGTTTGAGTTTGTG R 2 1 2 1 201000 r 74 goat snp7408-scaffold127-1272890 2 27102126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784104 Affx-122948461 AX-385271156 2 108132263 ATTTTATAAGCAAAAAAATCAAGCTGGTAATCTTT[A/G]TCAAATTAATAATGGCATTTTTCTTAACTAGTTTT R 2 1 2 1 101000 f 74 goat snp7409-scaffold127-1308896 2 27066164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400757 Affx-122959887 AX-123271112 2 108195639 GAGAAGAAAGAATGATGTTTTGTATCCTTCTGTAG[G/T]TCCCATGGGATTAAAAAAAAGACTTAAAAGACAAA K 2 1 2 1 101000 f 74 goat snp7411-scaffold127-1372272 2 27002823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416299 Affx-122947932 AX-123286648 2 108248211 CAAGGTAGGAACCTAAACATATAAGAATTCCACTG[C/T]ATCTGTGAACAAGGAACAGAGAAAATGAAGCTGTG Y 2 1 2 1 101000 f 74 goat snp7412-scaffold127-1424844 2 26949493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802110 Affx-122929270 AX-385289014 2 108298141 TATTCTATTAACAATAAGAACCAATGGATTTTGAG[C/T]AGGGTCCTGTCATGATCTAAAGAATGTCTTAGTTT Y 2 1 2 1 101000 r 74 goat snp7413-scaffold127-1474774 2 26899421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431186 Affx-122937177 AX-123301527 2 108335084 TACAAAGGAACTTCTCAAGTCTGCTGTAGGGTTTG[A/G]AATTAACTGAGACTGCAATGAGGAGTTTAAGGGTC R 2 1 2 1 201000 r 74 goat snp7414-scaffold127-1511717 2 26862142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453709 Affx-122919684 AX-123324042 2 108396783 TGAGAGAAAGAAAAGAACAGAGTGACTTCCTGAGT[C/T]TATGTTTCAGAACAGAATGAAGAAATGTCATAATG Y 2 1 2 1 101000 f 74 goat snp7415-scaffold127-1573416 2 26800016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792950 Affx-122938084 AX-385279928 2 108477285 ATGAATAAAAGTTTGTGGAGGGATGATATGTGTAC[A/G]TATTGTATCAAAGTATGTTCCCTATGAAATTTATG R 2 1 2 1 201000 r 74 goat snp7417-scaffold127-1653918 2 26719342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401299 Affx-122959858 AX-123271652 2 108508510 TTCATGTAACATATACCTCATGCCTGGGGTTAATC[A/G]CCAGTAGTTCTTGGCAGAATGAAATCTTTAATATA R 2 1 2 1 101000 f 74 goat snp7418-scaffold127-1685143 2 26688338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391677 Affx-122966543 AX-123262034 2 108566090 GCTAAGGACTCTGTCATTATTAGAGCTAAGGAAAA[C/T]GATGCTCAAATTTTAATAAATTATACAAGATCAGA Y 2 1 2 1 101000 f 74 goat snp7419-scaffold127-1742723 2 26631497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776174 Affx-122953761 AX-385263302 2 108597837 GAGCAGTGCAGAAAAATGCTATACAAAGGGACTGC[A/G]TATTTACAAAATATATGACCCATGAAATCCTGGAC R 2 1 2 1 201000 r 74 goat snp7420-scaffold127-1774470 2 26599805 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768024 Affx-122935029 AX-385255238 2 108627298 TGAAATGATAAGTAAAAATAACACTTTCAATTTGT[A/G]TATTTCAGTCATTTTATATGACCTTTTCTTTCATA R 2 1 2 1 201000 f 74 goat snp7421-scaffold127-1803931 2 26569636 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390494 Affx-122967259 AX-123260851 2 108680032 GTCACACCTAGGCAAAGGTTTCCACAGTCTTCAAG[A/G]GCTAGAGTTGTTCAGAGTGAAGGCATGGTCCTACA R 2 1 2 1 101000 f 74 goat snp7422-scaffold127-1856665 2 26516428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790621 Affx-122974733 AX-385277623 2 108746034 AGAGTCTAGAAAACAGGACAGACCTGACAGAACTG[C/T]ATCTGTTTACAAAGTAACAAAAACATTAAATATCC Y 2 1 2 1 101000 f 74 goat snp7423-scaffold127-1922667 2 26449758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452006 Affx-122920918 AX-123322339 2 108782068 GGATGGTTGAATTAATAACATCCTATTATTTTATT[A/G]TTGCATAAGAATTTATAGCTGTGCTGACACCACAC R 2 1 2 1 101000 r 74 goat snp7424-scaffold127-1958701 2 26415367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449319 Affx-122922996 AX-123319654 2 108811001 TAGCTCTGTGACTCCCAGTAGCCACATACAGACAC[A/G]TATACATATACCTAATATGAATCAGTAGCCACACA R 2 1 2 1 201000 r 74 goat snp7425-scaffold127-1987634 2 26386347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414770 Affx-122949243 AX-123285119 2 108852120 CTGTGAGAGCTTGACAGAGTGCATAAATCTTCCCC[A/G]TTGGAGACACCAAGCAGTCCCCATGGACAAGGGAG R 2 1 2 1 101000 f 74 goat snp7426-scaffold127-2028753 2 26347511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417322 Affx-122947746 AX-123287670 2 108931927 AACATCTATTCATTACTGAACTTCCTTGGTGGTAC[A/G]TAGGATAAGAATCTGCCTGCCAATGCAGGGGACCC R 2 1 2 1 101000 f 74 goat snp7428-scaffold127-2108560 2 26267626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383071 Affx-122973744 AX-123253429 2 108973238 CAGTGACGAATGGCTAAAGGATTTTGGTAGTAATA[C/T]TGAACAAAATAATTCATCTCCTTTTCTTCTCATAC Y 2 1 2 1 201000 f 74 goat snp7429-scaffold127-2149871 2 26226372 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789608 Affx-122933352 AX-385276616 2 109032239 AGTAGTAGTAGTAGTAAGAGCTTATTTTTACTGAG[C/T]AGTTACTATGTTCCAGACATGGTTCAGGTGCTTTG Y 2 1 2 1 101000 r 74 goat snp7430-scaffold127-2208872 2 26167025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423388 Affx-122943129 AX-123293734 2 109063319 AAGGAGATGAATATTGATCCCTGTCATTCTATACA[A/C]AGATGCAGCAGATAAAAGGAGCAATCTGAATTCTT M 2 1 2 1 101000 f 74 goat snp7431-scaffold127-2239952 NW_017191778.1 19486 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790829 Affx-122972291 AX-385277829 2 109103312 TCTCAATGCCTTCTTCCAATATGCCGATAATTTGT[A/G]TTTTTTCAGCTGTCATAACAGTGAAAAGCTCAACA R 2 1 2 1 201000 r 74 goat snp7432-scaffold127-2279945 2 26095746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434930 Affx-122934305 AX-123305270 2 109152789 CTCATGATGCAAAGACACACATGTTAATGTGAAAG[A/G]AGCATATCCACTTACTAAAGAAATAAAATTTTTTA R 2 1 2 1 101000 f 74 goat snp7433-scaffold127-2329422 2 26046119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789007 Affx-122974417 AX-385276020 2 109197254 ATCCCTCATGGCAGTTTCATTGTCATTAAAAGTAC[C/T]GCTCTATTGTGTGTATTCTCTATTCATATTCATGA Y 2 1 2 1 101000 f 74 goat snp7434-scaffold127-2373887 2 26000885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415536 Affx-122948663 AX-123285885 2 109243279 CAGTATACAATTTATACAGGCTACAACAAATTTCC[A/G]CATACATTATTGAACGAAATACTCACAACTGTGTT R 2 1 2 1 101000 f 74 goat snp7435-scaffold127-2419912 2 25955270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775265 Affx-122949522 AX-385262395 2 109274806 AATACTTACTGGACCTTTATTGCCACTTATCATCC[A/G]TCTGCTGATACTAGCCCTTGTTTTATAATCTTGTA R 2 1 2 1 101000 f 74 goat snp7436-scaffold127-2451439 2 25924416 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416930 Affx-122948042 AX-123287278 2 109306023 CAGCCAACTTCTCTTGGCAATTCCAACTTTAAAGC[A/G]TTAGTCCGAAGTCAACCACTTAATTAGAAATTTAA R 2 1 2 1 101000 f 74 goat snp7437-scaffold127-2482656 2 25893732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771891 Affx-122959245 AX-385259047 2 109348394 GACCTGTGGTTTTTCTGGATTCTCAAGTTCATTGA[A/C]TATATTAGACTCACTTAGAGTTGTCAGCATTTCTC M 2 1 2 1 101000 f 74 goat snp7438-scaffold127-2525027 2 25853644 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390491 Affx-122967589 AX-123260848 2 109390055 TAAGAAGAGATTGACTGCAGTGATGGACCCTAGAC[A/G]CTGATTTGGGAAGAAAGGACAGGCAGGAGGTGACT R 2 1 2 1 101000 f 74 goat snp7439-scaffold127-2566688 2 25811948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441552 Affx-122928696 AX-123311889 2 109420203 CACCCTCAGACCATGGGGAAAGAGAAACAGTGAAT[A/G]TCATTCCCACAGATGGCCTGTTGAGAAACCAAAAA R 2 1 2 1 101000 r 74 goat snp7440-scaffold127-2596836 2 25780634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449551 Affx-122923247 AX-123319886 2 109461964 TCCAAAAATGTTGTTCCTGTGACATTCTAGGAATT[A/G]TTGGATAACTCAGTCATAGCCTTGTGGGCCAAATA R 2 1 2 1 101000 r 74 goat snp7441-scaffold127-2638597 2 25738571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445207 Affx-122925517 AX-123315544 2 109527103 CGATTAGGACCTTTGCTCCCCTGTGTTACTGAAAA[C/T]GGCAGGACTGCAGTGCAGATGCTACCCATTATGAA Y 2 1 2 1 201000 f 74 goat snp7442-scaffold127-2703736 2 25673407 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449050 Affx-122923063 AX-123319385 2 109579566 AACAGAGGAGGTGTCCACGTAATAGAAAAGAGTGA[A/C]CTGGACAAAGACTTCTTCCAACAGTCATACGTACC M 2 1 2 1 101000 f 74 goat snp7443-scaffold127-2756199 2 25622049 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413408 Affx-122950710 AX-123283757 2 109671384 TGTCCATAACCCTTTAATACTTTATCTCTCTAAAG[G/T]TCATTTCCAGTATAGAATGTTATGGTTCTATGGCC K 2 1 2 1 101000 r 74 goat snp7445-scaffold127-2848017 2 25529092 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415763 Affx-122948928 AX-123286112 2 109717823 TATTCCCCCATTCTAAGGAAGTGCTTCCTAACAGC[A/G]CATGATTACAAAAAATTGTCTCAAGAAGTAGTCAG R 2 1 2 1 201000 r 74 goat snp7446-scaffold127-2894456 2 25482634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434396 Affx-122934689 AX-123304737 2 109748345 GAATTCATTGGCAGTTTTTTCATTATGTTTTTCCT[G/T]GTCCACATATTTCCTTTGGCTTTTTTGGTGGTTGC K 2 1 2 1 101000 r 74 goat snp7447-scaffold127-2924978 2 25451647 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390904 Affx-122967098 AX-123261261 2 109782359 GAGCCACATCTCTTCCGCACATATGTACAAGTACA[G/T]AGTTTATTTATATACTTTCAAGGAACACTTAACCA K 2 1 2 1 201000 r 74 goat snp7448-scaffold127-2958992 2 25417629 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380668 Affx-122975188 AX-123251026 2 109824326 TAAAGGCAGGGATTGCATTGCTTCTGCCTGTTTTA[C/T]ATCTAAATCAAAAGGTTAAGACCAAAAGATTGTAC Y 2 1 2 1 201000 r 74 goat snp7449-scaffold127-3000959 2 25375344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412734 Affx-122950727 AX-123283083 2 109852935 TGTATGTCAAGATTCATCTTGCTCAAGGGTGAATG[A/G]CATAGTAAAATAAAATCAAATGAAATAAAAATAAG R 2 1 2 1 101000 f 74 goat snp7450-scaffold127-3029568 2 25346689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436922 Affx-122933198 AX-123307260 2 109883401 GAGCAATAATTCAGTTTATGTCATTGTTGTACCTT[C/T]CTCTCTGGAACACAAATTCAAGCAAGCTGGTCCCC Y 2 1 2 1 201000 f 74 goat snp7451-scaffold127-3060034 2 25316263 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411293 Affx-122952298 AX-123281643 2 109933731 TGTGGTGAAATAATTGGTTGAAAAAGACAAATCTG[C/T]AAAATAAATAAATAAGGCGACATTTGACCTTTCAC Y 2 1 2 1 101000 f 74 goat snp7452-scaffold127-3110364 2 25265915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412454 Affx-122951406 AX-123282803 2 109969844 CCTGTTTTGTTGTTTTCTTTATCTGCTCTCACCCA[C/T]GAGGATTCAGAATTCTTTCATACAGTTTTTGTAGG Y 2 1 2 1 201000 r 74 goat snp7453-scaffold127-3146477 2 25229229 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426653 Affx-122939936 AX-123296999 2 110023009 AGTGGTCAGATCTCAGGTCCTTGACCATGGTCAGA[C/T]GTTTGGACTTTATTCTGAGTGCAGTGAGAAGCCAC Y 2 1 2 1 101000 f 74 goat snp7454-scaffold127-3199642 2 25176027 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777051 Affx-122924183 AX-385264174 2 110072664 ATATTTCAAATGTACTATAAGCATACTGAAATAAT[A/G]TAAATAATAGGACTGAAATGATATAAATAGGAGAA R 2 1 2 1 101000 r 74 goat snp7455-scaffold127-3249297 2 25126120 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275310 Affx-1111834828 AX-519548886 2 110105142 TTTCCTCCTCAATCTTCAAGTCTCTCTCAAATGCT[A/G]TTCCCCCA R 2 1 2 1 101000 f 74 goat GoatD01.055426 2 110105142 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445136 Affx-122926173 AX-123315473 2 110114801 TTATAAAGAGAAAACCTGCTACCTTGTGTAAAAGC[A/G]TGTAAGTAGTAGTAGAGGATAAGGAAAGATAAGTA R 2 1 2 1 101000 r 74 goat snp7456-scaffold127-3291434 2 25085251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377935 Affx-122977217 AX-123248294 2 110156019 TGCTGTAGTTTTAGAATTAAATTTCAGCTGACAAG[C/T]AGGGCATGTAAGAAGAGAAAGAAGACAATAATGAG Y 2 1 2 1 101000 f 74 goat snp7457-scaffold127-3332652 2 25044407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773631 Affx-122969904 AX-385260771 2 110191114 GTAAAGAAATGTTCGTTTCTGTATCAGAAATTATA[C/T]AATCTCTAAGTAACAAAAGTTATTCCTCCAGAGCT Y 2 1 2 1 101000 r 74 goat snp7458-scaffold127-3367747 2 25009382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389130 Affx-122968554 AX-123259488 2 110246935 CTTTCAATCTTACAACATTGTATTAGTTTTAGGTA[C/T]ACAACGTAGTGATTTGATTTCTCTGTTGCAGTATG Y 2 1 2 1 102000 r 74 goat snp7459-scaffold127-3423568 2 24952488 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464170848 Affx-1110347652 AX-515646306 2 110248285 ATATGTGGCACCTCTGCTTAGCATTCTTCCCATAT[A/G]CACTCAGTTTCAGTTTTGCTGAGCAGTGGTATGAC R 2 1 2 1 101000 r 74 goat 2_110248285_AF-PAKI 2 110248285 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414784 Affx-122949233 AX-123285133 2 110283180 TATGTTTTGCCCTCTTGGGAGCTATAATAAGAAAG[C/T]ATCTTATAGGGAGGAGATTAAACCAGTCTCAAATC Y 2 1 2 1 101000 f 74 goat snp7460-scaffold127-3459813 2 24915959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439038 Affx-122930339 AX-123309375 2 110316910 TTTTGGATTAGAGTGTACAGAATTTTAAAAAGGAT[A/G]GGAGGGTTGCAATCATCCTGGAACAAAACAAACAT R 2 1 2 1 101000 r 74 goat snp7461-scaffold127-3493543 2 24882096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425280 Affx-122940967 AX-123295626 2 110358077 ATTCAGCTTTGCCCGCCATATTGGAAAGCTGTCTC[A/G]TGGAGGAAGGGGTGTTGTCCACACGACAAAACGCC R 2 1 2 1 101000 f 74 goat snp7462-scaffold127-3534710 2 24840986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443407 Affx-122927383 AX-123313744 2 110392122 AGATCTGCATGTAGTCCTACCATTGTGACCTGGCC[A/G]CAAATACAGTGAGAACAGTTGCACTGAAGCAAACA R 2 1 2 1 101000 f 74 goat snp7463-scaffold127-3568755 2 24807290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398538 Affx-122961531 AX-123268893 2 110431871 GAACTGCTGTTTGGACACATTAACTTGCCCCCAGA[C/T]GACTGCGAGTAAGAGGGGAAGCTGTAATCAGACCC Y 2 1 2 1 101000 f 74 goat snp7464-scaffold127-3608504 2 24766973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439687 Affx-122930578 AX-123310024 2 110467014 TGGGGTTAGGTTGGAAAAGCCACCTGTTTACAGAA[C/T]GATGTGGGAGCTTTTCTGTAGAAATTCCATGGTTA Y 2 1 2 1 101000 f 74 goat snp7465-scaffold127-3643647 2 24731925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411080 Affx-122951933 AX-123281430 2 110554119 GTTTGTCAGTGTTTCTGTGTGTGAAATTTGAGCCA[A/G]TGGTTTTAGACATATGCATGTGTGAAACAGCTAAT R 2 1 2 1 201000 r 74 goat snp7466-scaffold127-3730752 2 24644687 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408933 Affx-122953943 AX-123279284 2 110588160 AACTTCTAGGCCAATCCAGTAGAGACCCCTTTGCA[A/G]AGCTATAAGTCAGCCATAAGCAAAGCACTTTGCGA R 2 1 2 1 201000 r 74 goat snp7467-scaffold127-3764793 2 24610368 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394679 Affx-122964363 AX-123265034 2 110641252 GTTGGGGCATAGACTTGGATAACTGTGATATTGAG[A/C]TATCAAAAGAGGCTCCTATATCTGAAAGGCTGAGA M 2 1 2 1 201000 r 74 goat snp7468-scaffold127-3817885 2 24557058 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772903 Affx-122968618 AX-385260048 2 110678922 TCTTGAACACTTGTATGTCTCAACAATGAAGACAA[C/T]GCCTGGCACATGCTTGGTGCTTAACAAACACTTCT Y 2 1 2 1 101000 r 74 goat snp7469-scaffold127-3855555 2 24518574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382581 Affx-122973754 AX-123252939 2 110727658 ACATGCACATGAAGACATGGGCAGAAGGAAGAACC[A/G]TCTGTGAGTGGGATGCCTGGGACTCCATTTAAGAA R 2 1 2 1 201000 f 74 goat snp7470-scaffold127-3904291 2 24469582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777334 Affx-122923846 AX-385264456 2 110777843 TCTGTGCATAGCCCAAATCAGTGCTGGACTCTGCT[A/G]CTCCTCAACACAGATGTGTTGACAAGATGAGGTGT R 2 1 2 1 202000 f 74 goat snp7471-scaffold127-3954476 2 24418472 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801636 Affx-122950068 AX-385288544 2 110867376 TGGCATCAGGAACCTGTGGCTTATTACATGACATA[C/T]GTGATCATTAAAGGAGATTTATTTGGAAATAAACA Y 2 1 2 1 101000 f 74 goat snp7473-scaffold127-4044009 2 24320629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421892 Affx-122944262 AX-123292239 2 110919212 CAACAGCTTGATGCTAATGAGCCTACTTAATAGCC[A/G]CATTTTCCTCCCCAAAGTCCAGCATCAATACACAG R 2 1 2 1 101000 f 74 goat snp7474-scaffold127-4095845 2 24267325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423464 Affx-122942584 AX-123293810 2 110969858 GTGATCTTTCCCATCTTTGCATCAGGTATTCAAAG[C/T]ATTGGAGCTTCGCCTTCAGTATCAGTGCTTCCGAT Y 2 1 2 1 303000 f 74 goat snp7475-scaffold127-4146491 2 24215685 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789057 Affx-122919403 AX-385276070 2 111020375 GCAGATGTTTGGCCAAGAAAATAGGAGATCATTTG[A/C]GATGAACATTTTTCTGTCCAGTTAAGTTAGGTCTG M 2 1 2 1 101000 f 74 goat snp7476-scaffold127-4197008 2 24164329 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395121 Affx-122964146 AX-123265476 2 111053952 GTGGCTTCTGTTTTGAACTTTTCAAGCACCAACAG[C/T]TGTCTAGCCTCAGGACAAAACATGAAAAACAAAAT Y 2 1 2 1 101000 r 74 goat snp7477-scaffold127-4230585 2 24130443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407588 Affx-122954659 AX-123277939 2 111112737 TTGCTTCTCCCCTGAACTCCATAGTCCATGTGTCC[A/G]CTTGGGTGGTTAATAGCTGTTCCCCACATACCCAG R 2 1 2 1 201000 r 74 goat snp7478-scaffold127-4289370 2 24070689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443378 Affx-122927405 AX-123313715 2 111197184 GCAAGTTCTGGCGCCAGGCTGCCCAGGTTTGAACA[C/T]TGTCTCTGCCACTGACCCAGTGTGGAGGTCTGATC Y 2 1 2 1 101000 f 74 goat snp7480-scaffold127-4373817 2 23988367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426931 Affx-122940432 AX-123297276 2 111226826 GATCTTATTAGATACTTTTTTATACTACTGTACCT[A/G]TTAAATCTTGTTTGGCTTGCCTATAACATAGTAAT R 2 1 2 1 101000 f 74 goat snp7481-scaffold127-4403459 2 23957954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439731 Affx-122930543 AX-123310068 2 111278227 ATTTAACTGTTGCAGATCTGAGGAGACTAAGCAGA[C/T]ATGACCTCTAAATGCTGTGTGATACCCTGGATTGG Y 2 1 2 1 101000 r 74 goat snp7482-scaffold127-4454860 2 23906619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393759 Affx-122965211 AX-123264114 2 111330478 CAACACATATACACAAACATACATATATGCATATA[C/T]GTATAGTTTAAAATGAGAATCTGTTCACTGGGACA Y 2 1 2 1 103000 r 74 goat snp7483-scaffold127-4507111 2 23854240 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788007 Affx-122919832 AX-385275028 2 111374018 ATGACATACTTCAGAGCTTAATTATATACTCCCAT[A/G]TTCATCTAGGTTTGCTATGCATGCGAGAAATTTCT R 2 1 2 1 101000 r 74 goat snp7484-scaffold127-4550651 2 23807723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436352 Affx-122933068 AX-123306691 2 111434531 ATGGAAATCCTGCCTGGAAATCATCTGACAACATC[G/T]ATAAAGAGCCTTAAGACTGTACATACCCTTGACCC K 2 1 2 1 201000 r 74 goat snp7485-scaffold127-4611164 2 23747345 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414936 Affx-122949093 AX-123285285 2 111463101 CTTTTTAAACTTCCTTACACTCCTGCTGATCCTGT[A/G]GAGGGCTCTACCATCAGTCTCCTTTGCCCTCCTAG R 2 1 2 1 101000 f 74 goat snp7486-scaffold127-4639734 2 23718556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391578 Affx-122966614 AX-123261935 2 111517801 CACAGCTCCTGGGTGGAATGAACCAGGTGAGGAAG[C/T]GGCATCTAGGGATTTTGTGTCAAAGCAGAGAGCCT Y 2 1 2 1 101000 r 74 goat snp7487-scaffold127-4694434 2 23663803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395260 Affx-122964093 AX-123265615 2 111553782 CCTTAATGCTTTGGGTCCTTGCTGAGTGCCCTCCC[A/G]CAGGCAGCCTCAAGTTCTCTTTCTTTCCATGCTGT R 2 1 2 1 201000 f 74 goat snp7488-scaffold127-4730415 2 23627967 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449353 Affx-122922970 AX-123319688 2 111617814 ACTGAGCACGCATGCATGCATGCATCCAATCCACT[A/G]TACTCTCCCAAACACAAAACAGGGAGAGGCTCAAG R 2 1 2 1 101000 r 74 goat snp7489-scaffold127-4794447 2 23563782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785412 Affx-122944591 AX-385272457 2 111706961 TATTTTAACTATCAGATAGATTATCATTTATATTA[C/T]GGAAGGTTCAATGATGACATTCTGCATTACATTCT Y 2 1 2 1 101000 r 74 goat snp7491-scaffold127-4883594 2 23474109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411757 Affx-122951500 AX-123282107 2 111744922 TGACTCAAGTCCCAAATCTTTACCCTAAGCTTTGA[C/T]GTTGCCACTTGGGTGTCTAATAAGTTTTCCAAATA Y 2 1 2 1 101000 f 74 goat snp7492-scaffold127-4921555 2 23435930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441519 Affx-122928717 AX-123311856 2 111779666 TTGGATACTGATTTAGAAATAAGATATAAAATGTT[A/G]CTGTGAGGGCAGTGAAATAATTCTATGTGTAAGAA R 2 1 2 1 101000 r 74 goat snp7493-scaffold127-4956299 2 23401218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793187 Affx-122965083 AX-385280165 2 111833601 ACTTTTCTTACATTCCCTTCAATTATGGGTTATTA[C/T]AAAATATTGCGTCTAGTCTCTGTGCTATACTGTGT Y 2 1 2 1 101000 r 74 goat snp7494-scaffold127-5010234 2 23347200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422933 Affx-122943033 AX-123293279 2 111904433 TTTGTAGGGCAACATCTAAGCAAGGCAGTTATGTT[C/T]TTATGCTTTTGCACTTGGGGAACATTTTTGTGGTG Y 2 1 2 1 201000 f 74 goat snp7495-scaffold127-5081066 2 23269545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440696 Affx-122929908 AX-123311033 2 111934280 AAGGCAACAAGCAGACGGGACCCTGGAGTGCAGAA[G/T]AAGGGACATGGGGCATGTGAGTGACACCCAGAGAG K 2 1 2 1 101000 f 74 goat snp7496-scaffold127-5110913 2 23239793 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412748 Affx-122950523 AX-123283097 2 111963489 AGAAGAGAGCAGTGGGATTAAAATAATCTCAGTCC[A/G]AAAATGTTTTGTATGATTCATTATTAAAATGACAA R 2 1 2 1 101000 f 74 goat snp7497-scaffold127-5140122 2 23210349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784446 Affx-122970141 AX-385271495 2 111996291 TGTCTGCATATACCCTGTCTTGAATAAATTCAATA[A/G]TGAATCTCTGAGATTTGCTATTGTTACCCTATCCT R 2 1 2 1 101000 r 74 goat snp7498-scaffold127-5172924 2 23177623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414580 Affx-122949373 AX-123284929 2 112061284 CTAAACAAACAAAAAACCCCAGCAAGCTGAAAATG[C/T]GCCTATTTACAAAATTCTTCATCAAGCTTCATATT Y 2 1 2 1 201000 r 74 goat snp7499-scaffold127-5237917 2 23112754 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800814 Affx-122960488 AX-385287730 2 112093225 CTAATCACTAACAATCTTGGTAAACACGGTACAGT[A/G]TATCATTAATAGCAGAGAACATAGATTTTGCTGCC R 2 1 2 1 201000 f 74 goat snp7500-scaffold127-5269858 2 33591271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385419 Affx-122971332 AX-123255777 2 112168733 GTAAACAGGCGTCAGGGCTACATTCTTTTTCTTCC[A/G]TGAACCATTTGGATCCTGAAGCCTGAATTTCACAC R 2 1 2 1 201000 r 74 goat snp7502-scaffold127-5345366 2 23005166 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397957 Affx-122961908 AX-123268312 2 112208827 GATAAAAGGATGTATATTACTTTTTGAGGCCTGCC[C/T]GAAAGCTCATCGTGTCTTTCAAAAGAGAAACAGAA Y 2 1 2 1 101000 f 74 goat snp7503-scaffold127-5385460 2 22966840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376434 Affx-122978068 AX-123246793 2 112240815 AAGCCAGCCTCCTTGCCCTTCCTTAAACACCAGTC[A/G]TTTTTGAGCCCACCCAGTCCTCTGGCGTTTGCTGT R 2 1 2 1 101000 r 74 goat snp7504-scaffold127-5417448 2 22935023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277885 Affx-1111836140 AX-519551380 2 112289093 CCCCTAATCCCACTGTTGCTGGCATCCAAAATAAA[A/G]CAAACTTTCCTTTCTACCAACCTGGCCTCTTTGAT R 2 1 2 1 103000 f 74 goat Random2.2K-259 2 112289093 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791239 Affx-122979186 AX-385278233 2 112294394 CCAACTGCAAGTCATGAGCTAAACAAAAACCATTT[A/G]CTTAGATATTACAGCCAGTCTTTTGGTTGTCATCC R 2 1 2 1 101000 r 74 goat snp7505-scaffold127-5471027 2 22880267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768609 Affx-122967113 AX-385255789 2 112325450 AAAGAGAACATAAACAAAAATTGAGAAATACAGTG[C/T]GGTACTCCTTACCACATGCTATCATTTTCTGCATT Y 2 1 2 1 201000 f 74 goat snp7506-scaffold127-5502083 2 22849605 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789554 Affx-122950627 AX-385276563 2 112357103 ACTCCTCAGAAGTAAGTACTGAAAATATTCACATT[A/C]TATTTTTAACAGTGTCTTAGAAGAATTGATAGCCA M 2 1 2 1 101000 f 74 goat snp7507-scaffold127-5533736 2 22818077 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771208 Affx-122976413 AX-385258366 2 112436433 AACTCCTGTGAATTCCATCTCCTTAACCGTTCTCT[A/G]CTGTTACCACCATTATCTGCTAGTACAGATCTTTA R 2 1 2 1 101000 f 74 goat snp7509-scaffold127-5613066 2 22737848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388097 Affx-122969500 AX-123258455 2 112493315 CTCTTTGGCAGCATTTAAAACTGGCCTCCCTCTTG[C/T]GTTGGGTGGCTTTCAGGGTTTTGGTTCAGAAAATA Y 2 1 2 1 101000 f 74 goat snp7510-scaffold127-5669948 2 22680948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389328 Affx-122968488 AX-123259686 2 112532443 CACCCAGTGAGGCAGTCGCGCCTCTCCCTGCTGGG[C/T]GATGGTAGCAGTCATGCAGAAGCAGAAAACCTTCT Y 2 1 2 1 101000 r 74 goat snp7511-scaffold127-5709076 2 22641981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431139 Affx-122936580 AX-123301480 2 112570443 AGAAGGTGTGCCCTGGAGAAGTTCCAGCATTTGTG[C/T]ATCAGGAGACTTAAAATAGCAAACAACAGAAGGAA Y 2 1 2 1 201000 r 74 goat snp7512-scaffold127-5747076 2 22604097 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418238 Affx-122947036 AX-123288586 2 112623877 CTCTGGTTGTTATTATTTTACATTAATTCATAACA[A/G]TGTGTAGAATGCTTGGGGAAGATACAGAAAGGAAC R 2 1 2 1 202000 f 74 goat snp7513-scaffold127-5800510 2 22550801 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379600 Affx-122976022 AX-123249958 2 112654847 TTTTTCCTGCCTATGAGTGGTTTATGTGTCAGATG[C/T]GGTTAAACCCATGGGCTTTATTGCCTCATTTGAAA Y 2 1 2 1 101000 r 74 goat snp7514-scaffold127-5831480 2 22520125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421897 Affx-122944257 AX-123292244 2 112691228 ATGTAGTTAATTTTCTGTCTTCCTCCACCTAGAAT[A/G]TAACTGTGTAGAAAGAGAAATTTGGCTGTTGGGCT R 2 1 2 1 101000 r 74 goat snp7515-scaffold127-5867861 2 22483507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407188 Affx-122954821 AX-123277539 2 112726765 CTTGCTCTCGTATCTCCTTTGGCCATATCCTTTTC[G/T]CTTGTCCTTCTCATGCTTTGTAGAAATCCTTAGTC K 2 1 2 1 101000 f 74 goat snp7516-scaffold127-5903398 2 22446414 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271848 Affx-1111833150 AX-519545631 2 112752513 GCTCTCACAAACCTGCTCCACCCATGATTTTGCCA[A/G]TCTCCCAAGATGGCAAATAAATCTTTCCATCGCCT R 2 1 2 1 101000 r 74 goat 2_112752513_AF-PAKI 2 112752513 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440611 Affx-122929974 AX-123310948 2 112756338 GATCCATTTCTTGTTATTCCACCTTCGCCAGGAGT[G/T]AAAGTACTAAAATCAAATTTATGATTTAATATAGT K 2 1 2 1 101000 f 74 goat snp7517-scaffold127-5932971 2 22416240 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394131 Affx-122965328 AX-123264486 2 112785453 TGAAATTTACTGTGATTGTGGGAATGTAATTAACC[G/T]AGGTGAAGAGACAATGGTCACATAAGAAACTTGAT K 2 1 2 1 101000 f 74 goat snp7518-scaffold127-5962086 2 22386580 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778758 Affx-122960891 AX-385265868 2 112823325 CTAGAAATCCACCTTTTCGGGGCTCACTTACTTAT[A/C]TTTCCCAAAGGAGACAGATGTTTTACTGGATTGGT M 2 1 2 1 101000 r 74 goat snp7519-scaffold127-5999958 2 22348757 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393986 Affx-122965036 AX-123264341 2 112854775 TGTAATGTGACCAGGAAATCTAGACATATGTGCTT[A/G]TGTAGGACTAGACAGTGGTTAAGACATATCCAAGA R 2 1 2 1 101000 f 74 goat snp7520-scaffold127-6031408 2 22317281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786842 Affx-122953297 AX-385273871 2 112883485 GCATAAAACAGACTAGAGACAGTGTACTCATTATG[C/T]AAACAAAACTTCAAGATAAATCTTCTTGCCTGTCC Y 2 1 2 1 101000 r 74 goat snp7521-scaffold127-6060118 2 22288714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425201 Affx-122941031 AX-123295547 2 112935878 TGTTTAAAACCTCTGATGAAGGGACCATTGACATG[C/T]AGAGCTCTCAATCACATCCACCATTGCTGGGTCAG Y 2 1 2 1 101000 f 74 goat snp7522-scaffold127-6112511 2 22235955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388868 Affx-122969315 AX-123259226 2 112965575 CATTACGGCTTAAAACCAAATTAAACATAAGAAAA[C/T]AACATAACAGAAAACCATGAGTGAAAGAACAATTC Y 2 1 2 1 202000 f 74 goat snp7523-scaffold127-6142208 2 22206414 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396791 Affx-122962755 AX-123267146 2 113008741 CCAATCGAGTCCAATTCGACTCAATGGACACGAAT[A/C]TGAGTAAGCTCTGGGAGTTGGTGATGGACAGGGAA M 2 1 2 1 303000 f 74 goat snp7524-scaffold127-6185374 2 22163284 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445186 Affx-122925532 AX-123315523 2 113083076 CTCCTATTGATTAGGGTCCATGATCTCTTCCGTAA[C/T]GGATACTTTGGCTTTTTGCCTGCCGGCTAGTATAC Y 2 1 2 1 101000 f 74 goat snp7526-scaffold127-6259709 2 22089011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415656 Affx-122948564 AX-123286005 2 113114685 CCCATACATCACTGAATGCCATAGTAGGCTTTCCT[A/G]AGGACATGGAAGAATGCCTTCATCCTATCCACGGA R 2 1 2 1 101000 f 74 goat snp7527-scaffold127-6291318 2 22057324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440834 Affx-122929269 AX-123311171 2 113150619 AATAAGACAGTAATGTTAGACTATGAATCAATTTC[A/G]TTTTGCTTCACAGTTTTCTAAATACAGCCTTCACA R 2 1 2 1 101000 r 74 goat snp7528-scaffold127-6327252 2 22021339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392754 Affx-122966005 AX-123263111 2 113186689 CTTTTAAATACTAATGTTTATGACTTACAGAATGG[C/T]TATCACATCTAGTCCCTGAAAAAACACTTGATCAA Y 2 1 2 1 201000 f 74 goat snp7529-scaffold127-6363322 2 21985033 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435488 Affx-122933437 AX-123305828 2 113229523 TGAGAACATGACCTTTGGGTGATTCCGTACTCTTC[A/G]CATGCCCAGAGAATTTCTACAACTAATCCTGCAGC R 2 1 2 1 101000 f 74 goat snp7530-scaffold127-6406156 2 21942232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769506 Affx-122921533 AX-385256676 2 113261782 TAAACACATGTTAAGCTTGAATTCACTAATAAAAA[C/T]GTTCATGAAAGCATATCACATTCATATAAGATCTC Y 2 1 2 1 201000 f 74 goat snp7531-scaffold127-6438415 2 21910044 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376930 Affx-122977783 AX-123247289 2 113323287 ATTTTTGTCATTTTTATATAAATGTTTTATATACA[C/T]GCTGAGAGGTCTCCTATTAAGTTGGTACAGAAGTA Y 2 1 2 1 103000 r 74 goat snp7532-scaffold127-6499920 2 21848080 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393762 Affx-122965208 AX-123264117 2 113351982 TGTGCCAATAGTGTCCTGCTCATTGGTAGGGGAAG[C/T]GATTGCATCCGGGCAAACAAAACTGTGCCAAATAT Y 2 1 2 1 101000 r 74 goat snp7533-scaffold127-6528615 2 21826745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791972 Affx-122933439 AX-385278960 2 113403831 TATTACTTAGATAAGAATGCTGAAACCTTTGGGTG[C/T]GAAGTTTTAAAATAGACTAGGTTTTTCTCCAGCTA Y 2 1 2 1 101000 f 74 goat snp7534-scaffold127-6580464 2 21774549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382691 Affx-122973642 AX-123253049 2 113460358 ATTCCCTAGACATATCTATCAAATACAGAGGCTTA[C/T]ATTTACCTGTAAAATTGGGAAATATTTAAATTTAT Y 2 1 2 1 101000 f 74 goat snp7535-scaffold127-6636991 2 21717553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415797 Affx-122948903 AX-123286146 2 113502466 AGGATGAAGAAAAGCCATACAAGCTTAAGAATTCT[A/G]CCACAGGAGGGAGCAAGATGCATGGGGCAAGCACA R 2 1 2 1 202000 f 74 goat snp7536-scaffold127-6679099 2 21674897 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436806 Affx-122932244 AX-123307144 2 113533981 GCCAATAAGGTGAAAGAAATGCCAAAGAAAGACAA[C/T]ACTACAGAAGCCAAAGGAAAAAGTTTTTAAGAAGC Y 2 1 2 1 101000 f 74 goat snp7537-scaffold127-6710614 2 21642658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390889 Affx-122967111 AX-123261246 2 113566684 TACATCTCTTGCAGTAGTTTTGAGTAAAACCTTAC[C/T]ATTCCAACATGTGATAGAATACTTTTTCTTCAACA Y 2 1 2 1 101000 r 74 goat snp7538-scaffold127-6743317 2 21610311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452616 Affx-122920366 AX-123322949 2 113599787 CATTTTCCCCTCCTGCCTGAAATGAGACTTAAGAT[A/G]CTGGGACAGAGAGAACAAGTAAGGGATGAAACATC R 2 1 2 1 102000 f 74 goat snp7539-scaffold127-6776420 2 21577734 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428876 Affx-122938339 AX-123299218 2 113660546 ATAAATATAAGTAATCTGATTCTATAGAGAATTTT[A/G]CTTTCATTATTTTCATTTTGATTTATTGAGACCTC R 2 1 2 1 303000 f 74 goat snp7540-scaffold127-6837179 2 21516318 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386397 Affx-122970830 AX-123256755 2 113711378 TGTCTTTCTCCTCTCACAGATATTGTCATTGTTTA[A/G]CCTTCTGTCTAGGTTATTATTATCATCACCAAACT R 2 1 2 1 201000 f 74 goat snp7541-scaffold127-6888011 2 21465466 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798529 Affx-122933391 AX-385285462 2 113741067 CTGAAAATTTGAGTTAGTTTACAGGAGAGGGATCC[A/G]CCCCTAGGGTGTTACATAATAGATGCTTTTCATTG R 2 1 2 1 202000 f 74 goat snp7542-scaffold127-6917700 2 21435388 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417649 Affx-122946845 AX-123287997 2 113791080 TTTCTCCTTTCTTCTCTCTTTTTCAAAAAGTTATA[C/T]ATCAGATTTAGGACAAAGGTGCTTCTCCTCTAACT Y 2 1 2 1 103000 r 74 goat snp7543-scaffold127-6967713 2 21385335 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439555 Affx-122930096 AX-123309892 2 113837007 GAATTTCTCTAAGTCTGTGCATTTCTAAACTTGTA[C/T]AAGCTCTTAATTTTCAAAAGAGTCATTTTCAAGTC Y 2 1 2 1 101000 f 74 goat snp7544-scaffold127-7013640 2 21339798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762277 Affx-986696808 AX-385250466 2 113871749 AATGCTCTCTATGCACCTGCCCTCCTCTGTATGCA[C/T]CCGAGCCACGGCGTCTGGGGTCGCTTCTTCTGTCC Y 2 1 2 1 600010 f 74 goat 2_113871749 2 113871749 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38407481 Affx-122954765 AX-123277832 2 113875009 TCTCATTCTAATTCCTCTTCTTTCCCTTCCATAAC[A/G]CAAAACCAAGGGGTAGAGGATATGAAACTTTGCAG R 2 1 2 1 103000 r 74 goat snp7545-scaffold127-7051642 2 21300495 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802947 Affx-986696095 AX-385289838 2 113907938 TGAAATTGGCGAAGGATTTCCCCATTTTGGAGGCT[C/G]AGCTGGGGTATGCAACACCTAGGTCTGAGAGCAAC S 4 1 2 1 600010 f 74 goat 2_113907938 2 113907938 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 320778444 Affx-122949876 AX-385265558 2 113911728 TTTAAAATAAAACCTACAGGGTTCAACCAACACTG[C/T]AGATCTATGCCTGGATGCCTGTAACCACCTTACTC Y 2 1 2 1 102000 r 74 goat snp7546-scaffold127-7088361 2 21263168 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447756 Affx-122924576 AX-123318092 2 114001580 TGAATTCATGGAAGATGGAGTTTCCAAGTTGGGAA[A/C]GCTGAGGAGAAAGGGAAATGAGAAGAATCTCAAAT M 2 1 2 1 101000 f 74 goat snp7547-scaffold127-7178213 2 21172551 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398792 Affx-122961420 AX-123269147 2 114033064 TGCCTAGCACATAATCTGTTTTCCCTGCCTTCATC[C/T]TCCTGGGTATTTTGTAGTAAGTAATGAAAAATTGA Y 2 1 2 1 303000 r 74 goat snp7548-scaffold127-7209697 2 21140519 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411493 Affx-122951782 AX-123281843 2 114062894 ATGTTCTTTATTGCCCCCACCCAAGTCACCAACGT[A/G]CATCCTTAGGATTGTTCAGCTCAAGGCTGAACAAC R 2 1 2 1 101000 r 74 goat snp7549-scaffold127-7239527 2 21109807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382161 Affx-122974034 AX-123252519 2 114141857 ATGATAAAGAACAGCCAGCAAGACTGGTCTTTCAT[A/G]TTGTTTTTAATTTTTATAAATATATTTACTAAACA R 2 1 2 1 103000 f 74 goat snp7551-scaffold127-7318490 2 21030095 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773266 Affx-122932848 AX-385260409 2 114185315 TATCCACTGCAAGCTGCATGTGACTTTGATTCTAC[A/G]TAGAAACCCTCACTGTAAGAAGAATATAATTATAT R 2 1 2 1 101000 f 74 goat snp7552-scaffold127-7361948 2 20986534 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405880 Affx-122955604 AX-123276232 2 114215351 TTGCACCTATGGAAACTGAGAGGACCAAAAGATCC[A/G]TATTTGAATCTCAGTTCTTTTTTTCCATAGAAAAT R 2 1 2 1 101000 f 74 goat snp7553-scaffold127-7391984 2 20956108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780223 Affx-122964593 AX-385267319 2 114254886 TTTCTTTGCAATTGTGGTTCCAAGAACTTAAACCC[A/G]TTAAGAAACCATGCTGGTGGCCCTGAGGAAAATGT R 2 1 2 1 101000 r 74 goat snp7554-scaffold127-7431519 2 20915944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431137 Affx-122936581 AX-123301478 2 114313739 CCTTATGAATTTGATTCGTTCTCTCCCAAAACTCT[A/G]CCGTGCGGGAAAAAAAGAATACATAAATGGGTTTC R 2 1 2 1 101000 f 74 goat snp7555-scaffold127-7490372 2 20856819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764612 Affx-122964328 AX-385252254 2 114353075 ACATATTATCCTTATGGCTACAATCTACATTAGGC[A/G]CATGTTAACAAATGTTATCATTCAAAATTATTCTT R 2 1 2 1 201000 f 74 goat snp7556-scaffold127-7529708 2 20816315 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386297 Affx-122970928 AX-123256655 2 114424290 AAAACAGCGACAAAGGGAGGATTTCGGGGTTAGGT[A/G]GGAGTTGCCAAAAGTGGGTCATAGATACCCAGCTC R 2 1 2 1 201000 r 74 goat snp7557-scaffold127-7600923 2 20745163 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767998 Affx-122945409 AX-385255212 2 114459292 TTGTTAGAAGTCAGGTGTGTTAGAAAAAGAAAAAT[A/C]TAAATTATGTAAAGAGAAGCTATCTGTGATCATAG M 2 1 2 1 103000 f 74 goat snp7558-scaffold127-7635925 2 20710088 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443537 Affx-122927769 AX-123313874 2 114513193 CATCAATAGACTGTAAACAGAAAAAAAAAGAATGC[A/G]TGACCTAATAAATGTATGACAAAAATTCATTATTG R 2 1 2 1 303000 r 74 goat snp7559-scaffold127-7689826 2 20656266 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453445 Affx-122919864 AX-123323778 2 114547461 TGAGAGCCAGCCTCTTGGACCAAGGTAGGGAATTT[G/T]CACCCTTCACTTATTTTAAAGTACATACCTCACAT K 2 1 2 1 101000 r 74 goat snp7560-scaffold127-7724094 2 20622167 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275486 Affx-1111834926 AX-519549058 2 114603951 ATTTGCAGTTGAAGTATATGATGAAAATCTAGCCC[A/C]ACGGAGT M 2 1 2 1 101000 f 74 goat GoatD01.059005 2 114603951 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38412042 Affx-122951723 AX-123282392 2 114648407 GTCTATGGAATTGCAAAGAGTCAGACATTACTTAG[C/T]GACTAACATTTTCCATTTTCAGGACACTTGAAAAT Y 2 1 2 1 303000 r 74 goat snp7562-scaffold127-7825040 2 20521428 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788047 Affx-122974105 AX-385275068 2 114701083 TAATCTGCCTTACTCTTATTTAACATACTGAATTA[C/T]ACCTGTTTCAGAAATTACCTCTTTCAACAACCGTT Y 2 1 2 1 101000 r 74 goat snp7563-scaffold127-7877716 2 20468799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398178 Affx-122962652 AX-123268533 2 114755140 CACATCGGGAAATAACTGAGCAAAGCCAAGAGAGC[A/G]TGTTGTGTGTTGGATGTGATGTCACATGGGCAGAG R 2 1 2 1 101000 f 74 goat snp7564-scaffold127-7931773 2 20414760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773077 Affx-122970321 AX-385260220 2 114793557 ATCTCTGCATAAATTCCCAGAACTGGAATTCCGGT[A/G]TGAAGGAATCTGAAAGTTCAAGATTCTTGATGTAT R 2 1 2 1 201000 r 74 goat snp7565-scaffold127-7970190 2 20376323 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383615 Affx-122972553 AX-123253973 2 114828619 ATGATAGTCTAGTTTTCACAAGGAGAGGACACATA[C/T]GAAGTTATTCAGTTGACTTTCTTTCTGAATTTAAT Y 2 1 2 1 101000 f 74 goat snp7566-scaffold127-8005252 2 20341155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387170 Affx-122970626 AX-123257528 2 114872666 GGCATTCTGTAATGGGTCATCTTGTAAAAAGGAAA[C/T]AAAACAAGAACAAAATAGCAAAGATTTGATAAACC Y 2 1 2 1 101000 f 74 goat snp7567-scaffold127-8049299 2 20296639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383952 Affx-122972953 AX-123254310 2 114984713 GAAAGGATTAGCTTTGCAGATGCAATCGAGCATCA[C/T]GGTCCTATGGAGCTCAGGGAACTGCTGCTGATGGG Y 2 1 2 1 101000 f 74 goat snp7569-scaffold127-8161346 2 20185700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782516 Affx-122945596 AX-385269592 2 115024015 TCAATGGCTTGTGATGGATAACCTCTGTCAACCTT[C/T]GTGTCAAAGTGATGTTCCCCAGGGATCATCCGGAA Y 2 1 2 1 101000 r 74 goat snp7570-scaffold127-8200648 2 20146405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765501 Affx-122961514 AX-385252986 2 115071872 CTGTTCTTACTAGTCATTCTCTGTGCCCCATTTTC[C/T]ACTCCCTCTTTGGGAGTATATATGATCTTTCTATC Y 2 1 2 1 102000 f 74 goat snp7571-scaffold127-8248505 2 20098635 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421673 Affx-122944425 AX-123292020 2 115103950 GGGTATGAAATAAATAATACATTGTGATACTATTA[C/T]ATGTGTTTTGGTGTGGGGAATTTGCCCCTTTCGTG Y 2 1 2 1 202000 f 74 goat snp7572-scaffold127-8280583 2 20066742 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435913 Affx-122932764 AX-123306252 2 115192820 GGATCAAGTACTGAAAAGAAAGTGATGAGTCACAA[C/T]GTAAGAAAGAAAATATTTTCTGTAGCTCAGTTGAG Y 2 1 2 1 101000 f 74 goat snp7574-scaffold127-8369453 2 19977226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421534 Affx-122943875 AX-123291881 2 115286607 TTCCTCTGCAGAGAAGCCCACAATGGATCACATAT[A/G]CTCAGTGACCCATCACTTCTCAAGAAGCACTTATG R 2 1 2 1 102000 f 74 goat snp7576-scaffold127-8463240 2 19883068 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447119 Affx-122924468 AX-123317455 2 115312608 CCATCTCTTTTGAAAAAATGAATTTTCCAAAGAAG[A/C]TCACACTCATCCAGCCACCATCACGGCCATCATCA M 2 1 2 1 303000 f 74 goat snp27036-scaffold287-2722095 2 19834813 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398358 Affx-122961671 AX-123268713 2 115379638 GCTCAAGAATAACTGATTAACCATGCCAGTAATTC[A/G]CTGTGTGACTGGGCAAGCCATTGTGTTCTCTGGGT R 2 1 2 1 101000 f 74 goat snp27034-scaffold287-2655065 2 19773571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437013 Affx-122933128 AX-123307351 2 115439012 ATTGGCAAGACGAAGGAGCTGATTATGTGCAGAGA[A/C]AGGGCAGGGTAAAGAAAGCCAGATACCTGGAGGCA M 2 1 2 1 101000 f 74 goat snp27033-scaffold287-2595691 2 19713818 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779013 Affx-122969571 AX-385266120 2 115473672 CAGTTAACAAGCATAAAATGCAATAATGTAGAGTC[C/T]GAGAACTCTTTCTACTCATACACACACAAAAACAA Y 2 1 2 1 101000 r 74 goat snp27032-scaffold287-2561031 2 19679549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395486 Affx-122963897 AX-123265841 2 115620295 ATTTTGTTCTGACCCCATGGGAGTTCTTTTTAGAT[A/G]CCTTTCTAATTCACTCTAATAAACTGGCTGACTAT R 2 1 2 1 101000 r 74 goat snp27029-scaffold287-2414408 2 19532160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399678 Affx-122960500 AX-123270033 2 115704151 TGAGAAACTTACCTAAATCATAGACCTTTTGAAAT[A/G]CCATGCTCTTTTCTCTCTGCTGAGAAAGTGGAACC R 2 1 2 1 201000 f 74 goat snp27027-scaffold287-2330552 2 19445779 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271850 Affx-1111833151 AX-519545633 2 115739013 GTGACTGCATGATTTTCAAAGACTTAAGCTTCTTT[A/G]CTCTAATTGTTGCTCTACCACCTTCAACACTCAGC R 2 1 2 1 101000 r 74 goat 2_115739013_AF-PAKI 2 115739013 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778670 Affx-122975738 AX-385265782 2 115809110 ATCATCCACTTGAGGGCAGAATTTGGACTAAAGTT[A/C]TACCTAATCACATAGAATAAAATTACTCTTTATTT M 2 1 2 1 101000 f 74 goat snp27025-scaffold287-2225593 2 19341412 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795253 Affx-122968619 AX-385282211 2 115840152 ATTATCAAGCATGCAGTTGACCTTAAATTTAGACA[G/T]AAATAGCCCTTGCTAAAATTGTAAATGCCATGTCT K 2 1 2 1 101000 f 74 goat snp27024-scaffold287-2194551 2 19310019 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388581 Affx-122969163 AX-123258939 2 115872917 TCAATACTAAGGAACTTGTGAGGGTATTTTGTTGC[A/G]TTTATCACCATGTTATAAAAAACAGGAAGGCATAT R 2 1 2 1 101000 f 74 goat snp27023-scaffold287-2161786 2 19276659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421699 Affx-122944405 AX-123292046 2 115924204 AAAATCACACTTGAAGTAGCAGGAGGCACTGACAA[C/T]AATGGCCAGAGCCACCAACACAAAGATGCATTTCA Y 2 1 2 1 101000 f 74 goat snp27022-scaffold287-2110499 2 19225099 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443179 Affx-122927605 AX-123313516 2 115976135 ATATTTACTTGTTTGCATCAGTGCTGCTTATATTC[A/G]TAAAAATACTTTTTGAAAAGGGTCAGTGTTGATAT R 2 1 2 1 103000 r 74 goat snp27021-scaffold287-2058568 2 19172913 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389820 Affx-122968190 AX-123260177 2 116012380 AATTTCTAATGAAAATCTTGTATCTAACAAAAATA[C/T]GGATCAACTGTCTAGGTTTAAACATCACAAACAAA Y 2 1 2 1 101000 r 74 goat snp27020-scaffold287-2022323 2 19136580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764411 Affx-986696810 AX-385252110 2 116016800 CGAATCTATGGGTGCTTTACCACCAGGCATTCCAT[C/G]ACCTTCTATGATACCACAAAATTGGAAAATAAAAA S 4 1 2 1 600010 r 74 goat 2_116016800 2 116016800 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320783724 Affx-122951070 AX-385270780 2 116064544 ATATACTCAAGACAACAAATTCCTTTATCTTAAAA[C/T]AATTCCTGATTGTAGCTTTTAAAGATCCCATAAAC Y 2 1 2 1 101000 r 74 goat snp27019-scaffold287-1970159 2 19084906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382865 Affx-122973522 AX-123253223 2 116093142 ATCATACACACACACACACACACATATACACTTGA[C/T]ATCAGCTAAATTAAAGCTTTACTCACCAAACGAAC Y 2 1 2 1 201000 r 74 goat snp27018-scaffold287-1941561 2 19055336 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798019 Affx-122946628 AX-385284955 2 116157574 GTTTTTATTAGTTTATGTGGAATTGAAGCTATATT[A/C]GCAACTTTTATATTATTAATTTTCTGGAGAGCAAT M 2 1 2 1 101000 r 74 goat snp27017-scaffold287-1877129 2 18990504 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453318 Affx-122919977 AX-123323651 2 116225618 GACCCACAAGGACCTGGTGTAGCCTCAGTCTTCCA[C/T]GGATGTAGGTAATTAAGTTGAGTAGCAAATGGAAA Y 2 1 2 1 101000 r 74 goat snp27015-scaffold287-1809085 2 18922107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799820 Affx-122962250 AX-385286746 2 116351103 CAAAAAGAAAAATTAGAGCTCAGCTCCTTTGTTCA[C/T]GTTCCTCTTTTTAAGAGTGTGGAAAGATCTTTTTT Y 2 1 2 1 101000 f 74 goat snp27013-scaffold287-1683600 2 18799644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784462 Affx-122939615 AX-385271511 2 116436924 GATTCCTTAATCAACAGAGTCAAAATGACTTCAAA[G/T]AGATTTCTTCATGGGAAAGTTTGGGCGGGAGTACA K 2 1 2 1 101000 r 74 goat snp27011-scaffold287-1597779 2 18713250 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771698 Affx-122959310 AX-385258855 2 116479751 CTGCAGAGCCCAGGAATCTTGGTGATTGTTGAGAG[C/T]GTCTATAGAGAACCTTAAAAGAAAATTAGAAATCC Y 2 1 2 1 101000 f 74 goat snp27010-scaffold287-1554952 2 18670170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397006 Affx-122963137 AX-123267361 2 116520050 AACAGCAGAGATGGAGGTGTTCATCTTTTGAACTA[C/T]GTTTACATGGAACTGCCCACCAAGTACTCTTTCCG Y 2 1 2 1 101000 r 74 goat snp27009-scaffold287-1514653 2 18629313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438100 Affx-122931508 AX-123308438 2 116549832 CCTGGGATTCAGCACCACTGCCTCTAGTTCATTAA[C/T]ATGCCAAGTAGTGTGTGGCTGACACACAGGGTTTT Y 2 1 2 1 101000 f 74 goat snp27008-scaffold287-1484871 2 18599451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777238 Affx-122932223 AX-385264361 2 116596850 TTCTTTATGTTTTTTTTCGCCCTCCATATTCAGAG[C/T]GGATGTTATCTAAGTCTAATTTATTTTCTCTTCAT Y 2 1 2 1 101000 f 74 goat snp27007-scaffold287-1437853 2 18552314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420016 Affx-122945159 AX-123290364 2 116692793 GTACTTGCTGTTGTGCTCAAGAGGTGTGTTCGTGC[A/G]TGCCAGGTCACTTCAGTTATCTGACTCTTGGCTCG R 2 1 2 1 201000 f 74 goat snp27005-scaffold287-1341910 2 18455984 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398672 Affx-122961878 AX-123269027 2 116748892 CAGGATGTCCTTTAAAGAAGCATCACCAAGACTTC[A/G]TTGGGAGGTCTTAGTGATCACTTTTTCACGTGTCA R 2 1 2 1 201000 r 74 goat snp27004-scaffold287-1285811 2 18399806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375981 Affx-122978429 AX-123246340 2 116784824 AACACAGATCCCAGGAATGACCAGTCACTCAGGAC[A/G]CTTGGAAAACTGAATGGACCCCCACATGGAGGGCC R 2 1 2 1 201000 r 74 goat snp27003-scaffold287-1249879 2 18364052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273963 Affx-1111833955 AX-519547568 2 116798673 CTGGCTTGATTATTTCTTGTCCCCTATGCTTTTAC[A/G]CTTTA R 2 1 2 1 101000 f 74 goat GoatD01.011549 2 116798673 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382734 Affx-122973609 AX-123253092 2 116816088 ATGAACTAGAAGAATGTATATACTTTGACTCCTTC[A/G]ACACTGGTTTTGGTGTCTTTTGTCTCTTTAGTAAA R 2 1 2 1 101000 r 74 goat snp27002-scaffold287-1218615 2 18332871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414998 Affx-122949042 AX-123285347 2 116851065 CTCTGAGTGGGAAAAGTCACTGTGGGCAAGGAGAA[C/T]GAGCCTAACAAGAGCCCTTAGAAGTCACCCCTCAA Y 2 1 2 1 201000 f 74 goat snp27001-scaffold287-1183638 2 18297999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380217 Affx-122975483 AX-123250575 2 116914329 CTGACTTCCCTATTTTTATACAGAGAAATCATTTC[A/C]TATTTTGCCATATCTGAGTTTGGGATCACTTCCAA M 2 1 2 1 101000 r 74 goat snp27000-scaffold287-1120374 2 18234834 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441290 Affx-122929464 AX-123311627 2 116953762 ACAGTCTCCCCGTTTATGATGGTTCCCCATCTGCC[A/G]TGCACACTGCTTCCTTCCAGTGCCCTCATTCAAAC R 2 1 2 1 201000 r 74 goat snp26999-scaffold287-1080941 2 18194691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776832 Affx-122961015 AX-385263956 2 116999916 TGATGATTCTTTAATTACCTTAAAGGTAACTGTCA[C/T]GGCTTTTTCTGATGTGGACCTTTCGCCTTCTTTTG Y 2 1 2 1 101000 r 74 goat snp26998-scaffold287-1034787 2 18152332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408633 Affx-122953485 AX-123278984 2 117041208 CATTACCATGACCTTATGAATATTTATACTGTTTC[A/G]TGGAAAGAAAGAGGTGACTTAACATTGTAACACAA R 2 1 2 1 101000 r 74 goat snp26997-scaffold287-993495 2 18110804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274766 Affx-1111834482 AX-519548352 2 117067105 TGCAGAGAGAAGACCTGTGTGTGCTTGCACTTGGG[A/G]TTCCCTC R 2 1 2 1 102000 f 74 goat GoatD01.037908 2 117067105 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443712 Affx-122927152 AX-123314049 2 117078794 TTTGCCTAAAGGGACATTTCAATGTTCAGAAACAA[C/T]GTTTGTAATGATTATAGCACCGCTGCAGAACATTC Y 2 1 2 1 101000 r 74 goat snp26996-scaffold287-955909 2 18072634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380908 Affx-122975028 AX-123251266 2 117137687 AGCATAACTTACTCTGAACCTTCATCGTTGCATGG[A/G]TCTTCACATCTTCACATGGCCTTTCCTGTGTCTCT R 2 1 2 1 101000 f 74 goat snp26994-scaffold287-897016 2 18014109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413504 Affx-122950637 AX-123283853 2 117166297 GATACCTGCCCATCCTCCCTGCTCTCACCCCTCTT[G/T]CCCAAGCTAACCTCTTCACGAAGGCAGTCTTCATC K 2 1 2 1 201000 r 74 goat snp26993-scaffold287-868406 2 17985615 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438901 Affx-122930441 AX-123309238 2 117200911 ACTTACTCATGAAATGAGCTATGCCTGTATGTTAG[C/T]GCCTGTGGAGCTCCAGGTGAGCTGAAGGTGATATA Y 2 1 2 1 101000 f 74 goat snp26992-scaffold287-833792 2 17950977 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382651 Affx-122973676 AX-123253009 2 117235479 AGTCGTTCCATCTTTCCTGATCACATCAGGAAGGG[C/T]GGTGTCTGCCTGTTACAGCAAAAGACAGCAATCAT Y 2 1 2 1 101000 r 74 goat snp26991-scaffold287-799224 2 17916271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376705 Affx-122978976 AX-123247064 2 117275782 CAGATTGATCTTGTTCCGCGAAGTCCTCAAGAACT[A/G]TATGAACTGACATCTCTGATTTGGTAAAGACTGGG R 2 1 2 1 101000 f 74 goat snp26990-scaffold287-758921 2 17876000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772216 Affx-122945027 AX-385259371 2 117307646 GCCTAATTAGTTTCTAAAAGTATTGGCATGAGTTA[C/T]TGAGTTTAATGGGTGAGGGCGAGAGATGTACTTCA Y 2 1 2 1 101000 r 74 goat snp26989-scaffold287-727057 2 17843807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408585 Affx-122953658 AX-123278936 2 117353558 AAATTCATGTTTAGAAGTAGAATGGCATCATTGAA[C/T]GTGTACCTTGTCCCGTTATTCTGGAGAGCTGGATT Y 2 1 2 1 101000 r 74 goat snp26988-scaffold287-681145 2 17797570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425849 Affx-122940664 AX-123296195 2 117384685 AAACAAGAACAACAATTAAGATTATCACTGCTTCC[A/G]TTTAATTCCCAGTTTTTCAGGAGTTTGAGCGGTTT R 2 1 2 1 101000 r 74 goat snp26987-scaffold287-650018 2 17766021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393879 Affx-122965128 AX-123264234 2 117419867 CTTCTGAAACATCAATGGGATTGTGTCAACTCTCC[A/G]CCTAAAACTCTTCCAGGGTTCCCCATCCCTTTCAA R 2 1 2 1 201000 f 74 goat snp26986-scaffold287-614836 2 17730585 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417427 Affx-122947215 AX-123287775 2 117453900 AAATCCCATGTCAATGGATGCTCAGCACTCCCTAG[C/T]CATATAGCTCCGGATTAGGTACTATTGTGCTTAGA Y 2 1 2 1 101000 r 74 goat snp26985-scaffold287-580803 2 17696165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779631 Affx-122971821 AX-385266733 2 117488585 TTCCATATAAGCAAAGTTTAATGCATGTAATATAC[G/T]AACCTCTTCAAGAATAAAAAGCAGTACTAGAAGTT K 2 1 2 1 101000 r 74 goat snp26984-scaffold287-546118 2 17661316 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389513 Affx-122968296 AX-123259871 2 117544515 GGATCTGGCAAGTTCCTTAACCTGTCTGTGCGCCT[A/G]CTTACTCACCTGTGTATGGGAGAATAAGAGCGTCC R 2 1 2 1 201000 r 74 goat snp26983-scaffold287-490188 2 17605329 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278037 Affx-1111836142 AX-519551529 2 117554114 TCCAAAAATGAGCTTTGTGTGTATGTGCACGTGGC[A/G]TATCTCAAAGGGAGAAGGTTCACAGCTTTCACCAT R 2 1 2 1 201000 r 74 goat Random2.2K-262 2 117554114 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412424 Affx-122951426 AX-123282773 2 117607678 CATCTGTATATTCCCCACTTCCTTTCTTCCTTGCT[A/G]TCTACTTATTGGATAACCTGGGGTCTTTGCCCTAC R 2 1 2 1 101000 r 74 goat snp26982-scaffold287-427025 2 17542418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277890 Affx-1111836143 AX-519551385 2 117629500 TTAAAGAGGAGAACCAGAACGTACACTTGTAGAGA[A/G]GACTTCCCTAGTGGTCCAGTGGTTAAGAATCTGTC R 2 1 2 1 101000 f 74 goat Random2.2K-263 2 117629500 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427598 Affx-122939457 AX-123297941 2 117639980 TGTAGGCTGGAATTTGACACAGATCTCATAGCACT[A/G]TGTAAGCAAGACGGTGACTGCCATTTGTGAGACGT R 2 1 2 1 101000 r 74 goat snp26981-scaffold287-394723 2 17510269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772941 Affx-122972317 AX-385260085 2 117687417 CAAGAAAGATGGTCCACGCAAGTAAGGAAGTGTCT[A/G]CTACTGAAGTTTCCCAAAACCATCCAAATGGAGCA R 2 1 2 1 101000 r 74 goat snp26980-scaffold287-347286 2 17462961 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453565 Affx-122919770 AX-123323898 2 117783936 CTCCTCACCTGAGGCTCTGTTCTCATGGCCTGCAA[C/T]GGTGGCAGAAGCTTCCTGAGGTCTCTCCTGCACAT Y 2 1 2 1 201000 f 74 goat snp26978-scaffold287-250767 2 17366481 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382956 Affx-122973367 AX-123253314 2 117829140 CCCTGAATTCCTGCTGTGACACTGCGTAGAGCAGC[A/G]CTCAATCCTAATTTTCAGCTGGGTGAACTTGTACA R 2 1 2 1 101000 r 74 goat snp26977-scaffold287-205563 2 17321392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436782 Affx-122932262 AX-123307120 2 117858211 CCGTGTTCAAACATGTTGATTCCCAAGGCAGGGCC[A/G]TGGAATGTGCACCTCTCCTCCCTCCCTTCTTTTAT R 2 1 2 1 201000 f 74 goat snp26976-scaffold287-176492 2 17292393 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443448 Affx-122927837 AX-123313785 2 117903395 CTCATCACACTTGAATCAAAATGACATTTGTTTAT[C/T]TCTCATAAGCAATTTCACTTAAAAGAAGAACTATT Y 2 1 2 1 101000 r 74 goat snp26975-scaffold287-131308 2 17246851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425621 Affx-122940906 AX-123295967 2 117946656 CAATTCAGGCCGTGTGTAAACAGAGAGCAACAGCA[C/T]GGCCCTGGATACCTCAGGTGGTGGTGGAGTTGCGG Y 2 1 2 1 201000 r 74 goat snp26974-scaffold287-88047 2 17203796 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451085 Affx-122921410 AX-123321419 2 117977485 TTTCAAGCCCCTATTATCTATGAGGCTTTACAGAT[A/G]TCATTAAACTAAGTGAAAAGTCAGAAAGAGAAGGA R 2 1 2 1 101000 f 74 goat snp26973-scaffold287-57218 2 17172975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767569 Affx-122923340 AX-385254821 2 118008843 TTATGCATTGCCTAGAATTTCCAGAACAATGCTAC[A/G]TAACAAATCATACAAAGCATCCTAACCTTCAAGTT R 2 1 2 1 101000 f 74 goat snp26972-scaffold287-25860 2 17141029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420863 Affx-122944638 AX-123291210 2 118056664 GTCTTAACTATCCCCAGATTCTAATGCGAGAATAA[C/T]ACATCCGTGTTTTCTTTGACACGCGGCACCCCTCA Y 2 1 2 1 202000 f 74 goat snp3654-scaffold1113-1450166 2 17092506 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410571 Affx-122952133 AX-123280921 2 118102854 GCATATCGAACGATCAGTAAAAACATGCAAAAGTG[A/G]GAAGGAAAAGGAAAGTAAACGCTGCATTCCCCCAA R 2 1 2 1 101000 f 74 goat snp3653-scaffold1113-1403976 2 17046370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438772 Affx-122931384 AX-123309109 2 118150389 TTTCTTACTGTCTGTAGGAAAAGGATCTGAAAACC[A/G]AAGGGTGAAATTGCCATTGCCTTGGAGTCCTTGGC R 2 1 2 1 201000 r 74 goat snp3652-scaffold1113-1356441 2 17001811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379227 Affx-122976275 AX-123249586 2 118193058 TTACTTCCTGATTTATCTATTGGAAAGCTCTTAAT[A/G]ACTGTTTTGTTAGATTTTAAAAAATGCCTATCATG R 2 1 2 1 101000 f 74 goat snp3651-scaffold1113-1313772 2 16959207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440316 Affx-122930209 AX-123310653 2 118225098 AGGTTCACGGAACAGGTGAGTCTGCAAGAAGGTGG[C/T]AATTCTCTGAAGTCAAGAGCAATGGATCTCTCAGC Y 2 1 2 1 101000 r 74 goat snp3650-scaffold1113-1281732 2 16926822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388809 Affx-122968907 AX-123259167 2 118261232 AACTAGCAACTAGAACTTTCATTGCAAGCATTTTG[C/T]GTATCAACCTTATCTCTAGCTTCACATTATTTCTC Y 2 1 2 1 201000 r 74 goat snp3649-scaffold1113-1245598 2 16890744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435376 Affx-122933578 AX-123305716 2 118296925 CTGGCAGGGAGTGACAGAAGGATCTGTAAACAAAC[A/G]CCAGGTGAACTGAACTATGAATCTTGAACAGGAAT R 2 1 2 1 201000 f 74 goat snp3648-scaffold1113-1209905 2 16856386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272017 Affx-1111833152 AX-519545783 2 118334565 GAAGCTGAAGCCCCAATACTCTGGCCACCTCATGT[A/G]AAGAGTCGACTCATTGGAAAAAACCCTGATTCTGG R 2 1 2 1 303000 f 74 goat 2_118334565_AF-PAKI 2 118334565 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439701 Affx-122930566 AX-123310038 2 118338551 TACACAGAGATGCAATGGGGGTAGGGAGGGCTAGG[C/T]AAGATATGGAGGAAGAACCTGCAAATTAGTAGAAA Y 2 1 2 1 201000 r 74 goat snp3647-scaffold1113-1168279 2 16814733 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409167 Affx-122953201 AX-123279518 2 118367405 TTGGCCACTGTCTTAATACTCCATGGTCTAAAAGT[A/G]TGTATGAACCTCTAAAGGACCAATGGAGATTCAGC R 2 1 2 1 101000 f 74 goat snp3646-scaffold1113-1139425 2 16785759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452877 Affx-122920700 AX-123323210 2 118403559 ATAAGAAATCCTTTCATCCAGGTCCTCTTTGTCCT[A/G]CAAGGAAGAGAGGATGTCTGAGATCTCCGGCTTCA R 2 1 2 1 101000 f 74 goat snp3645-scaffold1113-1103271 2 16749213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433374 Affx-122935124 AX-123303715 2 118434546 CTGAACATACCTAAATCCTTCCTGAAACCTGTGGG[C/T]TGAATAAATAGGACACAGCCAGGAGCTTTCCTGGC Y 2 1 2 1 201000 r 74 goat snp3644-scaffold1113-1072284 2 16717864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395026 Affx-122964215 AX-123265381 2 118487400 CCCCAGTTAAAAAATAACATCTGGCCGTGGGGGAA[G/T]CTGAGTAAAATACAGACATGCTCATTCCTTGTCAG K 2 1 2 1 101000 r 74 goat snp3643-scaffold1113-1019430 2 16664622 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390761 Affx-122967897 AX-123261118 2 118519831 GCGGATGCAAGCAGGTTCTGAGCCCTGGAGGACTT[A/G]TTTTGAGGCTGAGCTGTTCTAAACAGCAACTTCCC R 2 1 2 1 101000 r 74 goat snp3642-scaffold1113-986999 2 16632299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414886 Affx-122949132 AX-123285235 2 118597074 GGCCGCCAAGCAACAGACGGAGACACACACATGGA[C/T]GTACTCAGAGACACACAACGCTCGTACACAGACAC Y 2 1 2 1 101000 r 74 goat snp3640-scaffold1113-909756 2 16554578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429078 Affx-122938281 AX-123299420 2 118643526 TACGGAATATAGAATACTAATTCCAAGTGGCGAAA[C/T]GTGAAAAAATAACCTAAAATAAGATAGAAGAACAA Y 2 1 2 1 101000 f 74 goat snp3639-scaffold1113-863304 2 16507044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418646 Affx-122946334 AX-123288994 2 118685664 AATACTCTGGATTATATTGTGACTGCATGTGTTTA[C/T]TGAAACTCATTGAACTGTGCACCCGAAAGGGTGAG Y 2 1 2 1 101000 f 74 goat snp3638-scaffold1113-821166 2 16464989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401958 Affx-122958797 AX-123272311 2 118717538 TTGGTGCAAACGCACAGGTCTATCACCATGAAGCC[A/G]GCTCATGGGACCAAAGGCAGACAGGGCAGAAGCTG R 2 1 2 1 101000 f 74 goat snp3637-scaffold1113-789292 2 16432431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388768 Affx-122968938 AX-123259126 2 118751449 CAGCTGCCCCCACACACTTACCACACATACACACA[C/T]GTGCATACACGCACACACACACACATCCGTTGGAC Y 2 1 2 1 103000 f 74 goat snp3636-scaffold1113-755381 2 16398480 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381127 Affx-122974572 AX-123251485 2 118784056 CTCTCCAACAGGCACCTCTCTCAGGCCATAGGGGT[C/T]TTGCTGCCTTCACAACTTGCCACACCTTCCCTTTC Y 2 1 2 1 101000 r 74 goat snp3635-scaffold1113-722774 2 16365711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450467 Affx-122922943 AX-123320801 2 118827286 GTCAGATGGAGAGACCTGAAGTGCTTGTGGAATAC[A/G]GGGCGGGAGACTGGAACTCTTGCAGGACACAGGGC R 2 1 2 1 101000 f 74 goat snp3634-scaffold1113-679544 2 16322347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794397 Affx-122953925 AX-385281360 2 118873924 TCCCTTTTACTGTATACTAATATACCCTGTGGTGT[C/T]TGTCTTCCCCTCTACAATCCAAATGAATCCCTGAG Y 2 1 2 1 101000 f 74 goat snp3633-scaffold1113-632906 2 16274858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435504 Affx-122933422 AX-123305844 2 118907102 AGCAAAGCACAGAGCAGTCTTTGGAGCATGGACTA[C/T]AGATTCAGATTTTATTACCTCTACCACTGTGACCC Y 2 1 2 1 101000 f 74 goat snp3632-scaffold1113-599728 2 16241712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439406 Affx-122930247 AX-123309743 2 118937355 CACCACCCTCCAAGCAAGTGAAAACCCCCGGCGAT[C/T]AGTCTATAACAAATATTGACACGAGGGGGAAAAAA Y 2 1 2 1 103000 r 74 goat snp3631-scaffold1113-569475 2 16211260 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424612 Affx-122942194 AX-123294958 2 118974235 ACCTCCATTCTCCTCCTCCTCCACATACGATGGTT[A/G]TCTGGGTGGGTTCCCAAGATCTCCCCCAGCTCTGG R 2 1 2 1 201000 r 74 goat snp3630-scaffold1113-532595 2 16174232 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441982 Affx-122928441 AX-123312319 2 119017426 ATAGAATGGTGAAAGAAATAATTATCGCTACATTC[A/G]TAAGGGAAATGGATAATAATGGCATGTGAATAGCA R 2 1 2 1 101000 r 74 goat snp3629-scaffold1113-489404 2 16132857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278042 Affx-1111836144 AX-519551533 2 119032225 GTTTCATCTTGTGTATTCAAAGAAAATGGTGCTGA[A/C]TGGAATACCCAAGTGGGTTATGTGCCTTCATTCAT M 2 1 2 1 101000 r 74 goat Random2.2K-265 2 119032225 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382595 Affx-122973718 AX-123252953 2 119046372 TCCAATCCAATACCTAAAATCAACTGGTCTGTAAG[C/T]GTTGTGAGGTGAACACTATAAAATGTGGTATAAAT Y 2 1 2 1 101000 f 74 goat snp3628-scaffold1113-460458 2 16103527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398165 Affx-122962661 AX-123268520 2 119177304 TATGCCATTGAGTATGAAATGTTTCCTGAAGCATC[A/G]ACTCAGTGAAGTTTCTGGGTACCTGTGGGGTGTCA R 2 1 2 1 101000 f 74 goat snp3626-scaffold1113-329526 2 15972068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426856 Affx-122940490 AX-123297201 2 119210849 GAAAGGGTAGGTACATTTAAAATGTCGATAGCTAC[A/G]GAGGATTAGCTCTACTAACTTACATTTCAAACAAG R 2 1 2 1 101000 f 74 goat snp3625-scaffold1113-295981 2 15938173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448179 Affx-122924253 AX-123318515 2 119247191 GTCCTCATTTCCCAGTTTCCACCACACAGATTCCA[C/T]GTCCTCATCATCCAGGTTGGCACTTTTGCCCCATC Y 2 1 2 1 101000 f 74 goat snp3624-scaffold1113-259639 2 15901803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417430 Affx-122947213 AX-123287778 2 119295645 GTTTTGCAAAATAACACATATTAACATGCATAAAG[G/T]TACTATAAAAATGGAGAAAATTTTAATACCATATT K 2 1 2 1 101000 f 74 goat snp3623-scaffold1113-211185 2 15853549 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427423 Affx-122940056 AX-123297766 2 119331963 AATTTGGTCATTCTAAGCATATATTCCCAAGGAAA[G/T]AATCCGAAACAACTGTGATTAACAATGCATAAGAA K 2 1 2 1 101000 f 74 goat snp3622-scaffold1113-174867 2 15817125 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425592 Affx-122941411 AX-123295938 2 119362637 CTCTCGGGGTCCTGGCAGAATAAATGCCAAAGCAG[C/T]GAAAGGACACATGCACAACCCAGGAACGTATGGGA Y 2 1 2 1 101000 r 74 goat snp3621-scaffold1113-144193 2 15786105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419892 Affx-122945348 AX-123290240 2 119419591 TCTTCACCCAAGGAGACAGTGGAAAGGCATTCAAG[C/T]GAGGTAGCATCAACCACACGGTGCTCTTACAGACC Y 2 1 2 1 201000 r 74 goat snp3620-scaffold1113-87239 2 15728608 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385513 Affx-122971258 AX-123255871 2 119459374 ATAACTCGGATTTTCACATTTCTGTTCAGTCGGCC[A/G]TTTTACCTGCACTCACTTGCGTGTGTGTGGGTTCT R 2 1 2 1 102000 f 74 goat snp3619-scaffold1113-47456 2 15689267 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447858 Affx-122923888 AX-123318194 2 119513161 TCCAGAGCAGTTTCTTCCAGTTTCCTCCAGATAGC[A/C]GGCTGTCTTCCAGGTTATAGTCTTCAGTTTGGCTC M 2 1 2 1 102000 f 74 goat snp43284-scaffold5766-6232 2 15628886 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411890 Affx-122951192 AX-123282240 2 119562766 AGAGGAGCCAGAGGAGGGTGAGCTGGGGTCTGAGC[A/G]GACTTGCAGTCCATGCTGTGAGCTCCCTAATTTTT R 2 1 2 1 101000 r 74 goat snp43285-scaffold5766-55837 2 15579412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413742 Affx-122950055 AX-123284091 2 119576723 TTGAGGCAGCCAAGGGTGAAGCCCCAATATTTGGA[G/T]GAGTGAAGGTGACCCACTTTGTATGATGGCTCCTC K 2 1 2 1 201000 r 74 goat snp15998-scaffold1684-9957 2 15566111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415525 Affx-122948673 AX-123285874 2 119606957 CACTGCCTCACTTTCCTTTGATGAATGCTTCTGTC[A/G]TCCCTCCTGTAGGAGGACATTATTTCCATATGGAA R 2 1 2 1 202000 r 74 goat snp15999-scaffold1684-40191 2 15535776 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782161 Affx-122948368 AX-385269239 2 119654843 ATCTTCTGCTACTTAAGGGCATTCTTAATATTTGT[A/G]ATATAAATATTTACTTGGGCTTTTACTTCTAAGTT R 2 1 2 1 201000 r 74 goat snp16000-scaffold1684-88077 2 15487551 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773943 Affx-122934770 AX-385261082 2 119690582 ACCTCAGCTGACTTAATCTTCCATTAAGGTTCTAT[C/T]TGCATAGCCCATGATCTCGAAAGGCTTAGTGTGCT Y 2 1 2 1 101000 f 74 goat snp16001-scaffold1684-123816 2 15451904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427107 Affx-122939670 AX-123297450 2 119741095 TGCACAGCTTCCAGTTCTGAATCCCAAGCATACAA[C/T]GGTCCCTGAAGGAATTTCTGCACTTCTGTCCTTAG Y 2 1 2 1 101000 f 74 goat snp16002-scaffold1684-174329 2 15399427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418547 Affx-122946401 AX-123288895 2 119785761 CCCAAAACTCATAGAGCCCTGGTTAAAAAACCCAC[A/G]TCTACGAGAAAGAATAGACCTATAATGAGATGATT R 2 1 2 1 101000 f 74 goat snp16003-scaffold1684-218995 2 15354623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438489 Affx-122931601 AX-123308827 2 119807126 GAGAAAACAGTCTGCTGGCTTCTCAGTCTGCATCG[C/T]GGTGGCAGGGAGGTGAGGGCAGGTGCTCCCCCCCA Y 2 1 2 1 101000 f 74 goat snp38585-scaffold4896-36322 2 15332568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446946 Affx-122924675 AX-123317282 2 119839824 GCCATCCTCCTAGCCCCATGATGACCCGTCTACTG[A/G]AAACCTTGACCATGGCCTTTCTCAGCTCAGGGACC R 2 1 2 1 101000 r 74 goat snp38584-scaffold4896-3624 2 15301515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419026 Affx-122946036 AX-123289374 2 119860535 AATTGTTGAGGGATGGGATGGAAGAAGCAGAAATG[C/T]AGTTGCTATGAATAATCGCTGACATTTCTAGAGCA Y 2 1 2 1 201000 r 74 goat snp2519-scaffold1071-506828 2 15281009 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452266 Affx-122920763 AX-123322599 2 119890175 TGTCCTCATTTATCAAACCATAGAGTACCTGAACT[A/G]TACCAGACATTTCTCTTCAAGATCTTATTTAATCC R 2 1 2 1 101000 f 74 goat snp2518-scaffold1071-477188 2 15252241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442951 Affx-122928220 AX-123313288 2 119937671 TGCAGCCTAAGCAAAGATGCCAAGGAGATCACAGA[C/T]GCCAGAGAGCTTTATAAATGGCAACATTCTGGGCA Y 2 1 2 1 101000 f 74 goat snp2517-scaffold1071-429692 2 15204217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406814 Affx-122955687 AX-123277165 2 119990727 CCTTGGAAATACAATCTTGCTGCGTAGAAACGTGT[A/G]TGTGTGACACACACACAGAGAAGTACACAGACTAC R 2 1 2 1 101000 f 74 goat snp2516-scaffold1071-376636 2 15152105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444142 Affx-122926797 AX-123314479 2 120104480 TTCAGTGAGTAAGCCAGCAACTCTGCATCCTCAGG[A/C]TCAGATGGCAACATGACCTCCTCAGGAATGCCTTC M 2 1 2 1 102000 f 74 goat snp2514-scaffold1071-262883 2 15036122 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277894 Affx-1111836145 AX-519551389 2 120127359 AAGGATAATGTGAATGGAGGTTGCACAGTCATCCT[A/G]AAAAATAGAAAAGAAAGACCGAATGGATCATTATG R 2 1 2 1 101000 f 74 goat Random2.2K-266 2 120127359 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421597 Affx-122944492 AX-123291944 2 120151728 AGGCATTTAAGGTCTACCTGATCTGCCTCCAAGCT[A/G]TCTCCAGTTCCACCTCTTACCATAGATCCTAAATC R 2 1 2 1 101000 r 74 goat snp2513-scaffold1071-215635 2 14988763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392780 Affx-122965985 AX-123263137 2 120204442 TAGCATGTTAGCTTTATGTCAAAAATCTTCTAGAG[C/T]GCCCATCCCCTCAGGACGTTGAGGTCCATCAGAGA Y 2 1 2 1 201000 f 74 goat snp2512-scaffold1071-162921 2 14935720 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403763 Affx-122957998 AX-123274115 2 120237406 GATCTTAGGGCTCTACTGGTATATTCCTGTATCCT[A/G]TTGGACATAGAGATGCCTCTTAAGAGCAGCCTCAT R 2 1 2 1 101000 f 74 goat snp2511-scaffold1071-129957 2 14902755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420698 Affx-122944792 AX-123291045 2 120266153 GTAAAGTTAGCAAGTAATGATTTTTTTTTTTTCCA[C/T]TGAGGTTTGACCACATTCACAGGTCATTTCTACAT Y 2 1 2 1 101000 r 74 goat snp2510-scaffold1071-101210 2 14874009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423118 Affx-122942910 AX-123293464 2 120298954 ACAAGTCAGTGCTCTGAGAATCAGTGCTCTCACAC[C/T]AGGCTGGGCAGGAAGGACTCCAGGAGGGCTCTGAT Y 2 1 2 1 101000 f 74 goat snp2509-scaffold1071-68409 2 14841182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426392 Affx-122940850 AX-123296738 2 120347116 AGCGGTATCCCTTTGTCTCCTTCAGATGAGGACCA[C/T]GGAAACACTCACCCTGGGCTTCAGATGCTGTGCTT Y 2 1 2 1 201000 f 74 goat snp2508-scaffold1071-20247 2 14793427 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798476 Affx-122976086 AX-385285409 2 120379025 TACCTGCTGTATCTGTTAGGTCTTTTAGACCCAAC[A/G]CTTATTCTATCAAAGATGAGAGTGGTAAAAAGAAG R 2 1 2 1 101000 f 74 goat snp17729-scaffold1840-11563 2 14757356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775057 Affx-122932128 AX-385262189 2 120424238 GGGTAATTAACTAATAAATAGTTGAACAGAGTTTT[A/G]AAACTATGCTCTTTCTGATACTGCTACTGCTTTTA R 2 1 2 1 101000 r 74 goat snp17730-scaffold1840-56776 2 14712215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765741 Affx-122970351 AX-385253197 2 120453123 AAATAGCGATCCTTTTCTTTCTCACTAATGTCTAA[C/T]GAAGATTTAATAAAGGTCTTACATACACTGATGAC Y 2 1 2 1 101000 f 74 goat snp17731-scaffold1840-85661 2 14684639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434946 Affx-122933858 AX-123305286 2 120496511 GAGGAATAAAAACAAAATCTTCTCTAAGACTGTAC[A/G]TGAAGCAAGTGAACAGAGACTGGAATTCAGGCTGA R 2 1 2 1 101000 r 74 goat snp17732-scaffold1840-129049 2 14641854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381487 Affx-122974960 AX-123251845 2 120559805 AAAGAAAGCAAAAGATAACAAAACTCTTTACAAAG[C/T]ATATCTTTTACACCTTCATTTAGGTTTCCCTCTTG Y 2 1 2 1 101000 r 74 goat snp17733-scaffold1840-192343 2 14578507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438236 Affx-122931434 AX-123308574 2 120608593 CCTTCGTTGATTTTAAACTACCAGTGTGACATCAC[A/G]TAATGCAGAGTTAGGAAGAGATTACAGTAAGTCAC R 2 1 2 1 101000 f 74 goat snp17734-scaffold1840-241131 2 14529555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777024 Affx-122965809 AX-385264147 2 120696349 CTTGCGAATATAATCCAACTTTCTTAGGGTGGTGC[A/G]CCCAGCCTTTCGTGATCTAGTCCCCATTTACTAGC R 2 1 2 1 202000 r 74 goat snp17736-scaffold1840-328887 2 14443331 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430777 Affx-122937482 AX-123301118 2 120770835 ACTTCTGGTCAACACACTCAGACCCACCCTTAGCC[A/C]CCTGACTCAACAATTCTGTGGAGATACCAGTTTTC M 2 1 2 1 101000 r 74 goat snp17737-scaffold1840-403373 2 14368728 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427915 Affx-122939673 AX-123298258 2 120816129 TGGGGTCCCTGATCACCCCTATGCCTGGAGACTAA[C/T]AGGCACAGGACAAATTCCTAAAGGCACCGCTATGG Y 2 1 2 1 101000 r 74 goat snp17738-scaffold1840-448667 2 14323023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272930 Affx-1111833153 AX-519546617 2 120834877 ATATACTGTGATTGATCTGTTGGGCATTGTTGCTA[A/G]CACTATTTCCTTTATGTCCAGAATCAGTAATCTTT R 2 1 2 1 101000 f 74 goat 2_120834877_AF-PAKI 2 120834877 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412480 Affx-122951387 AX-123282829 2 120853662 AACACTCCACAGAGTGTGGGTCATCTCAGAAGGCA[A/G]GATCAGCCTCCACTCTGAATTGTAACCAGACAACC R 2 1 2 1 201000 r 74 goat snp17739-scaffold1840-486200 2 14285435 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786642 Affx-122923044 AX-385273674 2 120910373 TGTGTTGCAAATCCAGAAGCCAATTGCCTCTTGTT[A/G]CATCCCCCTATCGATGACCCAGAGACCCATCAAAC R 2 1 2 1 101000 f 74 goat snp17740-scaffold1840-542911 2 14228621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388522 Affx-122969205 AX-123258880 2 120969100 TTGAGGGTATGGGGCTCAGGACAGATACTCTTCCC[A/G]TTCAAATCCGTCTATCACATACTCGCTGGGTGGCT R 2 1 2 1 101000 r 74 goat snp17741-scaffold1840-601638 2 14171204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392604 Affx-122966050 AX-123262961 2 121034064 ATATATACAGGGCTGTAATGAACTTTGTGGTCCAT[A/G]CTTATCACAACCAATCATTTCCTTAGGATAAATTC R 2 1 2 1 101000 f 74 goat snp17743-scaffold1840-666602 2 14105708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409581 Affx-122953575 AX-123279932 2 121071860 GAAAAAGAAATATGACATATAATGAAAATGCAGGC[G/T]AAATAAAAGATATCAAATAAAAAAGGGAACCATAA K 2 1 2 1 101000 f 74 goat snp17744-scaffold1840-704398 2 14067775 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388219 Affx-122969407 AX-123258577 2 121106465 AATTCCCTCATCAGTGCTGAACTCTTAAGTGTTCC[A/G]GGGAGAGCAATAGGGATATAGGAAGGAGAGGCTTA R 2 1 2 1 101000 f 74 goat snp17745-scaffold1840-739003 2 14033123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431984 Affx-122935946 AX-123302325 2 121183086 CTTTCCCTTTTCTTTGCCTGCTGAGTTTTCAATCA[A/G]TCTTCAAAGCTCTGTACAAGTGTGGTCTTCTTTAA R 2 1 2 1 101000 r 74 goat snp57678-scaffold925-882815 2 13958321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392886 Affx-122965738 AX-123263243 2 121226636 GGTTCTACTGTAGACTGAAGAGCTACCTACGCACC[A/G]TCCACTAGCTATAGAACCGCACATTTCTTAATGTC R 2 1 2 1 101000 r 74 goat snp57677-scaffold925-839265 2 13914776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399097 Affx-122960871 AX-123269452 2 121289858 CCAAGCACAACAACCATGGCCTTGCTAGGTCTCAG[A/G]GACCCTTAGTCTTGACTTTCAGATGGTGGCTCAGT R 2 1 2 1 201000 r 74 goat snp57676-scaffold925-776043 2 13852698 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394484 Affx-122964562 AX-123264839 2 121348057 GAGAGTTGATCTGGGTGACTTAGCCTGACATGACC[A/G]TAAAGGGAATTCTGCCAGGCCCCAGACTCCATTTG R 2 1 2 1 101000 f 74 goat snp57675-scaffold925-717844 2 13795103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377385 Affx-122977631 AX-123247744 2 121381154 CCACCATTAATCCAGGTACTGAGCCTGTCCTGGTG[A/C]TGAGGTTGATACCCGCTGGGATCTGCCCATCTGAC M 2 1 2 1 201000 f 74 goat snp57674-scaffold925-684747 2 13761778 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376167 Affx-122978839 AX-123246526 2 121423580 ATCAATACAGGATGTGGCATGAATGACTGTTGAAT[A/G]TATGAAAGTGAGTGTGGGAAGAGACCCTGGAGGGT R 2 1 2 1 101000 f 74 goat snp57673-scaffold925-642321 2 13720247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419039 Affx-122946027 AX-123289387 2 121467416 GCTGCTCTAGGGGAAATGCCTGGCAGATAGTAGGC[A/G]TGAATGAATGACTACTGAATACTGAGGGAGGGAGT R 2 1 2 1 202000 r 74 goat snp57672-scaffold925-598485 2 13676347 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396234 Affx-122963338 AX-123266589 2 121496441 CACAGAGCAGTGAAAGGAGCCAGATACAGAAGGGT[A/C]CATACTGTGATTCTCTTGATATAACTTGGAAAAAT M 2 1 2 1 201000 r 74 goat snp57671-scaffold925-569460 2 13647358 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444413 Affx-122926578 AX-123314750 2 121537183 CAAAGGACCCATTTCATTTCACAATGCGGCAAATG[A/C]TGCCAGAGGAAGAAGTGTCAGATGCTTGTTACCTT M 2 1 2 1 201000 f 74 goat snp57670-scaffold925-528718 2 13608388 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453088 Affx-122920041 AX-123323421 2 121589528 GGCAGCAACAGAAGCACCTTGGAACTGGTTAGAAA[C/T]GCAAATTCTCGGTCTCCACCTTGGATCTACTGAGT Y 2 1 2 1 303000 f 74 goat snp57669-scaffold925-476373 2 13556112 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412119 Affx-122951105 AX-123282469 2 121619147 AGTAGGGGAACTCGAGCAGAGAGGCGAGACCTTCC[A/G]AGGAGTTGGAGTGGGACGAACTGGGAATGGGTGGT R 2 1 2 1 201000 f 74 goat snp57668-scaffold925-446754 2 13526536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405009 Affx-122956382 AX-123275361 2 121669214 GACATAGATTTTTTCCTATTTTTGTGGCTCCACCA[C/T]GCTGGGTCTATAATCTCAAGGTGCAAGGAAGCCAG Y 2 1 2 1 101000 r 74 goat snp57667-scaffold925-396687 2 13476890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382969 Affx-122973356 AX-123253327 2 121711062 TTGCTTTAGGTTCTAGGACTAGAAATATTCCCAGC[A/G]AGGCGGAAATAAAGAAAGAGCATGGGCATTAGGAT R 2 1 2 1 101000 f 74 goat snp57666-scaffold925-354839 2 13435239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392119 Affx-122966345 AX-123262476 2 121742020 TTCAAAAGGGAGAAAACCAATCATTCAGGATAAAG[C/T]GTCTTTTCTGTCAAAGACTTGAAGTACTTTCCAAT Y 2 1 2 1 101000 f 74 goat snp57665-scaffold925-323881 2 13404349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798823 Affx-122954144 AX-385285753 2 121771699 CTCTCTAGAAAAAGATTTTGTTAATTACACCTAGT[A/G]TATCCAACTGATATGAACACAGAGTGAATGCACAT R 2 1 2 1 101000 r 74 goat snp57664-scaffold925-294202 2 13374676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382883 Affx-122973420 AX-123253241 2 121859075 CTCAGCGTGGCCCTCCCTGACCCCCAGCTCCACCC[A/G]CTTAACCTCCCCACACATCATCGCTCTCAACACCA R 2 1 2 1 101000 r 74 goat snp57663-scaffold925-206826 2 13287445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781780 Affx-122972813 AX-385268862 2 121899171 CATACCTGATATCCAATTATTCAACCCATTGTACA[A/G]ACAAGGCAATTGAGACTAAGTAGTGAAGATAGACT R 2 1 2 1 101000 r 74 goat snp57662-scaffold925-166730 2 13249460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789669 Affx-122925160 AX-385276678 2 121935421 CTGTCCCAGTCTAGCAAATATTTAATCCCTTGAGG[C/T]ATGTGTTTTGTTTACTAACTTTCTTCTTTACGTGT Y 2 1 2 1 101000 f 74 goat snp57661-scaffold925-130480 2 13213289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429225 Affx-122937925 AX-123299567 2 121972121 GCTTGACTTGTACCTTCTCAGTGATGTTCAAGATC[A/G]TTAGAAAATTAGAGCAGGGAGGGGGACTTCATGAA R 2 1 2 1 101000 f 74 goat snp57660-scaffold925-93780 2 13176269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452634 Affx-122920352 AX-123322967 2 122016360 GTCAGGCAGAGCTGGGTGGCCTACAGCTAACTGGC[A/G]GTGGACAGGCTGCAGGATGGGCTGATAGTGCATTC R 2 1 2 1 101000 r 74 goat snp57659-scaffold925-49541 2 13132455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777669 Affx-122964823 AX-385264788 2 122060736 GACTGAATGGTTGAGAGCAAGAATAAATGCACGCA[C/T]TGAACATACAAGTACGGATTACTGGATGGCAGCAA Y 2 1 2 1 101000 f 74 goat snp57658-scaffold925-5165 2 13087911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388651 Affx-122969111 AX-123259009 2 122066938 TAAAATTCACGGTCCCTCAATCCTGTTAGCAGCCC[C/T]GCAAGGTAGGTTCTGTGGCCCTCTCTTTTTAAGGA Y 2 1 2 1 201000 r 74 goat snp52148-scaffold772-938 2 13078413 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438463 Affx-122931240 AX-123308801 2 122098388 AAACAATTAAGACCAGATCTTTAAGAGCAAGGTCC[A/G]TGGGCAAGTTTGGCCCAGCTGCCTCTTTGCATGAC R 2 1 2 1 101000 f 74 goat snp52149-scaffold772-32388 2 13046973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277895 Affx-1111836146 AX-519551390 2 122099294 GATAAGGAAAAATGAGGGTGCCAGGATTTGTGATG[A/G]CATCCACTACGGTAGTCAGTGTGGTCGTATTGAGA R 2 1 2 1 101000 f 74 goat Random2.2K-268 2 122099294 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376243 Affx-122978781 AX-123246602 2 122136726 ACATTCTTTCCGATCCCTGGATGTTCACAGTCTAG[C/T]GGGGAAGATGGGAAAATGGCACCGGGGACAGTCAA Y 2 1 2 1 101000 f 74 goat snp52150-scaffold772-70726 2 13008807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762283 Affx-986696814 AX-385250471 2 122166744 CTGAATCATGGTATGTTTAATGAAAGGTGAATGTA[C/T]AAAGAGACTACAGTGAAGACATGTAGCTTTTGACA Y 2 1 2 1 600010 f 74 goat 2_122166744 2 122166744 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 38440292 Affx-122930225 AX-123310629 2 122266053 TTCAAATCCTCCAGCTCCCTGAATCCAGTCCTCCT[A/G]CCCATCCACACTGTCTTTTCTGGGAGTGTAGGGGG R 2 1 2 1 201000 r 74 goat snp52153-scaffold772-200053 2 12882439 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278048 Affx-1111836147 AX-519551538 2 122303331 AGTTCTGGCTTGGGGTCTCTCATGAAGTTGCAGTC[A/G]GACAGTTGTCTCTGGGGTCACCTCTCACCCTTCAT R 2 1 2 1 102000 r 74 goat Random2.2K-269 2 122303331 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780763 Affx-122932397 AX-385267852 2 122306415 GCAGAAGCAGAACATGAGTGCTTGCATTTGCCATT[C/T]GCGCTGAAATCTTGCACGTGCTAAAACCCACCGGG Y 2 1 2 1 101000 f 74 goat snp52154-scaffold772-240415 2 12842770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429772 Affx-122938247 AX-123300113 2 122338484 ATTCTGCTCTCCAACCAGTCCAGCGGAGGGGCCTC[A/G]TCTATACATACCTGAACTGAGTGACTCCGGTGTCA R 2 1 2 1 101000 r 74 goat snp52155-scaffold772-272484 2 12810236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393858 Affx-122965145 AX-123264213 2 122368838 AAGGGCAGGGACTGGTCCTTGATCCCGCCAGGCAC[G/T]GCAAGGGAAAGGAGACCCGCGGCAAAGGAAAGCTG K 2 1 2 1 101000 r 74 goat snp52156-scaffold772-302838 2 12779744 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383382 Affx-122973511 AX-123253740 2 122405753 AGCCTCCCTTTTCTTCCTGTGTTCCCCCAGCGCCA[A/G]TTAAGCACTGTGCCAATCTCTGTGACAAAGATTAC R 2 1 2 1 101000 r 74 goat snp52157-scaffold772-339753 2 12743331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783714 Affx-122953015 AX-385270771 2 122456718 TCGATCAGAATCAATTAGAGGATAGATCCGAGGAA[C/T]GTAGAAGGCACAATTCCAGATGTTCCTAGTGATGC Y 2 1 2 1 101000 r 74 goat snp52158-scaffold772-390718 2 12691892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444343 Affx-122926722 AX-123314680 2 122502536 ACAAGAGAAATTGTGAAGATGGGTGAGGTGGACAA[C/T]GGAAAGGCAATGGATGAATGGGTGAGCAGATGGGG Y 2 1 2 1 101000 f 74 goat snp52159-scaffold772-436536 2 12645488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407851 Affx-122954520 AX-123278202 2 122534178 ACCACCAAAAATAAACTCTGCCAAATATTGGTTGC[A/G]TACACATATGTGTTTATATATATTTATGTTTTTCT R 2 1 2 1 101000 f 74 goat snp52160-scaffold772-468178 2 12614066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413608 Affx-122950563 AX-123283957 2 122573138 TTCAATTAGTGCATGGTTGGTTGAATCCGTGGAGG[C/T]GGAACCTGCGGATATGGACGGTTGACTGTAACTCC Y 2 1 2 1 201000 r 74 goat snp52161-scaffold772-507138 2 12575052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395286 Affx-122964076 AX-123265641 2 122616014 TCCCTGACCTCCCAGACAACTCACTCACACACACA[C/T]ATGTATACACACACACGCATACATGCACACACTTG Y 2 1 2 1 103000 f 74 goat snp52162-scaffold772-550014 2 12532035 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408422 Affx-122954464 AX-123278773 2 122644822 CAGATAAGAAGGTCCACAGAAACCTCAGTTCCTAG[C/T]GAGAGGAACCAGCTTTGAGCCCTCTCCACCCGCAC Y 2 1 2 1 101000 f 74 goat snp52163-scaffold772-578822 2 12503309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383811 Affx-122973181 AX-123254169 2 122688810 GTATCAAGTTCTAAATTTCAGAGTTCATTGACTCA[C/T]AGTATCTCAGAGCTGCAGAGACACTGGTCTAGGCA Y 2 1 2 1 101000 r 74 goat snp52164-scaffold772-622810 2 12459768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416391 Affx-122947862 AX-123286740 2 122729972 ATAGTCCACCAGCCAAGTCAGGCCTGCCCACGTTA[C/T]GCATGGGCTGCAAGCTGAGAGTCATTTTTAAAGTT Y 2 1 2 1 201000 r 74 goat snp52165-scaffold772-663972 2 12418787 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421155 Affx-122944182 AX-123291502 2 122774023 TTGCCATGGGCTGTGAGCCTCTCAGGACATCAGCA[C/T]GAATCCAGGAAAACACTCATCTTCTGGGAGGACTC Y 2 1 2 1 201000 r 74 goat snp52166-scaffold772-708023 2 12375042 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415667 Affx-122948555 AX-123286016 2 122804270 ACCAAGTCCTTTTCATGAACTATCACTTTCAATCC[A/G]TTTAAGAAGCCTGTGGGGTTGGGGTTACCCTCTGC R 2 1 2 1 101000 f 74 goat snp52167-scaffold772-738270 2 12345538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407531 Affx-122954699 AX-123277882 2 122836304 GACATTATTTTCAGTTAGAAAACTCCTGAAGAAGC[A/G]TGACCTCTCCTGATGAACTAAGCTGATGAGTAGAT R 2 1 2 1 101000 r 74 goat snp52168-scaffold772-770304 2 12313561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391129 Affx-122966796 AX-123261486 2 122866077 GAGAACCATGTTTCATCTAAAAGAAAAAGACAAAG[A/C]GTTAAAATATTATTTTCATTTTTTAAGGTCATGGC M 2 1 2 1 101000 f 74 goat snp52169-scaffold772-800077 2 12283827 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381141 Affx-122974563 AX-123251499 2 122916964 GTCTCCCACATTGCAGGCAGATTCTTCACCACTCC[A/G]CCACCAATGTATAAATCTCTCTCTATGAAAATCTT R 2 1 2 1 101000 r 74 goat snp52170-scaffold772-850964 2 12232894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401293 Affx-122959862 AX-123271646 2 122959134 AAAGCATATGTAAAAGGGAAATATATGGCAAAAAA[C/T]GGTACAAAGATGGGAATAAGGAATATATTGTTTGC Y 2 1 2 1 101000 r 74 goat snp52171-scaffold772-893134 2 12191145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449443 Affx-122922672 AX-123319778 2 122995842 GGAGCTCAACACTCACCGGCTGGTCCTTTCCCACC[A/G]CTCCCAGCTCTCTTTCCTTGGCGTAGGCCAGTTGG R 2 1 2 1 101000 f 74 goat snp52172-scaffold772-929842 2 12154443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382571 Affx-122973763 AX-123252929 2 123029036 TCCATTAAGTGAAGATTCTATGACCTGGGAATTTA[C/T]GATTCTGGAAGTCAAGGACTATCTGGTTCTAGGAT Y 2 1 2 1 101000 f 74 goat snp52173-scaffold772-963036 2 12121259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802782 Affx-122947256 AX-385289681 2 123090282 CAACCCCTAACTGCTTTCTGACCCTGTTGTTTCAC[A/G]TTTAAATAGGAGGGTGAATACACCTTGCAAAGGGC R 2 1 2 1 102000 f 74 goat snp52175-scaffold772-1024282 2 12060180 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416660 Affx-122947596 AX-123287008 2 123138551 CAGTTCTCCAAGAGCCCCAGGCAGGAGGCAGCAGG[C/T]GAAACTCATTTCCTGGGGTTTATGCCTCCTGCTCC Y 2 1 2 1 101000 r 74 goat snp52176-scaffold772-1072551 2 12010245 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432607 Affx-122935499 AX-123302948 2 123177744 GGATGCATCCCAATATCCTATTTATACCTCCCAGG[A/G]GAGCCTGGGAACTCCACCTGGACAGTCCCCCCTCA R 2 1 2 1 101000 f 74 goat snp52177-scaffold772-1111744 2 11970621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769074 Affx-122920081 AX-385256249 2 123254821 AGTCAATCGGTAAGTACATCCTTTTTTATTGAAAT[A/G]TAGTTGATTTGCCACGTGGTTTTAATTTCTGCTGT R 2 1 2 1 101000 r 74 goat snp52178-scaffold772-1188821 2 11894603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420551 Affx-122945289 AX-123290898 2 123286034 TTTGCAAACATAAGCCCTAAGCTTACTGTGGGGTG[G/T]AAGTGGAGGTGGAAAAAGAAGAACAGACACTCAAG K 2 1 2 1 103000 f 74 goat snp52179-scaffold772-1220034 2 11863421 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384299 Affx-122972287 AX-123254657 2 123332170 TCTTGTGCCTCCTGCATTGGCGGGTGGCTTCTTTA[C/T]CACTGTGCAACCTGGGAAGCTTAAAAGGAAGATGG Y 2 1 2 1 103000 r 74 goat snp52180-scaffold772-1266170 2 11816801 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407861 Affx-122954512 AX-123278212 2 123375503 TGATTTCTTGGCCTCGGATGCTACCTGGTCCACCA[C/T]GTCAGCACAGCAGGCACAGTTTCTCAGGCTCAGGG Y 2 1 2 1 101000 f 74 goat snp52181-scaffold772-1309503 2 11773023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272932 Affx-1111833154 AX-519546618 2 123447548 AGAAGACTGGGTGGCATTGCTGACTTGATGGACAT[A/G]AGTTTGAGCAAGCTCTGCGAGTTAGTGATGGACAG R 2 1 2 1 303000 f 74 goat 2_123447548_AF-PAKI 2 123447548 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795379 Affx-122930966 AX-385282335 2 123504007 AATTTTAATATATCAATAGTTCAGAGTTTTCTAAT[A/G]CAAAGAACTGTAGCTTCTGGTTCTCCCTGAGTATT R 2 1 2 1 101000 r 74 goat snp47652-scaffold670-6366 2 11643751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476170 Affx-1251763673 AX-586011597 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20000 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 539476425 Affx-1251763673 AX-586011826 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 4 1 4 1 20000 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165169 Affx-1251763673 AX-606940581 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165479 Affx-1251763673 AX-606940890 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165523 Affx-1251763673 AX-606940935 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165743 Affx-1251763673 AX-606941152 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165783 Affx-1251763673 AX-606941192 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562166126 Affx-1251763673 AX-606941534 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 38439429 Affx-122930195 AX-123309766 2 123572121 CTTCAGTCTGAAGTAGTCTGCCTGTATCATTCCCC[A/G]CTCCCACCCCACAACGTTTACTTTTCTTAGTCTCT R 2 1 2 1 201000 r 74 goat snp47653-scaffold670-74480 2 11575653 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777101 Affx-122945823 AX-385264224 2 123651037 GCCACTGTGAAATATTTCTTATATAGTTTAAAGGA[C/T]AGATTTGGCCTTCACTTATTTCATTGTATTTAAGA Y 2 1 2 1 101000 f 74 goat snp47655-scaffold670-153396 2 11497091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392223 Affx-122966267 AX-123262580 2 123688012 TTTGGGGCCAGTTTAAAATCACTAACATAATCTGC[A/G]CCATGGAGTTCTGGGTCATAGTCTCCCAGCTCAGA R 2 1 2 1 101000 f 74 goat snp47656-scaffold670-190371 2 11459478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770953 Affx-122963390 AX-385258116 2 123727230 AATTACTATGCAGAGCTAATGTCCTCAAGGACTAG[C/T]TGGGTTTATAGGGATGGTGAACTCTGCCATATGGA Y 2 1 2 1 201000 r 74 goat snp47657-scaffold670-229589 2 11417637 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796592 Affx-122975250 AX-385283538 2 123764156 TCATGTCATCCCTATAAAGAACACAGTCCAGAGCA[C/T]GGCTCATAATAAGTCATCATTAAATACTAGCATTA Y 2 1 2 1 101000 f 74 goat snp47658-scaffold670-266515 2 11380803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797302 Affx-122936347 AX-385284241 2 123823305 CTTTCTCTTGAAGCTGACTCTCCAGAAGTAGTTAT[A/G]TTGGCCCCATCCAATTGCAAGGGACTGAAAAGTAA R 2 1 2 1 101000 f 74 goat snp47659-scaffold670-325664 2 11321451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424998 Affx-122941898 AX-123295344 2 123854641 ACAAGCCTCCTTGCCTCCCTCTGAATTGCAGCTTC[C/T]TCACCTGTACACTGGAGGTGACAATGATGGAGATG Y 2 1 2 1 102000 f 74 goat snp47660-scaffold670-357000 2 11289600 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796428 Affx-122929840 AX-385283378 2 123910185 ACTTCCTTAAATTACTCTTTAAGACTTGGTTGGAA[C/T]AGACAGCTTGGAAAACTTCGCAGGTTGGGAAGGGT Y 2 1 2 1 101000 r 74 goat snp47661-scaffold670-412544 2 11233919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413616 Affx-122950558 AX-123283965 2 123946145 CCTTGTCTTCCCAACTGTCTGTATTCTACATCATA[C/T]AAGATTGATAAGCGATACCTCTAACTTGCTTTGTA Y 2 1 2 1 101000 f 74 goat snp47662-scaffold670-448504 2 11197814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413501 Affx-122950640 AX-123283850 2 123975015 GACATAGATTGTTACTAGCGTTTAAACAAGTGATA[C/T]TTGAAAATGCTTAGAAAAGTTCCTGGGGCCAGTCG Y 2 1 2 1 201000 f 74 goat snp47663-scaffold670-477374 2 11168622 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429733 Affx-122937603 AX-123300074 2 124069662 ATCTAGCCAGCTTCATCTCTACAGGGTAATGCATA[C/T]GGTTCAGAGCTCCTTCCCCAAGGACCCCAGTCCCA Y 2 1 2 1 101000 f 74 goat snp47664-scaffold670-572021 2 11073905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412496 Affx-122951375 AX-123282845 2 124154701 CATTGTCAGGCGGATTCTTTACCACTGAGCCACCT[C/T]GGAAACCCCACAGCTTAGATTTACAGAGAAACTGA Y 2 1 2 1 101000 r 74 goat snp47666-scaffold670-657060 2 10988232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804473 Affx-986696640 AX-385291042 2 124220951 TTATATTCTCTAAAAGATATAAGGTGTATCAGGTA[C/T]AAGGTATATCAGATATAAGGTATATTCTCTAAAGA Y 2 1 2 1 600010 r 74 goat 2_124220951 2 124220951 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320797485 Affx-122920336 AX-385284424 2 124233522 GTACAGCAGAGAACAAAAGAGAGCACCTATCTTCA[C/T]GAATCTTATATTTTTAGTAGGGAAGCAGTGATTAG Y 2 1 2 1 101000 f 74 goat snp47668-scaffold670-735881 2 10908197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401856 Affx-122959425 AX-123272209 2 124280780 AAACTTGGAATTGGGACAGAAGCTCAAGGGTTCCC[G/T]GAATGGGAAGCAACATTGAGGTTAGAGGTGATTCA K 2 1 2 1 101000 r 74 goat snp47669-scaffold670-783139 2 10862089 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776283 Affx-122973271 AX-385263411 2 124322803 GTCCATTTATAGTCTACTTTCAAAATGTCTCATTC[A/G]CTTTGAAGTGTTAATTTGCTGGTACCAGTGTTTTC R 2 1 2 1 101000 r 74 goat snp47670-scaffold670-825162 2 10820184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397518 Affx-122962051 AX-123267873 2 124365944 GGTGGCTGAGAAGGTGAATCCAGGCTGGAGGAAGA[A/G]GGTCTGAATTGGGGAGCAGAGCTAGGACTCGACTC R 2 1 2 1 201000 f 74 goat snp47671-scaffold670-868303 2 10777397 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794334 Affx-122946541 AX-385281298 2 124395493 ATATTTTTTAAAAGAGGTCAAGAATTTTCAGAGAA[G/T]CAGAATTTTTGGAGATGGAAGGGTCCAATTCCTTC K 2 1 2 1 101000 r 74 goat snp47672-scaffold670-897852 2 10747845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404426 Affx-122956765 AX-123274778 2 124435980 AATGCCATCAGTGCTCCTACTTGAGAAACCCTGGC[C/T]AAGAGCATGGAACTTGAATGCTTAGGTTGACTCAC Y 2 1 2 1 101000 r 74 goat snp47673-scaffold670-938339 2 10706455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431726 Affx-122936751 AX-123302067 2 124506565 TTCTTTATTACAATTACTCTCTTACTAATACCTTC[A/G]ATAATTTTGACTCTTGTACTGTCCTTGCTAAACCC R 2 1 2 1 101000 r 74 goat snp47675-scaffold670-1008924 2 10635416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776792 Affx-122968620 AX-385263916 2 124540570 TTGGTTAGGTCAGCACAGTCTTGTTTCTGGGCTTC[A/G]GTTTTATTGGCTCAAAAATTTTTTGTTACCATATT R 2 1 2 1 101000 f 74 goat snp47676-scaffold670-1042929 2 10601277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391612 Affx-122966591 AX-123261969 2 124610126 CACTGAGCCACCTGGGAAGCCCATGAGACAGGACA[G/T]CAGTTTATATAATGCCACCCAAGTGAGACTGAAAG K 2 1 2 1 101000 r 74 goat snp47677-scaffold670-1112485 2 10531540 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419807 Affx-122945839 AX-123290155 2 124641388 TGCCCAATGATAGAGTTCCCTGCCATCTTGGCATT[A/G]GCGTGATCTTACAGGAGTTCTGTGGTTCCCGAGCA R 2 1 2 1 101000 f 74 goat snp47678-scaffold670-1143747 2 10500206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767353 Affx-122930352 AX-385254629 2 124677535 GCCACATCAGAGGGGGTCTATAATTCTTCTAATAA[C/T]AGGGCTCTTGATCTGGTTAATGCACTAGCTACCTG Y 2 1 2 1 101000 f 74 goat snp47679-scaffold670-1179894 2 10463291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380229 Affx-122975474 AX-123250587 2 124718061 CACTTTGATGTTGATATGATCATATTTATTATTAG[C/T]ATGCAACTGAAACCCAACACTTTCTCAGTTTTGTA Y 2 1 2 1 201000 f 74 goat snp47680-scaffold670-1220420 2 10422960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382645 Affx-122973680 AX-123253003 2 124768983 TTTAATACTCACAGCAACCTTAAGGTAAGTAGAGA[C/T]AGAATTCAAACACAGGCAGTCCAACTTCAGAGCTA Y 2 1 2 1 201000 f 74 goat snp47681-scaffold670-1271342 2 10371129 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789581 Affx-122953753 AX-385276590 2 124806799 AAATCTCTGAAAAGGCCTCTTTGCCATTATCAGTG[C/T]ATAAACATGCTGGGAGAATGCCTGCAAAAACACAG Y 2 1 2 1 101000 r 74 goat snp47682-scaffold670-1309158 2 10332199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435515 Affx-122933413 AX-123305855 2 124835726 ATGGCAAGTTGGGAGGGTGGCGACGGGAGTCCCTT[C/T]GCAGGAGTCCTGTCCCCTCTGGGCCTCTGTTCCTC Y 2 1 2 1 201000 f 74 goat snp47683-scaffold670-1338085 2 10303289 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278050 Affx-1111836148 AX-519551540 2 124881504 CCTAGAAATTCCCTAAGTTTTTATCAGTTTTGGAT[A/G]ATTTTGAATAGCCAGCGATCTTTAATGTACCATCT R 2 1 2 1 101000 r 74 goat Random2.2K-273 2 124881504 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439103 Affx-122931112 AX-123309440 2 124885681 ATGCCAAAGCCTCATCTATTTGTGTAACTTTAGGT[C/T]AGGCTGGGGAGCTGCAAAGGGCCCCTAACAACTTT Y 2 1 2 1 101000 f 74 goat snp47684-scaffold670-1388040 2 10255073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427549 Affx-122939497 AX-123297892 2 124963602 CTTATCACACTCACAATGTAACATACACACCTAAA[G/T]CCCAAGCTCCAAAGAGGCCACACACCCAGGTTCAC K 2 1 2 1 101000 f 74 goat snp47685-scaffold670-1465961 2 10179462 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796584 Affx-122961115 AX-385283530 2 124997373 CTGGACTCATCAAGCAGCCTTTTTGAATACTTATT[A/G]TATGCTCCTTAATCACTCATCTCATTCTTGCATAC R 2 1 2 1 101000 f 74 goat snp47686-scaffold670-1499732 2 10145818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434273 Affx-122934782 AX-123304614 2 125092367 GGCAGGCTTGGAAGGATCCAAGCATCCATTGACAA[C/T]ATTCTTGGGTCCCTTGGGTCCTACAAGTAGATGGT Y 2 1 2 1 101000 r 74 goat snp47688-scaffold670-1594726 2 10051234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449763 Affx-122922446 AX-123320098 2 125133592 CAGATGCCTAGACAAAGGAAATGGAATCTGCTGGA[A/G]TGGGAAGGGGAAATGGGAGGACAAAGAAGGAAGGC R 2 1 2 1 101000 f 74 goat snp47689-scaffold670-1635951 2 10011372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779940 Affx-122942034 AX-385267039 2 125193122 GACAGAAACAAACTCATAGGTTCAACTGATTCAAA[C/T]GTAACATGATTTACTACGTTCCTATTACATACACA Y 2 1 2 1 101000 f 74 goat snp47690-scaffold670-1695481 2 9952181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774067 Affx-122925030 AX-385261205 2 125244093 TGCATAATCCCTGGTGATTTCCCTACACCTTGACC[G/T]CACCTTCTAAATTAGCTCCTTTGTACATATGACCT K 2 1 2 1 101000 f 74 goat snp47691-scaffold670-1746452 2 9900685 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423749 Affx-122942852 AX-123294095 2 125277229 TCTGTCTAAGCCACGACGAGTGTCTCTAACCCGGT[A/G]ACTCCAGCAGTCTCCTGGCCCACTCCCCTCCGCCT R 2 1 2 1 101000 f 74 goat snp47692-scaffold670-1779588 2 9867466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412742 Affx-122950527 AX-123283091 2 125308567 GTAGACCTGCTGGCTGTGAAGAAAAAGCAAGAAAC[A/G]AAGCGTTCTATCAACGAGGAGATCCACACGCAGGT R 2 1 2 1 201000 r 74 goat snp47693-scaffold670-1810926 2 9836255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380371 Affx-122975344 AX-123250729 2 125340059 AGGCCGTTTTCACTGCAGGAGGGGGAAGGCAGGAC[G/T]GGCCTTTCATCCACAAGGGGCTTGGAAACAATTTT K 2 1 2 1 103000 r 74 goat snp47694-scaffold670-1842418 2 9804968 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429907 Affx-122938113 AX-123300248 2 125374584 TTTTTAGTCTGCAGTGTCAGCCCTGAGGAGACAGA[C/T]ATGGGAGTAGGCAGCCCTTGAACCTGAGGACCTTA Y 2 1 2 1 201000 r 74 goat snp47695-scaffold670-1876943 2 9769949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771726 Affx-122969274 AX-385258883 2 125427347 TGGCTGTATCCCAGAAATACACTTATTGGGTCTTA[C/T]GGTACACAGATGTTCAACTGTACACGATATGACTC Y 2 1 2 1 101000 r 74 goat snp47696-scaffold670-1929706 2 9717367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403316 Affx-122957831 AX-123273669 2 125458128 GCTCCAAGTCTCCGTACAGGCAAGTCGTAATGTTT[A/G]GAAAGATTCATCCCAAGAGATGCTCTTCGGGGGCG R 2 1 2 1 101000 f 74 goat snp47697-scaffold670-1960487 2 9686517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428115 Affx-122939075 AX-123298458 2 125486718 TGTTCTAAGCCTTTCATTTTCTTATTGACGCTTGA[A/C]AACTATCCTATAAGGCAGGAGCTGTTGTCACCTGT M 2 1 2 1 101000 r 74 goat snp47698-scaffold670-1989077 2 9657402 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393162 Affx-122965534 AX-123263519 2 125522986 AGAAGAAGCAGATCACCAACTCCAGCACGGTGAGC[A/G]GCGCAGTCAAGGACCCACACGGGGACCAGGGCTGG R 2 1 2 1 101000 f 74 goat snp47699-scaffold670-2025345 2 9620945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422198 Affx-122943502 AX-123292544 2 125599802 AGCAACAAGCTAGGCTTCAGTTCTGTCACTTAAAA[C/T]GACAAGATGACTGGACAAATCTGAGTCTGTAATGC Y 2 1 2 1 201000 r 74 goat snp47700-scaffold670-2102161 2 9544314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775868 Affx-122928976 AX-385262999 2 125634026 CATTATCAATGCTTATCATCTGACCATTTCTGTGC[A/C]AAGCACAATCCTTCTTAGGACATACAATGAGGGAC M 2 1 2 1 101000 f 74 goat snp47701-scaffold670-2136385 2 9509950 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382648 Affx-122973678 AX-123253006 2 125684923 AGGAAGGAGAACAGGATGGGGCAAGTGCTGATCAC[A/G]TCTTGAGCACACTGATTCTTAAAGAACGCTGGCTA R 2 1 2 1 101000 r 74 goat snp47702-scaffold670-2187282 2 9458759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387897 Affx-122969615 AX-123258255 2 125717904 ATGGCTGATGGAATATCCCCAAAATGGGAGACAAC[G/T]GGCACTGTTGTTTCTAGCTGTAGACCCTTCTTTAC K 2 1 2 1 201000 r 74 goat snp47703-scaffold670-2220263 2 9425971 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452302 Affx-122920679 AX-123322635 2 125758527 GGCTAAAGTTGGGACAGGTCAAACCTTTCCTGAGA[C/T]CTGCAGGGGGTTCCCACCTCTCCCAACCCTGCACC Y 2 1 2 1 101000 f 74 goat snp47704-scaffold670-2260886 2 9385084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420888 Affx-122944618 AX-123291235 2 125834008 AATTGTGGTCTTCAATATACAAAATCTTTCAGGTG[C/T]AAATAACAGAATAAAACAGCTTAAACACTTGGGTG Y 2 1 2 1 101000 f 74 goat snp47706-scaffold670-2336367 2 9310575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430805 Affx-122937460 AX-123301146 2 125844386 ATTCTAGAAAACAGCAGAACCATCCACCCAACTGC[C/T]CAGGCCAAAACCTAAATGTTTTGCTTCCTAGTAAT Y 2 1 2 1 101000 f 74 goat snp8256-scaffold130-7687 2 9299981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396438 Affx-122962986 AX-123266793 2 125898238 ATTTCATGTTACGGTGGATGAGGACTTAACCTTGC[A/G]TACAAGGCCTACTTCTCCTTGCCTTTTCCTCCCAG R 2 1 2 1 201000 f 74 goat snp8257-scaffold130-61539 2 9245931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450028 Affx-122922840 AX-123320363 2 125929616 CCCCTGCATTAGAAGGCAGATTCTTAACCACTGGA[C/T]CACCAGATAAGGCCTGACAATAAGTCTTGACAGTT Y 2 1 2 1 101000 r 74 goat snp8258-scaffold130-92917 2 9214815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400897 Affx-122959744 AX-123271250 2 125971525 TGTGTTTCTCTGTGTCTGTGAATGCATGTCTGGAC[A/C]TGTGTCTCATTTATGTGCAATGAGGGCATGTGTGT M 2 1 2 1 201000 r 74 goat snp8259-scaffold130-134826 2 9172777 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386270 Affx-122970946 AX-123256628 2 126020330 GCCAAAATGAGGGGTGGAGTATGAGATGATGGTGA[C/T]GGAAGGCAATGGAAAACTGAGGAGTCTGTTAAATT Y 2 1 2 1 101000 f 74 goat snp8260-scaffold130-183631 2 9124075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440065 Affx-122929738 AX-123310402 2 126090340 AAGCCAGTGTCCTGGAAGCCATAGCAACACCCTGG[C/T]GAGAGAAGACAAGACAGGAACTAGAATGGGGTACA Y 2 1 2 1 202000 f 74 goat snp8261-scaffold130-253641 2 9053807 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449742 Affx-122922461 AX-123320077 2 126127554 TATTTAGCCAATGGTCACACAGGCCCTGGCAGGTT[A/C]AGTGGTTTGCATAGAGGCACAGTAAGCTTGGGGCA M 2 1 2 1 201000 r 74 goat snp8262-scaffold130-290855 2 9016846 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278052 Affx-1111836149 AX-519551542 2 126154061 CAAGCAACTGTATTTCTAAGGTGTTTAAGCAGTCT[A/G]TGAAGTAAAGGACTTTTAGAAGTATAAACACCCTA R 2 1 2 1 101000 r 74 goat Random2.2K-276 2 126154061 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437096 Affx-122932184 AX-123307434 2 126161122 AGATTGGCAAGTATCATGGCATAACAGGTGGCTTA[C/T]GTTATTTTTAGGTATTTGCATCACAGGTTTAAATA Y 2 1 2 1 101000 f 74 goat snp8263-scaffold130-324423 2 8983108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272934 Affx-1111833155 AX-519546620 2 126161417 TGTCCAACTCTGTGTGACCCCATGAATTGCAGCAC[A/G]CCAGGCCTCCCTGTCCATCACCAACTCCTGGAGTT R 2 1 2 1 103000 f 74 goat 2_126161417_AF-PAKI 2 126161417 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414782 Affx-122949234 AX-123285131 2 126241178 TAAGTTCGAGTCTGTGTATATGTGGGCTTCCCAGG[C/T]GGCTCGGGGGCAAAGCATCTGCCTGCAAATCGAGC Y 2 1 2 1 103000 f 74 goat snp8265-scaffold130-404479 2 8903721 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380950 Affx-122975000 AX-123251308 2 126271269 CTGAATTAGACCTTCTCTGTAGGCTCCAGAAGCCA[C/T]GCCCAGCCTCCTCTAGTTCCTGGAGTCTCCCAGAG Y 2 1 2 1 101000 f 74 goat snp8266-scaffold130-434570 2 8873361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388593 Affx-122969155 AX-123258951 2 126304799 GAAAGAGAGAGGAATCAAGGTTTTTTCATTTGTGC[A/G]CCCATCATTTGAAGGGAAGATGACCGTCCTTTATT R 2 1 2 1 101000 r 74 goat snp8267-scaffold130-468100 2 8838836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780152 Affx-122955663 AX-385267249 2 126336860 ATACTCATAGACTGCTCTACAAATCCTGAATGCCT[A/G]TTCACTTATTTACAGTGAGAAACGTGAGTGGAAAG R 2 1 2 1 101000 f 74 goat snp8268-scaffold130-500161 2 8807019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375368 Affx-122979230 AX-123245727 2 126367579 CAGGCAACAGTGTATTGCTAATTGTTTGCTTTGTG[C/T]GGTGTGTCTGCTGCCTGTATAATCCAGTTTTCCTT Y 2 1 2 1 201000 f 74 goat snp8269-scaffold130-530880 2 8776142 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440894 Affx-122929226 AX-123311231 2 126416573 AAAGTTGTTTGTATCTGGCCCGCGGTGATTCTCTG[C/T]GCACGCCTCAGCTGCCAAGGGCAGCACTGGCCAGT Y 2 1 2 1 101000 f 74 goat snp8270-scaffold130-579874 2 8726791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432294 Affx-122936317 AX-123302635 2 126456497 ACCTTTTCTTTCGCCAGGCTGCCTCTTCTAAAGGC[A/G]TTAGGACCACACCACCCTCCACCGACCCAGGCCTT R 2 1 2 1 201000 f 74 goat snp8271-scaffold130-619798 2 8687015 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408094 Affx-122954715 AX-123278445 2 126487270 TGGAAAGGAATGTCTGGGCCTGGTGTGACATCTCC[A/G]CGTCTCCAAGTCCTGTCTCCTCACAGAGGAAAAGA R 2 1 2 1 101000 f 74 goat snp8272-scaffold130-650571 2 8656873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781133 Affx-122966958 AX-385268218 2 126596717 TCACTTATGAGGTCTGCTCACGACTGAGCAGTTCA[C/T]ACATACATTGGCATGTCTAACAGTGACAGATTCTC Y 2 1 2 1 101000 r 74 goat snp8274-scaffold130-760018 2 8547620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385551 Affx-122971229 AX-123255909 2 126632716 CTGCTCTCCCTGGAAATCAGAGCAGACTTGCTGAC[G/T]GCTCTGCAGCAAACCAAGAGGTCCAGAGAGAAGCA K 2 1 2 1 202000 f 74 goat snp8275-scaffold130-796017 2 8511617 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405451 Affx-122956043 AX-123275803 2 126719639 ACAGAGAGAAAGAAAAAGGCCTTCCAGAGGGAAGG[A/G]TAGTAGGAACAGAGAGGGAGCTAGAACAGGCGTGA R 2 1 2 1 201000 f 74 goat snp8277-scaffold130-882940 2 8426507 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412457 Affx-122951404 AX-123282806 2 126751725 GAGGGGAAGGGTGGGAGGGGCAGGTCTTTCTTTGC[A/G]TGAATACAATATGCCACAGCCCACTGCAGCCTTTC R 2 1 2 1 101000 r 74 goat snp8278-scaffold130-915026 2 8394435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767196 Affx-122973409 AX-385254478 2 126835436 TGCTGTCCTCTAGCTTACTCCATTCACCCACAAGC[C/T]ATTCCTTTGCAGACTCACATCCACAATGCAGCGCT Y 2 1 2 1 101000 f 74 goat snp8280-scaffold130-998737 2 8310464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797337 Affx-122938965 AX-385284276 2 126866350 ATCACTAGCGATGACACTTACATTAAGAAGGCTAC[A/G]GTTGCTATAACACCACACGCATGGTAGGAATGGTT R 2 1 2 1 101000 f 74 goat snp8281-scaffold130-1029651 2 8279708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803167 Affx-122958443 AX-385290030 2 126896301 TGGGTATATATGTCCTGGACATCAAATTTGTTACT[A/G]TCTTTTAGGTAGTCTTGGTCACATTCTCATCCTTT R 2 1 2 1 101000 r 74 goat snp8282-scaffold130-1059602 2 8249237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413928 Affx-122949812 AX-123284277 2 126925995 GGCTGTCTCCATAGAGGGCTGCTTAGGACCAAGTT[C/T]AGGAAGTAGAATTGTCCTCCCGTAAACAGTGAGCA Y 2 1 2 1 101000 r 74 goat snp8283-scaffold130-1089296 2 8218437 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278054 Affx-1111836150 AX-519551544 2 126927246 CATCTCTAATACCCCCCACCCCTTTTCGTCCCTCT[A/G]TTATAGTGGCTATGTGCCTGCATCCTGCCATAGGC R 2 1 2 1 201000 r 74 goat Random2.2K-279 2 126927246 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427400 Affx-122940074 AX-123297743 2 126962003 GTGTGATGGTGAGATTGTGTGTGTGTGTGCGTGTT[A/G]CAGGAGTGGGACTGTCAATGGGACTTTCTTATTTG R 2 1 2 1 103000 r 74 goat snp8284-scaffold130-1125304 2 8181941 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436728 Affx-122932306 AX-123307066 2 126995453 GCTGGGAAAACTGCAGAGTGGATTCAGTTTCTGCT[A/G]CAAGAAGAAATTGCTGCTGCTGGGGTGAAGGGGTG R 2 1 2 1 101000 f 74 goat snp8285-scaffold130-1158754 2 8148605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378710 Affx-122977054 AX-123249069 2 127034435 AGATGCCGATATGATGAGAGGGGAAGCCTATGGAC[G/T]CTGCGACACTGCAAGGCTCAGTCTTGGCCCTACCA K 2 1 2 1 101000 f 74 goat snp8286-scaffold130-1197736 2 8109563 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388229 Affx-122969398 AX-123258587 2 127066370 AAAGTCAGGGGAGAAGGCACAGGCCACGATGGGAC[A/G]AGGGTCTCCGGTGCTTTCTGCATCAGCCAGGAAAC R 2 1 2 1 101000 f 74 goat snp8287-scaffold130-1229671 2 8077046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402866 Affx-122958236 AX-123273219 2 127096201 ACAGCAAGTTAAAACCTAGGACTCCAGGTTCCAAG[C/T]TTCTTTTCAAACTTCTGGGCTTCCAGGGGTCATAG Y 2 1 2 1 101000 f 74 goat snp8288-scaffold130-1259502 2 8047008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795097 Affx-122962653 AX-385282056 2 127183615 AGATGAAATATGGTTTTAAGTCTATCATTAATATC[A/G]TCAGAGTGATAAGAGAAGGTACTGCATCTGTGCAA R 2 1 2 1 101000 r 74 goat snp8290-scaffold130-1346916 2 7960797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784991 Affx-122949784 AX-385272038 2 127222564 ATGAACTTACCTGCCATCAGTAACGATGAATAATG[C/T]TCAGAAATGTAATCGTGTGGCTGCAATCCTATCCC Y 2 1 2 1 101000 f 74 goat snp8291-scaffold130-1385865 2 7922396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407637 Affx-122954621 AX-123277988 2 127267429 TGTAATAACAGCAGCCCTACCCTCTCCGTGATCCT[C/T]GGGCTCCTACCCCGAACAGGTCTTAGTGAAGCCTT Y 2 1 2 1 201000 r 74 goat snp8292-scaffold130-1430730 2 7877857 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446303 Affx-122925647 AX-123316639 2 127317363 TTTCAAGAGACCCCGCTCCAAAGCTGAAAGAAAAA[C/T]GGAAATGCTGTAAGAAGGAAAACCACCCAACCCCC Y 2 1 2 1 202000 r 74 goat snp8293-scaffold130-1480664 2 7827824 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408921 Affx-122953953 AX-123279272 2 127387562 GCTGAGAAGCTGATGAGTAGACAGCGATCCAAAAA[G/T]TAGAGAAGTGTTGGGAAAACAGTAAGATTCAGACT K 2 1 2 1 101000 f 74 goat snp8294-scaffold130-1550863 2 7757419 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412028 Affx-122951734 AX-123282378 2 127436666 TAGTCAGCTTTCTGTTGCAATTCTAAGTGCCTCCA[A/G]AAAACCACCTTCATTCAACAAGTCAGTCATTCTGA R 2 1 2 1 101000 f 74 goat snp8295-scaffold130-1599967 2 7707478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453214 Affx-122920438 AX-123323547 2 127467806 CCACCTCAGTTTTCCCCAGTAATGTTCTTCTTCTG[C/T]TCCAGGTTCCAAAAATCAGGATCCTACATTGCCTC Y 2 1 2 1 101000 r 74 goat snp8296-scaffold130-1631107 2 7676429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414603 Affx-122949355 AX-123284952 2 127528825 TCATGATAATAATGGTGGTTCCCATTTGGAAAGCA[G/T]CTGTTGGGTGCCAGGCACCACCTGAGTGACTTGTT K 2 1 2 1 101000 f 74 goat snp8297-scaffold130-1692126 2 7615147 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439199 Affx-122931040 AX-123309536 2 127560776 ACATCTGCTTTCCCCCTCCTGAGGGCCTGGGCAGC[A/G]TCTTGGGCTTGGTCATGCCCCAGCACATCACAGAA R 2 1 2 1 101000 r 74 goat snp8298-scaffold130-1724077 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405530 Affx-122955984 AX-123275882 2 127595070 TTATATCACAACATTTTAAAAAGATGGGATTCATG[C/T]GAATGGGAAAAACAATCATATTCTAGAAGAATGAA Y 2 1 2 1 101000 r 74 goat snp8299-scaffold130-1758371 2 7548666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439232 Affx-122931016 AX-123309569 2 127636574 TCTTTGCAATCTTTTTGTAAGATAAGGTGTATTAG[C/T]GGTTTCTGAAGCCTGAATGCTCTGAACAATTTCAT Y 2 1 2 1 201000 f 74 goat snp8300-scaffold130-1799875 2 7506832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447319 Affx-122924902 AX-123317655 2 127688235 TACAAAGGTTTTGCTGATACTGAGCACTGTAAGGG[A/G]TTCAGCCACCAGACCCTCATTTCCATCCAGGCTTT R 2 1 2 1 101000 f 74 goat snp8301-scaffold130-1851536 2 7455100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435478 Affx-122933446 AX-123305818 2 127730655 AGTCAGACTGCTCAGGTTTAAATTTATGCTTCCCC[A/G]TCTATTAGCTGTGGCCCCAACATCTCTGGGCCTCA R 2 1 2 1 101000 r 74 goat snp8302-scaffold130-1893956 2 7412880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450433 Affx-122922049 AX-123320767 2 127778030 AGCTCCAGTCTCTCTCTCCCAGGAAGTCACAGATT[C/T]ACTGTGTCAAAGCCAGAATGCCAGGTATGGAAAGC Y 2 1 2 1 201000 r 74 goat snp8303-scaffold130-1941331 2 7365505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388863 Affx-122969319 AX-123259221 2 127808411 AGGGACCTTGTCTGGCTCACTGTTGAATCTCCAGC[A/G]CCTTCCGTGGTGTCTGGCACACGGTCAGTGCCCAG R 2 1 2 1 101000 f 74 goat snp8304-scaffold130-1971712 2 7335190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765155 Affx-122975322 AX-385252707 2 127854226 CAGTGATACAACCACTGGGAAAAGAATGCGTTTTA[A/G]TAAGAACAAAGTACACTCCTCAGTACTTACTCAAG R 2 1 2 1 101000 f 74 goat snp8305-scaffold130-2017527 2 7288771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778406 Affx-122920426 AX-385265521 2 127889740 TTCTGTCTTGGCCTCTGCTTCTCAGAAGACCCAGA[C/T]GATCTCACCTTTTGTGAAAAGGTTGGAAAGTTAAA Y 2 1 2 1 102000 f 74 goat snp8306-scaffold130-2053041 2 7252648 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376638 Affx-122979027 AX-123246997 2 127924893 TGCCTCCCCATATTGCCAGGCAGGCTCTGCATTTC[C/T]CCTGTGTTAGAGGTGAGGAACAACTCAGGCTGTGA Y 2 1 2 1 101000 r 74 goat snp8307-scaffold130-2088194 2 7214762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784828 Affx-122931968 AX-385271875 2 127957397 TTGCTTGTTCGTCCTTAACTTCCCAACTGATTGAC[A/G]TAGAGTTGTTTTTCCTAGCAAATGCAAAAACTTCC R 2 1 2 1 101000 f 74 goat snp8308-scaffold130-2120698 2 7181877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379257 Affx-122976255 AX-123249616 2 128011373 CCTCACTCCCATCTAAGCCCCAGGCTAAGCCGACA[C/T]GGCCTCAGAAAACTGCTGTCCTAAATTTCTGTTCC Y 2 1 2 1 101000 r 74 goat snp8309-scaffold130-2174674 2 7130582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377208 Affx-122978180 AX-123247567 2 128041157 ATAATGACAAGTTGGCCTTTGTCATCACAGTGCAG[A/G]CCCTTCCACAGGGCTTGGCTTCAAGGAGGGGCTTA R 2 1 2 1 101000 f 74 goat snp8310-scaffold130-2204458 2 7101053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424366 Affx-122941846 AX-123294712 2 128081488 AAAAAAATTTTTTTTAATTATTGTTGTAATATAAT[C/T]TGTATGCAGAAAATACGTAAGTCTTAAGTGTGTAT Y 2 1 2 1 103000 r 74 goat snp8311-scaffold130-2244789 2 7060664 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441917 Affx-122928599 AX-123312254 2 128177212 GATGATACTGAAACCCACTGTTGCAGCAAAAATAG[A/G]GATGAGACTTTTCTTACATTATAATGAGACTTTTC R 2 1 2 1 201000 r 74 goat snp8313-scaffold130-2340513 2 6964062 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403811 Affx-122957961 AX-123274163 2 128219039 CTCAATTCCTCCTGGAAGAGAGGCTGGAGATGATA[C/T]AGATGGATGAGGAAGGAAGATCCAGGGAGAATAAG Y 2 1 2 1 101000 f 74 goat snp8314-scaffold130-2382340 2 6922494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778415 Affx-122952454 AX-385265529 2 128285587 GGGGCCTTTGCATACACTGTACTCTATCTGAAAAG[A/C]TTTTCCTGTATCCTCTTTACCTGGGTAAAGTTAAT M 2 1 2 1 101000 f 74 goat snp8316-scaffold130-2448888 2 6855899 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385666 Affx-122971150 AX-123256024 2 128334778 AGTTTTCACAAATGAGACCAAAGGTTCAACGTCAA[A/C]GTGTGTCTGCTCTGCAGCCATTTCAACAACCCAGG M 2 1 2 1 101000 f 74 goat snp8317-scaffold130-2498079 2 6806893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407237 Affx-122955368 AX-123277588 2 128381042 GGGACCAATCTTTTAAAGCAAAAAATAGAAATACT[A/G]TTTTACAGAAATACTATTACAGGGAAAATACTTTC R 2 1 2 1 303000 r 74 goat snp8318-scaffold130-2544343 2 6760614 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424182 Affx-122942521 AX-123294528 2 128436469 AAGTGCTAATGTTCTCTGAATGTCAGATGCTGGGT[A/G]TGCTGAGCATCTTCACATGGGAGGTGGGGACTGCT R 2 1 2 1 101000 f 74 goat snp8319-scaffold130-2599770 2 6704939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405287 Affx-122956852 AX-123275639 2 128496122 TGGAAACATATGGAACTCATTACCCTAAGTCGAAG[C/T]GGTCGCTGGCCAGCTGGCAGTTGGTCGGTTTGGGG Y 2 1 2 1 101000 f 74 goat snp8320-scaffold130-2659423 2 6645284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402398 Affx-122959018 AX-123272751 2 128575684 TGGGTTCATTTCATTTCCCCAATAACCCTATGTAG[G/T]AAAAACTATTATCATCCTTATTTCATAAATAGGGA K 2 1 2 1 201000 r 74 goat snp8322-scaffold130-2738985 2 6566020 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403414 Affx-122957758 AX-123273767 2 128615973 ATTGACGCCACGGAAACTGACAAACGCTACAAATC[A/G]ATTTTTTCCTTTGAGAACCTGCTGTTAAACATTTA R 2 1 2 1 101000 f 74 goat snp8323-scaffold130-2779274 2 6525690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402917 Affx-122958195 AX-123273270 2 128658131 ACAAAAAAGTCCTGAGCATATATGTGCCTGCTACA[C/T]AGAAACCACCATTCTTATTATTCAGTTGTTACCTG Y 2 1 2 1 101000 f 74 goat snp8324-scaffold130-2821432 2 6483527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272936 Affx-1111833156 AX-519546622 2 128665956 AACGACCTTCTGGAGTGCTCACAAGGCTAAGAGGG[A/C]AGAATAAACCTTTTTTTTTTTTCTGATATAAATAC M 2 1 2 1 102000 f 74 goat 2_128665956_AF-PAKI 2 128665956 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433383 Affx-122935117 AX-123303724 2 128697450 GGAGATCAGTATAACTGTGAGCCATTATTGTTACT[A/G]TTGTTGTTATTTAGATAAACTGAAAGGAAAATACA R 2 1 2 1 101000 f 74 goat snp8325-scaffold130-2860751 2 6443953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381133 Affx-122974568 AX-123251491 2 128746670 TGGCGTACCGATGACTTTCTCTTCCAGTCCCCTAA[A/G]AAAACAAGTTTTGTCAGCCTGAGTTCCCCTAATCT R 2 1 2 1 201000 r 74 goat snp8326-scaffold130-2909971 2 6394722 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414385 Affx-122949995 AX-123284734 2 128787850 CAATTTGTGAGCTCTGTATTTTGCAAGTTGTTTAC[A/G]TTTTTTGCCAATCTGATGAGAGAAGAAGATAGGAT R 2 1 2 1 101000 f 74 goat snp8327-scaffold130-2951151 2 6353510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389849 Affx-122968161 AX-123260206 2 128848143 CCAGGGAGGCCCCACGTCGTATATGCAGTGCTTCT[A/G]TGAACGCAGCCGCAAACCCAGTAACGCATCTACGT R 2 1 2 1 201000 f 74 goat snp8328-scaffold130-3011444 2 6293493 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422565 Affx-122943760 AX-123292911 2 128953125 AATGTCGAGAGGATAAACTCAAGAGAAGTTACCTT[A/G]GCCCTGTTTTTCTAGTCTGTAAAATGGAAGGGTTA R 2 1 2 1 201000 f 74 goat snp8330-scaffold130-3116426 2 6187588 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382153 Affx-122974040 AX-123252511 2 129017744 TCTGAAGTCTGCGCTCTAGCACTGCCCCAGTGCTC[G/T]GCTCACTGCTGGTGTCCCATGTGGTCCTTTGTTTC K 2 1 2 1 103000 r 74 goat snp8331-scaffold130-3181045 2 6122670 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275693 Affx-1111834957 AX-519549262 2 129115753 GAAAGGAATCCATCTCTGCTGTGTTTTCATTAGGC[A/G]CAGACAGAAATTCTAGTGGTTAATGTAACTTCCCA R 2 1 2 1 101000 r 74 goat GoatD01.059919 2 129115753 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417455 Affx-122947194 AX-123287803 2 129127295 TTCTGATTTCATTTGAAGCCGAGCTACCAAGTACT[A/G]TGCCCAGGGGTTCTACCACATTTTGACTAACCTGG R 2 1 2 1 201000 f 74 goat snp8333-scaffold130-3290596 2 6013043 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444285 Affx-122926764 AX-123314622 2 129168921 CCTGTCTTCAGTCCCATATTACAGATGGGGAAACT[A/G]AGTCACTTGTTCCACTAACTCAAGTAATAGGAGGC R 2 1 2 1 101000 r 74 goat snp8334-scaffold130-3332222 2 5972490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384120 Affx-122972824 AX-123254478 2 129217391 ACCCCCCAGGGGTAACTAATCTGGTAAAGAAGTCA[C/T]GGCCCCCCTGCTGTTCCTGGGAAGCTCCCAACCGA Y 2 1 2 1 101000 f 74 goat snp8335-scaffold130-3380692 2 5924230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399750 Affx-122960322 AX-123270105 2 129302407 CCCCTTCAGATTGGGAGCTGCCTGCAGGCAGTGCC[C/T]GGACTCTGAACAACATGCATTCAGGGCAGGAGGCC Y 2 1 2 1 201000 r 74 goat snp8337-scaffold130-3465708 2 5840648 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425106 Affx-122941230 AX-123295452 2 129358286 TGTGTCTTCTTCTCTCTTTCCTTTTCATCTGGCCC[A/G]TTTCCCATGCCCTCCTATGCATGAGCCAGGTGTGT R 2 1 2 1 201000 r 74 goat snp8338-scaffold130-3521587 2 5786063 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769428 Affx-122937722 AX-385256598 2 129396603 GATCCTTCACTGAAGGGACTCTGACCCTAATAAGG[C/T]GTTCTTAAGTAGAGCTGAAATCTCTCTTTCTGAAA Y 2 1 2 1 101000 f 74 goat snp8339-scaffold130-3559904 2 5747343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396903 Affx-122963217 AX-123267258 2 129425817 GCATCCTGTCCCCAAACCCCACTGCCTGCAGTGCA[C/T]GATGAATTAATATTTTTTTATAAAACCTGTAATTA Y 2 1 2 1 201000 r 74 goat snp8340-scaffold130-3589118 2 5717470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441644 Affx-122929202 AX-123311981 2 129473505 GCGGGCCTTGCTCCTGAGCATCTATTTGCTGTCTG[A/C]CTTACTCACCTGTGACGAGCAAACACCTTTCCATC M 2 1 2 1 101000 r 74 goat snp8341-scaffold130-3636806 2 5669979 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769453 Affx-122967163 AX-385256623 2 129510150 CAATAAAAGTTTCGTTATTGTCTGAAAATAGCAAA[C/T]GTATTCCTAAAAACTGGATGCAATTTACTATGTAA Y 2 1 2 1 101000 f 74 goat snp8342-scaffold130-3673451 2 5633270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802914 Affx-122924432 AX-385289811 2 129560672 CCAAATATATATACTGTTAGTAAGATTTTCTTCAA[C/T]GGAGGGAATTTAATTGCTGAAAACAGGGAAAGAGA Y 2 1 2 1 101000 r 74 goat snp8343-scaffold130-3723973 2 5582731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433893 Affx-122934404 AX-123304234 2 129597493 CGGGGGGAGAAGACAGGTGCTCAGTTGTTTAAGCC[A/G]TTGGCTCATTCATCCATTTGCCTACCATGTATCAA R 2 1 2 1 201000 r 74 goat snp8344-scaffold130-3760794 2 5547426 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384368 Affx-122972234 AX-123254726 2 129638803 CAGCCAGTGGAAGGAATGCAGACATCTGGCTCCCC[A/G]TGCAGCGTCTGCTCTTCTTGTTGGTGCTAAATCTT R 2 1 2 1 101000 r 74 goat snp8345-scaffold130-3802104 2 5505530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768391 Affx-122935985 AX-385255571 2 129678539 CTGAACAAACTGCCGTTTCATGGTGGAACGGCTCT[A/G]CTTGGTGCTTCTTACACTGAGTTGAAATCTGCTCC R 2 1 2 1 201000 r 74 goat snp8346-scaffold130-3841840 2 5465752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428213 Affx-122939446 AX-123298556 2 129709457 AGAGAAAAGAAGGAAAAGAAAGTCTCTCTCCCTCT[C/T]AGCCTACCCCAGCTACACTATCCAGAAATTTTTTT Y 2 1 2 1 101000 r 74 goat snp8347-scaffold130-3872758 2 5434382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425298 Affx-122940954 AX-123295644 2 129778513 GCACGAAGTGTGCGACACTTTGCGCATTTTCTTCC[A/G]TTTCCCACTTGTCCTTTCTTCAGGATAGGTGTGTA R 2 1 2 1 101000 r 74 goat snp8349-scaffold130-3941814 2 5367649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432992 Affx-122935258 AX-123303333 2 129818296 CCTCCAGAACGGAGAGAAAGAAGCTTCTGTTGTTT[A/G]AGCCACCCAGTCTAGGGTATTTTTATTACAGCAGC R 2 1 2 1 103000 r 74 goat snp8350-scaffold130-3981597 2 5328234 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377704 Affx-122977406 AX-123248063 2 129869185 TTGGAGATCTACGCTGAAGTTATGTGCAGCCTACA[C/T]GACAAGATATCTGGACTGTGTGTTGAAATAATGCC Y 2 1 2 1 101000 f 74 goat snp8351-scaffold130-4032486 2 5279720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414536 Affx-122949508 AX-123284885 2 129934389 TGGGTTCCTGGCACTATTTCTGCAAATGTTCTTTA[C/T]GCTTGAAATTATTTCCAGATAAAAAGTGTCTTAAA Y 2 1 2 1 101000 f 74 goat snp8353-scaffold130-4097690 2 5214859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436077 Affx-122932693 AX-123306416 2 129969898 ACAGTCTTTAACACTAATTACAGTATTCTTTAATT[C/T]CACCTCCATTTCTCCCCCTGGTTTCATCTGCTCCT Y 2 1 2 1 201000 f 74 goat snp8354-scaffold130-4133199 2 5179270 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429092 Affx-122938269 AX-123299434 2 130009324 CAGGATGTTCTTGGGGATGCAGCCTTGAGCAAGAA[C/T]GGTCCCAGCTTTCTTGGGGCTGCTTTAGTCTACTA Y 2 1 2 1 201000 f 74 goat snp8355-scaffold130-4172625 2 5139817 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406574 Affx-122955092 AX-123276926 2 130047736 GGAAAGGTTGAAAAATTTGTTCAAGACTGCACAGC[A/G]AGGCAGTACAGACAGGATTCTCCATCAGACTGAGA R 2 1 2 1 101000 f 74 goat snp8356-scaffold130-4211037 2 5101584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394370 Affx-122964640 AX-123264725 2 130115763 GGCTGTTCAAACAGTACAGCTGGGCTTGAACCCCC[A/G]TATTAGACCACAGAGCCTACTCCCTTAGCTGCCCT R 2 1 2 1 101000 r 74 goat snp8357-scaffold130-4279064 2 5033497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793460 Affx-122930825 AX-385280437 2 130177873 GTGTGTTATAATTTTTAAGGCAGATGGTAAACCTT[A/C]CTCTATGTCTTGAGGTTTCATCTTGTTGTGGGACA M 2 1 2 1 101000 r 74 goat snp2021-scaffold1059-1431982 2 4970733 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785576 Affx-122979127 AX-385272620 2 130230451 AAAACATTAGTAATCCTTGACTCCTCTTTTCCTCC[A/G]TATCCAGTCGGCAAATTTCTTCAGCTCTACTTTGA R 2 1 2 1 101000 f 74 goat snp2020-scaffold1059-1379404 2 4917390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378796 Affx-122976990 AX-123249155 2 130299246 CATCTGCAAAATAAGGCTGATGATGAACATAAGAG[C/T]ACCTACTTCAAAGGGTTTTGCCAAGGATTAACTAA Y 2 1 2 1 101000 f 74 goat snp2018-scaffold1059-1310609 2 4848689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425659 Affx-122940878 AX-123296005 2 130337330 TAGATGAGGGAACTTAGGAAAAGTACCCTGCACGG[C/T]GCAGGTGCCCAATACGTGCTTGATCCCTGAGTGAC Y 2 1 2 1 101000 f 74 goat snp2017-scaffold1059-1272525 2 4810894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412339 Affx-122950839 AX-123282688 2 130388646 GCCTTCGCCAGACTCCCAGTGCCCCGGGGAGCAAG[A/C]GGAGCAGGGAACTGGCAAACAGGTAGAGGGCTCAC M 2 1 2 1 101000 r 74 goat snp2016-scaffold1059-1221209 2 4759699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416217 Affx-122948228 AX-123286566 2 130428225 GTGGGAAAAACACACATTCATCTCCTACCATTGCC[A/G]ATCCACCCACTCAAGGCTGCTTCCTTCTTTGTGGT R 2 1 2 1 201000 f 74 goat snp2015-scaffold1059-1181630 2 4720020 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435730 Affx-122933293 AX-123306069 2 130492573 TGTTGCAAGAGGTGATTTTGATCCTGCAGAACAAC[G/T]TCACCCGGCACATCACACGGCTAGAGTTCATCGGA K 2 1 2 1 101000 f 74 goat snp2014-scaffold1059-1117282 2 4655005 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388926 Affx-122968832 AX-123259284 2 130545285 TCCTCTAACACGCGGCTCAGACACCACCTCCTCTG[C/T]GAAGCCCCCTCAGTCAGGACCCTCAAGGCTGTGCG Y 2 1 2 1 201000 r 74 goat snp2013-scaffold1059-1064570 2 4602598 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387650 Affx-122969847 AX-123258008 2 130581204 TGTTACACAAGTTTGGACAGAGAAACATGGGCTAG[C/T]TGTGGGAGGGATTCAAACTGACCACCGGTCTCTCC Y 2 1 2 1 201000 r 74 goat snp2012-scaffold1059-1028651 2 4566773 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377523 Affx-122977475 AX-123247882 2 130627489 CATCACGTTCTGGAGTAGTATCAATGAAGCACATA[C/T]ACATGTATCAAAAAGACAGTCAAAATATTCTTTCC Y 2 1 2 1 101000 f 74 goat snp2011-scaffold1059-982366 2 4521185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798511 Affx-122978152 AX-385285444 2 130673358 TTTAAACCCACAAAGCATTAAGTGAAGATACCTTT[A/C]AGAGATCTAATACTGAATTCTACCTTGAAGGAGGA M 2 1 2 1 101000 r 74 goat snp2010-scaffold1059-936497 2 4475288 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394954 Affx-122964284 AX-123265309 2 130733573 GTTTTCTGGAAATCACACTGACTTCTGAAATAAAA[C/T]AATATTGCAGTGAAAATAAAGGGACATTATAAAAA Y 2 1 2 1 101000 f 74 goat snp2009-scaffold1059-876282 2 4414530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437292 Affx-122931984 AX-123307630 2 130774690 TTGGAGTGAGTGGGATGGCCCTGTACGTAGCCAGA[C/T]AGGGGTCGTCTTTTCCTGTTATACTTCTGAGTTTC Y 2 1 2 1 102000 r 74 goat snp2008-scaffold1059-835165 2 4373075 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377058 Affx-122978294 AX-123247417 2 130815935 TCCAGCATTTATTTGCCAGGGCGTTTGCATCTGTT[A/C]TTTGACTTAATCCTCACACTGTTCTATGAGGTAGG M 2 1 2 1 201000 r 74 goat snp2007-scaffold1059-793920 2 4331418 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387461 Affx-122970364 AX-123257819 2 130880266 CCCGGGTCTCCCACATTGCAGGCAGACGCCTTACC[A/G]TCTGAGCCAGAAAGGAGGGTATTAATGAGAAATTA R 2 1 2 1 103000 r 74 goat snp2006-scaffold1059-729589 2 4266599 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408286 Affx-122953791 AX-123278637 2 130918440 CTGGGACTCCTAGGTAATTAGTGAATGAAAACTAC[G/T]AATGGGGGTGCTATGTTCTAAAAATCTTAACAGTT K 2 1 2 1 101000 f 74 goat snp2005-scaffold1059-691415 2 4228350 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800121 Affx-122972129 AX-385287044 2 130947979 TAAGTATCTACAAAGTGTGATTTGTTGTCAGAAGG[C/T]GTAGTCTTATTTCAGAGCAAGTTTCAGAAGTTGCC Y 2 1 2 1 101000 r 74 goat snp2004-scaffold1059-661876 2 4198674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452300 Affx-122920681 AX-123322633 2 130985203 AAGAAAGACAGTGATGAGTGTTTGAGCTAAGTGAG[C/T]GAAAGGGAAACAAGAGTACCAAAATAATATGGTTT Y 2 1 2 1 101000 f 74 goat snp2003-scaffold1059-624652 2 4161427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379804 Affx-122976237 AX-123250162 2 131014952 TCATACCTGTGGGTGCTTCAGTCTTGCTCTCAGCT[A/G]TGACACAGCTCTAAGGCAGGGCAGGTGTACCAGCA R 2 1 2 1 201000 r 74 goat snp2002-scaffold1059-594903 2 4132246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391638 Affx-122966570 AX-123261995 2 131102124 TAGCTGGCCTGCGGACCAAAGCAGAAAGGCTCCAC[A/G]GGAAAATGCCTTTTGGAAACACTGGGTTAGAGAAG R 2 1 2 1 101000 r 74 goat snp2001-scaffold1059-507731 2 4044884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386282 Affx-122970937 AX-123256640 2 131146469 CCATGGTTGAGGATAAAATCTACTTCCTCCAGTCG[A/G]CCTCCAGTCCCCAGTGACCCGGACAGCTCACCCCA R 2 1 2 1 101000 f 74 goat snp2000-scaffold1059-463386 2 4023897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437731 Affx-122931734 AX-123308069 2 131189012 ATGTGCAGGAAGACGACGCTGAAGATGAAGAGCCC[A/G]AGCATCATGGAGAAGGCGCTGGCGTAGTAGGGGTA R 2 1 2 1 101000 f 74 goat snp1999-scaffold1059-420843 2 3981243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271854 Affx-1111833158 AX-519545637 2 131215364 ATCCTCTCCGGTAGCTGAAGGGTGTGTGGAGTGGA[A/G]GTCAGACCCTTCCTGTGCGGGTGCTGGAGAAAATC R 2 1 2 1 202000 r 74 goat 2_131215364_AF-PAKI 2 131215364 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401153 Affx-122959370 AX-123271506 2 131228065 GTGTGCTCTCACACTGGGTTGACTCCCTGTGTACA[C/T]AGCTCCATTTTTGATCCTAAAAAAGAATTTTGTGT Y 2 1 2 1 303000 f 74 goat snp1998-scaffold1059-381790 16 28891921 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382260 Affx-122973943 AX-123252618 2 131292445 TCCTTTGATGAGGGGATGTCCAACCCGGAAGGAAT[C/T]AGTCCAACTTCTTCATCTGGCACGACCGTGTCCTA Y 2 1 2 1 201000 r 74 goat snp1997-scaffold1059-317410 2 3877149 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417185 Affx-122947321 AX-123287533 2 131325573 AACCTGGGCTCTCTTTCAAAGCACCTGCTAAAGGA[A/G]CACAGAACAGCAGATGCTTTTGAGATGCTCCAAGG R 2 1 2 1 101000 f 74 goat snp1996-scaffold1059-284282 2 3843922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415522 Affx-122948675 AX-123285871 2 131355119 TTTGCAACAGGCCCATCATCCAGGTAGGTGTTACT[A/G]TCTCCATTTAACAGATAAGCAAACTGAGGCTCAGA R 2 1 2 1 101000 f 74 goat snp1995-scaffold1059-254736 2 3814218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399826 Affx-122960263 AX-123270181 2 131414474 GAGACTGGATGGTTAACTAGATTCATAATCTGTCA[A/C]GTGACCCAATTTGAGGGATGCTGATAAATGAATCA M 2 1 2 1 101000 f 74 goat snp1994-scaffold1059-195381 2 3755879 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381389 Affx-122974382 AX-123251747 2 131469158 AAGCTTGCTTTCTCATTGGTGTGTGTGTGAGTAAA[G/T]CTGACTGTAACAGCTGGGGGCCTCCTTGTCCCTGC K 2 1 2 1 101000 f 74 goat snp1993-scaffold1059-140697 2 3701631 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427842 Affx-122939730 AX-123298185 2 131506543 AACAGACACTGAGGAGGGGCTGACCCAGCATCACA[C/T]GGCTGGACAGTGATAGCTGAGGTTCAAACCCGGGG Y 2 1 2 1 201000 r 74 goat snp1992-scaffold1059-103312 2 3664475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449744 Affx-122922459 AX-123320079 2 131557232 GCCTGAAAGAGACAAAGTCTTTGAGGGAGGAAAAA[C/T]CATGATCAAGCTGGCCAGGGATGCGTCACTGTGAT Y 2 1 2 1 101000 f 74 goat snp1991-scaffold1059-52623 2 3614876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439772 Affx-122930512 AX-123310109 2 131587507 CCAAGTTGTGGAATGAACTGTGTCCCACAAAAAAC[A/G]CATATGTTTAAGTCCTAACCCCTGTACTTCAAAAT R 2 1 2 1 101000 f 74 goat snp1990-scaffold1059-22348 2 3583972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422347 Affx-122943445 AX-123292693 2 131616130 TAATGTGGTGCCTATATGCTACCTTAACTGCTTCC[G/T]CTCCCAGCCCCATCTTCCTCAAACTGAGAACATGG K 2 1 2 1 101000 f 74 goat snp22271-scaffold220-6176 2 3557778 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390542 Affx-122967222 AX-123260899 2 131671619 GGACTCCAGGTGAACAGCATAATGGTGACCCTTAC[A/G]GACCTTGCAGGCTCCTTCCTCCTTCTGTTCTCCAT R 2 1 2 1 201000 f 74 goat snp22272-scaffold220-61665 2 3501685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450173 Affx-122922313 AX-123320508 2 131709295 GGGACCCTCTAAACTTAACCCACTGAATCAAGATC[A/G]CTGTCTAAGTTCTCCAAAGCTGAAGTGGGGACTGA R 2 1 2 1 101000 f 74 goat snp22273-scaffold220-99341 2 3463848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415501 Affx-122948691 AX-123285850 2 131791179 GCAGGCTACAGTGTGTGGGGTCACAAAGAGTCAGA[C/T]GTGACTGAGTGATTAATGCTTTCAGAGAGGAGGCA Y 2 1 2 1 103000 r 74 goat snp22275-scaffold220-181225 2 3381613 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416847 Affx-122948104 AX-123287195 2 131873585 TTCCTTAGTGTCCTCTGTGCTGGGCACCAGAGCTA[A/G]ATGTTAATTCAAAGGGACAGTGCCCCTGCTTCAGG R 2 1 2 1 201000 r 74 goat snp22277-scaffold220-263631 2 3299548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783807 Affx-122938984 AX-385270863 2 131916378 TGTGATTTCAGGCGATCAGGACTACTGTAAGCGCC[A/G]TCTGTGTCAATGTGATAAAAGAGCTGCCGATTGTT R 2 1 2 1 101000 f 74 goat snp22278-scaffold220-306424 2 3257108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803530 Affx-986696098 AX-385290341 2 131935537 CCTGGGTTTGATCCCTGGTCAGGGAGCTAAATCCC[A/G]CATGCCATAACCAAGATCCATCACAGCCACAGAAA R 2 1 2 1 600010 r 74 goat 2_131935537 2 131935537 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38398547 Affx-122961525 AX-123268902 2 131954563 ATCAGATGTACACAAACTCATGGACACAGAGGGAC[A/G]CACACAGAGACACATAGGCACACAGACACACGTGT R 2 1 2 1 101000 f 74 goat snp22279-scaffold220-344609 2 3218098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403366 Affx-122957793 AX-123273719 2 132067519 CATCACTGGAAGCTCTCTCAGATGACTGAAGGGAG[C/T]GTTGTGGTCTTTGCTGGAACAATGAATTCTTTGTG Y 2 1 2 1 101000 r 74 goat snp22282-scaffold220-457565 2 3104361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395797 Affx-122963653 AX-123266152 2 132149741 ACCTCTCTGTGCCTCGGCTGATTCATTTGCGAGGC[A/G]AAGCAGATTGCCCTTGCCTTTCAGGGACTCACCAA R 2 1 2 1 201000 f 74 goat snp22284-scaffold220-539787 2 3027549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278058 Affx-1111836152 AX-519551548 2 132152472 TTTTCTTATTTTTTAAAAATATCTTTTATAAATTA[A/G]CAATGTGGAATTTAAGACATACAAAAGAGTGTGTA R 2 1 2 1 102000 r 74 goat Random2.2K-283 2 132152472 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384861 Affx-122971948 AX-123255219 2 132182648 TCAGCAAAAGGCAGCTACCTCTTTGCTGTTCATCA[G/T]AGCTGTCAGTTGGGAGTCTCGGCATCCTGGCATCG K 2 1 2 1 101000 f 74 goat snp22285-scaffold220-572694 2 2995352 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449651 Affx-122922581 AX-123319986 2 132275886 TGGAACAAGAGATAAATAAACTTCCTCACTGAACT[A/G]CTAGGAGAGTAAAAACAGGATGGTATGATGGCATG R 2 1 2 1 101000 r 74 goat snp22287-scaffold220-665932 2 2901895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437039 Affx-122933109 AX-123307377 2 132319171 TCAGTATCAAATTTTATTCCCTGAAATATCTTGTT[A/G]CATCTGACTTGAAGAGCATCATTCTTGAAAATGAC R 2 1 2 1 101000 r 74 goat snp22288-scaffold220-709217 2 2858654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434754 Affx-122933905 AX-123305095 2 132348683 AAAGGTAAACTTCCCAAGGGCAATGATTTGTGTGC[A/G]TTTTGTTCCCTGCCAAGGACAGTGCCAAAGACGAT R 2 1 2 1 201000 r 74 goat snp22289-scaffold220-738729 2 2828264 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401301 Affx-122959856 AX-123271654 2 132385634 AGGCTTTTAGAGATCAGGTCTCTGGGGTGAGGAGG[C/T]GGAGGCTTGCCTGCTGCGGGAGCTCTGGCCCTCTT Y 2 1 2 1 101000 f 74 goat snp22290-scaffold220-775680 2 2791684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394605 Affx-122964420 AX-123264960 2 132415222 CTAGGTACGACTTTAAGAGGCAAGGGCCGAAGCTC[A/G]CTCCCAAGACTTAACCAGCATCACCCTGTCTATGA R 2 1 2 1 201000 f 74 goat snp22291-scaffold220-805268 2 2761810 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433482 Affx-122935041 AX-123303823 2 132472942 ATTTGACAAGAGGAGGAGGTGGGGTAGGGTTGGGA[C/T]GAGGGCAGGGAGAGAGTCATTAACTGATTGACTGG Y 2 1 2 1 101000 r 74 goat snp22292-scaffold220-862988 2 2704062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451377 Affx-122921217 AX-123321710 2 132518561 TTCTCATGGGAAGCTTTTTAGCTGTACACAGACTC[C/T]CTGAGAGTCTTGTCTCTGCCACCCTCTTTACCTTC Y 2 1 2 1 101000 f 74 goat snp22293-scaffold220-908607 NW_017189554.1 39948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404155 Affx-122957079 AX-123274507 2 132555542 TCAAAAAGTTTCAGGTGGCTTCAGGACTTTCCCAG[C/T]GGTCCAGTGGTTAAGACTCTGTGTTTCCAATGCAG Y 2 1 2 1 101000 f 74 goat snp22294-scaffold220-945588 2 2669860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404200 Affx-122957674 AX-123274552 2 132615813 GCCGGCCTCAGGTTCAGTTTATTGAAAACCACGAG[C/T]GCAGTAGTGTTTCCATTTGTTAGTCATCGTCCAGG Y 2 1 2 1 101000 r 74 goat snp22295-scaffold220-1005859 2 2609074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404089 Affx-122957133 AX-123274441 2 132657624 TTAATACTATATTTAATATTGCATGTAAAATTATC[A/G]TAACTGAACAATACTGTTACTATGGTGATCTAGGT R 2 1 2 1 101000 r 74 goat snp22296-scaffold220-1047670 2 2566911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413406 Affx-122950711 AX-123283755 2 132690073 CTGTCCCCATCGTTGCATGGCTGCAGAGCTGTCCC[A/G]TGTCCCCGTGGAGAATGCGGGGGGTTGGACGTGCG R 2 1 2 1 101000 f 74 goat snp22297-scaffold220-1080119 2 2534427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414201 Affx-122949655 AX-123284550 2 132752491 CCCCTCTGTCCGCACAGCACCCACCTTATTTTGGT[C/T]ACTCCCCACAGCCCTCTTCTCACCGGGGCAGTGCC Y 2 1 2 1 101000 f 74 goat snp22298-scaffold220-1142537 2 2472750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411038 Affx-122951964 AX-123281388 2 132808020 AAGGAGGTAATTGAACTACAGTGCTACAAACTCGG[C/T]GAAAGTTAGCCATTATTAATTTGAATTAGATTGTG Y 2 1 2 1 101000 f 74 goat snp27452-scaffold2925-417572 2 2422980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424778 Affx-122941402 AX-123295124 2 132853538 CAGAGCGGAAAAAGACTAGAGCTGTAACCTAGCAT[C/T]GCACAGACAAGGAGAGAGTGTTGCCAATAGACATT Y 2 1 2 1 101000 f 74 goat snp27451-scaffold2925-372054 2 2377168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419590 Affx-122945386 AX-123289938 2 132899800 GTTTCCCAAAGGAAGAGGCTGCACGGATGTCCTTA[C/T]AGAAGATGCCTCGAGGGGAAGGCTCTGGAATGTCC Y 2 1 2 1 201000 f 74 goat snp27450-scaffold2925-325792 2 2330570 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409507 Affx-122953634 AX-123279858 2 132938668 AGTCTCCCCGGATGGGGCTAAAAATAAGGTAGATG[C/T]GAAAATGTCCACGAAGGAGTCTATGGGCGGAGGGT Y 2 1 2 1 201000 r 74 goat snp27449-scaffold2925-286924 2 2296985 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38428649 Affx-122938660 AX-123298991 2 132985392 TTGTCGGGACCTATGATGGCCACCACGCGGGGCAC[A/G]TAGTGGCTGTAGTCCTCCTGGATGGGCAGGAAGTA R 2 1 2 1 101000 r 74 goat snp27448-scaffold2925-240200 2 2250497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384632 Affx-122972161 AX-123254990 2 133020710 CAAACCCAGGCCTTCCTGGCTCTGAAGTCCACAGG[C/T]TTAATTACGCTAAAGTGCCTGCTCGATAGGGGTTA Y 2 1 2 1 101000 r 74 goat snp27447-scaffold2925-204882 2 2214958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401384 Affx-122959227 AX-123271737 2 133059731 GCAGAGCTAGAATGGACTGAGAGACCCAGAGAAGA[C/T]TGGTGTGGGCTCTACCCAGGGTAGAGTTTTGAATA Y 2 1 2 1 201000 f 74 goat snp27446-scaffold2925-165861 2 2175518 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450839 Affx-122922245 AX-123321173 2 133125703 TCTAAAGGGCTTTTGCTAAATGTTGTGAATCCAGA[C/T]GTAGATGAGACATAGTCCTTGCTTTTACAGACGAC Y 2 1 2 1 101000 f 74 goat snp27445-scaffold2925-99889 2 2108792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775450 Affx-122977715 AX-385262581 2 133166886 CAACTCTAAAAATAATGGAATCACAGCATCCCAGC[A/G]TCTCAGAACCATGTGATGTTAGAGCCAAAAGGAGG R 2 1 2 1 101000 f 74 goat snp27444-scaffold2925-58706 2 2067806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444651 Affx-122926467 AX-123314988 2 133196053 GATTTGGGACTTCTGCGGGGAGTGGGGTTTGAGTC[A/G]TTCTGATGGCCACCCCAGTTGAGAGCCATTGGTCT R 2 1 2 1 201000 r 74 goat snp27443-scaffold2925-29539 2 2042758 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387448 Affx-122970377 AX-123257806 2 133228545 TCTCCGGGTTCCGGAGGCCAGAATTCCTCAGGGCC[A/C]TGTTGGAAGAGGCACCTTTCCCCCTACTCCCCAGC M 2 1 2 1 101000 r 74 goat snp1812-scaffold1050-2854 2 2018573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451191 Affx-122921331 AX-123321525 2 133273009 CTGGGCCATGGGGTGGGACTGAGGCAGGGTGAAGA[C/T]GATAAAAATTTAAGGAGACACTCGCTCTCATGGTT Y 2 1 2 1 101000 r 74 goat snp1813-scaffold1050-47318 2 1974008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453192 Affx-122920455 AX-123323525 2 133305214 GACGCGCATCTTCATGGGACTTGCCCCCTAGTGAA[C/T]GGAGACAGGTAATTTGCTCAGTGGATCTGCTGGAG Y 2 1 2 1 201000 r 74 goat snp1814-scaffold1050-79523 2 1943318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379830 Affx-122975819 AX-123250188 2 133339211 ATGAGCATGCTTGAGTCATCAGCACAGGCGGCAAC[A/G]GCAAGAAGCCTGAGCTTCCTTTCCCATCCCGTCTG R 2 1 2 1 201000 f 74 goat snp1815-scaffold1050-113520 2 1908972 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429386 Affx-122938544 AX-123299728 2 133373338 CAAGCCAAAGAAAAATCACACGCAGGAAAACAGAC[C/T]GGAGGGACCCACACCACAGCGGGGGTTTGTCTTTG Y 2 1 2 1 103000 f 74 goat snp1816-scaffold1050-147647 2 1874619 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448994 Affx-122923106 AX-123319329 2 133410959 CGTAGGGTAAGCAGACCCTGTGACCAGGGGCAGGC[A/G]TGGGTGGTCCTCATTAAAGACACCAGACACAGCCA R 2 1 2 1 101000 r 74 goat snp1817-scaffold1050-185268 2 1836674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424997 Affx-122941899 AX-123295343 2 133445185 GCAGCTTGGGGACGGGTGTCCAGAGGAAAAGAGAC[A/G]CCAGCGTTCAAGAGCCTCTTCCTGGAGCCCCATGT R 2 1 2 1 202000 r 74 goat snp1818-scaffold1050-219494 2 1802279 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380865 Affx-122975059 AX-123251223 2 133489874 CTGATCTTGCTGAATTCCCAGATGCCTAGGAGGAG[C/T]GGCTGAGAGAGCAGCCCAAGTATCCCACGCCGTCT Y 2 1 2 1 101000 f 74 goat snp1819-scaffold1050-264183 2 1758801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444460 Affx-122926543 AX-123314797 2 133519072 CTGGCTGGCACTGAGATCTCATCCAAGGTAATAGG[C/T]ATTTATCTTAGTGTGTTCAGCTGTGGGCTCGATGC Y 2 1 2 1 101000 r 74 goat snp1820-scaffold1050-293381 2 1730027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384990 Affx-122971887 AX-123255348 2 133568735 GAGGCTGAATTGTATTCTGGCTGCAAGGGAAAGAC[A/G]TTGCAGGGTCTTAAGCAGGGGAATTCTCTGACTTG R 2 1 2 1 201000 f 74 goat snp1821-scaffold1050-343044 2 1683916 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403108 Affx-122958129 AX-123273461 2 133635697 TGAAAAGAGCTGTGATTGATCTAGCCGGAGGTGCA[C/T]AAACAGACTCCCACTCCCTCCTGGATTCATCCCAC Y 2 1 2 1 201000 f 74 goat snp1822-scaffold1050-410006 2 1619247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447727 Affx-122924599 AX-123318063 2 133668127 CGTGCCCCAGAGTCACACAGCTGGTGGGTCAACAG[C/T]GGCCCTCGATAGAACAAGATGTGGAAAGGCCCCAG Y 2 1 2 1 101000 r 74 goat snp15936-scaffold1675-77883 2 1586567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411608 Affx-122951600 AX-123281958 2 133709501 TGTCACATTCTGATCTAAGGGGAACGTGAGTGTCC[A/G]TTCTGTCTGATTTTGTTCCACGATGTTTTCACATG R 2 1 2 1 101000 r 74 goat snp15935-scaffold1675-36509 2 1546389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412810 Affx-122950479 AX-123283159 2 133758810 GTTTTTAACTGTTTGGTCCAGTAGTGAGTATATTC[A/G]TACTGTTGAACAACCTATCTGCAGAGCTTTCTCAT R 2 1 2 1 101000 r 74 goat snp28313-scaffold3010-12701 2 1499822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441744 Affx-122929128 AX-123312081 2 133790626 TGGCGCAGTGTTCCCTCCGGCTCTGCTTCCCATCG[C/T]GTCTGTGGTCACATGGCCCTCTCACTCCGACTTCC Y 2 1 2 1 201000 f 74 goat snp28314-scaffold3010-44517 2 1467596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427644 Affx-122939333 AX-123297987 2 133821537 TTTTCAGGGAAAGAGGACCAGAGCTACAGAGAGAA[A/G]TAAAGGAAAACCCAGCCAGGAAAATAAAGGCACAA R 2 1 2 1 101000 f 74 goat snp28315-scaffold3010-75428 2 1436344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440445 Affx-122929403 AX-123310782 2 133868368 CAGGAGCTCAGGAGATGCTTGTATTCACATGAGAC[A/G]CCAGGAGAGGAGACACCAAACCTCCGTCTGTCAGA R 2 1 2 1 201000 f 74 goat snp28316-scaffold3010-122259 2 1388991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404569 Affx-122957372 AX-123274921 2 133917624 TCTCGCAAATCTGCAGGTAAGGGGGCTGCAGCACC[G/T]AGATGTTAAGTGACTCACCTGCCCAGCGGAAGTGG K 2 1 2 1 101000 r 74 goat snp28317-scaffold3010-171515 NW_017189527.1 62719 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380555 Affx-122975285 AX-123250913 2 133948996 GCTTAAGGCTGGAGGATCCTTAGAGAGCATCCTAG[C/T]CCAATCCTTCCATTCTCAAATGGGGAAACTGAGGT Y 2 1 2 1 101000 f 74 goat snp28318-scaffold3010-202887 NW_017189527.1 31447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414265 Affx-122949612 AX-123284614 2 133997193 GGCTGCAGCCATCACAGACCCCCACCCGCAGAGAC[C/T]GCATGAACGGAACTGTTTGTTGCTCTGAGCTGCTA Y 2 1 2 1 101000 r 74 goat snp28319-scaffold3010-251084 2 1180107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771186 Affx-122939957 AX-385258346 2 134032722 CTGTGCTAAGCACTTTGCTTGCAGGAGCTCACACA[A/G]CTCTATCCGTCACAAGGCAGGTAATACTACAATCC R 2 1 2 1 201000 f 74 goat snp28320-scaffold3010-286613 2 1214172 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450706 Affx-122921888 AX-123321040 2 134070125 AGATAATTCCAAAGGAAAGGACCAGCTAGCCAAGC[A/G]TGAGTCAGTCGGGAACAGCTGGTGCACAGGCGCGC R 2 1 2 1 101000 f 74 goat snp28321-scaffold3010-324016 2 1252615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272021 Affx-1111833159 AX-519545787 2 134118994 TATGGGGTCGCACAGAGTCGGGCACGAGTGAACCG[A/G]CTTAGCAGCAGCAGCAGCAGTTCAGCTTGAAAATG R 2 1 2 1 303000 f 74 goat 2_134118994_AF-PAKI 2 134118994 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791848 Affx-122941674 AX-385278838 2 134167673 TCCCGTAAGGATGGAGCCTCCGAGACAGAACAACA[C/T]GGCACAAGCCATTTAAAGCCAAGAAATAGAGTCGG Y 2 1 2 1 202000 r 74 goat snp17515-scaffold1811-66577 2 1350722 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415207 Affx-122948982 AX-123285556 2 134220701 ACCTTCCCTCCAGACGACATCGTCTGTGCCACTGA[C/T]GGCTCGATCAAACAGTGGAGACCAAAGCGCCTGAC Y 2 1 2 1 201000 r 74 goat snp17516-scaffold1811-119605 2 1092805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785837 Affx-122960035 AX-385272874 2 134250349 GTCTTTGCTAAGGGGTTTTGCGGGGGAAGAAGAAG[A/G]GTATTCAGACAAGTTCATTCTCGTAACAGCCAACC R 2 1 2 1 101000 f 74 goat snp17517-scaffold1811-149253 2 1119190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398758 Affx-122961446 AX-123269113 2 134350404 TCCCAGATCTAACAGAAGGCCCAGCATCTCCAGGA[C/T]GCCTCTCCACATGGCCCCTGTTCCCCGACCACCTC Y 2 1 2 1 101000 f 74 goat snp17519-scaffold1811-249308 2 1022414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419404 Affx-122945600 AX-123289752 2 134405745 TTTTCACACACGCATGAAGTGGTTTGGGAAGGAGC[C/T]GTCCTCTAGCGCATGGCATAGTAAGGACTGAAGGA Y 2 1 2 1 201000 r 74 goat snp17520-scaffold1811-304649 2 970824 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436396 Affx-122933033 AX-123306735 2 134473411 AATTCAAGACAACTCTGAGGACTCAGCCCCAGAGC[A/G]TCCCGGGGGGTTTCCCAACCCTCAGTGGCCGCTGG R 2 1 2 1 101000 f 74 goat snp17521-scaffold1811-372315 2 906258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383260 Affx-122972738 AX-123253618 2 134504835 TGTGTTCCTACAACAAGAAACAACTTTCTGCCCCC[A/G]GGGAGAGACCGTTTGACCTCCCCTGCTGGGAACAA R 2 1 2 1 101000 f 74 goat snp17522-scaffold1811-403739 2 876442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452738 Affx-122920278 AX-123323071 2 134561159 CTCCTGTTGGCCCACAGTCTGAGCACCCAGGACTG[A/C]CAAATCACAGCATCTCCGAGTCGGAAGGGGCTTTA M 2 1 2 1 101000 r 74 goat snp17523-scaffold1811-460063 2 820688 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447549 Affx-122924041 AX-123317885 2 134583606 GCTAGGGTACCGCTTCCCAGACGACCCTGAGAGGC[A/G]GGGAAAGGAGGCGGGCCAGAACTGCTAAGCGCCAG R 2 1 2 1 202000 f 74 goat snp25942-scaffold2682-290286 2 797285 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452394 Affx-122920610 AX-123322727 2 134636595 GTCTCGGGCTTTGCACCTCCTGCTGCCCTTCCTGG[C/T]GCTTGGATGCCCCAGACACACCCCTTCTTGTTCTC Y 2 1 2 1 101000 r 74 goat snp25941-scaffold2682-237297 2 744124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432048 Affx-122935899 AX-123302389 2 134671066 CTGTGAAAACTGAGTTTCGTTCAGTTTCCAAGTGT[C/T]GTGGACTAGGCTTTTGCTCCCGTCCCCACCGGTTA Y 2 1 2 1 101000 f 74 goat snp25940-scaffold2682-202826 2 709406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277908 Affx-1111836153 AX-519551403 2 134696915 TCAAGCCAAAAGTGCCTTTAGGCAGTGGTCCAAAT[A/G]CATGTGTTTTTAATTTATAAATGCCTCCCCCTGGT R 2 1 2 1 103000 f 74 goat Random2.2K-286 2 134696915 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422640 Affx-122943701 AX-123292986 2 134705993 CTGATGATGGTTGCTCTGAGTGATGCTCCCCACCT[C/T]CTTCGTCCCTCTGAGCCAGTGAGAAACTAGAGGAG Y 2 1 2 1 101000 f 74 goat snp25939-scaffold2682-167899 2 674028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426815 Affx-122940521 AX-123297160 2 134768458 CACTTAGCAGAGCAGCTCAGGCTAGAACTACCACA[C/T]GGCCTCATTAGAGGAGGCGTGTAGTGAGGTCACAA Y 2 1 2 1 101000 f 74 goat snp25937-scaffold2682-105434 2 614121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376722 Affx-122978964 AX-123247081 2 134797775 GTAGACTCCCTGGAGTTAGAAATTAGGGGTAGAGC[C/T]ACGTCCGGAGAATAAGAAAGTCTTGAAGGAGAAGT Y 2 1 2 1 201000 r 74 goat snp25936-scaffold2682-76117 2 584235 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416870 Affx-122948088 AX-123287218 2 134839728 CTTCAGACCCCCTTTTAGGGGCCTCCATTCCTGCA[C/T]ATCGGCTCCAGGGAGGACCAGGCCGTGAGCGGGAA Y 2 1 2 1 303000 r 74 goat snp25935-scaffold2682-34164 NW_017189886.1 4624 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278062 Affx-1111836154 AX-519551552 2 134865265 TTTCAGGAACACCAGAGCTCCATCTCTGTTTCTCC[A/G]AAATGCTAAACTGGTGTGGGAGCAAACTCGCACAG R 2 1 2 1 101000 r 74 goat Random2.2K-287 2 134865265 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436803 Affx-122932246 AX-123307141 2 134955186 GTTCAAATGTCTTTGGTGATGGCACTGGGTGTTCC[A/G]GTGAACTAACAGCAGCAGGCATTCAGGTTTTTATA R 2 1 2 1 101000 f 74 goat snp56621-scaffold895-81195 2 450930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420655 Affx-122944825 AX-123291002 2 135156332 TGGAAGAAAATACATGTGGATGTACATGGGACAGA[C/T]GTGGGTCTGTGTGACACTGTATGCATCTGTATGTC Y 2 1 2 1 101000 f 74 goat snp56625-scaffold895-282341 2 250290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777453 Affx-122976208 AX-385264573 2 135188495 TGGTAGAATATGCCACATGTAATGTGGAGCGCACC[A/G]TCTTAGCCATCTTTAAGCTTCGGCTCAGTGGCATC R 2 1 2 1 101000 f 74 goat snp56626-scaffold895-314504 2 224737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434515 Affx-122934603 AX-123304856 2 135223081 AAGTGGAAAGCATCATAACAGCGCCGAGTATGATA[A/G]CAGACTTATTGTGACGACTAAATGAATGTCAAGTG R 2 1 2 1 101000 f 74 goat snp56627-scaffold895-349090 2 181916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409742 Affx-122953017 AX-123280093 2 135255106 GGCTGTGCAGCCATCGATGCTGTAATTCCAGGACA[C/T]GCTCATCGCCCCCAAATGAGACTTCGTGCCTGTCA Y 2 1 2 1 101000 f 74 goat snp56628-scaffold895-381115 2 149547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413506 Affx-122950636 AX-123283855 2 135331490 GCTGTCCCCTCCCTAACCCCCTGCTCATCTTTCCC[A/G]CTCACACTGTCCTTGTCCGAGAGGGCAATGATGTT R 2 1 2 1 101000 r 74 goat snp56629-scaffold895-457499 2 90162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390364 Affx-122967677 AX-123260721 2 135369861 TTGATTCTGGTTGGATATTAAATGATTCCAAAGAA[C/T]GTTTTGTTAGGCATAATCAGGGCATTGCATAAATG Y 2 1 2 1 101000 r 74 goat snp56630-scaffold895-495870 2 51534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428111 Affx-122939078 AX-123298454 2 135409132 TCCTTCTTTTGTCCCTTACAAGGAACATTCTAATT[A/C]GATTGAGGGCCAGCCACACCCATCGTGACCTCACC M 2 1 2 1 101000 f 74 goat snp56631-scaffold895-535141 2 13915 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792507 Affx-122955333 AX-385279487 2 GACATGACTGAGTGACCCATCACCACCAATAACAA[C/T]GATCAGGTCCCATTGTTAAGGCTCCTCTACCTGTT Y 2 1 2 1 101000 f 74 goat snp19062-scaffold1917-98839 4 24436926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762302 Affx-986696833 AX-385250484 3 1965 AGTATAATATTGTCATACATTCCCTGGCCTCAGAT[A/T]TCAATTCTGTTCATTTTTCTTGGTTTTGACTAATA W 4 1 2 1 600010 f 74 goat 3_1965 3 1965 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 38438528 Affx-122931197 AX-123308866 3 23250 TCCAGATGTGGTATGCAGGCTCCTCTCTCATTGTG[A/G]CACCTGGTCAACACACTAGTTGTGCCCAGGGCCTC R 2 1 2 1 102000 f 74 goat snp32075-scaffold361-731478 3 120005149 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392964 Affx-122965681 AX-123263321 3 72885 GGAAACATGACCTCTCCGTAATCTCATTTGCCATT[A/G]TAAGACAGTTATTCATTTGACAAGTGTTTATTGAT R 2 1 2 1 101000 f 74 goat snp32074-scaffold361-681843 3 119954417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272064 Affx-1111833400 AX-519545828 3 79964 CAATCTCCAAACAAATCTCTACTTATTTCTCCCAT[A/G]AGGTCTTGGTGGCTGGCCAAGCTGACCTGACTGTG R 2 1 2 1 303000 r 74 goat 3_79964_AF-PAKI 3 79964 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403799 Affx-122957971 AX-123274151 3 172416 GCTGACAATTGGACTTCCTTATCCTCCACACCCCA[C/T]GCCAGCATCCTGTCTGTACCCCACACCAGCGGACC Y 2 1 2 1 201000 r 74 goat snp32073-scaffold361-582312 3 119853700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410253 Affx-122952534 AX-123280603 3 203015 CTCCTCTCTTCTGAAAGTCATTCTCTTGTTTTCTC[A/C]TGCAATGGGGAGGTACAATTGCCTGGCTGAGAAGT M 2 1 2 1 101000 r 74 goat snp32072-scaffold361-551713 3 119823011 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450092 Affx-122922788 AX-123320427 3 246193 AAGGTGGGTATTATATTTAAGCCTGACAATAATGG[A/C]TGACCATTGAAGGTGACAGGATGAATGTCTCTGGT M 2 1 2 1 101000 f 74 goat snp32071-scaffold361-508535 3 119779380 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429764 Affx-122938254 AX-123300105 3 314245 GGGAGGGCTATAGGAAAGAGAGTCCATGGCTTTCC[A/G]TTGGCTGATTCCTTCCCAGAAACTAAGAGGAATCT R 2 1 2 1 101000 r 74 goat snp32070-scaffold361-440483 3 119711529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391813 Affx-122967024 AX-123262170 3 343430 TCGAAGTCCTGTTTTGGGAACCAGGGGTAGAGACT[A/G]ATGTATGATTCTGTATTATCTCACAGATAGCATGC R 2 1 2 1 201000 r 74 goat snp32069-scaffold361-411298 3 119682046 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778893 Affx-122947358 AX-385266001 3 397115 AATATAATCGTGCTGATGACAAAAATTTATTAAAA[C/T]ATAAATATTGCCAGTGAGGATGATTGATAACAAAA Y 2 1 2 1 201000 r 74 goat snp32068-scaffold361-357613 3 119628310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278064 Affx-1111836155 AX-519551554 3 407597 CACCGTGCTCGATGCCCTGTGAGTGCCCCACAGAC[A/G]AGGATGTCCACTGCCAAGTGTGATTCAGCTGTGCC R 2 1 2 1 101000 r 74 goat Random2.2K-289 3 407597 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413912 Affx-122949825 AX-123284261 3 436705 AATTAAAATCAAAGAGGTTTCATTTGACCACTAAG[C/T]GAATAAAAGAGAGGAGAGAAAGGCTGTTGAGAAAG Y 2 1 2 1 201000 f 74 goat snp32067-scaffold361-318023 3 119587835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794456 Affx-122924789 AX-385281419 3 522636 CATTAAACATAATATATAGTGACCATCGGAAATGT[A/G]AAATTAGAGTTCCTCTTGGGGAATACAGAATTGAT R 2 1 2 1 102000 r 74 goat snp32065-scaffold361-232092 3 119502245 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388120 Affx-122969484 AX-123258478 3 568238 ATTATCTTGCCTTTAAAAAATCTCTTAATTGTCCC[A/G]CATTCCCCTCCAGACTCATGTCTTTGCTCCTTTTA R 2 1 2 1 101000 r 74 goat snp32064-scaffold361-186490 3 119456680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409452 Affx-122954082 AX-123279803 3 605675 CTATAAGAAAACAGATATCAGACTTTAAAGATGCT[G/T]CTTTATTGTGCTGTAGGGCTCTATACTAGGCTTTA K 2 1 2 1 101000 r 74 goat snp32063-scaffold361-149053 3 119418788 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434468 Affx-122934637 AX-123304809 3 687920 ACAGAGTAAGTGACTTTTACACACATGCAAATGTA[C/T]ACATATACAAATACTGCATAGAGGTGCTCCCAATG Y 2 1 2 1 101000 f 74 goat snp32062-scaffold361-66808 3 119335778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412653 Affx-122950787 AX-123283002 3 731044 CCAACTTGCATTTTGTTTATTTAGGCTTTATGACA[C/T]ATACTGATATTTCTCCTCTTATTTTTGCAACATTG Y 2 1 2 1 101000 f 74 goat snp32061-scaffold361-23684 3 119292994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275024 Affx-1111834547 AX-519548606 3 739234 CCTGCAGGGTCAGACAGTCGGGTGGTCAAGCTGGG[A/G]TGAGGTCGGCTCTGCTGCTGCAGGAGATGGACCCT R 2 1 2 1 202000 r 74 goat GoatD01.041204 3 739234 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783902 Affx-122956532 AX-385270957 3 763240 TGCTTTTACTTTATCTTCTATAAAGTGAAGAAATA[A/C]TAGTACCCAGCTCACAGGGTTATAAAGTTTAAATG M 2 1 2 1 201000 r 74 goat snp40756-scaffold522-8413 3 119260783 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768239 Affx-122930651 AX-385255420 3 800826 TTTCCACATCAAACTTTTTGTAATATATTCTACCT[A/G]CCTAGGAATTCATACCAAAAGAGGTGTCACCTAGT R 2 1 2 1 101000 r 74 goat snp40757-scaffold522-45999 3 119222421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765109 Affx-122945528 AX-385252670 3 895146 ATAGGAAGATGATGTAGGAATATTTTCCATTATGT[A/C]TTCTTTCTAAACTTCTGAACTATGTCAATATAGTG M 2 1 2 1 101000 f 74 goat snp40759-scaffold522-140319 3 119126876 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421590 Affx-122944497 AX-123291937 3 924689 AAGTGAAGAGCGAAGGCTCAGTGGCTTGGTCCACA[C/T]GAGGGGCAAGGAACATTTCTGAGCCTCATACGGTG Y 2 1 2 1 101000 r 74 goat snp40760-scaffold522-169862 3 119098678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786952 Affx-122946346 AX-385273981 3 977870 TGCACACCCAGAGTTTATGGCCTACTAAGGAACAG[C/T]GGTGATTAGGCAAGTATTTAAACCATGATCAGGAT Y 2 1 2 1 101000 r 74 goat snp40761-scaffold522-223043 3 119045920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421596 Affx-122944493 AX-123291943 3 1007730 CTGAATGATGGTCATGAAACGTGTCAAGCTCTCTC[A/G]TCACTTGAGGCATGTGGGAGGACTGCACTTCCTCC R 2 1 2 1 101000 f 74 goat snp40762-scaffold522-252903 3 119015999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437147 Affx-122932145 AX-123307485 3 1068387 CAATCATAACACGTACTCACTGTGTTCACTGCAGA[C/T]GACCGTGCGATAGCAGGGATCTGCCCTACAATGCC Y 2 1 2 1 101000 f 74 goat snp40763-scaffold522-313560 3 118955097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425875 Affx-122940646 AX-123296221 3 1099000 TCAATAATGGCCTAAGGCTTTTTCAACTTCTTCAG[A/G]TCTCTAAGGGGCTTCTAATGCTGTTACTGCCTAAA R 2 1 2 1 101000 f 74 goat snp40764-scaffold522-344173 3 118924291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454171 Affx-122919314 AX-123324504 3 1127874 CCATTCCAGGCATTCTCTGCAGAAGGGAGTGAAGA[A/C]AACTTCTGTCCAAACTAGAATCTCCAGGATTATGG M 2 1 2 1 101000 r 74 goat snp40765-scaffold522-373047 3 118895423 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786945 Affx-122931290 AX-385273974 3 1176469 AACAGAACACACACTGCAGATAAATATTGCAATCT[C/T]TGAACTTTTCCAGTAACTGTATTTCTCTTAATCTT Y 2 1 2 1 101000 f 74 goat snp40766-scaffold522-421642 3 118846961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444628 Affx-122926934 AX-123314965 3 1208726 CAAGGAGTCAATTTCCCCTTGTGTTCCTCCCTTGA[C/T]AACAGTGGAAAAACACCCCTGAATCAATATTAAAA Y 2 1 2 1 201000 r 74 goat snp40767-scaffold522-453899 3 118814860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780946 Affx-122922671 AX-385268033 3 1244943 CAGGTATTCTAAAAAGACTACTTCTGTAACCATTA[C/T]AGAAATTCACAGTAGAGAGTTTTGACCCATTTAGT Y 2 1 2 1 101000 r 74 goat snp40768-scaffold522-490116 3 118778598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378021 Affx-122977584 AX-123248380 3 1297858 CCAGAGTAACCCAAAGAGGTTTCAACAATCCTTCA[C/T]ATAAACAGGAAAAACTCAGCACAAAATATGGTCAC Y 2 1 2 1 101000 f 74 goat snp40769-scaffold522-543031 3 118725500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388635 Affx-122969122 AX-123258993 3 1334206 TCCATTAAAAGACAAGGGCATGTTTCATGCAAAGA[C/T]GGCCACAATAAAGGGCAGAAATGGTAAGGACCTAA Y 2 1 2 1 303000 f 74 goat snp40770-scaffold522-579379 3 118689653 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277915 Affx-1111836157 AX-519551410 3 1345661 CGTCCATAGCACACACCTATACATAGATCAGCCAC[A/G]TCATCTGTTCATCCTCCCTGATACTCAGCCATCCA R 2 1 2 1 101000 f 74 goat Random2.2K-291 3 1345661 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765065 Affx-122925568 AX-385252633 3 1366799 CTACAGTATAAGTGTCACTGAAGTTGCCTTTTTTT[C/T]TCTTACTTGTATTATAAAAGGAGCAAACAGAAAAA Y 2 1 2 1 102000 f 74 goat snp40771-scaffold522-611972 3 118657073 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781138 Affx-122943034 AX-385268223 3 1405778 ATTCTGGTCCAAAGAGTTTTCTATAAAGAGGAAAA[C/T]GAGGAAAGAACTCATTCAGGAGGGATACAGAAACT Y 2 1 2 1 102000 r 74 goat snp40772-scaffold522-650951 3 118618059 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790489 Affx-122965942 AX-385277492 3 1445861 TGACATCTGTCTTAGGCCAAAGATTGACCACATAA[C/T]GATTTTTATCTTTGTCTCGTCTATTAAATTAATGA Y 2 1 2 1 101000 f 74 goat snp40773-scaffold522-691034 3 118577946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797951 Affx-122941002 AX-385284886 3 1493505 TTTCGCTTTCATAAAGTACCTGTGGACAGGAGTCC[A/G]TTTTACTGAAACTTCACTGATTTCTTGGTATTAAG R 2 1 2 1 101000 f 74 goat snp40774-scaffold522-738678 3 118530481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400432 Affx-122959968 AX-123270787 3 1542525 TCAAGATTCTTCTCACAAGGGCAATTCTGTTTAGC[A/G]TGTTTTAGGCAGGTTGTGGCAAGAAGTTATTTAAT R 2 1 2 1 101000 f 74 goat snp40775-scaffold522-787698 3 118479957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792861 Affx-122931362 AX-385279839 3 1599829 ATGAGTCAGTGAATCTGAGAGATCACATTTGAAGA[C/T]GACCCAGTACACTTTTGAGAAGCTGGAGGTTTTAT Y 2 1 2 1 101000 f 74 goat snp40776-scaffold522-845002 3 118422769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380272 Affx-122975423 AX-123250630 3 1629362 GGGTCATTTCCACCTTGACGGACAGGACAGGCCAA[C/T]ATGAACGTGCATGTATGAGCTGCACCCCTTGGCCT Y 2 1 2 1 101000 r 74 goat snp40777-scaffold522-874535 3 118392553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423851 Affx-122942773 AX-123294197 3 1713638 GGGGAGATTAGCTAACTGTGCCAGTGGGTGATTAT[G/T]GCATATCGCTCTGAGAAGAGTACATGTTCCTGCTG K 2 1 2 1 101000 f 74 goat snp40778-scaffold522-958811 3 118306768 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793455 Affx-122934214 AX-385280432 3 1757727 AAGCAACAACAAGGAAAGTTGCAAAGAATTCAATG[C/T]GGATTAGAGTATTATGAAGACTCCTAACTTACGCA Y 2 1 2 1 101000 f 74 goat snp40779-scaffold522-1002900 3 118261861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411432 Affx-122951828 AX-123281782 3 1796484 ATACATGTGTACAGCAGTTTGTGTTCACCTGAAAC[G/T]AACACAGTGTTGTAAATCATGCGTGTGCTGTGCAT K 2 1 2 1 101000 f 74 goat snp40780-scaffold522-1041657 3 118222461 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426510 Affx-122940210 AX-123296856 3 1841681 GTGTTAGGCAAGATACATACATTCTCTGAGAATCC[A/G]TTTCTTCATCTATAAAATGGGTGTAATGATAATAT R 2 1 2 1 103000 f 74 goat snp40781-scaffold522-1086854 3 118177025 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406125 Affx-122956200 AX-123276477 3 1880254 CCATTTTCCCAAAGGACGGAGAGGACAAAAGAGGC[A/G]TTAATAGGACTCGTTGCTGCCTTTTTCTCCCAGTC R 2 1 2 1 201000 r 74 goat snp40782-scaffold522-1125427 3 118137999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799214 Affx-122952481 AX-385286144 3 1951684 GACATAAAATAAATATAGGTAGAGTCAGTGTGACA[C/T]GCCTCTCAAGTGTCTTCCAACATAAATTTTACTAG Y 2 1 2 1 101000 r 74 goat snp40784-scaffold522-1196857 3 118066229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789446 Affx-122932591 AX-385276456 3 2004670 CAAAGAAGTCTAGTCAATGGAGAACATTTGATTCA[C/T]ATATTGGGACAGATGTTAAGATTTTTTGTTTTTAC Y 2 1 2 1 101000 f 74 goat snp40785-scaffold522-1249843 3 118012823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452603 Affx-122920491 AX-123322936 3 2048588 AAACAAGGCTTGAAAGACTTCATATGCCCCACTTA[C/T]TTGTAGAATCACTAGGGAAATATGTGAAGATCTTG Y 2 1 2 1 201000 r 74 goat snp40786-scaffold522-1293761 3 117967000 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410618 Affx-122952098 AX-123280968 3 2083721 TTGCATTTAATTTATTCTGTGCTCATCTGTTGATC[A/G]TGAATGTGAGAGAGAATTTTTAGACTGTTCTATTA R 2 1 2 1 600000 r 74 goat snp40787-scaffold522-1328894 3 2083721 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777697 Affx-122952098 AX-385264816 3 2083721 TTGCATTTAATTTATTCTGTGCTCATCTGTTGATC[A/G]TGAATGTGAGAGAGAATTTTTAGACTGTTCTATTA R 2 1 2 1 101000 f 74 goat snp40787-scaffold522-1328894 3 117933056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417543 Affx-122946925 AX-123287891 3 2120870 GTAGTTTGAGATGGAGAATTGTCTCCAGCATTTGG[C/T]AGAGTGTGGTTTTACATATATTCTCAATTAGAAAA Y 2 1 2 1 201000 r 74 goat snp40788-scaffold522-1366043 3 117894247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377522 Affx-122977476 AX-123247881 3 2150216 GCTTTTCTAGAGCAAGCTTTCATATAAACCATTTC[A/G]TTTGAAATCTCCAATTTTCGAGTTGGCTTTAGCTA R 2 1 2 1 101000 r 74 goat snp40789-scaffold522-1395389 3 117864878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798535 Affx-122951278 AX-385285468 3 2184826 TGATTTTAACTGTCCCTATGTTTCTTCTTAATCTT[A/G]TATTTTGTCCATTCACTTAATTTTACTTTGGGTTA R 2 1 2 1 101000 f 74 goat snp40790-scaffold522-1429999 3 117831305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417302 Affx-122947232 AX-123287650 3 2235161 CCGCGTGGGTGATCTACAGTCTGGAGAATAATTAT[A/G]CCACAGAAGCTCTCTTACAGGAATGAAAATTCTGA R 2 1 2 1 101000 r 74 goat snp40791-scaffold522-1480334 3 117780616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413523 Affx-122950623 AX-123283872 3 2329615 AAAGCATGAGTACAATCTCAGGACAGAGGGCACAG[C/T]GTAGGGGGCCATGTGCCACTAGGTTTACAAAAATT Y 2 1 2 1 101000 f 74 goat snp40793-scaffold522-1574788 3 117683870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392136 Affx-122966331 AX-123262493 3 2361086 AATCATCAACTATGATTGGACTATGAAGTTTAAGA[C/T]GGTCTTTATGAAGTTTAAAGAAAAACTTCATCTTA Y 2 1 2 1 101000 f 74 goat snp40794-scaffold522-1606259 3 117652247 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415574 Affx-122948633 AX-123285923 3 2395582 AGGAAGTGGAGTGCCTTGTGCTTTGTGTTACACCG[A/G]AAGAAAGATCAAATTCACATCCTCATGGGTTTCGG R 2 1 2 1 101000 r 74 goat snp40795-scaffold522-1640755 3 117617165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440243 Affx-122930667 AX-123310580 3 2441361 TCCAAAGGATTATTAAACAAATATTTCCTGCAGTG[A/G]AATCCAAGCCTGAGGTCATATCCTCAGCTGCACTT R 2 1 2 1 101000 r 74 goat snp40796-scaffold522-1686534 3 117570387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784860 Affx-122923125 AX-385271907 3 2475829 GAGGGAAAATATGTTCACTGGGCTTAAGAGAGAAG[C/T]ACCCTGTTGGAGAGGAGGAAGGTCACAGCCTCAGA Y 2 1 2 1 202000 r 74 goat snp40797-scaffold522-1721002 3 117534750 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791165 Affx-122942142 AX-385278160 3 2501137 AGGAATGACAGGGCAGAAAGAGGGTAAAAAGACAG[A/G]ATCTTTGTTGATCTATGAATCATTAAATCAATTTG R 2 1 2 1 101000 f 74 goat snp55780-scaffold865-16545 3 117509571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383710 Affx-122972477 AX-123254068 3 2534062 ACATGCTATTAAAACTTCTATTATAGGACTTCACC[A/G]TCTTTTATATTAATTTCTTTCTTCCTAGACTGTGA R 2 1 2 1 101000 f 74 goat snp55781-scaffold865-49470 3 117476076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436070 Affx-122932699 AX-123306409 3 2568081 AGGTCAAGGGCTAAGTATATATCTGCAGTTCAAGA[A/G]CGCAGACCAGTTTACAAGGTAGCAATGAAACTCCT R 2 1 2 1 101000 f 74 goat snp55782-scaffold865-83489 3 117440950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272027 Affx-1111833381 AX-519545792 3 2594496 GAGAGATCTCTCGTCATCACTCATCAACAAGAGAC[A/G]TTCCTCTCTCACCTTGTTGCAAAACCTTGGGTCTT R 2 1 2 1 101000 r 74 goat 3_2594496_AF-PAKI 3 2594496 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436254 Affx-122932551 AX-123306593 3 2601445 GGCTGCTCTTGTATCTCACCTTCACGTTGATTAAT[G/T]TGTTGGGTTGAGGTCCCACTGGAGGGAAACTCAGG K 2 1 2 1 201000 f 74 goat snp55783-scaffold865-116853 3 117407740 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406282 Affx-122922901 AX-123276634 3 2653763 AGGTAGACAATGCCCACAGGGAACAGGAGCTACTC[A/G]TCTTGCCTTTGGAGTCACACATCTCAGCGAACCCA R 2 1 2 1 201000 r 74 goat snp55784-scaffold865-169171 3 117355703 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773979 Affx-122938356 AX-385261117 3 2734085 TTGTACAGCAAAGACCAATCTATTATTTATAACCA[C/T]GAAGAACTCTATTAATTCCCTGTCCTCAAATAGAG Y 2 1 2 1 101000 r 74 goat snp55786-scaffold865-249493 3 117274316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430697 Affx-122936914 AX-123301038 3 2777708 GAGGTGCAAACAGCTCTCTTCTGCTTCCAGAAAAT[A/G]CATATCTTGCTTTCTTTCTGATTATTAAAATGAAT R 2 1 2 1 101000 f 74 goat snp55787-scaffold865-293116 3 117229873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799509 Affx-122927252 AX-385286439 3 2823843 AAGAAAGTCTAGACTTCTAGGCCCTGAAAGCTCTC[A/G]TAAATAGCATTAGTCCAACAACCCAAGGCTATCTC R 2 1 2 1 101000 r 74 goat snp55788-scaffold865-339251 3 117183527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375788 Affx-122978577 AX-123246147 3 2914052 CCAGTAAGTTTGGAAAAACCTGTGTACTATCCTCT[A/G]TTCCCACTTAAACTTCTAGGCGGGAGTGACAGGGC R 2 1 2 1 101000 r 74 goat snp55790-scaffold865-429460 3 117094720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377505 Affx-122977486 AX-123247864 3 2958206 CCTCTGGGATAATTTTCCTTTCTCATTTTGTATAG[C/T]GAACTCCTACTCATTCTTCAGATCTCAAAGCCTTA Y 2 1 2 1 101000 r 74 goat snp55791-scaffold865-473614 3 117051881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405789 Affx-122955911 AX-123276141 3 2988548 TCCCCAGTATAAGACTGTTTTTCAGTGCAGGGAAT[A/G]TGAGTTTGACCCTGGTTGGGAAACTAAGAGCCCAC R 2 1 2 1 103000 f 74 goat snp55792-scaffold865-503956 3 117021588 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789424 Affx-122943523 AX-385276434 3 3027242 TCACCCAGGCTGTTTCATTAGCATCGCAATGGGTC[C/T]GTTTGATTCCCTCTTCTGGTTCTAATACAGCAACA Y 2 1 2 1 101000 r 74 goat snp55793-scaffold865-542650 3 116982853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390731 Affx-122967919 AX-123261088 3 3073323 CCTGGGCGTGTCAGAAGAGATGTCTGTTCCTTGGC[A/G]TTTTGAAGTCCATGGTCCCTTGTCATTTCACAGAG R 2 1 2 1 101000 r 74 goat snp55794-scaffold865-588731 3 116937160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278071 Affx-1111836158 AX-519551561 3 3153024 GCCCCTAGAATCCCTCCTGAAAAGAGAATTTTTAC[A/G]ACCACACATTCGCCAAATTGTCTGTTCCAGGACGT R 2 1 2 1 101000 r 74 goat Random2.2K-294 3 3153024 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275817 Affx-1111835024 AX-519549380 3 3179124 GCGTCCCCCAGCAGATCGCGGAAGCTGCTGCCCTC[C/G]CGCAGCGGCATGGACTCGAGCAGGTGGTTCAGGAG S 4 1 2 1 103000 r 74 goat ilmnseq_rs642262399 3 3179124 C G 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276097 Affx-1111835165 AX-519549648 3 3179289 TCCGTCCCCTCGGCAGGCGGGGCCCGGCTCAGTTC[A/C]ACCTCGGGGACCTCCTCTAGGTCTGAGGACTGGTC M 2 1 2 1 102000 r 74 goat ilmnseq_rs658495597 3 3179289 G T 1 neutral Goat_IGGC_65K_v2 Illumina 38450774 Affx-122921833 AX-123321108 3 3305056 CTCCAGCCTGTGGTCAGAGGTCAGGCAGTTGTAAA[G/T]CTGCACAGGGAATTTCATTCAGGCAGTTACTTTCT K 2 1 2 1 101000 f 74 goat snp55799-scaffold865-820464 3 116705300 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437416 Affx-122932417 AX-123307754 3 3346505 TTAAAAGGAGAGCTGTATATCTACAACACACACAG[C/T]GATCAAGGGCAGGAATCCGCTATTTTAGGGTAAAG Y 2 1 2 1 101000 r 74 goat snp55800-scaffold865-861913 3 116663779 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770479 Affx-122939915 AX-385257645 3 3375550 TAAAGGGGTTTGTAGGAATGAATTAAGTCAGTATA[C/T]GTAAAGCGTTTGGATCTATGTCTGGCTCATGGCAA Y 2 1 2 1 101000 r 74 goat snp55801-scaffold865-890958 3 116634943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376878 Affx-122977823 AX-123247237 3 3410690 CTGAACAATTGGAAAACAGTTTTCACTGACTGAAG[C/T]GGAGGTTCTAAGGGTGGGTGGCTAGGAAGCAGGTC Y 2 1 2 1 201000 f 74 goat snp55802-scaffold865-926098 3 116599562 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453898 Affx-122919501 AX-123324231 3 3515134 CTTCATAAACCAGTCTTCTCATTAAGGAACAGGAC[A/G]TGTCTCTGTTAAAATCTTTTACATCTTTCAGTGAT R 2 1 2 1 201000 r 74 goat snp55805-scaffold865-1030542 3 116495155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786539 Affx-122975940 AX-385273572 3 3581154 TACTATGTATTGACCTATATTTTAGGCAATCTTCC[A/G]TTTCAGCAAAACACAATGGATCCAAAACTGAATTA R 2 1 2 1 101000 f 74 goat snp48292-scaffold684-4653 3 116129166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375911 Affx-122978478 AX-123246270 3 3614393 ACAGGGATATAAAAGTACCTAAGAGGGCAAGCAGA[C/T]AGTGCATCGCAAGAAGCATTTAAATTGAGAATGAA Y 2 1 2 1 101000 f 74 goat snp48293-scaffold684-37892 3 116096397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405851 Affx-122955861 AX-123276203 3 3649112 CATCTGTTCTGTTTTAGTGCCAGGGAATTGCAAAA[C/T]GACCAGCAACTCTCACCTCCTGGTTCTGATTGGTC Y 2 1 2 1 101000 f 74 goat snp48294-scaffold684-72611 3 116061501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787453 Affx-122959006 AX-385274478 3 3689889 CTTCTTCAAAAGTCAGTATGTGTCATTCTGGAAGA[C/T]AGACCACTGTCCAGTTAGAGGAAGACATGTCTTCA Y 2 1 2 1 101000 r 74 goat snp48295-scaffold684-113388 3 116021038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275790 Affx-1111835086 AX-519549355 3 3733664 GTGGGTGTCCCGTTCAGGCGAACCTCTCCTCTTAG[A/G]GCTGGTGGGTCATCACGGGCTTCTGTGAAGCACAA R 2 1 2 1 201000 f 74 goat ilmnseq_rs649524942 3 3733664 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468276206 Affx-1111835220 AX-519549756 3 3733671 TCCCGTTCAGGCGAACCTCTCCTCTTAGGGCTGGT[A/G]GGTCATCACGGGCTTCTGTGAAGCACAAACACACA R 2 1 2 1 101000 r 74 goat ilmnseq_rs665215002 3 3733671 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276089 Affx-1111835236 AX-519549641 3 3735158 CCAATGGCAGGAAGAGTGCCGCCAACTACAGCTTT[A/G]CAGTGAGTTTTCTCTGTTCTCTGGGGCGGCTTAAA R 2 1 2 1 202000 f 74 goat ilmnseq_rs666925188 3 3735158 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275598 Affx-1111834989 AX-519549168 3 3735189 ACTGCAAAGCTGTAGTTGGCGGCACTCTTCCTGCC[A/G]TTGGGGTTTCTTTGGGTCAGGGATCCGCGGTACAT R 2 1 2 1 102000 f 74 goat ilmnseq_rs637141532 3 3735189 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468276136 Affx-1111835186 AX-519549686 3 3735190 CATGTACCGCGGATCCCTGACCCAAAGAAACCCCA[A/G]TGGCAGGAAGAGTGCCGCCAACTACAGCTTTGCAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs661607006 3 3735190 T C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276122 Affx-1111835251 AX-519549672 3 3735233 TTTTCCCCGAAGACAAAGATGATGACTGCTTCAGT[A/C]GGAAGTCCATGTACCGCGGATCCCTGACCCAAAGA M 2 1 2 1 101000 f 74 goat ilmnseq_rs668105767 3 3735233 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275997 Affx-1111835111 AX-519549553 3 3735260 TGTGATTAATAAACAAGCCCCCTTCTGTTTTCCCC[A/G]AAGACAAAGATGATGACTGCTTCAGTCGGAAGTCC R 2 1 2 1 201000 r 74 goat ilmnseq_rs653396172 3 3735260 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276274 Affx-1111835254 AX-519549818 3 3738469 GGGGCTCACGGTGCGGCCCTCGGGAAAGCCCCAGA[A/G]GAAGTCTAACCTCCCGGTGAGTGGAGGGACTTCGG R 2 1 2 1 202000 r 74 goat ilmnseq_rs668232262 3 3738469 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468275902 Affx-1111835067 AX-519549460 3 3738483 GCCTTGCAGGCAGCGGGGCTCACGGTGCGGCCCTC[A/G]GGAAAGCCCCAGAAGAAGTCTAACCTCCCGGTGAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs647065552 3 3738483 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275955 Affx-1111835091 AX-519549513 3 3738490 GATTGCAGCCTTGCAGGCAGCGGGGCTCACGGTGC[A/G]GCCCTCGGGAAAGCCCCAGAAGAAGTCTAACCTCC R 2 1 2 1 303000 r 74 goat ilmnseq_rs649926286 3 3738490 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468276212 Affx-1111835223 AX-519549762 3 3738495 TCCAGGATTGCAGCCTTGCAGGCAGCGGGGCTCAC[A/G]GTGCGGCCCTCGGGAAAGCCCCAGAAGAAGTCTAA R 2 1 2 1 303000 r 74 goat ilmnseq_rs665577468 3 3738495 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275855 Affx-1111835117 AX-519549417 3 3738540 CCAAGTGATGTCTATCTGTCATTCCTCCAGGTTTC[A/G]AATATCAAGTCCAGGATTGCAGCCTTGCAGGCAGC R 2 1 2 1 101000 f 74 goat ilmnseq_rs654226695 3 3738540 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38433334 Affx-122935154 AX-123303675 3 3739524 GCATGGCTGCTACCAATCTCAGGGCTGAAGGCAGA[C/T]GACTCACGCTCTTAAGTTCACCTTCGGGGAATCTT Y 2 1 2 1 201000 r 74 goat snp48296-scaffold684-163023 3 115971776 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275900 Affx-1111835066 AX-519549458 3 3740486 TGGGGGAAGGATCCGCTGAGTCCTGGGGACCCCGA[A/G]CAGCCCAGCAGGACCACGGAGGCAGAGCTGGCGGA R 2 1 2 1 202000 r 74 goat ilmnseq_rs647010203 3 3740486 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468276154 Affx-1111835195 AX-519549704 3 3740488 GCTGGGGGAAGGATCCGCTGAGTCCTGGGGACCCC[A/G]AACAGCCCAGCAGGACCACGGAGGCAGAGCTGGCG R 2 1 2 1 303000 r 74 goat ilmnseq_rs662667530 3 3740488 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275712 Affx-1111835047 AX-519549281 3 3740489 GCCAGCTCTGCCTCCGTGGTCCTGCTGGGCTGTTC[A/G]GGGTCCCCAGGACTCAGCGGATCCTTCCCCCAGCT R 2 1 2 1 303000 f 74 goat ilmnseq_rs644663602 3 3740489 G A 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275877 Affx-1111835055 AX-519549437 3 3740510 CTGCTGGGCTGTTCGGGGTCCCCAGGACTCAGCGG[A/G]TCCTTCCCCCAGCTGGGTGTTTGGTCTGCTGCCGT R 2 1 2 1 102000 r 74 goat ilmnseq_rs645584577 3 3740510 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468275927 Affx-1111835155 AX-519549485 3 3740547 CTCGTGGTCACATTTGGGGCTTCTGTCCTAGGTGC[A/G]CACGGCAGCAGACCAAACACCCAGCTGGGGGAAGG R 2 1 2 1 202000 f 74 goat ilmnseq_rs657425815 3 3740547 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276114 Affx-1111835174 AX-519549665 3 3740862 TCAGCCCCTGCATCCGTGCCCTCTTCCTCCTCCGC[A/G]GATGAGACCCCTTGGTCACTGATGTGGCTGGTCAA R 2 1 2 1 102000 r 74 goat ilmnseq_rs659534114 3 3740862 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275618 Affx-1111834999 AX-519549188 3 3740882 TCAAGAGAAAGCTGGAGGAGTTGACCAGCCACATC[A/G]GTGACCAAGGGGTCTCATCCGCGGAGGAGGAAGAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs638749927 3 3740882 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275731 Affx-1111835057 AX-519549298 3 3740954 ACCCACCCACTTGTCCATTTCAGCATCCAGGTGGC[A/G]ACGAGCCCACAGATGCCGACGTGGAAGAGGCGGCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs645789240 3 3740954 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276164 Affx-1111835272 AX-519549714 3 3747747 CCCGAAGAAGCAACCAGAATGTGTCCTTTCCACCT[C/G]CCTTTACCTGGCTCTCAGAGGCGGTCCAGCCTTTC S 4 1 2 1 102000 f 74 goat ilmnseq_rs669588432 3 3747747 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468275704 Affx-1111835043 AX-519549273 3 3747748 AGAAAGGCTGGACCGCCTCTGAGAGCCAGGTAAAG[A/G]CAGGTGGAAAGGACACATTCTGGTTGCTTCTTCGG R 2 1 2 1 202000 f 74 goat ilmnseq_rs643881729 3 3747748 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276029 Affx-1111835127 AX-519549583 3 3747769 TGGCCTCTCACCATCCCAGACAGAAAGGCTGGACC[A/G]CCTCTGAGAGCCAGGTAAAGGCAGGTGGAAAGGAC R 2 1 2 1 102000 r 74 goat ilmnseq_rs654993557 3 3747769 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275821 Affx-1111835026 AX-519549384 3 3747814 CCGACGTGGACACCTCGGACGAAGAAAGCATCTGG[A/G]CTCAGAGAGTGGCCTCTCACCATCCCAGACAGAAA R 2 1 2 1 102000 r 74 goat ilmnseq_rs642369280 3 3747814 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275647 Affx-1111835014 AX-519549217 3 3747833 CTGCCCTCCCAGTATCTGGCCGACGTGGACACCTC[A/G]GACGAAGAAAGCATCTGGGCTCAGAGAGTGGCCTC R 2 1 2 1 202000 f 74 goat ilmnseq_rs640800213 3 3747833 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275596 Affx-1111834988 AX-519549166 3 3750000 GCCTGTGTGGAAGACCACGGTCAAGCGCACTTACC[A/G]GGAGTGGCAGCGACCCCGGGGCCTGCAGTGCAGGA R 2 1 2 1 102000 f 74 goat ilmnseq_rs637083966 3 3750000 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276159 Affx-1111835269 AX-519549709 3 3750087 AGCTCCGAGAGCTCGTCTGGTCCAGCAGGCGAGAG[A/G]CCGACCCTCTGCTCTTCTGGACGGGGGTGGCACGC R 2 1 2 1 103000 f 74 goat ilmnseq_rs669419642 3 3750087 G A 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276184 Affx-1111835209 AX-519549734 3 3750099 GCCAGGGCCCCCGCGTGCCACCCCCGTCCAGAAGA[A/G]CAGAGGGTCGGCCTCTCGCCTGCTGGACCAGACGA R 2 1 2 1 103000 r 74 goat ilmnseq_rs663762137 3 3750099 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275830 Affx-1111835031 AX-519549393 3 3750109 CCAGGCTGATGCCAGGGCCCCCGCGTGCCACCCCC[A/G]TCCAGAAGAGCAGAGGGTCGGCCTCTCGCCTGCTG R 2 1 2 1 103000 r 74 goat ilmnseq_rs642583600 3 3750109 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275792 Affx-1111835087 AX-519549356 3 3750121 GGCCGACCCTCTGCTCTTCTGGACGGGGGTGGCAC[C/G]CGGGGGCCCTGGCATCAGCCTGGTCCAGGATCCCA S 4 1 2 1 103000 f 74 goat ilmnseq_rs649545123 3 3750121 G C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276008 Affx-1111835198 AX-519549563 3 3772277 ATCTTTCCAAGCTCACGGATGAAGAGGCCAAGCAC[A/G]TCTGGGAGGTGGTTCAACGGGACTTCGACCTTCGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs662818451 3 3772277 T C 2 neutral Goat_IGGC_65K_v2 Illumina 320777243 Affx-122966666 AX-385264366 3 3784110 CTGCAGAGAGAAAACTCTCAGGTTATAGACCAATA[C/T]ACTATCAGCTCTGGAAGTGAAACTGGAGATCATTT Y 2 1 2 1 101000 r 74 goat snp48297-scaffold684-207609 3 115926896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447098 Affx-122924485 AX-123317434 3 3828981 ATATGCAACATTAGGGTACCTTAAGCCCTAAGCCC[G/T]CATAGCCAACTGCATTTTTTAAAATTCAGCCCCAA K 2 1 2 1 101000 f 74 goat snp48298-scaffold684-252480 3 115881734 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38447022 Affx-122924543 AX-123317358 3 3874998 CATGAGAATCCCGCTCTGAACTCCTGAGGCAGCTC[A/G]CGGTGGTAGTTTACTCAAAGTGTTTTCTTTCCTCC R 2 1 2 1 201000 r 74 goat snp48299-scaffold684-298497 3 115835715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425563 Affx-122941434 AX-123295909 3 3922731 TATCTTCACTTGCAGAGCCTAGATCAGGCAAGCTA[C/T]GGGTCAGAGCCCAAAGCACAAAATGTCAAACAGGC Y 2 1 2 1 101000 f 74 goat snp48300-scaffold684-346230 3 115788538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425370 Affx-122941572 AX-123295716 3 3963722 GACAAAGACAGAATCAAGACCTTGGTTTAGGAAAG[C/T]GATAAGCATATGCTGGGTAGAGAATGAGAAGGAAT Y 2 1 2 1 101000 f 74 goat snp48301-scaffold684-387221 3 115747719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794865 Affx-122978186 AX-385281825 3 4000463 TGGAAATGAAGAAAGAAAAACACGCGTCTACTGAA[C/T]GCTCATCACATGCCTAGTGCCGTATTTGAGGCTTG Y 2 1 2 1 101000 f 74 goat snp48302-scaffold684-423962 3 115711253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447762 Affx-122924571 AX-123318098 3 4036443 TTGGAACCCTAAGCACTTCTTTTATTCCACAAAAG[C/T]GAGCAGCTAGAAGGGGAAAAAGGAACAGGTTAGAA Y 2 1 2 1 303000 f 74 goat snp48303-scaffold684-459942 3 115675114 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774075 Affx-122971560 AX-385261213 3 4070559 AAAGCCACTGGTTTAGTTATTCCTATATTTCTCTA[C/T]TAACTGGACTTTAAGACATGGAACGTTGCAAAGGC Y 2 1 2 1 101000 r 74 goat snp48304-scaffold684-494058 3 115641152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419317 Affx-122945662 AX-123289665 3 4127985 CTGTGCCAGAGAACACAGATGGTATGTTTATTGGA[C/T]TGGTGTGACTGAGACAGACATGGTCCCCTTTCTTA Y 2 1 2 1 101000 f 74 goat snp29472-scaffold3194-50498 3 115574011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799097 Affx-122977459 AX-385286027 3 4168641 TCAGTCTCTGGGATAGCAGTGGTTTTACAGGAGTA[C/T]AGGATTGAGATATGGGTTAAAAACAAATGGATTAA Y 2 1 2 1 101000 f 74 goat snp29473-scaffold3194-91154 3 115532674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386488 Affx-122970758 AX-123256846 3 4199898 TTGTTATCCAGCATATCTTAGAACTATTCTTCATT[C/T]CTCAGAAAATGAAGAACTCATTTGAATATAAACCC Y 2 1 2 1 101000 f 74 goat snp14634-scaffold159-8591 3 115495269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429218 Affx-122937930 AX-123299560 3 4268489 CTGTTTTTTTTTTTTTTAATACTTCCAGCATTTTA[A/G]CTGCTTCTCCAAAAGAAACTAAATCTGAAAAAGTG R 2 1 2 1 102000 r 74 goat snp14635-scaffold159-77182 3 115428879 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376700 Affx-122978980 AX-123247059 3 4330731 TAGCTCTCTTCTCCAGGGCATAGAGGGCTTTTATT[A/G]CTTCACAGAGCTCTAGGAAATGGAGCAGTAAATGC R 2 1 2 1 201000 r 74 goat snp14636-scaffold159-139424 3 115366759 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449537 Affx-122922597 AX-123319872 3 4341142 TTACCACTTTGAAAATACCAGTTACTATCCTAGGT[A/G]CTGAAAATACAAAAATTAATGAGACATAATTCTTG R 2 1 2 1 101000 f 74 goat snp7791-scaffold1280-234365 3 115356129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432046 Affx-122935900 AX-123302387 3 4392244 CTCTTCCTGCTCTCAGAATTTCTAGAAGATTGTCC[A/G]GAGATGCCTGTCAAAGGCACTTCACCATTCATCAC R 2 1 2 1 101000 f 74 goat snp7790-scaffold1280-183263 3 115304435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801983 Affx-122933841 AX-385288887 3 4447892 AAAATTAGTTAACTCTTAAGAAAACATAAATTAAA[C/T]GCTCTTTAATAGCAAAGTAAACTCCAGTTAAACTA Y 2 1 2 1 303000 f 74 goat snp7789-scaffold1280-127615 NW_017209692.1 415 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773107 Affx-122932854 AX-385260250 3 4500005 TACAAACAACATTTCAGTTAATTGTTGCAAAAGCC[A/G]TTTTGTTACCATTTAGTTCTATTTTACAGATAAGG R 2 1 2 1 101000 f 74 goat snp7788-scaffold1280-75502 3 115171649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277919 Affx-1111836159 AX-519551414 3 4520098 CAAGAGAAACGTGGAAAGACCCACAGTTAACAGTT[A/T]CCAGCCAGTGATGACCCAGGGCCTAGACAGGGCCA W 4 1 2 1 101000 f 74 goat Random2.2K-297 3 4520098 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405543 Affx-122955972 AX-123275895 3 4536105 GAGATCATTTCATAAGCACTTAAATGAATTATTAG[C/T]ATTTGTTAGTACTTTTTTCTTCAAAGTGGTTTTTA Y 2 1 2 1 101000 f 74 goat snp7787-scaffold1280-39402 3 115140101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795517 Affx-122967740 AX-385282472 3 4565301 GAAAGCATAGGTTTTTATCAAAGCATTCACATTAG[C/T]GCAATTCAGAACAGGTGTCTGATGTTCTCGGCTCC Y 2 1 2 1 101000 r 74 goat snp7786-scaffold1280-10206 3 115110635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797264 Affx-122977757 AX-385284203 3 4579860 TGAAATTATTTTCCAAAGCTGGTGGCAATTCTTCC[A/G]TTTCTATAGAGAAGATATTTGACTTCTTTTTTAAG R 2 1 2 1 101000 f 74 goat snp26961-scaffold2852-4254 3 115090070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783117 Affx-122938344 AX-385270184 3 4668825 TGTCCAATGAAATAGAAATGGGTTTAGTTTTGATG[C/T]GTGAGTATAACTAGAACCAGTGGGTAGAATATACA Y 2 1 2 1 101000 r 74 goat snp26963-scaffold2852-93219 3 114999672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425877 Affx-122940645 AX-123296223 3 4747526 GGGATTCAGATGCCCAATATTGCAAATTTGCTACC[C/T]CTGCTCACTGAGGCCTGGGAATGTTCTGCTTTCAG Y 2 1 2 1 101000 f 74 goat snp26964-scaffold2852-171920 3 114920595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769798 Affx-122972974 AX-385256968 3 4776395 ATATATGTGATAGTTGTTTCTTTATAAATTTATTA[C/T]AGTTTATGAATTTATCACCTGTTCTACCTCAGTAA Y 2 1 2 1 201000 f 74 goat snp26965-scaffold2852-200789 3 114891630 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772973 Affx-122949277 AX-385260117 3 4811854 CCAGAAATGCACAAAGGTATCAATAAACACTTCTT[A/G]TACAGCCTCAAGGAAATAGATCTCCAGTTCCATCT R 2 1 2 1 101000 r 74 goat snp50523-scaffold726-27321 3 114844820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441386 Affx-122928852 AX-123311723 3 4841440 ATGGAGACTTTAAACAAAGCAAAATGTACCATCTT[A/G]ATAATTTATTTCATTTCATATAATGAAATATGAAA R 2 1 2 1 303000 r 74 goat snp50524-scaffold726-56907 3 114814867 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797426 Affx-122975895 AX-385284365 3 4930128 AAATTGCATAAATGAGGATGAATATAGGGACATTC[C/T]ATTGGCTATAGTACATTGATTCTGCTTGCCCAGTT Y 2 1 2 1 101000 r 74 goat snp50526-scaffold726-145595 3 114725763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782358 Affx-122956739 AX-385269434 3 4967785 AACCTACTAATTTACTCCCACTAAAAACACTATTT[C/T]TTTTCGTGCTTTGCCAAATGAACCATGTTTTATAA Y 2 1 2 1 202000 f 74 goat snp50527-scaffold726-183252 3 114687272 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416794 Affx-122948148 AX-123287142 3 5020991 CAAAACCTTTCTACTTCTGGAGGAAAGACAGTAAA[C/T]TATCATGGGCACAGACCTTTTGAGATTCCCTATTG Y 2 1 2 1 201000 r 74 goat snp50528-scaffold726-236458 3 114633632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443268 Affx-122927488 AX-123313605 3 5070317 CTTGCATTCTACTTAGACTTGCTCCAGGCTATAAA[C/T]AAGGCTGAATAGTAGGTTGGTTTTAAATGCACTAA Y 2 1 2 1 101000 r 74 goat snp50529-scaffold726-285784 3 114583973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390139 Affx-122967992 AX-123260496 3 5104250 CTGGAACCTTATCTAATCCAGGTATTAAGTGATTC[A/G]AACCTGTTTACTTCCATTTAATATTTATATTTTGA R 2 1 2 1 101000 f 74 goat snp50530-scaffold726-319717 3 114550200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272045 Affx-1111833391 AX-519545809 3 5176243 CGCTGTGATGGGGGTCCAAGCACCAGGGCTGACGC[A/G]AGTACCACCGCGGTGCGTCCCGTTTCATGCCACAT R 2 1 2 1 202000 r 74 goat 3_5176243_AF-PAKI 3 5176243 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801065 Affx-122955869 AX-385287979 3 5191158 AACTCAAGGCTGCTTGTTGGGATCTATCCTGACTA[G/T]CCCAGTGCCTGATCCAAACCACTAGTAAAATATTC K 2 1 2 1 101000 f 74 goat snp50531-scaffold726-406625 3 114462193 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446192 Affx-122925728 AX-123316528 3 5240862 AGACCTGCTGTATATCCTGACACCACTCTGCCTTC[A/G]TAATAAGACTACTATGGAGTTTAGATGAGATCATA R 2 1 2 1 201000 r 74 goat snp50532-scaffold726-456329 3 114412300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278075 Affx-1111836160 AX-519551565 3 5299648 GCCCCTTACAATGGAAGTGCAGAGTGCTAACCACT[C/G]GACTTCCAGGGAACTCCCACAAATACAACTTTAAT S 4 1 2 1 103000 r 74 goat Random2.2K-298 3 5299648 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429404 Affx-122938529 AX-123299746 3 5300314 TGTGCAACCAACATGGTAAATATTAGGTTAAGCAC[G/T]AATCAATGAAATCTCAGAGAATTTTGCTATGAATT K 2 1 2 1 101000 f 74 goat snp50533-scaffold726-515781 3 114352299 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428331 Affx-122939000 AX-123298674 3 5365787 ACCTACCAAAAAGCACACAGTGTGAACAAAAACTA[C/T]GCTGAGCCCTTGGGGCAGTCGCATCTGCCAATTCC Y 2 1 2 1 101000 f 74 goat snp50534-scaffold726-581254 3 114287040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418866 Affx-122946124 AX-123289214 3 5396341 TACTTTTGCCTCAGGGATAGTAGCAGCCCTGAGCA[A/G]TTTTCAGGGATGGGCTCTGAAGCACTGTCCTATAT R 2 1 2 1 303000 r 74 goat snp50535-scaffold726-611808 3 114256474 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787604 Affx-122952086 AX-385274627 3 5443271 GTCGGATAGCAATTATTAACTGAGTGTGCATGCCA[A/G]TTTGGCACTGTATAAATCAGGTTGGATATTGGTAC R 2 1 2 1 101000 f 74 goat snp50536-scaffold726-658738 3 114209131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387528 Affx-122970310 AX-123257886 3 5490011 TGGAAAGATTGTATTGACAATAGACACAAATTCTT[A/G]TACTTTGTTGTATGGGGGAGTAAAGGCTCTACCTA R 2 1 2 1 201000 f 74 goat snp50537-scaffold726-705478 3 114162314 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786075 Affx-122926149 AX-385273111 3 5565183 TTAAGACAGATGAAACACTTAAAGTAGAACATGTC[A/G]TTGCATTTCCTGATCATATGCTAGATCTGATTGTT R 2 1 2 1 101000 f 74 goat snp50539-scaffold726-780650 3 114085817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403447 Affx-122957730 AX-123273800 3 5710826 ATATCCCTTTCTCCCCAAATTCTTCAGACAATCCA[C/T]GAAAGGAAATGATTTGGCTTTTAATTATGCCCTCC Y 2 1 2 1 201000 r 74 goat snp50542-scaffold726-926293 3 113939041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440320 Affx-122930205 AX-123310657 3 5769480 TGACACTCAGTTCTTTTAAAAAGATACCTTATTGG[G/T]ACAGTTCAGAGTCTATTACTAGTAAAGAGGCAAAG K 2 1 2 1 101000 r 74 goat snp50543-scaffold726-984947 3 113879651 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412287 Affx-122950876 AX-123282636 3 5800164 ATTGCTTGTTCTAATTTTCTCTGACTCAGATGGTC[A/G]TTTCCCAGGGCTCTGGAAAGGTCTTTTGTTTCTAA R 2 1 2 1 101000 f 74 goat snp50544-scaffold726-1015631 3 113848189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436255 Affx-122932550 AX-123306594 3 5845187 GTATAGCTGCAATCTGCGCATGCAGGCTCAGTTGT[A/G]CTCAACTCTTTGAGACTCTATGGAACGCAGCCCAC R 2 1 2 1 103000 f 74 goat snp50545-scaffold726-1060654 3 113802845 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801561 Affx-122927454 AX-385288470 3 5873764 TTTGTTATCTGTTCTTGACCAATCTTAAGGAGACT[A/G]TGGTTTAGGATTTGGGCAAGAGAGCGCTTTTAGCA R 2 1 2 1 101000 r 74 goat snp50546-scaffold726-1089231 3 113773571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779252 Affx-122927344 AX-385266356 3 5910490 TTTAAGTACATAATCACGACTTCCTCTGTTGGCTA[C/T]GATGGAGTACAATGAAACAACATATTGCTGCCAAT Y 2 1 2 1 101000 f 74 goat snp50547-scaffold726-1125957 3 113737002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453131 Affx-122920007 AX-123323464 3 5956363 GAGATAATGTGAAGCTCATTTCCAGTCTATAATAA[G/T]AACATGTGTGCCAGGAGGCAGTGTGGTGAAGTGAA K 2 1 2 1 201000 f 74 goat snp50548-scaffold726-1171830 3 113689052 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787842 Affx-122976855 AX-385274865 3 5980654 AAACAGAAAAGTATCACAATGATCAAATTTGCAAA[G/T]AACTTTGTGTGTTTCAGGTTACTAAAGGATGTTCC K 2 1 2 1 101000 r 74 goat snp26119-scaffold2721-225024 3 113664632 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794591 Affx-122942393 AX-385281553 3 6048656 TACATGAATAAGTTGTAGGGCAAAAATTATAAAAA[C/T]ACTTTACAGATATAAGCCATTATTCACCCTATGAG Y 2 1 2 1 101000 r 74 goat snp26118-scaffold2721-157022 3 113597256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390865 Affx-122967817 AX-123261222 3 6080021 AAGTGACTTACTATTCCATTTGCTTGTTTTCTTTG[C/T]AGCAGAACTTAGACCTGTCTTTGGTCTCTGTCTCC Y 2 1 2 1 101000 r 74 goat snp26117-scaffold2721-125657 3 113565061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803373 Affx-122937307 AX-385290207 3 6132056 GAAGGGACTTCAGTTTAGATTAAGATGGCCTCCTT[A/G]CTTGTTTCTTCTGTTGCTCAATGTCAGAAAGTCGT R 2 1 2 1 101000 r 74 goat snp26116-scaffold2721-73622 3 113514917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406382 Affx-122955405 AX-123276734 3 6174072 GTGTTGGAGGAAGAAGGGCCCATGGCATTCGTTTG[C/T]GGTGTTATGTACACTCATCCTGTCCCCTGAGTTGA Y 2 1 2 1 101000 r 74 goat snp26115-scaffold2721-31606 3 113472304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434068 Affx-122934185 AX-123304409 3 6215908 TTAATAAGAATTGTTTGCTACATGATCTTATAATG[C/T]ACTACTTTTCTTTTATAGCACTTTTTACACTTTTA Y 2 1 2 1 101000 f 74 goat snp17637-scaffold183-10131 3 113430423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393320 Affx-122965952 AX-123263676 3 6296876 TCATTATCTTCCCTTGGATACAGTCACTGGCTTTC[A/G]TTCCAAAGGCACCCAAGGCTGGTCACTGTTCCTCC R 2 1 2 1 101000 f 74 goat snp17639-scaffold183-91099 3 113350737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397148 Affx-122962440 AX-123267503 3 6347008 TAACCAGGGAGGAAATAAAGCTTATGGCTATGTAG[C/T]GCTGGTCCCCTCACTTCACCAGCAGCAGAAAAAAT Y 2 1 2 1 101000 f 74 goat snp17640-scaffold183-141231 3 113300813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396198 Affx-122963365 AX-123266553 3 6386394 CAGCTCCAAGTAAAGTGATGTTGAACACCCTGACT[A/G]TACTTAAGTTGTAAGAAATTTCCAAGATGGCCAAT R 2 1 2 1 201000 r 74 goat snp17641-scaffold183-180617 3 113260820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768916 Affx-122966195 AX-385256093 3 6418968 GGCAGTGCAACTGTTTATAATTGGGTGTGTACCAT[A/G]TATCTTTGTGTGGATGTGCCCTGCAGATTATATGC R 2 1 2 1 101000 r 74 goat snp17642-scaffold183-213191 3 113228064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780340 Affx-122941681 AX-385267435 3 6492695 TTTTAGTTAACTGCTTTTTACCACAAAAATTCTTA[C/T]ATTAAATTTTGCCTGCTCAAATTACTAGTGTGGTG Y 2 1 2 1 101000 r 74 goat snp17644-scaffold183-286918 3 113153820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274517 Affx-1111834238 AX-519548108 3 6509898 AACCTGTGGGGTTCCTGCAGCTGAAACCCAGAAGC[A/G]TGTGAGAGCCCCCTAAGTCTACAGCTTCTGGAAGT R 2 1 2 1 201000 r 74 goat GoatD01.026962 3 6509898 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770283 Affx-122935374 AX-385257449 3 6536576 AAGTTGTATAGAATACAGATATTCTTCTACAAATA[C/T]AGTAGCTTTTAGATTTGTTATTTTATATTTCACAT Y 2 1 2 1 201000 r 74 goat snp17645-scaffold183-330799 3 113108842 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409994 Affx-122953273 AX-123280344 3 6594362 AACTGGGGCCAACCTCTTTGTTCTTTAAAATCTGA[C/T]GGATTACAAGAAGGTCTTCATCACCCACATTTGTT Y 2 1 2 1 102000 f 74 goat snp17646-scaffold183-388585 3 113050745 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780951 Affx-122920869 AX-385268038 3 6632028 GCTTTCTGAGACAATTTCTGCCATTCAGAGGGTGC[C/T]CTGATGATCACATTTGGATTCTTACAGATATAATA Y 2 1 2 1 101000 f 74 goat snp17647-scaffold183-426251 3 113013005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401003 Affx-122959691 AX-123271356 3 6687585 CATGGGGTTCAAGGAGGGGGAGAGGGAGTTTGTAC[A/G]TAATGGGTGCAAAGTTTAGAGTTATGAGAACATCT R 2 1 2 1 201000 r 74 goat snp17648-scaffold183-481808 3 112957069 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444071 Affx-122926848 AX-123314408 3 6755065 CGCTCAACGGTCTGAGTGTTAAAAACATTCACAGG[C/T]ATGCTTTAAAATCCCCACCCTGACCTGTCTTAACT Y 2 1 2 1 101000 f 74 goat snp17650-scaffold183-549288 3 112889137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389173 Affx-122969091 AX-123259531 3 6789610 TCTGCAGTTTCTCTGTATCCACCATTCTGTATCCA[C/T]AGCCGCAACCAACCGCATATTGTGTATTTACTGTA Y 2 1 2 1 101000 f 74 goat snp17651-scaffold183-583833 3 112854560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451557 Affx-122921703 AX-123321890 3 6842520 CATGCGCTTGGCAACTAACACAGCCTTCTCTGTGG[C/T]ATCTCACTGAACCTTCATGAAACAGCTGAGGAAAC Y 2 1 2 1 101000 r 74 goat snp17652-scaffold183-636743 3 112802027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403895 Affx-122957491 AX-123274247 3 6880944 AGATTCCCTGGGTACAAAAGCAGGGGCAAGGGTAG[C/T]AGGGGTGAAGGCCAACCAGAATGATTAACCATCCT Y 2 1 2 1 102000 r 74 goat snp17653-scaffold183-675167 3 112763166 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391970 Affx-122966521 AX-123262327 3 6912888 TTACAGAAAAGGGGTTGCTAGATCAAAGAGTAAAC[A/G]CATATGCAATTGTACGAGGTACTGCCTATTCCCCT R 2 1 2 1 101000 f 74 goat snp17654-scaffold183-707111 3 112731681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391840 Affx-122967002 AX-123262197 3 6942994 ACTGGAATTTCATTTACGTCAGGGAAAATGTTTAC[A/G]TGGCAGTTTCTTTGGAAGGCAGTGGCATTTTGTCA R 2 1 2 1 101000 f 74 goat snp17655-scaffold183-737217 3 112701807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394270 Affx-122964718 AX-123264625 3 6976730 TGAAACAGGTGGTAGAAGAACAACCACTGATCCTA[C/T]AAATGCAAAGAGTAATGACAAGATTGTTCTGTTAA Y 2 1 2 1 101000 f 74 goat snp17656-scaffold183-770953 3 112668041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791841 Affx-122937402 AX-385278831 3 7014209 GAAGGTGGACATCTTCTAAGAGATCATCTAATGAC[A/G]GAGATCCTGATAATTGTCCCAAACCATGAAGACAG R 2 1 2 1 101000 f 74 goat snp17657-scaffold183-808432 3 112631010 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398258 Affx-122962185 AX-123268613 3 7044577 AAGCAGGGTGTTTGGATAGTCACTTAGAAGTTTCT[A/G]CTGCAAAGTAAGGATTGGGAAAGAAAGATTAATTC R 2 1 2 1 101000 f 74 goat snp17658-scaffold183-838800 3 112600146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381010 Affx-122974662 AX-123251368 3 7093613 AGGACTCTGAGGCAGGAAGCTGAGCTGGCCCAGCA[A/G]TGTGCAGTGGAAAGAGGGCTTTCATGGTGGAAAAT R 2 1 2 1 103000 r 74 goat snp17659-scaffold183-887836 3 112550518 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770706 Affx-122947842 AX-385257870 3 7129897 ACATCTGCAGCTTTTTTAGTAATTGTGTGCATCAT[A/G]TTTCTCTGTTAAGTCAGAGTCTCTCCAGCTATCAT R 2 1 2 1 101000 r 74 goat snp17660-scaffold183-924120 3 112514040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390665 Affx-122967129 AX-123261022 3 7193819 TACTACACAGTTGAATATAAGTATCTTTTTTTAAT[A/G]GCTTGAATTTCTCAGATCATCAGTATTTAGAGTCC R 2 1 2 1 101000 r 74 goat snp17661-scaffold183-988042 3 112448237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450597 Affx-122922019 AX-123320931 3 7241455 GAAAGAGAGTCATCAGGATATACAGAAATGGACTG[C/T]GTGCTAAATTATGGCATAAAGGGGAAAAAAAAAGT Y 2 1 2 1 101000 f 74 goat snp17662-scaffold183-1035678 3 112400019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804072 Affx-986696656 AX-385290742 3 7275293 CCAGGGATGGTCCTTCTGTGAGGCCAACGAGAAGG[A/G]GAAGAAGCCACTGTGGCCATCGGGGAGAGGGTCTG R 2 1 2 1 600010 f 74 goat 3_7275293 3 7275293 Ancestral_priority_1043 ancestry 0.458 neutral IMAGE 10K 10K ancestral 320787330 Affx-122938504 AX-385274355 3 7305057 TGAGGAGATGAGATTGAACAACTTGAGGAGGCTGG[C/T]GAAAGTGGCTGAGGTTCTGTCTTTATATCTTTAAT Y 2 1 2 1 102000 f 74 goat snp17664-scaffold183-1099280 3 112335839 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409064 Affx-122953348 AX-123279415 3 7334204 ATGGGATTTATGTCCTCTAGGTTTTAATTTCAATG[C/T]AGTCAGATTTATCAATCTTTTGTTAATGATCTCTG Y 2 1 2 1 101000 f 74 goat snp17665-scaffold183-1128427 3 112306142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383625 Affx-122972547 AX-123253983 3 7374576 TGACCAATGCTGAGCACTGACCCCTGGGAGGCATC[A/G]CTGCTTCTCCCAGTCTTTCCTCATTTCTGAACATG R 2 1 2 1 101000 r 74 goat snp17666-scaffold183-1168799 3 112265375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421614 Affx-122944478 AX-123291961 3 7408036 ATGACAAGACAAACAAAAAACTAGACAAACATTTG[G/T]GAAGCCTGATTAAGATAAACAGATATGACAGTCAA K 2 1 2 1 101000 r 74 goat snp17667-scaffold183-1202259 3 112232560 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778627 Affx-122962941 AX-385265738 3 7475270 GGACACGGGGGCTTGTGCATGGTTTTACTATTACT[A/G]TAATTCCCACCCCAATCCTACGCTCCACCACTACC R 2 1 2 1 101000 f 74 goat snp17668-scaffold183-1269493 3 112157042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417446 Affx-122947202 AX-123287794 3 7576409 CAGATCATTATGAATAATTAGGTTAGCAAACAAGC[A/G]TTAATACCAAATATGAATTTAATACTAAATATCAC R 2 1 2 1 101000 f 74 goat snp17670-scaffold183-1370632 3 112055110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764948 Affx-122964666 AX-385252529 3 7591446 CCAAAGGGATAAAAGAGAAAGGACTTGATCCCTAA[C/T]GGATATGGTGAGTACGAAAGGTTCTGAACTTATTT Y 2 1 2 1 101000 f 74 goat snp17044-scaffold1777-7639 3 112015390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452026 Affx-122920903 AX-123322359 3 7624985 CTGTTCCCATGCATTCAGTACTAAAGTTTCCAGTC[A/G]TGGAGATGCTTCCTCCTTCCCTCCTCTGAGTCTTT R 2 1 2 1 101000 f 74 goat snp17045-scaffold1777-41178 3 111981879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452560 Affx-122920522 AX-123322893 3 7662294 TCTATATATCTTCTCCCCAAGACCTGCTCCAAGAG[C/T]CAACTTAACTCTTTTTATCTCCTGCTAGCTGGGAC Y 2 1 2 1 201000 r 74 goat snp17046-scaffold1777-78487 3 111944041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418762 Affx-122946200 AX-123289110 3 7693631 TTATTAAAGATACTTGGGGCTCTTTCCCATTCTTA[G/T]GTAAACCTTCTTCACCAGAAATAGTGCACACGCTG K 2 1 2 1 101000 r 74 goat snp17047-scaffold1777-109824 3 111912650 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272225 Affx-1111833399 AX-519545972 3 7699659 AAGCCATGCAGGACTTGAAGGCAGCTGAAATCACT[A/G]AAGAGAGCCCAGAGATGGCGGATGGGGAGGGGGAC R 2 1 2 1 101000 f 74 goat 3_7699659_AF-PAKI 3 7699659 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446106 Affx-122925795 AX-123316443 3 7732226 ACAGACCAGCAACTACTAAGGGCTGAGGGGTGACT[A/G]TGGAGGGGGCTGGGGGAATTTGGGAATGATGGAAC R 2 1 2 1 201000 f 74 goat snp17048-scaffold1777-148419 3 111873951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785917 Affx-122943751 AX-385272954 3 7769340 ATATTTACTTCCCTACCCTAACTCATTCTTCATAT[A/C]TCATCTGAAACCACCTTTTCCCAAGACATCAGAAA M 2 1 2 1 101000 r 74 goat snp17049-scaffold1777-185533 3 111837021 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277923 Affx-1111836161 AX-519551418 3 7778398 CCAGGAATCCACCAAGTTTGCCTGGTTGTCAGGAG[A/C]CCTGAGCTTGGTGGGAAAAGGCGGGGAGAACAGGG M 2 1 2 1 102000 f 74 goat Random2.2K-299 3 7778398 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431232 Affx-122937142 AX-123301573 3 7798148 GTAGACCTTAATGTATTAACATTTTATTGTTAACA[C/T]GTCTAAGAGGGTGCTTCTGAACCAGTTGAACACCT Y 2 1 2 1 101000 r 74 goat snp17050-scaffold1777-214341 3 111808346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386110 Affx-122971427 AX-123256468 3 7853474 CCTGCAGCCCTTTCCCCTTTTGCTTTCTTCTGGCT[G/T]GGGCAAAGGCCATCATAGGTGAGAATGAAGTGATG K 2 1 2 1 201000 r 74 goat snp17051-scaffold1777-269667 3 111753373 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799208 Affx-122925123 AX-385286138 3 7891413 TACAAAGTCAGTTGAAATTCTACCACTCATTTGAC[A/G]TCTCTGTTGATGGTATAAAAGAAGAAAAAGCTAGA R 2 1 2 1 101000 r 74 goat snp17052-scaffold1777-307606 3 111715466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435264 Affx-122934058 AX-123305604 3 7943509 TAGTCCCCGCGCGGCGAAGCTGTGTGTGTTTCTAG[C/T]GTCGCAGTGACTGCTGTCGCATCGGGATCTTGATC Y 2 1 2 1 101000 r 74 goat snp17053-scaffold1777-359702 3 111662990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793175 Affx-122945229 AX-385280153 3 7972983 GTGGGAAGCAGGTGATGACAACCTCTAGCCTTCAA[C/T]GTTAGAACAAAGCCTAAGGTCCAGGTGGTCTAAAG Y 2 1 2 1 101000 f 74 goat snp17054-scaffold1777-389176 3 111633576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389596 Affx-122968772 AX-123259954 3 8012178 CTCAAGGAAGTCAACTTGTCTTCCATCTTGGGCCT[A/G]TTTGGTTCTATTATCTTATGTCATGTCCTCAGGCT R 2 1 2 1 201000 r 74 goat snp17055-scaffold1777-428371 3 111594078 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397580 Affx-122962002 AX-123267935 3 8066373 GACATCCATGAGACAGTTGGATATGGGGTTTCAAA[C/T]GCAGAAAATAACTGGCTGCCCTGTGAAATTTAGGA Y 2 1 2 1 101000 f 74 goat snp21715-scaffold213-40854 NW_017200692.1 8587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376137 Affx-122978861 AX-123246496 3 8114988 TTGCACAAATTGCCTTATCATTCAATTTTGATCTC[C/T]TAAATTTATAATTCACAAAATAGATGTAGCTCACA Y 2 1 2 1 101000 f 74 goat snp21716-scaffold213-89469 3 111159559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438743 Affx-122930828 AX-123309080 3 8152220 TTCTTTGGAAACCATGAGCACCATTGTTTACTCCC[A/G]GGGTAGAAAATTCTAGACAATTCTGGGTGAGAAAA R 2 1 2 1 101000 f 74 goat snp21717-scaffold213-126701 NW_017214458.1 12035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422157 Affx-122943533 AX-123292504 3 8186627 CACTGTTGAGGCTGAGTCCTTTTCAGAGGCTCCTT[G/T]CCCTGCAGAGACAAAAGAGGGACTTGGAGAAGCAG K 2 1 2 1 101000 f 74 goat snp21718-scaffold213-161108 3 111233829 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392053 Affx-122966394 AX-123262410 3 8228332 GAGACATGGTATAGTCAAGACCAGTATCCTCAGGT[A/C]GACCATCCACAAATAAGAGGACAACTGCAATTACA M 2 1 2 1 101000 r 74 goat snp21719-scaffold213-202813 3 111275816 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423166 Affx-122942742 AX-123293512 3 8272913 AATCACTTAATAAATATGTAAGATAAAGAAGTCCC[A/G]TGAGCTATGAATCTCCCAAGTGATTAAAGAATAAT R 2 1 2 1 101000 r 74 goat snp21720-scaffold213-247394 3 111325054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384760 Affx-122972027 AX-123255118 3 8336365 AACAAAGTGCAAAGGGAGGTCCTGAGGAGCAGCCA[C/T]GGGGAAGAGGGCCCTGTAGAGAGAGCTAGTGGGCA Y 2 1 2 1 303000 f 74 goat snp21721-scaffold213-310846 3 111389028 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420760 Affx-122944716 AX-123291107 3 8349748 AATCTACTGCTTCTCTCATTCTGCTATTGGTTCCC[C/T]CTAATGGCTTTTCACCTCAGTTATTGTGTTCATTG Y 2 1 2 1 201000 r 74 goat snp29272-scaffold315-1752872 3 111002050 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454110 Affx-122919356 AX-123324443 3 8418625 TGAAAGAGGTTGCTATTGGGCCTCATGTATTTAAA[C/T]GGAATCTGGTTCTCAATGGTAGTCATGGCCTGTGA Y 2 1 2 1 201000 f 74 goat snp29271-scaffold315-1683995 3 110932495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433860 Affx-122934430 AX-123304201 3 8520732 TAATTATATTAGCCACACTTCTGTGTTTTTCTACT[G/T]TGGGGCAGATGGAGATGGTAAAATCCTTGAGACAT K 2 1 2 1 201000 f 74 goat snp29270-scaffold315-1581888 3 110826227 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395813 Affx-122963642 AX-123266168 3 8682604 TTGTTATTTTTTAAAATGTCAGGATGAACTGTCAC[A/G]TGTATGGCTGTGTTTGTCTTTTGCTTCTCCTGTAT R 2 1 2 1 101000 r 74 goat snp29266-scaffold315-1420016 3 110662506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781022 Affx-122943949 AX-385268109 3 8713914 CACTGAGGTTGACCTCTTTAGGAAATCCTGTCACC[G/T]CAACATTCTCCTCCCTGCTAAAGAATTAGACTAGT K 2 1 2 1 101000 r 74 goat snp29265-scaffold315-1388706 3 110632974 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377763 Affx-122977361 AX-123248122 3 8761572 GCTCACTGCAAAGCCTTTCAGTGGAACAAGGTGGG[C/T]GACGGCTTGGCTTATGAAGATTTCAGTTTCCCCAT Y 2 1 2 1 101000 r 74 goat snp29264-scaffold315-1341048 3 110585048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413522 Affx-122950624 AX-123283871 3 8849859 ACCTTAGGCTCTGAAATTCAAAGAATGACCCCAAC[A/G]AAGCTGAAACTCATACTATAAAAAACATGTTTATA R 2 1 2 1 201000 r 74 goat snp29262-scaffold315-1252761 3 110496588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403214 Affx-122957906 AX-123273567 3 8883776 GCCACCCAACCCCCACCTGGAAGGGGCAAAGAGAA[A/G]CAAGGGGCAAAGAAGCCAGAGTTTGTGTTTGTACC R 2 1 2 1 202000 f 74 goat snp29261-scaffold315-1218844 3 110462688 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422875 Affx-122943077 AX-123293221 3 8966220 CAAGGAGCTCAAAGTCTAGCATCCAGTGCCTTGTG[A/G]TGAGTGCAGCCCCAGAATCATGCCTGGGATACAAG R 2 1 2 1 101000 f 74 goat snp29259-scaffold315-1136400 3 110380851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443308 Affx-122927458 AX-123313645 3 9070346 AGAGTGCTTAGGATGTTCAAAAAAAATTTCTCCAA[A/C]GCTCTCTCTGATCCATTCAGAACAATCAGAATCCA M 2 1 2 1 101000 r 74 goat snp29256-scaffold315-1032274 3 110276949 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396575 Affx-122962917 AX-123266930 3 9127193 GTCACTTACAAGATGAAATGAAAAGATTTAAGCCT[C/T]TCTAGATTCAGCCTGCCCTTGACTGTCCATTCTCA Y 2 1 2 1 101000 f 74 goat snp29255-scaffold315-975427 3 110219759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445763 Affx-122926072 AX-123316100 3 9194582 TTCTCCAAAGGCACTTATCGCTGGCTTTCTGAATT[A/G]CCTTGGCTCATCCCCGTGTTTTATCTCCCCTACAG R 2 1 2 1 201000 f 74 goat snp29253-scaffold315-908038 3 110152428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441522 Affx-122928715 AX-123311859 3 9262723 GGAGGATTGCCGTAAATATTAATATATGCACATGC[A/G]TTCCAGGATTCAGAGGCGAGGCCTGGTTCTCCTCC R 2 1 2 1 101000 f 74 goat snp29252-scaffold315-839897 3 110084129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386927 Affx-122970001 AX-123257285 3 9296460 AACCTCTGTCCATAGTTCTTCAGGCACTCTATCAG[A/G]TCTCACCATCATAAACATCATCTCCACCACACCTT R 2 1 2 1 201000 r 74 goat snp29251-scaffold315-806160 3 110050535 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388618 Affx-122969137 AX-123258976 3 9358962 CACAAGTGTCCTGAAATGTCCCTGCTTTCAGGGCT[A/G]AGCGGTACTGTAGAATCTCTTCCAGTCTTTTCTCT R 2 1 2 1 101000 r 74 goat snp29249-scaffold315-743658 3 109987902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406775 Affx-122955716 AX-123277126 3 9394836 GATAAGGAGATCTTAATGAAAAGGCTGAAAGTTCT[A/G]CCTAAATGCCATTAGTGCGTGTAGTATTTTTAGTG R 2 1 2 1 101000 r 74 goat snp29248-scaffold315-707784 3 109952453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449142 Affx-122923557 AX-123319477 3 9432476 AAAACTCCTCACCAAGTCTGCATGAGTTAGGACAC[A/G]CAGTTTTAAGGAGCACAGCCCACCATGTTCCTCTT R 2 1 2 1 101000 f 74 goat snp29247-scaffold315-670144 3 109914133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446681 Affx-122924752 AX-123317017 3 9463298 GAGATGGAGAGATTATGCTGGTGTCCAGGAGGCTC[G/T]ATATAATGACAGGGAGGAAGGAAGTTGGAGAGAAG K 2 1 2 1 201000 f 74 goat snp29246-scaffold315-639322 3 109882458 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434846 Affx-122934377 AX-123305187 3 9499083 AGAAGAACACCACAGAGTTTAAAAAATAACTGATA[G/T]ACCTGGAAAAACATTTTGTAAAGATAAACTCTGAC K 2 1 2 1 303000 r 74 goat snp29245-scaffold315-603537 3 109851197 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395258 Affx-122964094 AX-123265613 3 9549347 ATTACCTTAATAAGAATAAAATTTGGAAATAAAAG[C/T]AATAAAAGTCAAAACAAAAAAATTAGCCCTAAGGG Y 2 1 2 1 303000 f 74 goat snp29244-scaffold315-553273 3 109802334 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774548 Affx-122924011 AX-385261682 3 9618383 CTGCATTTACAAGAAAAGAAACTATTACAGAGTGT[A/G]TTGATATTTACAACAAATCATGTATGTTATTTAAA R 2 1 2 1 101000 f 74 goat snp29242-scaffold315-484237 3 109732311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443848 Affx-122927526 AX-123314185 3 9672353 TTTCCTCTTTGTCCGGTACTATTGGCCTTTCCTGG[C/T]GCACAGATGCTACAAAGCAAGGGGAAGTAGATGTA Y 2 1 2 1 101000 f 74 goat snp29241-scaffold315-430267 3 109677329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772912 Affx-122939120 AX-385260056 3 9788047 TCATTCAGTAAAATTCAATCAAACTCTTTACCATG[A/C]TCCATGATGACCCTCAATAGGAAATGCATATCATA M 2 1 2 1 101000 r 74 goat snp29239-scaffold315-314573 3 109558762 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435050 Affx-122933746 AX-123305390 3 9834695 ATATTCATCATGGACACTTTGCAAAATTCAAGAGA[C/T]GGTAGAAATTTATACCGTGAGTTATACCATGCAGA Y 2 1 2 1 101000 f 74 goat snp29238-scaffold315-267925 3 109516602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446049 Affx-122925837 AX-123316386 3 9875393 AAACATTGGGATTCTTTATGCTTTGTCCTGGAATC[A/G]TCTTTGTTTTCTAGCTACTCTTCCTCTCTCTTTAA R 2 1 2 1 101000 r 74 goat snp29237-scaffold315-227227 3 109476096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418215 Affx-122947053 AX-123288563 3 9910236 AGCCAGCTAGATACTTGTTGGGGTAACAAAACTAA[C/T]AGTAGGAGCAGATAGAGAAAGTTTCTACTGCTAGC Y 2 1 2 1 101000 f 74 goat snp29236-scaffold315-192384 3 109440956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411035 Affx-122951966 AX-123281385 3 9953630 TTTCCCCTGAGTAGTTTGTTCTCCACCTCCTAAAA[G/T]AATACACTGCACGTGACTCCAAACTGCATGTGTTT K 2 1 2 1 201000 f 74 goat snp29235-scaffold315-148990 3 109396960 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448962 Affx-122923131 AX-123319297 3 9989703 CTTTATCAAATAAATAAAACAGATCAAAGGAAAAC[G/T]ACTCTTTTGGAAACAGATAAATAAGACCTGAAACC K 2 1 2 1 201000 f 74 goat snp29234-scaffold315-112917 3 109360888 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423154 Affx-122942752 AX-123293500 3 10024829 TCCCCTACTGTCTGGCCAGGCACCTTTTCTTCATG[C/T]TGAGGAGTGAGACAAAAGCAACCTTCAAACTAACA Y 2 1 2 1 101000 r 74 goat snp29233-scaffold315-77791 3 109325802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412836 Affx-122950460 AX-123283185 3 10064906 ACATCTACATCACCTGGAAACTTGTTAGAAATGCA[A/G]CTTCTTGGGCCTCAAGCCAGATCAAATAAACCTGA R 2 1 2 1 201000 r 74 goat snp29232-scaffold315-37714 3 109285126 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402154 Affx-122958651 AX-123272507 3 10094387 ACACTGAGCAAGTCACTAATCTTATGCTTTAACTT[C/T]CTTGTCTCTAAAGTAGAGATATTAGTAGTACTTGG Y 2 1 2 1 101000 f 74 goat snp29231-scaffold315-8233 3 109255390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446900 Affx-122924707 AX-123317236 3 10122051 AAGAAAAGGGGGAGGAAAATGTTCTGAATTATGAC[G/T]ATTTCTCCCATGTCCTCTAACCTCTGATCTCTGGA K 2 1 2 1 101000 r 74 goat snp56497-scaffold89-1084978 3 109138720 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404717 Affx-122957251 AX-123275069 3 10151083 CTTAAGTCCTGTGCACATCTTCTCAAGGTGCTGCT[A/G]TGGTTACTTGTAAGAGATTCGCTGTTACTGATTTA R 2 1 2 1 101000 r 74 goat snp56496-scaffold89-1055946 3 109111988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793897 Affx-122973075 AX-385280866 3 10234090 CAGGGTGTACTTGTATGCAATTCAAGAGTGTTAAG[C/T]ATGTTGACTTTGTGCAACTAATCTCCAGAACTCTT Y 2 1 2 1 101000 r 74 goat snp56495-scaffold89-972939 3 109035337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783056 Affx-122944596 AX-385270123 3 10304067 TAAGTTCTTCCCAGTGCTCAGATTAGAATACAAAA[G/T]GGTAGAAATGCCTGACTGACAACGTTCTTACCCAA K 2 1 2 1 101000 r 74 goat snp56493-scaffold89-902962 3 108964864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409860 Affx-122952922 AX-123280211 3 10353865 AGAGCATTTTGTAAGTATGAAGGAGGCCCAGTAGG[C/T]GAACTGTGGACTCTCTCTTGGGAATCTGGTTCTTG Y 2 1 2 1 101000 f 74 goat snp56492-scaffold89-853164 3 108914528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387409 Affx-122970409 AX-123257767 3 10400624 CTCATTATTTTCAGAACTCCATCATGTTGATGGCT[A/G]CTAGCTTCTCTCAAGACCCTGGAAACCAAGGAAGA R 2 1 2 1 201000 r 74 goat snp56491-scaffold89-806405 3 108869326 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377271 Affx-122978131 AX-123247630 3 10444909 AGCTGAGCCACAAGGAAAGCCCCTATATCTTCCTA[C/T]AGCTCACAAAACAACTGCTCAATACTGACCTGTCT Y 2 1 2 1 101000 r 74 goat snp56490-scaffold89-762120 3 108823572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417931 Affx-122946717 AX-123288279 3 10477794 TCAATCCCATCATTTATAGCCTAAGAAATAGGGCT[A/G]TGCAGACAGCCCTGAGAAATGCTTTCCAAGGGGGA R 2 1 2 1 101000 f 74 goat snp56489-scaffold89-729235 3 108790706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272007 Affx-1111833372 AX-189289814 3 10496829 CCTGGAGTTCACTCAGACTCACGTCCATCGAGTCC[A/G]TGATGCCATCCAGCCATCTTATCCTCTGTCGTCCC R 2 1 2 1 303000 r 74 goat 3_10496829_AF-PAKI 3 10496829 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401762 Affx-122959500 AX-123272115 3 10508996 GTTTGTTTGTTTTTATTTGTTTGTGACTACCTTGA[C/T]AATTTTAGTGAAATTTCTCCTTCCCAGCCTTTTAC Y 2 1 2 1 101000 r 74 goat snp56488-scaffold89-698033 3 108760431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780573 Affx-122963025 AX-385267664 3 10561005 TTACCTAGAAAAATTCTTCCACTTTTATATCTCTA[A/G]TTATTTTATACCATCTATTAGTGTAGTGATCATAG R 2 1 2 1 101000 f 74 goat snp56487-scaffold89-646024 3 108708379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436120 Affx-122932654 AX-123306459 3 10590435 GAAGGAGGGGTAAATATTCTGCCTGCACATGTGTT[A/G]CAAAAATGGTCCCAGGGAAGAAAGTAGAGTCATGG R 2 1 2 1 101000 r 74 goat snp56486-scaffold89-616594 3 108678239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379073 Affx-122976326 AX-123249432 3 10623536 GTGTCATCTTCGATTCAAGAAAGAATGTGACTTGA[C/T]AAGAGTCATACAAAGAGGATATTATCAGTTGACAT Y 2 1 2 1 102000 r 74 goat snp56485-scaffold89-583493 3 108644869 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449465 Affx-122922652 AX-123319800 3 10656340 TGTCATAGAATATGCTTCCCTAGTCCATGGAACTT[A/G]CTTCCTTTCTATCAGCCATCTCTGAAAGACTGATT R 2 1 2 1 101000 r 74 goat snp56484-scaffold89-550689 3 108611762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776128 Affx-122938101 AX-385263258 3 10701613 TCCCTAAGAGAGACATCTTTGAGTATCTAGTACAA[C/T]ATTTTCCCATTTCTAGCCCAGAGTATATGAACTCA Y 2 1 2 1 101000 f 74 goat snp56483-scaffold89-505416 3 108565401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426187 Affx-122940578 AX-123296533 3 10739717 GAAGTCTGGGCTGAGCAATGGAACTAAAGAAAAGA[C/T]GACTTGATGGCCAAATTAAATTTGCTTTGATCCCT Y 2 1 2 1 101000 f 74 goat snp56482-scaffold89-467312 3 108527077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795540 Affx-122932452 AX-385282495 3 10812658 TGCAGTAATATCATGGCCTACTCATTTGCTTCAGG[C/T]TCCTCTGCCTGGCTTAGTATCTTTAGGTATTGTGA Y 2 1 2 1 101000 f 74 goat snp56481-scaffold89-394371 3 108455302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447282 Affx-122924931 AX-123317618 3 10903897 ACTAACCTCCATGGTATATTAGAAAAGGTCTTTTC[C/T]ATGACCAATTAATTTTCCTACTGTATTACCATAGT Y 2 1 2 1 101000 r 74 goat snp56480-scaffold89-303132 3 108367359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773978 Affx-122919755 AX-385261116 3 10932583 TAAAAATTGAGGGATAGAAATAAGAATAGAGAGAG[C/T]AATTCAAAACTGTGAGAGCCTTATTGATGATGTTA Y 2 1 2 1 101000 f 74 goat snp56479-scaffold89-274446 3 108338837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389690 Affx-122968698 AX-123260048 3 10963679 CATATCCTGGATACTTTCGTGAATATAATTTTCCT[G/T]ATATAGCAACTTATACAGTTTTGGAAAGCAAGTAC K 2 1 2 1 101000 r 74 goat snp56478-scaffold89-243350 3 108307563 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796060 Affx-122962207 AX-385283012 3 11006856 CAGCCACATGTTCATCACTATTGATCCTTTAAATT[C/T]TAATTCAGATGCCTCTTTCTTAACAACTTCCCTGG Y 2 1 2 1 101000 r 74 goat snp56477-scaffold89-200173 3 108264470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406330 Affx-122955449 AX-123276682 3 11055188 AAATCCATGCCTGATGCACACAGAGGCCAAAGAAA[C/T]GGAGATGTCAGAGTATGGAGAAGAGAAAGATTTAT Y 2 1 2 1 101000 f 74 goat snp56476-scaffold89-151841 3 108219133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394279 Affx-122964711 AX-123264634 3 11084563 CCACATTCACCAGATAAAGCTGCTCAGAACCCAAC[A/G]CTCTCCAATTTCTGGAGGGAGCAGGCAGAGAGAAA R 2 1 2 1 202000 r 74 goat snp56475-scaffold89-122466 3 108189786 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441310 Affx-122929447 AX-123311647 3 11124378 CTGGTGTCCTCAGGCTTGCAGAAATCTTACCTTTA[G/T]ACCTGAGATGTGTGTCTTCCTTGATTTTGGAGTAG K 2 1 2 1 201000 f 74 goat snp56474-scaffold89-82651 3 108149275 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407082 Affx-122954904 AX-123277433 3 11153156 TTTTATACCATTTAATTTGCAAAATTAAAAAGCTG[C/T]AGCAGCCCAGTGTTTGCAGGGATGTGAAAAAATTG Y 2 1 2 1 201000 f 74 goat snp56473-scaffold89-53873 3 108119600 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391902 Affx-122966954 AX-123262259 3 11188244 AAAGTCAACAACCTTTAATTCCTCCTCAAGGGACA[G/T]AGATAATATTCCAAACCATATCCGTGTGCTATTTT K 2 1 2 1 102000 f 74 goat snp56472-scaffold89-18785 3 108084233 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415025 Affx-122949022 AX-123285374 3 11222888 AGTAATATTTCTGCAAGCCTGAGGACACCAGAGGA[C/T]GTTCCACTGAAGTACAAGGCACTTGTTCATGTGAG Y 2 1 2 1 101000 r 74 goat snp16912-scaffold1767-15760 3 108040918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777742 Affx-122968176 AX-385264860 3 11252941 ATTGCATGCACAGAGAGCAAATTGTGTACAGCTGG[C/T]GCTTGAATAATGTGATTTGAGCTACATGACTCCAC Y 2 1 2 1 101000 f 74 goat snp16913-scaffold1767-45813 3 108009942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453881 Affx-122919513 AX-123324214 3 11296990 GCATTTCTCCCCTGCTTTTTAAATATGAGGTCCCA[C/T]ATTTATATTTGGTGCTGGACTCCAAAATTGAGTAG Y 2 1 2 1 201000 r 74 goat snp16914-scaffold1767-89862 3 107965476 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417159 Affx-122947343 AX-123287507 3 11353242 TAGCCCATGGTCTTATTCCAGCCTGTCATCTCTTT[C/T]TGAATGGTCCATAGACTAAGAATGGTTTTATGGCC Y 2 1 2 1 201000 r 74 goat snp16915-scaffold1767-146114 3 107907604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387407 Affx-122970410 AX-123257765 3 11389734 TGTCTTCCCAATGTCATGTTCCTTGCACTCATACT[A/G]CCCCCAGGGTACTGTCATGTTCCTCACATTACCCC R 2 1 2 1 101000 f 74 goat snp16916-scaffold1767-182606 3 107870714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774084 Affx-122959879 AX-385261222 3 11427176 AGATACACAGAGACACAATCATTCATTACTCACTC[A/C]GGTCAGGTCTACTGTCCTTATAGCCAAGAGTCAGC M 2 1 2 1 101000 f 74 goat snp16917-scaffold1767-220048 3 107834378 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448893 Affx-122923257 AX-123319228 3 11508793 TCCTTGATTGCATGCACGTGTCTAGTGAGCTTGTG[C/T]GTGTTAGTGCACATCTACACACAAGTGTTGGTAGG Y 2 1 2 1 101000 r 74 goat snp16919-scaffold1767-301665 3 107753918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442577 Affx-122928501 AX-123312914 3 11542727 CCAAAGATCGTTAATGCATAAATGTACTAATGTTG[A/C]TCAGAAAGGTGCCTGGCACATGGTTCATGCACAAG M 2 1 2 1 101000 f 74 goat snp16920-scaffold1767-335599 3 107719989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437399 Affx-122932428 AX-123307737 3 11573513 GCACACAGCTTGTTCACACTGACACAACTATCCAG[C/T]GGCCTGGGAGGAAAGGGGTTTAGCCAGGGAGCTGG Y 2 1 2 1 101000 f 74 goat snp16921-scaffold1767-366385 3 107689696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797301 Affx-122971681 AX-385284240 3 11613006 TCCTGAACAACTGTGCGTGTGGGATCCCAATAAAG[C/T]ACTGTTTCTATATCATCAGCATGCTGCTTGTGCTG Y 2 1 2 1 101000 r 74 goat snp16922-scaffold1767-405878 3 107650659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427406 Affx-122940070 AX-123297749 3 11653379 CCTCCTTCCCTCAGTTCCTCTATTTTCCCTCCTAT[C/T]TCCCCTTCCTACCTTCACAACATTCCTGTAGTACT Y 2 1 2 1 101000 r 74 goat snp16923-scaffold1767-446251 3 107610466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783560 Affx-122971288 AX-385270622 3 11683867 GACTGGAAGAGAGAAAAGGGGGAAGTTTCAGAAGA[C/T]GAGGAGTTTAGGGAACTGAGGTGAGGTTATCAGTA Y 2 1 2 1 201000 f 74 goat snp16924-scaffold1767-476739 3 107579628 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405434 Affx-122956058 AX-123275786 3 11715035 TGGGGCCTCCTTCCAGCCTTACATTTCAGTTCACT[A/G]TCTTCAGCCATCTGGGACATGGCCCTGTTTTTCTT R 2 1 2 1 101000 r 74 goat snp16925-scaffold1767-507907 3 107548331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375927 Affx-122978466 AX-123246286 3 11758923 ACACCCGCTATGCTTCAGAATCATCTATTCAGATT[A/C]TTTTCTAAAAATTATTTGTAAAAACAATGATTTGT M 2 1 2 1 103000 f 74 goat snp37056-scaffold4496-18196 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402782 Affx-122958302 AX-123273135 3 11797945 TGAAAATGGCAACATGTACCATGAACCATACAGCA[C/T]GCTGGATTTACAGAAAATTTTTTTAAGGCGTGTTT Y 2 1 2 1 103000 f 74 goat snp6327-scaffold1223-614225 3 107448791 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774085 Affx-122936868 AX-385261223 3 11835897 ACAAGACATATATCATCTACCATGTCTCCCTTGTA[C/T]GGTCACACCACAAGGACTTCAATTCGTATTTGATG Y 2 1 2 1 101000 r 74 goat snp6326-scaffold1223-576273 3 107410652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792283 Affx-122953516 AX-385279265 3 11881912 AGTTATAGAGCTAATAAATACACCACTCCTTTAGG[C/T]AACTTGGAGGAAACAATCAGGCTTAAGGAGCAGAA Y 2 1 2 1 101000 r 74 goat snp6325-scaffold1223-530258 3 107364229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390590 Affx-122967189 AX-123260947 3 11911621 AGACTCCCACTGTCCTTGAGGTTGTAAAGAAACTT[A/G]CATACTAGCAGAGATGGCAGATGTTATACAAATAA R 2 1 2 1 202000 r 74 goat snp6324-scaffold1223-500549 3 107334523 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801876 Affx-122952507 AX-385288783 3 11947863 AATTTTTGATTTAAGATCCTAGAATCCAAAATTTG[A/C]TACAGGAATGTCTCGACCAATATATATTAATTACA M 2 1 2 1 201000 r 74 goat snp6323-scaffold1223-464307 3 107298085 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398293 Affx-122962157 AX-123268648 3 11992886 CCAGATCTATCTGAGACTGAACCTAACGAATTCAA[C/T]AAAGAGATTCAACAGGCATTAACACTTGAATAAGA Y 2 1 2 1 101000 f 74 goat snp6322-scaffold1223-419284 3 107252718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769268 Affx-122947820 AX-385256441 3 12039298 TATAGGCAACCATGAACTGTACACTGATGATTCGT[A/C]TACATTTACAAATGTATGTCATACTGCAACAAAAC M 2 1 2 1 101000 f 74 goat snp6321-scaffold1223-372872 3 107206026 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424953 Affx-122941270 AX-123295299 3 12096695 CTCGCTCTGATGCTCGAATGCTTGTTAGTTATATC[A/G]CTGGCTCTTCTAGAAAACACGGCAGACAATGAAGC R 2 1 2 1 101000 f 74 goat snp6320-scaffold1223-315475 3 107152091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801819 Affx-122973508 AX-385288726 3 12153807 CATTTAGAATAAGAACAAAAAATGGCTTAAGATTT[G/T]TCACCTTCTGGTTAATCCACCTCTAGCAGAACCAA K 2 1 2 1 201000 f 74 goat snp6319-scaffold1223-258363 3 107093838 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783330 Affx-122923597 AX-385270395 3 12186613 GGACAAGTATCTACCCAAAAGTCGTGGTCCATAAA[C/T]AGAAAGACTATTTATTTGCCACACAGCCAAAAGCA Y 2 1 2 1 101000 r 74 goat snp6318-scaffold1223-225557 3 107060767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277927 Affx-1111836163 AX-519551422 3 12207071 CAGATGAATCCACAAACAAGTGCAAACATGTTAGA[A/G]TCAATGGCCATGGAAGACCATGGTCAAAGGCGATG R 2 1 2 1 101000 f 74 goat Random2.2K-300 3 12207071 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420437 Affx-122944900 AX-123290784 3 12322611 TGAGGAACATGGAAGAAGATTTAGAAAGAGAAGGA[C/T]GGCAGCAAAGCTTTGTGATCTACCAAAGATCTAAT Y 2 1 2 1 101000 f 74 goat snp6316-scaffold1223-89559 3 106924756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387616 Affx-122969870 AX-123257974 3 12389090 TTGGGCCCCTTGTTAGGGTAGGGCCACGTGTGTAT[A/G]CATGTTCACATGATCACAAGTCTGCAGTCATTGTG R 2 1 2 1 201000 r 74 goat snp6314-scaffold1223-23080 3 106857019 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418977 Affx-122946071 AX-123289325 3 12413784 AGATTGATCATCTCCTTGAGCAACAGTTAGGGAAC[A/C]CTGGGAACTACGGAGAAGGGAGCTGTTGTGACGAC M 2 1 2 1 101000 f 74 goat snp30036-scaffold3280-19323 3 106829459 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445962 Affx-122925897 AX-123316299 3 12468394 ACAGGTGGGGGAGATGGAGAGGAAGGTGAGGGCTC[A/G]TGAAGAGAACAAAACATAGCTTGGCTCCTGCACAC R 2 1 2 1 101000 r 74 goat snp55040-scaffold841-2879850 3 106688006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408432 Affx-122954456 AX-123278783 3 12498381 CATTTAAACATTCAATGATTCTGTGAGGCAGAAAT[G/T]TCCACTGCACAGGTGGAAAACTAAAACTTACAGAT K 2 1 2 1 201000 f 74 goat snp55039-scaffold841-2849863 3 106657436 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778619 Affx-122942991 AX-385265730 3 12543318 TGTGCACTAGACATGGTATATAGCTATATTATCAC[C/T]AAGTACTCTGCAAACAATCTGTGGGAGAAGTGCCT Y 2 1 2 1 101000 r 74 goat snp55038-scaffold841-2804926 3 106611750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393714 Affx-122965241 AX-123264069 3 12582852 TCAGCAAGCTGCCAAAGAATACAGACAGACCACTA[C/T]GCAAAATTTGGAAAACAATTTGTGACCAAAATGAA Y 2 1 2 1 101000 f 74 goat snp55037-scaffold841-2765392 3 106574152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400228 Affx-122960161 AX-123270583 3 12625178 ATATAATGGCAGTACTGTGGAAGTGCTCTGGTAGC[A/G]CAGAGGAGAGCCAGCCTAAATGTAAACAGCAACTC R 2 1 2 1 201000 r 74 goat snp55036-scaffold841-2723066 3 106534062 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452630 Affx-122920355 AX-123322963 3 12671268 TTGCAGGACAGGTAATTGGCATCCCAAACTAATTG[G/T]TGACAGAGCAAAGCCTTAAATCCAACACTGGATAA K 2 1 2 1 101000 f 74 goat snp55035-scaffold841-2676976 3 106487295 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451461 Affx-122921148 AX-123321794 3 12727653 AGGAGGGAAGCTATAGGATGGGGTGAGAGGTTGTC[A/G]CTTATGATAGACAGTGAGATGGAAAACCCTGTTAA R 2 1 2 1 101000 r 74 goat snp55034-scaffold841-2620591 3 106432372 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443544 Affx-122927764 AX-123313881 3 12756318 CTTACCCAGAGAAGTTGGCAGAAAAGAGGCAGTGA[C/T]GCTGGCTCTCTCATCCTCCTGAGGGGAGGAGTGGC Y 2 1 2 1 101000 f 74 goat snp55033-scaffold841-2591926 3 106403038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429827 Affx-122938176 AX-123300168 3 12801360 CTGTGGGTCAAGTAAGTTAAGGCAAGTGACAAGAA[C/T]GTACAAATGTTACTTGTTATTGTCAACATGGGGGC Y 2 1 2 1 101000 r 74 goat snp55032-scaffold841-2546884 3 106357583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431189 Affx-122937175 AX-123301530 3 12861613 GAGAGAGATTATATGCATTTCAGGCCACATTCCAC[C/T]GCCAAAAAGAAATTATCAGCATGGATAATCAAAGG Y 2 1 2 1 101000 f 74 goat snp55030-scaffold841-2486631 3 106297552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464190566 Affx-1110361225 AX-515665799 3 13006322 GTGGATAAACCTAGAGTCTGTCTTATAAAGTGAAG[C/T]CAGAAAGAGAAAAACAGATATCGGATATTAATGGG Y 2 1 2 1 101000 f 74 goat 3_13006322_AF-PAKI 3 13006322 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422724 Affx-122943260 AX-123293070 3 13047314 CCTGGTTCCTGCACTCCCTTCTCCCAAGGTACTTT[A/C]CACGGTCCTCACTCAGAAGATTCAGGTCTGAATCT M 2 1 2 1 201000 r 74 goat snp55026-scaffold841-2300930 3 106118041 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423595 Affx-122942390 AX-123293941 3 13162187 TACTTCTGAGAGTGAAAGAGGGTGCTGTTAATTGC[C/T]TGAAAGGAAAGGCATGATGGGACACATAGCCACCC Y 2 1 2 1 101000 f 74 goat snp55024-scaffold841-2186057 3 106003511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791774 Affx-122933536 AX-385278765 3 13205200 CCAACTGACCCTCAATTCACCTGTTTTAAAAAGGA[A/G]GTTAATACTTATCCATATCCAGGTGTTTGTTCTGA R 2 1 2 1 101000 f 74 goat snp55023-scaffold841-2143044 3 105960506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797474 Affx-122930695 AX-385284413 3 13240846 CCACTGGGTTCTAACAGGACTAAGATTTGCCATCA[A/G]TTTTATTAGCACCATTAGTATCTGTGTTATTCCTA R 2 1 2 1 101000 f 74 goat snp55022-scaffold841-2107398 3 105925065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376182 Affx-122978828 AX-123246541 3 13341792 TCACAGTTCACAAGGCCAGGGGCTTGATTAGAACA[C/T]GAGTTCCTTCACCTCCTGGCTGTGGGACTTTAGGC Y 2 1 2 1 101000 f 74 goat snp55020-scaffold841-2006452 3 105824803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449493 Affx-122922631 AX-123319828 3 13372807 AAATTAAAGTGGGGAGGGGGCATCCAGGTCCCAGG[A/C]GACCAAGAGAGCTGGGTCAATCAGCCTGCCTTCAG M 2 1 2 1 201000 r 74 goat snp55019-scaffold841-1975437 3 105793163 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391378 Affx-122967275 AX-123261735 3 13417893 ATGGGCAACAGAGGACAGCAAAGCTTCAATGATGG[C/T]TATCTGTATATTTAACTATATGCATAGATTAAACT Y 2 1 2 1 101000 f 74 goat snp55018-scaffold841-1930351 3 105748965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407178 Affx-122954827 AX-123277529 3 13487471 AAGATGGGGCCTTCATGCTCCAGCATCCTCTACCA[A/G]GAACGGAAGTCCTTCCTGCAGCCTCATGGCCTTCC R 2 1 2 1 101000 f 74 goat snp55017-scaffold841-1860773 3 105679897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383683 Affx-122972498 AX-123254041 3 13528976 CTATTACTTAGTCGGAAAGTATTTGTATTTGTTAC[A/G]CATTTCCCACTAAATGGAACGTTCTTGTATTCCTA R 2 1 2 1 101000 r 74 goat snp55016-scaffold841-1819268 3 105639432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384317 Affx-122972272 AX-123254675 3 13571150 ACTCACCAGCGCAGGTAGCAATACATGGCTTCCAC[A/G]TTATAGTACTTGCTGCCTGCAAGGGTGCCCAGCTG R 2 1 2 1 201000 r 74 goat snp55015-scaffold841-1777094 3 105597337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440714 Affx-122929897 AX-123311051 3 13686718 CCTTCAGCTTCTTTGACCCTGCTTGTCACTGCTCA[A/G]CCAGTATTGCTGAATCATCCTCTTCTCCCTGACCC R 2 1 2 1 101000 r 74 goat snp55013-scaffold841-1661526 3 105481913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434161 Affx-122934895 AX-123304502 3 13739435 CGTGGCACTTCGCTGGAGGCACCCCTTCCAAAATC[C/T]CATAGACCATCCAACTTTAGTGTGCGGGTGACCAC Y 2 1 2 1 101000 r 74 goat snp55012-scaffold841-1608809 3 105428930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773365 Affx-122960743 AX-385260507 3 13771428 TGCAAAATGATGCCACAGATTTATGGATACATGCA[C/T]AGGTAATAAAAGAATCAAAATGCCAAACACCAACT Y 2 1 2 1 101000 r 74 goat snp55011-scaffold841-1576816 3 105401309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389166 Affx-122968526 AX-123259524 3 13830541 AGAGGGGCAGAAATGCCCACATCAGCACAGAGACA[C/T]GGAAAGCAGGGAACAGAGGGTCTCGGAGAAAGAGG Y 2 1 2 1 101000 f 74 goat snp55009-scaffold841-1517703 3 105344102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409317 Affx-122953088 AX-123279668 3 13871074 AAGTTTAAACAGGTCCAAGTCAGAGGTGAATGAAC[A/G]CATGCAAACCCACCCTAAGGGATGGGAGGCGGAGG R 2 1 2 1 101000 f 74 goat snp55008-scaffold841-1477170 3 105303954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437576 Affx-122931877 AX-123307914 3 13942972 AGTCCTAAGGGACCTAGCTCTGGATCTTGTATAGA[C/T]CAATTGCCCATCAAAGTGGACTATGGGGAAGAACT Y 2 1 2 1 101000 f 74 goat snp55007-scaffold841-1405272 3 105232245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793578 Affx-122963208 AX-385280553 3 13973726 AACCAGACGAACTGAGATTAGAAAGAACAAAAACT[A/G]CTCTGGCATAAGGCTGTTCAATTCAGAAGGGATTA R 2 1 2 1 101000 f 74 goat snp55006-scaffold841-1374518 3 105201556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382154 Affx-122974039 AX-123252512 3 14031339 TACATCCCAACACAGTGATAGATGCAAAAGAAATA[C/T]AAAACCCTAGACTGCATCAGAGGTGATAAAGTGAT Y 2 1 2 1 101000 f 74 goat snp55005-scaffold841-1316905 3 105143741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779798 Affx-122949549 AX-385266898 3 14063962 GGGAAGGAACTCTTGAGATTTCTTTTGTGATTATA[C/T]TATGCTATTTAATGTAATGGAGAATGGCTGATGCT Y 2 1 2 1 101000 f 74 goat snp55004-scaffold841-1284282 3 105111029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428977 Affx-122938865 AX-123299319 3 14095988 GAATTTAACAATACTGAGCAAAAGGCAGATGCAAA[A/G]GAATACGTACTCCGATTACATAACAGACAGACAGA R 2 1 2 1 101000 r 74 goat snp55003-scaffold841-1252256 3 105078771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766973 Affx-122919255 AX-385254272 3 14134494 AGAAAGAAAAATGGTATAGTGATGAGGAATATTTA[C/T]TCTCAATTCCAATAACCATGTTTAGATCCAAGCCT Y 2 1 2 1 101000 f 74 goat snp55002-scaffold841-1213750 3 105040266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802488 Affx-122932622 AX-385289392 3 14168763 TCTATACAAGGCAAACCCTTTTCATAAAAAAAAGA[C/T]TCTCAAGAAACCATATTACTATACAATCTAATGAC Y 2 1 2 1 101000 f 74 goat snp55001-scaffold841-1179481 3 105006179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402631 Affx-122958397 AX-123272984 3 14203126 TTAACAGATACAGTAGGTGATGGGGAAGGGAGATT[A/G]CTTTCTCCTACTGCGCTAAAAGGGGATTTTGCTGT R 2 1 2 1 101000 f 74 goat snp55000-scaffold841-1145118 3 104971804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785079 Affx-122968551 AX-385272126 3 14379661 TTAATAAAATCAGATGAACAGAATGTTGGCAATTG[C/T]GAAATCTGAGTGACAGTTACCTGAGGGTTTATTAG Y 2 1 2 1 101000 r 74 goat snp54996-scaffold841-968583 3 104795782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453492 Affx-122919828 AX-123323825 3 14412584 AGGCTTCCTTAGCCCCTTTCAAACATACTTCCTCT[A/G]TGATAACACTCAACACCACAGTGTAAATGGGTTAA R 2 1 2 1 201000 r 74 goat snp54995-scaffold841-935660 3 104762986 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399300 Affx-122960535 AX-123269655 3 14450123 GAGACTAGCGAGGGGCCCAAGGTGGTCTGCTATGC[A/G]GAAGGAGAGACTGAGGTGGCTCACTGTGATGATAC R 2 1 2 1 101000 r 74 goat snp54994-scaffold841-898121 3 104725644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427123 Affx-122939658 AX-123297466 3 14501250 GTCTCCTTGTCACACAGGGCCTCAAATTTAGGCTT[C/T]GGATGTTACTTCTAGGTGTGGTTTCAGACAGTCTC Y 2 1 2 1 101000 r 74 goat snp54993-scaffold841-846994 3 104682487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434736 Affx-122933919 AX-123305077 3 14566478 ATGCCTTCCTGTGTCCACTATACGCCCCTCTCACT[A/G]CCAAGATGTGTGCATTCCTATGCAAAGAAAATTAG R 2 1 2 1 101000 r 74 goat snp54992-scaffold841-781766 3 104616958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450128 Affx-122922761 AX-123320463 3 14600266 TTTCCCTCTGAAGAATGGGGAGATTGAACAAATCT[A/G]TGAGGCCTGGTCACTAGAGATCAGTAATAGAGTGG R 2 1 2 1 101000 r 74 goat snp54991-scaffold841-747978 3 104584711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384609 Affx-122972568 AX-123254967 3 14691296 AAGTGGCTGAAGATGAAATCCTCAAAGTCGTCCAC[C/T]GCGTCGTCATCACCTGTTTCTCTCACTGCCACCTC Y 2 1 2 1 101000 f 74 goat snp54990-scaffold841-656948 3 104495297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417433 Affx-122947211 AX-123287781 3 14727299 AGAGTCAGATATGACTGACTGAACTGAACTATAGG[C/T]ATTATTTATTCTAGCCAAAAAGTATATCTCTCACC Y 2 1 2 1 201000 r 74 goat snp54989-scaffold841-620945 3 104459198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786625 Affx-122952682 AX-385273657 3 14757452 CTTTTCTGAATTTTTATAGGAAAGGCTTTCTCATC[A/G]TGAAAGGTTTGGAAAGAATAGAAGACAATAAAGAA R 2 1 2 1 101000 r 74 goat snp54988-scaffold841-590792 3 104428652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450111 Affx-122922774 AX-123320446 3 14789576 CCCAGTGCCTTCAAACTGCTCTTTCCTATTCCCCC[A/G]GGGCTCCCTCCCTCACCTCCTAAAGATCTCCCATC R 2 1 2 1 103000 r 74 goat snp54987-scaffold841-558668 3 104397583 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798940 Affx-122943327 AX-385285870 3 14851116 GAGGCTTTGCCCAGGGGACAGGATATGGCTTTTGA[C/T]GGTGTGGTTTGCTTTTGTGATGAATGAAAGAGTTT Y 2 1 2 1 101000 r 74 goat snp54986-scaffold841-497128 3 104337585 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799089 Affx-122973400 AX-385286019 3 14883292 GTGGTCTGGATGAAGTGAAACAATACCTGGCTGAC[A/G]CTATTGTTATCATCATTAGACTTATAAAATTCTTC R 2 1 2 1 101000 f 74 goat snp54985-scaffold841-464952 3 104305442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431956 Affx-122935965 AX-123302297 3 15024088 CTCCAAAGAGATCTTCACCCTGGAATTTCCTGCTA[C/T]GCTAAGGGGTTTGTTGACTTGTGAAGGAGATGGAG Y 2 1 2 1 101000 f 74 goat snp54982-scaffold841-324156 3 104164256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446206 Affx-122925715 AX-123316542 3 15058576 GAACACTGTAATGCCTTTCAGAAAAAATGTTCCTC[A/G]CCATCACAGGCCTTGAGTGTGTCCCACCAAAACCT R 2 1 2 1 101000 f 74 goat snp54981-scaffold841-289668 3 104129630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429483 Affx-122937877 AX-123299825 3 15089091 CTGGGCCATCAGGGAAGTCCCTTAACCTCTCTTCC[A/G]TTTATCAGGCATCTCTTTCGTGTCATGTCCTGAAC R 2 1 2 1 101000 r 74 goat snp54980-scaffold841-259153 3 104098878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434714 Affx-122933936 AX-123305055 3 15182681 CGATTTTTTTTTTTAAATAAAGTGGAAAAAAGTTT[A/G]TTCTTGGAGTCAGAAAGCTTTAACACTTATTTCTT R 2 1 2 1 101000 r 74 goat snp54977-scaffold841-165563 3 104005456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445865 Affx-122925993 AX-123316202 3 15216847 GTTCTCCGTTTTCCTGGTGCTCAGGTTGGTTGGGC[A/G]AGGTGGTCTCAAGGCCTGGACAGCCTTGTGAAAAA R 2 1 2 1 102000 r 74 goat snp54976-scaffold841-131397 3 103971044 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768666 Affx-122944032 AX-385255844 3 15257792 GATTATTGAAAAAATAAATCGCTCTGCCCAGCAAT[A/G]CTCTGATGCTCGGTAAACCTGCCCTGTCATGTGGT R 2 1 2 1 101000 r 74 goat snp54975-scaffold841-90452 3 103929170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766823 Affx-122976188 AX-385254146 3 15300792 CTCCTTCATTTAGCCTGTGTGTATCACTCTTTCCC[A/G]TAGGTCCAGAATCACCAACACCTCCATCCTTGGAT R 2 1 2 1 101000 f 74 goat snp54974-scaffold841-47452 3 103886063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777434 Affx-122961217 AX-385264555 3 15329551 CACAGTCAAGACTTTGCTGTGAATTATAGTGATCA[C/T]GGATGAACTTTCCTGTGTTTTTTGTTTACTCAAGC Y 2 1 2 1 101000 r 74 goat snp54973-scaffold841-18693 3 103857346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411773 Affx-122951487 AX-123282123 3 15394793 GATGTTATAAAAGAAGTAAATTTCAAGGTCTACCC[A/G]TTCTGAGAATTGCTCCTGTTGCAGGGAAGCTGCAG R 2 1 2 1 101000 r 74 goat snp24560-scaffold2498-586958 3 103792989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427805 Affx-122939757 AX-123298148 3 15460162 CTCTGAGAAGTTACATTATAAGTTTCAGGCATAGC[A/G]TAATATGTCCCCTTAAAGTGATGCTTCAGTTTGTG R 2 1 2 1 101000 r 74 goat snp24559-scaffold2498-521589 3 103730057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396879 Affx-122963236 AX-123267234 3 15514927 CACAAAGTAGATCATACACCTGGTAATAAGGTTCC[C/T]CACACTGTCTCAAAGGGTACACAGAGGTCACATAA Y 2 1 2 1 101000 r 74 goat snp24558-scaffold2498-466824 3 103675384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395160 Affx-122964116 AX-123265515 3 15550782 TTACCATGGTGACTATCACTGCCACTAAACTAAAA[C/T]ACTATATTCTTCTTAAAAGGGAACACAGTACTACC Y 2 1 2 1 101000 f 74 goat snp24557-scaffold2498-430969 3 103640970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392649 Affx-122966446 AX-123263006 3 15626524 CTCAGTTTTACCAAAGCCTTACTGCTCATTCACCC[A/G]TATCAGGCTTAGAGAGAGTAAGCCACTGTCCATAA R 2 1 2 1 101000 r 74 goat snp24556-scaffold2498-355227 3 103565769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464192323 Affx-1110362116 AX-515667538 3 15639658 GCAGAAGCAAGATACCCAGCGGATACAGGAGAGGT[C/T]GGGCAGGAGCACCTACGTGTTTGCGAAAGAGGTCA Y 2 1 2 1 202000 f 74 goat GoatD01.001881 3 15639658 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420963 Affx-122944585 AX-123291310 3 15657299 CAAAATAGCTTTAAAAAAGTTAATCACCTTAAAAG[C/T]TTGAAATGATGAAACTGCTGCTTATCTTAGAACTA Y 2 1 2 1 101000 r 74 goat snp24555-scaffold2498-324452 3 103535122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803266 Affx-122973211 AX-385290115 3 15755044 AGATAAAGGAACAGTAATAACTCCCATTTAATTGA[A/C]TACTCCAAAAGCCCAAGAAATAATGAACATTGAAT M 2 1 2 1 101000 r 74 goat snp24553-scaffold2498-226707 3 103437396 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407944 Affx-122954360 AX-123278295 3 15836282 AAATGAGGACACTATCATCTACCACACAGATCAAA[C/T]GAGATAACACAGGTAGAGACCTAGTGAGCACTCAG Y 2 1 2 1 101000 f 74 goat snp24552-scaffold2498-145469 3 103356062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417623 Affx-122946863 AX-123287971 3 15881880 CCAGCACAAGCCCTAGCCTCCTGGTGTTGCAGGAA[G/T]CAGGACCCCTTCCAGGGCCTAAAAGTGGGCTCTTG K 2 1 2 1 201000 f 74 goat snp24551-scaffold2498-99871 3 103316119 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387351 Affx-122970482 AX-123257709 3 15941147 TAAGTTTCAGAGGCTGAGCTATCTATAATCTTAAG[C/T]TCCTGGAACACAAATACCTCTTATCTCTTGCAAGG Y 2 1 2 1 101000 r 74 goat snp24550-scaffold2498-40604 3 103256760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272187 Affx-1111833377 AX-519545939 3 15974845 AGCAGCCTGGACATGACGTTTGCCAAGCAGGAATC[A/G]CACAGCAAGCTGGACACATATAGATATCCCAAATG R 2 1 2 1 201000 f 74 goat 3_15974845_AF-PAKI 3 15974845 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394388 Affx-122964627 AX-123264743 3 15981349 GATTGTCAGCCTGGCGACCGTGACTCTTGCTGATG[A/G]TCTCCTCCCTGGCTGGCTTAGGGATGGACAGTGCC R 2 1 2 1 101000 f 74 goat snp24549-scaffold2498-402 3 103216182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392009 Affx-122966489 AX-123262366 3 15994564 TTGAGTCTGGGGTGCTCAAGGGATGACCCAAGCTA[C/T]GGTCAGAACAGAACCAGAATTCTGAGGAAGTGCAC Y 2 1 2 1 201000 f 74 goat snp26817-scaffold2813-264011 3 103119670 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412391 Affx-122951454 AX-123282740 3 16043609 ACTCAGGGCACCTGGAAGAGTGCACTTTGTGTCCC[A/G]TATCACATAATACGGGCTCAGTCACACAGCCGTGC R 2 1 2 1 101000 r 74 goat snp26816-scaffold2813-214966 3 103070496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430541 Affx-122937195 AX-123300882 3 16076652 AATTCTCAGCGTGCACTCTGGATGCAGAGACAGGG[C/T]TCATCTGTGCATTTGGCAAATAAGGCAAGTGTCCA Y 2 1 2 1 101000 r 74 goat snp26815-scaffold2813-181923 3 103037580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417978 Affx-122946684 AX-123288326 3 16122788 CTACAATTAAAAGAGGGTCATACACACATTCATAA[C/T]GCTAAAGATTAGCCTTTCTGGTCATCTTCTTTTCT Y 2 1 2 1 201000 f 74 goat snp26814-scaffold2813-135787 3 102991921 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442613 Affx-122928473 AX-123312950 3 16158320 CTGGCTGAAGTGCTGTGGTGGGGCAGTCATGAGTG[A/G]TGGGTCTCTGAGGTTTTCTAATCCACAGGGTTATC R 2 1 2 1 101000 r 74 goat snp26813-scaffold2813-100255 3 102956199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396661 Affx-122962851 AX-123267016 3 16203807 TCTTAAACTCTTCCTTATCCCCAGCCCACAGGAGT[A/G]CCCGTCTGTACAGCGCTCCCGGTTCCATCAAGGCT R 2 1 2 1 201000 r 74 goat snp26812-scaffold2813-54768 3 102910341 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786974 Affx-122919930 AX-385274003 3 16234620 AACCTTTCTGTAACGTTTTTTCACTATGTATAAAA[C/T]GGAGGCAGTGGCTTTTCTCGTCTCATAGGATTTTA Y 2 1 2 1 102000 r 74 goat snp26811-scaffold2813-23955 3 102879224 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782064 Affx-122964358 AX-385269142 3 16288425 TTTCTGTAGAGATGATGTTACAGGTGTTTGCACAC[A/G]TCCAAACTCATATTTAGTTATGCATATTAAATATG R 2 1 2 1 101000 f 74 goat snp50663-scaffold73-1092297 NW_017189676.1 23826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424815 Affx-122941375 AX-123295161 3 16319077 CACAACAGAAATGTATGCATATGACACTAAAGCAC[A/G]TGTATGAAGATGCTCATAGCAGCAGAATTTGTAAT R 2 1 2 1 101000 r 74 goat snp50662-scaffold73-1061645 3 102808791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384186 Affx-122972409 AX-123254544 3 16458054 CCCTGACTCTGAGAACCATCTTCTTCCAGCTTCTG[C/T]GCCTGCAAAGACATGAAATGAACACAATAGCAACA Y 2 1 2 1 101000 f 74 goat snp50660-scaffold73-922668 3 102667984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422737 Affx-122943252 AX-123293083 3 16495115 CAGAGTCGGACATGACTGAGCACGCATACACGGTG[C/T]GCTATGGGACCTTTTGCAGACATCTTACTTCTTTG Y 2 1 2 1 101000 r 74 goat snp50659-scaffold73-885607 3 102630509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386292 Affx-122970931 AX-123256650 3 16555503 GCTGACAAACCTGTGCTGCGTGTGTACAGGTAAGC[A/G]TCCTCTGAGAACTGGAGTGGGGCCTTCCACAGAGG R 2 1 2 1 101000 f 74 goat snp50658-scaffold73-825219 3 102570237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394505 Affx-122964546 AX-123264860 3 16607125 AGAGCTATGAGGAACATGAACAAAAGATCAAGATC[A/G]TATGACACACAGCTCACAGTTCACTGCTTACAAAC R 2 1 2 1 101000 f 74 goat snp50657-scaffold73-773597 3 102518711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779490 Affx-122948119 AX-385266593 3 16649086 GATTCAATCTGAAGGGTTCTTAGAGTAGCAGCTCT[A/G]TAAAAGATGTTGGTGCACTGACTGAGGTGTTATAC R 2 1 2 1 201000 r 74 goat snp50656-scaffold73-731636 3 102476964 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783740 Affx-122937410 AX-385270796 3 16697698 CGTTTCATATTGGCAGTCAAGGATGAATCAACAAA[C/T]GAAAAATCCTTTGCTTACAACTCACAGTTGCTGCT Y 2 1 2 1 101000 r 74 goat snp50655-scaffold73-683024 3 102428514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787825 Affx-122954292 AX-385274848 3 16734614 AGAAAATACAAGCATAAATAAGTTATTTTAAGAAA[C/T]AACTTAAAATTCTATCCTCCACAGAAAATCATTTC Y 2 1 2 1 303000 f 74 goat snp50654-scaffold73-646108 3 102393561 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419431 Affx-122945510 AX-123289779 3 16824934 TAGCTCAAGATGGAAACTGAAAGGAAATAGTTTCT[A/G]TCAAACACGTACTGTGTGTAAGCAGTGTGCTGGCC R 2 1 2 1 101000 r 74 goat snp50652-scaffold73-555788 3 102301703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785932 Affx-122960684 AX-385272969 3 16873032 GAAATGTCAGAGTGTTTTTGGTGGAGAGGGTCTTA[C/T]AGTTATGTGAATAGAGTTACAAAACAGCTTTCTCT Y 2 1 2 1 101000 f 74 goat snp50651-scaffold73-507690 3 102253288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404239 Affx-122957643 AX-123274591 3 16943228 ATAGACCATGCAAATAATTTCTCCCAGTCTGTTAT[C/T]TGTCAGTTAACTTTGTCATGACATCTTTCACTGAA Y 2 1 2 1 201000 r 74 goat snp50649-scaffold73-437494 3 102178741 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414760 Affx-122949249 AX-123285109 3 16984128 TGGTATCCCCAGTGGTGGTGAGCATACCAGGGAAG[C/T]GATGTGGAACCCAGGCTCTTTCACTACTTCAGGGT Y 2 1 2 1 201000 r 74 goat snp50648-scaffold73-396594 3 102133965 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791284 Affx-122955565 AX-385278278 3 17016512 GGGTCTCAGTCATGTTATAATGCATTATGAGTATT[A/G]TCAGCATTGGGTAAACATCTCAAAGAGGTGCAAAT R 2 1 2 1 101000 r 74 goat snp50647-scaffold73-364210 3 102101194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451270 Affx-122921317 AX-123321603 3 17052405 AGAGTTAATACCACAACTGACCAGAGTAGGTTGGA[C/T]GGAGAAAAAAGGAAGCAGCAAAGGCCTTTGTACAA Y 2 1 2 1 101000 f 74 goat snp50646-scaffold73-328317 3 102065213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780170 Affx-122926320 AX-385267267 3 17092367 AAGTCACATAGGCTTACAACTTATACAATATGATC[A/G]TCAGGGATTGGGAAGGAGTGGTAGCAACTATTGGG R 2 1 2 1 202000 r 74 goat snp50645-scaffold73-288355 3 102024761 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408100 Affx-122954712 AX-123278451 3 17126094 TTTAATTTTTTAAGACTTTGCGTGTATTCGATAAC[A/G]TATAGTAGTTGTCTTTCTGAGTCTCACATGTCACT R 2 1 2 1 101000 f 74 goat snp50644-scaffold73-254628 3 101991367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424242 Affx-122942471 AX-123294588 3 17159042 TCCATCCATCATTCATTCAAAAGCCTTAATTATAT[A/G]CTTGTGATGTGCAAAGAACTGGGGATACAAAGGAA R 2 1 2 1 201000 f 74 goat snp50643-scaffold73-221680 3 101957547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771241 Affx-122945301 AX-385258399 3 17201583 AACTCTAAATGTCTATGGTTTTAGGTTACAGTTTC[G/T]ATTTGGAAAATCAGGGTTGGATATGCCTTGTCTTG K 2 1 2 1 101000 r 74 goat snp50642-scaffold73-179139 3 101917553 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406362 Affx-122955422 AX-123276714 3 17234818 CGTCTTTTGCAGACAACGCCCCAGGTGTATAATGG[A/G]CTGATTCATGGCCAGCCAAACCCCATTCCACCTGT R 2 1 2 1 201000 r 74 goat snp50641-scaffold73-145904 3 101883745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423098 Affx-122942923 AX-123293444 3 17283348 TGGGGAGGCGACTCAGAGCCTTCTCTGGTGTCATC[A/C]AGTCCGTGGAAGAGAGACTTTCAAGACGGAGAGGG M 2 1 2 1 201000 r 74 goat snp50640-scaffold73-97374 3 101835914 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376596 Affx-122979062 AX-123246955 3 17333233 CCTTGCAGATTCTGTGGAAAGAGCTCTGCCTCATG[C/T]CAGATGCTCAAGGACATGTAGGAAAAAGCATTTCT Y 2 1 2 1 101000 r 74 goat snp50639-scaffold73-47489 3 101785868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408877 Affx-122953986 AX-123279228 3 17377285 GTATATTAATATATAAAATGAGATCTTGGGGACTC[C/T]GTCCTCTTCTGTAAAAAGGGGGGTAAGAGTATGAC Y 2 1 2 1 201000 f 74 goat snp50638-scaffold73-3437 3 101741423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403493 Affx-122957696 AX-123273846 3 17420803 TAGGAAGAAGAGAAATAAGAAGGGAGGGAGGAAAC[A/G]CACACCAGGGAACCTGCTTAAGATGCTGTACTTGG R 2 1 2 1 201000 r 74 goat snp9904-scaffold1353-39982 3 101309344 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274121 Affx-1111834018 AX-519547724 3 17448212 ATCCTGGAGCTGTTCCGCTCGGCCGCCTACCGCCA[A/G]CCCATCCTCATTGCCGTGGTGCTGCAGCTGTCCCA R 2 1 2 1 202000 r 74 goat GoatD01.014314 3 17448212 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427218 Affx-122939579 AX-123297561 3 17454971 TGCTGGTATGTTCACCTTCTGATGTGGGCTCACTT[A/G]CTAGTTCGTATTTGGTAACTTCTCACTGTGTCCTT R 2 1 2 1 101000 r 74 goat snp9905-scaffold1353-74150 3 101274883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429016 Affx-122938330 AX-123299358 3 17483756 AGATGGCCTTGGACAACAACATCCTCCATCCTACA[C/T]GAGCCGTCAGAATTCAACACCCCATGTACAATTTT Y 2 1 2 1 201000 r 74 goat snp9906-scaffold1353-102935 3 101245273 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394803 Affx-122964810 AX-123265158 3 17565596 AGACCACCTCCCCCCAGTAAAATTCCTCTCAGGTT[C/T]TGAATATCAGCTATGATCAGTTTAGTCAGGCCAGT Y 2 1 2 1 101000 r 74 goat snp9908-scaffold1353-184775 3 101163811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394556 Affx-122964458 AX-123264911 3 17667374 CAAGCACTGGATTTGGAGGTACAAGAGGGAGTGAC[A/C]CAAAGCTACTGGCCTGGGCAAAGGATGAAACCAGA M 2 1 2 1 101000 f 74 goat snp9910-scaffold1353-286553 3 101067737 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407195 Affx-122954816 AX-123277546 3 17725368 ATGAGACATTAGGTAAATAATTCAATCTCAATCTT[A/G]TTTAACTTCAATTTCTTAACCCAAGTGGGGCTAAT R 2 1 2 1 102000 r 74 goat snp9911-scaffold1353-344547 3 101009226 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389830 Affx-122968175 AX-123260187 3 17779786 TGTCTTCCCCCAAACAACAGACAAGCAAACCCTGA[G/T]GCCTCAGGGTAAATATACTTGCCTTCCTGAGGTTT K 2 1 2 1 201000 r 74 goat snp9912-scaffold1353-398965 3 100955778 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378587 Affx-122976586 AX-123248946 3 17837501 CAAGCCATTTGGAGGTGAGCAGAAGGGAGGGAAGA[C/T]GAAGAGATATTTCTGAAAAAGGTGGACAATGAAAA Y 2 1 2 1 101000 r 74 goat snp9913-scaffold1353-456680 3 100897621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414581 Affx-122949372 AX-123284930 3 17892232 TTGCCCCCATTACACACACTCACTTCATTCTTGCC[A/G]TTTTCATTAGTTCAACATTTGGATCAAAAGGCTCA R 2 1 2 1 201000 r 74 goat snp9914-scaffold1353-511411 3 100842823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764438 Affx-986696826 AX-385252131 3 17937879 TTTGGAGAACACCTTGGAGGTCCCTCTCAGATTTA[A/C]ATTGTACCTATCTTTTCCTCAGCAAGCAAGTGTAC M 2 1 2 1 600010 r 74 goat 3_17937879 3 17937879 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 468278083 Affx-1111836164 AX-519551573 3 17987172 TCTCTCTGTATAGTTTGGGTAAGTTATATCACCTC[A/G]GTTTTTTCGGCATTCTGTGGTCGTAACAGAATCTA R 2 1 2 1 101000 r 74 goat Random2.2K-301 3 17987172 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397155 Affx-122962435 AX-123267510 3 18010329 AAGGTTAGACCAGTGTATGGAAGACAGAGACTCTG[A/C]GTGAAGACTTTTTCCCAGGCCTCCCTCTGACTCCA M 2 1 2 1 201000 f 74 goat snp9916-scaffold1353-629508 3 100723896 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445409 Affx-122925380 AX-123315746 3 18046498 ATGTTCTTTTTTGCCTTTGCTCCCTGGGTGGTCTT[A/G]TCCTCCTTTGCATTTCTGCTGTTTGCTTGTGCCTT R 2 1 2 1 101000 f 74 goat snp9917-scaffold1353-665677 3 100687387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384749 Affx-122972035 AX-123255107 3 18119660 AAGGTTAAAACCAGTTTCTACTCCTAAGGCCTGCT[A/G]CATAGCATGCATGTATGCTAAGTCACTTCAGTTGT R 2 1 2 1 101000 f 74 goat snp17385-scaffold180-1209310 3 100613549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788399 Affx-122923578 AX-385275417 3 18149809 ACCAGTTTTCAGATCAAAACTCCAGAAGTATTGGA[A/G]AGATGCCTATTTACAGGGCTCCCTCAGAAGAGCCC R 2 1 2 1 101000 r 74 goat snp17384-scaffold180-1179161 3 100582878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777035 Affx-122930104 AX-385264159 3 18284158 GCATTATTAAGTGGAAAACTGTTCTGATTTTAGAC[A/G]TAACTGTACTCTTAAACAAAGTATATAATCTGGCC R 2 1 2 1 101000 r 74 goat snp17381-scaffold180-1044812 3 100448021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435443 Affx-122933474 AX-123305783 3 18315726 GCCGAGGTCATCTTCGAGAAATGTAGTCAGATCTC[G/T]CTGTCAGAATCTACCACTGCCTCCCTGTCCAAGAA K 2 1 2 1 101000 f 74 goat snp17380-scaffold180-1013244 3 100416335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413381 Affx-122950132 AX-123283730 3 18392023 TGACTGGTTGGTTGTTCACTCTTAAGCAAGAGCTA[C/T]AACCTCAGAGTAGCAAAGCTACTTGTTAGTGCTAG Y 2 1 2 1 101000 f 74 goat snp17378-scaffold180-936947 3 100339710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418603 Affx-122946357 AX-123288951 3 18428123 CTTTGGCCCAGCTGGGATGCTTACCCCCAACCACT[A/G]AACTGAGGCAGCCAGCATGATGAGGCCGTGTCAGA R 2 1 2 1 201000 r 74 goat snp17377-scaffold180-900847 3 100303564 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399666 Affx-122960509 AX-123270021 3 18473971 AGTCTCCTGCCAACCAACAGACATGGCCATCATTA[C/T]ATGACATGTGTGTTGATAGGGGAGGAGGCATTTTT Y 2 1 2 1 103000 f 74 goat snp17376-scaffold180-854999 3 100256454 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451445 Affx-122921160 AX-123321778 3 18555824 TGCATGTATTGAGGGGCTGTTGGGTGCCACATACT[A/G]TGCTAAGAATTCAAAGACACAACATAATCTCTGCC R 2 1 2 1 101000 r 74 goat snp17374-scaffold180-773146 3 100174635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800599 Affx-122925385 AX-385287518 3 18586293 TGAGTAAAGGGAAGAGACTTTGGGGCCTAACAGAA[C/T]AGAGAATCACAGGAAATCATTCACTCTAGTAATCT Y 2 1 2 1 101000 r 74 goat snp17373-scaffold180-742677 3 100143884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407989 Affx-122954324 AX-123278340 3 18622242 CATGCATTATATGATTACATCTTCACAACAATCCT[A/G]TAAGGGAGGTTCTACTATTACCCACATGTTAAAGA R 2 1 2 1 101000 r 74 goat snp17372-scaffold180-706728 3 100107771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272020 Affx-1111833378 AX-519545786 3 18636994 GGCTGCCGGAGGTACCAGTTAGGGGCCCGAGGGCC[A/G]TGGTGAGCTGTTTCAAAGGAGCAGAGCGCAGCGGC R 2 1 2 1 102000 r 74 goat 3_18636994_AF-PAKI 3 18636994 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800293 Affx-122939527 AX-385287216 3 18650946 TAATGAATGATGGAGTAGGACAATACTGAGAGAGA[A/G]TAGAGAATATATTCATGGTTCTAGGACTGCGAGAA R 2 1 2 1 101000 r 74 goat snp17371-scaffold180-678024 3 100083865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436116 Affx-122932657 AX-123306455 3 18724451 CCCAAACACTGCCCTTCTCTCTGTGATACCGGGAC[A/G]ATGTCTCCCCAGTGCATTTTTGCCTTCAGCAGCTG R 2 1 2 1 101000 r 74 goat snp17369-scaffold180-604519 3 100010259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397226 Affx-122962379 AX-123267581 3 18777292 ACTTGACAGTAGATACAGAGGTGCAACTGAAACAT[C/T]CTCAGATATTATCCCAGTTTGTTTTTTTTTTTAAG Y 2 1 2 1 101000 f 74 goat snp17368-scaffold180-551678 3 99956996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437806 Affx-122931678 AX-123308144 3 18855200 ATTCACTGAGCACCCTTTCTGGATGTCATATGTAT[A/C]TATGTTACCTGTAATCCTAACATCAGTTCTGTAAG M 2 1 2 1 101000 r 74 goat snp17367-scaffold180-473770 3 99877977 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447707 Affx-122924610 AX-123318043 3 18899920 AAACTGCCTCACCTCCTACCTCTCCACATCACTAG[G/T]GCTCAAACATTGCCCCCTTGTGGTACAGCAGCATG K 2 1 2 1 201000 r 74 goat snp17366-scaffold180-429050 3 99833120 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401098 Affx-122959414 AX-123271451 3 18966716 CAACAGGGTCACCACTTCCCCTCTTGACAACAGCA[C/T]AGATGATGAATACTGAAAGAACATAATTCTACAAT Y 2 1 2 1 201000 r 74 goat snp17365-scaffold180-362254 3 99766411 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400023 Affx-122960792 AX-123270378 3 18999026 ATAAAAATTGATACAATTGATTTTTAAAAATCAAA[G/T]CACTGAAGCCTAATTGATAAAGGTTAGAAACCATC K 2 1 2 1 101000 r 74 goat snp17364-scaffold180-329944 3 99734083 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413025 Affx-122950999 AX-123283374 3 19035500 CTAATGCCTAGGCTCTGGCAGGAAGAAGGAGAGGG[A/C]TAGTGGAATACTCTACACCCGAGTGGGGACCTGGA M 2 1 2 1 201000 r 74 goat snp17363-scaffold180-293470 3 99697929 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439119 Affx-122931098 AX-123309456 3 19123479 TCAGTGTTTTGAGTCTTTATCATTTTATTCATATC[G/T]ATGTTCAGGAATCTTTAATGGCTTAATTTTACTTC K 2 1 2 1 101000 r 74 goat snp17361-scaffold180-205491 3 99609500 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783912 Affx-122969489 AX-385270967 3 19169651 GTGCTACTTTACCTGACTGGAATGCCATTCAAGTC[A/G]GTCAGCTTCATCTCCACTTCACAGGTGACACACCC R 2 1 2 1 201000 r 74 goat snp17360-scaffold180-159319 3 99562497 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779437 Affx-122964899 AX-385266540 3 19209089 GATGATCCCAAATACGAAAATCCAAGTCATTAATA[C/T]ATAAAAAGGAAGTCTTACAGACCTAAAATTATGCT Y 2 1 2 1 101000 r 74 goat snp17359-scaffold180-119881 3 99522928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443085 Affx-122928115 AX-123313422 3 19239428 GAGAATGATGAGAGGGATCTTGAGAGATGGGACTA[C/T]TGGGGATTGCCAAGGAAAGGATCCTAAGATTCTAA Y 2 1 2 1 101000 f 74 goat snp17358-scaffold180-89542 3 99492564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417521 Affx-122946941 AX-123287869 3 19271082 TCCTCCAACACTCATGAAGTAACAGTGAAGTAAGA[C/T]AGGAAGCTGCAGGATTGAGAAGAACCATGGGTCTT Y 2 1 2 1 201000 f 74 goat snp17357-scaffold180-57888 3 99461379 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378471 Affx-122976674 AX-123248830 3 19314358 GACAATGTGTCAGTTTTGCTTTCACACTTGTAAAT[A/G]TAATGCTGGTGCTAAAGGGAACTATTGATTGATGG R 2 1 2 1 101000 f 74 goat snp17356-scaffold180-14612 3 99409068 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400587 Affx-122960402 AX-123270942 3 19342516 ACAATAGAGTAATAATCCTGTCAATGTTCTCAATA[G/T]ACCACTTTATCAAAAGCAAGTTTATAACAGAAGAA K 2 1 2 1 101000 f 74 goat snp23402-scaffold2345-165737 3 99388787 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381935 Affx-122974128 AX-123252293 3 19401074 CATAGAGGAGAATCCGGCTTTCTCAGGCTGAGTCT[C/T]CGGCTCATTCACCGTCCTCTCAGAAGGCCCCTTCT Y 2 1 2 1 101000 f 74 goat snp23401-scaffold2345-107179 3 99329745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429817 Affx-122938185 AX-123300158 3 19445161 CAAGTGGGGTGGGTTATGGCAAAATGTGTAGCTGC[A/G]TTTATCTCCCCCCAAACCCAGAAGTTCTACTACCG R 2 1 2 1 101000 r 74 goat snp23400-scaffold2345-63092 3 99285246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425103 Affx-122941232 AX-123295449 3 19480032 ATATATATGTGTGTATATATATGGAGAGAGAGATC[G/T]AAAAGCTACAAGAGTCCTAGGAAGTTACATTCCCT K 2 1 2 1 101000 r 74 goat snp23399-scaffold2345-28221 3 99250573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446483 Affx-122925056 AX-123316819 3 19531719 CTCCTCTTGAAAATCTAATGAGAGATATAAGCCCC[A/G]TCCTCAGAGAATGCTCAAGTATGTCTGTGCTTTTC R 2 1 2 1 101000 r 74 goat snp50889-scaffold737-1255532 3 99171914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416760 Affx-122948183 AX-123287108 3 19564394 AATAAGAATGGACCCTGAGTGGTATCTCAGGACTC[A/G]AAGCCTGTGGGTTTCACAGTTACATCCCCATGTTC R 2 1 2 1 101000 f 74 goat snp50888-scaffold737-1222857 3 99139226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452016 Affx-122920911 AX-123322349 3 19652308 GCTAGTCCCTCTTCCCCTTCCCTGGCAACACCAAC[A/C]AAAAGGCCAAGATAGGTCTTCAGCTATGGAGGAGG M 2 1 2 1 101000 r 74 goat snp50886-scaffold737-1134943 3 99051256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785291 Affx-122925632 AX-385272336 3 19686388 AGGTGAAAGAGAGGGCTTAGTAACTCCAGATGGCA[C/T]AGGTATTTACTTTGCCAGTTCTGAAGGAAAGTATA Y 2 1 2 1 101000 f 74 goat snp50885-scaffold737-1100863 3 99017096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800241 Affx-122945250 AX-385287164 3 19715723 GTTTCATAAAGGCAGGGTTCAGATCAATTTTGTTT[A/G]CCATTATACCCCTAAAACAGTCAGGTATTCAATAA R 2 1 2 1 101000 f 74 goat snp50884-scaffold737-1071528 3 98987342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414369 Affx-122950006 AX-123284718 3 19765405 AACAGTACAGACATTAGAAATGTTAGTTGCCTTTG[A/C]TTCCACAAGGCTCTGAGAGGCTTGGGTTTGCCCTT M 2 1 2 1 101000 f 74 goat snp50883-scaffold737-1021846 3 98938370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418980 Affx-122946069 AX-123289328 3 19797853 CAGTGTCCATGTCTTTGTCTGCTCTGCTCTACGAG[A/G]GAGATAAGACTTGTCCCACACACGTGGTAGACCCA R 2 1 2 1 101000 r 74 goat snp50882-scaffold737-989398 3 98908213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439924 Affx-122930011 AX-123310261 3 19845983 TATTTGTCCCTACCCCATCAACTTGCCTAAATTCT[A/G]TTCATACTATAAAGCCAGAGCTCAAGTGCTACCTT R 2 1 2 1 201000 r 74 goat snp50881-scaffold737-941268 3 98859862 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434112 Affx-122934935 AX-123304453 3 19878438 ATAAAACAAGGATTGGAAAATGTTGAATTTTGCAA[G/T]CAGAAGTAAATTCCTGACCATATTATGATAATGGC K 2 1 2 1 101000 r 74 goat snp50880-scaffold737-908813 3 98827409 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387830 Affx-122969666 AX-123258188 3 19927863 GAGTAATAAGCAGGCTTCAGACAGCAGAGGGCCCC[A/G]TTCACCTTGTTAAAGGGCACAAGCTTCATCCTGCA R 2 1 2 1 101000 r 74 goat snp50879-scaffold737-859388 3 98778194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789670 Affx-122926375 AX-385276679 3 19990805 CTTCTTATTTTACTTTTCATTCTACGAACACTCCA[C/T]TGAAGCAGCTTCCATAACAAGCTCACATTGTATAG Y 2 1 2 1 101000 r 74 goat snp50878-scaffold737-796446 3 98715490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789786 Affx-122970884 AX-385276794 3 20019783 GAAGTAAAGCCCACTGTTACTATATACCCTAAGCT[A/G]TGAGCCTTCATCTCATCAGTAAGAAAGGGCATGAT R 2 1 2 1 101000 r 74 goat snp50877-scaffold737-767468 3 98686329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404394 Affx-122956791 AX-123274746 3 20060829 CACCACCACCAAGGCCGATAGGATCTGAAGTGATA[C/T]GTAAAAGGGATCTAATATACCCATTACCCTCTCCT Y 2 1 2 1 201000 r 74 goat snp50876-scaffold737-726422 3 98645285 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375475 Affx-122979149 AX-123245834 3 20100621 ATAATTCCATGTCTGGGTTTAGAAAAACAAGCACA[C/T]GGCAAGTGATACTGCTCCTCATCCAGGCAGGGGCA Y 2 1 2 1 101000 f 74 goat snp50875-scaffold737-686630 3 98604333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775463 Affx-122955979 AX-385262594 3 20219799 TACTAATTCTTACGTTTCCTGAGATGTGTTTCTGG[C/T]GATTATTCCAATTATCTTTAAGAATGTGTGTGTGT Y 2 1 2 1 102000 f 74 goat snp50873-scaffold737-567452 3 98484513 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430474 Affx-122937250 AX-123300815 3 20275954 GAAAAGTCAGTGGCAAGATAGACGATATAAAAGAA[C/T]AGTAAAGAGCAAGAGCTTTGGATCAAACAGAACCA Y 2 1 2 1 201000 f 74 goat snp50872-scaffold737-511297 3 98428183 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273682 Affx-1111833738 AX-519547294 3 20311446 TGTAGAAGTTCTGTATATTAAATGTACATTTGCTT[A/G]CTATTTTTCTCTTCAATAGAGAATTACCTCCAAGC R 2 1 2 1 201000 r 74 goat GoatD01.003271 3 20311446 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402689 Affx-122958352 AX-123273042 3 20346916 ATGGAAGCCAGAGATACTGTCCTTCCCCTGAGCTT[A/C]CATGGGGCCCTAGAAATTTCTCTATCATTGAAATT M 2 1 2 1 202000 r 74 goat snp50870-scaffold737-440335 3 98357680 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388446 Affx-122969258 AX-123258804 3 20393402 ATTTGCCACTAAAGCATGGTTCCTGGACCAGCAGC[A/G]TGGCATCACCTAGGAGCTTGTTGGAAATGTAGATT R 2 1 2 1 103000 f 74 goat snp50869-scaffold737-393849 3 98310296 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774409 Affx-122962425 AX-385261545 3 20423457 TTCACTTTTGTAATTTAGCTATATACAAATGATGC[A/G]TTACTTTTCTCTTTGTGGGATCTCCTTCCATGAAA R 2 1 2 1 101000 r 74 goat snp50868-scaffold737-363794 3 98281805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783036 Affx-122942542 AX-385270104 3 20471456 TTCAGAAAATAGTACTGTAATTAAAGAGCTAAACA[C/T]GGCTGGTGTTCAAGAAAGTCCATTGAATTTTCTAG Y 2 1 2 1 101000 r 74 goat snp50867-scaffold737-315795 3 98232773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399039 Affx-122960919 AX-123269394 3 20502168 GTCTCTTAACCTTGAAAATCCTTCCTGCTCTCCTC[A/G]TTTCTCACCACTTATCCCAGGACAAACACTGGTGG R 2 1 2 1 201000 r 74 goat snp50866-scaffold737-285083 3 98201775 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425730 Affx-122940754 AX-123296076 3 20555915 TGTTAAGATGGTGTGTGAACCACTCAACTATAATA[C/T]AAAGCTTAAAGGAAAATAGTAAAAGTAACTATAGC Y 2 1 2 1 101000 f 74 goat snp50865-scaffold737-231336 3 98148042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453440 Affx-122919868 AX-123323773 3 20594146 TTTATAATGTTTACTCAGTATGACCCCTGAGAACA[C/T]AGTTGTGTTCTTTTGACGTATTTGGCAAGGTTGTA Y 2 1 2 1 102000 r 74 goat snp50864-scaffold737-193105 3 98109507 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413102 Affx-122950943 AX-123283451 3 20649710 CCTACGCATCTAGTGCGGCATGCCATGCTCTTGTG[C/T]ACAAAAACAAGCAGTGGAAGACCTTCCCTTTGTGA Y 2 1 2 1 201000 r 74 goat snp50863-scaffold737-137541 3 98052775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377713 Affx-122977398 AX-123248072 3 20682672 ATCTGATCCCTGAATCTATATGTCAGCTCCTTTTT[A/C]GTACTTCAAATGGCACATTTTCAAATCCCTTAACC M 2 1 2 1 101000 f 74 goat snp50862-scaffold737-104579 3 98019711 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394285 Affx-122964707 AX-123264640 3 20769475 ACTTTAACTCAGAACATGTATTATTATTTCTTGAC[C/T]ATCTTTGTCTCTGCATTCCCTCACTCTAATTAGTT Y 2 1 2 1 101000 r 74 goat snp50860-scaffold737-17776 3 97932548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430072 Affx-122937546 AX-123300413 3 20830408 CAATGACCCACAGAGCACCCTCCTTACCCAGGCCA[C/T]GAGGCAGATCTCAGCTCCTCGGCCAGCTTCCCTTC Y 2 1 2 1 101000 f 74 goat snp47051-scaffold659-43058 3 97691794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395826 Affx-122963633 AX-123266181 3 20859358 GTTTAGAAAAGAATAAAGAATACATCTACGGAGTA[C/T]GTTTTATGTTAGGAAAAGGGGACACAGGCATGTTA Y 2 1 2 1 101000 r 74 goat snp47052-scaffold659-72008 3 97662792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404716 Affx-122957252 AX-123275068 3 20918215 GTCACAAAGCCACACACTGTATGACTCCCTTTATA[C/T]GAAATGTCCAGAGCAGACAAACCCAGAAGAATAAA Y 2 1 2 1 303000 r 74 goat snp47053-scaffold659-130865 3 97604126 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767737 Affx-122952810 AX-385254968 3 20950412 AGAATAAATGAATGTCATCTAGGCTTAGGGAGAGA[C/T]AGTGAGGAAGAGAAAAGTCTAAGCTAAAACTCAAA Y 2 1 2 1 101000 f 74 goat snp47054-scaffold659-163062 3 97571938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781587 Affx-122973456 AX-385268671 3 21002782 GCCAGAGCTGGAGTCTAGGAACGTTTTAGGTGCAA[C/T]CTGAGAGCAAATGCAGCCCTAACAGAGTTATAGGA Y 2 1 2 1 101000 r 74 goat snp47055-scaffold659-215432 3 97518859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417339 Affx-122947734 AX-123287687 3 21066665 GGGAAGAAGGTGCCAACTGTGTCTAGACCCTACTC[A/C]TTTATTGAGTTTGGTAAGTTTTTGTGCCTCACTTC M 2 1 2 1 101000 r 74 goat snp47056-scaffold659-279315 3 97454325 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790372 Affx-122966112 AX-385277375 3 21104160 TAAAGACAGCAGATTAAGTACATGCATTGTGTTCC[A/G]CTCCCTCGTAGACCTTAACCAAAAGTTAACATTTG R 2 1 2 1 101000 f 74 goat snp47057-scaffold659-316810 3 97416267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394235 Affx-122964881 AX-123264590 3 21151975 ACCTGTTCGAATGCCTGAGGACATGAATACCACAG[C/T]AAAGCTCCAAGTCAGGTTAAAAGGCTTGGTTCTTT Y 2 1 2 1 101000 f 74 goat snp47058-scaffold659-364625 3 97368452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272192 Affx-1111833379 AX-519545944 3 21155934 GCTAAAAGGAGAGGCAATCTGAGGCAAGAATCAGG[A/G]CTTGGTCTGGAACAAGGCCAGGAGTCTGAGGTTAG R 2 1 2 1 101000 f 74 goat 3_21155934_AF-PAKI 3 21155934 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444421 Affx-122926572 AX-123314758 3 21193605 TCTTAGAGTTCAGTTATATGGTTTTATATTGTGAT[A/G]TATACATTGTACACATTCTAAAAGTTCTTTTGGTA R 2 1 2 1 101000 r 74 goat snp47059-scaffold659-406255 3 97326485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421690 Affx-122944412 AX-123292037 3 21228626 AGCTGAATACATGGGCCAGGCTTGGCTAATGCTGC[A/G]TTTCTGAGAAGTGGCCTTGACCATGAGAACTCAAT R 2 1 2 1 101000 r 74 goat snp47060-scaffold659-441276 3 97290881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453875 Affx-122919518 AX-123324208 3 21263106 ACAGTAGCTTCTGCTAAGGAATGAAGAAAGCAAGG[C/T]GTGATTGATGTCTGCCCACTCACCAGACTGCAGTG Y 2 1 2 1 101000 f 74 goat snp47061-scaffold659-475756 3 97256492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447935 Affx-122923788 AX-123318271 3 21294093 CTCACTAAGTACTTAAAGCACAGTATACTACCCAG[A/C]ATCACTGCTAATGCCTTTTTTCACCTGTGATCTTA M 2 1 2 1 101000 f 74 goat snp47062-scaffold659-506743 3 97225533 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423424 Affx-122942614 AX-123293770 3 21364720 AGACATGACTGAGCACACACAAAGAAGTTGTGGGA[C/T]ACTCATGATAAAGAGTGTCTCCTTGGACTATTTGG Y 2 1 2 1 303000 r 74 goat snp47063-scaffold659-577370 3 97154728 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435065 Affx-122933735 AX-123305405 3 21398118 AAGGACACTCTAAAAAGTAAAGCAACAAATAACAG[A/G]TTGGCCGAATTGACTTCCAATTTATAAGTAGCTCC R 2 1 2 1 101000 r 74 goat snp47064-scaffold659-610768 3 97121334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392580 Affx-122966068 AX-123262937 3 21438099 TGTGTGATTAAAGCAAACGTCATAAATTCCTGAGG[C/T]AAGAAGATATAAGAACTTCAGAAACTGCCTGGGAT Y 2 1 2 1 101000 f 74 goat snp47065-scaffold659-650749 3 97080527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401668 Affx-122959569 AX-123272021 3 21482315 ATATGAGAACATTTCTTTGGGGAGTACATCATAAA[C/T]AACATAATAGTGTATAAACAGAGTGAAGGGGGAAA Y 2 1 2 1 101000 f 74 goat snp47066-scaffold659-694965 3 97036174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409476 Affx-122954061 AX-123279827 3 21511827 GGGAAGAGGTAGGAGGCAGCATGTGGCTTCCCAGT[A/G]CAAAATATAGATAGCCACCCAAAACAGGATACATA R 2 1 2 1 101000 r 74 goat snp47067-scaffold659-724477 3 97006774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434749 Affx-122933909 AX-123305090 3 21549939 GTTAAACACCTTGCCCAGCATCACTCAGCCAGAAG[C/T]AGCAGAATGAAGTCAAAGCCAAGGAAGGCATCCCC Y 2 1 2 1 101000 r 74 goat snp47068-scaffold659-762589 3 96968636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396776 Affx-122962765 AX-123267131 3 21585507 GTCCATTCGATAGTGAAGAAATATTTACAGAGAGT[A/G]TATTTGCCTGGCACATAGTATGTGCTCAATAAACA R 2 1 2 1 101000 f 74 goat snp47069-scaffold659-798157 3 96932930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769907 Affx-122922403 AX-385257076 3 21614550 ATATAGACTTATTTTAGAAGATTAGTGGACCAAAT[A/G]TCTTTCTAATCTTTGGCATACATAGGTGATGGAAA R 2 1 2 1 101000 r 74 goat snp47070-scaffold659-827200 3 96903960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787242 Affx-122973594 AX-385274268 3 21676808 TGAAAAACGGGTGGTAAACGTTTTATCAATACTAG[G/T]CTTCTGGAGCCTGGCAATGGCCTTATATGCTGAGC K 2 1 2 1 202000 r 74 goat snp47071-scaffold659-889458 3 96846692 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796862 Affx-122977010 AX-385283805 3 21730682 TCTTTTGTATATAATAGATAACTCATGGGAACCGA[C/T]GGAGTGACTTTGCAGCAAAGCCTTCCTTTGCTAGG Y 2 1 2 1 201000 f 74 goat snp47072-scaffold659-943332 3 96792816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448389 Affx-122924094 AX-123318725 3 21762825 GATGGCCTCAATCCAGACCCTGCCCCCTTAACCAC[C/T]CAGTTAACGTGAACGTGACCCACAGCTCCAACCAC Y 2 1 2 1 101000 r 74 goat snp47073-scaffold659-975475 3 96760620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769722 Affx-122927094 AX-385256892 3 21795243 TTTTGTTTTACTGAAACTAATGTGAAAATAAGAAG[A/G]TTTCTTTCTACAAAGATGGCAAGTTATACAAGGAA R 2 1 2 1 101000 r 74 goat snp47074-scaffold659-1007893 3 96727164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795126 Affx-122965845 AX-385282084 3 21852378 AATTGCTTTCACAAGATATAGTAGCATACATCATG[A/C]TTTCACAAGATATAGTATGATAAATTCTCCAGTCA M 2 1 2 1 101000 f 74 goat snp47075-scaffold659-1065028 3 96669569 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770859 Affx-122962347 AX-385258023 3 21892625 CCTAACACTCCTATGAAGGTTTAATCAGTACCTCT[A/G]CTCCAATATCTCGCCACCTTTATTTGGTGAGTAAT R 2 1 2 1 101000 f 74 goat snp47076-scaffold659-1105275 3 96629629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409034 Affx-122953863 AX-123279385 3 21930822 CATTTCCTCTGCTTGTTCCTCTTTCTTCAGTCACC[C/T]TTTCCAAAAGGCCATTCCTCAAGATTCCATCAGTG Y 2 1 2 1 201000 r 74 goat snp47077-scaffold659-1143472 3 96590965 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443130 Affx-122928083 AX-123313467 3 21975667 ATGACTAGAATGCTTTCTTCAAAAATAACAGAGAT[A/G]CAAAGTGAGAAGATGGGCGAGATTAAAGTAATTAG R 2 1 2 1 101000 r 74 goat snp47078-scaffold659-1188317 3 96545958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778625 Affx-122953605 AX-385265736 3 22017615 GTAACATACTAGGCAAGTTACTGAAGCTCTTTGAA[C/T]ACCCTTTATAATGTCTATAATAAGGATATTTAAAT Y 2 1 2 1 101000 f 74 goat snp47079-scaffold659-1230265 3 96503671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390143 Affx-122967988 AX-123260500 3 22060696 AGAAATACTTCAAAGTATATTCTGCCTGACTACAA[G/T]AGTAGTTGGCCTAAGAATTCCCTGACAGTCCAGTG K 2 1 2 1 201000 f 74 goat snp47080-scaffold659-1273346 3 96460100 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439523 Affx-122930124 AX-123309860 3 22099700 TGTCCAGAATGCTGTTTCCTCCATCCCCCAGGATA[C/T]GGATAGGGGTTGAGGACCTAATATCGAACTTTACC Y 2 1 2 1 101000 r 74 goat snp47081-scaffold659-1312350 3 96421723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414244 Affx-122949629 AX-123284593 3 22129501 CAGTGACCTTGAAGATGGGGGAGCTGGTGGCAAAG[A/G]TGAAGGCACAAGTGTGGTGAAGAGCTTCAGGTGTT R 2 1 2 1 101000 r 74 goat snp47082-scaffold659-1342151 3 96392020 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788110 Affx-122961370 AX-385275130 3 22168302 TTCCACTTTTCTGTACTTGGAAGAGACCAACATTA[G/T]CTTCTGTTTAGTCCAAGGTATAAAATGATATGCTT K 2 1 2 1 101000 f 74 goat snp47083-scaffold659-1380952 3 96353204 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451476 Affx-122921137 AX-123321809 3 22198443 AAAGCCATTTCCTGGCAAGAGAGAGGACTGTGAGA[C/T]GAGGTATTAGAGTGCTGAAAATTAACAGGAGGAAA Y 2 1 2 1 201000 r 74 goat snp47084-scaffold659-1411093 3 96323103 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395235 Affx-122964476 AX-123265590 3 22227863 TCAGCTGCTCTTAACTTCTATGAATTGCCCTCCTC[C/T]CCTCTGAAGCCCCAGGCTCCTAGTACATCCCTTAG Y 2 1 2 1 101000 f 74 goat snp47085-scaffold659-1440513 3 96293682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420792 Affx-122944692 AX-123291139 3 22319616 TTACTCATTCTGATTAAGCCTGTTCTCCATATTTA[C/T]GGCCAGTATCTGATGTGTAAATTAGAGACTTTGTT Y 2 1 2 1 101000 f 74 goat snp47087-scaffold659-1532266 3 96201078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787579 Affx-122919816 AX-385274603 3 22351015 ACTCTGTAGCAAGACTGATTTGCGTAAGTAAAATA[G/T]CTTTAGGCTTCTCCTCTCTTTAGCTTAAGTTTCTT K 2 1 2 1 101000 r 74 goat snp47088-scaffold659-1563665 3 96169571 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419166 Affx-122945733 AX-123289514 3 22381404 GAATGGATAGTTAGTGCCAATAACAGCAATGTGGT[A/G]TTGTTTTATCCCTTCTGTAACCTTGCAGATAAAGA R 2 1 2 1 101000 r 74 goat snp47089-scaffold659-1594054 3 96139216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412688 Affx-122950762 AX-123283037 3 22418850 CTGAGGAAAATGCTGTTTTAGTACCATCACCTGGG[C/T]TCCTCTTTCTAGTCACTTGTATAAACATGTGCTAC Y 2 1 2 1 600000 r 74 goat snp47090-scaffold659-1631500 3 22418850 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772043 Affx-122950762 AX-385259198 3 22418850 CTGAGGAAAATGCTGTTTTAGTACCATCACCTGGG[C/T]TCCTCTTTCTAGTCACTTGTATAAACATGTGCTAC Y 2 1 2 1 101000 f 74 goat snp47090-scaffold659-1631500 3 96101707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449486 Affx-122922635 AX-123319821 3 22450724 TAAGTATTCAAGAATTGTTTGTGTTCCTTCCCAGG[C/T]GAGCCCCTCCCTCCTGATGGATACTTTCATTCACA Y 2 1 2 1 201000 f 74 goat snp47091-scaffold659-1663374 3 96069301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436186 Affx-122932606 AX-123306525 3 22489522 TTCAATATTTCAGTGTCTAAAAAAGAATATAATTA[A/C]ACTTCTTTCTGATGTGGCCTGTAATTCTCTTTGTA M 2 1 2 1 101000 r 74 goat snp47092-scaffold659-1702172 3 96031091 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433805 Affx-122935178 AX-123304146 3 22534993 AATGGAATGAGGATGGGCCAAAACTCCAAGGGGGC[A/G]CTCAGAAGATGAGCTTAAACTTGTAGATGAAATAT R 2 1 2 1 201000 r 74 goat snp47093-scaffold659-1747643 3 95985020 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424026 Affx-122942086 AX-123294372 3 22577891 AGCTTGCTACTTGGGGCTCCAGGAACGAATCAAGC[A/G]ACAGCTCATAAAAAAAGAGGGTTTTATGATTTTCC R 2 1 2 1 102000 r 74 goat snp47094-scaffold659-1790541 3 95941565 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766177 Affx-122957457 AX-385253579 3 22610490 TAACATCTGGTCTTATAATCTGATACTCTGGGTGC[C/T]TCACTTATGTCTGAATAGCTAGTATGCCTCACCAG Y 2 1 2 1 101000 f 74 goat snp47095-scaffold659-1823140 3 95908052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396959 Affx-122963172 AX-123267314 3 22642105 AACTTCATTATTCCTTTTCTTTGGTGCATACTCTG[C/T]GGCACATGTAAGCACATCTGACTCTCAATACATCA Y 2 1 2 1 101000 r 74 goat snp47096-scaffold659-1854755 3 95876256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421498 Affx-122943906 AX-123291845 3 22723414 AAGGATGGTGGTATGGCTATTAAACCATGTCTATT[A/G]AAGTCTAGAGCACTTAAAATTCACCTGCTTGCTTG R 2 1 2 1 101000 f 74 goat snp47097-scaffold659-1936064 3 95794259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429188 Affx-122937956 AX-123299530 3 22780229 AAGTAAAGCAAACATAATTCTGTTGTGTTTCCATC[A/G]CTGGCCTAATTCTGAAGGACATTCAATGAAATAGA R 2 1 2 1 101000 r 74 goat snp47098-scaffold659-1992879 3 95736908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382708 Affx-122973628 AX-123253066 3 22823066 AAAGGAAAGAAAAGAAGGAAGATAGTCTTCTCCCT[A/G]CCTTTCCTCCTCTCCTACGGCTCTGGCATTCGGCT R 2 1 2 1 103000 r 74 goat snp47099-scaffold659-2035716 3 95693458 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409892 Affx-122952901 AX-123280243 3 22857327 GTAGCTCACTTAAAGTTCTTGAGCTAATAGATGGT[A/G]GAGGCAGAGTTTGAACCAAATTCTAACTTTTGAGT R 2 1 2 1 101000 f 74 goat snp47100-scaffold659-2069977 3 95659096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398567 Affx-122961510 AX-123268922 3 22889721 GATAGGCAGCATATCCCTGTGATGAGGAACTGCTG[C/T]ATAGACAGTGGTTTTCTCCTGCTCCTTACCACTTT Y 2 1 2 1 101000 r 74 goat snp47101-scaffold659-2102371 3 95626935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391715 Affx-122967505 AX-123262072 3 22933035 ACTCCATAAATGCTGTGAGCAGACACTGCTCTAAG[C/T]GCTTTATGTGGATTAATTTTAACCCCCAGAACAAC Y 2 1 2 1 101000 f 74 goat snp47102-scaffold659-2145685 3 95583712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802889 Affx-122959248 AX-385289787 3 22972661 GTCATTCATAACTGGAGGAATGATGAAAACAAATG[C/T]AGTCATTCTTCCTATTATACCACAACCACCCACCT Y 2 1 2 1 101000 f 74 goat snp47103-scaffold659-2185311 3 95543985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390556 Affx-122967214 AX-123260913 3 23027986 AATTTTTTAAGGCTAACAGTATAAAATTATTTCTG[C/T]ACTGTTATTTCTTTGAAATGTGAACAAAGTAATAA Y 2 1 2 1 303000 r 74 goat snp47104-scaffold659-2240636 3 95491610 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414644 Affx-122949324 AX-123284993 3 23121413 CCAAAAAAAGCAAGAGAATTAGAATTTGAATTAAG[A/G]TGGTAGGAATGAATATGAGAGGCATGATATGAAAG R 2 1 2 1 101000 r 74 goat snp47106-scaffold659-2334063 3 95397604 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441336 Affx-122929428 AX-123311673 3 23172950 AAAATGTTGACATTTGGCTTTTAAGTTAGTGTCAA[C/T]TTGCATTTAGAACATAGCAAACATATAGGAAGGAA Y 2 1 2 1 101000 r 74 goat snp47107-scaffold659-2385600 3 95345743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431570 Affx-122936189 AX-123301911 3 23203011 ATCTCTCACAATATAGAGATTATGACTGAGCATGA[C/T]GTCCTGTTCTTACCTGTGGAAGCAAATATCCTTTA Y 2 1 2 1 101000 f 74 goat snp47108-scaffold659-2415661 3 95315608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785046 Affx-122922984 AX-385272093 3 23242604 CGTAACCAGCAGGTTCTTTTCTCGTAGAAACAATG[A/C]TTGTGTGATGGCGTCCTTGTGACCCTTTAGACGGT M 2 1 2 1 101000 f 74 goat snp47109-scaffold659-2455254 3 95275957 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443276 Affx-122927482 AX-123313613 3 23276841 AGGCACCATTATTTTGTAGAAAAGTCTCTGAAAAA[C/T]GACTTAAGACTACTGGTTTTTGGTCCCAGTTCTAC Y 2 1 2 1 101000 r 74 goat snp47110-scaffold659-2489491 3 95241824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785791 Affx-122942908 AX-385272831 3 23310407 AAAGAATCAGCTACTACCACAGAGAATGTCAGTTA[C/T]ACAGTAATATGAGTAACACGGTGTTGTTGGAACTC Y 2 1 2 1 101000 f 74 goat snp47111-scaffold659-2523057 3 95207934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388374 Affx-122969327 AX-123258732 3 23340370 TTCCCTAAGGACACCCTGTGAATGATGGTGGGGTC[A/G]ATGGGAATTCAGGCTCTCGGGCTCCTCAGGCAGCT R 2 1 2 1 101000 f 74 goat snp47112-scaffold659-2553020 3 95177895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397092 Affx-122962709 AX-123267447 3 23371002 CCTTCTCAGGTTGGCCTTGAGAACAATAGTACAGG[A/G]CTGTTAAGCCACTGATGACCACCTGCCCTCAAGGG R 2 1 2 1 101000 f 74 goat snp47113-scaffold659-2583652 3 95147501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787389 Affx-122943352 AX-385274414 3 23468125 ATTCTCTCTCTCCATCTATCAGAGCAGCCTAGTAT[A/C]TGATTTCCAGCCTTGTGCCCATCTAAGTCTTGTAG M 2 1 2 1 101000 f 74 goat snp47114-scaffold659-2680775 3 95051123 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386358 Affx-122970857 AX-123256716 3 23516687 CTAAAGCCCATGAAAATGATTGTCCATCCCAATGC[C/T]GTACCAAGGGTGAAAATCTTCAAATATCTCATTTT Y 2 1 2 1 101000 f 74 goat snp47115-scaffold659-2729337 3 95002983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442783 Affx-122927731 AX-123313120 3 23552991 CACCTCCCACATGCAGTCAGCAGGAACCCTGATCT[A/G]AAGGTGTCAGTGATGTAGTTTGGTTTCAGAGCTGA R 2 1 2 1 101000 r 74 goat snp47116-scaffold659-2765641 3 94966933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430171 Affx-122937367 AX-123300512 3 23593613 GAGGGCTCAGTGTGGCCTGTCCCTTCATCTGGCCA[G/T]CATTCCATGGGCCCTTGGTCACATGGATGACAGGG K 2 1 2 1 202000 f 74 goat snp47117-scaffold659-2806263 3 94926825 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444773 Affx-122926354 AX-123315110 3 23635074 ATTGATCTGTCATTTACGGATATGAGATGGTCAAC[C/T]AAGATGGAATTGCAGCTATTACATATTAAAAATGA Y 2 1 2 1 101000 f 74 goat snp47118-scaffold659-2847724 3 94885280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801832 Affx-122952778 AX-385288739 3 23664213 TCAAAATTTCAAACTGCTTGGTTAAAATCTACCAA[C/T]TGAAGCCCTGGGTTGTCCTAGAGAACATCACAGAG Y 2 1 2 1 101000 r 74 goat snp47119-scaffold659-2876863 3 94855248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793084 Affx-122962025 AX-385280062 3 23696307 TGAAATGTGAAAGTCAGAACTGTACAGTAATATGA[C/T]GAATCCTTTCATAACGCTGGTATTCTATGAATTTT Y 2 1 2 1 101000 r 74 goat snp47120-scaffold659-2908957 3 94823167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393837 Affx-122965160 AX-123264192 3 23782705 CACCTTCTGAACTTAGATGGTTGTTTCCTTTGAAA[C/T]GTTGTGCTGTACTTAGTCACTCAATCATGTGCGAC Y 2 1 2 1 101000 f 74 goat snp47122-scaffold659-2995355 3 94735771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785263 Affx-122929746 AX-385272308 3 23848965 TAGGATCAGAACCTGACAGGACAAAAACTAATTGC[A/G]TCATTCTCGCAATAGCAATATTAATCAGTATATTA R 2 1 2 1 101000 f 74 goat snp47124-scaffold659-3061615 3 94668956 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272194 Affx-1111833380 AX-519545946 3 23867537 ACTGCATAGCTTGAGAAGTCCAGCACAAAATGAAA[A/C]TGTAGGCCTCTTACTCAAAAATTAGTATGTTCCCC M 2 1 2 1 101000 f 74 goat 3_23867537_AF-PAKI 3 23867537 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413369 Affx-122950140 AX-123283718 3 23911840 ACACCAGGGATTCAAAAGAAAAGTTTCCAATACGT[A/G]TACACTCAAAAGAATGACGGGGCCAATAAAAATAC R 2 1 2 1 101000 f 74 goat snp47125-scaffold659-3124490 3 94605780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443132 Affx-122928081 AX-123313469 3 23948002 AATAAGTTAATAGACTATTGAAATAGTCCAACAGC[G/T]AACTGAGAGCTTGAACTAGAGCAGGGGCAATGGGG K 2 1 2 1 201000 f 74 goat snp47126-scaffold659-3160652 3 94568902 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409720 Affx-122953033 AX-123280071 3 23979986 CTAGCTAAAAACTTAGATCCCAACTGACCACAATC[G/T]ACCCAAACATCAAGGATCTAAGAGACCAAAGTTTC K 2 1 2 1 101000 f 74 goat snp47127-scaffold659-3192636 3 94536756 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393423 Affx-122965874 AX-123263779 3 24027875 TGCACTCATATTACACAGCTAAACTGCATACTACC[G/T]TCTTTCATATTTTTTCTCCCAAATCTCCCACATGA K 2 1 2 1 101000 f 74 goat snp47128-scaffold659-3240525 3 94488568 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375762 Affx-122978599 AX-123246121 3 24065455 GGGGAGGCAGAGTGGGCAGAGTAGTAGGGAGATGT[A/G]CTCTTAGAATTTCTTGGCCCCTGGGATAGGATGTG R 2 1 2 1 101000 r 74 goat snp47129-scaffold659-3278105 3 94451014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782018 Affx-122954501 AX-385269097 3 24101130 TTTTAGAAGGGCAGATAAGAAATGACTTACACATC[A/G]CTTCTCTCCACATTCCACTGACTTAGAACTGCGTA R 2 1 2 1 101000 r 74 goat snp47130-scaffold659-3313780 3 94415356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788416 Affx-122927297 AX-385275434 3 24144179 CAAAAAAACGGAGATGAATATTTTGGCAATCCTAA[C/T]GTAAAAAGGGAATGACAAAATCCTGCAGCTGAGAG Y 2 1 2 1 102000 r 74 goat snp47131-scaffold659-3356829 3 94372586 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396472 Affx-122962962 AX-123266827 3 24185398 GGACTGTGCTAGATGCTTCATATGCGTTTGTGTTA[C/T]GACCCTCATTTTATGAGAAAGCTGAGTAACCAGGG Y 2 1 2 1 101000 f 74 goat snp47132-scaffold659-3398048 3 94331545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782816 Affx-122953543 AX-385269888 3 24229062 TGCTGGGTTTCCTTTGTGTTCCTAATAGGAAACCA[A/G]ACACACCACAAAGTATACCCTTTCTCACTAACCCC R 2 1 2 1 101000 f 74 goat snp47133-scaffold659-3441712 3 94288511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415707 Affx-122948524 AX-123286056 3 24265011 TGGCTGGTACATACTGTCATTCGGGGGCTAGGAGA[C/T]GGAGGGTGGAAGTGAGGGTAAAACCATCTGCTGGG Y 2 1 2 1 101000 f 74 goat snp47134-scaffold659-3477661 3 94252299 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438016 Affx-122931570 AX-123308354 3 24316059 ACACTTTACTGAATGGCTTTTCTTTCCCTGTGGCA[G/T]AAGCCTTCGGGGTCCCTGCTTCACTATGTTTTTGG K 2 1 2 1 101000 f 74 goat snp47135-scaffold659-3528709 3 94201075 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407622 Affx-122954633 AX-123277973 3 24376226 TTCAGTTTCTCCTTCTGAAAATGGGAAAAATAATC[A/G]TGTCCCACAGAGATGCTGGGAGAATTATATAAAAT R 2 1 2 1 101000 r 74 goat snp47136-scaffold659-3588876 3 94140531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398050 Affx-122961754 AX-123268405 3 24411782 TTCATTATTTGCACTCATTCACATTTATTTCAGAC[A/G]CACATATGATTTGGTAGTACTCTCTTAGTTCTAAG R 2 1 2 1 101000 r 74 goat snp47137-scaffold659-3624432 3 94104790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792589 Affx-122966434 AX-385279570 3 24447361 TTGTTAAAGTGCAATTGAGAGTGCTTTTTCTTTCA[A/C]ATGGTGTGTAAATAATGGTGCCGGTTAAAATCAAT M 2 1 2 1 101000 f 74 goat snp47138-scaffold659-3660011 3 94068980 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429991 Affx-122938044 AX-123300332 3 24506258 AACAGACAAGAGCAGAGCTGCTTGGGAACACTCAA[C/T]GAAAAAGCAACTGTAACAGAAGAGACATGTTACAT Y 2 1 2 1 101000 f 74 goat snp47139-scaffold659-3718908 3 94009660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277932 Affx-1111836165 AX-519551427 3 24514908 ATGAACTCCATCATCACACATGTTATTTCCTTCTA[A/G]GAGGAAACTTGTTAATTTATTTCTTTGGAGATATT R 2 1 2 1 101000 f 74 goat Random2.2K-303 3 24514908 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800226 Affx-122919721 AX-385287149 3 24536748 ATTTCAAATTTCACAAGATTGTACCAGTTAACTGT[G/T]GCTCGTCAGAAACCCTAAAGCTTAGTGGCTGGACC K 2 1 2 1 101000 r 74 goat snp47140-scaffold659-3749398 3 93979076 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385879 Affx-122971599 AX-123256237 3 24629878 GGGAGTGATGCCCTGTAAGTCATTCTGCTTAAGGC[A/G]AGAGGAGACTGTTTTTTCCATTGATGCCGAAGTTG R 2 1 2 1 101000 r 74 goat snp47142-scaffold659-3842528 3 93887784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386731 Affx-122970148 AX-123257089 3 24696956 TAGTGGTTGTACCAATTTACCTTCCCACCAACAGT[A/G]CATGAGTTTTCTTTTCACTTCAGTCTTGCAACTCT R 2 1 2 1 101000 r 74 goat snp47143-scaffold659-3909606 3 93818159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405669 Affx-122956565 AX-123276021 3 24734393 CTCCAAATATAGTCACAGCAGGAGTTAGGGTTTCA[A/G]CGTGACTTTCAGGGGATGGATCATTCACACTGCTT R 2 1 2 1 101000 f 74 goat snp47144-scaffold659-3947043 3 93780301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437017 Affx-122933126 AX-123307355 3 24763345 CCCATAGCCTCTCCTAAAAATTAACCAGGTAGTCA[C/T]TCAGTACCTGTTATTATTTGTTATGCTAAGCCTTC Y 2 1 2 1 101000 f 74 goat snp47145-scaffold659-3975995 3 93751703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775874 Affx-122936739 AX-385263005 3 24793389 TATCTGGTATGGCTTTTTGCACAAACCAGCTCTTA[C/T]GAAATAGGAATGCCAAAGGTCAGGCACTCAGAATC Y 2 1 2 1 101000 r 74 goat snp47146-scaffold659-4006039 3 93721759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432307 Affx-122936307 AX-123302648 3 24829767 GGAACGTTTAAGGCACAGATCTCTGGACTCCACTC[A/G]GACCTACCCAAACGCATCTCTGTGGGGTGGCTTAG R 2 1 2 1 101000 f 74 goat snp47147-scaffold659-4042417 3 93685570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431779 Affx-122936708 AX-123302120 3 24885573 CTCTAACCTTTCTCTGAAGTCAGAAGAAATAATAA[C/T]GGTCACGTGTATATGGGGCTCCTTCCACCCCCTCC Y 2 1 2 1 201000 f 74 goat snp47148-scaffold659-4098223 3 93629355 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444933 Affx-122926700 AX-123315270 3 24929562 TGAAACTGAAGTTTCTGGGCCTGTTGGGGGCTGCA[C/T]TACTGTTGTCCCTTTTTATTTATGCTTGAAAGAAT Y 2 1 2 1 201000 r 74 goat snp47149-scaffold659-4142212 3 93585150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424737 Affx-122941663 AX-123295083 3 24961211 GTATAGACAACCAATCACCCGACTCATCCCAAAGT[A/G]GCCTGTTCCCACACCGGGGAGGTGTCCTAATATCC R 2 1 2 1 101000 f 74 goat snp47150-scaffold659-4173861 3 93553329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772978 Affx-122944845 AX-385260122 3 25028419 GCAAGGATGAATGCAAAGCCCAGATTAGTGATCAA[C/T]AGCATTTACTACTGTAATTATTTATTACCACCATA Y 2 1 2 1 201000 r 74 goat snp47151-scaffold659-4241069 3 93486187 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403675 Affx-122957504 AX-123274027 3 25061122 TGCTGGTAAAGAACCAAAAGAGGGAGGCATTTACA[A/G]TGTTTCACGTCTACTGACATAACGTTACCTTCTTT R 2 1 2 1 101000 f 74 goat snp23724-scaffold2397-22213 3 93453320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388489 Affx-122969228 AX-123258847 3 25091536 TAGCTCTCTTAGCATCAGTTTCCCCAACTTTTGCT[A/G]TTGGTGCCTGTGGCAGAAGCCTGGGAGTTTATAGG R 2 1 2 1 201000 f 74 goat snp23725-scaffold2397-52627 3 93423085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410492 Affx-122952194 AX-123280842 3 25127978 GCCTTGATACCACAGAAGACAGGTCTCCCTACCCA[C/T]GCCTACCCCCCAAGGCAGGGTCAATCAAGGCAGAT Y 2 1 2 1 101000 f 74 goat snp23726-scaffold2397-89069 3 93386783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782597 Affx-122959572 AX-385269671 3 25168211 ACAAGCAAAAGTACATGCAAATCCTTTGCTTTCTA[C/T]ACAAATGGAGTTTCATATTGTTCAGCAGTTTGGTT Y 2 1 2 1 101000 f 74 goat snp23727-scaffold2397-129302 3 93346132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424705 Affx-122941688 AX-123295051 3 25225286 AAGAGAGATCTGGGGTCCAAGGTTAGAAGAAATGG[A/G]TTTTATAGTCCTTCCTCTCCTCCTACCGGGAGGCT R 2 1 2 1 101000 f 74 goat snp23728-scaffold2397-186377 3 93288682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384785 Affx-122972008 AX-123255143 3 25245278 ATAGAACATGCCTGTCCCTTCCTTGGGACTGCATA[C/T]GTGGTTCATCAAAACCACTCTTCCCTTAAATAACT Y 2 1 2 1 201000 r 74 goat snp47869-scaffold675-11017 3 93269368 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402533 Affx-122958474 AX-123272886 3 25275282 TGAGTACAAACCCACTGTGCTGCCCAGTAAACTTG[C/T]AAATTCTGTACCTCTGACATGCTTTCTATAACTGC Y 2 1 2 1 201000 r 74 goat snp47870-scaffold675-41021 3 93239480 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438160 Affx-122931460 AX-123308498 3 25335685 CATATGTTTTGGACTTTTGTTTTTGAATCACTTTT[A/C]GTTTCTTCTAGAAGTGTTACTGTTTTATCCACTTT M 2 1 2 1 101000 r 74 goat snp47872-scaffold675-101424 3 93178738 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403922 Affx-122957474 AX-123274274 3 25382309 TTGGCATGTCTTGGGCTACTGAAGGGCTTGGTCAT[A/G]CTTTCTGGTCTCTGCTTTCCTCCTTCAGAGGCATT R 2 1 2 1 101000 r 74 goat snp47873-scaffold675-148048 3 93132294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378072 Affx-122977175 AX-123248431 3 25431366 AAGGGACTTCTACTTGAACAGTCTCCTCAGCCCTC[A/G]CCCTGCTGCCAGGCTGCTGGTGTGGTAGTCATCCC R 2 1 2 1 101000 f 74 goat snp47874-scaffold675-197105 3 93079276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778799 Affx-122963533 AX-385265908 3 25466890 TGGTTTACCCTTCACTTTTGTATATAAGCAATTAT[A/G]TATATGCAAAATATGGATAGGTAGGTACATCTTTC R 2 1 2 1 201000 f 74 goat snp47875-scaffold675-232629 3 93041757 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793266 Affx-122938368 AX-385280244 3 25525676 ATGTCCTTTCTACCTTAGTGAATTAAGAGAATTAA[A/C]TGAATAAAAATTCCCCATAAAATTTTAAGAAGCTG M 2 1 2 1 101000 r 74 goat snp47876-scaffold675-291415 3 92983106 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387328 Affx-122970499 AX-123257686 3 25556409 CATGAAAGTGAGGTCAGGCTATAATTAAAAACTCA[A/C]TGGGCTCTTCACTAAAAACTCTGAAAGACACTGAG M 2 1 2 1 101000 f 74 goat snp47877-scaffold675-322148 3 92952348 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410898 Affx-122952070 AX-123281248 3 25599660 ACCCCTTTTAAAAAGTATAGTCGATTGGCTCCAAG[A/G]ACTGAAACAGAAATGCACTGTGTTCAACTGTGTGA R 2 1 2 1 101000 f 74 goat snp47878-scaffold675-365399 3 92910642 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378197 Affx-122976939 AX-123248556 3 25688805 GACTGACCCTCCTCTAAATAAGAGAGGGTTGGGAA[C/T]GCGGTACAGAGATTCAGAGATGACCACGGTGAATC Y 2 1 2 1 202000 r 74 goat snp47880-scaffold675-454544 3 92822823 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411372 Affx-122952240 AX-123281722 3 25754158 TAGAAATTGGCAAGCCTTATTAAGGTACAGGCTTG[A/G]CCAAAATTGTCCTCCACTGTTTGAAGAGTGGGCTT R 2 1 2 1 101000 r 74 goat snp47882-scaffold675-519897 3 92758128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427213 Affx-122939583 AX-123297556 3 25804796 TAGATCAGCATTCTGAAAAGACTTGCATGCCTCTC[A/G]CCCTCATCCTGATTAGTCATGGCACTTAAAAATCC R 2 1 2 1 101000 f 74 goat snp47883-scaffold675-570535 3 92707466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427782 Affx-122939777 AX-123298125 3 25864085 ACTACTAAATTAATAGAAAATGCCAAATAAGTAGC[A/G]CATCAGTGCTATTGCAGTTTCAGCCACAGCAATTA R 2 1 2 1 101000 r 74 goat snp47884-scaffold675-629824 3 92648489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397421 Affx-122962245 AX-123267776 3 25898508 CTAAGACTCAACACAGCCAAATAAATACATAAAAA[C/T]GAAAAAAATCCTCCAAAACAAAATAAGGAACTTGC Y 2 1 2 1 303000 r 74 goat snp47885-scaffold675-664247 3 92614002 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389231 Affx-122969047 AX-123259589 3 26018663 CTATAAGTAACTTTTAATTTCCTCTTTATCTTTGA[C/T]CCATGGGTCTTTTCCCCCCAAATTAATGATATTAG Y 2 1 2 1 101000 f 74 goat snp47887-scaffold675-784402 3 92493875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783880 Affx-122936154 AX-385270936 3 26055504 GTGTAATTCAGTAGTCAGCAAAGGCTTCCCTTATG[C/T]GACATTGCTCTAAATATATTGTTCAGTTTATTTGT Y 2 1 2 1 101000 f 74 goat snp47888-scaffold675-821243 3 92457018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448657 Affx-122923345 AX-123318993 3 26104227 GGGAGCAACAGATGTTCTGTGGAGAGCCCAGCACA[A/G]TCCCCATCCTTGATGCTCACAGTCAGACAGGCAAC R 2 1 2 1 101000 r 74 goat snp47889-scaffold675-869966 3 92407169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278088 Affx-1111836166 AX-519551578 3 26113319 ATGGCACACTGCATTTTCCAAAAATGGCCTATAAT[A/G]GTATTTCTCATCCTACAAGCTCTTCTAGAACTTTG R 2 1 2 1 101000 r 74 goat Random2.2K-304 3 26113319 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396656 Affx-122962855 AX-123267011 3 26133536 TGAGGCTCCCCTTGATTTCCCCACTTGAATGTGCC[A/G]TCTATTTCTCACTGGTATCCCGACCTCATGGAGCA R 2 1 2 1 201000 r 74 goat snp47890-scaffold675-899275 3 92377814 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429902 Affx-122938116 AX-123300243 3 26183953 TTTGTACTTGTGGGTTTTCCCCACCAGAACTTAGA[A/G]TACTCTGAGAGCAGGAAATTTTTGTCTGCCTTGTT R 2 1 2 1 201000 r 74 goat snp47891-scaffold675-949692 3 92327379 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447496 Affx-122924082 AX-123317832 3 26219766 AAATAAAGGAAAACATCCTCTCCTAGTTTTGTGCA[C/T]ACAACAGAGACAAGCTAAGGAAATAAAAATACACA Y 2 1 2 1 101000 f 74 goat snp47892-scaffold675-985505 3 92291786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386189 Affx-122971368 AX-123256547 3 26249119 AGTGCATAAAACTGGAAACAAAGAGAAATCCCATT[A/G]TATCAGTTAAGATAGAATAAGTTTTGCCAACAATA R 2 1 2 1 201000 r 74 goat snp47893-scaffold675-1014858 3 92262331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429174 Affx-122937967 AX-123299516 3 26324601 CTACAGTAGTATCAAAAGTAAATTGATACTTGAAA[C/T]GATTTTATTATTTGAAATGATTTTATTAATTTATT Y 2 1 2 1 101000 f 74 goat snp47894-scaffold675-1090340 3 92185137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768868 Affx-122938008 AX-385256045 3 26385287 GTCTTTTCTGCAGATCTGGCACAAGTTTCTTTGAG[G/T]AGATTACATAAATGTCTTGTAGCATTATTCCTGGA K 2 1 2 1 101000 f 74 goat snp47895-scaffold675-1151026 3 92124371 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381587 Affx-122974802 AX-123251945 3 26471855 TATTCTGTTAGGAAAGAGTATTAGAAAGCAGCTAA[C/T]GACAGTCTTTACACTGAATAGTTTTTAACCATTGT Y 2 1 2 1 101000 r 74 goat snp47896-scaffold675-1237594 3 92037016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417271 Affx-122947255 AX-123287619 3 26527131 AGTTTTCTCAAGTATGTTCTAAGCACAGAAGTATC[C/T]AAGTGGGGCCAAAATTCAGACTTGAAAATGTCCTT Y 2 1 2 1 201000 f 74 goat snp47897-scaffold675-1292870 3 91981688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453605 Affx-122920136 AX-123323938 3 26573366 TGAGACTCTTAAGTTTTATTTATTAACTTTAAATG[A/C]GTTCTTCAAGTGTGATGTTTTTGAGTTCAGTGATA M 2 1 2 1 101000 r 74 goat snp47898-scaffold675-1339105 3 91935510 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407818 Affx-122954548 AX-123278169 3 26625734 CACTGGGAGGTGTGGGACTATCCTAATTTTACAGA[A/G]TAAGAAGCTGAGTGAGAAGAGGAAGCATCAATTTG R 2 1 2 1 101000 f 74 goat snp47899-scaffold675-1391473 3 91882394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786978 Affx-122925508 AX-385274006 3 26661549 TAGAGACTTAACATCAGAAACAAGAGTGCTACTGA[A/G]CTCCTATTTCTTTTCCACATAATTAGCTTTAGGTT R 2 1 2 1 201000 r 74 goat snp47900-scaffold675-1427288 3 91846582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464198750 Affx-1110365364 AX-515673899 3 26695999 AAGGTACACTCTGATATGTCAGCTGTCACAATGCA[A/G]TTTAACAAAATTGTTTTAAATGAAGTTAAAGACAA R 2 1 2 1 101000 f 74 goat 3_26695999_AF-PAKI 3 26695999 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780932 Affx-122962104 AX-385268019 3 26750210 TTATGCCCATTTGTTAATGTATATGACTGCTTTCA[C/T]GCTACAGTGGCAAAATGAGTAGCTGTGGCAGGTTG Y 2 1 2 1 202000 r 74 goat snp47902-scaffold675-1515949 3 91757873 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800908 Affx-122955976 AX-385287823 3 26804805 TGCTCCTTCCCTACCACAAGTTTCAGTGAGTCAGT[A/G]TCATTCTAGTGAATCCCACTTTTGATGTTAACTAT R 2 1 2 1 101000 f 74 goat snp47903-scaffold675-1570544 3 91701815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449575 Affx-122923228 AX-123319910 3 26834961 AGCTAAGAGAATCAGAAGGAGCTTGTAGCCAAAAC[G/T]ACTTTATTGTTCATTTGTTTTTCAAGCTAAAGTTA K 2 1 2 1 101000 f 74 goat snp47904-scaffold675-1600700 3 91671606 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444966 Affx-122926673 AX-123315303 3 26869042 TTCATCTTCACTATCGGAAGCATTTCATTAGTAGT[A/G]CCTGCCTGCGGCACCATGTGCAAAGTTCTCAGACT R 2 1 2 1 201000 f 74 goat snp47905-scaffold675-1634781 3 91637523 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429657 Affx-122937666 AX-123299998 3 26903559 AAATGAAAGAGCTGAGGCTCAGAGTTGTTAGGTCA[C/T]GTGCTCAAGGCCCCAGAGTTAGTAAGTGGCAGATC Y 2 1 2 1 101000 r 74 goat snp47906-scaffold675-1669298 3 91603590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383778 Affx-122973205 AX-123254136 3 26934483 GCTTTCAAATTTTATGGGATGCAGCTAAAGCAGAA[C/T]GTAGAGGGAGATTTACACGTTTGTATGTAGCGCTG Y 2 1 2 1 101000 r 74 goat snp47907-scaffold675-1700222 3 91572543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783787 Affx-122930849 AX-385270843 3 26965574 ACATTTCCTAAACTACAAGTGCCATCAGAGTTAAA[C/T]AGTTACCTTTTGGTATACTTTTCTTTTTGTCGTAT Y 2 1 2 1 101000 r 74 goat snp47908-scaffold675-1731313 3 91540861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778719 Affx-122959169 AX-385265830 3 27070003 TCTCAGTTGTAATGAGAGACCAGCAGATATATCAG[C/T]GTTTTACTCTACCTGTTTCCAGTGTCAGTGGCATG Y 2 1 2 1 101000 f 74 goat snp47911-scaffold675-1835742 3 91435770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439166 Affx-122931064 AX-123309503 3 27111429 CCTCTCCTGTTCACTGACTATTTATCACCTGGCTT[A/G]CTTGCCCTCTCTACCTGTCATGATTCCTGGTGACT R 2 1 2 1 201000 r 74 goat snp47912-scaffold675-1877168 3 91394291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396085 Affx-122963431 AX-123266440 3 27157688 CGTGACCGTTTTGCTCAGCATCAGCCTTGCCAAGA[A/G]CTGGTGGAGCCCCACTGGAGATGAGGTCATTGGTG R 2 1 2 1 101000 f 74 goat snp47913-scaffold675-1923427 3 91347488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429206 Affx-122937939 AX-123299548 3 27195815 TGTATAAAAATGCGTGCCTGTGCTTTTAGCCCCCA[C/T]AGTTGAAGTCCCTTTATAAAGATGCATCTAAAAGC Y 2 1 2 1 201000 r 74 goat snp47914-scaffold675-1961554 3 91309415 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434613 Affx-122934089 AX-123304954 3 27241018 CTCCTTTTGCTTTTTCTATAAGGTGGGAATAATGA[C/T]GCTAGCGCTATTTTCCTAGAAGTTTGCTGAGAGGG Y 2 1 2 1 101000 f 74 goat snp47915-scaffold675-2006757 3 91264444 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393734 Affx-122965228 AX-123264089 3 27303314 CTGACTCCCACTGAAGCCAGAAACATTCTGTTGCC[C/T]GATCACTGGGGTTGCCCCCATGCATTTAAAGGTCA Y 2 1 2 1 201000 r 74 goat snp47916-scaffold675-2069053 3 91203559 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422308 Affx-122943473 AX-123292654 3 27341252 AATATAATCTGTTCACTAAGTTTGAAGAGATGCCA[C/T]GAAACAGCTGCCTAGGAATGGCACTCTGGAGGCTA Y 2 1 2 1 201000 f 74 goat snp47917-scaffold675-2106991 3 91165377 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779682 Affx-122951264 AX-385266783 3 27372615 GATCAAACCCGCATCTGTTGCAGAATAATGATATT[A/G]TGGCCTTCTCAGAATATCACACCCAAAGTCAGATG R 2 1 2 1 201000 r 74 goat snp47918-scaffold675-2138354 3 91134160 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796352 Affx-122974558 AX-385283302 3 27415028 GGGCCATCTTATCTTAGATGAAGCTAGCTGTGTAC[A/G]TGCCGTAGTGTTTCTCGAAGTGCAGTTCACTTACC R 2 1 2 1 101000 r 74 goat snp47919-scaffold675-2180767 3 91091802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804486 Affx-986696653 AX-385291047 3 27453924 TGATGCTCAGCGTCTTGGCACAGGTGGCAGGTTTT[C/T]TGCATCCTCTCACCTTTGTGTTTCTCACATGGTGC Y 2 1 2 1 600010 r 74 goat 3_27453924 3 27453924 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38396035 Affx-122963468 AX-123266390 3 27476125 TCCAGTACTTTCTGACTTGTTTTATGCAATGAACA[A/C]CACCACCAACAGCCAACAGTTATTGAACACTGATA M 2 1 2 1 101000 f 74 goat snp47920-scaffold675-2241864 3 91030637 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397501 Affx-122962066 AX-123267856 3 27504736 GCACTGGGTGAGGGAGAAGAATGGAGTATTAAAAT[G/T]ATTTGGACAAATGAGCGGACTCTGGTGACAAAGTC K 2 1 2 1 101000 f 74 goat snp47921-scaffold675-2270475 3 91002130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389111 Affx-122968566 AX-123259469 3 27569763 GTGTTACCTTCTAACCCTGGTGGATAGCAATATGC[A/G]CAAGGTATGACCAGCCAGAGAAACTCACCTAAGCT R 2 1 2 1 101000 f 74 goat snp47922-scaffold675-2335502 3 90913204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401739 Affx-122959515 AX-123272092 3 27607009 AAGGAAAGAGATGACTGCAAAACCATGAGACACCC[A/G]CCTGCTTGTTCATACGCAGAGGTGCCCTCAGCTCT R 2 1 2 1 101000 f 74 goat snp47923-scaffold675-2372748 3 90875949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449292 Affx-122923015 AX-123319627 3 27679206 GAGAGCTGAGGAACACCACCACTTGCTTGGTAAAA[C/T]AGTTATCAGAAAAGTATTCTAGAAGACAGTGACGT Y 2 1 2 1 101000 f 74 goat snp47924-scaffold675-2444945 3 90803165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777405 Affx-122972164 AX-385264526 3 27713602 TGGGCTTGGTTCTCTTTCTGCAAAGTGGCACTGAG[C/T]AAGATGGCGATCATAATTCTTTCCATTAATAAACA Y 2 1 2 1 101000 f 74 goat snp47925-scaffold675-2479341 3 90768462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778656 Affx-122953597 AX-385265767 3 27745989 GGCAACACTGCGGACTATGAGACAAGGAGAACAAG[C/T]GGAGGGCACCAAGACCAGCGCAGAATAAATGTAAC Y 2 1 2 1 101000 r 74 goat snp47926-scaffold675-2511728 3 90736196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425356 Affx-122941582 AX-123295702 3 27793463 TGGTATCAAAAAATGAACCTATGGAGCATCATAAA[C/T]AAAAGAGTAGCATGACTGCATATGTGGGAAAAAGT Y 2 1 2 1 201000 f 74 goat snp47927-scaffold675-2559202 3 90688705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375926 Affx-122978467 AX-123246285 3 27841491 AGTGATAGAAAACACAGATGTCACAGCAGCAGAGA[C/T]GGCAGGTAGGACAGACACGAGCTAACCTTGTACAG Y 2 1 2 1 202000 r 74 goat snp47928-scaffold675-2607230 3 90640832 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405626 Affx-122956598 AX-123275978 3 27871395 GGGGCTGGAGTATTGAGGGGTGGAAGGGTCTATGA[C/T]GACAAGGTAGTAGAAAGAATTCTGGGAAGAATATT Y 2 1 2 1 201000 f 74 goat snp47929-scaffold675-2637134 3 90610853 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464199324 Affx-1110365661 AX-515674470 3 27896703 TCCTCCAGAAAGCCCTCCTTGGCTTCCTCCAAAGA[C/T]AAGCTCCCTCCCCCCAACCTCCATCATCTCACGGG Y 2 1 2 1 102000 f 74 goat Random2.2K-305 3 27896703 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395461 Affx-122963913 AX-123265816 3 27901633 CAGGCAGCTTCACTAATGATCCCATCAAGACTGCA[C/T]GTGGCAGGGAGGGACAATCCCCCAGGAAAAAATGA Y 2 1 2 1 101000 f 74 goat snp47930-scaffold675-2667372 3 90580733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408056 Affx-122954274 AX-123278407 3 27958173 ATAAAGAGGCTGCTCCTTTCCAGAGCCCAAAATCT[A/G]GTAGGAGCAGAGAGATTATAAAAACAAATAAGCAC R 2 1 2 1 201000 r 74 goat snp47931-scaffold675-2723912 3 90524363 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400447 Affx-122959958 AX-123270802 3 27988740 GTCCAGGCAGTGCCTCTGGGCGACAGAAATCAAAA[G/T]ACACTTTGCAGTACTACGTGATAACATTCAATTCT K 2 1 2 1 201000 f 74 goat snp47932-scaffold675-2754479 3 90493869 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441709 Affx-122929153 AX-123312046 3 28029118 AGAAACTAGGTTTCTGCTGTCTGGTGGACAATGTC[A/G]TTATTATAGCCTAATTCCCCTTGAAATCTCTGGCA R 2 1 2 1 201000 r 74 goat snp47933-scaffold675-2794857 3 90453077 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438800 Affx-122930802 AX-123309137 3 28085684 CAAACAAATGAAGAGAATTTATGCATCCCTACTGA[G/T]ATGAAGTGGTAATTGGGTGGGGGACAGAGTATTTC K 2 1 2 1 101000 f 74 goat snp47934-scaffold675-2851423 3 90399377 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801287 Affx-122952323 AX-385288199 3 28133226 AGTCAGTCATTAATAACTGGATCATCTGTCATCAT[A/G]TGATACGAAAAATAAATTTCCAGCCAAGGCCACTT R 2 1 2 1 101000 r 74 goat snp47935-scaffold675-2898965 3 90351782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772690 Affx-122920058 AX-385259837 3 28171444 GATCCAACCTTACCCACCACAAAGTAGATCACTTA[C/T]GAGAGATGAAACTGTCCACCAAGTACCATAACCAC Y 2 1 2 1 201000 r 74 goat snp47936-scaffold675-2937183 3 90313098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443549 Affx-122927761 AX-123313886 3 28203846 TATGCATGCAAAATTTCTGGAAGGACACACAAGAC[A/G]CTATCAACAGGGATGGCTTCTAGACTTTAGAAAAT R 2 1 2 1 201000 r 74 goat snp47937-scaffold675-2969585 3 90280105 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277936 Affx-1111836167 AX-519551431 3 28255892 TCCCCGCACACTACTTCCAGCTTCTCTGCCGAGCC[A/G]TGTCCTGTAACCTCCTGGGTCTCCCTTGCTTGTGC R 2 1 2 1 202000 f 74 goat Random2.2K-306 3 28255892 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277938 Affx-1111836168 AX-519551433 3 28289202 TTGCGCCACACATAGCTTGTGCGTGTGACATGTAC[A/G]AGGTGGTGCGTGTGTGTGTGCTAAGTCACTTCAGT R 2 1 2 1 201000 f 74 goat Random2.2K-307 3 28289202 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391625 Affx-122966580 AX-123261982 3 28317199 CAGGGCACTTGTAGCTTCTGCTTTCTCTCAGATCA[C/T]AGCCTATAGTATGCTAGATAAGGAAGCCAGTCTAG Y 2 1 2 1 101000 r 74 goat snp47939-scaffold675-3082938 3 90166033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444085 Affx-122926840 AX-123314422 3 28380435 CAGAGTGTTGTTAAGTACAAGTCAATAAAGCTAAA[C/T]AAAACATGTCCTTTAGAGAGTTAAAAACCCCCTTC Y 2 1 2 1 201000 f 74 goat snp47940-scaffold675-3146174 3 90101356 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426417 Affx-122940832 AX-123296763 3 28410342 GAGGGGCATTTTAAGACAATTTTATCTGTTTCTTT[A/G]TTCATCATATACATAATATCTGAAAGCCAACCACA R 2 1 2 1 101000 r 74 goat snp47941-scaffold675-3176081 3 90070651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398659 Affx-122961888 AX-123269014 3 28445157 AGGGTCAGAGGAGTGGACTCTCGGCTAAGCCCACA[A/G]GGGTAACACATGGAACTTCATCCAGCTGACCCTCC R 2 1 2 1 101000 r 74 goat snp47942-scaffold675-3210896 3 90035553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791104 Affx-122971292 AX-385278099 3 28512379 GATGAGCTGCCAGGATAGGAATATGGACAATAGAA[C/T]GAAAAGAATACTTTGAGGATAATTATGGCAAGATT Y 2 1 2 1 101000 f 74 goat snp47943-scaffold675-3278118 3 89967486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415799 Affx-122948902 AX-123286148 3 28546443 CAGTTGTCATATCATATCTATGTCACCTGTGTATT[C/T]TGAGATCACACCTGTACCTGCCAATAAACCTGGGA Y 2 1 2 1 201000 f 74 goat snp47944-scaffold675-3312182 3 89933466 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450178 Affx-122922310 AX-123320513 3 28578297 GTATTTCTTAGAAACTATTCTAGTAGTAACCAATT[A/G]TAAGTCTGGGTATATGTAGACAAATAGGTAGGGAA R 2 1 2 1 101000 r 74 goat snp47945-scaffold675-3344036 3 89901645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446806 Affx-122925292 AX-123317142 3 28637431 TGTGACATCTACTAAAATAAATTGATGAGCAGACT[A/G]CATTCTTACACTTTGAGGAAAGGGCCAGAGACATC R 2 1 2 1 101000 r 74 goat snp47946-scaffold675-3403170 3 89842511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454095 Affx-122919367 AX-123324428 3 28670908 GTGTGTGTGTGCTGCATTCCGAATTCCCTGTGCAG[C/T]CTCCTTAATCTGCAGCCTGCTGTCAGTACCTTACA Y 2 1 2 1 101000 r 74 goat snp47947-scaffold675-3436647 3 89808849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792662 Affx-122925738 AX-385279642 3 28715924 AATGATCCATTCTGTGCTTTTGCTGCAGAATCACA[G/T]TCATATGGCAGTCTAATTTCAGGCACTTTTAAAAC K 2 1 2 1 101000 f 74 goat snp47948-scaffold675-3481663 3 89763874 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444061 Affx-122926855 AX-123314398 3 28771119 GAGATCTTGCTCAAGCTCTTTCTCCTTTCTGGGCC[C/T]GAGCCCTGCAGCTGAACATCTAAGGGTTGGTTGAC Y 2 1 2 1 201000 r 74 goat snp47949-scaffold675-3536858 3 89708973 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787492 Affx-122925796 AX-385274517 3 28805573 GTAAGTACTTGTAGATCAGTGTGAAGTATTTCCCA[C/T]GGTAATTTTGTTTGGATTAACAGAATTTGCCCAGT Y 2 1 2 1 101000 f 74 goat snp47950-scaffold675-3571312 3 89674432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800967 Affx-122975335 AX-385287882 3 28835068 AAAGTGTGAATTTAACCTAAATTTTGTATCTGATG[C/T]GTAAATATTTTCTAACCTTTCTCATTGTCTAAGCA Y 2 1 2 1 101000 r 74 goat snp47951-scaffold675-3600807 3 89644687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434609 Affx-122934092 AX-123304950 3 28881722 CAGGGTCCTCACTAGCAGATCCTCCTGAATCTTGT[C/T]TCTAGGCAATGAATGCCGTGAGTTCCAACTGCCTG Y 2 1 2 1 201000 r 74 goat snp47952-scaffold675-3647461 3 89598649 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426095 Affx-122940644 AX-123296441 3 28929732 AAAAGAAGGAGAGGCCTGGGGTCATTCTTTGGAAA[C/T]GAATGGGCAAGTGGAGTAAAGAATGAAGGGGAGCC Y 2 1 2 1 201000 f 74 goat snp47953-scaffold675-3695471 3 89551317 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425681 Affx-122940862 AX-123296027 3 28985552 TGAACTGAGAGGCCACCAGTTCTACAACTAACTTT[A/G]TTAGTTTGCTAAGGCTGCCATAAGGAATATAACAG R 2 1 2 1 103000 f 74 goat snp47954-scaffold675-3751291 3 89496039 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779899 Affx-122969393 AX-385266998 3 29067209 CCCAGTAGGAAAGACAGATAAGTAATAAGAAACAA[C/T]AGGATCCCATGAGAGACACAAAAGTGTCCAAGTAT Y 2 1 2 1 101000 r 74 goat snp47956-scaffold675-3832948 3 89414322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408116 Affx-122954252 AX-123278467 3 29116334 GTGAAAATCATGAAAGGAAAAAAAGAAAGCTAACC[A/G]TGGCAGTAACGCACTAAGGTGATCCCCAGTGAGTT R 2 1 2 1 101000 r 74 goat snp47957-scaffold675-3882073 3 89364966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798638 Affx-122937950 AX-385285570 3 29160713 CAGAGTGTGGAGAAACTGAATCAACACAATTTATT[A/G]TTAGATGAAAGTCAGACGCAGCAAAAAAGAGCAGA R 2 1 2 1 101000 f 74 goat snp47958-scaffold675-3926452 3 89320747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277940 Affx-1111836169 AX-519551435 3 29205567 CGCTGTTCTTGCTTCATGGCTTGGGAATTGCCAAA[A/G]AAAGCTTACAGCCAGAAGCCCTGGGACAACCAGCA R 2 1 2 1 101000 f 74 goat Random2.2K-309 3 29205567 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428612 Affx-122938689 AX-123298954 3 29217572 CTGATTTGCAGGACAGTAGAAAGCAGGCAGGGTCT[A/G]CCCATGGTCTCCCCAGGTTTATATTCCTGAGTCCC R 2 1 2 1 201000 r 74 goat snp47959-scaffold675-3983311 3 89264170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436276 Affx-122932536 AX-123306615 3 29268640 AGTTACACTGAAGAGCCTTTGCTTTTCTTGGTACT[A/G]TTTGTTAGTTCTATCTCCTTCCTCCTGCTGATCAA R 2 1 2 1 101000 f 74 goat snp47960-scaffold675-4034379 3 89213420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272518 Affx-1111833382 AX-519546236 3 29297461 TATAGTCCAACTCTCCCATCCATACATGACTACTG[A/G]AAAAACCATAGCTTTGACTAGATGGACCTTTGTTG R 2 1 2 1 103000 f 74 goat 3_29297461_AF-PAKI 3 29297461 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416328 Affx-122947908 AX-123286677 3 29321173 TTACAGCTTTTCATTGTAAAATTTATCATGATAAT[G/T]ATTAGTTGATATATCTTATCCTAGGTGGTGCTAGC K 2 1 2 1 101000 r 74 goat snp47961-scaffold675-4086912 3 89160896 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773287 Affx-122963958 AX-385260430 3 29353247 CCGCATTGTGGATTAAATGTAGATCTGAGCAATAA[G/T]GTAATGATATGACTTCAAAAACCTCCCCTGAAAAT K 2 1 2 1 101000 r 74 goat snp47962-scaffold675-4118986 3 89133272 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390659 Affx-122967134 AX-123261016 3 29403522 ACGAGGAATCAGCTTGGGCGTCTTCTTCCTTCTAG[C/T]CCCTCAGGACGAGAGTCCCTCCCTCTTCTTCCTTC Y 2 1 2 1 101000 f 74 goat snp47963-scaffold675-4169261 3 89083478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798698 Affx-122972888 AX-385285630 3 29463896 TGTAAAAATGTTACCCAGTTGGGCTGTTGGCCAAA[C/T]GGCAAACAATTTACACTTGTCCATGGAAGGATATG Y 2 1 2 1 201000 r 74 goat snp47964-scaffold675-4229635 3 89023520 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432514 Affx-122935569 AX-123302855 3 29495225 AAAATCATAAGAAGCCCAAGGAAAAAGTTTAGATA[C/T]AGAAGAACTAAGTTATGAAAATATATAGATTTTCT Y 2 1 2 1 101000 f 74 goat snp47965-scaffold675-4260964 3 88992051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772647 Affx-122934073 AX-385259795 3 29546702 TTTGAACCACTCTCTATCAATGTGAACTAAACAAA[C/T]AGGGTGGAGATAGGAAACTATCTCTATCCCTGGAA Y 2 1 2 1 101000 r 74 goat snp47966-scaffold675-4312441 3 88940448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396425 Affx-122962996 AX-123266780 3 29607718 TTTAGATCTGGGGGCTCTACTAAAGATGTTCATCT[A/G]AGGTTACTCAGTAACCCAAGGCTGAGTCTGTCCTT R 2 1 2 1 101000 f 74 goat snp47967-scaffold675-4373457 3 88879524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794869 Affx-122930366 AX-385281829 3 29628400 TAGATGGGAGTTATAAAAAAACATGTGGGTCTGAC[A/G]TTTCACTCTACCTGTAAGCCAAAAAAGTTAGCCTG R 2 1 2 1 101000 f 74 goat snp43515-scaffold580-4578 3 88858705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420075 Affx-122945113 AX-123290423 3 29661431 AGAGCAATAAACCTGAAGGTCTAGCAATAGAAATG[A/C]TGCCAAATGAATCAGGGAGAAAGAAATTTAAAAAA M 2 1 2 1 101000 f 74 goat snp43516-scaffold580-37609 3 88825363 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775408 Affx-122948567 AX-385262539 3 29694774 CCCTAGATATAGAAGGGGACTTTGTTCCCGACAAG[A/C]TCCCCATCAAACTTTTTGGGGGATCTTTTTTGTTT M 2 1 2 1 202000 r 74 goat snp43517-scaffold580-70952 3 88792453 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431700 Affx-122936773 AX-123302041 3 29758731 AAAACAAGTAATGTAAAAATACCTGTTACAACCCC[C/T]GCTTCTGTAACAATGCCAGTTGCCTCTTTCTAAGC Y 2 1 2 1 101000 r 74 goat snp43518-scaffold580-134909 3 88728896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382541 Affx-122973785 AX-123252899 3 29818865 GGGCCAGGAGCCCAGGAGGGTGTGAACTAACAAAA[A/G]CAAAATAAGTGTATGTGTACCAAAGAAATGAGGGA R 2 1 2 1 202000 f 74 goat snp43519-scaffold580-195043 3 88668156 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802308 Affx-122942403 AX-385289212 3 29853494 TGGTGAGAATCCAGTCCATTGGAGACTTAATGACT[A/G]TACCAGGTAGACAGTCCAATGGTTTAATCAACATG R 2 1 2 1 201000 f 74 goat snp43520-scaffold580-229672 3 88632930 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396157 Affx-122963383 AX-123266512 3 29930073 CTATATGGTGCAATGGTTAAGAATCTAGACTTTGG[C/T]GTCAGCTATACCTGGTCCTCAAGCCCCAAAAGACA Y 2 1 2 1 201000 r 74 goat snp43521-scaffold580-306251 3 88554321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380035 Affx-122975584 AX-123250393 3 29964237 TTTATTTCTTGAGACTCTGGGCTGAGCTGAAAGCA[C/T]ATTGGAGGGGCTGACCTTACCTTGATTCTGAAGCT Y 2 1 2 1 202000 r 74 goat snp43522-scaffold580-340415 3 88519330 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377282 Affx-122978124 AX-123247641 3 30025861 AGGCCTGTCTGAGCTGGAGCTTGAGTGGGTTGCAG[C/T]GGCAAAAGATACACAGGACCCTTCACGTGGCAAGT Y 2 1 2 1 101000 r 74 goat snp43523-scaffold580-402039 3 88448719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446415 Affx-122925563 AX-123316751 3 30074010 GCTGTCCACAGTAGGCCCATCATCAGTAGTGCATC[A/G]TTGTTAAACAGATGAATGAGCAAGTGAACTCTTGA R 2 1 2 1 201000 f 74 goat snp43524-scaffold580-450188 3 88400189 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417039 Affx-122947530 AX-123287387 3 30112426 TGTACAGAGAACACAAATGTTGTTGCAGGATGGAA[C/T]AGGAGACTGGGGTTACCGAATTGAAGTTAAAGTCA Y 2 1 2 1 101000 f 74 goat snp43525-scaffold580-488604 3 88361845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784985 Affx-122958980 AX-385272032 3 30149276 GAAAACAAGATGTGGAGTCAGAAAATAGTTGAAGA[C/T]GAACATTGTAGATAAGGTGGTTGAAGACCATGAAA Y 2 1 2 1 101000 f 74 goat snp43526-scaffold580-525454 3 88325088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436654 Affx-122932479 AX-123306992 3 30180595 CAGTGATCAACTGATTTGCAGAAGAATCTCTGAAG[A/G]TTAACAAGGTTTTTCTTTTTAGAAGAAGTGGGTCC R 2 1 2 1 101000 f 74 goat snp43527-scaffold580-556773 3 88293459 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442369 Affx-122928021 AX-123312706 3 30215704 CATCACCCTGATACCAGAAACCAATAAAGATAGCA[C/T]GAAAAAGAAAATTGTAGGGTCATATCACTGGTGAA Y 2 1 2 1 101000 f 74 goat snp43528-scaffold580-591882 3 88257210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450136 Affx-122922755 AX-123320471 3 30298510 CAGTTTGATGTGCATGTAGTTTTGTACTGTGTGTT[A/G]TTATCTTTGTTTATGTGATTTGAGTGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp43529-scaffold580-674688 3 88174479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377379 Affx-122977636 AX-123247738 3 30337693 TCTTCTGTCTAGGATCATTGTACATGCTTTAAAGT[A/G]CATATCTCCCCAACTCCCCAGCCTCCCACCCCTGG R 2 1 2 1 101000 f 74 goat snp43530-scaffold580-713871 3 88134866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420669 Affx-122944815 AX-123291016 3 30397915 AGATTTTGACAGCAGAAGGGTGTCAGTTTTTCCAG[C/T]GGGGTTGGCTGGGGTGGTAAGTCCATGCCTGACTA Y 2 1 2 1 101000 f 74 goat snp37607-scaffold460-1208717 3 88069189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379901 Affx-122975765 AX-123250259 3 30440599 AGTCACAAGATCAGGGGTGCCAGATACGAGTACAC[A/G]CTCTTTGGAGTGGGCTAAAAAGAGAATTCAGGGAA R 2 1 2 1 101000 f 74 goat snp37606-scaffold460-1166033 3 88025765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385271 Affx-122972073 AX-123255629 3 30490449 AGGAAGAAAAGCAGAGGCCATTATTAGCAGATGCA[C/T]GGTAGGAGTGAGTACAGTTCAGAAAGACCTGCTCT Y 2 1 2 1 101000 f 74 goat snp37605-scaffold460-1116183 3 87974034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423030 Affx-122943408 AX-123293376 3 30520865 ATTTACAGTAACGATAGTCACTGCCACCATAGCTT[A/G]AAAACTTCACATCCATCATCTCCTTTAATCTTGCA R 2 1 2 1 101000 f 74 goat snp37604-scaffold460-1085767 3 87942897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448887 Affx-122923261 AX-123319222 3 30552942 GAGTATCATGTGTTAATTGCTCATGCTGTCCTCCC[A/G]CTGCCTAGAATGCCCTCCTGTTCTGTGCCCTAGCC R 2 1 2 1 101000 f 74 goat snp37603-scaffold460-1053690 3 87910322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451163 Affx-122921353 AX-123321497 3 30585768 AGCTGTGTCAAATGGATTGATTAAGCTACAGATCT[A/G]TAATTTGCCTGCTGAGATATATGCTGTGACCTGAG R 2 1 2 1 101000 r 74 goat snp37602-scaffold460-1020864 3 87877415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439660 Affx-122930598 AX-123309997 3 30643238 TAGGGTATATATATTTTTCCCAGGGTGCTGATGGA[C/T]ATGCACTGATCCAGTCACATCTCCTCCCATGAATC Y 2 1 2 1 101000 f 74 goat snp37601-scaffold460-963394 3 87819430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423079 Affx-122942937 AX-123293425 3 30682678 TCCTGGTGTCAGAACTGAGGCCATAGATGAAATAA[C/T]AAGAAGAAAAATTCCAGTTCACCAGAGCTAGACCT Y 2 1 2 1 101000 f 74 goat snp37600-scaffold460-923954 3 87782696 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384835 Affx-122971970 AX-123255193 3 30737338 CAGTTGATTGGAATCATTTATTCATCAGCATAATT[A/G]CCCACTTTGCACGAGGAGCCTTTCTCCTTTCTTAA R 2 1 2 1 201000 f 74 goat snp37599-scaffold460-869294 3 87727935 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415974 Affx-122948414 AX-123286323 3 30788842 GGATATCAAGAAAGTGGTGGAGGAGGTCTGGGAGG[C/T]AAGAGGAAAGTGAATTCCTGTAAACTTCCAGAAAG Y 2 1 2 1 101000 r 74 goat snp37598-scaffold460-817790 3 87676187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451026 Affx-122921453 AX-123321360 3 30825501 CATCTCTCATTAAAACAGTTGAACTTGAGCATTTC[A/G]TTTACCGATGATGTTTTTGAGAAAATTAAAACAAA R 2 1 2 1 101000 f 74 goat snp37597-scaffold460-781131 3 87639807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445970 Affx-122925891 AX-123316307 3 30870653 AAGCAGAACAGAAGGACACCCCAGAGGCGACAGGA[A/C]TGTGGGGTGCGATGCATGGAGCTGACTGGATCGTT M 2 1 2 1 303000 f 74 goat snp37596-scaffold460-735979 3 87594496 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408649 Affx-122953473 AX-123279000 3 30903478 GTCCTTCTCCTGGGACTTTATGTTCTTTATGTACA[C/T]GCAACTGCAAGAGCACAAGCATGGCAACACCCACC Y 2 1 2 1 201000 f 74 goat snp37595-scaffold460-703154 3 87561326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392162 Affx-122966312 AX-123262519 3 30981545 ATAATATAATTTAGGTTTTCTTTGCTGTATTTTAA[A/G]TGGGATCAAAAATTTTGAAGAGGATTTTTCTGTTT R 2 1 2 1 201000 f 74 goat snp37594-scaffold460-625087 3 87482497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379258 Affx-122976254 AX-123249617 3 31012777 AGGCACAGCAACCAGAACAGAGTCACTCTGCAATC[C/T]AGGGACAAAGGCATGCTGGGCCACAGCCCTGTTCC Y 2 1 2 1 101000 f 74 goat snp37593-scaffold460-593855 3 87451268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425694 Affx-122940782 AX-123296040 3 31044128 GGCCCTAGATGGGAAGTGTTCTGCGTTTCTTAAGC[C/T]GGTTCCTTCATTCATTCTGTAAACATTTACTATGC Y 2 1 2 1 201000 f 74 goat snp37592-scaffold460-562504 3 87419998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411538 Affx-122951656 AX-123281888 3 31087786 CACCCACAATCTGAGAGCACAGTTTGCTTTCCCTT[A/G]CCTCTGGATTTGGGCTTGTACCCATTACTGTGGCT R 2 1 2 1 101000 f 74 goat snp37591-scaffold460-518846 3 87376548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451810 Affx-122921484 AX-123322143 3 31123522 TCTGGGCAGGATGGCCTCCCTCCTTGCCAACCCTG[C/T]ACCCTGTTTCATCCTGATACTCCCAGCTCCAGAAT Y 2 1 2 1 101000 r 74 goat snp37590-scaffold460-483110 3 87341066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398444 Affx-122961610 AX-123268799 3 31181998 TTGAAAATAATTCTATTAGTGAAACTCAAACTTAC[A/G]TTAGCTCCTTTAGCAGAATTTCACGTTGCTGCTTC R 2 1 2 1 101000 r 74 goat snp37589-scaffold460-424634 NW_017211741.1 1958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448163 Affx-122924266 AX-123318499 3 31221653 GCCTCTCTGCCAACCCACGAGATTCCCACCAGACC[C/T]CATTCTTGGGCCACTGGTTTCTGTCTGGCAAAGAA Y 2 1 2 1 101000 r 74 goat snp37588-scaffold460-384979 3 87245594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380003 Affx-122975607 AX-123250361 3 31276876 GGAGATAGCCTCCATTTTCCTTGCCCAAGTTCAGG[A/G]AGTTGAGTTAGAGGAGTAGGCAGGTGGAGATTCAT R 2 1 2 1 101000 r 74 goat snp37587-scaffold460-329756 3 87190283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771811 Affx-122969865 AX-385258968 3 31330854 GCTTTTTGCTTTGAATTCTCAAAATGCAGCATCCT[A/G]TCTCTAACTTCAAAAGAGGTCAATTAGTAGACAGA R 2 1 2 1 101000 f 74 goat snp37586-scaffold460-275778 3 87136133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451336 Affx-122921269 AX-123321669 3 31360161 TGCTTATTGGCAGAGGGGAGGCTCAGATCCAAATG[C/T]GCCTCTCTCCAAAGTCATGAGGTAACCTCCATGAC Y 2 1 2 1 101000 r 74 goat snp37585-scaffold460-246471 3 87106651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438626 Affx-122930919 AX-123308963 3 31443956 TACACACAAAACCTGTCCAAGAGAACAATGCTGCC[A/G]TGCAGAGGACAGTAAGAAAGCAGGGCAGGGAGAAC R 2 1 2 1 101000 f 74 goat snp37583-scaffold460-162676 3 87022692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784913 Affx-122926550 AX-385271960 3 31498517 TTTGGAATCATGAGGGCATTATATTATGTCCCTTA[C/T]AGCTTTATCCCTGAGTCTATTTTGTCATACTCAAG Y 2 1 2 1 101000 r 74 goat snp37582-scaffold460-108115 3 86970991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387254 Affx-122970560 AX-123257612 3 31545686 TGGGTAGGTGCCTCGCCTGGCCTCTGCAGCACAGA[C/T]ACTTGGAACAGAGCCCCTAAACCCCTTAGGGCATG Y 2 1 2 1 101000 r 74 goat snp37581-scaffold460-60946 3 86923796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775309 Affx-122955983 AX-385262440 3 31618061 GTAGGTTATATGATTGCTTGTTCATTTCTATCTCC[A/G]CTTCATGTACCTCTGTGTCTTAGCATCAGATCTCT R 2 1 2 1 101000 f 74 goat snp25341-scaffold261-1157571 3 86826111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769626 Affx-122961141 AX-385256796 3 31688141 TTCTTTCCAGAGGACAAAATTTGGCTGTAAATTTC[A/G]TAAAAGTGAAGGCAAAGGGTGAAGTACAATTTGTT R 2 1 2 1 101000 f 74 goat snp25340-scaffold261-1087491 3 86754555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785006 Affx-122923974 AX-385272053 3 31783185 ACCATTACATAGTGAATGCCAAAGTTGAAAACTGC[A/G]TTTACACAGGATGGTTCCAAAGTTCTTGTACACTG R 2 1 2 1 201000 f 74 goat snp25338-scaffold261-992447 3 86658898 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379848 Affx-122975806 AX-123250206 3 31823088 GGGGCCCACAAGACAGCAAGTCCCTCAGGAAGGAT[A/G]CAGCTGAGGAGGGTTTGGAAGTGAGGCGCCTCTAT R 2 1 2 1 101000 f 74 goat snp25337-scaffold261-952544 3 86618728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799639 Affx-122949408 AX-385286568 3 31894974 TTCTGTTTTAAGAAGGAAAGCCATGTACTTATATC[A/G]TTTATACACACTGCTGCCAGATTAATATTCCTGAA R 2 1 2 1 101000 f 74 goat snp25336-scaffold261-880658 3 86546808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798556 Affx-122961037 AX-385285489 3 31937505 TTAAAATTAAACATAGTAGGGCATTTTTTTAGTAA[C/T]ATTCACTACTAGTATTTAGTATAATTTGAAAACTG Y 2 1 2 1 101000 r 74 goat snp25335-scaffold261-838127 3 86504211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272198 Affx-1111833383 AX-519545949 3 31957556 TTTCCAGTGAGTCAAGTCTTCGCATGAGGTGGCCA[A/G]AGTACTAGAGTTTCAGCTTTAACATCATTCCCTCC R 2 1 2 1 303000 f 74 goat 3_31957556_AF-PAKI 3 31957556 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441195 Affx-122929535 AX-123311532 3 31967093 GGTTTCAACTCATTTAGAAAACTACTAACAGTACC[A/G]CAGTGCCAGTACATGCTGGTCACATGCCACACCTG R 2 1 2 1 101000 f 74 goat snp25334-scaffold261-808539 3 86474467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453865 Affx-122919526 AX-123324198 3 32008750 ATTTGAGTTTTATTTCCATTTTGTGGAATCTTATT[C/T]TGGGGTCTGGCTTTGTTGTGCAATTGACACAGGTC Y 2 1 2 1 202000 f 74 goat snp25333-scaffold261-766882 3 86432804 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422426 Affx-122943362 AX-123292772 3 32039846 GCATGGTGAGGACGGAATCTCCTGATGGCCAGTGG[C/T]GGGTGGAGGCCCAGCCACCCAGCTTTTACTGAGGG Y 2 1 2 1 101000 f 74 goat snp25332-scaffold261-735786 3 86402597 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390803 Affx-122967863 AX-123261160 3 32068579 CTAGACATTTGCCAAGACAAAAAATTGGGGGAGAT[A/G]TTTTTCAATCTAAAAAAACAATTGTATTAATTTAA R 2 1 2 1 101000 f 74 goat snp25331-scaffold261-707053 3 86373671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430515 Affx-122937215 AX-123300856 3 32144148 TTAGCACGTATGCATGCAAGGTGGAAATGAGATGA[C/T]ACTTGGAAAGATTTGGAGCAATTCCTGGCATTAGA Y 2 1 2 1 101000 f 74 goat snp25329-scaffold261-631484 3 86296541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799079 Affx-122938314 AX-385286009 3 32187694 GTCCTAAATCCTTATCTTTTCAGCAGGATGACTCC[A/G]AATTGCAAATATTGCCCAATAGGATTAGTTTCTAG R 2 1 2 1 101000 f 74 goat snp25328-scaffold261-587938 3 86252637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392309 Affx-122967518 AX-123262666 3 32250834 AAATGGAGGTTCATAATATTTGCTATGGTCTGAAC[A/G]TTAGTGTCTTCCCAAAATTCATATGTTAAGTGATG R 2 1 2 1 201000 f 74 goat snp25327-scaffold261-524798 3 86188582 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376823 Affx-122977923 AX-123247182 3 32321234 AGTCAATACAGAGATGAAACCAAAGATGGAAAATA[C/T]ACTGGTTCACTCTAATTAACTTCTGCTGAGGACCC Y 2 1 2 1 101000 r 74 goat snp25325-scaffold261-454398 3 86117458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392401 Affx-122966214 AX-123262758 3 32371884 TTGCTCTGAATATGCTAATTTCCTTAATGTGCCTG[C/T]GTGCCATGTCGCTTCAGTCATTTCTGACTCCTTGC Y 2 1 2 1 101000 f 74 goat snp25324-scaffold261-403748 3 86067035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453878 Affx-122919515 AX-123324211 3 32401290 GTTGCCAGGAGTGGGGTACTCTCGAGGTGGAGTGC[A/G]TGGCTTCTCATTACAGTGGCTTCTCTTGTGGAGCA R 2 1 2 1 201000 f 74 goat snp25323-scaffold261-374342 3 86037798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418924 Affx-122946515 AX-123289272 3 32441749 GCTGTAGCTGTGATTCTTAACCAAGGGGCTTATCA[A/G]AGTCAGGGGAAATTTAGAAGAAACATTCCCACAAG R 2 1 2 1 10000 f 74 goat "023;ins-del_024;snp25322-scaffold261-333883" 3 85996844 A G "ins-del_024;023" 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403747 Affx-122958011 AX-123274099 3 32533999 TGAGGGCCTGCTATATGCTGAGCATCGTTAGCTGA[C/T]GAGCATACAAATCAAATAAGGCATGATTGCTACAC Y 2 1 2 1 101000 f 74 goat snp25320-scaffold261-241633 3 85904780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396507 Affx-122963526 AX-123266862 3 32580882 AGTCCTATTTTGAGACTCGATCTGATTTTACTAAT[A/G]AATTAATTACCCATTAGTAAGTAAAGTCAAGTCAC R 2 1 2 1 101000 f 74 goat snp25319-scaffold261-194750 3 85856559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387307 Affx-122970516 AX-123257665 3 32631342 AACACCATTTCCAAATAATAGTACTCTAGGTATTC[A/G]TTCCATCATTCTTTTAGCTTTCAGCCAGAATTTGA R 2 1 2 1 101000 r 74 goat snp25318-scaffold261-144290 3 85805974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435609 Affx-122933788 AX-123305949 3 32669537 CCCAGCTTCTCCTTCTAGGAGAGCAAGAATGAGGC[C/T]GTGTTAGGTCATGCCTTTTACTACCTAGGAGTCCT Y 2 1 2 1 102000 r 74 goat snp25317-scaffold261-106095 3 85768825 G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383196 Affx-122972789 AX-123253554 3 32716037 AAAATTATTGTGGAAGTCCCTCTCTTGTTTAGATC[A/G]TTACAGAATTTCATTCTCCCTTTTGAAGGATATCA R 2 1 2 1 101000 r 74 goat snp25316-scaffold261-59595 3 85722276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787980 Affx-122926815 AX-385275001 3 32749401 TTAACAGCTATTTCAGGAGCAAGCTTGAGAACATT[C/T]GTACCATTTCCTCTCCACAAAGAAATGACTCCGCC Y 2 1 2 1 101000 r 74 goat snp25315-scaffold261-26231 3 85688470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425769 Affx-122940724 AX-123296115 3 32781675 CCTTACTCAAACCTCACCTGCATTGCACATTGCAG[A/C]GTTGGCAACATTCTCAAACTCTCTAGTTACCATTT M 2 1 2 1 101000 r 74 goat snp30451-scaffold3351-51973 3 85655654 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796826 Affx-122936426 AX-385283769 3 32823822 ACCTCACACTCCATTAAACTCAATGGGATAAAATA[C/T]GTGAAATTCCAATATGACCCACAGATTATGATTTG Y 2 1 2 1 101000 f 74 goat snp30450-scaffold3351-9826 3 85610855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782933 Affx-122947105 AX-385270003 3 32861779 TTAGAGGAGCAGAGACTAGAGAAATGAGATGACTA[A/G]ATACGAGATGTTGCTATCATTCAGAGAAGTGATAA R 2 1 2 1 101000 f 74 goat snp46868-scaffold654-28032 3 85556043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772422 Affx-122947096 AX-385259574 3 32951624 CACTCATATAATTTTTGTGTAAAGAGGAGTGACAA[A/G]ATAATATTTATTTCAGTGACCACTTCTCCATTTTG R 2 1 2 1 201000 r 74 goat snp46870-scaffold654-117877 3 85465268 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422808 Affx-122943201 AX-123293154 3 33008949 ACATTCAGTCTATAGTATCCCCGGTGCCATTTTCT[A/G]CTGTTGCTCTGGATATACCTGCTCAGCTGAAGTTG R 2 1 2 1 201000 r 74 goat snp46871-scaffold654-175202 3 85406909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800671 Affx-122934412 AX-385287589 3 33055792 ATTTTGTTAGTTTTCATGATAGTAATAGTAAGAAA[C/T]GAGTCAGGCAATTTATCTCCTCGTCTGTAAAATAA Y 2 1 2 1 101000 r 74 goat snp46872-scaffold654-222045 3 85359533 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784484 Affx-122977464 AX-385271533 3 33089434 AAGAAGCTCACAGTTCTATTAAGGAGATAGGCATG[C/T]AGACTGTAATGCAAGGTTAAAGAGCAAAAACAAAA Y 2 1 2 1 101000 f 74 goat snp46873-scaffold654-255687 3 85325841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451799 Affx-122921492 AX-123322132 3 33132072 CTGGCAGGCTACAGTCCGTAGGGTCGCAAAGACTG[C/T]GCGACTAAGCACACAGGGCAGCTTGGAAGAGGGAA Y 2 1 2 1 103000 r 74 goat snp46874-scaffold654-298325 3 85282998 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421387 Affx-122944033 AX-123291734 3 33161601 GTTTGCTCTCAGAAGTTAGTAGGTTTGGATGGGAT[A/G]TTGCTTGAAACCAGTTTACTTTGAAGGAAGAGCAT R 2 1 2 1 101000 f 74 goat snp46875-scaffold654-327854 3 85253553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388677 Affx-122969007 AX-123259035 3 33192392 GACCCTGCTTGGAATTAAGGACAGTCACAAATTTA[C/T]GTTCTGCCTTTCCCCAGTCATGAGCATTTAATGGA Y 2 1 2 1 101000 f 74 goat snp46876-scaffold654-358645 3 85222683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439953 Affx-122929988 AX-123310290 3 33248522 CCCGCTCCCTCTTCTCACATTCGCCTCTCCTTCTC[A/G]TTTCTCTGCTTTGCCTTCACCCTTTCTCTGCTTTT R 2 1 2 1 101000 r 74 goat snp46877-scaffold654-414775 3 85165384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428503 Affx-122938769 AX-123298845 3 33293650 AATAGCCTTCAAAATACTCACAAGAAGGTTTACAG[C/T]AATGAAACAGCAGTTTAAAAAGTCCTGAAATATCT Y 2 1 2 1 101000 f 74 goat snp46878-scaffold654-459903 3 85120156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791266 Affx-122940159 AX-385278260 3 33348074 ATCAGTTTTAAGTTTTGAGCTTCTGATAACATTTT[A/G]TTGAGCCAAAAGCAGGCACCACAGACCAGAGAGTT R 2 1 2 1 101000 r 74 goat snp46879-scaffold654-514327 3 85065869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377921 Affx-122977228 AX-123248280 3 33388815 CAGTCAATGTACGCTGCAAGGTACATGGGAAGGGG[C/T]AGTGGGAGAATGGACACTTCGACTTGAACCTCGTC Y 2 1 2 1 101000 r 74 goat snp46880-scaffold654-555068 3 85025157 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408612 Affx-122953500 AX-123278963 3 33421585 TGTCTGGTACTCAGGTAACACTGGCTATGAATTAC[A/G]TAAGTCACTGGAGGTATGAACGCAGTGTGAAAACA R 2 1 2 1 101000 f 74 goat snp46881-scaffold654-587838 3 84992393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433594 Affx-122934959 AX-123303935 3 33451459 CTTAACCACTGGACCACCAGGAAATATCACTTCTT[A/C]GAGTTTTGAACCTAAGTCCTGTGTTCTCTTGATTC M 2 1 2 1 201000 r 74 goat snp46882-scaffold654-617712 3 84962474 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387406 Affx-122970411 AX-123257764 3 33492472 TTCTTTCCTGCCTGTGTACCTTGGCTCCTGCTCTT[A/G]CTTCTGGCCCAAATAACCTTACCCCTCTTCTCTGT R 2 1 2 1 101000 r 74 goat snp46883-scaffold654-658725 3 84920760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794916 Affx-122923252 AX-385281876 3 33521333 CTTTTGAGGTAACCTGGACAGTTAGAACTGAATGA[C/T]GGTCATTCATTCTCCTCTATTTAGTGCTACAGTTT Y 2 1 2 1 101000 f 74 goat snp46884-scaffold654-687586 3 84892259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450058 Affx-122922816 AX-123320393 3 33563672 AAGCTATTTACCTCCTTCCTCCCTCCTCTTTTTCT[A/C]TTTTTGTTGTTGTTCCCAGAAAGACATATTGCGTT M 2 1 2 1 201000 r 74 goat snp46885-scaffold654-729925 3 84849923 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388028 Affx-122969556 AX-123258386 3 33592325 ACCTACATGAGTGATTGTCTGAAATATTATAAAAT[A/G]TACTTGATACAGAATAAGAACTTAGTAATTCTGAT R 2 1 2 1 101000 f 74 goat snp46886-scaffold654-758578 3 84820723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444108 Affx-122926824 AX-123314445 3 33683337 ATGAGAAATAAATGCATTTTTTTAAGGTACTCTGA[C/T]ATTGGGGATTGTTTGTTACTTTAGCAGATTCTAGC Y 2 1 2 1 103000 r 74 goat snp46888-scaffold654-849590 3 84730073 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274689 Affx-1111834366 AX-519548275 3 33701290 GGCTGGGAAACTGAA[A/G]TGGCCCCACATGCTCCTGTGAAGGCAGTGAATGGG R 2 1 2 1 102000 r 74 goat GoatD01.032245 3 33701290 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320768189 Affx-122965559 AX-385255380 3 33739867 TTTCTCTCTCTTCTTGAACAAAATATTTTTAGAAG[C/T]GTTTTCAAAATTGCCAAGCAAAAAGCAAGGAACTG Y 2 1 2 1 201000 f 74 goat snp46889-scaffold654-906120 3 84673014 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782835 Affx-122942701 AX-385269906 3 33776242 AAACACTCAATATTATAAGCTTGTTTCAGAAGATA[C/T]GTGGATATTCTAAATATCTTTAGAATCTAAGAAAC Y 2 1 2 1 201000 r 74 goat snp46890-scaffold654-942495 3 84636519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771044 Affx-122935781 AX-385258204 3 33820770 TGTATTCAAGTTGTGTTCACCCATTCTGTGGTTTA[C/T]AGTAACCAGTTACATTAGATTTCTTCTTTTTTTTC Y 2 1 2 1 102000 f 74 goat snp46891-scaffold654-987023 3 84591854 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409884 Affx-122952906 AX-123280235 3 33859837 CTGCCTATTTTTCATATAATTTCTGCTTATACATT[A/G]TGGGATTTTGGTACATTTTACATTCTTTGTGCTGC R 2 1 2 1 101000 r 74 goat snp46892-scaffold654-1026090 3 84552819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444972 Affx-122926668 AX-123315309 3 33903498 CAGCTATTCTTGAAACTTGTCTTCTAGGGTCAGGA[G/T]AAGATGTTAGCATAGGAATCTTTCAAGTGGTGAAA K 2 1 2 1 101000 f 74 goat snp46893-scaffold654-1069751 3 84509180 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446270 Affx-122925671 AX-123316606 3 33948157 TGGGCTACAGTCCACAGGGTTGCAAAGAGTAGGAC[A/G]TGACTGAAGCAACATAACACAATAAAACTTTCAGT R 2 1 2 1 103000 f 74 goat snp46894-scaffold654-1114410 3 84464505 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452652 Affx-122920337 AX-123322985 3 33985812 AAAACAACAACAACAAAAAATCTCGAAAAGTTTCT[A/G]CAAACTGTCATGGCATAGCAAACTTTGGTAAGGTG R 2 1 2 1 101000 r 74 goat snp46895-scaffold654-1152065 3 84427455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277944 Affx-1111836171 AX-519551439 3 34019423 TCTGGCTTTGAGGGCCTGTGGGTCTTAGTTTCAGA[A/G]GACCCACAAGACTGGGAGAAATAGAGACCTCACTC R 2 1 2 1 202000 f 74 goat Random2.2K-311 3 34019423 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424857 Affx-122941343 AX-123295203 3 34040199 GATTTTCAAAAATTTTTCTTGTACTTACCAGAACT[C/T]GAGACCAACACAGACATCTACTCACTTAGTAGAAC Y 2 1 2 1 201000 f 74 goat snp46896-scaffold654-1206452 3 84372587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451903 Affx-122921034 AX-123322236 3 34098168 TAGGTTTAGATTTGGGGCTCTTATAGGGGACATCA[C/T]GGTCTTTGGAGGCATCTGTGATCTGATCCCCAACC Y 2 1 2 1 101000 f 74 goat snp46897-scaffold654-1264421 3 84314585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412128 Affx-122951100 AX-123282478 3 34132776 ATGAATATTTACTAAGAGCCAGTGGGTCAGGCACT[A/G]TTTTAGGTGCTCAGAATACATGGAGGAGTGTGCTA R 2 1 2 1 201000 r 74 goat snp46898-scaffold654-1299029 3 84279599 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453963 Affx-122919462 AX-123324296 3 34167630 ATACAAAAATCACCACCTTTTGTGTTCATTTTCTA[G/T]AAAGGATTTTTTTGTTTTTGACAGAAGTGCCTCTT K 2 1 2 1 303000 f 74 goat snp46899-scaffold654-1333883 3 84244335 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784333 Affx-122965756 AX-385271384 3 34202428 ATATAAATCCGAAGATGTTAGTGAGATTTAGGATA[A/G]TAGGATATATAAGAATTTTGGTTATGGGATAGTGT R 2 1 2 1 201000 f 74 goat snp46900-scaffold654-1368681 3 84208755 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390320 Affx-122967708 AX-123260677 3 34253688 ATGGAATGATAAGCTGTTTGGCATCTTCCCAGTCA[C/T]GCCTTTGCATAAAGAGGGAGATTGGGACTGTCACC Y 2 1 2 1 101000 f 74 goat snp46901-scaffold654-1419941 3 84162741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415361 Affx-122948773 AX-123285710 3 34288551 TGCTGATAAGGCTTGTAGATAGCTATTAAGGATAA[C/T]GTCATTTGGTATAAACATTATTGATTTTAGCTTGG Y 2 1 2 1 101000 f 74 goat snp46902-scaffold654-1454804 3 84127650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385174 Affx-122971737 AX-123255532 3 34392806 TTCTGTAATGTCCAAATACAGAAAGCCTCACTCAA[G/T]TGTAGATTTTTGTCTTTACAGTCAGCCTTGAAACT K 2 1 2 1 101000 f 74 goat snp46904-scaffold654-1559059 3 84022361 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800031 Affx-122945970 AX-385286954 3 34427081 ATGTCAGTACACAAGCCTGAAGTCTAGGGGAGCAA[C/T]ATATTGCTAGCAAATAAGAAATAACTGTACCTCTC Y 2 1 2 1 101000 f 74 goat snp46905-scaffold654-1593334 3 83987913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795106 Affx-122927624 AX-385282065 3 34458581 TACTTGTAAGTTTGACATGAATTCCTTACTGTTGC[A/G]TTGTTCTTCCTTGACATCTTTTGTTGTCAATTATA R 2 1 2 1 102000 f 74 goat snp46906-scaffold654-1624834 3 83956545 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421490 Affx-122943913 AX-123291837 3 34503046 TGAATCATGATATTCAACTGAAGAAAATTAAAAGT[A/G]TCATCTTGGCAACCAATAATGAGAAGGTATAATGC R 2 1 2 1 101000 r 74 goat snp46907-scaffold654-1669299 3 83912790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386021 Affx-122971494 AX-123256379 3 34532918 AGATTTATGAGTTTACTTCCTTTTTTTTGCCAAGT[A/G]CCTAATCTTCCTTTGAAAATTGCTTGATTATCCTC R 2 1 2 1 101000 r 74 goat snp46908-scaffold654-1699171 3 83882765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272199 Affx-1111833384 AX-519545950 3 34538516 TTGCCAAATTCAGAATTAAATTCAAGAAAGTAGGG[A/G]AAACCACTAGACCATTCAGGTATGACCTAAATCAA R 2 1 2 1 303000 f 74 goat 3_34538516_AF-PAKI 3 34538516 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406953 Affx-122955063 AX-123277304 3 34569642 TATAGTGCTGGCTTCTCTATTAGATGCTCAATAAA[C/T]ATGTCTGGAGGAAATTTAATATATTTCCAGACACA Y 2 1 2 1 101000 f 74 goat snp46909-scaffold654-1735895 3 83845924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396976 Affx-122963161 AX-123267331 3 34605119 CTTTTCATTGCCTTTCAAGGATTTTGTATTTGCAC[A/G]TGGCAACTAGAGAAGAGATGACAGCTTCTAAAGCA R 2 1 2 1 201000 f 74 goat snp46910-scaffold654-1771372 3 83811085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801887 Affx-122947416 AX-385288794 3 34638803 AACATAGTTGGAGAGATTTCTCTTGGCTCTGTTGT[A/G]GTGGATAGAGAATGTCTTAGGTGATCAGAAGACGT R 2 1 2 1 101000 f 74 goat snp46911-scaffold654-1805056 3 83777169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440814 Affx-122929822 AX-123311151 3 34679195 CTATTAATGTCGCAGTTATTGTTCCTTTATGATAC[A/G]TATTGTAATAAATCTTTTTTTATTATTAATCTATA R 2 1 2 1 101000 f 74 goat snp46912-scaffold654-1845448 3 83736997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785230 Affx-122965008 AX-385272276 3 34731476 CCTTCTTCCCCTTTCTTTAAAATCAAAGGTACTCC[A/G]ATTGTAGACTAAGGAAACTGACTCTCCCAGTGTTG R 2 1 2 1 101000 f 74 goat snp46913-scaffold654-1897729 3 83687752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434355 Affx-122934717 AX-123304696 3 34775568 CTCTTTAATGTCCAGGAAATATTTGATTCCCAGAA[A/G]ACTGCACTGTAGCCCCTGATATAATTTTCTTGTGG R 2 1 2 1 101000 r 74 goat snp46914-scaffold654-1941821 3 83642788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385652 Affx-122971161 AX-123256010 3 34859131 AAAGACTGCACAAAAAGCTAAAACTGAACCTTATC[A/G]TTTGCTCTCCAGAGATTCTAACACTCCAACTTGAC R 2 1 2 1 101000 r 74 goat snp46915-scaffold654-2025384 3 83559366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407760 Affx-122954976 AX-123278111 3 34905943 GTCTCTGCCAAAATCAACATGAATCAGCCATAGGT[A/C]TACCTATGCTCCCCTCCTTGAACCTCTCCATAAAT M 2 1 2 1 103000 r 74 goat snp46916-scaffold654-2072196 3 83511357 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787839 Affx-122925282 AX-385274862 3 34973592 GACACAAAATTATTCACATTTGTAAACACCATAGA[C/T]GATTTTAGAAGGATTCTAGCTGAGTTAGAGAGTAT Y 2 1 2 1 101000 f 74 goat snp46918-scaffold654-2139845 3 83442371 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435487 Affx-122933438 AX-123305827 3 35025388 TCCAAAATAATTGGGAAAGTTATTCTCTCTTCTTG[A/G]ATGTTGGCTTAGACAGCTGGATACAGTTTTCCTAC R 2 1 2 1 101000 r 74 goat snp46919-scaffold654-2191641 3 83390302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442906 Affx-122927639 AX-123313243 3 35061779 ATAATTTGATTTGATGTCAAAGTAAAAGCACACTG[C/T]TGACTTATGTGTATGTGTTTTATATAAATAGGAGC Y 2 1 2 1 201000 f 74 goat snp46920-scaffold654-2228032 3 83353816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416955 Affx-122948022 AX-123287303 3 35097738 TCAAGAAAACTAAAAAAACAAGATAGAAAATGTTG[G/T]GACACAGTAGACCATCAGGCCATTTCAAGATCCAG K 2 1 2 1 101000 r 74 goat snp46921-scaffold654-2263991 3 83317330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383193 Affx-122972792 AX-123253551 3 35156719 TGATGGAAATAATTGTTTTCTTTTTCCCACAGAAA[C/T]AGACTCATTGAATGCATGCCTTGTTTATTAAAAAG Y 2 1 2 1 101000 r 74 goat snp46922-scaffold654-2322972 3 83257856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442164 Affx-122928311 AX-123312501 3 35186389 GCATCTTTGAACAAAGTCGATTTTGTATTTTTCTT[A/G]CTAATCTTTATACTTTTGATTTCCTTTTCTTGTCT R 2 1 2 1 103000 f 74 goat snp46923-scaffold654-2352642 3 83228108 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769339 Affx-122924037 AX-385256510 3 35221433 AGCTCTTCACATCTACCCTTAGCTCTGCAGAGTTA[G/T]ATATAACTTCACAATTACTTTACTGTCTGGAGACA K 2 1 2 1 101000 f 74 goat snp46924-scaffold654-2387686 3 83193001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795594 Affx-122975160 AX-385282549 3 35253167 CTCCTCATGGCCAAATTTCTTGCTTAAGCCATTCT[A/G]TATTCCCTTGGCTAGTCATGGTTTCTTACATGGTT R 2 1 2 1 101000 f 74 goat snp46925-scaffold654-2419420 3 83162197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433924 Affx-122934300 AX-123304265 3 35289018 TAAACATATCTTCCTTTTTAAAAATCAGTAACTGA[C/T]GAGATATATTTAGTGTCAATCATGTTAAACCAAAT Y 2 1 2 1 101000 r 74 goat snp46926-scaffold654-2455271 NW_017199951.1 11865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794669 Affx-122955688 AX-385281630 3 35318224 GTATTGAGATTAATTTTCCTAGAATCTACCATAAT[A/G]CCTAATTCTCAATAAGCAATTTTAGAATGGATGAT R 2 1 2 1 101000 r 74 goat snp46927-scaffold654-2484477 3 83096351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278100 Affx-1111836172 AX-519551590 3 35322375 TTTATTCAACCCTAAATAATTCAACCTATCTTTTC[A/G]TGGGCCATTTTCTTTGGTCTAATAGGAAATTCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-312 3 35322375 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431634 Affx-122936141 AX-123301975 3 35369406 CTGGGTAGAGAATGAAAAAACACACTTCAGTAACC[A/G]CATTTCTATTGACAGAAGTAATTGGAAGTTTGCAA R 2 1 2 1 101000 r 74 goat snp46928-scaffold654-2535659 3 83044556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803179 Affx-122931305 AX-385290041 3 35400517 CAATAATGTTAATAATCTGAGTCACACATTTATTT[A/G]CTGGTTTAAAGGAAACAAAGTTTTCTGATATATTA R 2 1 2 1 101000 r 74 goat snp46929-scaffold654-2566770 3 83013155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797585 Affx-122929887 AX-385284524 3 35461132 GCATGACCTTGAAGTACGTTAAGCAACTGCATGTA[C/T]GAAAAGGTGACTTCCAAAATTCATGGCCCTTTCAG Y 2 1 2 1 101000 r 74 goat snp46930-scaffold654-2627385 3 82952150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441134 Affx-122929582 AX-123311471 3 35511357 TCTGTTGCCTTACTAAACTTCTTTCTGGTTAATCT[A/G]TTGATGTCCGTGGGGTGTTAAAAACTCCTACTATT R 2 1 2 1 101000 f 74 goat snp46931-scaffold654-2677610 3 82901927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451330 Affx-122921273 AX-123321663 3 35527664 AACAGAATTGTTATTCAAATATACCTCAGGCTTAA[C/T]TGCAGATTTACCCTTTGACATAACATATGGATTGA Y 2 1 2 1 101000 r 74 goat snp43590-scaffold582-14146 3 82883735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412080 Affx-122951694 AX-123282430 3 35558017 TTTCCCTTCTCTTTCATTGAGTTTCTATTTTTTCT[A/G]TCTTTTCAATGCCAATCCAAAATATATAATCAACT R 2 1 2 1 201000 r 74 goat snp43591-scaffold582-44499 3 82853631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803494 Affx-122943928 AX-385290315 3 35607221 TAGTTTTCCAGATTCATGCATACTTGTTTTCCAAT[C/T]CTGACTCAGTGTGTTTTTACTTCAGTTCTGTATGG Y 2 1 2 1 101000 r 74 goat snp43592-scaffold582-93703 3 82803560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381786 Affx-122974293 AX-123252144 3 35639323 CAAAAATAAAATTTTTACATTTGCAAGAATGAATA[G/T]AACAGAAAAGAAACAGACTTTGAGGTGAATGACTT K 2 1 2 1 202000 f 74 goat snp43593-scaffold582-125805 3 82771183 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409223 Affx-122953158 AX-123279574 3 35674225 CTTTGACATATGATTTTTAGAATTAAAAAACAAAC[A/G]TGATCCAACACATTGCCATTGGGATTCTGTTGCTT R 2 1 2 1 101000 r 74 goat snp43594-scaffold582-160707 3 82735707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394744 Affx-122964858 AX-123265099 3 35719873 ATTCTTCTGATCTATGTGGTTGTTGGCTGGGATAA[C/T]AGAGCAACAGCAGTCTTAGATTCAACTGTGGGTTC Y 2 1 2 1 101000 f 74 goat snp43595-scaffold582-206355 3 82689652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775374 Affx-122960351 AX-385262505 3 35752482 TAAGGACACCTAAATTCACTGTTTCTCCAGACTAA[C/T]GGCAATAACTTCGGTCTGTCACTTTACTCTCTGTC Y 2 1 2 1 201000 f 74 goat snp43596-scaffold582-238964 3 82656523 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783475 Affx-122930186 AX-385270538 3 35803400 TGAAGAGATCTAAATAAAAGACCCATCTTTATGAA[C/T]GCTTCACCAAACTTTTACTAAACTCTTCTTTCTTA Y 2 1 2 1 101000 r 74 goat snp43597-scaffold582-289882 3 82605682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432882 Affx-122935342 AX-123303223 3 35838212 TAAAAGACTGGTTGTTCAACTCATAGTTACTATTA[C/T]AAGTGTGTATTTTATGCCTTTGGTCCTAACAGAAA Y 2 1 2 1 101000 r 74 goat snp43598-scaffold582-324694 3 82570793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395553 Affx-122964247 AX-123265908 3 35895281 ACTTACTTATAGATCTATGTAAAATAATAAATAGC[G/T]AATTTTAAAGACATTAATATGTAGTGTGTTTGTTA K 2 1 2 1 101000 f 74 goat snp43599-scaffold582-381763 3 82516140 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275542 Affx-1111834961 AX-519549113 3 35914102 GTTCCATCAGGTCTCAATCTGCAGTTTTCCAGACA[A/C]CCTCAGACATGTCTAG M 2 1 2 1 101000 f 74 goat GoatD01.060076 3 35914102 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424358 Affx-122941853 AX-123294704 3 35952253 AAATGATAAATCAAGTTTCTATACTTTCTCACATC[A/G]TTTAATTTTAAAACACAGAATTGAAATGTATTTTT R 2 1 2 1 303000 r 74 goat snp43600-scaffold582-438735 3 82457915 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764424 Affx-986696818 AX-385252122 3 35969269 CTTAAAAATGGTATTTCCTATTCAGAAATTAATCA[A/C]ATTAAATTTGGAAGGAATTTGATCCTAAAGATGGT M 2 1 2 1 600010 r 74 goat 3_35969269 3 35969269 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 468277947 Affx-1111836173 AX-519551442 3 36011916 CGCTTGCTTTCATCAGAAGATGTTCACAAAATCAC[A/G]GCAGTTAAGGCAGAAACTTTGGCATCAGAACATTC R 2 1 2 1 101000 f 74 goat Random2.2K-314 3 36011916 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424676 Affx-122941713 AX-123295022 3 36030712 CAGCCAGCGACCCTCAGCACTCTTTGGCTTTTAGA[C/T]GTATCAGTCCAGCTGGGGCCTCCATCTTCATACAG Y 2 1 2 1 101000 f 74 goat snp43602-scaffold582-517194 3 82381273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795430 Affx-122932677 AX-385282386 3 36059562 TTATGTCCTGCTTCCTTCAGTAGTATATGAAGGCA[C/T]GTAGTGATATTCTTCACTATTTTATCTTAAATTAT Y 2 1 2 1 101000 f 74 goat snp43603-scaffold582-546044 3 82352402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798598 Affx-122920130 AX-385285531 3 36098469 ATTTATGCAAGATGATATTATATAGTGAAATAAAA[C/T]ACAGCCTTGTTGTGTCATGGCTTGCCATTTAACAT Y 2 1 2 1 101000 r 74 goat snp43604-scaffold582-584951 3 82313126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772215 Affx-122966462 AX-385259370 3 36145082 GTTCACTGACAAACATTTGACACCTTATCCACTTC[A/G]TGACTGTTCCATGATTGCTTCAATACTATCATACA R 2 1 2 1 101000 f 74 goat snp43605-scaffold582-631564 3 82268189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381397 Affx-122974377 AX-123251755 3 36194076 TACACCGCTCTGTGAACAATTATGAAAACAGAAAA[C/T]AAAATCTTGAGTAGTAGTACCACTTTGGAGAATAC Y 2 1 2 1 202000 r 74 goat snp43606-scaffold582-680558 3 82218791 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793435 Affx-122951073 AX-385280412 3 36270427 TTTGAAATATCATTATTATAGAACTTGAAGTAGTC[A/G]TTTTCACACTTCAATTTTGTTGCTGAGCCAGAGAG R 2 1 2 1 202000 f 74 goat snp43607-scaffold582-756909 3 82142073 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385269 Affx-122972075 AX-123255627 3 36300937 CATGCTACATTTTGGAACTATCAGTCTCTCTCAAA[A/G]GAAATTATAAATCAAATATGCTAATATGTAAAGTC R 2 1 2 1 101000 f 74 goat snp43608-scaffold582-787419 3 82111640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426266 Affx-122940323 AX-123296612 3 36349407 GTGCCCTGATAAATACTTATACCTAGCTGGCTACT[A/C]TCTAATATGCCCACACAGTTTTGGTCCTGTCCCAC M 2 1 2 1 101000 f 74 goat snp43609-scaffold582-835889 3 82063158 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428824 Affx-122938378 AX-123299166 3 36394559 CCAAAACACCTCTTCTGTCTTTAAAAAACTAAACA[C/T]AGAACTGGCATATGATACGGCAATTCCACTCCTGT Y 2 1 2 1 101000 r 74 goat snp43610-scaffold582-881041 3 82018719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766073 Affx-122962020 AX-385253489 3 36450778 ACCAATTGGAAACACAAAAATCTAAAAGGTTAATA[C/T]TCCAATGGAATACATCAAGAAGTGAACCTTGTGAA Y 2 1 2 1 201000 f 74 goat snp43611-scaffold582-937260 3 81962222 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795672 Affx-122951879 AX-385282627 3 36488368 ATGTTTAGTCAATACATTTCTCTCAGGGATAATTT[A/G]TTCTTTGTTAAATGAAGAACAGTGAAGGCAAGGGT R 2 1 2 1 201000 r 74 goat snp43612-scaffold582-974850 3 81924701 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775526 Affx-122942944 AX-385262657 3 36517197 TTGATGTTTGCAACAGTCCTGAATTCAGATTAAGA[C/T]GAGAGATGTTTGCCTGACAAGGAAACAAGACTAAG Y 2 1 2 1 101000 r 74 goat snp43613-scaffold582-1003679 3 81895836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402645 Affx-122958386 AX-123272998 3 36606841 CCCTAATTTGGATAAGTAATACCTCTAATCCCTCA[A/G]TTATGTCAGTTACAAGTTATATCAAGGAAGCATAA R 2 1 2 1 101000 f 74 goat snp43615-scaffold582-1093323 3 81806198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778472 Affx-122962590 AX-385265586 3 36646518 GTACTTTGTAAGCGTAAGTAACTATTGAAAAGGGA[A/C]TCATTGAATGAATAATCCATCCATGTGTTTTTATG M 2 1 2 1 202000 r 74 goat snp43616-scaffold582-1133000 3 81766469 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771544 Affx-122951178 AX-385258702 3 36716489 GAAAGTAAATATGTGACTTTCTTATAAGAAGTACC[A/G]TTATAAGAAATTGTATAGAAAGAATCTCTCAAGGT R 2 1 2 1 101000 f 74 goat snp43618-scaffold582-1202971 3 81694860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774801 Affx-122920003 AX-385261935 3 36766020 GTACATTTTTAGGTTGGATCTTCTTTTCCATGTGT[A/G]CATTTGCTTTGTTGTTTCTAATTGTTCATGGTATT R 2 1 2 1 101000 r 74 goat snp43619-scaffold582-1252502 3 81644702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802208 Affx-122977328 AX-385289112 3 36824846 GAATGATCCTTGGCTAGATGCTTATGTCAGGACAA[C/T]AAACTTGAAATATCATGCAGCACTTGCAGTTCAGA Y 2 1 2 1 101000 f 74 goat snp43620-scaffold582-1311328 3 81584393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440709 Affx-122929900 AX-123311046 3 36909248 CAAATGCCAGATAAATCTACCCCACAAACCAGTTG[C/T]TATAATCATTGCCCTGACCCAAGACCTAAGATGAA Y 2 1 2 1 201000 r 74 goat snp43621-scaffold582-1395730 3 81498859 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437713 Affx-122931747 AX-123308051 3 36917405 TTTTAAACTCAAGCTCTAACAGACTGTAGGTGTCC[A/G]TTTTATTCTTTTCATTAGAAGTAGTTCCTCTGCTT R 2 1 2 1 103000 f 74 goat snp21571-scaffold2102-137705 3 81490846 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772232 Affx-122959340 AX-385259387 3 37014595 ACATTTTACTCCTTTCATTTTTGCTGCCATGCACT[A/C]GAATCAAACTCAGTGAATTAATTTTTTCCTATCCA M 2 1 2 1 101000 f 74 goat snp21569-scaffold2102-40515 3 81392350 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384679 Affx-122972128 AX-123255037 3 37071006 CTCTGTGGAAGTCAGGTCCTGGGGTTCTCCTCTCT[A/G]TTTCTGGGATTTTTAAAAAATGAGGTTTGCAGGTG R 2 1 2 1 201000 f 74 goat snp22465-scaffold222-1353540 3 81342067 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272032 Affx-1111833385 AX-519545797 3 37106836 TAAACAATCAGATTATGAGAAGCATTTCTTAATCT[A/G]TTTTTCTTACATTGTAATCAACTTTTAATTCTGTT R 2 1 2 1 101000 r 74 goat 3_37106836_AF-PAKI 3 37106836 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424128 Affx-122942012 AX-123294474 3 37231756 TTGGTTGTCGACATGAGAATTGCTAAGACGTAGAC[A/G]TCAATTTCTCAGGGAGGAAAAATACAGAAATATGC R 2 1 2 1 101000 f 74 goat snp22461-scaffold222-1192790 3 81178869 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777547 Affx-122965338 AX-385264666 3 37322030 CAAAGCAGAAAGAGACAGGCTATAAGTTGGGAGCC[A/G]CTTTGCCAGTTTTTCTGAGTAAGGAAACTCTATGC R 2 1 2 1 101000 r 74 goat snp22459-scaffold222-1102516 3 81088564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386933 Affx-122969996 AX-123257291 3 37407941 ATTTCTTTGTTTAAGGCTCGCACTCTTCTAAAGAG[C/T]ATTTAGATGTGCACTGCAACAGTTACTTCACCTTT Y 2 1 2 1 101000 r 74 goat snp22457-scaffold222-1016605 3 81001841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388965 Affx-122968800 AX-123259323 3 37447199 AGGTAAAGCAGTGCTTGAAAATTGCTTTCTTAAAA[C/T]GTTGATTTTATGGATTTTAAAATTTTCCTTCTAAA Y 2 1 2 1 103000 f 74 goat snp22456-scaffold222-977347 3 80962409 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791574 Affx-122923292 AX-385278565 3 37492889 ACGTTAACATTGTCACTCTTCCTGATGCTTTTTTA[C/T]AATCTTTTGCCATCATATTCATATAAATTATGTGT Y 2 1 2 1 101000 f 74 goat snp22455-scaffold222-931657 3 80916281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768740 Affx-122956626 AX-385255918 3 37525247 GTGATGCTAGCTTTTGCTTTGCTGTTCAGAATCAC[A/G]TTTTACAAGCCCATCCATTAAGAGATTCTTCCTAA R 2 1 2 1 101000 f 74 goat snp22454-scaffold222-899299 3 80883442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768292 Affx-122952204 AX-385255472 3 37572717 ACTTGCTGAGGGGCATTTACTTGGTAAAGTCATCA[G/T]ATTTTAGATCTGACTTTAGTCTTCGACAAACATTG K 2 1 2 1 201000 r 74 goat snp22453-scaffold222-851829 3 80835937 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376474 Affx-122978040 AX-123246833 3 37601963 CGTTTTATTGCTGTGAAATCCTGTGAAAGAGAAAA[C/T]AAGTCTGGAAGAATATTCAGGTACAACACTGTCAC Y 2 1 2 1 201000 f 74 goat snp22452-scaffold222-822583 3 80806355 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774821 Affx-122921617 AX-385261955 3 37730445 ATAATATCCATATGAGAAGTAGGATTTTTGAAGTA[G/T]TAAATGTAAGTTACTTTGTTCAGTGCCTCTAGTGT K 2 1 2 1 201000 f 74 goat snp22450-scaffold222-694101 3 80675857 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416745 Affx-122948196 AX-123287093 3 37831940 CCCCTTCTCTCTCTCTCTCTCTTATAAGGAGCTTG[C/T]GGAGATTAAATGAGATGCTATACAGGAAGGCCCTG Y 2 1 2 1 101000 r 74 goat snp22448-scaffold222-592606 3 80571972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431424 Affx-122936521 AX-123301765 3 37898920 GCACTAAATAGGGGAAAGAAACTTTTATGTATTAA[C/T]AAAAATTAGTTCTATATCAAAGCTTTAAAAATCTT Y 2 1 2 1 202000 r 74 goat snp22447-scaffold222-525626 3 80506857 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768819 Affx-122933374 AX-385255996 3 37930325 CTAGGCTTCAATCTTTTATGTATAATATGACAATT[A/G]TGTCTTACAAAAGGCAAATATGAGGGGTAACTATT R 2 1 2 1 202000 r 74 goat snp22446-scaffold222-494221 3 80476865 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420789 Affx-122944694 AX-123291136 3 37959263 CCGAAATATTTTAAAAACGAAATAGATGACTGAAA[C/T]GCCTAAATAATTGACTCAAAGGTTACTTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp22445-scaffold222-465283 3 80447899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429630 Affx-122937689 AX-123299971 3 38031438 ATTCTGCTTTAGGTGATATTAAGGCTGATGGCCCA[C/T]GGTCCACATTTTGAGTAGCAAAGATTCTAGAAAGT Y 2 1 2 1 201000 f 74 goat snp22443-scaffold222-393108 3 80375226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793048 Affx-122962650 AX-385280026 3 38109840 CTTCAATAATCTCATGCTCTCTGAGCTACAAATTG[C/T]TGCATTAATTTAATAGGTTTGTCACATTCTTTTTA Y 2 1 2 1 101000 f 74 goat snp22441-scaffold222-314706 3 80296779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419706 Affx-122945916 AX-123290054 3 38144920 TAGGGAATGTATTTGTTCAACTTGGGCTTCCTCGG[C/T]GACTCAGCAGTGAAGAATCTGCCTGCAATGCAGGA Y 2 1 2 1 101000 f 74 goat snp22440-scaffold222-279626 3 80261738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397210 Affx-122962391 AX-123267565 3 38209784 GCTTTCAAGGACAGGAAAAAAAAATTCACCAAGTA[C/T]TTTTCAAACCATTATGAAAAATCCCCCCATAATTG Y 2 1 2 1 303000 r 74 goat snp22439-scaffold222-214762 3 80197099 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390442 Affx-122967627 AX-123260799 3 38257075 AATCACTACATTCAGCAGTACAATAAAGGCAGCTA[C/T]AGTCTACTTAAAATTCTCAACTCCATTCATTGAGA Y 2 1 2 1 101000 f 74 goat snp22438-scaffold222-167471 3 80150162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801717 Affx-122949339 AX-385288625 3 38293519 AGGGCCCTGTAAAAGACCCAATGCAATTTAAATAC[A/G]TAATGCACTGAAAGTGCCCCTCACTCACATACTAC R 2 1 2 1 101000 r 74 goat snp22437-scaffold222-131027 3 80113827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436538 Affx-122932927 AX-123306876 3 38353202 TAAATTTAGATTCTTCATTTTACAACCCTGCAAGA[C/T]GGTAAATGCCTTTCCTATTATGGATATCTTAGCCC Y 2 1 2 1 101000 r 74 goat snp22435-scaffold222-71344 3 80053840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772763 Affx-122922511 AX-385259908 3 38384297 TTATTTTTAAGAAAGACTAGAGTGAAAATGGATAA[C/T]GTAATTTTTCTAAGAGGATAGGCAGTTTTCCTAAA Y 2 1 2 1 101000 r 74 goat snp22434-scaffold222-40249 3 80024879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378520 Affx-122976636 AX-123248879 3 38416038 AAAAATAAAAATCTGTGTATTTGTGTAGCTTTGTA[C/T]GAATACTATTATAGGGAGAAATGCCATTATAAGGC Y 2 1 2 1 101000 r 74 goat snp22433-scaffold222-8508 3 79993119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425716 Affx-122940765 AX-123296062 3 38447841 GTGTTGCAAGTCTACTTAGACATAAATCATCTTTG[C/T]GTTTGTGTGTGAGAGAGAGACAGAGAGAGAGCAAG Y 2 1 2 1 202000 f 74 goat snp21085-scaffold2063-155139 3 79959916 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439010 Affx-122930359 AX-123309347 3 38531229 CTTGGATCCCTCCTCAGCCTATGTGCTTGGTGATT[A/G]TAAACAAGCATTACAGTTCTTGGGAAAAGCAGAAT R 2 1 2 1 101000 r 74 goat snp21083-scaffold2063-71751 3 79875903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444364 Affx-122926706 AX-123314701 3 38587080 ACGGCTAGCCTTCTCCTATTCTCTTTGGATCAGGG[A/G]CTGCTTCTCCTGAAGGTGGCTAGGTTTCGACCTAT R 2 1 2 1 101000 f 74 goat snp21082-scaffold2063-15900 3 79819376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771780 Affx-122921957 AX-385258937 3 38603587 CAAAATATTCAATTGTGCTAACTGAGGTGATTCAT[A/G]TAGCACTATATTTTTTCTTATGAGTCTTAAAAATT R 2 1 2 1 201000 r 74 goat snp6600-scaffold1236-508 3 79803271 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380941 Affx-122975006 AX-123251299 3 38634418 TGCTTTCCATAACACTTCAGATGAAGACTTGTAGG[C/T]GGATTAATTGTAAAAAGTTGTTTCTTTTGGTTTAT Y 2 1 2 1 101000 f 74 goat snp6601-scaffold1236-31339 3 79769740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773105 Affx-122978384 AX-385260248 3 38758113 TCAGCATCAGAGAAAATGTAGGAATAAGTATGCCA[A/G]TTCAGCAGCCAACCTCTCTTTTGTTAATGTGAAAG R 2 1 2 1 201000 f 74 goat snp6604-scaffold1236-155034 3 79644136 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405809 Affx-122955895 AX-123276161 3 38792547 TGTGACTCCACTCCAAGTATATACTCTAGACACAC[A/G]CATGCTCAATTACACAGATGTTGCTCACATTGAGA R 2 1 2 1 101000 f 74 goat snp6605-scaffold1236-189468 3 79612716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386919 Affx-122970008 AX-123257277 3 38821456 GCACATTTTTTAAAATCTATTTGACAATTAGCCTG[C/T]ATTATTTCAAACTATCTACATTTTTATTGCATTAT Y 2 1 2 1 303000 r 74 goat snp6606-scaffold1236-218377 3 79584165 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445411 Affx-122925379 AX-123315748 3 38852602 TTTTAACCCACTTAACAAATAATCTTGAAACAATT[A/G]TAGATTCACAGGAAGTTGCAAAGATAGTATAGTGA R 2 1 2 1 303000 f 74 goat snp6607-scaffold1236-249523 3 79552698 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785188 Affx-122952237 AX-385272235 3 38910979 TTGAGAATTATTACCTAAATAAACCTTATTAACAT[A/G]AGATTTACCTGCACCTTTTTTATACCCCTTCAACC R 2 1 2 1 201000 f 74 goat snp6608-scaffold1236-307900 3 79496338 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442484 Affx-122927928 AX-123312821 3 38956482 GTACTTCTGCCACTACTTTGTGCTTAGTTGCTCAG[C/T]AGTGTCCAACTCTTTGTGACTTATATATATATATT Y 2 1 2 1 103000 f 74 goat snp6609-scaffold1236-353403 3 79450839 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396810 Affx-122963287 AX-123267165 3 39011834 TCCAGTAGAATACAGCTGTGTCCTGTCACTCATCC[A/G]TGATTAAACATGTAGTGGTGGTACACATTCTCAGG R 2 1 2 1 101000 r 74 goat snp6610-scaffold1236-408755 3 79396945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769213 Affx-122920343 AX-385256388 3 39062185 GGTGTAAGGAAAGGTCTGCTACAGCTGCTGTTGCA[A/G]TTACTGACGCGACTGCGAGAATAGAAGCAATGACA R 2 1 2 1 102000 f 74 goat snp6611-scaffold1236-459106 3 79346608 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785818 Affx-122968237 AX-385272856 3 39094937 TTACAGTTACCTGAGGAATCATACTAGAACAAGGA[C/T]GATTATAGCCCTTGGTTGAGATCATGTTTAATTTC Y 2 1 2 1 101000 r 74 goat snp6612-scaffold1236-491858 3 79314238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796685 Affx-122947400 AX-385283630 3 39141947 TATATGTAATATGATATGTTGTTTGATAAATGTTT[A/G]CTCATGCTAATGGAAGACCCTAGATTGTATAGTAC R 2 1 2 1 101000 r 74 goat snp6613-scaffold1236-538868 3 79267264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396175 Affx-122963773 AX-123266530 3 39193860 ATAGCGGGTCAGAGTTCCTTAAGTGGAATTTAACC[A/G]TAAAAAGGGTAATTTGAATTTATCTAATTATATAC R 2 1 2 1 101000 f 74 goat snp6614-scaffold1236-590781 3 79215406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788746 Affx-122972345 AX-385275762 3 39253735 AATTTTTAAGATATTTGAAAAAAACATGGATTCTC[A/G]TGAATATGAACATCCTCCAGTCTTTGACCATTTCT R 2 1 2 1 202000 f 74 goat snp6615-scaffold1236-650656 3 79155971 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409586 Affx-122953571 AX-123279937 3 39306859 TGCTTGCATTTACTTTTTGTTGTTCTTTTCTTTTT[A/G]CTTTTACTGCATTTGTTCTCAGGGACTGTCAAAGT R 2 1 2 1 103000 r 74 goat snp6616-scaffold1236-703780 3 79101788 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390857 Affx-122967822 AX-123261214 3 39382198 AAATATACACTGAATTTATTCTTATCTGATCTATT[A/G]GCTAGGTTGCTTATTTTTCATTTATTTTCTCACTC R 2 1 2 1 201000 f 74 goat snp6618-scaffold1236-779119 3 79026201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779737 Affx-122971609 AX-385266837 3 39421778 AAGAGGAACAGCTTAATTTGCCAAAGTCATTAGAG[A/G]TTAAACTTTATCTGGTCCTTAAGTTGTAACCATAG R 2 1 2 1 101000 f 74 goat snp6619-scaffold1236-818699 3 78986488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777633 Affx-122927791 AX-385264752 3 39469402 AATGTTGGTGCTATGACAAAGATGTACAAGGTACT[A/G]TAAGTATTTTTAATAGGAATTAAAGGATGTCAGGG R 2 1 2 1 101000 f 74 goat snp6620-scaffold1236-866323 3 78937099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785681 Affx-122951092 AX-385272722 3 39481925 TGACTATTAAATGAGTATTAATCTTTCCTTCTCAA[C/T]AGCTGTTTAATCAAGATTTTTCTCTAGGTGGGAGA Y 2 1 2 1 101000 r 74 goat snp56242-scaffold879-1912984 3 78923218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800270 Affx-122930649 AX-385287193 3 39510953 ATATCCTAGCATCTGATCAGGAACACAAAACACTG[A/G]CTAGTTGAATGCCCACTCTCCTAAACACAGTGCTA R 2 1 2 1 101000 f 74 goat snp56241-scaffold879-1883956 3 78893608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449311 Affx-122923002 AX-123319646 3 39547483 ATAAAAAATTAATTTTAAAAGATTTAAAAGATTAA[G/T]AAAACCTGACATTAGGTCACATGTAACAGTGTGAG K 2 1 2 1 103000 r 74 goat snp56240-scaffold879-1847426 3 78856396 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767836 Affx-122936366 AX-385255056 3 39588658 GCTTTGGGGATTTGGATGAAGAAGAACCTCTCCTA[C/T]ATCAGAGTCCTGTGCCTAGTTACTACCAGAAAAAT Y 2 1 2 1 201000 f 74 goat snp56239-scaffold879-1806251 3 78815388 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412372 Affx-122950814 AX-123282721 3 39618985 TTAGTGAGCATCTGAAACATAGCATCATCATTTAC[C/T]TGGAAGGGGAAAATAGGCCTGTTTTAAATGTAAAT Y 2 1 2 1 201000 f 74 goat snp56238-scaffold879-1775924 3 78784766 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785432 Affx-122937485 AX-385272477 3 39670240 AAGCTTCCTCTGACCTCTGCAGACTTTGTTTAGTG[A/C]CCTTCATCAGTATCCCTTTGATCCTCTGTGCTCTG M 2 1 2 1 101000 f 74 goat snp56237-scaffold879-1724669 3 78733141 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423721 Affx-122942875 AX-123294067 3 39727019 CAATAGTGTTCCTCACCTCTCAAGGTTTCACAGAA[A/G]AGGTGCTGGAAGAGGTGGTGGTAACCATAAAGGTG R 2 1 2 1 101000 f 74 goat snp56236-scaffold879-1667890 3 78676301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377534 Affx-122977466 AX-123247893 3 39756393 CAATGGCATGTTTTCTTGCGGCTAGACTGTGACTG[A/C]ATCCTGTCATTTCATATTTGCAGGCTGCTCCATCT M 2 1 2 1 201000 r 74 goat snp56235-scaffold879-1638516 3 78645053 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416532 Affx-122947760 AX-123286880 3 39790183 TGTTGTCTTCTGAGCATGTACAAAGAAAAATGACC[A/G]TATGGGCTATATTTCTGGCTAGTCTCTTTTAATTC R 2 1 2 1 101000 f 74 goat snp56234-scaffold879-1604726 3 78611056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385183 Affx-122971730 AX-123255541 3 39834683 ACAGGGTCTGTTAAAGGCAAAAAGAGCAAAGCAGG[C/T]GGAGATCAGAGAAGAATTTTACAGGTGTGAGTTTT Y 2 1 2 1 101000 f 74 goat snp56233-scaffold879-1560226 3 78566522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272035 Affx-1111833386 AX-519545800 3 39849930 AGAAATTCTCTTTACCACTATGTAGAAGAGATCCA[A/G]TGGTACAGTGGCCTATCACCGTCATCAATTTTTTT R 2 1 2 1 101000 r 74 goat 3_39849930_AF-PAKI 3 39849930 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438343 Affx-122931335 AX-123308681 3 39882101 CCTTTTGGTTGTTAAAAACCCTTCCTTTTTCTTGA[C/T]GGGTCTTCTGTACTATTATCACTCTTTGTCTTTTT Y 2 1 2 1 101000 r 74 goat snp56232-scaffold879-1512808 3 78519545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434312 Affx-122934752 AX-123304653 3 39917972 GAGAAGAGGTGTGTTCAGTGGGGATCTGCTTCTGG[C/T]GGTCTCACCAATGCTCCATTTTACTTGCTTTGAGA Y 2 1 2 1 101000 r 74 goat snp56231-scaffold879-1476937 3 78483085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398753 Affx-122961450 AX-123269108 3 39951875 ACAAAATCAGATTTGAAAATGAATAGAATAAAAGA[C/T]GTCACAACAAACTGCTAATTTTAAAAAGCCAGCAG Y 2 1 2 1 201000 f 74 goat snp56230-scaffold879-1443034 3 78448708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414437 Affx-122949955 AX-123284786 3 40016315 AGAAAGACTGCCTTGAAAAATAGTGCAAATAATTC[A/G]TGCAAGTTAAGCTTGGAAAAGCAGAATCTTAAAAA R 2 1 2 1 101000 f 74 goat snp56229-scaffold879-1378594 3 78382963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407145 Affx-122954855 AX-123277496 3 40053449 TTTTCCACTACAGAAATCAAAGCAAAAAAGTTTTC[A/G]TTTTCTCATTAAACTAGAAAACTCATTCAGTCAGA R 2 1 2 1 303000 r 74 goat snp56228-scaffold879-1341460 3 78344760 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788651 Affx-122972549 AX-385275667 3 40100659 ATTCCTCAGTTGTGATCAGAAGATGAGAATAATTA[C/T]GTCCAGCTATAGGCTTGTTTTGTGGGTTAAAGAAA Y 2 1 2 1 101000 r 74 goat snp56227-scaffold879-1294250 3 78296821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386666 Affx-122970196 AX-123257024 3 40141457 TAAGTAGTTTGAGTTGTGATTTAAGTTTTCTCTTT[G/T]TAGTGGCATCCCTACCATTGTTTTTTCTTTCCTGC K 2 1 2 1 101000 r 74 goat snp56226-scaffold879-1253452 3 78255635 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376213 Affx-122978806 AX-123246572 3 40187382 TAAAGAACAAGGAAGTAAATATTTTAGGTTCTGAA[C/T]GCCACAAGGTCTCTGCCAAAACTACTTATTGCTGC Y 2 1 2 1 101000 r 74 goat snp56225-scaffold879-1207527 3 78211486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275273 Affx-1111834694 AX-519548849 3 40194763 AACTCA[A/G]TTTAGATATCTGAGCTTCAAATACTGCAGGACATA R 2 1 2 1 101000 r 74 goat GoatD01.046382 3 40194763 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802225 Affx-122940554 AX-385289129 3 40274913 CCCTACTTTTTATTAGAAGCAAAGAATTAGAAACC[A/G]TGTTACTTACAAAAGGATTTGCTAGCCAATCTTTA R 2 1 2 1 201000 f 74 goat snp56224-scaffold879-1119996 3 78124736 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396762 Affx-122962775 AX-123267117 3 40309644 AGACTGAATTATTTTTAGAACTTAAAATTTTCTAT[A/G]CTGTGTTCTAAAAAGTATATGCAGGTGACTAGGCA R 2 1 2 1 101000 r 74 goat snp56223-scaffold879-1085265 3 78090704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774865 Affx-122922381 AX-385261999 3 40371352 ACAAAGACAGCAGACATGCTGAACAGCATCAAATC[A/G]TGTGCAAGGAAGGCCACAGAGTTATACAGAGAGAA R 2 1 2 1 102000 r 74 goat snp56222-scaffold879-1023557 3 78028731 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787772 Affx-122922833 AX-385274795 3 40428048 TTAGCTGCATGGGTTTGGGTTCTGCTTCCTCTTCA[C/T]GGGTTTGGGTCGGTTGTTGATTAAATTGGAATGTT Y 2 1 2 1 201000 f 74 goat snp56221-scaffold879-966861 3 77972270 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427971 Affx-122939188 AX-123298314 3 40469474 GTATCTTTCACTATATGAGACCTTACTCAAATTTG[C/T]AATCTACAGCCACAGATCTCTCATGATCTTGGATG Y 2 1 2 1 101000 r 74 goat snp56220-scaffold879-925435 3 77930440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382578 Affx-122973756 AX-123252936 3 40502514 ATATAACACAGTGCAGCAAGTATATTCCTTCCTCC[A/G]CACATCAGTCATTCAACTATCCATGGCCTTCGTGT R 2 1 2 1 201000 r 74 goat snp56219-scaffold879-892395 3 77896836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779080 Affx-122977601 AX-385266185 3 40590549 TAATAATAATATTGATATTAACTTGCTCAGTGTCA[C/T]GTAAGTGGTCGAGATTTGAACTCAGGAATTCCTGA Y 2 1 2 1 101000 r 74 goat snp56217-scaffold879-804360 3 77808526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782960 Affx-122971834 AX-385270029 3 40619440 TAGCACCCCCTCTTCACTCACTGAGTTTTGGACCA[C/T]GTAATACATAAGAACATGTATGTAAATGGTGACCC Y 2 1 2 1 303000 f 74 goat snp56216-scaffold879-775469 3 77779666 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796142 Affx-122953993 AX-385283093 3 40655248 AGAAAGTAGAAAATAATTGCATTAAGTTATTTTGA[G/T]CTGGGTTGAAATGTTAATTTATTCCCACCCAGTTC K 2 1 2 1 201000 r 74 goat snp56215-scaffold879-739661 3 77743009 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380610 Affx-122975246 AX-123250968 3 40687427 AGGCTTCTCACCATCACCAGCAACCATGTGGCTTT[A/G]TTTCAGGGGATTTGTTGCTCCTAGAGCAGCTGAGA R 2 1 2 1 101000 f 74 goat snp56214-scaffold879-707482 3 77711066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380616 Affx-122975243 AX-123250974 3 40735904 GTGTGTATGTGTGTGCACATGTGCACACTCGTATG[C/T]GCAGGCACACACATTTAATTAGAAAAACCAGTTTG Y 2 1 2 1 303000 r 74 goat snp56213-scaffold879-659005 3 77662044 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773920 Affx-122972297 AX-385261059 3 40785725 ACTGACTTTCTTTTATGGTGTGTTCAAAGACTATA[C/T]GAGACAACATACATTCCTTCTGCTCTCATTCAATT Y 2 1 2 1 101000 r 74 goat snp56212-scaffold879-609184 3 77612335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377017 Affx-122977720 AX-123247376 3 40814459 ATTGCTGGTTTTGTGTGTGTGTGAGTACTCATTCT[A/G]TTCCCAATGGCCTTTGTTTTAATTTTGTGAATTAA R 2 1 2 1 303000 r 74 goat snp56211-scaffold879-580450 3 77583562 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406171 Affx-122956160 AX-123276523 3 40853028 AGAGAGCAGGAAAGTTCAACGTAAAGCAGAGGAAA[C/T]GAGTTTGTTCAAATAAGGCCAAGTTTCATGCATTT Y 2 1 2 1 101000 f 74 goat snp56210-scaffold879-541881 3 77545004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380988 Affx-122974677 AX-123251346 3 40893242 CTCTTAGTAATTAATTTTTTTTTAATATTGTGCCT[A/G]TTGTAGGTGTTAATGCAGACAAGGTTGGAATTGAA R 2 1 2 1 101000 r 74 goat snp56209-scaffold879-501667 3 77504423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430468 Affx-122937255 AX-123300809 3 40947572 AGGGTTATTGTGAGGATTAGCTGTAATGTTATGTA[C/T]GGCATCTGGCTCAGAAGTGCTGAAACGATGGAGGC Y 2 1 2 1 101000 f 74 goat snp56208-scaffold879-447337 3 77449737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277949 Affx-1111836174 AX-519551444 3 41030095 CCTGCCACTACTACTGAGAGCACTGGAAACGATGC[A/G]TGTGAAAAGTAGAAGATAGCATTATTTCTGCTCTT R 2 1 2 1 101000 f 74 goat Random2.2K-317 3 41030095 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797203 Affx-122957389 AX-385284142 3 41062043 GATAAAATAAAAATAATCGATCAATACCTTTCACA[C/T]AGCTATTTATCATCAGTCGATAAGATTAAGCCTGT Y 2 1 2 1 101000 r 74 goat snp56206-scaffold879-332866 3 77333772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377411 Affx-122977558 AX-123247770 3 41090637 TTTTTACAATTGGAGTATATACCTCAGGGGATTGC[A/G]TAACACTTTTTAAATGAACTGAGTTCTAAATCGAT R 2 1 2 1 101000 f 74 goat snp56205-scaffold879-304272 3 77305201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783279 Affx-122972961 AX-385270344 3 41131551 TAATTAGGACTGGCTGTGTTACTTTGCTGAGGCAA[A/G]CCTAGTCTCAACAAGACACAGGCCTAATATATTCC R 2 1 2 1 102000 f 74 goat snp56204-scaffold879-263358 3 77264274 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790572 Affx-122963571 AX-385277575 3 41208730 AGTCTGCTACTAGAAACCAGACAGCAAGAAGCCTT[A/G]AAATAAATCGACCCTTCTCTGGTCATTCTAAATAG R 2 1 2 1 101000 f 74 goat snp56203-scaffold879-186179 3 77186614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775925 Affx-122952520 AX-385263056 3 41290350 TAGTAACTGAAGCCCTTCCTTGTCTACTAGTTCAA[C/T]ATCTGTGTCATTCATGGATTGTGTTTTCCTCCTTC Y 2 1 2 1 101000 f 74 goat snp56201-scaffold879-104559 3 77104449 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796460 Affx-122925610 AX-385283410 3 41322717 TTGAGTAATATTTTAACTGAAAGTCTCTGACTTCA[C/T]TGATTCTGTTATAATGAACTCAACCAGCATAAAAC Y 2 1 2 1 201000 f 74 goat snp56200-scaffold879-72192 3 77071786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443893 Affx-122927060 AX-123314230 3 41356367 TTGGATCTTGTCATCCCAAGACGACAGACCTCTTC[A/G]TTTAAAAGGTTAAAAGAGAGATTATCCTGATTCTC R 2 1 2 1 201000 r 74 goat snp56199-scaffold879-38542 3 77037688 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407493 Affx-122954754 AX-123277844 3 41415684 CATCCTTGCACAAAGTTCCACGTCATTAAAGTTTT[A/C]GTCTTTATATATTTAATGAATAAATCAGAAATTTT M 2 1 2 1 101000 f 74 goat snp15520-scaffold164-3351664 3 76968822 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405142 Affx-122956957 AX-123275494 3 41465676 TTTTAAGAACAAAATTTTATACTTTAAGAACAAAA[G/T]CAAAAGACAGTTGCCCAATGTAACCAAACACAGTG K 2 1 2 1 101000 r 74 goat snp15519-scaffold164-3301672 3 76919076 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394968 Affx-122964272 AX-123265323 3 41536334 AATTCAAGAATTATTAGAAATAAAATACTAGAACA[C/T]GCCTTGAGAGATTGTCCATCATCATTTTACATCAA Y 2 1 2 1 101000 r 74 goat snp15518-scaffold164-3231014 3 76847834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394476 Affx-122964567 AX-123264831 3 41619391 TATTTTCATTCTCTGCACATTAAAGAAAGAGCTTA[C/T]GAACCTATGAAACATGCCAATATGTGCATTAAAGT Y 2 1 2 1 101000 r 74 goat snp15516-scaffold164-3147957 3 76764046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801446 Affx-122943979 AX-385288355 3 41715167 CTACCCCTCTTCCTTATCTTCTGCAAAATGTCTCA[A/G]CAGTCTGTCCAATGGTGATCCCTCTTTACTTTCTT R 2 1 2 1 101000 f 74 goat snp15514-scaffold164-3052181 3 76665007 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432984 Affx-122935265 AX-123303325 3 41750445 GTAAAGAATTGCTTCTTTGCTTAGCTGCCCCCAGC[C/T]GCTTAGAGCTGTTTGGACTTCATCTTCACCACCAC Y 2 1 2 1 201000 r 74 goat snp15513-scaffold164-3016903 3 76629470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786958 Affx-122967600 AX-385273987 3 41782700 ATGTATTACTGACATGGGCCAGTTTTAGCTGATTC[C/T]GCCTATCTTTTCTTAAGCTCTAAGTGTTAGAATAA Y 2 1 2 1 101000 f 74 goat snp15512-scaffold164-2984648 3 76597055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445361 Affx-122925418 AX-123315698 3 41839503 CCTATCACAAATGAGAAAACTGTGGCTTGAAAAGG[C/T]TAACTGAGTTACCTAAAAACACTATGGTTAATATC Y 2 1 2 1 303000 r 74 goat snp15511-scaffold164-2927845 3 76539807 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774077 Affx-122924697 AX-385261215 3 41883348 GATAGAATTAAATAATTCAGCACTGGAATAGTGTA[C/T]AGGAGAAGCATGTATCTGAATTTTGGCAATCGTAT Y 2 1 2 1 101000 r 74 goat snp15510-scaffold164-2884000 3 76495500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788621 Affx-122934167 AX-385275638 3 41919667 GTTGGTTGATTGTCTAAAATATTCTCTGTCCTCAG[C/T]GTAGCTAAAGAACTGTTCATTCTTCAATTGCAGTA Y 2 1 2 1 101000 f 74 goat snp15509-scaffold164-2847681 3 76459068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791334 Affx-122973412 AX-385278327 3 42038549 AGAGGCTGAGAAAGAGAATGCTTATTTTAGGTAGC[A/G]CTTTTAAAATACGCTTATTACAAAAGAAGATGAGA R 2 1 2 1 101000 f 74 goat snp15507-scaffold164-2728799 3 76339511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767947 Affx-122970566 AX-188959500 3 42095647 GTATGTTACTATGGTGAGCATTAAACAAAGGAACA[C/T]ATTAAATTTATGTTACACAGTGTCTGGTACATAGG Y 2 1 2 1 101000 f 74 goat snp15506-scaffold164-2671701 3 76281773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415048 Affx-122949488 AX-123285397 3 42135080 AAGCAACTATACCCCAATTAAAAAACATCCCCCAG[C/T]AAGGAACTGGAGCAAGTGTCATGTATCATAATAAT Y 2 1 2 1 201000 r 74 goat snp15505-scaffold164-2632268 3 76242293 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384565 Affx-122973005 AX-123254923 3 42166500 GCTCTGAATAACAACCCTTCATCACTGACACATTT[A/G]CCTTATTCCTTAAGTGCAGCCGTGGCTAGTTTCAC R 2 1 2 1 101000 f 74 goat snp15504-scaffold164-2600848 3 76210810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381584 Affx-122974804 AX-123251942 3 42212200 TTGACTTTGAAGCCCTCCATAGAGTCCCAAGGACC[A/G]TCTAGCAAAAGGGAGCCGATCTGAGAGAAGGGGAG R 2 1 2 1 101000 r 74 goat snp15503-scaffold164-2555148 3 76166488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410764 Affx-122952685 AX-123281114 3 42262089 TTACTTTCCCTCCTCCACCTGGTCACATTTGAGCA[C/T]GTATTCATTATCTCATCTTTCTTTTCTTCTAATAT Y 2 1 2 1 103000 f 74 goat snp15502-scaffold164-2505259 3 76115330 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789331 Affx-122964147 AX-385276341 3 42307012 TTATGTGTCAAGCACGGTCTTAATTGCTGAACATG[C/T]AACAGTGAATGCCACAGAACTATCTGTTCTCATTG Y 2 1 2 1 202000 r 74 goat snp15501-scaffold164-2460336 3 76072374 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782623 Affx-122928856 AX-385269696 3 42337602 AAAATGCATATGATATCATCCATCTGTGTGAATAA[C/T]GGCATAAGAATGAACTCACTGTTAAGAATCACTTG Y 2 1 2 1 101000 r 74 goat snp15500-scaffold164-2429746 3 76041936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422562 Affx-122943763 AX-123292908 3 42370900 TTGCCGACGCTGGACGCAGGATAGGTCCTGATGTA[C/T]GTAAAGGAGTGGTAGGCTTACACTGACAAAGAAAG Y 2 1 2 1 101000 r 74 goat snp15499-scaffold164-2396448 3 76007824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786516 Affx-122942355 AX-385273550 3 42468923 ATGGCTACCCTGGGAAAGTTTTAGTTTTATAAACA[G/T]TTATATTCATGGGCACTAAGATTATTAGGATAAAT K 2 1 2 1 101000 f 74 goat snp15497-scaffold164-2298425 3 75908770 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429583 Affx-122937725 AX-123299924 3 42501568 AAAGGGAAGAGAAATGGAAATAGTGTTGCTGGAAC[A/G]CAAGGATGCTTGGAGCTGTGGAAAAGGGGCCACTT R 2 1 2 1 101000 f 74 goat snp15496-scaffold164-2265780 3 75877446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381357 Affx-122974408 AX-123251715 3 42530207 CAACTATAAGGTTTAATAATTATTGATATATAAAA[G/T]AAATTGAAGCACTTTGACTAATGTGACCTAGGAAG K 2 1 2 1 102000 r 74 goat snp15495-scaffold164-2237141 3 75848446 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443102 Affx-122928103 AX-123313439 3 42594938 GGCTTTGGCACAGAAGACATTGCAAATGATGCCTC[A/G]TTTGCAATGAGGCATGGACATAAACACTCCTGTAT R 2 1 2 1 101000 r 74 goat snp15494-scaffold164-2172410 3 75782939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786371 Affx-122949865 AX-385273405 3 42669057 TTTCTCATCAAGTTTGGTCTTGTGTGGATCATCAC[A/G]TTAAAGCTTGTTTTTCAGCTTGGTGAAAGCCATGA R 2 1 2 1 101000 f 74 goat snp15492-scaffold164-2098291 3 75708022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794771 Affx-122948821 AX-385281731 3 42698333 TGGCTCATTTAGTGAATAGAAAACTCATCTTCTAG[C/T]AGTATATATGTTTTCACGGAAATAAAATTGGAAAA Y 2 1 2 1 101000 f 74 goat snp15491-scaffold164-2069015 3 75678719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454060 Affx-122919390 AX-123324393 3 42760113 TTTTAAAAGGCAGTTAACAAAATAATTGTAGTTTT[A/C]TTAACCTCTTTACTTAAAAAAATAGTCAGTGCAGT M 2 1 2 1 303000 f 74 goat snp15490-scaffold164-2007235 3 75617051 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795437 Affx-122970195 AX-385282393 3 42805323 GGAATTCCCTGGAGAACAATGTGTTTATTATATGC[A/G]TCTACAAATGATATTAAGGTGATTTCCTAAGTTGT R 2 1 2 1 101000 f 74 goat snp15489-scaffold164-1962025 3 75572120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412202 Affx-122950938 AX-123282552 3 42867352 CATGCCTTGGGAGCTTCTTCCATGCTTCCACATGC[A/G]CTCACAACTCTCTGGGTACTTGGCCAATGTATTTC R 2 1 2 1 101000 r 74 goat snp15488-scaffold164-1899996 3 75509672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430749 Affx-122937500 AX-123301090 3 42929033 ACATTAACATGAAAATACACGACCACAACTTAAAA[G/T]CTAGAATAGTAAATTTTTATTTTGTTTGCTTTTGA K 2 1 2 1 103000 f 74 goat snp15487-scaffold164-1838315 3 75447742 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789917 Affx-122975930 AX-385276923 3 42974643 ATTAGAAATACATTCCTTTGTACTTTCTATTTCTG[C/T]ATCTAGAAATCATGCCTGAATCTATTACATTTCTA Y 2 1 2 1 101000 f 74 goat snp15486-scaffold164-1792705 3 75401657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419439 Affx-122945504 AX-123289787 3 43061010 TGATCCTCTGTTTAGAAAACAAGGGCATCCATGCC[A/G]CAGATGCTTTGATGGTGAGCAAATTACCCTACTTA R 2 1 2 1 101000 r 74 goat snp15484-scaffold164-1706338 3 75317364 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379008 Affx-122976376 AX-123249367 3 43115661 TACCACTCTTACGTCTCCATTTAAAACAATGCTCC[A/G]CTTTCTCTTATTGACACTGACTTTTCTCTCCTTTG R 2 1 2 1 101000 f 74 goat snp15483-scaffold164-1651687 3 75263058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454263 Affx-122919644 AX-123324596 3 43155034 TGTATTAAATATACTAAAGATGTGATTTGATTTCT[A/G]TTCTTTGGTGTGTGAAAATCACTCACTCAGTAATA R 2 1 2 1 202000 f 74 goat snp15482-scaffold164-1612314 3 75223903 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426042 Affx-122941110 AX-123296388 3 43193982 TTGTAAACACTAGCATATTAATTGTACCTATTTTC[C/T]AAAGAGCAGGTCATTATTATTGACATGCTACTGGC Y 2 1 2 1 101000 r 74 goat snp15481-scaffold164-1573366 3 75185301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784541 Affx-122973072 AX-385271590 3 43290315 TGACTCTTCCAAGTAGCACAAATACATTTCACAAC[A/G]TGATCTTTGATAAGTGTCCAAATGGATTTTAAAAC R 2 1 2 1 101000 f 74 goat snp15479-scaffold164-1477033 3 75088456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451962 Affx-122920950 AX-123322295 3 43326733 GAAAAGTTGACTCAAAGAATAAAGGTTATCAAACC[C/T]AAAGGTTATATTTTTAAACCAAAGGTTCTTATGGA Y 2 1 2 1 101000 f 74 goat snp15478-scaffold164-1440615 3 75052016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408576 Affx-122953664 AX-123278927 3 43394000 CAACAGAAGAATTAAGAACTTCAGATAACAGTAAA[C/T]AGTGCATTAGATAAAAATTTCAATCTTCAGGGAAG Y 2 1 2 1 201000 f 74 goat snp15476-scaffold164-1373348 3 74984604 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793773 Affx-122926939 AX-385280745 3 43423086 GCAGCTTAGACTCAAAAGCAAACAGACATAGTTCA[C/T]AAAAATCTCTCATCACCTCAATATCCATTTCTCAG Y 2 1 2 1 101000 f 74 goat snp15475-scaffold164-1344262 3 74955066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418638 Affx-122946341 AX-123288986 3 43474557 ATGACGATAATTTAGCCCACTTGAAGATGAGTACC[A/C]TGCAGTTCCTCCTGCAAGTGAAAGCATCCTGGCAT M 2 1 2 1 101000 f 74 goat snp15474-scaffold164-1292791 3 74903713 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38419735 Affx-122945893 AX-123290083 3 43514929 GGTCAGATGGTCTGGGTTACTTTATTTATAGGAAA[C/T]AGCTAGCATGAACAAGTCAGATAATACAAAGCATA Y 2 1 2 1 101000 f 74 goat snp15473-scaffold164-1252419 3 74863471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802972 Affx-122929109 AX-385289858 3 43561811 CATCATTTCTTACATCCCTCTTTCATTCCAAGTTT[A/G]TCTCAATTATGCTGAAGAATAATTTTTTTAAGAAT R 2 1 2 1 201000 r 74 goat snp15472-scaffold164-1205537 3 74816599 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766965 Affx-122960160 AX-385254265 3 43618622 CATCAGGAGAGACTATCTTTAGCAAGAAATTTTGT[A/C]TTACCAGTCAATAGATAAAATTTACTGACCAATAT M 2 1 2 1 101000 f 74 goat snp15471-scaffold164-1148726 3 74758949 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398381 Affx-122961653 AX-123268736 3 43649525 ATTGACAAAAGGAAAGCTCAAAGAATGAATATCCC[A/G]CTCTTGCATTAAAATTCCTAAGTTAATGAGACCAG R 2 1 2 1 600000 r 74 goat snp15470-scaffold164-1117823 3 43649525 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780384 Affx-122961653 AX-385267478 3 43649525 ATTGACAAAAGGAAAGCTCAAAGAATGAATATCCC[A/G]CTCTTGCATTAAAATTCCTAAGTTAATGAGACCAG R 2 1 2 1 101000 f 74 goat snp15470-scaffold164-1117823 3 74728152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769575 Affx-122941204 AX-385256745 3 43746023 TTTCTACTCTTGCTTGTTAACTCAGTATTTCCCAT[G/T]TGAAAGATTGACAAGACTGAATAGGCCTCTCTAAA K 2 1 2 1 101000 r 74 goat snp15468-scaffold164-1021325 3 74631714 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449774 Affx-122922438 AX-123320109 3 43787182 CCTTTCCTAATGACCATACTTTGAAGATCAAGAGA[A/G]AAGAATGAAAAATGGCAGCTATGTTAACAGCTAGT R 2 1 2 1 101000 f 74 goat snp15467-scaffold164-980166 3 74590318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791662 Affx-122967963 AX-385278653 3 43838982 GTCATAAACTGAGAAAGGGCTTCAGTAGAAATGAC[A/G]TATCTTATAACAGGAGTATTACATACCATTGTTCC R 2 1 2 1 101000 f 74 goat snp15466-scaffold164-928366 3 74538470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397542 Affx-122962033 AX-123267897 3 43890890 AGTGAGATGATTCGCTGTTTCCTAACCACCTAAAA[G/T]CATTAAAGAATGAAAATAGGGTAGCACTGGCCCCT K 2 1 2 1 101000 f 74 goat snp15465-scaffold164-876458 3 74486017 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452381 Affx-122920619 AX-123322714 3 43955403 AATCATACACATTAAACCTTCACACTTGATGCCAA[C/T]ATTTAAAACTGTGGAAACAGATTCTGGGAATATAG Y 2 1 2 1 101000 f 74 goat snp15463-scaffold164-811945 3 74423865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451248 Affx-122921942 AX-123321581 3 43998548 CAAAGTTCACAGGCTTTCAAATCCAGATAGAATAA[A/C]TTTTAGATTACTAAGTGACATTTGTACCTTATTAG M 2 1 2 1 201000 r 74 goat snp15462-scaffold164-768800 3 74380893 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398737 Affx-122961825 AX-123269092 3 44049812 ATGCTCAGGGTGTCCGTCGTCACACCTGCTCTACC[A/G]CCAAAATTTTCCTTTTATTCTCATTCTTTTTACTT R 2 1 2 1 101000 f 74 goat snp15461-scaffold164-717536 3 74329119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380469 Affx-122975727 AX-123250827 3 44086287 TGGCTTGGTTAAATATTCTGGTCCTTCAGGTACTT[A/C]TGCAGACCTCAGAACAAAACACTGGACTGAAGTCA M 2 1 2 1 101000 r 74 goat snp15460-scaffold164-681061 3 74292332 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794707 Affx-122943386 AX-385281667 3 44144130 CTTGTTATAAGATAGGCAGCAAAATCAGTACACAC[A/G]TGGAAAATTAACATTGATAACAAATCCAGCTATCT R 2 1 2 1 101000 f 74 goat snp15459-scaffold164-623218 3 74234315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450222 Affx-122922276 AX-123320557 3 44199555 GAAGATTAATCAATCTTTTTTAGATTTACATACTA[C/T]AATACCTAATATTTTCCTACATGGAAACACCTGGA Y 2 1 2 1 101000 r 74 goat snp15458-scaffold164-567793 3 74178155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376779 Affx-122977958 AX-123247138 3 44270264 AAAATAATTCAATTTTAAAACCCACCAGAACATAA[C/T]AAGTGAACAAGTTTGTTTTCCAGGCTCATCAGTGC Y 2 1 2 1 201000 f 74 goat snp15457-scaffold164-497084 3 74107032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788754 Affx-122939929 AX-385275770 3 44298968 AGAAGAAGGTAGGGTTCCACTTCAAAGGAATGCAG[C/T]GTTCACTATAGTTGAATCATTTGGTTGACAACATA Y 2 1 2 1 101000 f 74 goat snp15456-scaffold164-468380 3 74078372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441347 Affx-122928880 AX-123311684 3 44329234 GTGCCATAAAACTTTTTCAGGAAGGAATCTGGAAA[C/T]AATGGGGGAAGGAACAGGTCACACAGAACCTTAGG Y 2 1 2 1 201000 f 74 goat snp15455-scaffold164-438114 3 74047864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392006 Affx-122966492 AX-123262363 3 44369843 CTATGATTTACTGGAGCACGAAAGTTGGACTTCCC[A/G]TTTCCTGTGCATAAACTTGCCTATCTAAGTCTATT R 2 1 2 1 101000 f 74 goat snp15454-scaffold164-397505 3 74007657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419219 Affx-122945690 AX-123289567 3 44433231 TTTCCCAGTAAAACCAAAAGGTTTAGTTTGTTTTT[C/T]AAGTTAAATTCTGGAAAAAGGTGAAAAAAAAAATA Y 2 1 2 1 201000 r 74 goat snp15453-scaffold164-334117 3 73943645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383462 Affx-122973450 AX-123253820 3 44508071 CGAGATGATTAAAACACTGGTCTGGGCCTCCCCAG[C/T]GAGAGTAAATCTATTAACATTTCCTTATTGACTCT Y 2 1 2 1 201000 r 74 goat snp15452-scaffold164-259277 3 73867638 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393895 Affx-122965114 AX-123264250 3 44578001 TTTATACAGAAAATGTTTATTTTTCTAATAAAAAA[G/T]CAACAATATATTCCCCTGTTCTCTAGTTTGTTCCA K 2 1 2 1 103000 r 74 goat snp15451-scaffold164-189347 3 73797164 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790626 Affx-122942394 AX-385277628 3 44709045 ACTTTCGGATCAAAAATTATATGCAGCTTAAATAA[C/T]GGAAATCCCAACATAGAAAATCCATTACTGTATTT Y 2 1 2 1 101000 r 74 goat snp15449-scaffold164-58303 3 73663707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389329 Affx-122968487 AX-123259687 3 44754515 AATTCATTCAGAATCACAAAGGAGTAAAAGAACTA[G/T]GTGGTCAAAACCATAGCAATGTTAGGAAAATCACA K 2 1 2 1 101000 r 74 goat snp15448-scaffold164-12833 3 73618270 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393282 Affx-122965446 AX-123263638 3 44768442 TTCCGTCATCTTCTTACTCATTCTTTCTCATGGAG[A/C]GGAAGTGAAACAACTGAGGTGTCCGCATTTAATGA M 2 1 2 1 101000 r 74 goat snp29695-scaffold321-5715610 3 73362598 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795257 Affx-122977446 AX-385282215 3 44807117 CAGTACTCCTCCTTCCTTACAGTCTATTTTGTCCT[A/G]TCTTATTCTTCGCAGTTGAGTTCAAATAGCACCTT R 2 1 2 1 101000 f 74 goat snp29694-scaffold321-5676935 3 73322575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785963 Affx-122960627 AX-385272999 3 44887977 GAAGAGTTATTATCAAAATGCAAAGCTACACTCAT[A/G]TTCCTTTCATGGAAGCAGAGTTGAAGATGTGGCTA R 2 1 2 1 101000 r 74 goat snp29692-scaffold321-5596075 3 73239950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399168 Affx-122960638 AX-123269523 3 44934087 CTGACATACAAGAAAAGGGGAGCCAGCATTAATGG[C/T]GCCACAGTGGAGGGATTTCGGGCAAGAACTACAAC Y 2 1 2 1 101000 f 74 goat snp29691-scaffold321-5549965 3 73193411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416381 Affx-122947868 AX-123286730 3 44985068 AACTATCCCACCCAGGAGACCACCCATAATTTCAA[C/T]ACCAAGAGCTAATTGTTGTTCAGTTGCTAAGTCGT Y 2 1 2 1 103000 f 74 goat snp29690-scaffold321-5498984 3 73142431 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272039 Affx-1111833388 AX-519545803 3 45013233 AGAAGAAAATATAGAAATTAGAAGGAAAGAAACAT[A/C]AAGACAGATCCATACATTTAGGGGACTTCTTTTGT M 2 1 2 1 102000 r 74 goat 3_45013233_AF-PAKI 3 45013233 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449593 Affx-122923216 AX-123319928 3 45046560 CAGCACGTATTTCATATATCTGTACATATGTGCCA[C/T]GTGTGCTATCAAACTTTGGAGAATATTATGAATTC Y 2 1 2 1 201000 r 74 goat snp29689-scaffold321-5437492 3 73080920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436417 Affx-122933016 AX-123306755 3 45091046 ATAAATACGACACCTGAGCAGATAGACCTGGGGTA[G/T]AAAGGGAGCTCTCCCCGTGAGGCTTGCTCAGGGAG K 2 1 2 1 101000 f 74 goat snp29688-scaffold321-5393006 3 73039121 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385176 Affx-122971735 AX-123255534 3 45173746 GTTGAATAAAATTATCCATTTGTGTATGTCTTCTC[C/T]GAGGTAATAATTTTTCTGAGGGTGAGAAGCAATTT Y 2 1 2 1 101000 f 74 goat snp29686-scaffold321-5310306 3 72955673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785057 Affx-122973027 AX-385272104 3 45234219 TATTAAACTCCTGGTGAGGGACAATTCAACTTTCT[A/G]CTAAGAATTCTAACCCCTTCTGGACACTAGCTCTT R 2 1 2 1 101000 r 74 goat snp29685-scaffold321-5249833 3 72894170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385925 Affx-122971565 AX-123256283 3 45302247 ATTATCTTTCACTTGGCAATTTGATTCCTACAACT[A/G]CCCTGCTATTCATGGAGCCCTGACTTAGACCCCTG R 2 1 2 1 101000 f 74 goat snp29684-scaffold321-5181805 3 72825699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768967 Affx-122960635 AX-385256142 3 45379868 GCTTGAAGCTCCAGTGCTAAGAAATATCATCACCT[A/G]TTTGTCCATCTGAAAGCAAGGTTTATCCTCCTCTT R 2 1 2 1 101000 r 74 goat snp29682-scaffold321-5104184 3 72746713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436071 Affx-122932698 AX-123306410 3 45441055 TTTAAAAAAAGCGTTATTTAGGAATGGATGTTTTT[A/G]TTTTTGCTCTTCATTATTGACTTGGCTTGATTTCC R 2 1 2 1 101000 r 74 goat snp29681-scaffold321-5042997 3 72685746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390006 Affx-122968041 AX-123260363 3 45489847 GGGGGGTTGAGAAGTCCTTTTCATGGAAATAAAAA[C/T]GGAGATGAAAGAAAACAGCAGTTCCAATTTTCGAT Y 2 1 2 1 101000 f 74 goat snp29680-scaffold321-4994205 3 72645696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385826 Affx-122971018 AX-123256184 3 45571454 CCCTAGCCCTTCACTTCTTAATACTTGGTTTTCTT[C/T]GAGAATTCAGTTCAATCATCACCTGCTCAGCTCTC Y 2 1 2 1 101000 r 74 goat snp29678-scaffold321-4912598 3 72563797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415771 Affx-122948923 AX-123286120 3 45612322 CCCTTTTCACCTAACTGGGAATAGAGACCAATTCT[A/G]CTTCCAAAGTAACTCTCACCTTGATCTCAGCATTC R 2 1 2 1 101000 f 74 goat snp29677-scaffold321-4871730 3 72522396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801213 Affx-122977877 AX-385288126 3 45667981 GGAAGAAGAATAAGTAAACAGGCAGAGTGTCCTGC[A/G]CTAAAGTACACCAGTGTCCTGATAAGAGTTCCAGC R 2 1 2 1 101000 f 74 goat snp29676-scaffold321-4816071 3 72466537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408384 Affx-122953720 AX-123278735 3 45771830 TCAGGCCAAAAGAGTATAAAATAAGACAAAGAAAG[G/T]TATTTACACTTATTCCAATTATCTATTGTTTCATA K 2 1 2 1 303000 r 74 goat snp29674-scaffold321-4712222 3 72362095 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397189 Affx-122962407 AX-123267544 3 45837529 TAGATAATTTGGGGCACTATCAAGGAGAGACAATG[A/C]GATGTACTTGGAAGATAATGGATTTTGGATTTAGA M 2 1 2 1 101000 f 74 goat snp29672-scaffold321-4646523 3 72295657 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412154 Affx-122951081 AX-123282504 3 45880438 ACACAGAGTTGAATATTCCAGTCCACATACTACAT[A/G]TGATAAAGTAAATAGAAAGGTTTTCCCAGAAAAGT R 2 1 2 1 101000 f 74 goat snp29671-scaffold321-4603614 3 72252371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427511 Affx-122939528 AX-123297854 3 45928159 GCCTATGTATGTTGGAATGAAGGAGTGTTCTACTT[A/G]GGTAAAAAGTGGTACATTCCAAAAACATAAGGGGT R 2 1 2 1 101000 r 74 goat snp29670-scaffold321-4555893 3 72200351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432713 Affx-122936018 AX-123303054 3 45975181 TTAGGAAAGAGTGGTAGTAAAAATGATATACTTTA[C/T]TGAGTGATGTTTTGATCTATTGCTTAATAGCAAGC Y 2 1 2 1 101000 r 74 goat snp29669-scaffold321-4508871 3 72153287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431291 Affx-122937094 AX-123301632 3 46035837 CACCCAACCACTGTGTGTTCAATTTCTGAAATCGT[A/G]CAATCTCCAAAATTTTCCCACTTTAATTTTAAAAC R 2 1 2 1 101000 f 74 goat snp29668-scaffold321-4448215 3 72092458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390353 Affx-122967685 AX-123260710 3 46070422 AAGGGACTTTCACTAAGTAGGAGTTCATTTTGTGA[G/T]GCCAACCATATCAGAACAGCAGACTGGACAATGTT K 2 1 2 1 101000 f 74 goat snp29667-scaffold321-4413630 3 72057922 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411129 Affx-122951897 AX-123281479 3 46110649 TCAACAAATGTAATGATGCTTGGCGTTCTTCTTGG[C/T]ACTTGGGTTTGGGAAGACAAGTAAGCCATCAGGGA Y 2 1 2 1 101000 f 74 goat snp29666-scaffold321-4373403 3 72017633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775537 Affx-122969822 AX-385262668 3 46165843 AGTAAAGTACATAAACATAGTCTATCCCTTTTAAA[C/T]TCTGTTAAAAAAAACTCTATCTCCTCTTTTGGCTC Y 2 1 2 1 101000 r 74 goat snp29665-scaffold321-4318209 3 71961688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415408 Affx-122948735 AX-123285757 3 46198025 ACGCTGATTCCACTGAAAGGATTCCTAAAGGTCCA[C/T]TTGCAAACCTTGGAAAGAACACCACAATAGTCTAG Y 2 1 2 1 101000 f 74 goat snp29664-scaffold321-4286027 3 71929307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476174 Affx-1251763678 AX-586011601 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20000 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 539476429 Affx-1251763678 AX-586011830 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 4 1 4 1 20000 r 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562165064 Affx-1251763678 AX-606940476 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 r 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562166102 Affx-1251763678 AX-606941511 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562166355 Affx-1251763678 AX-606941763 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 320782234 Affx-122925434 AX-385269312 3 46228202 GGCATTAAGGCCCTTCTGCTTTGAAACAGAGAATG[C/T]AAAGCACTCCTTAGTCCAGCCAGGCACTGATGTTT Y 2 1 2 1 201000 f 74 goat snp29663-scaffold321-4255850 3 71899081 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441700 Affx-122929162 AX-123312037 3 46269546 CTCATCTGGACTAGTGAATTCATCCTTGCATGCCA[A/G]CAAATGACTGTAGCTGGAACAGTGGTGACGTGTTA R 2 1 2 1 101000 f 74 goat snp29662-scaffold321-4214506 3 71857518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406880 Affx-122955640 AX-123277231 3 46301388 AAGAGGAGAGAATTATTTCCAGAGGAGAATACCAT[A/G]CTATTTTTCTGTAATACCTTTTTTAAAATTTGATT R 2 1 2 1 101000 f 74 goat snp29661-scaffold321-4182664 3 71824970 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419496 Affx-122945461 AX-123289844 3 46338318 CAGTTATTTTCCAGTCAATATATTTGTAAGGTGAC[A/G]AGTCACCCACTCCCATTTTTCAAAGGTTGAGCTGA R 2 1 2 1 201000 f 74 goat snp29660-scaffold321-4145734 3 71788042 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420731 Affx-122944767 AX-123291078 3 46376373 ATTTTTAAAGGACATTGGGGTTCACATTTCTGTTC[A/G]TTTTGTTTTAATTTTTCTCCTTTAACTTAATTTAG R 2 1 2 1 101000 f 74 goat snp29659-scaffold321-4107679 3 71750706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387964 Affx-122969605 AX-123258322 3 46435238 TTGTAATTTCATAGCTTTTCTTAAGGCATGCCCAC[A/G]TTATATAGACTCCTAGGACCCCAAACCAGAGCCAG R 2 1 2 1 101000 r 74 goat snp29658-scaffold321-4048814 3 71690634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417955 Affx-122946702 AX-123288303 3 46469079 AGATGAATGATTATGATTGGCCAATCCCCTGTCAC[A/G]TGGCCACCACTAATAGGAGGGTGATGGAAAAGCTT R 2 1 2 1 201000 r 74 goat snp29657-scaffold321-4014973 3 71657369 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395629 Affx-122963798 AX-123265984 3 46498154 AAAGCAGAGCATTTCAGGAGGAGGTGATGACCAGC[A/G]TGGAGCTTAGCATGAGACCAGGTCCTGGGCCAAAA R 2 1 2 1 201000 f 74 goat snp29656-scaffold321-3985898 3 71628337 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403703 Affx-122958041 AX-123274055 3 46574052 AAAAGACATACAACTTTGCAAAATTTAATTTTCTC[A/G]CATCCTTGAACTGAAATAGCAAGTCCAGGTTTAGC R 2 1 2 1 101000 r 74 goat snp29654-scaffold321-3910000 3 71552837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412436 Affx-122951418 AX-123282785 3 46609186 TTAAAACTGAAAAAGGTTTTTCATTGTTTTGTGGC[A/G]AGCTTACTGGGTAGCCAGAGCTGGCCTGAACTAAC R 2 1 2 1 101000 r 74 goat snp29653-scaffold321-3874866 3 71517837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415210 Affx-122948979 AX-123285559 3 46638930 GACCAGTGTTTTCTTGACAAAATTTTTATGCAAAT[A/G]TGACTTTAGAACTATGGAAGAATTAATTTTAATAC R 2 1 2 1 201000 r 74 goat snp29652-scaffold321-3845122 3 71490073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777415 Affx-122953023 AX-385264536 3 46701612 CTTTATTATTACACACCAAATTTTAGTAACTTCTT[A/C]AGTTTCCATTCTGGTGGGTAACACACAGTGCTAGA M 2 1 2 1 101000 r 74 goat snp29651-scaffold321-3782440 3 71428033 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398143 Affx-122961685 AX-123268498 3 46753775 CTGTCCCAGCTTGTTGTTTCTTGTGCATGCATGTT[A/G]AGTCTCTCACTCATGTCTGACTCTTTGCGACCTCA R 2 1 2 1 101000 f 74 goat snp29650-scaffold321-3730277 3 71375476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393743 Affx-122965223 AX-123264098 3 46793902 TAAAAAACTTCTTTGTTTTTTGTTTGCTTGCTGCC[A/G]TCAATGTATTCATAAAAATGTTTACCAGAGAGCAA R 2 1 2 1 201000 r 74 goat snp29649-scaffold321-3690150 3 71335899 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769384 Affx-122943992 AX-385256555 3 46849079 TGCACTTATCCAAGTTCCCATAGATGATTCATGTT[G/T]CCCTATCCAGACTATAATCTCAAGGAAATCATAAC K 2 1 2 1 101000 f 74 goat snp29648-scaffold321-3634973 3 71280967 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792781 Affx-122960941 AX-385279760 3 46878304 GGTATATATGCTGACAGATTGCTCATGATTTTTAG[A/G]TGTTCACAAATAGATGAAACTATTATAATACTAAC R 2 1 2 1 101000 f 74 goat snp29647-scaffold321-3605748 3 71251692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770321 Affx-122972173 AX-385257487 3 46910110 GGTTGTGGGGAAAAAACACCCTTACTGATGTACAA[C/T]AGCTTATATGCTATGTATGAACAAGTGAAGTGAAA Y 2 1 2 1 101000 f 74 goat snp29646-scaffold321-3573942 3 71219932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277951 Affx-1111836175 AX-519551446 3 46945463 AAAGTAACTGTTACTCAGAGGCTACAAGAGCCAAA[A/G]TTGTTTTTGCTTGTTTAACTTAGTTTTCCGCATTA R 2 1 2 1 101000 f 74 goat Random2.2K-319 3 46945463 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404611 Affx-122957339 AX-123274963 3 46978631 GGACACTCATCAGAGAGGCACACTGAGGAGCCAGA[C/T]ATTACTTGCTGCTTCAGTGACAAATAGCAACCAAC Y 2 1 2 1 101000 r 74 goat snp29645-scaffold321-3505421 3 71161831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400618 Affx-122960380 AX-123270973 3 47036111 GACCTGGGCTCCATCCTGGCTGTTTTATCAGGCAG[A/C]TGATTCACAGTCATGTTTCCTGCTGTGTCTCTCTA M 2 1 2 1 101000 r 74 goat snp29644-scaffold321-3447941 3 71104053 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432540 Affx-122935549 AX-123302881 3 47077709 CCACCTGGGAAGCCCCAGTAATTAAACATATTCAT[C/T]TCAAAAAAATTATCTGGAAAGCAGGGAGGGGCCTA Y 2 1 2 1 103000 f 74 goat snp29643-scaffold321-3406343 3 71061802 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421841 Affx-122944299 AX-123292188 3 47108410 ACTTCATTGTTTATTAAGTGGGTTAATAAAATACT[A/G]CTTATTCCAAGCTAGGTTTGAATTGAATTCCTCTA R 2 1 2 1 101000 r 74 goat snp29642-scaffold321-3375642 3 71030839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385952 Affx-122971543 AX-123256310 3 47147748 GCTGGTTTAGTCTAGATTTGCCTGTTTGTACAAAG[C/T]ACCAGCTGCAAAGGCCTTGGTAAGGTTCTTGCCCC Y 2 1 2 1 101000 f 74 goat snp29641-scaffold321-3336304 3 70991431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795221 Affx-122919490 AX-385282179 3 47219287 ATTCTAGTCAGATGCTTTGGGGAGTTTTTTAAAAT[A/C]ATTTTGTTTCAATCTTAACTGCATGCTTTCAATAA M 2 1 2 1 201000 f 74 goat snp29640-scaffold321-3264765 3 70919733 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386204 Affx-122970994 AX-123256562 3 47250405 TCCATGAGTCGTGCTGTGAAGGAACACAGGGAGGT[C/T]TGGCCCTCTGTGTTTCTGCCCTGGAGGTCCATCTG Y 2 1 2 1 101000 f 74 goat snp29639-scaffold321-3233647 3 70888375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401203 Affx-122959333 AX-123271556 3 47279469 CTTTTTGTGGCTATTACTATTCATTTCTCTTGGGT[A/G]TGTACTTAGAAGTGGAGCTGCTGGGTCATAGGAAG R 2 1 2 1 103000 r 74 goat snp29638-scaffold321-3204583 3 70859283 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782946 Affx-122919654 AX-385270016 3 47319420 TCACTGCCAATCAATCAGGTGACTACCATGGTAGC[A/G]TCCTAGTTCTAATTTGAATCTCTGATTATGAGTGA R 2 1 2 1 101000 f 74 goat snp29637-scaffold321-3164632 3 70821809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452068 Affx-122920872 AX-123322401 3 47355664 CTTAAATATCTATTATCTGTCCAACATCTGTACTG[C/T]ACTTGAGCATCCCTGATGGGCTCATGGAAGGCTAA Y 2 1 2 1 201000 f 74 goat snp29636-scaffold321-3128388 3 70785680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436314 Affx-122933261 AX-123306653 3 47403482 CGCCTCACCTGCCACTGCTTGTTTATGTCTTTTCC[G/T]CAGGGCTGTAAGCTCTGTGAAGTCAGAGGCTGCTT K 2 1 2 1 101000 f 74 goat snp29635-scaffold321-3080570 3 70737743 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442119 Affx-122928343 AX-123312456 3 47451480 GGCATTTTCTTTCCCAGGTAACTATCTAAGTAAAA[C/T]AAGACAGGGAAATGCATACCAAGGGTCAATGGGGA Y 2 1 2 1 101000 f 74 goat snp29634-scaffold321-3032572 3 70689361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769168 Affx-122977948 AX-385256343 3 47544313 TGCTTATCTAGTATTTGGATGTAGCCTTTGACACT[A/G]TTAACAGGATCATTGGCATTAGTCCAGATGGCAGA R 2 1 2 1 101000 r 74 goat snp29632-scaffold321-2939739 3 70596375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793009 Affx-122961542 AX-385279987 3 47638535 AATTTGGATCACTGTCTTCCAAAGAATAAAGGAAA[C/T]ACTACCCATAATGACCTCAGAAAATTAAATATGAA Y 2 1 2 1 101000 f 74 goat snp29631-scaffold321-2845517 3 70501494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770588 Affx-122957603 AX-385257752 3 47678859 AATGCTTAGTTTGAGTTTCCGTACTTAACTCATTG[C/T]AGACAATTACATGATGATACGGTTATGATACAGAT Y 2 1 2 1 101000 r 74 goat snp29630-scaffold321-2805193 3 70460801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434580 Affx-122934113 AX-123304921 3 47749848 AATGGAAAATGAGCATTGGCTTCAAGTCACCATCT[A/G]CGTTAGCCCCTAACAGAAGGTGAGCCAGTCTTTGC R 2 1 2 1 103000 f 74 goat snp29629-scaffold321-2734204 3 70390569 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410034 Affx-122953244 AX-123280384 3 47779125 CAATTCTAAATAACATTCCAAGCATACAGTTTCTC[A/G]CATTAGAATAAGATTGAACGATAGCTTAATGTTGC R 2 1 2 1 101000 f 74 goat snp29628-scaffold321-2704927 3 70360714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272208 Affx-1111833389 AX-519545957 3 47824803 CAACAGGTACATGAAAAGATGCTCAGCATTACTAA[A/C]CTTCAGAAAAATGCAAATCCTAACCACAATGAGAT M 2 1 2 1 103000 f 74 goat 3_47824803_AF-PAKI 3 47824803 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782599 Affx-122972940 AX-385269673 3 47877266 GAAACATATGAGATTGAGATCCCTAAATGAAAAGA[C/T]CATGCATAGTTCTTTTCAATATCAGATGATGACAG Y 2 1 2 1 101000 f 74 goat snp29627-scaffold321-2606786 3 70263726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384997 Affx-122971882 AX-123255355 3 47921055 ATTGTATTGGTACCTATTGCCCCACAATACATTCT[A/G]TTATACTTTTTTAAAAGAAGCTCAATTAGGTCTCA R 2 1 2 1 103000 f 74 goat snp29626-scaffold321-2562997 3 70220028 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450060 Affx-122922814 AX-123320395 3 47963595 ATGATAATACAAATCCACACGAGTCAAGAAAATTT[A/G]TTTGTCCTATGCATTATTTCTTGGTTGATGGCCTC R 2 1 2 1 101000 r 74 goat snp29625-scaffold321-2520457 3 70177343 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417412 Affx-122947226 AX-123287760 3 47997775 CTATCCTTATTCCCTCAAGCCTATCCTTCTTTCTC[C/T]CATAGGTAACTATTTTTAAAATTGTGTGTTTATCA Y 2 1 2 1 101000 f 74 goat snp29624-scaffold321-2486277 3 70142982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781825 Affx-122938618 AX-385268908 3 48061961 ATTAAACCAGTGGTAAGGATGACTTGAGCCCAGGT[A/C]ATAGATTGTGAAGGTGGAATTGATTTTTTTTTTTT M 2 1 2 1 101000 f 74 goat snp29623-scaffold321-2422091 3 70078706 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791036 Affx-122939504 AX-385278031 3 48106764 CAATCTAAGTATGTTTCTAAACAGAAAAAATCCTG[G/T]ATGTGTTAACACTAAATGCTGATATTATATAGCTG K 2 1 2 1 101000 f 74 goat snp29622-scaffold321-2377288 3 70033816 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399716 Affx-122960468 AX-123270071 3 48152000 ATTTTCTTTTTTCCTTTTTTTGCTTTGCTCTGCAG[C/T]AGGTAGAAGCCACAGAGTAAAGGAAACCACGCAGA Y 2 1 2 1 103000 r 74 goat snp29621-scaffold321-2332052 3 69987786 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449544 Affx-122923251 AX-123319879 3 48199413 TAGATCAGGAGGTTCCTGGGAATAACTTTTGTAAA[A/G]ACCTATCAGAAATAAGTGGAAAATAGAAATAATGG R 2 1 2 1 101000 f 74 goat snp29620-scaffold321-2284639 3 69939507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448396 Affx-122923684 AX-123318732 3 48255064 TCCTCAAGGGTTCCGGAGCTGCCAGAGCAAAGAAG[C/T]AGCGGACTGAAGAAGGAAAGATCGGGTGAAAACTG Y 2 1 2 1 101000 r 74 goat snp29619-scaffold321-2228988 3 69884658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800025 Affx-122962858 AX-385286948 3 48330560 TTGCAAGCCACATTTATATCTTACTCATCTGTATA[G/T]CCCTTTATATTGTCTTTGTATTTAGCTCAAAACAA K 2 1 2 1 201000 r 74 goat snp29618-scaffold321-2153492 3 69808469 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432164 Affx-122936414 AX-123302505 3 48378096 GTTCCTGAGGGAGAAATGGTTCCATGAAGAGACAG[C/T]AAACTGGAAGTTAAGGCAAACCACTTTGAGGCCTC Y 2 1 2 1 101000 f 74 goat snp29617-scaffold321-2105956 3 69760772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435925 Affx-122932756 AX-123306264 3 48434023 GCACAACAGGGCGACAGATACAAGCGGAAAGCTCC[A/G]CTGGGGTATTTTGATTCAATAGCCGGCTTTAAGGG R 2 1 2 1 101000 r 74 goat snp29616-scaffold321-2050029 3 69704954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405603 Affx-122955923 AX-123275955 3 48508033 ACCTAAGTTCTAAAAGTCATAATGGGAGAGCAGTT[A/G]ACTAGATTTCAATCAGTTCTACTTACCCCACAATG R 2 1 2 1 101000 f 74 goat snp29615-scaffold321-1976019 3 69630859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778290 Affx-122969510 AX-385265405 3 48647322 CCATTTTTTTGTCCTCTGTTAGCTTGTTTTTATAC[A/G]TTCTTTTACTAATCATTAATTGGTTTCCCTAGATT R 2 1 2 1 201000 r 74 goat snp29613-scaffold321-1836730 3 69491100 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766078 Affx-122967619 AX-385253494 3 48685317 TCACCTGTCTCAATCTCACAATCAGTCCTCTCTAT[C/T]CTACTCTAAAACTTCCTGCAAGTGCTACACAGTGC Y 2 1 2 1 101000 f 74 goat snp29612-scaffold321-1798735 3 69452908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781445 Affx-122929657 AX-385268530 3 48716588 TTTGTGGATCATGTCTTATTTATGAAATAATACTG[C/T]AGAACTTTATCACTTGTAATATTAAGGAATGTTAT Y 2 1 2 1 101000 f 74 goat snp29611-scaffold321-1767464 3 69421249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381244 Affx-122974498 AX-123251602 3 48760627 AGTCCTTCTTATCCCTCAGTTGACAGAAAAATAGC[A/C]TGTAGTAATTAACTTGGTGCAGCAGCAGAGAAGGG M 2 1 2 1 101000 f 74 goat snp29610-scaffold321-1723425 3 69377191 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412402 Affx-122951443 AX-123282751 3 48808361 CTGGGAAATTTTAGACTTGGCCTATTTTCTTAAGC[A/G]CAATGTAAATAGCTTAATGCTCTACTAGTTACAAC R 2 1 2 1 101000 f 74 goat snp29609-scaffold321-1675691 3 69328998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440944 Affx-122929007 AX-123311281 3 48866784 AGGAATGGGGAAGGGGGTGACTTGGGTGAGGCTTT[A/G]TAGGTGATGGTTGAGTGATCTTTTAGGGATTGATT R 2 1 2 1 201000 r 74 goat snp29608-scaffold321-1617268 3 69269829 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438634 Affx-122930912 AX-123308971 3 48940882 ACACAGGAACTAATACGGAAGCATCTGGAACAGAA[C/T]ACAAAGGAACCAAAAGTATTTCAAGAAAATCAGAG Y 2 1 2 1 101000 f 74 goat snp29607-scaffold321-1543170 3 69196632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432896 Affx-122935330 AX-123303237 3 48971043 AGCCTGAAGGAAATGTTGAAGTGAACCATAAGGCT[A/G]TCTCCTGACCGGTGGAACAAATAGTCTGCTTATGC R 2 1 2 1 101000 r 74 goat snp29606-scaffold321-1513009 3 69166198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798877 Affx-122937061 AX-385285807 3 49058272 TCCCCTCCGTCTTGATATAAAAATTCTAAAACCTG[A/C]GGTAAACCTCTCGCATACACCCTAGCAAAGGCCCC M 2 1 2 1 101000 f 74 goat snp29605-scaffold321-1425780 3 69077420 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377840 Affx-122977291 AX-123248199 3 49143542 ATGGAAAGTGTTTGTTTAGTAACTGAATTTCACCA[A/C]TATACAGTGTCTGTGTGTGAGGGGTTTACTTTGAT M 2 1 2 1 201000 f 74 goat snp29603-scaffold321-1340510 3 69005783 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446228 Affx-122925701 AX-123316564 3 49173968 AGCCAGGCATAGCAAGAACCCAATGTCGACATGAT[A/G]TGAGTACTGGATCACTCATTTCCATCTGCAAACTG R 2 1 2 1 101000 f 74 goat snp29602-scaffold321-1310084 3 68974868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765702 Affx-122959955 AX-385253164 3 49213328 TGAACAAACTACAAGAGTTTACTTTTGAAGCAGAA[A/G]TATTGCTTCTTCAGGCTCAACACCTTTGATATGTA R 2 1 2 1 101000 f 74 goat snp29601-scaffold321-1270724 3 68935630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779112 Affx-122923852 AX-385266217 3 49247222 TGAGCATCAAACTTACTAAAAAGTCAGATTTGTCA[A/G]CTCTGTAAAACTTTAGGCCTGTGGTTCATTGCCTC R 2 1 2 1 101000 r 74 goat snp29600-scaffold321-1236830 3 68903434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419304 Affx-122946230 AX-123289652 3 49318111 GAAGCATCTAGGCAGTGTGGGTTGGAGAGGGAAAG[A/C]GGGGTCAAATTTTGGAGGGTCTTAAAAAATAGGCA M 2 1 2 1 201000 f 74 goat snp29598-scaffold321-1165941 3 68832678 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397944 Affx-122961919 AX-123268299 3 49382119 AGAAGACCTTGACAGCTGAGCCCCTCCTCAGCACC[A/G]TGGGGTCTTGCAATGAGCTCCTCTCTAAAGTCTTC R 2 1 2 1 101000 r 74 goat snp29597-scaffold321-1101933 3 68768728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783286 Affx-122971430 AX-385270351 3 49444092 AAATGTGACTTAAACTATTAAGAAAGATTAGAATC[A/G]TTGCTATTGAGAATGCTGAAATAATTTTATGGCTT R 2 1 2 1 101000 r 74 goat snp29596-scaffold321-1039960 3 68706807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420041 Affx-122945140 AX-123290389 3 49474834 GAAGCACTTTCGTTTATGACCTATGGATACCCTTA[C/T]ATCATCTTCTATTACCTCTTCCCACACACCCTTAT Y 2 1 2 1 101000 f 74 goat snp29595-scaffold321-1009218 3 68676051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448267 Affx-122924189 AX-123318603 3 49511488 TTTTAAAACTTTATATGCGTTTCCATATAAATTTT[A/G]TAATCAGTTTGTCAAGTTATAAAAACATAAAAATC R 2 1 2 1 103000 r 74 goat snp29594-scaffold321-972564 3 68638919 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443128 Affx-122928084 AX-123313465 3 49551442 TCAGCCAAAACAAACAGAAATGCAATGAAATAAAA[C/T]GCTTTAAAATTATGACTTCAAATATAATGCTGATG Y 2 1 2 1 303000 r 74 goat snp29593-scaffold321-932610 3 68598601 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278109 Affx-1111836176 AX-519551599 3 49604174 CTCTATAAAGAAAATAACAATGTACTTGTAAATGG[A/G]TAAACAAGATATCTTTGAAAGAACCTGTAGCAAAT R 2 1 2 1 101000 r 74 goat Random2.2K-323 3 49604174 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384055 Affx-122972876 AX-123254413 3 49620219 TTAAAGCAAAATAAATCATTAATGTGAAATAGAAA[C/T]GCATTTGAAGTGAATACATAAAATTACTTTAACAA Y 2 1 2 1 303000 f 74 goat snp29591-scaffold321-863833 3 68529544 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797040 Affx-122959815 AX-385283981 3 49668131 GCAAAGCTCTTCCGGAAGACGATGACCATTGATAC[A/C]CTAGAGAATCAGTTGTGTTCAGTTAATCACACCCC M 2 1 2 1 101000 r 74 goat snp29590-scaffold321-815921 3 68480915 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451143 Affx-122921367 AX-123321477 3 49707793 AGAAGAGGCGACGACATTGATTAAAAGTAACAATC[A/G]TTTAAGGAAACAAGGGGTCAGGACCTTTGACTGCT R 2 1 2 1 201000 f 74 goat snp29589-scaffold321-776259 3 68441785 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398798 Affx-122961415 AX-123269153 3 49746826 CTGCCAAGTTTTACATGGCAAATGTATGCTTTTCT[C/T]GTCAGTGTCATCTTCCTCATTACTAACAATATCAT Y 2 1 2 1 101000 f 74 goat snp29588-scaffold321-737226 3 68402418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788873 Affx-122952046 AX-385275888 3 49781063 TTATAAGAAAGGGTCATTTAATTTGTCCATCATCA[G/T]CAGTACTACATATATAATCTTACAGAAAATAAGTG K 2 1 2 1 101000 f 74 goat snp29587-scaffold321-702989 3 68368303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381207 Affx-122974528 AX-123251565 3 49830973 TTCTACTCTTAAACACAATTCCTACTGAAATATAA[C/T]GGGGAGCAATCTAGAACAAAGTAACATCAAAAATT Y 2 1 2 1 201000 f 74 goat snp29586-scaffold321-653079 3 68317931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423830 Affx-122942791 AX-123294176 3 49886261 GAGTTTATAAATGTAATACAGAATTCTCCACTTAG[A/C]AAACAAAAAACATTAATAAAGCTGATAAAAACTTC M 2 1 2 1 101000 f 74 goat snp29585-scaffold321-597791 3 68262076 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451391 Affx-122921204 AX-123321724 3 49929144 TGTCCTAGCTAAGATTTCAAGGTAAAGTGTTCAAG[C/T]TGCTGCTTGGGTTCTTGTGGCTGCTTCCAGTAAAA Y 2 1 2 1 201000 f 74 goat snp29584-scaffold321-554908 3 68219111 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434492 Affx-122934620 AX-123304833 3 49974831 GGCTGCCTGGTGGCAGTGAGACTGTGGCAGGAAAG[A/G]GCATTGTCAGTGTGGGTAATTTTCACCCTGAACAC R 2 1 2 1 101000 r 74 goat snp29583-scaffold321-509221 3 68173255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779213 Affx-122922047 AX-385266317 3 50007532 TTTGGAAATATACAGAACGAAGCTCGAATAGAATC[A/G]TCTCCACTCACTAGTTTATACTAGCTTCATGAAGT R 2 1 2 1 101000 r 74 goat snp29582-scaffold321-476520 3 68140186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386191 Affx-122971366 AX-123256549 3 50045880 TATGGTACCATTCAGGGGGAAGTCCGAAGAAGAAG[G/T]TTCCAGAGCAAAATGCACTCATTTATTCTCATCCA K 2 1 2 1 101000 f 74 goat snp29581-scaffold321-438172 3 68101762 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796986 Affx-122945537 AX-385283927 3 50075248 TCGTAACTGCTGTCAAATACAGTTAAGTAAATATC[A/G]TTAGGAAAGAGCTCCGTTAAGAGAAATGCCAATCC R 2 1 2 1 101000 f 74 goat snp29580-scaffold321-408804 3 68072163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405560 Affx-122955957 AX-123275912 3 50113964 CTTTCAAAGGTTCAGTGCTGAAGGTCTCATATTCT[A/G]GGAAACCCCTCAGTCCAAGACAAACTGGTACATTC R 2 1 2 1 101000 f 74 goat snp29579-scaffold321-370088 3 68033400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431674 Affx-122936793 AX-123302015 3 50144249 ACTTGGTCCCACTGCTCTTTATATTATCTCTCATT[A/G]TCTTACCCTAGAGTTGTATCACATTTCCACATACT R 2 1 2 1 101000 r 74 goat snp29578-scaffold321-339803 3 68002652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765367 Affx-122971746 AX-385252880 3 50175356 AATGAATAAAACAGAACAGAGCACCCAAGAGTTGT[A/G]GGATAATATCAAACGATCTAACATACCAGGAAAAA R 2 1 2 1 101000 f 74 goat snp29577-scaffold321-308696 3 67970317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431062 Affx-122936639 AX-123301403 3 50207434 TACTTTATAATATCTAATTACATATACAATAGGCA[C/T]AATCTGGGACTATAGGAATGTGCAATTTTAATTGG Y 2 1 2 1 101000 r 74 goat snp29576-scaffold321-276618 3 67942376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764786 Affx-122940250 AX-385252397 3 50242134 AATGTGTGTACCATTCCCTACTAAGGCAGGAAACA[G/T]TCTAAAATGCTTCAGCCACAGAAGTTAAAAAAAAA K 2 1 2 1 101000 f 74 goat snp29575-scaffold321-241918 3 67907255 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429928 Affx-122938095 AX-123300269 3 50303632 AGACATGGTGGTGGTGTCAGAGAGAGTGCTTTGGC[A/G]TGTACTGGGAAATCCTATGGACAGAGGAGCCTGGT R 2 1 2 1 101000 f 74 goat snp29574-scaffold321-180420 3 67845229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779609 Affx-122978349 AX-385266711 3 50345509 CCTCTCTCCAAGAAAATTCCACTCACTTTTACTCT[A/C]GTTGACATGTAAGATTTATAAAAGTTTAATATTTG M 2 1 2 1 101000 f 74 goat snp29573-scaffold321-138543 3 67802888 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393405 Affx-122965888 AX-123263761 3 50386489 TGCATATGAAAATATGCTCAATCTCATTAGCAACT[G/T]AGAAATAATAAGTAAAATGAAAATGAGGCACCACT K 2 1 2 1 101000 f 74 goat snp29572-scaffold321-97563 3 67761345 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772434 Affx-122932753 AX-385259586 3 50460296 ACTTTAACAAATTTAGTAACAAATTTCTCACTGCA[C/T]GCTCTGTTTGTGCTGTAGTAAATGCAGCTTGTTTG Y 2 1 2 1 101000 r 74 goat snp29570-scaffold321-23756 3 67687811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799499 Affx-122925622 AX-385286429 3 50508183 TTCTGAGTTAATAATTATTGATATCTAAGCTACTG[C/T]GTTAGTGCTTTACACAAAGCATTTAATACTGGCAA Y 2 1 2 1 101000 r 74 goat snp195-scaffold1004-24032 3 67640152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444026 Affx-122926885 AX-123314363 3 50542879 TTTAAGGTGCACTCGCAGTGTCTCCTAGACTGTCC[C/T]TAGGGGAAGGAACCCCAGCTGCCCATAGCAGCAAT Y 2 1 2 1 201000 f 74 goat snp196-scaffold1004-58728 3 67605292 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272209 Affx-1111833390 AX-189023032 3 50563539 AAAAACCCTGATGCTGGGAAAGATTGAGGGCAGGG[A/G]GGAAAAAGAGGTATAGAGGATGAGATGGTTGGATG R 2 1 2 1 303000 f 74 goat 3_50563539_AF-PAKI 3 50563539 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448195 Affx-122924240 AX-123318531 3 50576242 CACTTCGTGAACGTGCGATAGAGGAGCAATAGCGA[C/T]AGCCCTCCCCATAACTAGCTTGTGATCCAGGACAG Y 2 1 2 1 101000 f 74 goat snp197-scaffold1004-92091 3 67571921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420842 Affx-122944654 AX-123291189 3 50608206 CGAGCAGTATGAGCTGGTGAGAGTTCTCATAGTGC[A/G]TCTACAAGCCACTTCTTCTGCAGGCCACCTCTGTC R 2 1 2 1 101000 r 74 goat snp198-scaffold1004-124055 3 67532270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775851 Affx-122973064 AX-385262982 3 50700682 AAGGGTTGACACTGGAGATTGACACTTCTGCATCT[G/T]TCAGTAATTCTGAACAAGTTTTTCTTTAGCAGTGG K 2 1 2 1 101000 f 74 goat snp201-scaffold1004-216531 3 67439041 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408020 Affx-122954303 AX-123278371 3 50735223 AGCAGAGTGCCCAGAAAATGATGAACACACAATAA[C/T]ATTAGCTAATCTGATTATCACTGACTCTATGAGCA Y 2 1 2 1 101000 f 74 goat snp202-scaffold1004-251072 3 67403724 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427628 Affx-122939345 AX-123297971 3 50790553 TAGGTTTAAGGTTTACACAGCATCAACAATGAAAC[A/G]TAAGTACAACCAAAACTGTACTGCATTAAAATAAA R 2 1 2 1 101000 f 74 goat snp203-scaffold1004-306402 3 67348535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376487 Affx-122978031 AX-123246846 3 50834433 AGCAACTGATGAGCAGGACTGATGAACAGGAACTT[C/T]AGTTCCTTAGCATTTCAGTCAGCACAGGTTACATT Y 2 1 2 1 101000 r 74 goat snp204-scaffold1004-350282 3 67304843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277955 Affx-1111836177 AX-519551450 3 50895881 CGTTACCTCATCTAATTCTACCACACCCCAAGGTG[A/C]TTTCTATTATTATCTGTATTTTTCAAGTCAGTAAA M 2 1 2 1 103000 f 74 goat Random2.2K-326 3 50895881 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449447 Affx-122922669 AX-123319782 3 50956852 CAAGGCAGCGATTATGAACACATGGTCTGGAAAAG[C/T]GATCTGAGATCTAGTTCCAGTTTGCAAACTATAGA Y 2 1 2 1 101000 f 74 goat snp207-scaffold1004-472701 3 67181921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437411 Affx-122932420 AX-123307749 3 50994987 CAAGGGGCTCAAGTTGGGCCCCATGGTCGGCTAGG[A/G]CTCCCCAGTATCTATTCGCCCTCCTTCTGCCCACC R 2 1 2 1 101000 f 74 goat snp208-scaffold1004-510836 3 67143823 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407356 Affx-122955277 AX-123277707 3 51038936 TGGCATTTTCCTGAGTGAACCTTTGGGAGCCCTTG[A/C]ATCCCTTCTGGGATCCTCTGGAAGCGCCTTTGTTG M 2 1 2 1 101000 f 74 goat snp209-scaffold1004-554785 3 67100127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781194 Affx-122938490 AX-385268279 3 51088754 TGAATTTCAACCCCACAAAAAATATTCATTAAATA[A/G]GCAGAATCATATGGGAGAGTGAACAATGTTCAGCA R 2 1 2 1 303000 f 74 goat snp210-scaffold1004-604603 3 67050343 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440753 Affx-122929867 AX-123311090 3 51121146 TCCCTGCAGCAGTTCCGCTGTCACGCGTGGCACGG[C/T]GATCAAGTAAGACAGATGCAGAGTCTTCCTGCAGA Y 2 1 2 1 101000 r 74 goat snp211-scaffold1004-636995 3 67017922 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768322 Affx-122926195 AX-385255502 3 51159118 TCTTTTTAAATTCTTATGCTGAAAGTTAAGCTTCT[A/G]TCTCTTTTCAAAAGAGATATACAATCACTCTTTAG R 2 1 2 1 101000 f 74 goat snp212-scaffold1004-674967 3 66981540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435033 Affx-122933758 AX-123305373 3 51194094 ATCTTGGGCTAAAACTGAGCTTCTCTCTGCTTCAT[C/T]ATCCTCCTCTGAGGATTTCATTCAATCATTTAACA Y 2 1 2 1 201000 r 74 goat snp213-scaffold1004-709943 3 66946532 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788254 Affx-122968871 AX-385275273 3 51231658 CTATAACTAGAACCTAGGTCCTCAGGATAAAATCT[C/T]AAGGCTCGTCCACACCAGACCACATTGTCTAGGCC Y 2 1 2 1 101000 r 74 goat snp214-scaffold1004-747507 3 66909070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439390 Affx-122930259 AX-123309727 3 51266129 AGAAAATGAGGCAATTCTATTGTCATGTCTAAAGA[C/T]ACTGCCTCGGGGTCTAATGAGCCCACCTGTAAACT Y 2 1 2 1 201000 f 74 goat snp215-scaffold1004-781978 3 66875699 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377474 Affx-122977507 AX-123247833 3 51312057 TAACACCTGCAATTCCAAATGGTGTGCCATGTGAA[C/T]ATCACAGAAATATTTGAAAGTGGTGATTTTCTTCA Y 2 1 2 1 101000 f 74 goat snp216-scaffold1004-827906 3 66829584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419526 Affx-122945437 AX-123289874 3 51343822 CTGTCTACGTTCTGGCCATTTTCAATTGCACTAGA[C/T]GGCTAGGGATTTGAAATCCAATGAAAGGAAATACT Y 2 1 2 1 101000 f 74 goat snp217-scaffold1004-859671 NW_017197361.1 8021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388228 Affx-122969399 AX-123258586 3 51376938 TTCTCTCCTCATTTCAATTAACCTTTAGAGAACTT[A/G]CAGGGGCTTCTCAGGTGGCTCAAGGGTAAAGAATC R 2 1 2 1 103000 f 74 goat snp218-scaffold1004-892787 3 66762272 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789830 Affx-122935094 AX-385276837 3 51420321 TAATTTGTCTTAATAGTTGATTCTTCATGTCACCC[A/G]CTTTACCTCAATGCCATCTTATTGGCTACAGATTT R 2 1 2 1 201000 r 74 goat snp219-scaffold1004-936170 3 66718559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452447 Affx-122920568 AX-123322780 3 51495741 CAGAAACTTAGACCATCTGGGGAGAAGTATGTCTA[C/T]AGGTTGAGGAAGTAAAATGACTTTTTTCTGCTTTA Y 2 1 2 1 101000 f 74 goat snp3256-scaffold1099-48913 3 66437903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797448 Affx-122951718 AX-385284387 3 51531024 CCCATGCCTTCCTTTACAGAGTTCACCCTAATCTC[A/G]CTGGACAGTTGAGGTAGCTACCAGTTAATTTCTCT R 2 1 2 1 101000 f 74 goat snp3257-scaffold1099-84196 3 66402575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795336 Affx-122977749 AX-385282294 3 51583255 TCTGTTCACTGTATGCCTCATGTGGGCAAGGTTGC[A/G]TTAGGGTTCATTTAAGGATCAATAAGATAACATAC R 2 1 2 1 101000 f 74 goat snp3258-scaffold1099-136427 3 66349662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804118 Affx-986696680 AX-385290772 3 51635295 GTGTTTGAGGAAAAGAGGGGTCAGAGAGCTTTAGT[A/G]GCCTGAAAGTAAAGATTCTCAAGATTTCTGCTTCA R 2 1 2 1 600010 f 74 goat 3_51635295 3 51635295 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320804514 Affx-986696682 AX-385291064 3 51635408 GGAATGAAAAGAGAAACAGCCAGCCAGCAACCAGA[C/T]ACTCTGTCATCATTTGTACAAACTACAAGACCATA Y 2 1 2 1 600010 r 74 goat 3_51635408 3 51635408 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38439077 Affx-122931136 AX-123309414 3 51636958 CCATACAACTGGTCTTTCTACACAAATGTTTCTCC[A/G]TCCTTTTTTTTCTTCTAGTCACCACTTTCCAACCA R 2 1 2 1 101000 f 74 goat snp56514-scaffold890-747830 3 66250196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804522 Affx-986696690 AX-385291071 3 51667998 TGAAACTATTGCAACATTTTTAATCAGCTATACAC[C/T]GAAATAAAATACAAAGCTTTCTTTAAGAAGTAATA Y 2 1 2 1 600010 r 74 goat 3_51667998 3 51667998 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 38405571 Affx-122955948 AX-123275923 3 51703790 TGAAAACACCAAGCAGTTTCATAGTCCAGTAACTG[C/T]CCCTCTTCCTCAGGGGGAAAAAAGCTATCACAGAA Y 2 1 2 1 202000 f 74 goat snp56512-scaffold890-680998 3 66182410 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801736 Affx-122958321 AX-385288644 3 51787233 CCCAGATAGGTCTTTTTAGAGTTTTGAGATACTCT[A/C]GAAATTATCTAGATTTAGAATGATCTAGAAAAGTT M 2 1 2 1 101000 f 74 goat snp56510-scaffold890-597555 3 66098310 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793457 Affx-122972106 AX-385280434 3 51843536 GCCCAGAATTACCAAACTAGCTAAAGAACTCTTCA[A/G]TCTAGTATTTTTTTATCCACGTGTTCAATAATTAC R 2 1 2 1 101000 f 74 goat snp56509-scaffold890-541252 3 66041968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454241 Affx-122919661 AX-123324574 3 51928836 TTCATTTTAGAGGAGACCTAGAAAATATGGTATTG[C/T]AATTGATGTTTGGAGGTCACTCCTGATAAAACAGT Y 2 1 2 1 101000 r 74 goat snp56507-scaffold890-455952 3 65956182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796636 Affx-122937217 AX-385283582 3 51964957 TTTTTAAATATTCCTAATGTCATGAAGACTGCTAT[A/G]ATTCTTAAACTGACTTCTATCATAAAACAATCATT R 2 1 2 1 101000 f 74 goat snp56506-scaffold890-419831 3 65919195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416042 Affx-122948359 AX-123286391 3 52025863 CATCTCTTCCAGCTGTGTTCACTTTCAACAATGAT[A/G]TCACCCCAATCCCTTGAGGCACTCAGATTAGAAAT R 2 1 2 1 201000 r 74 goat snp56505-scaffold890-358925 3 65857679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804142 Affx-986696692 AX-385290791 3 52027301 TGTGACTTAGGACTAATTCCATGATAAGAAAAATA[A/C]TAGTAGCAGCAACTACTGAGTTCCTCTTTTGCTGG M 2 1 2 1 600010 f 74 goat 3_52027301 3 52027301 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804526 Affx-986696694 AX-385291075 3 52029406 TAAGGATGGATAGGATGAAGGGAGGAAACCGATCA[G/T]CTCATTCTACTACTAAAAATCCTTGCGATGGGCTT K 2 1 2 1 600010 r 74 goat 3_52029406 3 52029406 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38438734 Affx-122930835 AX-123309071 3 52059258 CCTCACCACCTTACCTCTACAGACGACTCTCAGCT[A/G]GTTGGCTCCACCCTCCTGCTCCCTTCATTTGTCAC R 2 1 2 1 201000 f 74 goat snp56504-scaffold890-325530 3 65824345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453673 Affx-122919712 AX-123324006 3 52124148 ACATGTCAGCAATGCAGGTGAATTTGGAAGAATTC[A/G]CACAGCAGTATTTCTGTCACACTCTAGACATTTAA R 2 1 2 1 101000 r 74 goat snp56503-scaffold890-260640 3 65757557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776318 Affx-122941984 AX-385263446 3 52166853 AAACTTCATTGTTTTGAGCCTGTCTCATGAGCTAA[A/C]CATAACCTTTGACAACATTTCAGTGATACAATGCT M 2 1 2 1 101000 f 74 goat snp56502-scaffold890-217935 3 65714961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413854 Affx-122949866 AX-123284203 3 52203529 GTAGATTAGAGTTCTCTAAGCCATAAAAGAGCAGG[C/T]GGAGGAGGGCTGAGAGGAGCTACTCCATGCGCAAG Y 2 1 2 1 101000 f 74 goat snp56501-scaffold890-181259 3 65677585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778954 Affx-122920503 AX-385266061 3 52263791 ATTGCTCCACTGTAAAACCCAAGGCAGAATTAAGC[A/G]TAAAATCAACACATCTGTTGAGTACCTGCAGTGTC R 2 1 2 1 101000 r 74 goat snp56500-scaffold890-120997 3 65617004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781200 Affx-122955594 AX-385268285 3 52358141 TTAAAATTAAATTAGGGAAATTTTATAATTTCATA[C/T]GATTACTCAAGCCCCAAGCCTACCAGTATCAAGTA Y 2 1 2 1 202000 f 74 goat snp56498-scaffold890-26647 3 65522396 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409269 Affx-122953124 AX-123279620 3 52391932 CTGTGGGAATGCAAAGCCCAGCCCATCAATGGCAG[C/T]AGGAATGGCCACTCAAAAGAGGGGAGTTTAAGTTG Y 2 1 2 1 101000 r 74 goat snp1694-scaffold1047-2361794 3 65488387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385016 Affx-122971869 AX-123255374 3 52421122 GAAACCATAGCCACGTAAGAGTTTTAAGCCCTTCA[C/T]ATATCATTCCGTCACTCCAAGAAGGAAAATATAAG Y 2 1 2 1 101000 f 74 goat snp1693-scaffold1047-2332604 3 65465811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401751 Affx-122959508 AX-123272104 3 52453435 CATTTTCTGCATAGCAGTCCCCATCTTCCTTCTTC[A/G]TTTTGACTACTGCAAACTTATAGTGCCTTTTATTC R 2 1 2 1 201000 r 74 goat snp1692-scaffold1047-2300291 3 65433264 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443305 Affx-122927460 AX-123313642 3 52483983 AGAAGGATTCATGTCTCCATTCTCTGTACCCCTGT[A/G]AAACTAGAATTGTTGAATCATTCTGCTCCATTGGC R 2 1 2 1 201000 r 74 goat snp1691-scaffold1047-2269743 3 65402815 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790494 Affx-122921963 AX-385277497 3 52527335 TCTGGTCCAGGAATAAGAAGGTTTTTTGAGCAGCC[A/G]CAACACCCTCTTTGCTTGCAACTTCTGATCTGTGG R 2 1 2 1 101000 r 74 goat snp1690-scaffold1047-2226391 3 65358878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802530 Affx-122964727 AX-385289434 3 52584704 CTTTTTAATTAGGAGTAAAAGCTAGCAAGTAACTT[A/G]TCAATCCTATTGGAAATCTCACACAAACTTGAGGA R 2 1 2 1 101000 r 74 goat snp1689-scaffold1047-2169022 3 65301469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413917 Affx-122949821 AX-123284266 3 52614961 CTCTACAGATGTAAACAAGGAACACATGTTGAACC[A/G]CATCATTTTGATGCCTCTGGTAGATACATATGGTT R 2 1 2 1 101000 f 74 goat snp1688-scaffold1047-2138765 3 65271258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431451 Affx-122936498 AX-123301792 3 52693621 TCCTTCCACAGGCACCCCTCACCCTGCAAGACAGC[C/T]CTTCCGGACACTGTTATTCATCAGGACAGAAAAGC Y 2 1 2 1 101000 r 74 goat snp1686-scaffold1047-2060105 3 65192724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768308 Affx-122977243 AX-385255488 3 52733890 GCACTTTTACTCTTCCCCGTGAATTTGAAGAATTC[A/G]TTTCTTGTGTCCTATAGTCCATTATTTTGCCTGTA R 2 1 2 1 202000 f 74 goat snp1685-scaffold1047-2019836 3 65152096 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401257 Affx-122959294 AX-123271610 3 52790898 TAAACCTATTATGACCAAACACTTCAGCAGGCTTT[A/G]AGCAGAAGGTGCTTTCATTTGCTTCCAGAGCACAT R 2 1 2 1 201000 f 74 goat snp1684-scaffold1047-1962828 3 65094698 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421637 Affx-122944460 AX-123291984 3 52825309 TATTACAGACACTGCTTCTCCTCATTCCTGAAAAC[A/G]GGGGGTTGGAGGAGGTAATTCCTTGAGAACAGGAA R 2 1 2 1 101000 f 74 goat snp1683-scaffold1047-1928417 3 65060270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394298 Affx-122964698 AX-123264653 3 52868133 TTATTTTCCTGTACAAAGTTTTGTGCATACTGCTT[A/G]TTCCTTGACCTTACATTCATCTTCTTCTCTAAGAA R 2 1 2 1 101000 r 74 goat snp1682-scaffold1047-1885593 3 65016428 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382376 Affx-122973856 AX-123252734 3 52899763 CATTTTTCAAGGGAGAGCCATACATTTCAAATACC[A/G]TAGATCTGCAAACATTTTCAATGAAATCAAATGAA R 2 1 2 1 101000 f 74 goat snp1681-scaffold1047-1853963 3 64984832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418235 Affx-122947039 AX-123288583 3 52966912 TCTTGTTGGCCTGCATGATATCTTTTGGCTTACCA[G/T]AACAAGTACAAAGGCAAGACAGAAAAAATTTTCCT K 2 1 2 1 101000 f 74 goat snp1680-scaffold1047-1786814 3 64917528 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409964 Affx-122954108 AX-32597095 3 53025113 CTGTGTAATTTTAATTTATCATTAAGTAACACTTC[A/G]CTTTTTAACATAAAGAATTCAGTGTGCTTGATGGA R 2 1 2 1 101000 r 74 goat snp1679-scaffold1047-1728613 3 64858534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380085 Affx-122975545 AX-123250443 3 53064066 TGTTGTGATAAAACAACCAGCTACACAAAGCAGCC[A/G]CTGGATCTGTGACTTAACACATTTATTTCATTACC R 2 1 2 1 101000 f 74 goat snp1678-scaffold1047-1689660 3 64818942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783127 Affx-122951950 AX-385270194 3 53098362 AACTGAAGGCTCTGGAGTTAAATAATCAGTATAAA[G/T]CCTTGCTTAGAGGCAAAATAATATCTTCTTGATAT K 2 1 2 1 101000 r 74 goat snp1677-scaffold1047-1655364 3 64784122 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392541 Affx-122966098 AX-123262898 3 53139823 AGCTTGCCATTGATTAAGTGGCTTTATTTCTACAA[C/T]AGCAGAGGGTTGGCTCAGATGAGAAGTGGGTAGGC Y 2 1 2 1 101000 f 74 goat snp1676-scaffold1047-1613903 3 64742195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437774 Affx-122931704 AX-123308112 3 53245194 GGCCATGACAGAGGAGGGTGTGGAAGGTGATGGAA[G/T]AGGGCTGGAACCTGGAAAACAAATTCTACAACTTG K 2 1 2 1 101000 r 74 goat snp1674-scaffold1047-1508532 3 64636477 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435221 Affx-122933623 AX-123305561 3 53366887 CTGGGTCTAAAACTGCAAAAGACCCCAGTGCAATA[C/T]GGAGCTGAGTAGTATGGCTATGTTTAGCGCAGGGA Y 2 1 2 1 201000 r 74 goat snp1672-scaffold1047-1386839 3 64515050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402947 Affx-122958173 AX-123273300 3 53412936 AAGAGAGGGAAGACTTGTTGCAGAAATTGGGATTA[C/T]GGATAGGTCTTCTCTTTTTGAGAGTTTGAATTTTA Y 2 1 2 1 101000 f 74 goat snp1671-scaffold1047-1340790 3 64468830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390281 Affx-122967735 AX-123260638 3 53441834 CAAGTCACTGGTAGAACCTGGGAGCCTACAGTCTT[A/C]GAATCTAACTGGACTGAATCCAATTGAGTTAGGAG M 2 1 2 1 201000 r 74 goat snp1670-scaffold1047-1311892 3 64440013 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417638 Affx-122946851 AX-123287986 3 53472177 GTGATCCATTCTGTCGGCATAAAACTCAGGCACCC[A/G]CAGAGAACTGACCAGGTGGAGGAAACAACCTATGA R 2 1 2 1 101000 f 74 goat snp1669-scaffold1047-1281549 3 64409786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801975 Affx-122951553 AX-385288879 3 53514860 AGTAAGAAACAAAATCCTTAGGATTTTTTAACTGG[C/T]ATTTCAAGTTCTTGTGAGGATTTTATTTCCACTTA Y 2 1 2 1 101000 f 74 goat snp1668-scaffold1047-1238866 3 64366556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272213 Affx-1111833392 AX-519545960 3 53543437 CAGGCTACAGTCCGCAGAGTCACAGAGTCGGACAC[A/G]ACTGAGTGACTTTCAGTTTCACTACTCTTAGGTGA R 2 1 2 1 303000 f 74 goat 3_53543437_AF-PAKI 3 53543437 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776029 Affx-122948947 AX-385263159 3 53601620 CTTTTCCTCTTATCAAGATCCACAGTTGGTTCCAC[A/G]TTAAGCCGTGGCACACTCGATGGTAAAAGGATTTG R 2 1 2 1 101000 f 74 goat snp1667-scaffold1047-1152106 3 64279781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424929 Affx-122941288 AX-123295275 3 53671081 GGAGCTTTTTAAAAATATTTATTCCTAGTACTTTC[C/T]CAGACATGCAGAAGCTATTATGCCCTGGATTCTAT Y 2 1 2 1 101000 r 74 goat snp1666-scaffold1047-1082645 3 64209744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399996 Affx-122960809 AX-123270351 3 53703095 GTTGGTACAGTGAAGCTTTCCTCTTACCCATTTTG[A/C]TGCAGTTGTTCTTGGCTTTGTGCTGCCTGGGGTAC M 2 1 2 1 101000 f 74 goat snp1665-scaffold1047-1050631 3 64177620 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400542 Affx-122960437 AX-123270897 3 53753070 CCCCAGACTCTCACTATTTAAAGTTCTGGTTCTCA[A/G]CCTTGGTTCCACCTAGGATTACCTGAGAAATTGAC R 2 1 2 1 101000 f 74 goat snp1664-scaffold1047-1000656 3 64127518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404586 Affx-122957359 AX-123274938 3 53787794 GCAAGCAAAACAGTAGAGAAGGAAATTTTAAGGGA[C/T]GTTGATGCCAGTAGTAACTGTAATCATTGTGTGTG Y 2 1 2 1 101000 r 74 goat snp1663-scaffold1047-965932 3 64092456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774010 Affx-122972825 AX-385261148 3 53819460 TACAAATTGTGGTAAATTTTCAATGCCTTATCATC[A/G]TAAGAATCTTTGGCAACACATACATTCACATACAA R 2 1 2 1 101000 r 74 goat snp1662-scaffold1047-934266 3 64060676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432538 Affx-122935551 AX-123302879 3 53848513 CATGAAAATTACTGTATCAGACTGTGCATCATTTC[A/C]AGAACTTTCTCAAGAAAATGCTGTTATTTTTAAAA M 2 1 2 1 101000 f 74 goat snp1661-scaffold1047-905213 3 64031606 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438653 Affx-122930895 AX-123308990 3 53901807 TTGAGCATTTACCAAGTATCTGACGCTGCTCCAAG[C/T]GCATTATTTCATTTGACCTTCTCAGCACATTTAGA Y 2 1 2 1 101000 f 74 goat snp1660-scaffold1047-851919 3 63977951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790515 Affx-122973647 AX-385277518 3 53933320 GAGCTTGATTTGAGGAAATTTTTGAGATGTTAAGC[A/G]TATTTAATTTTTTAGCAAGAGAGAAATTAGTAAAA R 2 1 2 1 201000 r 74 goat snp1659-scaffold1047-820406 3 63946406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396523 Affx-122962957 AX-123266878 3 53967993 TGAAACAGGCCTACTAGTGAATCATCACAAATGAC[A/G]CCTTAGAAGCAGGCTTCCTCTAGTTAAACACACAG R 2 1 2 1 101000 f 74 goat snp1658-scaffold1047-785733 3 63911346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777387 Affx-122956824 AX-385264509 3 54018966 TTATATATACCAATAGAAGTAACGAAAATTACTAA[G/T]ACAGTTAACTAACAGTCATTTTATCCAGTCCTGGG K 2 1 2 1 101000 r 74 goat snp1657-scaffold1047-734760 3 63860330 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793686 Affx-122927649 AX-385280658 3 54056151 TTTCCCTTTAAGGTGGTAAAATGAAAGCAATATGC[A/G]TATCAACAGACAATATCTCAGAGGCTTTTAGTGCT R 2 1 2 1 101000 f 74 goat snp1656-scaffold1047-697575 3 63823048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412054 Affx-122951713 AX-123282404 3 54137042 CGAACAGCAACAGGAGATGCATTTGTGGTTTCCAA[C/T]GTTCCACAGTCTCCCTCATTACTTGACCTCTTCCC Y 2 1 2 1 101000 f 74 goat snp1654-scaffold1047-616684 3 63740963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382111 Affx-122974886 AX-123252469 3 54191488 ATTAATCTGACTTGGACAGCTCCTGGGGATGATTA[C/T]GATCATGGAAGAGGTAAGCTGAATGTGGTATGGAC Y 2 1 2 1 101000 r 74 goat snp1653-scaffold1047-562238 3 63685964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420139 Affx-122946002 AX-123290487 3 54252378 AGCTATCTGGGAGATTGTAATTTGTTGTTTTGGCT[A/G]TTCTTTTCTTTGATGTCACAGGTAATATTCAGATG R 2 1 2 1 201000 r 74 goat snp1652-scaffold1047-501348 3 63624055 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443377 Affx-122927406 AX-123313714 3 54288410 GGGTCTTTACCTGAAGATTCCATGAAAAAAAAGAG[A/G]GGCCTTCTGGGATCAGCCTGAACTGTAGATTTAGA R 2 1 2 1 201000 f 74 goat snp1651-scaffold1047-465316 3 63588184 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394261 Affx-122964723 AX-123264616 3 54317038 TCCGGAAGCAGGCGAACTCCTAGAACGGCCTGAGT[A/G]GAAGAATGCCCAACGGGGAGCAAGCGGGACAAAAC R 2 1 2 1 201000 f 74 goat snp1650-scaffold1047-436688 3 63559551 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436931 Affx-122933189 AX-123307269 3 54357932 ATAGAACAGTAAATCCTCGTGAAGTTTAAAATCTA[A/G]TAAGACAAATATGAAACATATAATTATGCAATTAA R 2 1 2 1 101000 f 74 goat snp1649-scaffold1047-395794 3 63518445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436323 Affx-122933255 AX-123306662 3 54435846 ACAGAACTGTAAGAGGAGATATATTTGGGATATTT[A/C]TGGAAAATATGTTTGGAGGAGGTGGTCTGAGCAAA M 2 1 2 1 201000 f 74 goat snp1648-scaffold1047-317880 3 63440470 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788715 Affx-122924669 AX-385275731 3 54482822 CCCAATAATGACAGACTAGATAACTTGATAATAAC[C/T]GGGAGATTGGACAAAATATACTTTAACTATGTCAC Y 2 1 2 1 101000 r 74 goat snp1647-scaffold1047-270904 3 63393166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447956 Affx-122923773 AX-123318292 3 54538215 ATAGTTTAGAAAGGGGATATCTATTTCTGCCAAAG[C/T]AAAAATTTAATATAAGCTGCATCAAAGTCTAAAGA Y 2 1 2 1 101000 f 74 goat snp1646-scaffold1047-215511 3 63337398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376452 Affx-122978056 AX-123246811 3 54572015 TACCCACTTTCTACTGTTCTGTATAATCTCAGCCA[A/G]ATCGTCTTGCCAGAATTAAGACTCAAAGATAGTGC R 2 1 2 1 101000 f 74 goat snp1645-scaffold1047-181711 3 63303493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787844 Affx-122958843 AX-385274867 3 54623942 GTGAACTCAGTTCCATTACAGCAATGAAATTCTTA[C/T]AACTCTAGATTAAACTTGATAATTTGTTAGTATAA Y 2 1 2 1 101000 f 74 goat snp1644-scaffold1047-129784 3 63251315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424974 Affx-122941916 AX-123295320 3 54668385 AAAAAGGAAGACGTAAGAACTACATTATCTCAGTA[C/T]GCAAAAGCATGAGTACACAAATGTTGACTAATATG Y 2 1 2 1 101000 f 74 goat snp1643-scaffold1047-85341 3 63206935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419426 Affx-122945514 AX-123289774 3 54717382 TAAGCTAATAATTATACTTTGCTTATATTTTGTCA[C/T]AGATAGTTATTTTAGTGTTTTCTTCTGACATGGAA Y 2 1 2 1 101000 r 74 goat snp1642-scaffold1047-36344 3 63157987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405295 Affx-122956848 AX-123275647 3 54769413 AGAAAAGGAAACCATATTTTTACTCTGAGGGTCCA[C/T]AGATTAAAAATATGGATAAATTGTGTGCATTTTCA Y 2 1 2 1 201000 r 74 goat snp18857-scaffold190-14530 3 63102011 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792568 Affx-122930653 AX-385279549 3 54805353 TAATTATAAGAATGAGTATTTTGCTGTGAAGATAA[C/T]TTATAGTGCCTTCCTGGTTTCATAAAGTCAAATTT Y 2 1 2 1 101000 r 74 goat snp18858-scaffold190-50470 3 63065761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391484 Affx-122966713 AX-123261841 3 54839132 ACCAAAATTACAAAAAAACAAAGAAAAACAGATAT[A/C]TTGGACTGCATTAAAGTGAAAAGTTTTAGAACTTC M 2 1 2 1 101000 r 74 goat snp18859-scaffold190-84249 3 63031029 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383631 Affx-122972541 AX-123253989 3 54873629 TATATTAATCTGTTTTTCTTTTCTTAAATAAATCC[A/G]TCCTAGTTGTTTATTCATATGAACCGTGGCGCTGT R 2 1 2 1 101000 r 74 goat snp18860-scaffold190-118746 3 62996559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794970 Affx-122940944 AX-385281930 3 54938851 TACTAAATATATGTTACTGAAACACAGCCACGCTC[A/G]TTCATCTCTTTATTATCTAGGGCTGTTATCACACT R 2 1 2 1 101000 f 74 goat snp18861-scaffold190-183968 3 62931252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379212 Affx-122976287 AX-123249571 3 54997863 TTAAGGCATTGACTGACATTATCAGACTTGTGTTT[A/C]GCAAAGATGCTCAAGCAGCAGTCTGGAAAGTACAC M 2 1 2 1 201000 f 74 goat snp18862-scaffold190-242980 3 62870831 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434044 Affx-122934203 AX-123304385 3 55034533 CAGCAAAGCGCCAGCTGCCAAAGTGAGGAGGACAG[C/T]GCACCATGATGCCTTGTGCAGGGATGGTGGACAGA Y 2 1 2 1 201000 r 74 goat snp18863-scaffold190-279650 3 62834856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785683 Affx-122961512 AX-385272724 3 55070625 TTACTTCACTGGTCTATTATCGAACTACAAATGTC[A/G]TGCTTTAGGGTGCCTAAGTTGCTGAGAATATTCTG R 2 1 2 1 101000 r 74 goat snp18864-scaffold190-315742 3 62798549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804150 Affx-986696696 AX-385290799 3 55101554 TAGAAGCTGAAGAGGGACAGGGAACTTCTGGTGAA[A/G]CAGAGAAAGCAAAAAACTCCGCACAGGGGACCAAA R 2 1 2 1 600010 f 74 goat 3_55101554 3 55101554 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 38438220 Affx-122931446 AX-123308558 3 55134783 GGATCATCCACCAAATCAAAAAAAGATGATTTTTC[A/G]TGCATGTATTGCAGGGCCAGAGTGAATCAGAGGCT R 2 1 2 1 101000 r 74 goat snp18865-scaffold190-379900 3 62734234 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788623 Affx-122944507 AX-385275640 3 55187906 TCTTTCCAAAGGAAAGAAGTAGGGTGTATATGTGG[A/G]AGGATCAGTTATCTCCTCTTCTCGTTGTTAAGATT R 2 1 2 1 101000 f 74 goat snp18866-scaffold190-433023 3 62680684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803536 Affx-986696101 AX-385290344 3 55218052 AAACATTAACTCAAAATGAGTTACAAAATTAATTG[C/T]TAGAGCTAAAATTATTAAATTTCTAGAAGAAAGCT Y 2 1 2 1 600010 r 74 goat 3_55218052 3 55218052 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320804154 Affx-986696698 AX-385290803 3 55218106 ATTTCTAGAAGAAAGCTTTAAGACAAAATCTTTAT[G/T]ACATTGAGAAAGGCAGATTTCTTAATAGACTCTAA K 2 1 2 1 600010 f 74 goat 3_55218106 3 55218106 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320804532 Affx-986696700 AX-385291081 3 55218115 AGAAAGCTTTAAGACAAAATCTTTATGACATTGAG[A/C]AAGGCAGATTTCTTAATAGACTCTAAAAGCCACAT M 2 1 2 1 600010 r 74 goat 3_55218115 3 55218115 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320796055 Affx-122959175 AX-385283007 3 55246127 AAAGTGGAATGTAAATATGATGGAATATCATTGTT[A/G]TCCTATCTTTCTCCTTCACTCCACAACCATCTAAA R 2 1 2 1 101000 f 74 goat snp18867-scaffold190-491244 3 62621929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426383 Affx-122940237 AX-123296729 3 55281270 AAGTGGCAGGGTCGCACTAATCTCTACATATCATC[A/G]TAACACATGAGAAACTTGTTATTCACAGTCAGTAC R 2 1 2 1 101000 f 74 goat snp18868-scaffold190-526387 3 62588904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776989 Affx-122941516 AX-385264113 3 55310446 AATAACAAACAAGGGTTAATTCCATCTATTCACCC[A/G]CAGACTTTTTCAGTCCTCCCAGAGCTAATTCGAAG R 2 1 2 1 101000 f 74 goat snp18869-scaffold190-555563 3 62559500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796803 Affx-122936063 AX-385283746 3 55346089 TTATTTTTTAAAAAGATTACCCAGACTTTCTCACC[A/G]CTGCTGTCCTAAGGGTCAGTACATTGCACAACTCC R 2 1 2 1 101000 r 74 goat snp18870-scaffold190-591206 3 62523564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277957 Affx-1111836178 AX-519551452 3 55364970 ATCACAGGAGTTAAAGTGAAGTACAAGAAAAAGTC[A/G]CTGGAGTTAAAAAGATCAAAGCACTGAGAATCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-329 3 55364970 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778242 Affx-122948478 AX-385265357 3 55397572 ATAGTTTTGCATTGCGTGACAGTATATCCAGTCTG[C/T]ATTTGAAAGATTCTTAATTTAAGATCTGTCATTTA Y 2 1 2 1 101000 f 74 goat snp18871-scaffold190-642689 3 62472223 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403309 Affx-122957836 AX-123273662 3 55429401 TGTTCCAGAAAAGAAACAAAAAAGAATGCTCTTTC[A/G]TGTGCACAGACTCTCCTCTAACCCCAAGCAACTCT R 2 1 2 1 303000 r 74 goat snp18872-scaffold190-674518 3 62440182 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798271 Affx-122925474 AX-385285206 3 55489082 TAGTTAAGACTGGGATATTGATAACCACTAAAGAA[C/T]AAAAGAGTGTTGTGTTATTCAAGATTTGTGCCAGT Y 2 1 2 1 101000 f 74 goat snp18873-scaffold190-734199 3 62382357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786727 Affx-122967494 AX-385273758 3 55535965 GGCTCCCTGGCGGTGGAAAATAGTTAACTATTCAA[C/T]GTTAAACAATGACTTATTTACCTTTTCTTTTTTTA Y 2 1 2 1 201000 r 74 goat snp18874-scaffold190-781082 3 62334677 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442099 Affx-122928357 AX-123312436 3 55576900 GATGAATACAGTCCAATGTACAGCATTGCAAATAC[G/T]CTTCCAAAGCCCTGAGTGATGAAAATGGCAATTTG K 2 1 2 1 101000 f 74 goat snp18875-scaffold190-822017 3 62293567 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417237 Affx-122947283 AX-123287585 3 55616220 AGGCAACATTTATTAATCACTAACGACATGCCAGA[C/T]GTTTTACATCTGTTTACACTGTCTTTGTAGGAGGT Y 2 1 2 1 101000 f 74 goat snp18876-scaffold190-861337 3 62253788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443482 Affx-122927814 AX-123313819 3 55644829 GAAGCAGACTCAGAAGTGAAGATTAAGTTTAAGGC[A/G]GAGATCTGAGCCCCAACAGCTGTCCCCTTCAGGCG R 2 1 2 1 101000 f 74 goat snp18877-scaffold190-889946 3 62224561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419740 Affx-122945889 AX-123290088 3 55678084 CCACCATCCCCCACACAGTCATCTTTACTCATTAC[G/T]ACCTCCTGCTGGTGATCCTTGGAATTGACGGAATT K 2 1 2 1 101000 r 74 goat snp18878-scaffold190-923201 3 62191819 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432701 Affx-122936028 AX-123303042 3 55711868 GGAATAAGACAAGGCCCTTACTTTCAAAGAGCTAA[C/T]GTTCCTCTGTTTACCTTCTTCATGCCATCTACTAA Y 2 1 2 1 101000 f 74 goat snp18879-scaffold190-956985 3 62157608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785453 Affx-122945455 AX-385272498 3 55778331 ACCTTCACAGGTTCCTTGGGGGTTTATGATCCTAG[C/T]AAGGTTAAGAATTGCTGATAATTTGTTCTGTGTTG Y 2 1 2 1 101000 f 74 goat snp18881-scaffold190-1023448 3 62091951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769827 Affx-122935286 AX-385256997 3 55795268 GCACGAGAACCTTTGTTTTATACGGATGTCCCTCT[A/G]TTATATTACCAAGACACCTTAGAATCGAGTTACAG R 2 1 2 1 101000 f 74 goat snp52103-scaffold770-397235 3 62074627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798676 Affx-122950530 AX-385285608 3 55847679 GCAAAAGAATGCTGTAATATGACCCTAACATTCTT[A/C]TCTCCAGGATTGATTGTTTCAACTGGATTTCGTAG M 2 1 2 1 101000 r 74 goat snp52102-scaffold770-344824 3 62022192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438780 Affx-122931378 AX-123309117 3 55883071 TTCTAGTCAACTCCTGTTAATCCTTCAGATCCCGG[C/T]GTAAATGTCCCTTGCTCCAGGACCCTGGTCCTTGA Y 2 1 2 1 201000 r 74 goat snp52101-scaffold770-309432 3 61986484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376731 Affx-122978957 AX-123247090 3 55911849 CCCATGAGACCCTAGGAAATTCTCAGGGGCTCCTC[C/T]GTCATTTGTCAATACCCACCACTGTACTTGTAAAT Y 2 1 2 1 101000 r 74 goat snp52100-scaffold770-280654 3 61957865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415635 Affx-122948582 AX-123285984 3 55957733 AGTGCTGAGCTCTGGGCAGTCCAAGGTGGGAAGGC[A/G]TGTAATTCTGGGGCCACATCTCTGCCAATCCAGCC R 2 1 2 1 101000 r 74 goat snp52099-scaffold770-234770 3 61911997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775500 Affx-122927546 AX-385262631 3 55992256 ATCTGCATATGGCCCATAGATTCTAGGAGACTACC[A/G]CGTGTATTATCAACAGCTCTGGTTAAATAATGAGA R 2 1 2 1 101000 f 74 goat snp52098-scaffold770-200247 3 61877694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782443 Affx-122964031 AX-385269519 3 56020799 CTTCTGTTGGATGATGCTGAGTCATGGACAATAGA[C/T]GCTTTGAGTATGAAAGGTCTGGTCATAAAAGACAA Y 2 1 2 1 101000 r 74 goat snp52097-scaffold770-171704 3 61848551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795256 Affx-122953034 AX-385282214 3 56070409 TCAACTTTCATCAACTACACACCCTACACCCTACT[A/C]TATTGTAGGAGAGGAAGGAATATACAATTTGTGAG M 2 1 2 1 201000 r 74 goat snp52096-scaffold770-122094 3 61798436 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444398 Affx-122926589 AX-123314735 3 56115506 TCTTCAGGTTATGACCCCAGAGTCCAGATGACTAC[A/G]TCTCTCATGTCCACTCCACTGACGTCTTCTAACTG R 2 1 2 1 201000 r 74 goat snp52095-scaffold770-76997 3 61753408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774058 Affx-122972403 AX-385261196 3 56191330 GATCAAAAGGTAATGGCAATGGATGAAGAAAATAT[A/C]TCCTTTTCTAGGTCTTACAGAATTGAGTCTAAGAG M 2 1 2 1 101000 f 74 goat snp52094-scaffold770-1173 3 61677119 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790064 Affx-122924521 AX-385277070 3 56203225 TGTTTATTGCTGTATCCTCAGCATTTAAAACAGTG[C/T]TGAGAACTGAGGTGCATAGTAGGCTCAATCAAAAT Y 2 1 2 1 101000 f 74 goat snp42040-scaffold55-10623 3 61665777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272215 Affx-1111833393 AX-519545962 3 56226061 AGTTCTTGCAATCTAACAACAAATACTCAGCCGCT[A/C]TACTAACCACTTCTATCAGAGCATGCGCATTTTCA M 2 1 2 1 101000 f 74 goat 3_56226061_AF-PAKI 3 56226061 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417393 Affx-122947691 AX-123287741 3 56259446 TTTTCTGTGGTTATACTATAACTTAAATTATACTT[C/T]ATCAAATATTGAGGTTTCCAAATTTGAGGCTACAC Y 2 1 2 1 303000 f 74 goat snp42041-scaffold55-66844 3 61608140 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429255 Affx-122937900 AX-123299597 3 56299752 TCCAGGGTGTCCACCAGATGGTTGTATTAAGCTTT[A/G]CAGCTCACCACAGAGATTGTGAGCAGAGCCAGCCC R 2 1 2 1 101000 f 74 goat snp42042-scaffold55-107150 3 61567864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396352 Affx-122963052 AX-123266707 3 56334953 GAATAGGAAGGATGACAGTAGGTGACCTGTAATGA[A/G]TGGGTGGGAGAGCAGTGGGACAGTGGCTCGAGAGA R 2 1 2 1 101000 f 74 goat snp42043-scaffold55-142351 3 61532420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429085 Affx-122938275 AX-123299427 3 56385438 TTTGCGTTCTGCCTAAACCATGGCAGTAGTGAACC[A/G]TCTTGGAGAATGTAAGATGTTTTATACTGCATGAA R 2 1 2 1 101000 f 74 goat snp42044-scaffold55-192836 3 61481872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424015 Affx-122942094 AX-123294361 3 56436121 CAACCAATCCAGGTTCTCTGATTCCTATACCTGGT[G/T]CAGTGGGGATGAGGGTGGGGGTGGGAATCAAGAAA K 2 1 2 1 101000 f 74 goat snp42045-scaffold55-243519 3 61433065 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429947 Affx-122938080 AX-123300288 3 56472522 CTGCTCAGGGTACTGTTGGAAGCAGTTGGTCTAAC[A/C]GACACATTAAAAAAAGCATCTCCTTCTTTCACTCT M 2 1 2 1 101000 f 74 goat snp42046-scaffold55-279920 3 61396736 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417618 Affx-122946866 AX-123287966 3 56508577 GTGTAACAAATTCCATAAAGATGTAAAAAATGGTC[C/T]ATATCCAAAAATAATGTTTAAAAACCACCCTAAAA Y 2 1 2 1 101000 f 74 goat snp42047-scaffold55-315975 3 61360269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764679 Affx-122956211 AX-385252308 3 56542179 GATAGGACACAATTCAGCCCTCATCAGAAGGCATA[C/T]AGAAAATGTTCAGCAAAGCTAAACTGAAGGTATTT Y 2 1 2 1 101000 f 74 goat snp42048-scaffold55-349577 3 61326258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791941 Affx-122946835 AX-385278931 3 56585330 TTAGTGTAAAATTAACATCAGATTTGGGAACTTGA[C/T]ATGAAAAAAAGAATACGAAACACCTTAGTAATTTT Y 2 1 2 1 101000 f 74 goat snp42049-scaffold55-392728 3 61282858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427477 Affx-122940015 AX-123297820 3 56626813 CAAAGAGTTGGACATGACTGAGCAACTGAACTGAA[C/T]TGAGCTCCGATTCTATCTGAAAAACATCCATATAC Y 2 1 2 1 201000 r 74 goat snp42050-scaffold55-434211 3 61241642 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380711 Affx-122975153 AX-123251069 3 56679208 CAACTCTTGATCTCCCTCATGACCCTCCTCCAAAA[C/T]AAAAAAATATATAAATGAAGAGATGAATTATAATA Y 2 1 2 1 103000 f 74 goat snp42051-scaffold55-486606 3 61188892 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430168 Affx-122937369 AX-123300509 3 56735393 CCCACATGCTAGTGTTTAATAGTGTCCCCTATTAT[C/T]GACATTCTCCACCAGATTGGGGCATTTATTGCAAT Y 2 1 2 1 101000 f 74 goat snp42052-scaffold55-542791 3 61131465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787787 Affx-122937124 AX-385274810 3 56786645 AATGATGGGTTATTGGTTTCCAGAGTATTCCAATA[C/T]GCTAAAACCCAAGTTAGGAATAATCCACTTGGATC Y 2 1 2 1 202000 f 74 goat snp42053-scaffold55-594043 3 61079565 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801902 Affx-122943960 AX-188760460 3 56831368 CGTTTAGTAATAGATGAAATGGGATTTATGAAAAC[A/G]CCAGATGAGGATGAAACAAGCAATCTTATATGGTG R 2 1 2 1 101000 r 74 goat snp42054-scaffold55-638766 3 61034464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400622 Affx-122960376 AX-123270977 3 56890899 CTTGAGGATGAACACTGAGAATATATTTATTTTCC[A/G]TTTGCTCATGGAGTAGGGTAATTTTGCATTGATTG R 2 1 2 1 101000 r 74 goat snp42055-scaffold55-698297 3 60977101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400911 Affx-122959734 AX-123271264 3 56962815 GGATGGTTGCTCATAAACCTTTCTGAAGAGCCCCT[A/G]CACTTAATGCTGAATCCACCTCATCTCACCTTCTT R 2 1 2 1 201000 r 74 goat snp42056-scaffold55-770213 3 60903830 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444024 Affx-122926887 AX-123314361 3 57000694 TGAACACTATATTGTTAGTGGATTAGATAGTCACC[A/G]TCTCTTGAAGCTGTCACTTTTTTCTCTATGGATAA R 2 1 2 1 101000 f 74 goat snp42057-scaffold55-808092 3 60866030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444676 Affx-122926449 AX-123315013 3 57057441 ATGTAACAGGTCACTGCCTATTGATGGTAACAATC[A/G]TATCCACGTCGTATCCAGTGTTATAAAAACTGTGC R 2 1 2 1 101000 r 74 goat snp42058-scaffold55-864839 3 60809300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786426 Affx-122938315 AX-385273460 3 57100117 AGGGGACAAACTGACTGTGGCTGGCATATTTTGAG[C/T]ATTTACTTTTTAGCAAGAACCAAGTAGATGTAGGT Y 2 1 2 1 101000 f 74 goat snp42059-scaffold55-907515 3 60766558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419212 Affx-122945696 AX-123289560 3 57142821 GCCGCCTTAACTGCATTTTTGTGAAGTAGCTGCAG[C/T]GGCACTTGATAGCTGATTATGTTAATCCTTTAGGG Y 2 1 2 1 101000 r 74 goat snp42060-scaffold55-950219 3 60722674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769404 Affx-122926257 AX-385256575 3 57178049 ACAGCCTACTATATGCTACTCTAAAATTTGAGGGT[A/G]TAAAGCTAAATCAGTTTATGCCCACAAGAAAGTGA R 2 1 2 1 201000 f 74 goat snp42061-scaffold55-985447 3 60687436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426949 Affx-122940415 AX-123297294 3 57213014 CATAGAAATGTTAGCTTATTTGGCCATCCTTTCCC[A/G]CACGTGGACTTTTTTCTGCTCTAAAGGTAGTCTTC R 2 1 2 1 101000 f 74 goat snp42062-scaffold55-1020412 3 60652451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378002 Affx-122977597 AX-123248361 3 57258179 AAAAAATAATTTTCCAAAAGTAGAATTTCAGGTAC[A/G]TAACAACTTGATGGGAAAGGCTGTTTGGGGTCTAG R 2 1 2 1 201000 f 74 goat snp42063-scaffold55-1065577 3 60607278 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447565 Affx-122924032 AX-123317901 3 57309029 GGTCTATCAAATGTGCTACCCAACTGGTTATTGAG[C/T]GTATTCTGTGCACTATCTTGAACATTCTCTCTTGT Y 2 1 2 1 101000 f 74 goat snp42064-scaffold55-1116427 3 60556134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438069 Affx-122931530 AX-123308407 3 57365953 GGCTTGCCAGTTGCCAGTGGGAAGTGAACATAATT[A/G]TGACTTCACAGCTGCTTCTCCTAAAGAAAAAGGTG R 2 1 2 1 101000 f 74 goat snp42065-scaffold55-1173351 3 60499216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780863 Affx-122973568 AX-385267951 3 57394786 CAGTTATAACCACTTATATACTAACATTAAATTTA[C/T]ATGAAATGATTAACAGTATACAAATAGATGGATAT Y 2 1 2 1 201000 f 74 goat snp42066-scaffold55-1202184 3 60470027 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400706 Affx-122959930 AX-123271061 3 57430158 CACCAGAGGACGAGAGAGAGTGTTTGCTAAACATC[A/G]TGGCATGGAGCATTCTTTCCTCTTGGGTAAGGATT R 2 1 2 1 101000 f 74 goat snp42067-scaffold55-1237556 3 60434201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426000 Affx-122941141 AX-123296346 3 57503098 CTTCGAGACTTGATTGTAGGTCAACATTAGCATGG[C/T]GCTGTTGGGAGGCTACCATAAGAGTAAAATCAAAG Y 2 1 2 1 201000 r 74 goat snp42068-scaffold55-1310496 3 60360911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421968 Affx-122943804 AX-123292315 3 57557194 ATGTAAACACTGAACATGATTGCTGAATCATATGG[C/T]AAGAGTATGTTCAGTTTTCTAAGAAACTGCTAGTC Y 2 1 2 1 303000 f 74 goat snp42069-scaffold55-1364592 3 60306913 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413939 Affx-122949804 AX-123284288 3 57606903 AGAATAAAGTTCTTGCATTGGTGAAAGAGGGTGTG[A/G]CCCAGTATATTATTGGAGAATTTAGACATATTAAC R 2 1 2 1 101000 f 74 goat snp42070-scaffold55-1414301 3 60256911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445624 Affx-122925096 AX-123315961 3 57645538 GCAGCAGAAGAGGTTTGATGAGGTAAAGAGAGAAG[G/T]GCAAATGTGGAATTTTTGATTGATTTTAAATTGTT K 2 1 2 1 101000 f 74 goat snp42071-scaffold55-1452936 3 60218387 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798983 Affx-122937633 AX-385285913 3 57675115 ATCTCCACTTAATCACAAACTCCTACAAATTCTAG[A/G]TTTTAAATATTGTTATTTCTCTGACATAGAGAAAA R 2 1 2 1 303000 r 74 goat snp42072-scaffold55-1482513 3 60188791 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434512 Affx-122934605 AX-123304853 3 57722408 TAGCCAAATAAGGTAAGTCATTTGTTATCTGAGCC[A/G]TAAATATTTACATCCACTAGTGACAAATGTATAAA R 2 1 2 1 101000 f 74 goat snp42073-scaffold55-1529806 3 60141029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384410 Affx-122972198 AX-123254768 3 57783386 TTTCTTTTTAGATTCCACATGTAAGAGATGTCATA[C/T]GAGGACAAATATTCTTTTAGTCAGGAGCTCTAAAT Y 2 1 2 1 101000 r 74 goat snp42074-scaffold55-1590784 3 60079280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433082 Affx-122935732 AX-123303423 3 57843271 GGCTTTTAATGAAGAACTACTCTAGAAGAAGTATG[C/T]TGCATATAATAAATAATGATGAGCATTAAAAAATA Y 2 1 2 1 101000 f 74 goat snp42075-scaffold55-1650669 3 60019651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392736 Affx-122966019 AX-123263093 3 57900451 CTTCTCCCACAAAGCCTTTCCTGAGGACCTTCTTG[C/T]ATCTTGCCTTTGCACTTACTGGTAGTTTTCTTTTC Y 2 1 2 1 201000 r 74 goat snp42076-scaffold55-1707849 3 59961512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784474 Affx-122938591 AX-385271523 3 57933045 TGTCAAATGCCATGGAATGAATACTTTAATTACCC[G/T]AAAATTCATGTGAGGTCAGTCCTTGAAGGAAAATA K 2 1 2 1 101000 r 74 goat snp42077-scaffold55-1740443 3 59928726 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451218 Affx-122921964 AX-123321552 3 57970557 TTTTAAAGAACTGAATGAAGCTGATAATTTGCTGG[A/C]GACTGCTATCTGATTCCCTTAGGAAAAAGTACTAG M 2 1 2 1 101000 r 74 goat snp42078-scaffold55-1777955 3 59890507 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399363 Affx-122961344 AX-123269718 3 58012878 GTTAAATGCCGTCTTCGGGTTCTGTTGCTAAATAA[G/T]GAAGGCGAGCACTGATGTAGAGGCGGAAGTTTCTA K 2 1 2 1 101000 f 74 goat snp42079-scaffold55-1820276 3 59847968 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781498 Affx-122979060 AX-385268583 3 58059077 ATTATAGTGTCATCAAATCATCTCAAATTGGTATA[A/G]AGGAGAAAAGCTCTATACTGATTACAGTGTCTGAA R 2 1 2 1 101000 r 74 goat snp42080-scaffold55-1866475 3 59801799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792341 Affx-122970550 AX-385279323 3 58089080 CAACTCTGATCTTTTCTATTAAATCCCTTTGTGTA[G/T]GACACATCAAGAATGGTTTTGTTCCTTAGCCAAAT K 2 1 2 1 101000 r 74 goat snp42081-scaffold55-1896478 3 59771806 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420396 Affx-122944928 AX-123290743 3 58131154 ATATGTTTGAATTCTCACAAATTCTCTGATGTTAA[C/T]GGGTGATTCTTTCCATTATTTTATTTTCAACATTA Y 2 1 2 1 101000 f 74 goat snp42082-scaffold55-1938552 3 59729245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780789 Affx-122921468 AX-385267878 3 58178246 TACAAAAGCTAACTAAAGAGGGCATGCTAAATGCA[A/G]CTCATTGGTTGGTTCTAACAGAGCTTGGAGTTTAA R 2 1 2 1 101000 r 74 goat snp42083-scaffold55-1985644 3 59682120 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405925 Affx-122955570 AX-123276277 3 58212938 GTCAGACAGGACTGAAGCAACTTAGCAGGCATGCA[C/T]GGAGAATGAATGGAACTGTTTCTTAAAGGAAATAA Y 2 1 2 1 201000 r 74 goat snp42084-scaffold55-2020336 3 59647782 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452367 Affx-122920629 AX-123322700 3 58242774 TCTCTCTGTTTTGTCTTGGCCTCTTCTACTTCTCT[A/G]TTCATCTTGGACTGCATCAGTTCAGTTCAGTTCAG R 2 1 2 1 103000 f 74 goat snp42085-scaffold55-2050172 3 59617527 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392824 Affx-122965783 AX-123263181 3 58272530 CAGAAGAATGTGTGTATTCCCCAGTACTCAGCATC[A/G]TTTCCTTGAACACTGAGAGAACATATTAAATGAAA R 2 1 2 1 201000 r 74 goat snp42086-scaffold55-2079928 3 59587578 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775824 Affx-122971465 AX-385262955 3 58303604 TCTGAATCCCTTGTGAGGCTTGCTTAGATCTCAGG[A/G]GAATTTCTCTTAACTAAAATCATCATTGTTTGGAC R 2 1 2 1 101000 f 74 goat snp42087-scaffold55-2111002 3 59556674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404545 Affx-122957390 AX-123274897 3 58346730 GTATACAAATGTCACAATGCAAAAATATATGAAAT[A/G]CAAAATCAGCATCAGACAGGATAAGATCACACTTG R 2 1 2 1 303000 f 74 goat snp42088-scaffold55-2154128 3 59513055 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432706 Affx-122936024 AX-123303047 3 58375557 AAACTAAAAAAAGCAAACCCCTGTCTGGGTGCATA[G/T]GTATGAAAATTATATTGGACAGGTACTGTCTCATC K 2 1 2 1 201000 r 74 goat snp42089-scaffold55-2182955 3 59484224 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424948 Affx-122941274 AX-123295294 3 58455240 ATAAAATATCCTTGTATTCAGCCAGCATATAGTCT[A/G]TTTAATCTTTTTCACTTCCAGGTCACAGTCTTTAG R 2 1 2 1 101000 r 74 goat snp42090-scaffold55-2262638 3 59402827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789918 Affx-122929533 AX-385276924 3 58507342 ACCAAAAATATTTATGGCTAGTATAATTGAAAATT[A/G]CTGTTTTATAACTGAAACTCAGATTATGTTCTCAA R 2 1 2 1 101000 r 74 goat snp42091-scaffold55-2314740 3 59349314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398141 Affx-122961687 AX-123268496 3 58569030 GTTCTTGATCCCGGAGGCAGGAAAGAAAGTGAGCT[A/G]TTGAGAGAAGACTGCTGTAGAACAAATGCAGTGAG R 2 1 2 1 101000 r 74 goat snp42092-scaffold55-2376428 3 59287427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438259 Affx-122931416 AX-123308597 3 58657496 TTGCACTGACAACCAAACAATTCTTGTGAATGAAT[A/G]CTGATTATGTATGCACAGCAGTTTATCTAGCACAA R 2 1 2 1 101000 r 74 goat snp42094-scaffold55-2464894 3 59199236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392024 Affx-122966477 AX-123262381 3 58689508 CAGGTTGATGCATGACAACTGCATGGAGATCAAAT[A/C]CCTGGGCAGGTTGAGGCATCTTGGCTTCCTGAGAA M 2 1 2 1 101000 f 74 goat snp42095-scaffold55-2496906 3 59166962 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447353 Affx-122924874 AX-123317689 3 58718905 GGCATAGATTAAGCTGAAAAAAATGGCACACCATT[A/G]TAGACAAGACTTTCCAAAAGATCTAGAAAACACTC R 2 1 2 1 101000 r 74 goat snp42096-scaffold55-2526303 3 59138103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435959 Affx-122933528 AX-123306298 3 58765578 CTTGGGAAGATTCAAGAGTCCAATAGCTATTATCT[A/G]TTCTGTCTATCAGAAATGCTCACTTTTCCTAATTA R 2 1 2 1 101000 f 74 goat snp42097-scaffold55-2572976 3 59090785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440080 Affx-122929728 AX-123310417 3 58796038 GATATCAGCAACAGGGCCAGCAATTTCAACATGGA[A/C]AGTGGAAGTCTCATCATTCATAAAGCTGCCAAGAG M 2 1 2 1 101000 f 74 goat snp42098-scaffold55-2603436 3 59059388 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420591 Affx-122945258 AX-123290938 3 58826456 GGCAGAAGTAGAATCCTGGGTCGTCTTTCTGGCAC[A/G]CTGCCTTCCTGATGATCATTAACATAATGCAAAAC R 2 1 2 1 101000 f 74 goat snp42099-scaffold55-2633854 3 59028955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802639 Affx-122934973 AX-385289540 3 58867316 CTGAATATCAGTACAGGGAATATTCATTCTCTGGT[A/G]AATAGAAATTCATCCTAGAAAATAGCATCATGAGT R 2 1 2 1 101000 f 74 goat snp42100-scaffold55-2674714 3 58987593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395911 Affx-122963604 AX-123266266 3 58900854 CTCTTCGCCAAAGATGAATCAGATTATATTTTGTT[A/G]GCTATTTTGGGGGCAGGGTGGATATATGTATTTTT R 2 1 2 1 201000 f 74 goat snp42101-scaffold55-2708252 3 58953998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401567 Affx-122958892 AX-123271920 3 58938497 GAAATTATAAATGGAGCAATGGAGCAGTCATCAAG[A/G]ACCCCAGGAAGATAATTATGGGTTGATAGTGGCCG R 2 1 2 1 201000 f 74 goat snp42102-scaffold55-2745895 3 58914688 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384332 Affx-122972259 AX-123254690 3 58974652 TATCTCTCTTAGAAAGTAAGACCCTTATGGAGGCT[A/G]GTAAGTCCCAAGATCTGCAGTTGGCAAGTTCATGA R 2 1 2 1 201000 f 74 goat snp42103-scaffold55-2782050 3 58878587 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396505 Affx-122963527 AX-123266860 3 59022214 TCGTACAATATAAAGTGATTCAGAGTTGGTAGTGC[A/C]GACAGAAACAGATAACTGCCAGAAGGAAATATAAA M 2 1 2 1 101000 f 74 goat snp42104-scaffold55-2829612 3 58831002 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429298 Affx-122938609 AX-123299640 3 59081981 AGAATCTTAAAATACCTGGTTGGCATCTCTTTTCT[C/T]TGTAACAAATAATTCATTTTAGTATACTCTGTGTA Y 2 1 2 1 101000 f 74 goat snp42105-scaffold55-2889379 3 58769802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794483 Affx-122957057 AX-385281446 3 59127894 TAATAGGAAACATGACAAGTCACAATAGAATTATA[C/T]TGTAAATCTAAACCCTACTGTTCACAGCCTTCCCG Y 2 1 2 1 201000 f 74 goat snp42106-scaffold55-2935292 3 58723821 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432628 Affx-122935484 AX-123302969 3 59162319 GAAATCAGTTTTGTCTCTTACTTAATTTATTAAAT[C/T]GTTCCCATGTTCAAAAAGCTAGACTTTTTTCCCTT Y 2 1 2 1 101000 r 74 goat snp42107-scaffold55-2969717 3 58689505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777249 Affx-122931210 AX-385264372 3 59203121 TGAAGCTTTCTCTACTCATTTCAACCATTAAATGG[C/T]ATAAAAGTAAAATTACCTGTGTACTTTTTAATGCT Y 2 1 2 1 202000 f 74 goat snp42108-scaffold55-3010519 3 58649859 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385639 Affx-122971172 AX-123255997 3 59325353 GGAATTCTTTGGTGGGCCAGTACTTGGGAATCAGT[A/G]TTTTCACTGCGAAAGACCCAGGTTCAATCCCTCAT R 2 1 2 1 101000 f 74 goat snp42110-scaffold55-3132751 3 58529698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383906 Affx-122973110 AX-123254264 3 59373361 CTGTAGGGTATAGGCAGGCAGCTCAGCAAATCCCA[C/T]GAGATGGGTTAAGGTGATGAGTCCAGGGAAGGACA Y 2 1 2 1 101000 r 74 goat snp42111-scaffold55-3180759 3 58482423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413262 Affx-122950223 AX-123283611 3 59420062 AATTTTACATTAATTATGCCCCTGTATTTTGACAG[C/T]GCTTTTTGTAGAACGCTGAATTTTTACAAAACCCA Y 2 1 2 1 101000 r 74 goat snp42112-scaffold55-3227460 3 58435598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413834 Affx-122949880 AX-123284183 3 59451796 CTTCCTACTGGTAAAGTATAGGTACAAATGCTTCC[A/G]TTGGCACCTCCGCAAATATTTATTAAATGCCTGCT R 2 1 2 1 201000 f 74 goat snp42113-scaffold55-3259194 3 58404560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424799 Affx-122941387 AX-123295145 3 59480622 CATTCTCATTTATTGAGTAAGCCAAAAGAATACCT[C/T]CACATCTGTATGCAAATATTTCACAATTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp42114-scaffold55-3288020 3 58375779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384219 Affx-122972381 AX-123254577 3 59522355 GCGATGTGACCCTGAAGGCATTGTCAACAAACCAG[C/T]GGGTGAGACGTTTCAGTTATAGGAATAAGCGAAAC Y 2 1 2 1 101000 f 74 goat snp42115-scaffold55-3329753 3 58334328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476175 Affx-1251763679 AX-586011602 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 4 1 4 1 20000 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 539476430 Affx-1251763679 AX-586011831 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20000 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562165156 Affx-1251763679 AX-606940568 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562165207 Affx-1251763679 AX-606940619 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562166256 Affx-1251763679 AX-606941664 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562166261 Affx-1251763679 AX-606941669 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 38423467 Affx-122942582 AX-123293813 3 59575877 TGTCATCTTATCCCTGACCATCCATTCTTCCCTCC[A/G]CTATTATTTTTAAAAGTTTTTTTTTTTCCATTACT R 2 1 2 1 103000 f 74 goat snp42116-scaffold55-3383275 3 58280826 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432895 Affx-122935331 AX-123303236 3 59607644 CCTATAGGTTTGCTAAGACATGTCAACAGAACTAA[C/T]GCCAATTGCCATTCATATAGTACCTCTTATGTCCC Y 2 1 2 1 101000 f 74 goat snp42117-scaffold55-3415042 3 58249118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409264 Affx-122953127 AX-123279615 3 59647481 GCTCTGCTTATATTTGTGTGTAATTTCTCATTTAA[C/T]GTGGACAAGTAAAAAGTCCACAGTGCCTGCACTGT Y 2 1 2 1 101000 f 74 goat snp42118-scaffold55-3454879 3 58209445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275091 Affx-1111834592 AX-519548670 3 59658069 CTGAACTAAACTGAGCCACCAGGAGAGCCCAGCAT[A/G]TAGGACTTATGCACAAATGACCTGCAGAAAATACT R 2 1 2 1 201000 r 74 goat GoatD01.042516 3 59658069 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770775 Affx-122933842 AX-385257939 3 59678001 CACTATTGTTTCTGATCAGGAAACATTACAGGAAT[A/G]CCACTATTAGAATGGATGAAAGCAGAAATCTGACG R 2 1 2 1 101000 f 74 goat snp42119-scaffold55-3485399 3 58177723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407479 Affx-122954766 AX-123277830 3 59720662 GCAATATGAAGCACAAAAGGTCTCAAATTACCTGA[C/T]GTTTATTGTCATTAAATTTTACCACTGAAAGATCT Y 2 1 2 1 101000 f 74 goat snp42120-scaffold55-3528060 3 58135295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443552 Affx-122927759 AX-123313889 3 59757273 CCCCTTTATTTGATTTAAATGCTCATTTTTCAAAA[C/T]GCATCCCTTGACAGTATATTCCATCCCATGATATC Y 2 1 2 1 101000 f 74 goat snp42121-scaffold55-3564671 3 58098157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385872 Affx-122971605 AX-123256230 3 59797155 AAACTCCAGGAGTCATATACCAGGCATTTTGCATC[G/T]CTGTCAAGAAGTTCCTTCATTTGATCCCACCTACA K 2 1 2 1 101000 r 74 goat snp42122-scaffold55-3604553 3 58058882 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408178 Affx-122954201 AX-123278529 3 59846837 CACTGAGCCACCTAGGAAGCCCTGGACTAACTTAG[C/T]AGAGAGTTAATTTGAGATACATTTGTAGGTAGAGG Y 2 1 2 1 201000 r 74 goat snp42123-scaffold55-3654235 3 58008530 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773957 Affx-122947697 AX-385261096 3 59914644 TTCTGGGAAGTCAGATGACTGAGAAAGGAAGACCT[A/C]GAAGAAGGATATTTCAGTGGTCTGATTTCAAATTT M 2 1 2 1 101000 f 74 goat snp42124-scaffold55-3722042 3 57941793 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787543 Affx-122943600 AX-385274567 3 59956199 TCCAGACCCAAGACATGACTATTTCAACTAGAAGA[C/T]GGTAAAACATCTCTGAGCAAAAGAAACAGTGGAGA Y 2 1 2 1 101000 r 74 goat snp42125-scaffold55-3763597 3 57899693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277959 Affx-1111836179 AX-519551454 3 59959339 GAACAATGGTTACTATGGCCCTGGACATGAGAGAA[A/C]TAGAAAGATGTTGGTCAAAGGGCACATATTTTTAT M 2 1 2 1 101000 f 74 goat Random2.2K-333 3 59959339 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769009 Affx-122937524 AX-385256184 3 59991756 AATCACAATAATGAGATTTCGGAGAAAAGGAATCG[C/T]GGAAATCACTCAACACTTCCTAGCAATGGGTAATA Y 2 1 2 1 102000 r 74 goat snp42126-scaffold55-3799154 3 57863626 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277961 Affx-1111836180 AX-519551456 3 60013636 AGGGAACAATTTGAGGAACTCTAGAAGAAACCAAT[A/G]AAATATAGGTAGGAAAACAATCTTATGTCAGGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-334 3 60013636 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399471 Affx-122961194 AX-123269826 3 60028741 AGCAATTTATACCCCAGAGCTTTTCAGAAGAGTTA[A/G]TACAATGGCTGTGCATGTCAGAAATGATTTTCTTT R 2 1 2 1 101000 r 74 goat snp42127-scaffold55-3836139 3 57827460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781013 Affx-122937150 AX-385268100 3 60061917 TGTAGTGGCAATAACTGGTCTGAAAATGACCCTCT[C/T]AAACATTTGTGAACTATCAAGCAGGGACTGAAATT Y 2 1 2 1 101000 f 74 goat snp42128-scaffold55-3869315 3 57795018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438507 Affx-122931212 AX-123308845 3 60098471 ACTAATACTTCTTCCTTTTTTAAAATGAGAAATGT[A/C]TCCTGCTTGGGCTTTAGAGATATGAACTTAAAAAG M 2 1 2 1 101000 r 74 goat snp42129-scaffold55-3905869 3 57757315 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765214 Affx-122978103 AX-385252753 3 60130712 TGTATATAGTTTCTTCATTTGGTTTTTAGAACACC[A/G]CACTCTCTTAGATTTCCTCTTATTTCAATTATTTT R 2 1 2 1 101000 f 74 goat snp42130-scaffold55-3938110 3 57725075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275117 Affx-1111834607 AX-519548696 3 60153208 GTCAACACTGCAGGGAAGGTGTCAGTCTCAACTCC[A/G]ACTGTCTAAAATGGAAAGTTCACCTGCAGCCCACT R 2 1 2 1 101000 r 74 goat GoatD01.042967 3 60153208 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770591 Affx-122968704 AX-385257755 3 60188447 TGGCATTCTCCTGTTTACTGATGAGTGGTGAACAC[A/G]CAAATTTTGCTCAGCCATAGTAATGAGCAACTAGA R 2 1 2 1 101000 f 74 goat snp42131-scaffold55-3995845 3 57667151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393803 Affx-122965179 AX-123264158 3 60239826 AGCCTGTACAGATGACACACGCATAAAGAGTTAAA[G/T]ACTCAAGAGTAGTCAAAAGTTGGCCGTTTTATTTT K 2 1 2 1 101000 f 74 goat snp42132-scaffold55-4047224 3 57615564 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780610 Affx-122926040 AX-385267700 3 60268696 GTGTTTTTCTGAACTGGCCCTCAGGTATTTAGGGT[A/C]TGTTGGGTCCTACATCTCTTTGTAAGAGCTACTTG M 2 1 2 1 101000 f 74 goat snp42133-scaffold55-4076094 3 57586611 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394144 Affx-122965317 AX-123264499 3 60305135 GGGATAGACAAAAACAAAGCCAGTAAAAGTACTTG[C/T]ATTATTAGGCTTGGGATCCTGTACATATGCTCTCT Y 2 1 2 1 101000 r 74 goat snp42134-scaffold55-4112533 3 57550226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779635 Affx-122965052 AX-385266737 3 60334684 GTGTGCAGGTTGAATCAGATTGGCCTTGGTAGGAC[A/G]CAGTCTGTGCTGGTATCGATTAGAATCTCGGGGAG R 2 1 2 1 101000 f 74 goat snp42135-scaffold55-4142082 3 57519074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769638 Affx-122934418 AX-385256808 3 60383235 AAAAAAATTTTTAACTTTACTCTTCATATTTTATT[A/G]TTTTGTTGTTTTGGCACAAAGGATGACAAGGAAAG R 2 1 2 1 303000 f 74 goat snp42136-scaffold55-4190633 3 57469911 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797024 Affx-122936932 AX-385283965 3 60419793 CTGACAAGTGAAGTAGAATTTTAAGCGTGTCCCAC[A/G]TTTGTTTCATTAACCTTTTTTTCTCTAGAGCCTAG R 2 1 2 1 101000 f 74 goat snp42137-scaffold55-4227191 3 57433219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400269 Affx-122960128 AX-123270624 3 60468095 GGACAGGAGGATGTTAACATGCTGCAACACACTTA[C/T]GCACAGTCCCGAACTTGACAGCAGTAGACAGATTT Y 2 1 2 1 101000 f 74 goat snp42138-scaffold55-4275493 3 57384144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278120 Affx-1111836181 AX-519551610 3 60471020 AAAAAAAAGAACAAATAATAATAATAGCAAGCTAT[C/G]TGGAAGGAATCTAAACTCACTGTTTTCACTGTTTT S 4 1 2 1 101000 r 74 goat Random2.2K-335 3 60471020 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434534 Affx-122934151 AX-123304875 3 60502935 CAGACTTGACTAAGTGACTGAACTGAACTGAATCA[C/T]GTAGGTCCATTCAGAGGATTGAGAAAATGTTTGTG Y 2 1 2 1 201000 r 74 goat snp42139-scaffold55-4310333 3 57348250 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452295 Affx-122920685 AX-123322628 3 60558110 TAGAGAAGAAAAAACTCATTAGTTGTAAGACTTGA[A/G]TGTCCATGTAATAAATGGCTAAATATAACATTTCA R 2 1 2 1 101000 f 74 goat snp42140-scaffold55-4365508 3 57293372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423208 Affx-122942711 AX-123293554 3 60602762 TTTTACTTAGGTTAAAATAAACAAGGATGAGAACC[A/G]TTGGATTTATCAACATGGAGTACACTGAAGATCTT R 2 1 2 1 201000 r 74 goat snp42141-scaffold55-4410160 3 57248671 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797389 Affx-122949184 AX-385284328 3 60681285 CAACTTAATATTCAACAATTTTTGAGACCCTGAGT[C/T]CTCAGAAAATTTAACTAGGTGATAAACTTCTTTAT Y 2 1 2 1 201000 r 74 goat snp42143-scaffold55-4488683 3 57172140 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786810 Affx-122959052 AX-385273839 3 60723967 TGCTCTTTCTATGTTTTAGGATATGATATTATTGA[A/G]CTTATGCTTTAATATTATTTGAAAACATGGTGTAA R 2 1 2 1 201000 r 74 goat snp42144-scaffold55-4531365 3 57129182 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379434 Affx-122976103 AX-123249792 3 60756302 TCATTAGGCCTCTCATATCCACTTGGGGGCAGTGA[A/G]TCATCCCCAGACTGGGGCATTAAAACTCTTCTATC R 2 1 2 1 102000 f 74 goat snp42145-scaffold55-4563700 3 57096327 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770356 Affx-122968252 AX-385257522 3 60835078 AATCTGGGAATCCTTTGAACTAGATTTTTTTTATC[A/G]TGGGTTTGAATACTTGACCTTTGAACCTGCTTTTG R 2 1 2 1 101000 r 74 goat snp42147-scaffold55-4642476 3 57017014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784273 Affx-122949073 AX-385271324 3 60885655 ATACTGTTAACCAGGCTTATCTTTTACTGGCCTCT[A/G]TCTGGCTCAGACTAATATGATAAAAAGTTTTCCAA R 2 1 2 1 101000 f 74 goat snp42148-scaffold55-4693053 3 56966101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383097 Affx-122973280 AX-123253455 3 60954429 CTCTCCTTATTTACAACTTCTTGGTACCTTCCAGC[A/G]CTCCGTCCATTTCCTTCCCCTCATGCTATAAATTG R 2 1 2 1 101000 f 74 goat snp42149-scaffold55-4761827 3 56895440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779983 Affx-122975796 AX-385267082 3 61003556 AGAAGACACTCAAATTCTAGGAAATAGTCTTGGCT[C/T]TGTTATTTCTCTATTCTTCAGTCATTAATTCTTCC Y 2 1 2 1 101000 f 74 goat snp42150-scaffold55-4810954 3 56846760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397743 Affx-122962536 AX-123268098 3 61041488 GCAACACATGAAAACCTTTGACTTCTCTCACATTG[C/T]AACTATTTCACATAAAAGCAAAGAACAAGAAACAT Y 2 1 2 1 101000 f 74 goat snp42151-scaffold55-4848886 3 56808148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407161 Affx-122954841 AX-123277512 3 61076132 TGAAGCCTCACTTAAACTAATATAAAAGCAAAGGA[A/G]AAGACCCTGACTTTGGGAAAGATTAAAGGCAGAAG R 2 1 2 1 201000 f 74 goat snp42152-scaffold55-4883530 3 56773531 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789633 Affx-122969598 AX-385276642 3 61107560 ATTATCTAGTGTTTAAGAAACAATTTAAAACATTG[C/T]AATCACAATGAGTTCACTGAATACATTTTGAGCAT Y 2 1 2 1 201000 f 74 goat snp42153-scaffold55-4914958 3 56741635 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438326 Affx-122931347 AX-123308664 3 61148397 CCTAACCAAACATACACCCCCATGGAATGTATTAA[C/T]GCTTCCGTCTGCACCATGTGGGTGAATGTAGGATA Y 2 1 2 1 202000 r 74 goat snp42154-scaffold55-4955795 3 56700488 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429618 Affx-122937698 AX-123299959 3 61205793 TTGTTCATCGCTTTGTAACTGAAGCATTCTGTATC[A/G]CACCAACTGAGAATGGTTTTGTTCCTGCTTCTGAG R 2 1 2 1 101000 r 74 goat snp42155-scaffold55-5013191 3 56642564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448284 Affx-122924176 AX-123318620 3 61234595 TAATCTTCATGCTATACACCTGAAGTCTCTCCTAA[C/T]ATTCTTTTTATGTGATGCTGAATGATACTACACTA Y 2 1 2 1 201000 r 74 goat snp42156-scaffold55-5041993 3 56613869 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411640 Affx-122951575 AX-123281990 3 61327346 CAATTAGTAGTTTTCAAGGTAAAGAACCAGTTTCC[G/T]TCTCACCCTCTCATTTTGACAATTTTTAGGAACTC K 2 1 2 1 101000 f 74 goat snp42157-scaffold55-5134744 3 56519628 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464218132 Affx-1110375202 AX-515693068 3 61361916 TAGGCCAATGTTACATATTCACAATGAATTGTATA[C/T]TGTACAATGTATATTCTGTATCTAAAAAAATGGGA Y 2 1 2 1 101000 f 74 goat 3_61361916_AF-PAKI 3 61361916 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445271 Affx-122925468 AX-123315608 3 61383058 CAGATTCTTTACTCTCTGATCCACCAGGGAAGCCC[A/G]CACATCCATTTCCTTCTTCTTAAATATAAATATGT R 2 1 2 1 101000 r 74 goat snp42158-scaffold55-5190456 3 56464287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794834 Affx-122965430 AX-385281794 3 61386356 TTATCTGTTGCTCTGGCAGCCTGATTTTCCTATTA[A/C]TTCATATGAATTCATTGTAAATTAAAGAAATTAGC M 2 1 2 1 202000 r 74 goat snp21579-scaffold2108-2142 3 56461127 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379187 Affx-122976307 AX-123249546 3 61439592 CTTAAGTAAGTTTTATGGCTCCTGTATGACTTGGA[A/C]TATACCACTGGCAACAATATCCTAATAATTTTTCT M 2 1 2 1 101000 f 74 goat snp21580-scaffold2108-55378 3 56406649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788490 Affx-122936590 AX-385275507 3 61491968 GAGTCTACCCCCTCTAGTCTAAAAATGATATTACT[A/G]TCACTAGTAAACATAGGTTTCCTAGGCATGTTTAC R 2 1 2 1 202000 f 74 goat snp21581-scaffold2108-107754 3 56353243 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398961 Affx-122960975 AX-123269316 3 61526390 AAAGGTTATATAACAAATTATTATAAATAATTAAT[A/G]TACAGTCATATCTGATTTAAGAATATTTGGTTAAT R 2 1 2 1 103000 r 74 goat snp21582-scaffold2108-142176 3 56318729 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376525 Affx-122978005 AX-123246884 3 61556039 TACAAGTCTTAATTTTGTGTGTGTGATCCCAATGT[A/G]ATTTCTGTCAATCACAATGCCCTAAAAAAAGAATA R 2 1 2 1 201000 r 74 goat snp21583-scaffold2108-171825 3 56288381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452828 Affx-122920737 AX-123323161 3 61631099 AGTTGGAAATGATCTGAGAAACCATAGATAACTTC[A/G]TTTATATTATACAAAGAAATAAAAACGGATGCCTA R 2 1 2 1 103000 f 74 goat snp21585-scaffold2108-246885 3 56211068 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378454 Affx-122976690 AX-123248813 3 61660450 AGGGCTCTTCTAATCCTTAATCTAAGATCCCTTTA[C/T]AAATTTTTGCAGAGTTCTTCTAATGCCCATAGATC Y 2 1 2 1 101000 f 74 goat snp21586-scaffold2108-276236 3 56182055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386829 Affx-122970093 AX-123257187 3 61688614 GGGAAAAAGCTGACTGGGTGAAATCCAAATGCCTT[C/T]AGTAGCAGAATGGCAGGAAAGTTGGGAAAGCCATA Y 2 1 2 1 101000 f 74 goat snp24971-scaffold257-12862 3 56152999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410886 Affx-122952078 AX-123281236 3 61724032 ACTACCAACGTGGGTAGAGTAAGAGAAGTTTTCAC[A/C]TTTTGCCATTTTAAATGTAAGAAAACAAAACACAA M 2 1 2 1 101000 f 74 goat snp24972-scaffold257-48280 3 56117250 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451874 Affx-122921059 AX-123322207 3 61862222 GAGGCTGCATTTTCACCCTCTGAAAGGCTAATGAC[A/G]TCAGACAACTTCGGGTACAAAAGTCTCTTCCCCTA R 2 1 2 1 101000 r 74 goat snp24974-scaffold257-186470 3 55976482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392196 Affx-122966288 AX-123262553 3 61916325 AAGACCCAGAAGCACTGTCCTATATAAGTGATTTA[C/T]ATCACCTCCTCCTGCACTCCTCACTTAGGATGCCT Y 2 1 2 1 201000 r 74 goat snp24975-scaffold257-240573 3 55922300 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425719 Affx-122940763 AX-123296065 3 61957490 ATGATGGGAGAATAAGAGCACTGCAGTAACTATCC[G/T]AGTGAGTGAGAAAAGAGTAATGGCTCTCTCCAGAA K 2 1 2 1 201000 f 74 goat snp24976-scaffold257-281738 3 55881947 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409127 Affx-122953304 AX-123279478 3 61993723 AGGGTAGGGTTGCTGTCAAATGTTTGAATATCTCA[C/T]GGGGATGGGTCTTTCTGCAAACAATAACACAAAAT Y 2 1 2 1 101000 f 74 goat snp24977-scaffold257-317971 3 55845677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429543 Affx-122937829 AX-123299885 3 62050007 TTTAGCATAAAGAGAATTTTTTTGTAGTATAGTTG[A/G]TTCACAATATTGTGTTACTTTCAGGTGTACAGCAT R 2 1 2 1 303000 f 74 goat snp24978-scaffold257-374255 3 55788625 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388440 Affx-122969263 AX-123258798 3 62095554 AGATGACTATTGTACTTTACATTTGCAATGCTAGG[A/C]TCTGTCTAAATACCCACTGAAAGAGATTCAGTTTA M 2 1 2 1 101000 r 74 goat snp24979-scaffold257-419802 3 55743248 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798255 Affx-122927180 AX-385285190 3 62129105 TGTTTTGCTTTTACTTTAAAAAGTAGACACTGCCA[A/G]CTCCATCAAAGTGTAGTTTGCAAAATATGAGATTA R 2 1 2 1 101000 f 74 goat snp24980-scaffold257-453353 3 55710010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274408 Affx-1111834237 AX-519548000 3 62175990 AGAAATTTATCCTTTAGTGTTAACTACCAAGACCC[A/G]GGAAATATTTAACTGCAGAGTAGAAGAAGATGTCA R 2 1 2 1 101000 f 74 goat GoatD01.026894 3 62175990 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787723 Affx-122926606 AX-385274746 3 62176284 TCCCTTTCATGGGAGTAGGGAGAGAGCAAGACATA[C/T]GTAACAGTCATCATGGCCCATAGAAATTCTGAAAT Y 2 1 2 1 101000 f 74 goat snp24981-scaffold257-500532 3 55662520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435927 Affx-122932755 AX-123306266 3 62223940 TGTGTCACATCACACTCTTTTTTTCACTCCCCCAC[A/G]TTTTTCTCACAGCTCACAGAACTCAGTCCACGTTG R 2 1 2 1 101000 r 74 goat snp24982-scaffold257-548188 3 55615003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775280 Affx-122973311 AX-385262411 3 62266002 TGAGTCACTGGGGATGACATTGGACACATTTTATT[A/C]TTCCTAAGCCTGAGATCTTAATTTGACTAACAGTA M 2 1 2 1 101000 f 74 goat snp24983-scaffold257-590250 3 55571260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434095 Affx-122934165 AX-123304436 3 62300492 ACTTAAGTGATTGGTTGACTTGTTTTCCTAAGGCT[A/G]TGCAGATTGGTCTCTTTCCCACTGGTGTTTGCTCC R 2 1 2 1 101000 r 74 goat snp24984-scaffold257-624740 3 55536059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798670 Affx-122932707 AX-385285602 3 62343648 TCTGTTTCAGGGTGAACACTGGTGTGATTTATACC[C/T]CTTATAAATCACATACTAAGTTTTCAACAGTTTGC Y 2 1 2 1 101000 f 74 goat snp24985-scaffold257-667896 3 55492344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425401 Affx-122941550 AX-123295747 3 62412212 ACTTTGAGCCAGTTATTTAACTTCCCTATGCTTCT[A/G]TTGCCATAAATGTGAAATACATGTAATGATACAGA R 2 1 2 1 201000 r 74 goat snp24987-scaffold257-736460 3 55423232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787777 Affx-122960764 AX-385274800 3 62449452 ACGGAGGAGTTAGGCCTCACCTCTTGATCAGAAAG[C/T]GGTTAAGATAATATTGAAGAAAACATGTGAGGTAG Y 2 1 2 1 101000 f 74 goat snp24988-scaffold257-773700 3 55385933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419306 Affx-122946229 AX-123289654 3 62482359 CATACGGTACATTTGCTTTGTACTATTTTCTACAC[A/G]TTTGTTGAAATTTAAAATGAAGAGTAATCATATTA R 2 1 2 1 101000 f 74 goat snp24989-scaffold257-806607 3 55352802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452586 Affx-122920504 AX-123322919 3 62511638 TTAGTGATTTTCTTAATTCCTTTATCAGACAGATC[A/G]TTTCCTGCGCTTTCCCCTTCAGTGTCTCCCACTGC R 2 1 2 1 101000 r 74 goat snp24990-scaffold257-835886 3 55323960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801158 Affx-122977554 AX-385288072 3 62652617 TGTGCAGCTAGATATTGACTATTATCCTAACTATT[A/G]TCTGACTGACCCCAGTGTCCTGCATTTTCTCCAGC R 2 1 2 1 102000 r 74 goat snp24993-scaffold257-976865 3 55182338 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440786 Affx-122929842 AX-123311123 3 62682937 CTCAGGAGTCTCAGGGAAACAAGAAATGAGAGATT[A/G]TAGAAGAATTAAGATTTTGTTAGGCATGTCCCTCC R 2 1 2 1 303000 f 74 goat snp24994-scaffold257-1007185 3 55151148 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410074 Affx-122952850 AX-123280424 3 62758861 GGCTGGCTCATTGGAACTTGGATTCCAGAGAGTTG[C/T]GCATAGATTCTCATCACTCATGCAGTCTTTCATCT Y 2 1 2 1 101000 f 74 goat snp24995-scaffold257-1083109 3 55074064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416269 Affx-122947954 AX-123286618 3 62828377 TGTGCCAGAAGAAGGAAAAAAACTGAGAAGAAATT[A/G]CTTCATCAGAATTAAAAGCTTGACCTTAAAATAAG R 2 1 2 1 201000 r 74 goat snp24997-scaffold257-1152625 3 55003964 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398742 Affx-122961822 AX-123269097 3 62877145 TATAATGGCCAGCAATGGTGACATTATTTATACAG[C/T]GGAAAAGCCCATAGTGTAAACATATAAGACATACA Y 2 1 2 1 101000 f 74 goat snp24998-scaffold257-1201393 3 54953622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425464 Affx-122941504 AX-123295810 3 62957936 TTTCTTTGAAACTTCTATTTGCTACCAGTTTCCTA[C/T]AGAGCTATCATTAAATCCTTTATCAGGGCTTACAT Y 2 1 2 1 101000 f 74 goat snp10420-scaffold1373-55295 3 54870680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274051 Affx-1111833976 AX-519547655 3 62982439 TGGTTTGAGACTAGTCAGCTTA[A/G]CACATCTGCAGTAAATGAGTCTACCATGCTGTTTT R 2 1 2 1 101000 r 74 goat GoatD01.012499 3 62982439 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320789600 Affx-122971262 AX-385276609 3 63040093 AAAACTCAGCTAAGAAATGGCATCATCAGGAAAGT[C/T]TCTTTTGGACCCTCACCCAGCTTACAAGTGACCCC Y 2 1 2 1 101000 r 74 goat snp10421-scaffold1373-137452 3 54781829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410822 Affx-122952638 AX-123281172 3 63071753 GGTAACCCATAGAAGGCAGCCTCCTGAATCCCAGC[A/G]CAGGACAGAGAAAGAGAAGCAGACTAATGATTTTG R 2 1 2 1 201000 f 74 goat snp10422-scaffold1373-169112 3 54749819 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447673 Affx-122923953 AX-123318009 3 63105880 CACCAGCAACTTTTTCTCTGTCCCAAGTGAGAAAT[C/T]TAACACAGTGGCTCAGATGGTAAAGAATCTGCCTA Y 2 1 2 1 201000 f 74 goat snp10423-scaffold1373-203239 3 54715276 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386967 Affx-122969969 AX-123257325 3 63135959 CAGATGGAATAGCTGTCAGCAGGGAAAGTAGGCCA[C/T]GACCGTGTAAGTACAAGGAGCTGCTCTTTGGGACT Y 2 1 2 1 101000 f 74 goat snp10424-scaffold1373-233318 3 54685736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438672 Affx-122930880 AX-123309009 3 63166445 TTCCGGGGTGACAGTGATGGGCTATAACTGGGTAG[C/T]AGTTACAGGTGTTCCCTTTTCTCAACCATTCATAC Y 2 1 2 1 201000 f 74 goat snp10425-scaffold1373-263804 3 54657521 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433501 Affx-122935024 AX-123303842 3 63197978 ATCAAAGAAAAGAGAAATAAGACATTTTTACATGC[A/C]ATCTCTTGAATGTTGAGGCATACATGGGGGAAATC M 2 1 2 1 201000 f 74 goat snp10426-scaffold1373-295337 3 54625021 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780477 Affx-122959672 AX-385267568 3 63230161 ATGACCCGATAGAATTATTAGGGGCTGCTGTTATC[A/G]TGTAATAGATCTGTGTATATTCTGCATTTTTATCG R 2 1 2 1 101000 f 74 goat snp10427-scaffold1373-327520 3 54593013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783217 Affx-122964063 AX-385270283 3 63264968 AATAATAATACTTCTCAGGTATTAAGTGGATTGAG[C/T]AAAGTCATGCATCTTGAGCTCAAAATAATAACACA Y 2 1 2 1 101000 f 74 goat snp10428-scaffold1373-362327 3 54558229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425428 Affx-122941530 AX-123295774 3 63319277 TCTGAGTCTCTACTTCTGCTTTGTGACTAAGATCA[C/T]CCATACCAATTTTTTCAGTGGTTTCCTTGTTTTAA Y 2 1 2 1 101000 f 74 goat snp10429-scaffold1373-416636 3 54503497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450943 Affx-122921763 AX-123321277 3 63368370 GTAAGAGTTGGAAGCCATGAAAATAAAGGGGTAAT[A/G]TAAGAGTAGAATTTGAACTGTCAGGTAGTGCGTCT R 2 1 2 1 101000 r 74 goat snp10430-scaffold1373-465729 3 54454410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432959 Affx-122935282 AX-123303300 3 63399027 TTTTTAAAGAACTGCCAAACTGTTTTCTAAATGCC[G/T]GTACTATTTTATCTTCCCACCAATATGAGAGCTAT K 2 1 2 1 101000 r 74 goat snp10431-scaffold1373-496386 3 54423995 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436591 Affx-122932524 AX-123306929 3 63429802 ATAAAAGTCTTGGCTAAAGTACGTATCTTCAAGGT[A/G]TGAAGCATAAAAACAAAGCTTTTGAGAATGAAACT R 2 1 2 1 101000 f 74 goat snp10432-scaffold1373-527161 3 54393259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385138 Affx-122971765 AX-123255496 3 63471984 ACTTATTTGCAAATGAGTATAAAATCAGCCATGAA[C/T]ACTTGATGGCAAATACCTATCTGCAAAAAATCTCA Y 2 1 2 1 101000 r 74 goat snp10433-scaffold1373-569343 3 54350758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404525 Affx-122956691 AX-123274877 3 63506716 ATTGGGATGTTGAGAAGACAAATGTAATAACACTT[A/G]TAAAGCACTAAGATTTTCATATAACTTTTTAACTT R 2 1 2 1 101000 f 74 goat snp10434-scaffold1373-604075 3 54315961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384270 Affx-122972309 AX-123254628 3 63560550 GTGCCCTATGTTCTGCGAAGTTGTATGTCCACATT[A/G]TAATGCTACACATGTAGAAATCAATTGCTAACCAT R 2 1 2 1 101000 f 74 goat snp10435-scaffold1373-657909 3 54261686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779904 Affx-122975403 AX-385267003 3 63602815 CTAGGTCCTAGTATAGGGGCCTGTAACCAGATTCA[A/G]TAAAGGCTTGTTGATGTGTCAATATAAAAATATAC R 2 1 2 1 101000 f 74 goat snp10436-scaffold1373-700174 3 54219080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278123 Affx-1111836182 AX-519551613 3 63626024 GGGTGACTAGAGCAGGGTGACTAAAGCACATCAGC[A/C]CTGCTACAATGTGAAATCTCAGATCACAGAAGATC M 2 1 2 1 101000 r 74 goat Random2.2K-339 3 63626024 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445799 Affx-122926042 AX-123316136 3 63651442 ATTTTGGAATACGTAGATGTGTATTAAATTTTTTT[A/G]TGACATTACCTAATGTGTTTTTTAACATTTGAAAA R 2 1 2 1 101000 r 74 goat snp10437-scaffold1373-748801 3 54170450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792025 Affx-122930127 AX-385279013 3 63715292 GTGGCACTCTTTTTGCCTTAGGATATATTCCACTA[C/T]AGAAATAACATTAAATCACACTTTTTAAATATTCT Y 2 1 2 1 201000 r 74 goat snp10438-scaffold1373-812651 3 54106574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800823 Affx-122967290 AX-385287739 3 63808010 TTAAAGTGAATGTTGACCATAAAGTCACACCTGAC[G/T]AGAGTCTTACCAAGGAGAGTTATTTGGCCTTTACC K 2 1 2 1 101000 r 74 goat snp10440-scaffold1373-905369 3 54017849 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391228 Affx-122967396 AX-123261585 3 63848339 AAAGATGATGAAAAAGCATTAAGTGGAATTGGCAA[C/T]AGATTGTCAGTGACCTTGATAATGGCTTTATTTGA Y 2 1 2 1 101000 f 74 goat snp10441-scaffold1373-945698 3 53977455 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272217 Affx-1111833394 AX-519545964 3 63879650 CTCTCACAACAAGAACTATCTTAGAAATTCTTTGA[A/G]AAGACTGATTTCCTAACAGAGAAAATTTTTTCTAT R 2 1 2 1 101000 f 74 goat 3_63879650_AF-PAKI 3 63879650 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388274 Affx-122969765 AX-123258632 3 63884982 CCACAGAGATCTTTGAGGCTGGTCTGAATAAGGAA[C/T]GAATGCCCAACCCTTGTGATATTCTGTGGGCAGAG Y 2 1 2 1 201000 f 74 goat snp10442-scaffold1373-982341 3 53939312 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454312 Affx-122919250 AX-123324645 3 63923585 TTCACTTGGCTGGCCATGTTTATTTTTTCTCTTTA[C/T]GTCTCCTGTCTAGGATGTGATTAGGGTATTGGCTT Y 2 1 2 1 101000 r 74 goat snp10443-scaffold1373-1020944 3 53900613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399539 Affx-122961143 AX-123269894 3 63963680 TGCAGAACAGTACCTAATTTACACAGCAAAGTCAA[C/T]GATAACACTTATTTTCTCTTCATATGAAATTTGGA Y 2 1 2 1 101000 f 74 goat snp10444-scaffold1373-1061039 3 53860458 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278127 Affx-1111836184 AX-519551617 3 63991471 CCTACAAAGAGAACAGGAGGAAGGCCAAGGTGGAG[C/G]CAGGCAGCACAGAGAAGTCCAAACACAGAAAGAAG S 4 1 2 1 202000 r 74 goat Random2.2K-340 3 63991471 G C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451611 Affx-122921630 AX-123321944 3 64007599 TCAATTCTGCCATTAAAACAGGTTGCTAGATACTT[A/G]TTCTTCCACTTAGCTAACATTTATGGGTTACATAT R 2 1 2 1 101000 f 74 goat snp10445-scaffold1373-1104958 3 53816397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786328 Affx-122919573 AX-385273362 3 64077488 GTCCTTTATTCTGGAACTCAAGGCCTTTGTAGTCT[A/G]TCTATATCTAATATTCTGATCATTTCAGTTTTTTA R 2 1 2 1 101000 f 74 goat snp10446-scaffold1373-1174847 3 53746657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437874 Affx-122932064 AX-123308212 3 64110673 AATCATCACTGTCCCTATCACCCTTAATCCTCAGG[C/T]GAGGTTGCAAGAACTAATGGATAAAAAAAAAACTG Y 2 1 2 1 202000 r 74 goat snp10447-scaffold1373-1208032 3 53711863 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422600 Affx-122943734 AX-123292946 3 64146330 AATGCAAAAGGCAGAGGGATAATTAGAATGAAAGC[A/G]TTGCAAAATACTATTCTTATTGGAGAAATGATAAA R 2 1 2 1 101000 f 74 goat snp10448-scaffold1373-1243689 3 53675420 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406548 Affx-122955113 AX-123276900 3 64217184 GAAAAAAGTTACTCCCTTTCTTTATTTCTAGTTCT[A/G]ATAGTCTTGGGAAAGAACTGATTAACATTGTTGGC R 2 1 2 1 101000 r 74 goat snp10449-scaffold1373-1314543 3 53601007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420013 Affx-122945161 AX-123290361 3 64299669 CCCCAGTGGGAGCTGGACTGTGAGAGTGTGTGTGG[C/T]GTTTGTCAGCACGTGGGCTTTGCTGACTCTGGGGG Y 2 1 2 1 103000 r 74 goat snp10451-scaffold1373-1397028 3 53519153 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790461 Affx-122925458 AX-385277464 3 64350177 TAGTCCCTATCTTGCTCAGTCCTACTGATTATCTC[A/G]TCTCAAGATCAAAGACATTCAGACCAATTATGTCT R 2 1 2 1 101000 f 74 goat snp10452-scaffold1373-1447536 3 53467914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414448 Affx-122949947 AX-123284797 3 64394264 TGTTTAGATGTTTCTTTTCAGCTTCAGCCTCCGTC[C/T]CCTCTCCCCATCACAAGCATCTAAGAAAGGCAGCT Y 2 1 2 1 103000 r 74 goat snp10453-scaffold1373-1491623 3 53424142 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788655 Affx-122956918 AX-385275671 3 64423223 TAGATTTTAACCAGAGCACTGAAAGACAAATTCAC[G/T]CCTTGTGGTTGGTTCCTAGTGAGCACTAAAGATGT K 2 1 2 1 101000 r 74 goat snp10454-scaffold1373-1520582 3 53394706 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428449 Affx-122938810 AX-123298792 3 64456639 GAGAGGAGACCACCTTCCACCCCATACTTCAAACA[G/T]ATCTACACCTGGTGAGATTTATTATGCAACAAAAG K 2 1 2 1 303000 r 74 goat snp10455-scaffold1373-1553998 3 53360997 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794983 Affx-122954513 AX-385281943 3 64487158 TAAATTGAAGGAAAATCTATGGAATTATTGTCATG[C/T]GGTATGTGGAAAATGTTTAAAACATAAGAAGCTTT Y 2 1 2 1 101000 r 74 goat snp10456-scaffold1373-1584517 3 53330835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386421 Affx-122970811 AX-123256779 3 64557505 ATCCAGGTGACAGCGTAACCATGGACAACAAGCAC[A/G]CTAGCAATCAAAATGATCCAGAATATATCTGTATT R 2 1 2 1 101000 f 74 goat snp10458-scaffold1373-1654864 3 53260034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407126 Affx-122954868 AX-123277477 3 64604738 GGGGCTTTGAAATGCACTGCATGACTTCTTTGGCA[A/G]AGGATTTACATCTTATTTGCTTTGCTTAAGCTAAT R 2 1 2 1 201000 r 74 goat snp10459-scaffold1373-1702097 3 53212771 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450646 Affx-122921980 AX-123320980 3 64662665 ACTTTTAATTAGAATCAGGGGAGAAACAAGGTGTC[A/G]TTTCACCCATTCTGCCAGGATAGGATCCTATCTAT R 2 1 2 1 101000 r 74 goat snp10460-scaffold1373-1760024 3 53176780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406318 Affx-122955458 AX-123276670 3 64698601 GTACTACTGCTTGAATATTCCTTATAAAATGCCAG[C/T]TCATCTCTACCTAATGCCTCTTACTGGCTTCCCTC Y 2 1 2 1 101000 r 74 goat snp10461-scaffold1373-1795960 3 53140851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453733 Affx-122919621 AX-123324066 3 64730963 TTAATCCCGTATGCTAAAGTTTTCATGTCTAGAAA[C/T]GTCAGCATAAGGAAAACAGCTATAATAATTTAAGA Y 2 1 2 1 201000 r 74 goat snp10462-scaffold1373-1828322 3 53108400 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389851 Affx-122968160 AX-123260208 3 64760891 TCTCTGAGCTCCTCTCTCAGTAATTCAACCCTCTA[A/G]TATTTGACAAGCAACAAGTGTCTGGAGAACAATGT R 2 1 2 1 201000 r 74 goat snp10463-scaffold1373-1858250 3 53079077 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401640 Affx-122959588 AX-123271993 3 64796853 CTTAACCAAGCTGTCAGTAGTCAGGGCTGCCATTC[A/G]TTTTTTTTGCAATCCTTTTCTCTCATTCTTTCTTT R 2 1 2 1 102000 f 74 goat snp10464-scaffold1373-1894212 3 53043473 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786272 Affx-122919775 AX-385273307 3 64859673 CTGGGGCAATTTAACCTATTTATTCTTCTCAATTT[A/G]CCTCTAAGTTTTCAGCTACAACAGGAACACAATAA R 2 1 2 1 101000 f 74 goat snp10465-scaffold1373-1957032 3 52980042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769232 Affx-122941940 AX-385256406 3 64895958 ATTTGAAGTCACTTTTTTAAAGATAAAGGGAAGTA[A/G]ATTACATTATTTAGTTACTTCTTCCCCACTAAAGG R 2 1 2 1 202000 f 74 goat snp10466-scaffold1373-1993317 3 52943468 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410121 Affx-122952818 AX-123280471 3 64965596 AATGACAAATTTATTGAGCTTTTCAAGTATTTGTT[A/G]GATAGAGATAAAGTATTGTGTAGGAACCAGAGGTT R 2 1 2 1 101000 r 74 goat snp10467-scaffold1373-2062955 3 52873538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415239 Affx-122948954 AX-123285588 3 65004655 CACGTCTAATAAAATCTCTCATGTTTCCAGAGAAG[C/T]AAAAATTCAATTCAATAAACATTTGTAGAGCTCCT Y 2 1 2 1 101000 f 74 goat snp10468-scaffold1373-2102014 3 52834633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432298 Affx-122936314 AX-123302639 3 65069725 CTAAAATCCTATTAAACACTGGAGCACAGACAGCA[C/T]GTTCCTGGGACCCCCTCTAAGTAGTGTAAGACACT Y 2 1 2 1 101000 f 74 goat snp10469-scaffold1373-2167084 3 52769710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424315 Affx-122941959 AX-123294661 3 65125645 GCCTTTCCTACCTGTTCATTTTCCTCCCCAGTATC[A/G]TCCCCTCACTCCTAACCTATCTACCCTAATAGAGG R 2 1 2 1 201000 r 74 goat snp10470-scaffold1373-2223004 3 52713823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771637 Affx-122941680 AX-385258795 3 65176424 AGAGGAGTTTTCATCTTCTTTGAATACCAGGAAGG[C/T]GAAAGCTTTTCCTGTAAATTCATTTGCCATTTAGA Y 2 1 2 1 101000 f 74 goat snp10471-scaffold1373-2273783 3 52662478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452444 Affx-122920570 AX-123322777 3 65240670 TCATAGAGGTGAGACCCTAATCCAATTGGACTGAT[A/G]TCCTTATAAGAAAAGAAAGAGACACCACAAATACA R 2 1 2 1 103000 f 74 goat snp10472-scaffold1373-2338029 3 52598136 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427480 Affx-122940013 AX-123297823 3 65301414 CTTTTCATCTCTGTCCTTACTGCATGTGTCTGGCA[C/T]AGGAAAGGCACTAAATAAAATGATTGTTCAATGAA Y 2 1 2 1 101000 f 74 goat snp10473-scaffold1373-2398773 3 52537302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785165 Affx-122929407 AX-385272211 3 65333324 AATAAAACTGAGTCTATCAAAGATGACTAGATGAT[A/G]CATTATAGACTGCAACTTTACCACTAATTTCAAAA R 2 1 2 1 101000 r 74 goat snp10474-scaffold1373-2430683 3 52505328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408816 Affx-122954033 AX-123279167 3 65383770 AATAATACCCATCCTGTAATCTTGCTGAGGGATAA[C/T]AAATATCTGTAAAATATCTGGCGGGCTGTCTGCCA Y 2 1 2 1 201000 f 74 goat snp10475-scaffold1373-2481129 3 52455131 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795215 Affx-122975031 AX-385282173 3 65421391 AGGCAAAAGGACTTAATATCTCCAAGCTTCAATTT[A/C]TTCAAAGTAGTCAAGAATAATAATAACCTTAACCA M 2 1 2 1 101000 f 74 goat snp10476-scaffold1373-2518750 3 52417457 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787438 Affx-122977995 AX-385274463 3 65452475 TCGAGCACCCAGTGACCATCAAAATGCCATGTTAA[C/T]ATTTCACAACTCAGATCCACCATCTATTTTGTGGA Y 2 1 2 1 101000 f 74 goat snp10477-scaffold1373-2549834 3 52386974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793944 Affx-122973707 AX-385280913 3 65492185 GTTGGGCCTTACTATCAATGATTTAATTGAATTGA[C/T]GAGATTTATTTCTTTCTTAGTGCAAATAAAATGGC Y 2 1 2 1 101000 r 74 goat snp10478-scaffold1373-2589544 3 52346985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393604 Affx-122965370 AX-123263960 3 65546057 TATTTATTCCCTAGAAGGATGTAGTTTATTTGCAC[A/G]TGGGAAAATCTAGCATATTAACTCATTAGAGCTCC R 2 1 2 1 101000 r 74 goat snp10479-scaffold1373-2643416 3 52292768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788244 Affx-122941145 AX-385275263 3 65633061 ATTTGGAAAAGAAAAGGGGTTGGCAAGTAGAAAAC[A/G]GAACACCTGGCTATTAGGTAATTACTCCTTCCAGA R 2 1 2 1 101000 r 74 goat snp10481-scaffold1373-2730420 3 52204607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450891 Affx-122922205 AX-123321225 3 65702635 GTGCATAATGTTAAGTTTTCTCAACTGAGGGAACT[A/G]GAGGGACCTTGCAGGATGACAGGCTCTCCTGCAGT R 2 1 2 1 101000 f 74 goat snp10482-scaffold1373-2799994 3 52134603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389853 Affx-122968158 AX-123260210 3 65741050 AAAACATGGGTTAGTATCTTTCCTCTAAATTCATT[A/G]CTATACTTATCCCAGTGGTAAACAGTGAAATACTA R 2 1 2 1 101000 r 74 goat snp10483-scaffold1373-2838409 3 51861918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770978 Affx-122947401 AX-385258141 3 65774953 GTACATTAAGTTCTTCTAACCATCTCTCTATGCTA[C/T]AATTTTTTAGCTTGTTTCTAACATTTTATACATTA Y 2 1 2 1 201000 r 74 goat snp10484-scaffold1373-2872312 3 52064848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802053 Affx-122950257 AX-385288957 3 65806441 TTTCTACAAGAGTACTTAAGGAATGATCCTGGAAA[G/T]CTAAAAGCTTTTGATAATAACCAAGCTTTCAAATC K 2 1 2 1 201000 r 74 goat snp11968-scaffold144-5847631 3 51619756 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277971 Affx-1111836185 AX-519551465 3 65842975 ACTCTTGAAGCTATCTGGACATTCATGTTCACTCT[C/G]CCTTGTACCTTAGTGTGTAACAATCCTTCTTCCTA S 4 1 2 1 101000 f 74 goat Random2.2K-342 3 65842975 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418076 Affx-122946608 AX-123288424 3 65847418 CTAATTTGACCTATTTTTTAAAATTCATAGAAGGG[A/C]AGAATTAAGAGTAGAAAAGAGTGGTATTATTCGGT M 2 1 2 1 101000 r 74 goat snp11967-scaffold144-5806654 3 51576804 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401991 Affx-122958770 AX-123272344 3 65898539 TCTCCTTTTCTGACTGCCTTGTCTGCCTCTACCTC[A/G]TGGCAACAAACACATTTCAGGGTGCCTAGTCACCA R 2 1 2 1 201000 r 74 goat snp11966-scaffold144-5755533 3 51525239 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420576 Affx-122945271 AX-123290923 3 65955636 AAAACTGCTGTGTCCCTCTGTTCTCAAATTATTCA[G/T]CAAAAGGGGAAATTCCAACCATTTATCTAGAGCCT K 2 1 2 1 201000 f 74 goat snp11965-scaffold144-5698436 3 51466538 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792351 Affx-122951057 AX-385279333 3 66044770 TATCTAGTGATATTCAGGTCTGACAATAGGGGCAC[C/T]AGTTTCCTATCAAGTGTAAAACTACAATCTCTGCC Y 2 1 2 1 101000 f 74 goat snp11964-scaffold144-5609302 3 51378239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441159 Affx-122929561 AX-123311496 3 66089847 TATGAAGATGTCCATATTTTCAAGTCAGCAGTAGA[C/T]GGGCATTTTACTTCATTCACAAGATTGTTTTTTCC Y 2 1 2 1 101000 f 74 goat snp11963-scaffold144-5564225 3 51332805 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411583 Affx-122951620 AX-123281933 3 66135244 ACAAAAATTATCTAGTTTGGGCTCCCACGTGATTC[G/T]CAGAGAAACATCCAGGTCCTGCTAAATGATGTACT K 2 1 2 1 101000 f 74 goat snp11962-scaffold144-5518828 3 51286127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794153 Affx-122966447 AX-385281119 3 66204031 TGAAAAATGGAAATTTGAAAATGGCCATTTGATGA[C/T]GGCCTATTTAAGAAGGAGTATTTTTAGGATCAAAA Y 2 1 2 1 201000 f 74 goat snp11961-scaffold144-5450041 3 51217296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437906 Affx-122931655 AX-123308244 3 66276921 AGTAATAGTATCTAATCCTGTCTTTACAACAATTA[C/T]ATTCAAGTGAAAAAGTCAGTCAAAAAGAGTAAACA Y 2 1 2 1 101000 f 74 goat snp11960-scaffold144-5377151 3 51145176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804502 Affx-986696669 AX-385291058 3 66282835 TTCATCTTTCAGTGTCTTATCTTTTTGCCTTTTCA[C/T]ACTGTTCATAAGATTATCAAGGCAAGACGGCTGAA Y 2 1 2 1 600010 r 74 goat 3_66282835 3 66282835 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 468277973 Affx-1111836186 AX-519551467 3 66329663 AGTGATCATGGTTTAGAGAAATGAAGTGGTTAAGA[A/G]TGAGGGACTGGACAGTTACAGCAGAGTGAAAGGAA R 2 1 2 1 101000 f 74 goat Random2.2K-343 3 66329663 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804102 Affx-986696671 AX-189342110 3 66344680 CAGACGGAAACCTGCCCAGAAAGAGGAGGAAGCAA[C/T]GCACAGTAAGAGCAGATAGTCCAGGCTGCCCATGG Y 2 1 2 1 600010 f 74 goat 3_66344680 3 66344680 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 38415450 Affx-122949177 AX-123285799 3 66361278 CATACCAGACACATATTTACTGCATGCACGCACGC[A/G]TGAAAGACACCAGTCTAGACCCACTGTTATACGCT R 2 1 2 1 201000 r 74 goat snp11958-scaffold144-5292794 3 51059679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277975 Affx-1111836187 AX-519551469 3 66364459 TGAAATTTTATCTTCTTGCTTTGAGCCCTCACTTG[A/G]GATGGGTTTTTAAAAGCATGATTTTATATATTATT R 2 1 2 1 101000 f 74 goat Random2.2K-344 3 66364459 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789712 Affx-122922645 AX-385276720 3 66405007 TATGTCAGAAGGTGGTAAGGGCAAAGAGAAAAACT[A/G]TAAAGAAGGGAAGCAGGTTATAGACTATCAGGAGG R 2 1 2 1 101000 r 74 goat snp11957-scaffold144-5249065 3 51016019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771371 Affx-122971904 AX-385258529 3 66446223 TGTAGAAAATATAACATGGGAATCCTGTGCCAAGT[A/G]CTAGATAACTTATCTTTTACTCTATTATTTGCAAA R 2 1 2 1 101000 f 74 goat snp11956-scaffold144-5207849 3 50974797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764546 Affx-122971391 AX-385252203 3 66497979 TTGTTTTTTACTTTTTTATGGTAAAATATCCATAA[C/T]ATAAAATTCACAATTTTAGCCATTATTCAGTTCAT Y 2 1 2 1 303000 f 74 goat snp11955-scaffold144-5156093 3 50922301 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391526 Affx-122966655 AX-123261883 3 66532830 CGTATGTTGTTAGGAAGGGGGAGATAACAAACACA[C/T]GAAGAAATAAATGAATAAAGTAAATTCAGAGAATG Y 2 1 2 1 101000 f 74 goat snp11954-scaffold144-5121242 3 50887622 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275224 Affx-1111834777 AX-519548803 3 66538300 TTACTTGTCCTTTTCAATCCCTGTTTGTCTGCCTG[A/C]ACTGG M 2 1 2 1 102000 f 74 goat GoatD01.052504 3 66538300 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38452316 Affx-122920669 AX-123322649 3 66573552 AGGAGACATAGATGCCAGCGTAGGAGGATGGCAAA[C/T]ACTGCAGTGTTAGTAGAGAGATCAGCAGGGGAGAG Y 2 1 2 1 101000 f 74 goat snp11953-scaffold144-5080520 3 50846254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791531 Affx-122967261 AX-385278522 3 66615773 TGTACACATCAGTTTTCCCACCTTCTACTGTTTAG[A/G]AAAGATTGAGGGCCCCTGGTAGGGATGCCATGTGT R 2 1 2 1 202000 r 74 goat snp11952-scaffold144-5038299 3 50804074 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451704 Affx-122921563 AX-123322037 3 66647107 TAGAGCATAAAGTCTTTGAGAAGAACAGGGAAAGA[C/T]AGGTGGAGAAATACATTCTTCTTATCTGTTATGCA Y 2 1 2 1 101000 r 74 goat snp11951-scaffold144-5006965 3 50772167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376622 Affx-122979039 AX-123246981 3 66680980 AGTGGTGAATTAGCTCCCGGGGTTGTCAACACAAA[C/T]GCAGAGAAAAGGAAGCTGTCATTCTTTTTAAATGA Y 2 1 2 1 101000 f 74 goat snp11950-scaffold144-4973092 3 50738219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411326 Affx-122952274 AX-123281676 3 66722851 CCTCTCGGGTGACAGAGAATGATTCCAGCATTATG[A/C]TCACAATTATAGCAGTACTGTGAGTCAGAAGCCCT M 2 1 2 1 303000 r 74 goat snp11949-scaffold144-4931221 3 50696532 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382108 Affx-122974888 AX-123252466 3 66766433 GTGGACTTGAGTTCAAATTCAAGTTCTAACACTTA[C/T]AGGTTATGTGATCTTGGGCAAGTTAGTTGAGTTCT Y 2 1 2 1 101000 f 74 goat snp11948-scaffold144-4887639 3 50652310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413415 Affx-122950704 AX-123283764 3 66798528 ATCAAGGTGGGAAACTATGTCAGATATTTTCTCCA[C/T]GGGTAATAAGCATTCATTAATTCCCAAAGAAACCC Y 2 1 2 1 101000 r 74 goat snp11947-scaffold144-4855544 3 50620338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425087 Affx-122941243 AX-123295433 3 66849673 CTAAAGTCTGTTTTACACAAAATATATTCAAATTA[A/G]CCTTATAATCTCAGGTTCAGAAAAAACTGAAAAAT R 2 1 2 1 101000 r 74 goat snp11946-scaffold144-4804399 3 50568968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801222 Affx-122926932 AX-385288135 3 66881851 TGTCTACAGGGTTACTTTGAAAAAATCAGGATGTT[A/G]CATTAGTATTTATATTGATTATTCACAACCATATT R 2 1 2 1 101000 f 74 goat snp11945-scaffold144-4772221 3 50536712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272218 Affx-1111833395 AX-519545965 3 66910631 ATAAATTAAGGGAGGTCAGAGGCCATATGTGATCT[A/G]GTCTGTGGATGGGGTCTTATATAAGTAGCTTTGCC R 2 1 2 1 201000 f 74 goat 3_66910631_AF-PAKI 3 66910631 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398825 Affx-122961393 AX-123269180 3 66927020 CATAAGTAATTGGATAATTGAGAATTAACACTTCC[A/G]TACTTTTTTGTTTATGTTTTGTTTAATCATAGCTT R 2 1 2 1 101000 f 74 goat snp11944-scaffold144-4727052 3 50490235 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378875 Affx-122976508 AX-123249234 3 66977058 CACAGGATGACCATTGGTGACCTATGCATGAAGTC[A/G]CTATGAAAATGAAGAATCACATAAACACTGCTGGC R 2 1 2 1 101000 f 74 goat snp11943-scaffold144-4677014 3 50440323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382493 Affx-122973821 AX-123252851 3 67032499 TTGATTCAAGTATAACTTTATATGATGCTGAGTAA[A/G]TGGTCATAAGAACCCATGGGGATATAATGCATGTA R 2 1 2 1 201000 f 74 goat snp11942-scaffold144-4621573 3 50384632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427831 Affx-122939739 AX-123298174 3 67066839 GTAGAATTCAAGAATTCAAGAGGAAAACAAAAGTA[A/G]GAGACTACAGCTCAGTTTTGACAAAATGCTATTTA R 2 1 2 1 103000 f 74 goat snp11941-scaffold144-4587233 3 50349308 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800239 Affx-122961965 AX-385287162 3 67109825 ATCATTCAAATGGTTCATATTAGTTTTGCTTTACC[A/G]TTTCATTGTAAGAGGGTATCATATTGCCCTGAAAA R 2 1 2 1 101000 f 74 goat snp11940-scaffold144-4544247 3 50305519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423566 Affx-122942413 AX-123293912 3 67167543 ACAATTCACCAATTAAAAATTTTCACCTGAATTAA[A/G]TAACATTAAATAACCAAAAAAAATTAGAAGAATAA R 2 1 2 1 103000 f 74 goat snp11939-scaffold144-4486529 3 50247017 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448964 Affx-122923130 AX-123319299 3 67250068 CCTAACCTGCTGGCCTGCAGAGTCCTACGGGAAAC[A/G]GAATGCTTTTACACAACTGCCTTTCCTGTTAGCCT R 2 1 2 1 101000 r 74 goat snp11938-scaffold144-4404004 3 50158290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416932 Affx-122948040 AX-123287280 3 67313545 AAGAACCTAACTAAGTTACGGTGTATCTGCCTTGA[C/T]GTCTTTGGAATTCTTCATACTTATGTGGATTCCCT Y 2 1 2 1 101000 f 74 goat snp11937-scaffold144-4340527 3 50093997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778115 Affx-122951728 AX-385265230 3 67391508 TTATCTGTCACAATTCTGTAGGCAAGCAGTCCATG[C/T]AGATTCAGCTACAATATTGACCCAGGGCCTCGCAA Y 2 1 2 1 101000 f 74 goat snp11936-scaffold144-4262564 3 50014007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396525 Affx-122962955 AX-123266880 3 67421392 ATCACATGGCTATACCCATCCATTTATTGTAAATT[A/G]TTATTGAGAGAGGTCTAAGAAGAAAAGCCTGGGGA R 2 1 2 1 101000 r 74 goat snp11935-scaffold144-4232680 3 49984428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448355 Affx-122924120 AX-123318691 3 67482326 TGCTATGGATACACATCAGTAGTACCTATTAACCT[A/G]CTACTCTAACCCATTAAGAGGGCAGGCTGGAAGTT R 2 1 2 1 101000 f 74 goat snp11934-scaffold144-4171746 3 49923374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377528 Affx-122977471 AX-123247887 3 67525041 TTTCCCCGTAAATAACAGCATGGAGCAAATATATC[A/G]CATTCCCAACTTCTTTGAAAAGGCTAAAAATAACC R 2 1 2 1 101000 f 74 goat snp11933-scaffold144-4129031 3 49881475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476177 Affx-1251763681 AX-586011604 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 4 1 4 1 20000 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 539476432 Affx-1251763681 AX-586011833 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 4 1 4 1 20000 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165087 Affx-1251763681 AX-606940500 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165331 Affx-1251763681 AX-606940742 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165408 Affx-1251763681 AX-606940819 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165431 Affx-1251763681 AX-606940842 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165504 Affx-1251763681 AX-606940915 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165942 Affx-1251763681 AX-606941351 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 320799186 Affx-122927025 AX-385286116 3 67586389 CATTTTCCAGTGTGTTGCTGTATAATTCTTCATAG[C/T]AATTTCATGATTCATGATTGCTTGCATTTCTGTGA Y 2 1 2 1 201000 f 74 goat snp11932-scaffold144-4067683 3 49819629 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453059 Affx-122920065 AX-123323392 3 67617695 ATTCTAGAGAGTTTTTTAGGATTTACCCAATTTGG[C/T]GGTTTTATATAAACTGGCTGATGAGAGTCAGAGAA Y 2 1 2 1 101000 r 74 goat snp11931-scaffold144-4036377 3 49786673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277977 Affx-1111836188 AX-519551471 3 67621592 CCTGATGCTGTGTGGACTGTGTTGGGCTGCAATTT[A/T]TTTTGTTCAATTATTTACATGCACTTGGCCAAATA W 4 1 2 1 102000 f 74 goat Random2.2K-345 3 67621592 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800895 Affx-122963551 AX-385287810 3 67675866 AAATCCCTGAACTCTAACTAGTCTGGTTCTGAGTC[A/G]TATTAAATCCTATGATCCATGGGGGTGGCCTGAGA R 2 1 2 1 202000 r 74 goat snp11930-scaffold144-3978206 3 49727265 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453327 Affx-122919972 AX-123323660 3 67710970 AGCAATGGTTGCCTTAGCAACTCTTTAATAGGCTG[C/T]GACTCTCAAAACCTGTCTTTTCTAGAGAGTCTTCA Y 2 1 2 1 201000 r 74 goat snp11929-scaffold144-3943102 3 49691854 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381247 Affx-122974496 AX-123251605 3 67773504 TAAAATTTCCCTAGTTCTGTCAAATGCCATTTCTC[C/T]ATGGAGCTTAATTATTTCTTCTTTTTCAGAAGTGA Y 2 1 2 1 101000 f 74 goat snp11928-scaffold144-3880568 3 49629347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780092 Affx-122930401 AX-385267189 3 67803625 TGCAGCACTTGGTAACTCTGTGATTTCATCATAAC[C/T]CTACTTCAATAGACTCAAAATCAAAATAATAATAG Y 2 1 2 1 101000 f 74 goat snp11927-scaffold144-3850447 3 49598635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424585 Affx-122942213 AX-123294931 3 67848109 AAACAGGGATTATAAAGTTTCATTCAAAACCAAAA[C/T]AATAGGCTATTACATACTAGAAGAATTGAGATTGC Y 2 1 2 1 101000 f 74 goat snp11926-scaffold144-3805963 3 49553302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767714 Affx-122958067 AX-385254948 3 67877996 GCAGGAAAATGTAAGAGAGGACTTTGTCCCTTTAG[C/T]ATATTCTAGGCCTACGCAGTGTGTAAACAGATGAA Y 2 1 2 1 101000 f 74 goat snp11925-scaffold144-3776076 3 49522555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274529 Affx-1111834349 AX-519548120 3 67913669 GCATAGAAATCACTTGTCTAAAAAGGAAGGTACCA[A/G]CAAGAGCAGGGGTGGAGGCAGGGCTGCAGGGGGCC R 2 1 2 1 101000 f 74 goat GoatD01.031083 3 67913669 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388116 Affx-122969486 AX-123258474 3 67929293 ATGGACAATCAATAAAAGGCAGGGGTCCACTCTAG[G/T]TCCAAGACTGGTTGGATTTTCACAGAGCATGAAGC K 2 1 2 1 101000 f 74 goat snp11924-scaffold144-3724779 3 49470479 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449735 Affx-122922465 AX-123320070 3 67998264 TGTCCACTGAGATAAAACAAGTGAGAGTGTTAGTC[A/G]CTCAGTTGTGTTGTGTCCTGCTGTTTGTGATCCCA R 2 1 2 1 103000 r 74 goat snp11923-scaffold144-3655808 3 49401007 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785604 Affx-122921185 AX-385272648 3 68043979 CTATTTCTAAAATTCTAAGTCACAAAGCTTGTTTC[A/G]CATTTTGTTTAATGATTCTAAAGTTAGCCAGACAA R 2 1 2 1 101000 f 74 goat snp11922-scaffold144-3610093 3 49354316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278137 Affx-1111836189 AX-519551627 3 68087601 TATTGGAAGAGATGCTGACTCTAAGCAGGACTGGA[A/G]GGACAGAGAATTGTGAGAAACGTTGTTCCTGGCTA R 2 1 2 1 101000 r 74 goat Random2.2K-347 3 68087601 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800911 Affx-122954154 AX-385287826 3 68092561 CCAAATAATTCATTTTATATACAACTTTACTATCT[C/T]GATGCCAATGTTATTCTTCCAACTTGCTATGGATT Y 2 1 2 1 101000 r 74 goat snp11921-scaffold144-3561511 3 49305057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431711 Affx-122936763 AX-123302052 3 68134137 TACTTGGAACTTGCTCAGAGGGTGAATCTCAAATG[C/T]ACTCACCACAAAAAGGAAATGGAAATTCTAGGTCT Y 2 1 2 1 101000 f 74 goat snp11920-scaffold144-3519935 3 49273742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771365 Affx-122955956 AX-385258523 3 68164267 TACGATCTGTTTCTCCTCAAGCCACCAAAATTGCC[A/G]TATTTTGTGGGATTATTTTCCCTTCGTTGTGGTCC R 2 1 2 1 201000 r 74 goat snp11919-scaffold144-3489805 3 49243432 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443320 Affx-122927450 AX-123313657 3 68196422 GAAACTCAGCTGACTGAAAAGAGAAATAAATGGTC[A/G]TTTACTTCCATGGTTGATTCTCAGATCTTTACTGT R 2 1 2 1 102000 r 74 goat snp11918-scaffold144-3457650 3 49210658 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410004 Affx-122953266 AX-123280354 3 68247295 GCTATCTATATATCTCTGTCTCTATCTCTACATTA[C/T]GATATCTAACTGCATATTCCTGGCCCAGTTCTGAA Y 2 1 2 1 201000 r 74 goat snp11917-scaffold144-3406777 3 49157484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783221 Affx-122921163 AX-385270287 3 68277351 TGTAGCAGTTGTCATTTTCTTGGAAATTTGTGATT[A/C]TCTAGGATTCAAAAAGATTGATCCTTCCAGGTCAA M 2 1 2 1 101000 f 74 goat snp11916-scaffold144-3376721 3 49126714 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399207 Affx-122960609 AX-123269562 3 68321829 GTTAAGCAAGATGAAAAAATTCTGTATACCTCTAT[A/G]CAATGATGTGCACATATGATTAACAAAACCGTACT R 2 1 2 1 101000 r 74 goat snp11915-scaffold144-3332243 3 49081495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451767 Affx-122921514 AX-123322100 3 68423843 CAAGGAGAGGGCAGCCAAGAGCAAGAAGTAAACTG[C/T]GTTTTTAAAATGAAAGTAAGGGAAAGTGAAACCAA Y 2 1 2 1 101000 f 74 goat snp11913-scaffold144-3230229 3 48978573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396311 Affx-122963082 AX-123266666 3 68475868 TAGTGCTTCAGTTCCTTGCTCTTTCCTTCATGATA[C/T]GCCTTAAATAAATACAACATTTATTTATGTCAAAT Y 2 1 2 1 103000 f 74 goat snp11912-scaffold144-3178204 3 48926546 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385326 Affx-122971664 AX-123255684 3 68524246 GGACTCTAGGTCTCCAAAACAGGATGATAAAACAC[A/G]TACACATCCATTTATTTCTGTAAACTCTGGTATCG R 2 1 2 1 101000 f 74 goat snp11911-scaffold144-3129826 3 48878375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783695 Affx-122976719 AX-385270753 3 68558100 GTACAATATTGCAGTATATTTTTCACTTTCTCTGG[G/T]ATAGCTAATTCCTTAGCAAGCTGCATAGTCAATAC K 2 1 2 1 202000 f 74 goat snp11910-scaffold144-3095972 3 48844113 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384267 Affx-122972311 AX-123254625 3 68604035 AATCTATCGTGTTATAGTTTTTATACTAATTTATT[A/G]TTGAATTCTTGAGAAGATCCTCTATAGTTGAGAGT R 2 1 2 1 201000 f 74 goat snp11909-scaffold144-3050037 3 48796734 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796440 Affx-122971215 AX-385283390 3 68700158 ATGTCTTTCATTACTGTTGCAAACTTGAAAATTTC[A/G]TTCCCTGAGATGGCTAAATCGAGATTTTGAGCTTA R 2 1 2 1 101000 r 74 goat snp11907-scaffold144-2953914 3 48700651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417882 Affx-122946757 AX-123288230 3 68754491 CTCTTCAATGAGTGACATTAAGTAATATGTATGAG[G/T]AATTGCTGAGTTTACTGCTCATTACCTCTTTAAAA K 2 1 2 1 101000 f 74 goat snp11906-scaffold144-2899581 3 48646284 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423228 Affx-122942695 AX-123293574 3 68834817 AAATGAAAGGAAAGGAAACTTGCAAGTAACTGAAG[C/T]AATTAAGGAAAGAAACTGATATTATCTGGTCTAGA Y 2 1 2 1 201000 r 74 goat snp11905-scaffold144-2819255 3 48567748 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423994 Affx-122942112 AX-123294340 3 68868067 TCTTTAGTTCTTCTACATATTTGTTAAAAATTTCA[C/T]GCATGTTCTCAATCTTCTCCTCCATTCTATTTCCA Y 2 1 2 1 101000 r 74 goat snp11904-scaffold144-2786005 3 48535683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783448 Affx-122923026 AX-385270511 3 68918232 GCTGATTGTCTATATTATGGGACTCATATTCAAAT[A/G]CATTTCTCTCTACCAAACTGCCTAAAGGTATTGAT R 2 1 2 1 101000 r 74 goat snp11903-scaffold144-2735840 3 48485063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389150 Affx-122968540 AX-123259508 3 68971867 ATCATTTTCTGCTTCCTAGATATACAAGTCTGATG[C/T]GTAGCCTGCAAGATTCTGTACAAGAAAAATACCCA Y 2 1 2 1 101000 r 74 goat snp11902-scaffold144-2682205 3 48430850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401823 Affx-122959449 AX-123272176 3 69025806 CACTCCAGATCACTCTGCTGGGCACATGCATCATG[C/T]GGCAGGCAGACCTAGGTGTCAGGTGCAGTGGTTTT Y 2 1 2 1 201000 f 74 goat snp11901-scaffold144-2628266 3 48376340 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402729 Affx-122958342 AX-123273082 3 69056471 ATGGACTGGATATTTTATTGAGAGAATTAATCTGA[C/T]GTGTTTGATTAGATCTAAATCTTCATGCATGTATA Y 2 1 2 1 101000 r 74 goat snp11900-scaffold144-2597601 3 48345568 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377200 Affx-122978185 AX-123247559 3 69096867 AGGTCTTGGCTAAAACACAACTTCCACAGAAGTAG[A/C]GAGAAGCTTCACAAATATCCTAAGTGGACCCCCTC M 2 1 2 1 101000 f 74 goat snp11899-scaffold144-2557205 3 48304460 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790208 Affx-122930993 AX-385277212 3 69128844 TGTTCATCATACAACAAAGACTCAAAGGTAGATCA[C/T]GAAATAATTTTATAGGGCTTGGTAAGTAAGAAATA Y 2 1 2 1 101000 f 74 goat snp11898-scaffold144-2525228 3 48271750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447638 Affx-122923978 AX-123317974 3 69194116 TCTTCCTAATAAGCTTAATTTTTCTATTAACAGCA[A/G]ATAGAATACTACTGGATTACCTGTTGAAGTCTGGT R 2 1 2 1 101000 r 74 goat snp11897-scaffold144-2459956 3 48205079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420647 Affx-122944830 AX-123290994 3 69244695 GCCTTCCTCAGCCAACATGTATGGCATAGCAACCA[C/T]GCCAAGTTCCCCCAAATTGCCAACTCCCTCTCAAG Y 2 1 2 1 101000 f 74 goat snp11896-scaffold144-2409377 3 48153678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435176 Affx-122933652 AX-123305516 3 69290450 CAAGGTATATCATCATGATTTCATGAATGCTAGAA[G/T]ACGTGGGACTCATGAGTCAGGGGCAAGTGAAAGTT K 2 1 2 1 201000 f 74 goat snp11895-scaffold144-2363622 3 48107740 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439992 Affx-122929796 AX-123310329 3 69347622 TTTAATAAGCATTAAAGCCTAGTAAGCAGTAAATT[C/T]ATCAATTGTTTTTATATTTTCTTAGGGAGAGACAT Y 2 1 2 1 101000 f 74 goat snp11894-scaffold144-2306450 3 48050077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445401 Affx-122925388 AX-123315738 3 69406580 ATCCCCTTCCTATGAGAAAGTATCCAGGTATATTA[C/T]ATTACAGGGAAAAAGGGTACATTCAAAATGAATTA Y 2 1 2 1 101000 f 74 goat snp11893-scaffold144-2247492 3 47990661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273595 Affx-1111833713 AX-519547210 3 69426418 GTTAGGTCTGGGATTGGCTGCTTGCCTTCAACCTT[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.002236 3 69426418 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406212 Affx-122956127 AX-123276564 3 69454078 CCAATTATTTCCTTCAAGTTGCAGCTTATCTTATG[C/T]TGAACTGCTGCCCTGAGAGCCCAAATGACCCTCTA Y 2 1 2 1 101000 f 74 goat snp11892-scaffold144-2199994 3 47943361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397947 Affx-122961917 AX-123268302 3 69499528 TGTTGCATATTTATATATACCATGATTATACTTAA[A/G]CTTTAAATTTGGGGGTGTTCAATTAAGTAATTTTT R 2 1 2 1 102000 r 74 goat snp11891-scaffold144-2154544 3 47898164 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389814 Affx-122968194 AX-123260171 3 69548410 AGCGGGCAGTAGGCCCACTTACAGGGAGTTGGAAC[A/G]CTTGCTTCCTTGCCTTCTCTCTGGGTAAACCTGAG R 2 1 2 1 101000 f 74 goat snp11890-scaffold144-2105662 3 47849162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272220 Affx-1111833396 AX-519545967 3 69616332 CTCTTTCATTTGTGAAAGGCTCTCAGAGTTGTGAC[A/C]ATTTTCTGTGTTCAAGGTTATTTTCCTGGTGCTAT M 2 1 2 1 101000 f 74 goat 3_69616332_AF-PAKI 3 69616332 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408358 Affx-122953738 AX-123278709 3 69628197 AGACCACCTGATGTATTTTCATGTTGGGTGGCATA[C/T]ATATTATTTCATTTTTATATAATACTGAAATATAT Y 2 1 2 1 103000 f 74 goat snp11888-scaffold144-2025875 3 47767613 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793502 Affx-122930314 AX-385280479 3 69760522 GAAGTGAAAATATAGTAATTAAATTGTTGCTATAA[C/T]GAATTATTATAATTATCTGAAGGTTTCTGGCATCT Y 2 1 2 1 101000 r 74 goat snp11886-scaffold144-1893550 3 47635252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777637 Affx-122976900 AX-385264756 3 69800141 CAAAGTAATGTATGTGCTATTTGTTGTTAACAAAG[C/T]AGATATAAAAGAATTTGGGGACTATTTCTTTTCTT Y 2 1 2 1 202000 r 74 goat snp11885-scaffold144-1853931 3 47595636 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406150 Affx-122956179 AX-123276502 3 69829510 GCTTATGTGTGTTAGCTTCCTAGAGGTTCAAGTGT[C/T]TTCAATTAAAAAATGGTCAACACTAGAAAATGTCG Y 2 1 2 1 101000 f 74 goat snp11884-scaffold144-1824562 3 47565691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769793 Affx-122954265 AX-385256963 3 69865419 TGATATCACTGCTTATTGGATGTTTAGTAATAGGC[A/G]TTTGTTAGTTTCAAAAATCACATGGGAAGTTGCCA R 2 1 2 1 101000 f 74 goat snp11883-scaffold144-1788653 3 47529940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446676 Affx-122924756 AX-123317012 3 69908457 CATGGGCTAGTAATTTTTACAAAAGACACTCATAT[C/T]CCTGGAACTCATTAAATATTTGTCAGATGGTGAAA Y 2 1 2 1 201000 f 74 goat snp11882-scaffold144-1745615 3 47486926 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390083 Affx-122968031 AX-123260440 3 69939804 ATAAACTGAAGAAAGGTAATAGAATGATGACATGA[G/T]ACTTAAAGCAGGAACTCCATGTTGCTGAGCATTGG K 2 1 2 1 101000 r 74 goat snp11881-scaffold144-1714268 3 47455575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439050 Affx-122930329 AX-123309387 3 69978062 GCAGGGTGACTTTAGGCAAGTTACACTTGATCAAT[A/G]TCCTTATCTTTAAAATGGACATAATAATAGTATCT R 2 1 2 1 303000 r 74 goat snp11880-scaffold144-1676010 3 47416956 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795903 Affx-122966039 AX-385282855 3 70016793 AAAACAACAAGAAATGCGTATCTGAAAATGTTACA[C/T]GCATATTTCCATTTTTGTGTACTGATATATTTTTA Y 2 1 2 1 201000 r 74 goat snp11879-scaffold144-1637279 3 47380018 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447058 Affx-122924516 AX-123317394 3 70054532 GAATGTTTCTGAGAGCAGTCTGCTTTGTGTGAGAC[A/G]TTTTAGGTCACATATATTGTCTGTGTTGTTCTCAT R 2 1 2 1 201000 r 74 goat snp11878-scaffold144-1599540 3 47342065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770434 Affx-122966654 AX-385257600 3 70086056 ACTGCATACATAGTTAAAAGCTCCATGGATATTTA[C/T]GGGATGAATGGTGGATGACTCCTTACCATTGGACA Y 2 1 2 1 101000 r 74 goat snp11877-scaffold144-1568016 3 47310295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433165 Affx-122935665 AX-123303506 3 70114646 GCCATGGGGTGTAAGTAATCAATATGGAGAGGGAA[G/T]TCTCAAATACATTTCATTTTGAGGCTAAAATTATA K 2 1 2 1 101000 f 74 goat snp11876-scaffold144-1539426 3 47283058 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396568 Affx-122962924 AX-123266923 3 70147436 ATTCAGCAATTATATGTTTAACAAAATGTATTGTT[A/G]TCTGAGACTGTAAGAGAAAATTTTGTTAATATTAA R 2 1 2 1 101000 r 74 goat snp11875-scaffold144-1506636 3 47250255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380307 Affx-122975395 AX-123250665 3 70177181 ACTTCTGTGCATATAGGGGGTATATAACTTCTGCT[A/G]TTTCATTGGCCAAAGCAAGTCACATAAACACTTGA R 2 1 2 1 201000 f 74 goat snp11874-scaffold144-1476891 3 47220492 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802655 Affx-122936658 AX-385289554 3 70207324 CCTAACAATGCTGTGAGTTATATACTATTATTAAT[G/T]CCCTTTCTGTAAATTAGATAACAGAGCACAGATAA K 2 1 2 1 201000 f 74 goat snp11873-scaffold144-1446748 3 47190355 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393384 Affx-122965904 AX-123263740 3 70237588 GAACTCATATTTTGTTTTGTTTTAAATATACAATC[G/T]CCACTGTTTTAAGAAGCTAGATAGAAAAGGTGAAG K 2 1 2 1 101000 r 74 goat snp11872-scaffold144-1416484 3 47159717 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779341 Affx-122954060 AX-385266445 3 70333762 GAATAAGGTTTTACTGTAAAGCTCAAGAGCACTGT[A/C]GGGAAGGTGATATCATCAAGCAATAATGCAGGATT M 2 1 2 1 101000 r 74 goat snp11870-scaffold144-1320310 3 47063686 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403539 Affx-122957607 AX-123273892 3 70406458 TTGAATTTTCTAGTTTTTGGAATAAGGTTTCACAG[C/T]GTGCATGCTAAGTTACTTCAGTGCTGTCCAACTCC Y 2 1 2 1 201000 f 74 goat snp11869-scaffold144-1247614 3 46990737 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422013 Affx-122943637 AX-123292360 3 70462834 AGCGCTTGGCCCTGTTTTGCTTAAGATCTTTTTCA[C/T]TGGGCATCCAATCTATTTTCTTCTGTATGGCTATA Y 2 1 2 1 101000 f 74 goat snp11868-scaffold144-1191238 3 46933038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435743 Affx-122933283 AX-123306082 3 70513872 AGAAAGTCTCTAATTCAAAAGTCCCCTATTGTATA[C/T]TCTCACAGCTTTCTCCATTTTCCTCTCATAGCCCT Y 2 1 2 1 202000 f 74 goat snp11867-scaffold144-1140200 3 46881871 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436226 Affx-122932575 AX-123306565 3 70583249 TGCTCTGTGCACAGATATGCTCTGCCATCATTTTG[A/C]TCTGCCATCCATAAGATACTGACATCATTTCCTTC M 2 1 2 1 101000 r 74 goat snp11866-scaffold144-1070823 3 46812087 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402611 Affx-122958413 AX-123272964 3 70633089 ATTCAGTCTCAGCCAACCTGACAATAAAGTGATCC[A/G]TTTATCCAACACAAGCAGGCAGAGAAGGAGATACT R 2 1 2 1 101000 f 74 goat snp11865-scaffold144-1020983 3 46761419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796154 Affx-122959126 AX-385283105 3 70669452 TTAAAATCTAAGATATAAACTTATACACATAAAAT[G/T]AACTAGTATTTAACTTTGGATATGAGCCCAGTAGC K 2 1 2 1 101000 r 74 goat snp11864-scaffold144-984620 3 46725075 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382942 Affx-122973378 AX-123253300 3 70701465 ACAAGGACCATGCCATTTGCTGTATCAGGTTGTAG[C/T]ACAGTGTCTTGCACACAACTGATAGTAAGTGTCAC Y 2 1 2 1 101000 f 74 goat snp11863-scaffold144-952607 3 46693038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443381 Affx-122927403 AX-123313718 3 70730930 TGCTAAATGCAATTATCAGTAAAACATTCCTGACA[C/T]GAGTTGGCATCAGGAAAGAAAGACAGGGCCATTTC Y 2 1 2 1 101000 f 74 goat snp11862-scaffold144-923142 3 46663626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780690 Affx-122976703 AX-385267780 3 70763100 GAGACCTTGAACTGGCCAGAGGCCTATTAATGCAC[A/G]TAATTGTTGGGTTGAATAATGAAAACTTGTTGTTG R 2 1 2 1 101000 f 74 goat snp11861-scaffold144-890972 3 46631099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426687 Affx-122939908 AX-123297033 3 70798041 AAACTATAAATATGTTCTAGAAAATAAAATTAAGG[C/T]GATGTGTCCTGTATGGCCATGTATTCTGCCTAAGA Y 2 1 2 1 101000 r 74 goat snp11860-scaffold144-856031 NW_017199931.1 72 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777091 Affx-122946616 AX-385264214 3 70832734 TTCACTGTATCTCAGATACTTGCTATAGTGCTTGA[C/T]GCTTAGAGATGGTTTCATAAATAAACTGAATGCCT Y 2 1 2 1 101000 f 74 goat snp11859-scaffold144-821338 3 46560644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441702 Affx-122929160 AX-123312039 3 70873831 TCCTAAAGTCATGCACCTGAGTAAGTGGCAGTGCT[A/G]TGATTTAATCTAGATCAGGCTGATGCCTTCTCCTA R 2 1 2 1 101000 r 74 goat snp11858-scaffold144-780241 3 46521726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277980 Affx-1111836190 AX-519551474 3 70877334 CTCTCCACAGGCTGCTTGAGCTCCCTCATAACATG[A/G]AGGCTGGGCTACAGAAGGGAGCATCTCAGAGAGCA R 2 1 2 1 102000 f 74 goat Random2.2K-350 3 70877334 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796948 Affx-122921858 AX-385283890 3 70960497 GTAGCAAAGCCCTCATAATAAATCCATTTACCTTC[A/G]GTTCAGGTTATAGCTTCTTTCCTAAAATGCCAGGC R 2 1 2 1 101000 f 74 goat snp11856-scaffold144-693575 3 46435516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425279 Affx-122940968 AX-123295625 3 70998989 CCACTCTGCTTTGTGTATCTTTCAGTGTCTTCTTA[A/G]CATTTTCTGCATTATGAACTTGGTAGGAGGAATAA R 2 1 2 1 201000 r 74 goat snp11855-scaffold144-655083 3 46396422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429775 Affx-122938244 AX-123300116 3 71039197 AAATGATTAGACATAGGCTTGAAAGGATTATGTTT[A/G]AAACAAGGAAATCAAGCAGGAAAGTATTTGAAGCA R 2 1 2 1 201000 f 74 goat snp11854-scaffold144-614875 3 46355720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436953 Affx-122933173 AX-123307291 3 71097324 CTGGAACCAGCATTTCATATTCCTGTAGTAAGCAA[C/T]AGTGGGACTAGACATATTTTCTTGTCTCTATATTA Y 2 1 2 1 101000 f 74 goat snp11853-scaffold144-556748 3 46297462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411335 Affx-122952269 AX-123281685 3 71138052 CACAGAGTCATACAGGACTTAGGGACTGTGCATGC[A/G]TGCACAAACAAATATTGAAAATAATTGGCTTGATG R 2 1 2 1 101000 r 74 goat snp11852-scaffold144-516020 3 46256354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425975 Affx-122941161 AX-123296321 3 71183306 AGGAAAGAAACAAGAATACATCCTGACCTTAAAGC[A/G]TGATGAAGCACAGATGATGTACTGTATGGCCATAG R 2 1 2 1 101000 f 74 goat snp11851-scaffold144-470766 3 46210805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791706 Affx-122955758 AX-385278697 3 71260765 CAAAGAAATACAAGATTAAGCTATGTGCAGTGTGT[C/T]CTTTTATTAAAATCATGGAAATCACTATTGATGCT Y 2 1 2 1 101000 f 74 goat snp11849-scaffold144-393307 3 46126286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375523 Affx-122979114 AX-123245882 3 71321087 TCAACAAGACTAACAGGCTCAAAAACAGATGAAAC[A/G]CAACCAACCACAGAGTTAAACCTCACATATCCTGG R 2 1 2 1 201000 f 74 goat snp11848-scaffold144-332985 3 46065557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384227 Affx-122972377 AX-123254585 3 71381949 TATACGTCCCCCATCTTAGTAGAGACTAATGAATC[G/T]AACTTAACCTTTTACTGAGCACTTTACCTCATCAT K 2 1 2 1 201000 r 74 goat snp11847-scaffold144-272123 3 46004239 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408505 Affx-122953715 AX-123278856 3 71435758 TTTAAATTGTTCATGTTTTATCTTTACCTCACCAC[C/T]ACTTATAGGTATAATAGAGTAGTCAAATAATGTTA Y 2 1 2 1 101000 r 74 goat snp11846-scaffold144-218314 3 45950462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384445 Affx-122973099 AX-123254803 3 71465271 AGATCCTTTAAAAAGAGGAAGACAAAATGAATGAA[C/T]GAACAAGTAGATAAAAAAATAAATGAAGGATCCCT Y 2 1 2 1 303000 f 74 goat snp11845-scaffold144-188801 3 45920781 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427824 Affx-122939744 AX-123298167 3 71515876 CTTTTTTTAAATATATATAATGAATTTACTTTACA[C/T]GCCAGTGTTCCAAGTATTTTGTTATGATTTTCACA Y 2 1 2 1 101000 r 74 goat snp11844-scaffold144-138196 3 45870111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778038 Affx-122940527 AX-385265155 3 71546697 AGAGTTGTCTCACCCTAAGGAAGGAAACAGCCTTT[C/T]GTATCATGGTACCAGTCATTGAGGGCTTCATAAGT Y 2 1 2 1 101000 f 74 goat snp11843-scaffold144-107375 3 45838988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412493 Affx-122951376 AX-123282842 3 71625346 TTCCATGTGTTACATAGGTATGGGGGGATGTGTGT[A/G]CCCCACCCTTTTTCTCTTTTAATCTCTCATTCCCT R 2 1 2 1 101000 f 74 goat snp11842-scaffold144-28726 3 45760189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277982 Affx-1111836191 AX-519551476 3 71632335 GTGGCACCACTGCTCCTGTGGACAAAAAAAACATC[A/C]CCTGCCGTTTCAATGAACAAAGGATGCTGCAGGCA M 2 1 2 1 101000 f 74 goat Random2.2K-351 3 71632335 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796589 Affx-122945781 AX-385283535 3 71662172 ATTCCCAAATAAAAGTTTCAGATCCAGTAAATTAC[A/G]TCTTATACTGTGATAAGAAAAGACTAATGTAGTTT R 2 1 2 1 201000 r 74 goat snp15138-scaffold1615-551675 3 45716037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420695 Affx-122944795 AX-123291042 3 71710044 CGTGAGTCCTTGCCCTGTCTTCCCTTCTGCACCAT[A/G]CTTGGCAGTCTTTCCCTGAATTCTGTTGTGAAGGA R 2 1 2 1 101000 r 74 goat snp15137-scaffold1615-503803 3 45667972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801497 Affx-122951661 AX-385288407 3 71743648 AGTTAAACTCTGCAACAACATGCAGTAGTTCTGTT[A/G]GATAATTATTTTGCTGAACTATGTTGCATTTCTGG R 2 1 2 1 102000 f 74 goat snp15136-scaffold1615-470199 3 45634152 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780574 Affx-122973793 AX-385267665 3 71792585 ATATGAAAAATTTGGAAGCACACATCCATCTAGGA[G/T]ATTGCTTGAATGTATTATGATACATCCATATGACA K 2 1 2 1 101000 f 74 goat snp15135-scaffold1615-421262 3 45584499 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380792 Affx-122975097 AX-123251150 3 71825307 TATGAATTTACTGTTTACTTCACATCTATTAAAAC[A/G]TTTATCTGAACTACTACATTGATAAGAAATTGAGA R 2 1 2 1 101000 r 74 goat snp15134-scaffold1615-388540 3 45551137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801639 Affx-122946864 AX-385288547 3 71856277 GGTGATTTTGTTGATATTCGTGTTGATGATGTTTT[A/C]TTCTTAATGTTTTTGGGGGTTTCCTGTGTTCTCAT M 2 1 2 1 102000 r 74 goat snp15133-scaffold1615-357570 3 45519222 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792491 Affx-122972881 AX-385279472 3 71943703 AGTAAAGAAAAAATACATGGAGTATGTATTTTCTT[A/G]TCTGTTTAAGACAAGGTAAAGTTAGAAAATCATAG R 2 1 2 1 201000 f 74 goat snp15131-scaffold1615-270144 3 45430197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394727 Affx-122964330 AX-123265082 3 71985375 TAATAATAAAGCTAAAGCATGTTCCTTTTCATACC[A/G]TTCCAGTTCCCCCTGGATACCTTAACAAACTCAAT R 2 1 2 1 101000 r 74 goat snp15130-scaffold1615-228472 3 45390274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766433 Affx-122933829 AX-385253807 3 72024837 AGATCACTTCTCTTCCATACCTCCTGATTACTAGA[C/T]ATTAGACTTCAACTAAATGCACAAAATAAATAGTA Y 2 1 2 1 101000 f 74 goat snp15129-scaffold1615-189010 3 45350079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429903 Affx-122938115 AX-123300244 3 72054644 TGCTACCTTGAATTTCAAAGATGAGGTGAGTGGCC[A/G]TTCTTAGGTGGTTATCCCTCCAGTACATATTACAT R 2 1 2 1 201000 r 74 goat snp15128-scaffold1615-159203 3 45318949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771162 Affx-122949102 AX-385258322 3 72085810 TCTTTGGACCTGGAGAAGCAAAGTATGTATCTAAA[A/G]CTTTTTTAGAAGACAAATTATGACTTTCATGTTTC R 2 1 2 1 201000 f 74 goat snp15127-scaffold1615-128037 3 45287029 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433735 Affx-122934514 AX-123304076 3 72123325 CAAGATGACTTTGGGGGAAACATTAATTCATATCT[A/G]TGACAAAAAACAGACCTTCAGTTTGTGCCAAGCCA R 2 1 2 1 101000 r 74 goat snp15126-scaffold1615-90522 3 45249665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771262 Affx-122939412 AX-385258420 3 72205640 TATTTTTGCATTTCCAGTATTGCTGATGGTAAAGG[C/T]GGTAAGGGTGGGAGTTCTAAATTTTTAGATATTTG Y 2 1 2 1 201000 f 74 goat snp15125-scaffold1615-8207 3 45165600 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782073 Affx-122935699 AX-385269151 3 72225962 GCCCATAAGAAGGACTTCTTCTCTACAGTAATGCC[A/G]TTATGATGAATAACTTTGCATGCAAATGAAGTAAA R 2 1 2 1 101000 f 74 goat snp54382-scaffold83-4509273 3 45145295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770934 Affx-122927298 AX-385258097 3 72266966 AGCTGTTTCCTTCAATGTATGCATTATAATTTAAC[A/G]TATTTGGGAAGGTACCATAGAGTGATTTAGAGCAC R 2 1 2 1 101000 r 74 goat snp54381-scaffold83-4468269 3 45103514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382552 Affx-122973777 AX-123252910 3 72305435 TAATCTTTTTAATATTATAACTGAAAAAGAAAAAA[C/T]AATGAGGTGATTTATGTTGGCCTTTGGAGACAGAC Y 2 1 2 1 103000 r 74 goat snp54380-scaffold83-4429800 3 45066094 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412383 Affx-122950806 AX-123282732 3 72336377 CTGGGTGAGTATACTCATAAAGTAAAGGTGTGAGA[C/T]GAAATATATGTAATGGTGTGTGCTGAAATAATTTG Y 2 1 2 1 101000 f 74 goat snp54379-scaffold83-4398858 3 45035114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272222 Affx-1111833397 AX-519545969 3 72349145 CAATCCATTTTTTTTTTGTGAGAAAGATTGAATGG[A/G]ATAATGTTCTCTTTTTTGTCTCTTTTTCAAAGTTC R 2 1 2 1 201000 f 74 goat 3_72349145_AF-PAKI 3 72349145 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423123 Affx-122942907 AX-123293469 3 72368531 TCTTATTTTCCTAATTTCAAGGGTCTTATGGGAAG[C/T]ATCACAGTGTCTTTCATCTACTGACATTAGTGAAA Y 2 1 2 1 101000 f 74 goat snp54378-scaffold83-4366704 3 45002177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451090 Affx-122921406 AX-123321424 3 72401845 TACTGATGAGTTTCCAGACAAGTTTCAAGATGGAT[A/G]TTTATCATTATCTTCCATGATCTGTTAAGGCTTAT R 2 1 2 1 201000 r 74 goat snp54377-scaffold83-4333390 3 44968737 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429595 Affx-122937716 AX-123299936 3 72443320 GTAATTCACTGTGTATTTTGGAAAAATGTTTAACC[C/T]CTCTCAGTCTCATTTTCCTAATTTTTAGCAGTTAT Y 2 1 2 1 101000 r 74 goat snp54376-scaffold83-4291915 3 44927282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444411 Affx-122926580 AX-123314748 3 72481678 ATCAACAGACATCATGAATTTGTTTAAAAGAATAA[C/T]AGCCTTAGGGTGAAGTTGCAATCTCTGCCCAGTTT Y 2 1 2 1 101000 r 74 goat snp54375-scaffold83-4253557 3 44888292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800485 Affx-122953378 AX-385287405 3 72519423 TTCATAGAATTATTATGAGGAACAAATGGAATATC[A/G]CATGTGTATCAGTGAGTAGAGTGACACCACCAGGC R 2 1 2 1 101000 r 74 goat snp54374-scaffold83-4215812 3 44850765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442700 Affx-122927874 AX-123313037 3 72569588 ATTCATTAAAAGTATAAAAACCTAGAAATAATCCT[A/G]GGATAATGATAATTGACAATGATGCCATTATTCTT R 2 1 2 1 101000 r 74 goat snp54373-scaffold83-4165647 3 44801261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429351 Affx-122938570 AX-123299693 3 72633085 TGAAAATTGTAATTATATATACACAGAAATGCTAC[A/G]TAATCTGTCCCCTCCTTTAAAACTGAAAGGTGTTT R 2 1 2 1 101000 r 74 goat snp54371-scaffold83-4102150 3 44736997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787907 Affx-122962123 AX-385274929 3 72678225 TTGAGAGCTTCTGAGTTGGTTAGCATATCCACATG[C/T]GAAGAGGGTGGTGCATCCCAAACTCCATGAGGTAA Y 2 1 2 1 101000 r 74 goat snp54370-scaffold83-4057010 3 44691741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409246 Affx-122953141 AX-123279597 3 72739366 TAGGTTAAGAGTAATAGTCCAGCCATAGCTGTTAT[C/T]GTATTGTGAAGCAATGGGACTAATTCTTCAAGTTG Y 2 1 2 1 101000 f 74 goat snp54369-scaffold83-3995869 3 44630053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404194 Affx-122957677 AX-123274546 3 72828891 TTAGGAAAACTTTTAGAAGTGATGACCCTTAGAGA[C/T]AGGACATTCAGGCAGATCTTAGGGGATGTAACCAT Y 2 1 2 1 201000 f 74 goat snp54367-scaffold83-3906344 3 44539574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416289 Affx-122947941 AX-123286638 3 72862420 ATTTACTCAAAATATTAAGTAATAAATGTATTAGT[A/G]TTCTCTCAGAATGAATTAATGCATCTCTATGTAGT R 2 1 2 1 101000 r 74 goat snp54366-scaffold83-3872815 3 44505951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430735 Affx-122937509 AX-123301076 3 72926786 TTCTGAAATATATCTGACAACTTCTCTAAATTGCC[A/G]TTATTACTTTTTAAAAATCATAAGATGTGTTGTTA R 2 1 2 1 103000 f 74 goat snp54365-scaffold83-3808449 3 44441313 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277984 Affx-1111836192 AX-519551477 3 72938055 TCGCTGGAGACAGGCTTCATGGCTTCAGTTCAGTT[A/C]AGTTCAGTTCAGTCGCTCAGTCGTGTCCGATTCTT M 2 1 2 1 103000 f 74 goat Random2.2K-352 3 72938055 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320775841 Affx-122938791 AX-385262972 3 72960255 ATTTTAGAGTGGCTTAATAAAAGTGGTAGCACTTA[A/C]GTTTTGCAAACTAAGACGGTATTTCAAAAATTAAG M 2 1 2 1 101000 f 74 goat snp54364-scaffold83-3774980 3 44407892 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376450 Affx-122978057 AX-123246809 3 72991369 CCTGAATAAGAACCCCCAAATACCATTTTCATGAA[A/G]ACAACAGAAATGCTGCAGTGTGAGGGGGAGGAATT R 2 1 2 1 202000 f 74 goat snp54363-scaffold83-3743866 3 44376403 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447361 Affx-122924868 AX-123317697 3 73039152 AGTCCATGGAGCTGCAAAAGAGTCAGACACAACTC[A/G]GTGACTAAACAGCAAACTTACAGTAACTTAAGAAA R 2 1 2 1 303000 r 74 goat snp54362-scaffold83-3696083 3 44328121 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782002 Affx-122926438 AX-385269081 3 73135324 GCCTCTCTTGTCTTTCTATATTCATAGGAGAATAT[A/G]CTATAATGAAGGTGGTCTCATCTCTCAGAATTATG R 2 1 2 1 101000 r 74 goat snp54360-scaffold83-3599911 3 44231723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778181 Affx-122952065 AX-385265296 3 73190475 TTCTTGAAGGAGGTTACAGGTACAGATTGGTGCCT[A/G]TGTTATAATTTGTACTGGACAACTCATTTAAGCTT R 2 1 2 1 101000 f 74 goat snp54359-scaffold83-3544760 3 44141902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772385 Affx-122946883 AX-385259538 3 73240173 GAAAGGGAACTATTATCAATTGATACCATCCTGTA[C/T]GCATACTTGTGCTAGGCACTTTATACATTTTATGT Y 2 1 2 1 101000 r 74 goat snp54358-scaffold83-3495062 3 44092203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392564 Affx-122966079 AX-123262921 3 73273623 TGACAAGACTGCCTAATTTAGGCACTTATTTTTTA[G/T]TAAGCATTTACTATGTGCCACATACCATCAAAAGG K 2 1 2 1 103000 f 74 goat snp54357-scaffold83-3461612 3 44057356 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799359 Affx-122957767 AX-385286289 3 73326652 TTAGCAGTCCACTGACTGCAAAATGTTGTACAAGA[C/T]ACAAAGATGGTCATGAGCCCAATGAAATTACAATG Y 2 1 2 1 102000 f 74 goat snp54356-scaffold83-3408583 3 44003594 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764922 Affx-122966311 AX-385252509 3 73368890 CCTTTAAGTCTAACCAATTCTGTCTCTATGGTTCT[A/C]CTTACTGATTTGCAACCAGGCTGCACCTCATTGTT M 2 1 2 1 101000 f 74 goat snp54355-scaffold83-3366345 3 43974786 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430456 Affx-122937264 AX-123300797 3 73403021 CCATTGAGAATATTGCCCTTGGTGGTCCTGACTTT[A/G]TGGCAAGGGTCTTTGATCCAACCTCCCATTTCACT R 2 1 2 1 201000 r 74 goat snp54354-scaffold83-3332214 3 43940659 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776027 Affx-122957059 AX-385263157 3 73455754 ATTGAATTTAACTGAAGTTGGGACAAGAGAATTAA[C/T]ATTTATTGAGTACCATCAAAAGCTGGAACCAGTAC Y 2 1 2 1 101000 f 74 goat snp54353-scaffold83-3279481 3 43887348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391377 Affx-122967276 AX-123261734 3 73504414 CTGATTTCCCCATGCTGTCTTTTCTTTGTGTCCTA[C/T]AAGTAGAAGCAAAATTATCAGAGGCCAGGAAATGG Y 2 1 2 1 101000 r 74 goat snp54352-scaffold83-3230821 3 43841202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425455 Affx-122941512 AX-123295801 3 73558033 TTCTTTCTTTTAAAAAATATTGAAAAGTCGTATAT[A/G]TTTATATCTTAGTATGAGAGGATTTTAAATGCTTA R 2 1 2 1 101000 r 74 goat snp54351-scaffold83-3177202 3 43787687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787565 Affx-122929182 AX-385274589 3 73609489 CCACAGAAGATGATCCAGAAGGAGAGAAGCATTGC[A/G]TAGAAGATGCCCTGTCGGATATCACCAAACAACAG R 2 1 2 1 101000 f 74 goat snp54350-scaffold83-3125746 3 43736453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390116 Affx-122968010 AX-123260473 3 73640686 GGAGGCCAGGAAGAGGGGCAGACACATGATGGAGA[C/T]AGGAAGGAGGGTCAGATTCCAAGACCACATACACA Y 2 1 2 1 101000 r 74 goat snp54349-scaffold83-3094549 3 43705263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407511 Affx-122954739 AX-123277862 3 73689585 TTTGTCTGCCTTGTTTTTAACCAAGCATTTCATGT[A/C]ATTCCAATTTCTCTCCTCTCTTAGTCTATCAATTT M 2 1 2 1 101000 f 74 goat snp54348-scaffold83-3045650 3 43656470 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409239 Affx-122953147 AX-123279590 3 73729809 GCAGAGCCAAAGGGGCAGGCAGCCTAGGACACGTT[A/C]GTGTGCCTTTATCAGCAGCGATTCTGATTTGGGCC M 2 1 2 1 101000 r 74 goat snp54347-scaffold83-3005426 3 43618546 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767782 Affx-122958117 AX-385255008 3 73805718 ATCTAGTGTGGGTGTGGATCAAAGTTCCCAGTGCT[C/T]AAGTTTTATTCTGCTTTACTAACATTGGCAGCCAA Y 2 1 2 1 101000 f 74 goat snp54345-scaffold83-2929517 3 43542371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397520 Affx-122962050 AX-123267875 3 73851066 GGAGCTTTTATTCAGATTATTCTTCTGAATGGAAG[C/T]ATCCTTCCCATTACTGACCCCCTGCTTTTCTGACT Y 2 1 2 1 101000 f 74 goat snp54344-scaffold83-2884169 3 43496497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414853 Affx-122949155 AX-123285202 3 73884614 GACCTATCTTGCAGAGGATGGGAGTATTTTTGTCA[A/C]GGTATCATAGAAAGAAATTATCTGAATGCTTCTGA M 2 1 2 1 101000 f 74 goat snp54343-scaffold83-2850621 3 43462947 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387172 Affx-122970624 AX-123257530 3 73923851 ATGTTCATTTTTGAATCATGTAAAGAGTATGAAAT[A/C]TACTCTAATGGATAAAAATGATTTTTTTTGTGGAA M 2 1 2 1 303000 f 74 goat snp54342-scaffold83-2811384 3 43423648 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444298 Affx-122926756 AX-123314635 3 73957531 GAGAGATAAGTCACAAGGCGACGTCTTTTCTCTCA[C/T]GTTCCTTCTCCTTCCAGGAGGCCACCCCCTCCAGC Y 2 1 2 1 101000 f 74 goat snp54341-scaffold83-2777704 3 43389916 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414436 Affx-122949956 AX-123284785 3 73996029 ATAAACACAGTTAAAGACTCATTTCCCCAGTTGCA[C/T]GAGCCACAGTCAAGTGATCAGGCAGACACAGAAGC Y 2 1 2 1 101000 r 74 goat snp54340-scaffold83-2739206 3 43353764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417150 Affx-122947350 AX-123287498 3 74044365 CCTTCAGAATCTGAGTTTGCAATGATGGGGGAAAC[A/G]TTTAGGAAAACTGCTCTGCTCTTTCAGGCAGTGAT R 2 1 2 1 101000 r 74 goat snp54339-scaffold83-2690870 3 43307590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415337 Affx-122948792 AX-123285686 3 74130356 GCATGCTCTTTCCGTGTTTTAGATGTCTGCCCAAG[C/T]GTCACCTTTGCAGAGAAGCATGCTCTGACAACCGA Y 2 1 2 1 101000 f 74 goat snp54337-scaffold83-2604879 3 43221490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769522 Affx-122976216 AX-385256692 3 74174497 TAACAAAATTATTTGAACCAAGATGGCTACAAAAC[C/T]GAGCTTGTAGATAGTGGTTGATACAGAATCAGAAG Y 2 1 2 1 101000 r 74 goat snp54336-scaffold83-2560738 3 43177319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440194 Affx-122930704 AX-123310531 3 74216064 CATATAGATTCACTGAGGTTTGTTCTTGTTTAGTC[A/G]CTAAAGTCATGTCCGACTCTTTTGCGACCTCATGG R 2 1 2 1 103000 f 74 goat snp54335-scaffold83-2519171 3 43136449 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772631 Affx-122941506 AX-385259779 3 74260674 ATGAAGCAGCTCTTGGAGGAGGTAATGTATGAACC[A/G]GGTCATGATAGGAATGATGTCCATTCAGACATAAT R 2 1 2 1 101000 f 74 goat snp54334-scaffold83-2474561 3 43091767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788842 Affx-122959715 AX-385275857 3 74305031 AAAGAGATAAAAAACTGACACATTCTGCCAAGAGA[C/T]GCACTGAAGTGTTAATGAAGGTTGCCTTTGGATTG Y 2 1 2 1 101000 r 74 goat snp54333-scaffold83-2430204 3 43046873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791319 Affx-122972705 AX-385278312 3 74340381 AGCTGTCAGTTTTCCCTACCTACTAAGTGATGGAA[A/C]TGGGATCTGTCAAAGGAGTATCAAACACTATACCT M 2 1 2 1 101000 f 74 goat snp54332-scaffold83-2394854 3 43011274 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376895 Affx-122977811 AX-123247254 3 74371575 AAACTGATATTATGTCCAATATTTAAAACCAGTTT[A/G]TAATAGGGGGAACATCTAAATCCTTAATTAAAAAA R 2 1 2 1 201000 f 74 goat snp54331-scaffold83-2363660 3 42979982 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403379 Affx-122957783 AX-123273732 3 74413392 GTGAAGAAGCTGATCCACACACAAACCCATGAATA[G/T]GTGGAGCTTAGTGTGTGACAGGGGTGGTACCACAT K 2 1 2 1 101000 f 74 goat snp54330-scaffold83-2321843 3 42938006 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391731 Affx-122967492 AX-123262088 3 74442832 TGAACATTAAATTTTTACAATAAAAATGTAGGATT[A/G]TGATTCTTTCCAGTATTTTGGTATTTCCAGGATTA R 2 1 2 1 101000 r 74 goat snp54329-scaffold83-2292403 3 42908836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411778 Affx-122951483 AX-123282128 3 74492290 ACATCTGTCTGGCATCTCTAAAATGAAATTTAAAT[A/G]CCAAGCTCACACATCTTGACTTTCTTTTATTTCCG R 2 1 2 1 101000 r 74 goat snp54328-scaffold83-2242945 3 42858734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436837 Affx-122932220 AX-123307175 3 74549732 AAGGTAAAGGTGCTTAGGGCCCATGAAAGTCACAC[C/T]GTGACCCTGGATGGTCTTGATTATGTTTTCAAAAA Y 2 1 2 1 201000 r 74 goat snp54327-scaffold83-2185503 3 42801082 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431886 Affx-122936055 AX-123302227 3 74581111 AGTAAAAGTAATAAATAAGTGTTGGTCCTTTGGTC[A/G]TGTCCAACTCTTTGCGACCCTATGGACTGTAGCCT R 2 1 2 1 303000 f 74 goat snp54326-scaffold83-2154124 3 42769785 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399066 Affx-122960896 AX-123269421 3 74625870 CATAGTTACACAAAATGAGAAAATACATGGAAATG[A/C]TTTGTGCAAAGGAGGCTCCTGGAAAAGTAAGACTA M 2 1 2 1 103000 r 74 goat snp54325-scaffold83-2109365 3 42725065 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414199 Affx-122949657 AX-123284548 3 74672605 AATATATCAAAAACTTACTTCTTGATCATGTTTCA[C/T]GAGGACTATGGGTTGGCTGAGGCTCTTCGGGCCTT Y 2 1 2 1 201000 f 74 goat snp54324-scaffold83-2062630 3 42678319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785192 Affx-122970803 AX-385272238 3 74719735 GTTGCAATTCTTCTAAACTACCAAGACTTGTTTTA[C/T]GGCCCAGAATGTAGTCTATGTTAGTGCACTGTTCC Y 2 1 2 1 101000 r 74 goat snp54323-scaffold83-2015500 3 42630367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377894 Affx-122977248 AX-123248253 3 74758001 ACTCTTGACAAACTGCATTGGGAAAAGAAGCCTTC[A/G]TTAATAGTTACTTAGTCTCCCTCACCCCATACCTA R 2 1 2 1 101000 r 74 goat snp54322-scaffold83-1977234 3 42592228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410422 Affx-122952410 AX-123280772 3 74805955 GAGCCTTAAAGAGCAGTAAAAGCACAGGCATTGGA[A/G]TCAGCAGATCCAGAATTAAAGTTCTGTTCTTGGCA R 2 1 2 1 201000 r 74 goat snp54321-scaffold83-1929280 3 42543811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396227 Affx-122963345 AX-123266582 3 74836057 AGGAAATGCCTGACACATAGTAATCATAAATAGGT[A/G]TAGACTGCAGTTATGTAGGCTGACTGAAGCATGAG R 2 1 2 1 101000 r 74 goat snp54320-scaffold83-1899178 3 42513590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420797 Affx-122944688 AX-123291144 3 74893609 AGCCATCCTGGATATTTACTGAATACTCTATTTCT[A/G]CCCCTCTGGCCAGTCAGAAATCAAATGTGTCGCAG R 2 1 2 1 101000 f 74 goat snp54319-scaffold83-1841626 3 42455432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272223 Affx-1111833398 AX-519545970 3 74919350 AGAATAGAGCCAGATCATTGCTTGTTTAACAAAAA[A/C]TTTTAGTAAGTGTCAAGTTAGTGTTTGCTTTTTCA M 2 1 2 1 102000 f 74 goat 3_74919350_AF-PAKI 3 74919350 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406137 Affx-122956190 AX-123276489 3 74941806 ATGAACGAGAAGTCTTTATTAGTTAAAGCCACTGA[C/T]ATAGAGTAATTATTGATTGCAGCAACATCAGCAAA Y 2 1 2 1 101000 f 74 goat snp54318-scaffold83-1793429 3 42406710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784602 Affx-122971199 AX-385271650 3 74994578 TATCTTATCCAAAAACTAAACTATCATCCCTACTT[A/G]CATAATTTTCATTCACTTCTTCTTCAGAGCAAATT R 2 1 2 1 102000 r 74 goat snp54317-scaffold83-1740657 3 42353327 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428257 Affx-122939413 AX-123298600 3 75074520 TGGAAATAGACCCTGGATAGACATTTTGACCCAAC[A/G]CGCATGACATGGTTTTCCAGCAAAATAGAACCCCC R 2 1 2 1 101000 f 74 goat snp54315-scaffold83-1660715 3 42273700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443110 Affx-122928098 AX-123313447 3 75127712 CTGGATATGTTGGAAATAACTGTGTATGAGAATAA[C/T]GTGGGTCAAAATATTTCCATTTAAATATGTACATA Y 2 1 2 1 101000 f 74 goat snp54314-scaffold83-1607523 3 42220541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801317 Affx-122925301 AX-385288229 3 75177745 TAAATTCTGAATGAGAGTAAGTGAACTCAAAGTAA[C/T]AGGAGGGATATTATAAGGCACCACATTTGTGAAAC Y 2 1 2 1 101000 r 74 goat snp54313-scaffold83-1557490 3 42170706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440482 Affx-122929373 AX-123310819 3 75212644 ATTTATTGATGGTGAAAATTGAAGTCCTCAGAGAG[A/G]TGAAGTTGATTTGCCTAAGATAAGAAAGCTAGAAC R 2 1 2 1 101000 r 74 goat snp54312-scaffold83-1522591 3 42136493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440535 Affx-122929332 AX-123310872 3 75242099 ACTCTTCTACACAGCAGTCTCTGAGAACTGTCTAA[C/T]AACATTACACCTCTGGATGCATCACCCAATTACTA Y 2 1 2 1 101000 r 74 goat snp54311-scaffold83-1493136 3 42107550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452017 Affx-122920910 AX-123322350 3 75283852 AGTATAACTTTGGACTAGCAACTTGATTTCTCTTG[A/C]TTCAGCTTTCTCATATGTGATGTAGGAATACTGGC M 2 1 2 1 101000 r 74 goat snp54310-scaffold83-1451383 3 42066001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384057 Affx-122972875 AX-123254415 3 75312772 AGAATATTTTCCTGATCACTTTTTCCCACTCCATC[A/G]TCTTATTCATCCCCCATCAAACATGCAAAAAAGCA R 2 1 2 1 101000 r 74 goat snp54309-scaffold83-1422463 3 42036482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428928 Affx-122938901 AX-123299270 3 75355389 GAATAACCCCAGGGGTAGGATCCATTACGTTCTCC[C/T]TTCTGTGGCTGAGACTGTGCACACCCCCACCTCTT Y 2 1 2 1 101000 f 74 goat snp54308-scaffold83-1379846 3 41994837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381761 Affx-122974311 AX-123252119 3 75386535 CATCCTGGGCTGGCTCCCTTTCGTTTTAAAACCGC[A/G]GCATATTTTAAAGTTATCAGGGAAAGAATGTTGAG R 2 1 2 1 101000 r 74 goat snp54307-scaffold83-1348700 3 41963557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423889 Affx-122942294 AX-123294235 3 75438669 AAAATCTATGTCATAATAATAATGCTTTCTATCTC[A/G]TGGGATTTATTTTTCAAGGAAAAAATGAGATCTGC R 2 1 2 1 201000 f 74 goat snp54306-scaffold83-1296566 3 41911457 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772930 Affx-122971107 AX-385260074 3 75471752 AAATCCATTATTACCTAATGTCCTTACTGTGTCCC[A/G]TTTCCGTGAATGGATGTTTGTGTTCCTAGGTTTCA R 2 1 2 1 101000 r 74 goat snp54305-scaffold83-1263483 3 41877647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401596 Affx-122958869 AX-123271949 3 75558310 CACCAGGGAGGAATACCACATTCATTGTATGTGTC[A/G]TGTTTAAAGAAAGACTAGGTAGCTGGGTGATTTCT R 2 1 2 1 101000 f 74 goat snp54303-scaffold83-1176925 3 41790683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770386 Affx-122927975 AX-385257552 3 75605469 GCTTACATGTTGATTGCTAAGTCATTTGTATTCAT[A/G]TCGAAAATGATATCTACTCTGCAGTGGGAAGTGGC R 2 1 2 1 101000 r 74 goat snp54302-scaffold83-1129766 3 41743540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278145 Affx-1111836193 AX-519551634 3 75631736 TTCCTAAAAATTTCACTTACCATTATGAAAATCAT[A/G]AGGAATTATTCATGAACATTATTCTAATGGATGGA R 2 1 2 1 101000 r 74 goat Random2.2K-353 3 75631736 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444632 Affx-122926931 AX-123314969 3 75662559 GTTGGACATTTTGTGTACCTATGAGCACAGTACCC[A/C]TATTTCAATGATATTCAAGTAGATGTTAGAATGAT M 2 1 2 1 101000 f 74 goat snp54301-scaffold83-1072676 3 41686839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443989 Affx-122926915 AX-123314326 3 75692028 GCCTTAACTCTATCTTGGGAGCGAATGCTGTCTAG[C/T]AGAATGTATATGGGGCTTTTTGAACTAGAAGAACC Y 2 1 2 1 101000 f 74 goat snp54300-scaffold83-1043207 3 41657498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436144 Affx-122932635 AX-123306483 3 75725476 AATCAAATATTAATTTACACTGTATCCATAGAAGT[A/G]TGGATTTCAGAACTCTGGAAATCCTTCTCTGGCAC R 2 1 2 1 201000 f 74 goat snp54299-scaffold83-1009759 3 41623915 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796149 Affx-122920475 AX-385283100 3 75779045 ACATGTATAGGTACTCTGAAGGCAGATAAACATGG[A/G]TTTTAATCTTGACTTCACTAAACTGTAATTCAGAA R 2 1 2 1 101000 f 74 goat snp54298-scaffold83-956190 3 41569224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451334 Affx-122921270 AX-123321667 3 75824971 CTCACTGGCATGCCCTTGTGAACCAAATACACACA[C/T]GCTAGCAAGTAAAGATACCCACACACAGACACTAT Y 2 1 2 1 101000 f 74 goat snp54297-scaffold83-910264 3 41523616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453093 Affx-122920038 AX-123323426 3 75875466 ACAGACTCCTTCTATCATCATTAACCTCATTAGTC[A/G]TCCCCAAATGAGGAAAGCCCAGGATGAGCTTTGAG R 2 1 2 1 101000 f 74 goat snp54296-scaffold83-859769 3 41472632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782350 Affx-122932866 AX-187886881 3 75911972 ACTGAGAACTCATATGGGCGTGTGGCTCCCACATC[A/G]CTTACTCAGTCACATAGCCTATGTGATCAGTCTTG R 2 1 2 1 102000 f 74 goat snp54295-scaffold83-823263 3 41435942 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441677 Affx-122929180 AX-123312014 3 75970786 CTGAACAAGTCTCTGGGAGCCTCTTACTTAGACAC[G/T]CAGGACAAGGAGAGACTGGCTTATCTCTATGAACT K 2 1 2 1 201000 f 74 goat snp54294-scaffold83-764449 3 41376935 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391101 Affx-122966818 AX-123261458 3 76032437 ATTGGATAGTTAAATGTTATATCACATCCTGCCAG[C/T]GAAATCTAAGCAAAAATCTATGTATGCAGTATTTT Y 2 1 2 1 101000 f 74 goat snp54293-scaffold83-702798 3 41313589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796845 Affx-122951208 AX-385283788 3 76063264 GATACCATTATTTTGCAGAACAACTAAGAAATAGG[C/T]AAGTGCTTACCCAACATACTCTAGATGTTCATCAT Y 2 1 2 1 101000 r 74 goat snp54292-scaffold83-671971 3 41282517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452761 Affx-122920260 AX-123323094 3 76092978 ACTTAGCTCTTTTGTTGGAGGGAAAATTATGAGAA[A/G]AATTATTCCTGTTAAGATTAGGAGACATACTGAGG R 2 1 2 1 101000 r 74 goat snp54291-scaffold83-642257 3 41252908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397103 Affx-122962699 AX-123267458 3 76154266 ATTAAGCTGTTTTGTTTGAAGATAAATCATTTGTC[A/G]GGGTTAATAAGATTATAGATCTCCTAGGTTAAAAC R 2 1 2 1 101000 f 74 goat snp54290-scaffold83-580969 3 41189888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801352 Affx-122939814 AX-385288264 3 76209578 GTTTTTTTTAATAGCAGGAATTCACATTTGTCAAA[A/G]TAACATAATTTTCTGATTTATAGTTTTTACCAAGT R 2 1 2 1 102000 r 74 goat snp54289-scaffold83-525657 3 41133466 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787412 Affx-122971873 AX-385274437 3 76260075 GTAAATATTTAGATCATCTTTCAGTCTAGCTTAAA[A/G]AATCACATTCAACTTGAAGTTAATATTTGCAACAC R 2 1 2 1 101000 r 74 goat snp54288-scaffold83-475160 3 41082612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403241 Affx-122957888 AX-123273594 3 76323917 TAGGGAAAGGCAAAAGGGACACAAGAGTTGAGCAT[A/G]CTTGGGATAAAACTTCAAAATTTCATTACAGGACG R 2 1 2 1 101000 f 74 goat snp54287-scaffold83-411318 3 41018020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787978 Affx-122944664 AX-385274999 3 76398899 TAAATTATTGGCAGCATTTCTCTTTTGCCAGTTAA[C/T]GTTTAAGGGCTAACACAGTAAATTTTTTACTGTAG Y 2 1 2 1 101000 f 74 goat snp54285-scaffold83-336336 3 40943705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410556 Affx-122952145 AX-123280906 3 76434231 GAAAAGCCACACAGCTCTTTCCTGTTCCCTTCTGC[A/G]CCTCCAAGCTCCTTATTAGAGTTGTTTAGTTGCTA R 2 1 2 1 101000 r 74 goat snp54284-scaffold83-301004 3 40908405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380404 Affx-122975319 AX-123250762 3 76484390 TCATTTGCAAATCCCCCATCTCCAAAAACTGTAAC[A/G]TTAGGGTTTAGTGCTACAAATATGAATTGGGGGGA R 2 1 2 1 201000 r 74 goat snp54283-scaffold83-250845 3 40858326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398390 Affx-122961645 AX-123268745 3 76523602 TGATGAGAAGAGTGCCTGGCACAGAGTAGGCACGG[C/T]ATGTGTGAATTCTCTTCCCCTTGCCTTGTGGCTTG Y 2 1 2 1 101000 r 74 goat snp54282-scaffold83-211633 3 40818782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414479 Affx-122949553 AX-123284828 3 76569755 CAGGGTCACCCTAGACTTTAATATCATCCTCCCTG[C/T]GTGACATTGCACATTAACATGGTCCTGAACGCCAA Y 2 1 2 1 101000 r 74 goat snp54281-scaffold83-165480 3 40772890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392218 Affx-122966271 AX-123262575 3 76599717 GTCTTCGCCGTATGCCTTTTAGTTGGATAAGAAAT[A/G]CTCTTTTTTGTATTAATATGTGTATACAGATGTGG R 2 1 2 1 101000 f 74 goat snp54280-scaffold83-135518 3 40743500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408606 Affx-122953641 AX-123278957 3 76649896 AACTTATTAGTCACTTAACATGTTTCTGTGCCTGC[A/G]TTAGGTAGGGGGAGGTATGCACAAGTGTCCTTGAG R 2 1 2 1 201000 f 74 goat snp54279-scaffold83-85339 3 40692675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777417 Affx-122952725 AX-385264538 3 76685019 ACTCCGCCATTTGGAGTGGTATTACACGGCTAGTG[C/T]GCGTTAACTACCTATTAGTTAGCTGAATGCCAAAA Y 2 1 2 1 101000 r 74 goat snp54278-scaffold83-50216 3 40658133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441669 Affx-122929185 AX-123312006 3 76729241 GGCCTCATCACAAAAGGACTTCTTTCCTCTCTTTG[A/G]CTTGGAGTCAGGTTGGGCTTGTGAATGTTTTACAT R 2 1 2 1 101000 r 74 goat snp54277-scaffold83-5994 3 40614702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785772 Affx-122963802 AX-385272812 3 76743803 GGATGGTAGTTTAGATTGGAGATGACTTGCAAGCT[C/T]TTTACCTGGTCCTACACAGGAAAACTTCTCTCTAA Y 2 1 2 1 101000 f 74 goat snp48419-scaffold687-3117450 3 40600219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799269 Affx-122922483 AX-385286199 3 76815353 TTGATATGCATACTAACGCAGAGGTAAACAATGAG[C/T]GTGGGCTTTCTAGCAAGAGAGATTTTAGCTCTTCA Y 2 1 2 1 101000 r 74 goat snp48417-scaffold687-3045900 3 40528381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387881 Affx-122969627 AX-123258239 3 76866319 TAATTTTTTCCAACAGCTCTGTGTGACGGCCAAAG[C/T]GGATATTTTACAGATGAAGAAAATAGGTGCCTGAG Y 2 1 2 1 103000 f 74 goat snp48416-scaffold687-2994934 3 40477345 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439529 Affx-122930118 AX-123309866 3 76909749 GCTGGTTGGAGACAAACAGGATTCGATATTTCAAA[C/T]GCAATTTCATACCCCAAGTATTTCTTCCTCTTTAG Y 2 1 2 1 101000 f 74 goat snp48415-scaffold687-2951504 3 40433828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409712 Affx-122953040 AX-123280063 3 77026193 GAGGGAGGGACCCCAGCTAAGTAGGTAAGCGTGCA[A/G]TTTTGTTGCTGGCAGCCCTTATTGAGGTGGAATAG R 2 1 2 1 101000 r 74 goat snp48412-scaffold687-2835060 3 40316707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451558 Affx-122921702 AX-123321891 3 77079867 GTGGCGATTGGCTTCTTTGTATGTGAGTGTATAGA[C/T]GTTGAGAGGCTAGAGGATGGACAAGGAGAGCTGGT Y 2 1 2 1 101000 f 74 goat snp48411-scaffold687-2781386 3 40263047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420346 Affx-122944967 AX-123290693 3 77119164 AAGGCCTCCTCACCTTGCCTGAGTTCTTGACACTC[G/T]GTGCTGGGTTTCCCTTCTGGGCAGGTGTCCTTCTC K 2 1 2 1 101000 f 74 goat snp48410-scaffold687-2742089 3 40223260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454277 Affx-122919278 AX-123324610 3 77149039 GGAGTCACAGAGCTGGACACGACTTAGCAACTAAA[C/T]GAAGGCACTGTGTTTTATGTCATAACGTTAGACAT Y 2 1 2 1 101000 r 74 goat snp48409-scaffold687-2712214 3 40193445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793982 Affx-122960525 AX-385280951 3 77203072 TGGGGCATTGTCATTTTAAAGCAGTGTTCTAATTA[C/T]AGTGATGTATTTTAGATTCACATTCTGTGATCCAG Y 2 1 2 1 101000 r 74 goat snp48408-scaffold687-2658181 3 40139324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444915 Affx-122926245 AX-123315252 3 77289716 TCTCTCAGGTTTGTAATGATTAGATGAGTTAATCT[A/G]TGTAAAACACTTGGAATATTCTTGATACAATGTAA R 2 1 2 1 101000 r 74 goat snp48406-scaffold687-2571537 3 40052189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404139 Affx-122957091 AX-123274491 3 77323767 ATAAGAAGAGAAACAAAGAGCTTATCCCAAAGACA[C/T]AGTTAAATTACAAGAGACATGTGTTCATATACTTG Y 2 1 2 1 101000 f 74 goat snp48405-scaffold687-2537486 3 40017870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774172 Affx-122965938 AX-385261309 3 77353881 CATTTTTTTGAACAAATATTTCTCCATCTTATTCC[A/G]TAATATCTGTGGAAGTGTTGTAAGGGTTGTAAAAT R 2 1 2 1 201000 f 74 goat snp48404-scaffold687-2507372 3 39987761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406361 Affx-122955423 AX-123276713 3 77407509 TTAATCTCTCTGGTTCTGTTTCCTCATCTATAACA[C/T]TGGAGTAAATAATACTTCACAGAGCTGTTATATCA Y 2 1 2 1 303000 r 74 goat snp48403-scaffold687-2453744 3 39934094 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389813 Affx-122968195 AX-123260170 3 77442937 ATGAACCGGCATCCAGTTAGGTCATAAGTAAGGAG[C/T]ACAGGGCAGGCTGGGGAGAAGCTTAAACTAGCAGA Y 2 1 2 1 101000 f 74 goat snp48402-scaffold687-2418316 3 39898691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384926 Affx-122972333 AX-123255284 3 77475067 CCACTTCACAGTTGGCTACCGTGGGTGGGTCTTTC[C/T]AGAAAGGCGAAGAGAAACCATACCTCTGGATGGTC Y 2 1 2 1 101000 r 74 goat snp48401-scaffold687-2386186 3 39866341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787631 Affx-122931996 AX-385274654 3 77512318 CTATCTGGTGACAGTTCATTTAAGAAAAGCAGTTA[C/T]AGTTCTTCCAGCTGAGGACATAAGAGAAGAAAAAG Y 2 1 2 1 101000 f 74 goat snp48400-scaffold687-2348935 3 39828337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785499 Affx-122947415 AX-385272544 3 77545279 AAGACCATCAATGGACAACTTTGATGAAGCAAAAC[G/T]AAGTTTATTAGACTTACTACGTGAAGAGTGAACAC K 2 1 2 1 201000 f 74 goat snp48399-scaffold687-2315974 3 39795070 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381694 Affx-122974719 AX-123252052 3 77574657 GAATGAGGATAGCACCAAGGAAAACATAGAGACAC[A/G]CCAGCACTAAGTAATAATGGCATTGCTTGAAATCC R 2 1 2 1 101000 f 74 goat snp48398-scaffold687-2286596 3 39764842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464228483 Affx-1110380459 AX-515703292 3 77605259 CCTGTCCCGGGATCTTCCTTAGTTCTCTCCTCTAC[C/T]GCGCTCTGCCTCAGCCTTGTTCACTGGTGCCAGCC Y 2 1 2 1 102000 f 74 goat 3_77605259_AF-PAKI 3 77605259 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790289 Affx-122931788 AX-187869299 3 77610485 AACTAGCATAGCAGGCTGGAAAAAGGATGAACCCA[C/T]GTTACATCACAGCAAAACCATTGACAAAGTGTTGC Y 2 1 2 1 101000 f 74 goat snp48397-scaffold687-2250768 3 39728506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417336 Affx-122947737 AX-123287684 3 77640915 AGACTGTCTGCTGTGTCCCTAAGATGCTAGAACCC[A/G]CATGTACCCGGTTATCTTACTGTAAAATGGAAATA R 2 1 2 1 201000 r 74 goat snp48396-scaffold687-2220338 3 39697587 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451949 Affx-122920962 AX-123322282 3 77674459 TGTTTTTTCTTTTTTCAAAGAACAGAGTAGGAACT[A/C]AGAGGGCAAATAATCAAGGTCATTGACTCCCAATA M 2 1 2 1 101000 r 74 goat snp48395-scaffold687-2186794 3 39664309 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392120 Affx-122966344 AX-123262477 3 77707105 GTCTTACAAAGAAGCTGTACCATTTTCCATTCCCT[A/C]TCCAGAGATATTTAAGGATTTAGTCATTAGGCTTT M 2 1 2 1 201000 r 74 goat snp48394-scaffold687-2154148 3 39631650 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429363 Affx-122938561 AX-123299705 3 77739234 CAGATCTTTCCTAAAGATTGCAAGATCTTTCCATT[A/G]GATATAAATAATTTTTCTTATTTTTTTATAAAAAT R 2 1 2 1 103000 f 74 goat snp48393-scaffold687-2122019 3 39599414 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404771 Affx-122956687 AX-123275123 3 77774236 CAGGTGTTCCAGGAAAAGGTTTTGTGAAATTGATC[A/G]TTTTAGTTACTTTCCATGCTTCTTCCAAAGCAAAT R 2 1 2 1 202000 r 74 goat snp48392-scaffold687-2087017 3 39564311 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451614 Affx-122921628 AX-123321947 3 77818803 AATGAGAAAGGAGGCAGGGTCTATGGAGCAGACCA[A/C]GGAGGGGTAGTTTAATCAAACTTCTCTTCTTAAAG M 2 1 2 1 101000 r 74 goat snp48391-scaffold687-2042450 3 39519734 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391869 Affx-122966981 AX-123262226 3 77879511 AGGAGTCTGCTTTCTGTGGCTTCTTCTTTAGGGTC[A/G]TTAAAGATAGATGGCCCAGGGAGACTCCTTTTGTG R 2 1 2 1 102000 r 74 goat snp48389-scaffold687-1981742 3 39458856 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381590 Affx-122974800 AX-123251948 3 77932953 CTTTATATCATTTAATCCACATAACAATCTGAGGC[A/G]GCAGGTATTAATAGAGCTGAGAGGTACATTTGCCC R 2 1 2 1 101000 r 74 goat snp48388-scaffold687-1928300 3 39406774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408344 Affx-122953747 AX-123278695 3 78048935 TTTCAGAGTGAACCTCATTTTTTTAATGTGTAAAA[C/T]AGAGTTGATAACACTGACCTCAAATGGTTGTGAGG Y 2 1 2 1 102000 r 74 goat snp48385-scaffold687-1812318 3 39290148 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790542 Affx-122920165 AX-385277545 3 78086750 CTCTTGAAGGTTAATAATAGCTACCCCAGAGAGCT[A/G]TTATATGTATCAAATGATGTAATAGGTGTGGAAAT R 2 1 2 1 102000 f 74 goat snp48384-scaffold687-1774503 3 39252378 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387834 Affx-122969663 AX-123258192 3 78144864 CCCAGTATTTCACCCTGCGGAGGCATGTGTGTGTG[C/T]AAACACTCTTGCCCTGGGAGCTTCTCCTTGTTTAG Y 2 1 2 1 102000 r 74 goat snp48383-scaffold687-1716389 3 39194406 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399939 Affx-122961257 AX-123270294 3 78181406 TCCTTACTGATTACAGAGTAAGTACCAGTGCCCTT[A/G]CCACATCCTTGCACCACTGCAGAACCTACCTACCA R 2 1 2 1 101000 f 74 goat snp48382-scaffold687-1679847 3 39158028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798131 Affx-122931957 AX-385285066 3 78219755 CCCAGACTAGAGGGTCTTCAATTGGGGTACCTGAA[A/G]TTAAGGCTATGCAAACCCCCAGAAATAATACACAA R 2 1 2 1 101000 f 74 goat snp48381-scaffold687-1641498 3 39119621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784976 Affx-122961388 AX-385272023 3 78275117 ATCCTTTTGTGTTGAGGTTTCAAATCAACCATCTA[C/T]GAGGCCAGATTACTATAGGTTCTGGAATTTGGGGA Y 2 1 2 1 101000 r 74 goat snp48380-scaffold687-1586136 3 39063732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447933 Affx-122923789 AX-123318269 3 78308144 AGGAAGTCAGCCTATTTCCTAGAGAGAACTGTGGC[C/T]GAGACAAGGCTTCCTGGTGCAGACATGGCTACCCC Y 2 1 2 1 101000 f 74 goat snp48379-scaffold687-1553109 3 39030614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376924 Affx-122977788 AX-123247283 3 78336730 CCTCGCCACAGTGACCCTTGGCGCCTGGAGTATCC[A/G]TTTCTCAAAATGTTGGCCCTGTGGCTTTTTTCCCT R 2 1 2 1 101000 r 74 goat snp48378-scaffold687-1524523 3 39002031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413070 Affx-122950966 AX-123283419 3 78389731 AAGCCTAAAATGTTAGCTTTTCTCTTTTAGCTTCT[A/G]TGCTTTGTCCCTCCCTTGATTTCTCCAGTGCTGAT R 2 1 2 1 101000 r 74 goat snp48377-scaffold687-1471522 3 38949102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423490 Affx-122942568 AX-123293836 3 78431362 ATGAGAACTGGAATTCTGATCTTTTCACATGGGTA[C/T]TCCTTGGGTTAATATTTGTAAAACACTTGAAACAG Y 2 1 2 1 101000 f 74 goat snp48376-scaffold687-1429891 3 38907666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427855 Affx-122939721 AX-123298198 3 78472990 ACTCTTAGCTGGGTGAGAGATCTCTCTCAGTTTTC[A/G]TATCTGTAACAGGTTCAGAAAGTACCTGACCACTG R 2 1 2 1 201000 r 74 goat snp48375-scaffold687-1388263 3 38866070 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386194 Affx-122971364 AX-123256552 3 78559173 CAGTCAGTATTCTCACAGCACTCTTGTGCCCCGCT[A/C]TTTAGTTTCCCTTTCACTGTCTGTCTACTCTCAAA M 2 1 2 1 201000 r 74 goat snp48374-scaffold687-1302080 3 38779227 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389721 Affx-122968674 AX-123260079 3 78594489 GTGTCCTTATTGCTAAAAGTGATGGGGAATAAAGT[A/G]CATGTATGTATGCTTTGATTTGCAGGGCAAAGTTT R 2 1 2 1 101000 r 74 goat snp48373-scaffold687-1266764 3 38743654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418785 Affx-122946184 AX-123289133 3 78640979 CAGTTCTGCCACTTACTAGTCATGTGACTGTGTAA[C/T]CTTACTGTTATTTAGTGTCTTCATCTGTAACAAGA Y 2 1 2 1 201000 r 74 goat snp48372-scaffold687-1220274 3 38697569 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793877 Affx-122962748 AX-385280846 3 78722316 TTTCCAGATCTGGAAATTAAGGTCAAGAGAAGTTG[C/T]AAGACTTGCCCGTAGTCTTAAAGCTAGTTAATAGC Y 2 1 2 1 202000 r 74 goat snp48371-scaffold687-1138937 3 38615480 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441196 Affx-122929534 AX-123311533 3 78761013 GAGCATTAGTTATGCATCCTTTTTGCTTTGCATTG[C/T]AATAAATGCTGCACTTTCCTACATCACAAACTGGT Y 2 1 2 1 101000 f 74 goat snp48370-scaffold687-1100240 3 38576668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437810 Affx-122932118 AX-123308148 3 78799505 GGCAGCCAGGACCTTGTCTGCTTTGGTAACTGCCT[A/G]TATGCCCCGTGCCTCAAACACTGTCTGGTATAAAA R 2 1 2 1 201000 r 74 goat snp48369-scaffold687-1061748 3 38536884 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778679 Affx-122943710 AX-385265790 3 78838385 CCAAAGTGCTCACACTCACAGGTGCTATGAGGAAC[A/G]TAAACTATAAGTTAGATATATTCTTTGCCCTCAAA R 2 1 2 1 102000 f 74 goat snp48368-scaffold687-1022868 3 38497587 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409844 Affx-122952934 AX-123280195 3 78867639 TTGCTACATCTATGAAGCCTCTAATGTAGTCCCTG[A/G]CACATATTATATGTCAGTTACCTTTTCATTTACTC R 2 1 2 1 101000 f 74 goat snp48367-scaffold687-993614 3 38467823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381266 Affx-122974481 AX-123251624 3 78902836 CTTTGTCCCTTCACATAGTCGCAGGCTCTATTCCA[C/T]GCTCACCCCCTGCACAAAGCACCCCCACCCCAAAC Y 2 1 2 1 101000 f 74 goat snp48366-scaffold687-958417 3 38432783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451001 Affx-122921720 AX-123321335 3 78937808 CATTCATTTTTACCTAACAAACAGTGGTGGTAGCT[C/T]AGTTGTGTCCGCCTCTTTGCGACCCCATGGACTGT Y 2 1 2 1 101000 f 74 goat snp48365-scaffold687-923445 3 38398011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428107 Affx-122939081 AX-123298450 3 78969176 GGTATTAAATTCCACTGGTGCTCAATGTTTCCATA[C/T]GTAAAAACAGATAATAGATTGATGTGAAGTGTAGG Y 2 1 2 1 101000 f 74 goat snp48364-scaffold687-892077 3 38366653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431590 Affx-122936175 AX-123301931 3 79011807 AAGGACATAAGACCACAGCCCAGGGAAGTGATCAA[C/T]AAGAGTAATTGTTCACTTTCATTACTATAGGTGTT Y 2 1 2 1 101000 f 74 goat snp48363-scaffold687-849446 3 38322981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784343 Affx-122927177 AX-385271394 3 79051982 ATGCCTTTTGCTTGCATTTTGTCTAAAAGGACTAC[A/G]TTTTCAGAACTGGGAATTATTTACTAATTGCAAAT R 2 1 2 1 101000 f 74 goat snp48362-scaffold687-809271 3 38282790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795268 Affx-122945732 AX-385282226 3 79111751 TTTCACCTGCAATGTTTGTTAAAAGTACATCTCAG[C/T]GCTACTGGATCTGAATCGCTGGGTTTGGGTGGGAG Y 2 1 2 1 101000 r 74 goat snp48361-scaffold687-749502 3 38223142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425754 Affx-122940737 AX-123296100 3 79167467 TCAGTGAATCCCAAATTGACAGAGGCTATATAAAG[A/G]TTGTTGGTGTTCCCACAAAATTCCAGGTATTACTT R 2 1 2 1 101000 f 74 goat snp48360-scaffold687-693786 3 38167041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442147 Affx-122928322 AX-123312484 3 79196426 GAGACTTTTAAAGTCATCTTAATTACTTGAGTGGC[A/G]CATGGATCACAAATTCTCCAGGGCTTGGCAAGTTG R 2 1 2 1 101000 f 74 goat snp48359-scaffold687-664827 3 38138132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409368 Affx-122954163 AX-123279719 3 79228242 CTTCTACTCCCTTTGTGCACTATAACTTATTGCTT[A/C]TGTAAAATGTAGATCATTGCAGAGCCTCAGACTCT M 2 1 2 1 201000 f 74 goat snp48358-scaffold687-633011 3 38106422 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442134 Affx-122928332 AX-123312471 3 79269808 TAAGTTCTGGTCCACAAACACTTGCCTGTAGGAGG[C/T]TCAGTACTTGAGAAAGAATTTGTAATAAACCAGAC Y 2 1 2 1 201000 r 74 goat snp48357-scaffold687-591445 3 38063130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422557 Affx-122943767 AX-123292903 3 79318306 GAAGGATTTGGTGTGCCAGGCTAAGGAATGTAAAG[C/T]ACACACTAAAAGAAATGGCAGTTCAGTTCAGTCCC Y 2 1 2 1 101000 f 74 goat snp48356-scaffold687-542947 3 38014216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409226 Affx-122953156 AX-123279577 3 79349577 AGTTGGGGTGAAGTCACTAAGAAAGTTTGGACCCT[A/G]AGGCCCCTTACCACCATCCCTGTATCTTCAGCAAA R 2 1 2 1 101000 f 74 goat snp48355-scaffold687-511676 3 37982473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794643 Affx-122927021 AX-385281604 3 79396925 TCCCAGTAGTTCACTATTGTATTCTAAGCAGAATA[C/T]AGAATTGATATTCTTTTATCCCATTATTTTAAATA Y 2 1 2 1 201000 r 74 goat snp48354-scaffold687-464328 3 37935083 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431527 Affx-122936224 AX-123301868 3 79426085 TTGCTCTATAGACACTATGCTATTTTTACATACAA[C/T]GTTAGATTTGATCCTTAGAGTAATCATTCAAACAC Y 2 1 2 1 101000 r 74 goat snp48353-scaffold687-435168 3 37905940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776800 Affx-122975849 AX-385263924 3 79466927 CTCATCACAAAAATGGTTGACTGTTAGAATTCTCT[A/G]TTCTTTATCAGACACCACTGAATACCTACACAACA R 2 1 2 1 101000 r 74 goat snp48352-scaffold687-394326 3 37865097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450305 Affx-122922147 AX-123320640 3 79532351 AATTAGGGAATACCATCCCTATTTTGTCAGTGATA[C/T]GTATTTTACTTATGTGCCGGGTTTTTTTAATCTGA Y 2 1 2 1 101000 f 74 goat snp48351-scaffold687-328902 3 37799675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428588 Affx-122938705 AX-123298930 3 79574600 GCGCTTGCTGCTGAACTCACCATGTCGGTGTGCGT[A/G]TTTTCTGGAGGGAGAATGACGTGTCAGTATACTAA R 2 1 2 1 101000 r 74 goat snp48350-scaffold687-286653 3 37757452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426441 Affx-122940813 AX-123296787 3 79626650 TTTTCTCTTCTTTTTTGTGTCCAGGGCCAGGTTAC[A/G]CTGCAGTAGCAGTGCTAACACCTCAATGGCTTGGC R 2 1 2 1 202000 r 74 goat snp48349-scaffold687-234603 3 37705429 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438527 Affx-122931198 AX-123308865 3 79659390 TGTGCATTGTGTTTCCTTCTGCTTGGAATTTTCCT[G/T]CCTCCAAATTCTTTCTCTGGATAATTAATACTCAC K 2 1 2 1 201000 r 74 goat snp48348-scaffold687-201863 3 37672593 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415009 Affx-122949033 AX-123285358 3 79694557 TACCAGTGTTTACTGTTAGAAAATGTTTAACCACA[C/T]GAATTAATCATCAAAAAGATGCCAAAGAAACATCA Y 2 1 2 1 101000 r 74 goat snp48347-scaffold687-166696 3 37637367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385393 Affx-122971349 AX-123255751 3 79728713 AATCACTTTGGGCTGGGGTGGATAGCAGAGTTAAA[C/T]GGATTGTTGGGAGACAGTTTTCTATAGCGTCTTGG Y 2 1 2 1 101000 f 74 goat snp48346-scaffold687-132540 3 37603383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773262 Affx-122961276 AX-385260405 3 79757596 CTTAGCACACATGTAGACGTTTGGAAGCCAGACCA[A/C]CTGGATCTTGAATACAAGGCTAGAGCTGACTACAA M 2 1 2 1 101000 f 74 goat snp48345-scaffold687-103657 3 37574013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377821 Affx-122977305 AX-123248180 3 79812201 TACTTACTTACTGTGCTTATTTACTTACTGTGAGG[A/C]GCTTACTAATGAAGACCTTGTGGAATTGGAGTCCC M 2 1 2 1 201000 f 74 goat snp48344-scaffold687-49052 3 37518506 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443570 Affx-122927340 AX-123313907 3 79850260 TGGAAGATTTAGTCAGTCTAGGAGGGAAGGGGGCT[A/G]GAGAGTCTGTTAGAACTTTCTAACCAGTTCTCAGG R 2 1 2 1 201000 r 74 goat snp48343-scaffold687-10993 3 37480037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443903 Affx-122927055 AX-123314240 3 79869480 TTGTGCTCAGCTGCTCATTCATGTCTGACTCTTTG[C/T]GGTCCCAAGGACTGTAGTCTATTGAGCTCCTCTCT Y 2 1 2 1 303000 r 74 goat snp54276-scaffold829-108064 3 37454032 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422488 Affx-122943314 AX-123292834 3 79902662 TGGCTATTATAAACAGTGCTGCGATGAACATGTTC[A/G]CTTATACATTGATTCGGGATTTGACCTTGTGCCTA R 2 1 2 1 102000 r 74 goat snp54275-scaffold829-74882 3 37419725 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401173 Affx-122959355 AX-123271526 3 79934139 ATGCAATACCATTTAAGTACAATGTACAACCTAGA[C/T]AGCATATTGAAAAGCAGAAATATTACTTTGCCAAC Y 2 1 2 1 303000 f 74 goat snp54274-scaffold829-43405 3 37387751 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415000 Affx-122949041 AX-123285349 3 79980416 ACTCTGGTCACAGGCAGAGGTGCAGTGCCCTTTCC[A/G]TTTTCCTGTGATACTGTGACTTTAATAAAAAATAT R 2 1 2 1 201000 r 74 goat snp15923-scaffold167-1887521 3 37485170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764775 Affx-122964636 AX-385252388 3 80023478 GTAGTCCATAAACAGTTTGCATCAGTATTCTGGTG[C/T]AGGCAGATATACACTTAGGAATCAAAATCTGCCTT Y 2 1 2 1 101000 f 74 goat snp15922-scaffold167-1844459 3 37299576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278147 Affx-1111836194 AX-519551636 3 80088755 CTTGCAAAATTTGAAAACACTATCAAGTGAAGAAA[C/G]AGAATGAAAAACTATGATACTTACAGGAGGGCCTT S 4 1 2 1 101000 r 74 goat Random2.2K-356 3 80088755 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402009 Affx-122958757 AX-123272362 3 80120019 ATAGAATTTTAGAACTTGGGTAAATCCTGTACATC[C/T]TCTGGCCTTTCTTTTCCCTGTTGAAAAATGAGCAC Y 2 1 2 1 201000 f 74 goat snp15920-scaffold167-1747918 3 37202790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396824 Affx-122963275 AX-123267179 3 80171223 AATAGAGGTCATAATTCCACTGTCGTTGGACATTT[A/G]TTTCAGATTCAGCATGGTCAGCTATTTTGGTGGTT R 2 1 2 1 101000 f 74 goat snp15919-scaffold167-1696714 3 37151417 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436715 Affx-122932316 AX-123307053 3 80228628 TCTGTCAACTCTCTTAACTCAAACCTCTCTTCTTT[A/G]TGGATGTTCTCCTTGATGTCCAGTTCAGATACAGA R 2 1 2 1 101000 f 74 goat snp15918-scaffold167-1639309 3 37093708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448856 Affx-122923285 AX-123319191 3 80282810 TCTTCGCCTCTAGGACTAATTTAAGAGGTCAGATG[C/T]ATACTGAAAGGGAAGATCTCTAGGAAGGAAGAATG Y 2 1 2 1 101000 f 74 goat snp15917-scaffold167-1585127 3 37039301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769824 Affx-122931074 AX-385256994 3 80333306 GTATTAGCTATGGTGCCTTACTCTTCCATAATAGA[C/T]GAGTGTCATGACCACCAGCTTTGATTCTGTTATGT Y 2 1 2 1 201000 f 74 goat snp15916-scaffold167-1534631 3 36988381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406707 Affx-122955766 AX-123277058 3 80427040 ACTTTGACAACCTGGAGATAATGTATTACAAGATA[C/T]GTCATTTTTGAATGAGAAGACATGAAACTATTTGC Y 2 1 2 1 101000 f 74 goat snp15915-scaffold167-1440897 3 36893595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448490 Affx-122923469 AX-123318826 3 80479087 CTGCAACCAAAGGAATGAGAGAATACTAAAAAATG[A/G]GCAATCTAGCTTAACCGAAGCCAAAAATATTACTG R 2 1 2 1 101000 r 74 goat snp15914-scaffold167-1388850 3 36842504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272229 Affx-1111833401 AX-519545976 3 80504373 TGGTCAAAATTTCATTTTACTCAGCTAAAACTGTA[A/G]CCCCTTAGAATGAAGTGACTGGCTCTTTAGTGCAT R 2 1 2 1 201000 f 74 goat 3_80504373_AF-PAKI 3 80504373 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320799280 Affx-122971089 AX-385286211 3 80538292 CACAAAAATTTGGGAAGCTACATATGGAGCAGAAG[C/T]AATCTTCTTGTCATTATTTCCGCTAACAAGCAAGA Y 2 1 2 1 101000 f 74 goat snp15913-scaffold167-1329645 3 36783110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394902 Affx-122964734 AX-123265257 3 80611159 ACTAAAGGAATCCCCAGGGGATTTCCAGCATTGGC[A/G]TGGGTGCAGCAAGCTCGAACCTGAAATCTATGCTG R 2 1 2 1 201000 r 74 goat snp15912-scaffold167-1256778 3 36710282 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383396 Affx-122973500 AX-123253754 3 80664734 GGGATGCAGTCCCAAGGCTGCCTCACACACAGTTA[C/T]GGGATTAATCAAGGAACTCACCGTGTGTTTGTGCC Y 2 1 2 1 101000 r 74 goat snp15911-scaffold167-1203203 3 36656663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442913 Affx-122927634 AX-123313250 3 80734106 TTACATCAAGTTGACCAATACTTGAACTCAAGATG[C/T]TCGAAGTAGTTTATTATAGTTTGCTATTTCTGTAA Y 2 1 2 1 101000 f 74 goat snp15910-scaffold167-1133831 3 36587339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403829 Affx-122957951 AX-123274181 3 80777856 CTCCGTCCCCTGCTCTGTCACTGTCTTCAGCACAG[A/C]CGCCGTGCCTTAGGTGGCAAAGAGCTGGTTCATCA M 2 1 2 1 101000 r 74 goat snp15909-scaffold167-1090081 3 36542899 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424753 Affx-122941649 AX-123295099 3 80807095 ATAGAATAAGAGCATTCCAATACTAGATCTAATTC[A/G]TCTACTTTAGGAATCCCCAAAATTTTTATTCCTCA R 2 1 2 1 101000 r 74 goat snp15908-scaffold167-1060842 3 36513699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786079 Affx-122966702 AX-385273115 3 80861741 ATTCATAGCACTGTCAAAGGAGACTGTCGTCTGCC[A/G]TGGCAGTATCTTTTAGTATCCCCAAAGGTTTTCCT R 2 1 2 1 101000 f 74 goat snp15907-scaffold167-1006196 3 36459759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803224 Affx-122976247 AX-385290079 3 80894117 TATGTTTAGAATCTCCCTGCACTTAAAAAATCTTA[C/T]ATAGGTGTGGTTTGTATAAGAAAGATGCTGCATTT Y 2 1 2 1 101000 r 74 goat snp15906-scaffold167-973820 3 36427349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439118 Affx-122931099 AX-123309455 3 80931631 TTGCCTCTACAAGGGGTATTGACAGTGTTTATATT[A/G]TGGCATTGTTATGAAGAAAAAATGAGGTAATATTA R 2 1 2 1 101000 f 74 goat snp15905-scaffold167-936306 3 36389985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795189 Affx-122973639 AX-385282147 3 80975420 TTGCATGTTATAGGGTCAAGTTATTCCAACATCCT[A/G]TACCGTCTATATTATCTTAAACAATAGTAGATTCA R 2 1 2 1 101000 f 74 goat snp15904-scaffold167-892517 3 36346016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399801 Affx-122960283 AX-123270156 3 81008973 AGAGAATCAAGCCCTCCCCACAGAGTGAATGGCAT[A/G]CTTAGTAAATATTCTTCAAATATTGCTGGGTGAAC R 2 1 2 1 201000 r 74 goat snp15903-scaffold167-858964 3 36312405 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768355 Affx-122965044 AX-385255535 3 81060087 ATTTAATGTTAGTACCACTCTATTTCAAATTGTAA[C/T]CCTAACCTTAAACCAAAGGTGGATTTTGTGGCCGA Y 2 1 2 1 101000 r 74 goat snp15902-scaffold167-807850 3 36261316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385709 Affx-122971110 AX-123256067 3 81092873 CTTTGAAGCAAGTGTCATGCATATTATGTTTTCAG[G/T]ACTTACTCAAATACTATGCTTCTACATAAGAGTGT K 2 1 2 1 101000 r 74 goat snp15901-scaffold167-775064 3 36228252 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449222 Affx-122923495 AX-123319557 3 81123009 GCACCAGGCTCCCTCTTTCTCTCTTTTTCTGGGAA[C/T]GGATTTGATGCAGGGAGAGGGAAATGGCTCTTTAA Y 2 1 2 1 101000 r 74 goat snp15900-scaffold167-744928 3 36197830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425670 Affx-122940870 AX-123296016 3 81153983 ACTAGGAGTGTACATGGCCTGATTTGGGCTTTGCC[A/G]CTAACCTAGTCTATGACCTTAGTCTGTGACCTCAT R 2 1 2 1 101000 r 74 goat snp15899-scaffold167-713954 3 36166694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415386 Affx-122948754 AX-123285735 3 81182577 AATCTTGAATACATTTTAAGGGAAGAGCAGGCCTC[A/C]CTTGCCACCTTGCACTTTTTCCTACATGGAAAAGA M 2 1 2 1 101000 r 74 goat snp15898-scaffold167-685360 3 36138156 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277990 Affx-1111836195 AX-519551483 3 81230869 ACTCTGTAGCAAATATTTCTCAATGTAAGTTGCTC[A/C]AATTCCATTCTATTTCTTTGAACACAATAAGATCT M 2 1 2 1 101000 f 74 goat Random2.2K-357 3 81230869 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394053 Affx-122964984 AX-123264408 3 81237220 TTGGATAAAGAAACTGACCCCTGATGGCTCAGCAC[A/G]TAAAGAATCTGCCTGCAATGCAGGAGACAAAGAAG R 2 1 2 1 303000 f 74 goat snp15897-scaffold167-630717 3 36083582 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381298 Affx-122974456 AX-123251656 3 81285471 CTTTGGATTTAGAGGCAAAGAAATTGCTCCCCTAA[C/T]ATGTTGGATTAATCTGCCCTAGCAACTCAGTTTGG Y 2 1 2 1 201000 r 74 goat snp15896-scaffold167-582466 3 36034750 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779969 Affx-122960265 AX-385267068 3 81322292 TTCCTATTATGGGCCCAGAATTAAATGGGTACCAA[C/T]AGACTGTACGTAGTACACAGAAAGCTACCGTTGGT Y 2 1 2 1 101000 f 74 goat snp15895-scaffold167-545645 3 35998069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391523 Affx-122966657 AX-123261880 3 81355489 TCCAGAGCAGCAACTGAAGATGAAGATATGACAGA[C/T]GTCAGTGCAAGACAGAAAAGGACTTTGTCTCTTAA Y 2 1 2 1 101000 f 74 goat snp15894-scaffold167-512448 3 35964819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764743 Affx-122964828 AX-385252357 3 81411656 CATTTAATTGAATCTCCTCTGAACTAAAAAGGGCT[A/G]CTATGTCCACTTGTACAGATACCTTAATATCACTG R 2 1 2 1 101000 f 74 goat snp15893-scaffold167-456281 3 35908554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799714 Affx-122941328 AX-385286642 3 81467208 CCCACAAGAGAAGACACGTGGCTTATACTTAATCC[A/G]TAGACTAAGTAGAGCTTCTCTAGCCAACTTGTTAG R 2 1 2 1 101000 f 74 goat snp15892-scaffold167-400729 3 35852039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771777 Affx-122973919 AX-385258934 3 81538656 AGAGGGGTAAGAGGAAAAGATTGAAAGAAGGGAAA[G/T]AAATTATTTGCAGAATAGTTTCACCAAGAAAAGAC K 2 1 2 1 101000 f 74 goat snp15891-scaffold167-329281 3 35780063 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793789 Affx-122978410 AX-385280761 3 81571539 AAGCAATGATAAAGATGATGTCTGGCAGGGTTGAA[A/G]TTTATTCAAGCCTTGTGCTCCTGGAAAATAGCAGT R 2 1 2 1 101000 f 74 goat snp15890-scaffold167-296398 3 35746846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278151 Affx-1111836196 AX-519551640 3 81651248 AAACACTATTTCTCACAAGATGATAGTGTTTAACC[A/G]ACATATCTTCACAACACTTTCCAAGATATGACACT R 2 1 2 1 101000 r 74 goat Random2.2K-358 3 81651248 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398054 Affx-122961750 AX-123268409 3 81670173 AGGCAACTGCAAAAGGCTCACTAATAGATCATTGG[C/T]AGGAATCAATGGAACTTTCAAAACAACTGAAATCC Y 2 1 2 1 101000 f 74 goat snp15889-scaffold167-197764 3 35643825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427569 Affx-122939481 AX-123297912 3 81699472 ATTCTGCTGTCCACCAAAGCCACTGGGTACACATA[G/T]ACTGTATAGGGATGCTCCCACATGAGAACCTCCAC K 2 1 2 1 101000 r 74 goat snp15888-scaffold167-168465 3 35613593 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803540 Affx-986696103 AX-385290347 3 81708893 CTATATAACCCCACCATAATATTACTAAACCTAAT[C/T]ATTTATATCATTATAACCTCCACCATATTCACACT Y 2 1 2 1 600010 r 74 goat 3_81708893 3 81708893 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320784961 Affx-122975762 AX-385272008 3 81732129 GGCAATAAGAGGGGTTGAAATAATCACAGAACTTT[A/G]CGATCCAGTCATTCTCCAAACCAACATGAGACTAA R 2 1 2 1 101000 f 74 goat snp15887-scaffold167-135808 3 35579957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379418 Affx-122976113 AX-123249776 3 81794313 TTGTATTTATGGAGATGCCCCTCCAAACAAAGGGA[G/T]AATGTACTATAATAACATCAGCATAAGCATTCATT K 2 1 2 1 201000 r 74 goat snp15886-scaffold167-73624 3 35517938 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399788 Affx-122960293 AX-123270143 3 81835732 CAGGAAAAAAAGGGAAAGAAGAATATTGTTTCATA[C/T]AACTGCTGCATTTTTGTTTCCTCAGCTCATTGATC Y 2 1 2 1 101000 r 74 goat snp15885-scaffold167-32205 3 35476471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450643 Affx-122921983 AX-123320977 3 81865081 TTATATGCATGTGCATGTGTATGTAGCATGTGTAT[A/G]TATATAATTTTCTCTATCCATTCATGTGATGAATA R 2 1 2 1 201000 r 74 goat snp15884-scaffold167-2856 3 35447280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773904 Affx-122947488 AX-385261043 3 81939947 GTCAGTGAAATTCAACTTCTCTTAATCCTTTATTT[A/G]CAAGTTTAGGCCCTGAGAAAGACTTTTGTTTAGGT R 2 1 2 1 101000 r 74 goat snp5214-scaffold118-3285247 3 35371152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448133 Affx-122924292 AX-123318469 3 82023212 AAGAGAATCTCAGACCACTCTCATTTATGAAAACA[C/T]TTTTCCTCTAATTTCCATTTTCCATATTCAAAAAG Y 2 1 2 1 101000 f 74 goat snp5212-scaffold118-3201982 3 35288216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375922 Affx-122978469 AX-123246281 3 82054172 GAGATATAAAGTGCTGTCTGTGAGAGATTAACCAA[G/T]ACCCTGGAAAGTACAGACAAGCCTCAGTGTTTCCA K 2 1 2 1 201000 f 74 goat snp5211-scaffold118-3171022 3 35257406 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772078 Affx-122930709 AX-385259233 3 82112247 TCACATAAGGGAGTAGGAACATGAATGAAATTAGC[A/G]TGATTATCAAGCAGTCCTAAAGTTCTGCTTGAGTT R 2 1 2 1 101000 f 74 goat snp5210-scaffold118-3112947 3 35198755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388808 Affx-122968908 AX-123259166 3 82193636 GTGTCCTACATTGCAATTCCATTCTGACACTATCT[A/G]CCTGGAGTTGAAAAGACCCCACAGGTTAAGGTCTC R 2 1 2 1 201000 f 74 goat snp5208-scaffold118-3031558 3 35116836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421567 Affx-122943850 AX-123291914 3 82269590 GGAGATGTGTTTACTGTGACTCCCTCCAGCTTGCC[A/G]TGTGATTACAGGTAAATCATCTAACTTCTTGAGGC R 2 1 2 1 201000 r 74 goat snp5206-scaffold118-2955604 3 35040660 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775997 Affx-122970528 AX-385263127 3 82304397 CACTGGACATGGTCATATGCAATTTTATATTGAAT[A/G]TCCCACATGAATCTGAAGTTATTGTGTGTTCCTGA R 2 1 2 1 101000 r 74 goat snp5205-scaffold118-2920797 3 35005840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788310 Affx-122963323 AX-385275328 3 82334863 TATGTCATGGATCTGGTAAAGGAAAATCCTTTACA[C/T]GTGAATACATTTATGCATAAATGCAGTTCACCAGT Y 2 1 2 1 201000 f 74 goat snp5204-scaffold118-2890331 3 34975317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804515 Affx-986696683 AX-385291065 3 82474191 ACTAATCTAGGTGTTGTGAAAGTATATTGTGGATA[C/T]GGTCAACATGTACAATAAATTGGCTTTAAGTAAAA Y 2 1 2 1 600010 r 74 goat 3_82474191 3 82474191 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38387029 Affx-122969923 AX-123257387 3 82474590 TGTCATTTGTCCCCACTCCTTTCCATGCCATTTTG[C/T]ATGACAGCCTCTGGGTATTTTCATGCCAATGAGTA Y 2 1 2 1 102000 f 74 goat snp5201-scaffold118-2750604 3 34834404 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449463 Affx-122922654 AX-123319798 3 82524959 AAGCATTATTCAAAAGAATAACAATCAGTGGCACC[G/T]GCATGCAGAGGAAAACTACACAGAGTAAATTAGAA K 2 1 2 1 101000 f 74 goat snp5200-scaffold118-2700235 3 34782555 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784660 Affx-122959385 AX-385271708 3 82600665 CATTAATGATCAAGTTTCACAAGAACTTAGAAGAG[C/T]AGCACATTTTAGCACTCAGTATGGTTATGACAGAG Y 2 1 2 1 101000 r 74 goat snp5198-scaffold118-2624529 3 34702985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447594 Affx-122924010 AX-123317930 3 82699626 CTGTCACTATGAGATGCTACTCTAGGCTCAGATAC[A/G]TTCTCTCTGCCCCTAGAATCATCATTTGTCCAAGG R 2 1 2 1 101000 f 74 goat snp5196-scaffold118-2525568 3 34602967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408532 Affx-122953694 AX-123278883 3 82773787 AAAATCGAGCAAATCACAATTCCAGTGGATTACTG[C/T]GAGGTTTAATGTCTCCAGTGTCCCAGCCCACTTAA Y 2 1 2 1 201000 f 74 goat snp5194-scaffold118-2451407 3 34528774 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440087 Affx-122929722 AX-123310424 3 82861737 GAACCACTGGCAGTCCACACCCTCCTCATGTCCCC[A/G]TATTTTTACCACTTCATTTAGTCTCTAATTTAGTA R 2 1 2 1 201000 r 74 goat snp5192-scaffold118-2363457 3 34443332 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424683 Affx-122941707 AX-123295029 3 82915477 GGTCTGTGCCAGGCACTGGAGGGAAATGGTAAGCA[C/T]GAGTAGACACAGACCTTACAGTCTGATGGGGAAGA Y 2 1 2 1 201000 f 74 goat snp5191-scaffold118-2309717 3 34389786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390689 Affx-122967950 AX-123261046 3 82981247 GAGACACTTTTTGTGCTGGAAAACTGGACTCCATT[A/G]CTGTGAATATTTTAACAGATTTTCACAGTTTCTCT R 2 1 2 1 201000 r 74 goat snp5189-scaffold118-2243947 3 34324162 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420544 Affx-122945295 AX-123290891 3 83014857 CCGCGTTGTGATTACCACCACACAGGATAGGGATC[A/G]TTCATTTGTTGTTTTGTTTTGCAAGCCCTTGACAT R 2 1 2 1 101000 f 74 goat snp5188-scaffold118-2210337 3 34289640 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272230 Affx-1111833402 AX-519545977 3 83117470 ACAATTGCACTCATCTCACATGTTAGCAGAATAAT[A/G]CTGAAAATTCTCCAAGCGAGGCTTCAACAGTACAT R 2 1 2 1 303000 f 74 goat 3_83117470_AF-PAKI 3 83117470 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453047 Affx-122920075 AX-123323380 3 83202449 ACATAGGGTTGTCATTAATCAGAGCATGGAGGGGG[C/T]GTTTCTGATGGTTGAGTGTCTGAGAAGTTTTCACA Y 2 1 2 1 101000 r 74 goat snp5184-scaffold118-2022745 3 34100971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399248 Affx-122960575 AX-123269603 3 83258540 TGAATGAATGGGTGGATGATTAAATGGTTAGTCAA[C/T]GGGAAGATTCCTGGGCCAGATTCCTGGTCAATATG Y 2 1 2 1 201000 f 74 goat snp5183-scaffold118-1966654 3 34044693 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800968 Affx-122977846 AX-385287883 3 83346185 GTTGTTGTTGGTATATAGCAGAAACACAGCCACTT[A/G]TTGATTCCTTCCTATGTGCCAACACCATGCTAACA R 2 1 2 1 101000 f 74 goat snp5181-scaffold118-1879009 3 33955774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770575 Affx-122937433 AX-385257739 3 83439394 TAGGTGTACCGACACGCATCTCTACCAAGTCGCTG[A/C]TAGCACAGTGCACCTGACTTGGCATGTGTGCTCAG M 2 1 2 1 202000 f 74 goat snp5179-scaffold118-1785800 3 33862642 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784835 Affx-122962232 AX-385271882 3 83484799 ATCTCCTGAAACTAATTAGTGATTTTTACAAGATC[A/G]CTTGTTGTACAGATCAGTATACAAAGGTCAGTTGC R 2 1 2 1 101000 r 74 goat snp5178-scaffold118-1740395 3 33816569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389832 Affx-122968174 AX-123260189 3 83576058 CCTTGGTGCCAGCTCTCCAGTCTCCCAGAGCACGC[A/G]TGTTCCTTTTCTTCCCTTGACCCCTAAGAGCAGCA R 2 1 2 1 101000 r 74 goat snp5176-scaffold118-1649136 3 33726657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275422 Affx-1111834793 AX-519548995 3 83586520 TTGACTTTTTATTTGTTTAATTCCAGTGGTGATTA[A/G]TTCACATAGACTCAAACTGTAAACTCCCTTCCACA R 2 1 2 1 101000 r 74 goat GoatD01.053299 3 83586520 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380188 Affx-122975505 AX-123250546 3 83766825 AAAACAACTCCAGATCTTAGTGACAAAAAAGTTAT[A/G]TTTCTTCTTTGTTCCGCGTCTGTCAAGGCTTGTCA R 2 1 2 1 101000 r 74 goat snp5173-scaffold118-1458369 3 33537474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381955 Affx-122974113 AX-123252313 3 83813887 AGGTTGGAGAGTATGAATGGAGGAGGAAGGATAAA[C/T]GAGAGGAAGATTGGGGCATCTCATAACTGCTGAAA Y 2 1 2 1 101000 f 74 goat snp5172-scaffold118-1411307 3 33500933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395115 Affx-122964151 AX-123265470 3 83999161 GAAGATTCTTCATTGGCTAGGTGGTATGTGAGTTA[C/T]GGACACAGCATAAAATTCAATCCCTGACCTCACAA Y 2 1 2 1 101000 f 74 goat snp5169-scaffold118-1226033 3 33315513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442987 Affx-122928190 AX-123313324 3 84070677 CTCAGTGATAACAGGTTGGCTGTGCTGAGAACCCC[C/T]GAGGTACCGAGACTATAATGCCATCAACGAGCCCA Y 2 1 2 1 201000 r 74 goat snp5168-scaffold118-1154517 3 33242187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377929 Affx-122977222 AX-123248288 3 84102263 ATTCCGGTTCAAGGAGTCATATGGCTCCAATTTTA[C/T]GCATGGCAAATAAGCCATATGGTGTCTCTTTTTGT Y 2 1 2 1 101000 f 74 goat snp5167-scaffold118-1122931 3 33210558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277994 Affx-1111836197 AX-519551486 3 84128924 TATCTTCTGTTTATGGCAACTCCATAAGGTAATGC[A/G]GTTATCATCCTCATTTTATACATAAGACCCTGAAC R 2 1 2 1 101000 f 74 goat Random2.2K-359 3 84128924 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376605 Affx-122979054 AX-123246964 3 84188900 TCTAAGCTTTAGTTGCATCATGAATAAAATTGAGA[C/T]AGTCATAGTTCATACCTGCCCCTCAGCTGTTCTCA Y 2 1 2 1 201000 f 74 goat snp5165-scaffold118-1036294 3 33123644 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408651 Affx-122953472 AX-123279002 3 84243949 TAGCTCTTTTTTTCACCCTCTGGGATCTATCTTGG[G/T]TATCCACAGTAGGACTATGTCCAAGTCTTGAACTC K 2 1 2 1 101000 r 74 goat snp5164-scaffold118-981245 3 33068371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428931 Affx-122938899 AX-123299273 3 84278101 AATAGATAGTAAAAGCATCTACCTCTAGGGTTATC[A/G]TGGAAAGTTCATCACGTAGTATACTACCCAGGATG R 2 1 2 1 101000 r 74 goat snp5163-scaffold118-947093 3 33034035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432357 Affx-122936271 AX-123302698 3 84331064 TCATTTTACAGATATGAAACCTGAGGTTCAGAGAG[A/C]TAAGTAATTTACCCAAATCACCCAGGTAGGAAGTG M 2 1 2 1 202000 r 74 goat snp5162-scaffold118-894130 3 32981332 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380496 Affx-122975705 AX-123250854 3 84364915 AAGGAGACTGTATTCTAGTAGGAGAAATAGACAAG[A/C]GCACAAATAGCTGTAGGAAGTTACAAGGGTCACAG M 2 1 2 1 101000 f 74 goat snp5161-scaffold118-860279 3 32946937 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769619 Affx-122972175 AX-385256789 3 84421431 GGTCACCCAGAGATCTTTTATCCTCATTCAAGGCT[A/C]TCAAGTATTTTCTGAATAGATAAAGTTGGTGGAAA M 2 1 2 1 101000 f 74 goat snp5160-scaffold118-803763 3 32890373 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433547 Affx-122934992 AX-123303888 3 84519568 AAATACGTGCAGATCAAACATCCTGACAACATATC[A/G]TAGAAATACATCCACGTTTAGCCATTGTGTGGCTG R 2 1 2 1 101000 r 74 goat snp5158-scaffold118-705626 3 32795023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277998 Affx-1111836199 AX-519551491 3 84553966 ATTTTGGTAGTAAAATAATACTGGAATCTTTACAT[A/G]TGCTTCTGTTAATAGCAAAATCTAATAGAACAATC R 2 1 2 1 101000 f 74 goat Random2.2K-360 3 84553966 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767488 Affx-122976903 AX-385254752 3 84590504 TGGTGATGAGGAATATGAAGAAAGGTTCTGTTACC[A/G]TATCATGAATAAGAGCAAGGTGTCCTGGTGGCTAG R 2 1 2 1 101000 f 74 goat snp5156-scaffold118-634690 3 32724308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767079 Affx-122944672 AX-385254368 3 84640026 TTGCTATGGAACACTTCCTAAAATGAATGTGCTTG[C/T]ACTGCAAGTCGTCTTCTGCCTTTGCGAGAAGTGGC Y 2 1 2 1 101000 f 74 goat snp5155-scaffold118-585168 3 32674374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443415 Affx-122927378 AX-123313752 3 84903570 TCTTATGGCATAAATTCAGTTATTCTCACTGCTTC[A/G]TTGACATTTCATAATTGTTGCTAACGTGGTTCACA R 2 1 2 1 101000 r 74 goat snp5149-scaffold118-321624 3 32409999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394970 Affx-122964270 AX-123265325 3 84970047 TTTTACAGATTATCAGATATCTGTTCAGTGCTCAC[A/G]TTTGCAACCTATCTTTTCAATTTTGTTTTCACATG R 2 1 2 1 101000 f 74 goat snp5147-scaffold118-255147 3 32343273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275438 Affx-1111834801 AX-519549011 3 85036073 A[A/G]GGGGCCTCCCTTCAGGAGATTCACCCCCAGTGGTG R 2 1 2 1 103000 r 74 goat GoatD01.053514 3 85036073 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423679 Affx-122942326 AX-123294025 3 85054209 TGTCTGTATTCCCTACCCTCCAATAATATAAATAA[A/C]ATGAGGGCAAGGAACACAACTACTTTATCCATAGC M 2 1 2 1 600000 f 74 goat snp5146-scaffold118-170985 3 85054209 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776138 Affx-122942326 AX-385263268 3 85054209 TGTCTGTATTCCCTACCCTCCAATAATATAAATAA[A/C]ATGAGGGCAAGGAACACAACTACTTTATCCATAGC M 2 1 2 1 102000 r 74 goat snp5146-scaffold118-170985 3 32258961 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402708 Affx-122959199 AX-123273061 3 85104995 TGTATCTCCACACTGGAGACACACATGGGTGCTTT[C/T]AGGCGGTCCTTGAGGCTACAGGTGTATATGGGGTA Y 2 1 2 1 201000 r 74 goat snp5145-scaffold118-120199 3 32207475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401636 Affx-122959591 AX-123271989 3 85146436 TTGACATGCTTGACATTTGGTAAAGAGCTCAGTGC[A/G]TGAGTGAATGAATGAATAGATGCATGACCACAGGA R 2 1 2 1 101000 f 74 goat snp5144-scaffold118-78758 3 32165663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771390 Affx-122938880 AX-385258547 3 85237081 ATCTTGTTTTAAACAGGAAGCATCGTTGGAACCTC[A/G]TTTTGAGCGCCCCAAACACACACATCCTCTCCTCC R 2 1 2 1 101000 f 74 goat snp8031-scaffold129-2939905 3 32075029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423095 Affx-122942924 AX-123293441 3 85310866 TTTCTGTCTAATCTGAGAGCAACACAGCCCATCCC[A/G]TTCAGATGACTGACGTGGAGGAGAGAGAAGTTACC R 2 1 2 1 201000 f 74 goat snp8029-scaffold129-2866120 3 32001389 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766505 Affx-122939170 AX-385253869 3 85369297 GTGTGCTGTGCTCTCAAGAAGATAAAAAGGGAGAA[C/T]ATAAAATTATGTACACACAAACAATGATGGATGCC Y 2 1 2 1 101000 f 74 goat snp8028-scaffold129-2807689 3 31942193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782857 Affx-122977578 AX-385269928 3 85398112 ATTACAGCAAAAATCTATAGCCTTTCATAATTTGT[A/G]CATGCTTATCAATACAGAATAATGGGCCCACAGCA R 2 1 2 1 101000 r 74 goat snp8027-scaffold129-2778874 3 31913352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410072 Affx-122952852 AX-123280422 3 85434537 AGGAAGGAATATGAGGTACCCATTCAAACCCTCCT[C/T]CCCATTTTACAGATGAATGACCTAGAAGACATCAC Y 2 1 2 1 101000 f 74 goat snp8026-scaffold129-2742449 3 31876887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411213 Affx-122952358 AX-123281563 3 85463418 TATCCTAGCTGTGGAGTATGACTTCAACCATCAAA[C/T]GTGATAGTCATAACTGCCTTATTAGGGCTGTCGTA Y 2 1 2 1 101000 f 74 goat snp8025-scaffold129-2713568 3 31848276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423742 Affx-122942858 AX-123294088 3 85494508 TGCAGGACTAGTGATGTTGAGCATCTTTTCATGTG[C/T]TCATTACCCATTTGCCTATCCACTTTGGTGAAATG Y 2 1 2 1 303000 r 74 goat snp8024-scaffold129-2682478 3 31817061 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442004 Affx-122928423 AX-123312341 3 85527180 ATCAACCTCCCTGGAAAAAAAAAGACCAAAGCATT[A/G]AAAATATACATACTTGTTGACCCAGCAATTCTGGA R 2 1 2 1 202000 r 74 goat snp8023-scaffold129-2649806 3 31783945 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769815 Affx-122964545 AX-385256985 3 85556071 ACTAGGGAATACAAAGACAATACATCACAGTCTCT[A/G]TCCTCAGGTGGTTCAGATACAAATAATGATACTAG R 2 1 2 1 101000 f 74 goat snp8022-scaffold129-2620915 3 31755908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439812 Affx-122930481 AX-123310149 3 85640881 CATAAGCATTGTTAGGAGTATAGAAATAATACATG[C/T]AAAGCATGGAGAAGGTACATATAATTGGCATCTAA Y 2 1 2 1 101000 r 74 goat snp8020-scaffold129-2536105 3 31671232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388710 Affx-122968982 AX-123259068 3 85674180 TGGGAGTCCAAGATCATGGTGCCAGCAGATTTGCT[A/G]TCTGGTGAGACTCCCTTCTTGGTTCATAGCCGTTT R 2 1 2 1 101000 r 74 goat snp8019-scaffold129-2502806 3 31637873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769108 Affx-122949588 AX-385256283 3 85706810 CCTGTGACGTTATGTTCGAAATCTGAGTACGATTC[A/G]TATTCTGTCAACGTAAATTCAGATTTGCCTCGGGT R 2 1 2 1 101000 f 74 goat snp8018-scaffold129-2470176 3 31605195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418666 Affx-122946318 AX-123289014 3 85744554 AAACTGGGTGTTGAGAGTTAATTAGAGGGTTAGCT[A/G]CTCATGGCACTTTGGATCATCCAAAAAGAAAAGAA R 2 1 2 1 101000 f 74 goat snp8017-scaffold129-2432432 3 31567278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400144 Affx-122960702 AX-123270499 3 85804633 TGGTTCGTCTATAGCGATGCTGAGGTCTCCCAGGG[C/T]GATGAGAGGAACTGGAGTAGAGAGGAAGCTGATAA Y 2 1 2 1 101000 r 74 goat snp8016-scaffold129-2372353 3 31507166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272069 Affx-1111833403 AX-519545833 3 85852238 GTTGTTGTTGTTGTTATTTATAAACTTTCAGTGCA[A/G]TAGTGTGGTTGATGGAAACGTTGAAGAAGTTCCCA R 2 1 2 1 101000 r 74 goat 3_85852238_AF-PAKI 3 85852238 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802416 Affx-122938399 AX-385289320 3 85860091 TGAGGTCTTGTCCATTCATGCACATACTGAGCAGT[A/C]GAACAGTATTTCCAGCACGTTCTTCCTGATTCCAA M 2 1 2 1 101000 f 74 goat snp8015-scaffold129-2316895 3 31452256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450421 Affx-122922057 AX-123320755 3 85893431 AGGTACCGGAAAGTCTCTAAAGACTGCAATCAGGA[A/G]AGAGACACAGTAGGTAACCCCTATGCATTCAAGTT R 2 1 2 1 101000 f 74 goat snp8014-scaffold129-2283555 3 31418601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448925 Affx-122923161 AX-123319260 3 85934818 ATCCTCTCAGTAGCACATGTGGAAACTGAGGCTTG[A/G]AGAGCTTCAGTAACTCACTCAAGACAGCACCACTG R 2 1 2 1 201000 r 74 goat snp8013-scaffold129-2242168 3 31377449 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798219 Affx-122921349 AX-385285154 3 85967072 GAGGAGATCAGGAAGTTTCATACCAAAGTTGCTTC[A/G]TTGTCACAAAAGACCCATTACGGGCATCTTCCTGA R 2 1 2 1 101000 f 74 goat snp8012-scaffold129-2209914 3 31343915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421527 Affx-122943880 AX-123291874 3 86001920 TATATATATATATTTTGTGAATGTTAAATGATCAG[C/T]GGAAGGATCTGTCTTCTAGCAACTGTGTGCTATGG Y 2 1 2 1 101000 r 74 goat snp8011-scaffold129-2175066 3 31309168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384262 Affx-122972315 AX-123254620 3 86036783 TCTATAATGTTGAGAATGGAGTGAGTGATGGAAAG[A/C]GAGGTAGTTCATGAGGTCAGAGAGTGGACATGGAC M 2 1 2 1 201000 f 74 goat snp8010-scaffold129-2140203 3 31273881 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771732 Affx-122925894 AX-385258889 3 86096751 TTCTTTAGAGTTTAGTTTATGAAGGACATTATTGT[A/G]TCCCTCTATCTCACACAAATAATTATTTCTGGCTC R 2 1 2 1 101000 r 74 goat snp8009-scaffold129-2080235 3 31214080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433158 Affx-122935670 AX-123303499 3 86154811 CTGAGAGGCGATCACGTATATAGCTGTATCTTCAG[C/T]GGTGAAAGGATGGGAAAAAAGAAATCAGTCTTATC Y 2 1 2 1 201000 f 74 goat snp8008-scaffold129-2022175 3 31155684 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417503 Affx-122947155 AX-123287851 3 86184250 TTGAGCGAGTTACTCCCCATCTCACGACCCCCTTC[G/T]CATCTGCTCAATGGGAAAAATGAAGACTTGCTTTG K 2 1 2 1 101000 r 74 goat snp8007-scaffold129-1992736 3 31126289 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404450 Affx-122956746 AX-123274802 3 86216553 GTCTGAACTATCATCCCTGAGAGGTGTTGGTGACA[C/T]AAGCAGAATAACACATATATTGACTAGGGTCCCTG Y 2 1 2 1 201000 f 74 goat snp8006-scaffold129-1960433 3 31093965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419117 Affx-122945768 AX-123289465 3 86273908 CACAGCATAATTAAAAGCATGGGCTCCAGGACAGA[C/T]GGCCTGAGTGTGAATCTCAGTTTCATTGCTTATTA Y 2 1 2 1 201000 r 74 goat snp8005-scaffold129-1903078 3 31036186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783851 Affx-122974798 AX-385270907 3 86348522 TTAGGGAAACCATCTGTTGATCCCTCTGAACTTCC[A/G]TTTCTCACCTTAAAACAGATACTTGATAAATCATA R 2 1 2 1 101000 f 74 goat snp8004-scaffold129-1828464 3 30960624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397244 Affx-122962367 AX-123267599 3 86442489 AGGAAACTAATTCCCCAAATGAAATTAAGTGCTGT[A/G]AGGAAGTGGAAATCAATTCTGGGAAGCTAAACAAT R 2 1 2 1 201000 r 74 goat snp8002-scaffold129-1734497 3 30866511 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419055 Affx-122946016 AX-123289403 3 86480190 TCTCCTGCAGTGGAAAGTGGATTCTTTACCACTAG[C/T]GCCACCTGGGAAATCCTCTAAAAGTCAAGTCATAT Y 2 1 2 1 303000 r 74 goat snp8001-scaffold129-1696796 3 30828800 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798154 Affx-122950630 AX-385285089 3 86515877 CAAAACCCTAATGTAGTGTAAATTGACTTGTAAAT[A/C]TGACCTCTCCTCAACATTTTATCACCTCATGCCCC M 2 1 2 1 101000 r 74 goat snp8000-scaffold129-1661109 3 30793142 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376775 Affx-122977961 AX-123247134 3 86545839 CTCCACCATCCTGAGCCAGCAGCAGGACCACCTTT[C/T]CCTCTGTTTCCCATGGGTCTTTCTGTGTGGCGGAC Y 2 1 2 1 101000 r 74 goat snp7999-scaffold129-1631147 3 30763316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789269 Affx-122938463 AX-385276280 3 86584650 AGGTGAGAAATTAATATTATTTGTAGAAATAGTAG[C/T]ATTATAAAGAATCCAACAAATGCTACCTGAATTCA Y 2 1 2 1 201000 f 74 goat snp7998-scaffold129-1592336 3 30723160 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417698 Affx-122947457 AX-123288046 3 86665212 TCACTTATATGGAGGTTGAGGTTATATTAATAGCT[A/G]TATGTTTTATTTTATTTTATTTTCTTATCCATCGT R 2 1 2 1 101000 f 74 goat snp7996-scaffold129-1511774 3 30642462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798055 Affx-122938606 AX-385284991 3 86704834 GGGGGCCTGGAAAGAGGAAATGTGTAGCATACAAG[C/T]GTATAAAGGCATGCTACGAAGGTAACAGGCCTTCC Y 2 1 2 1 101000 f 74 goat snp7995-scaffold129-1472152 3 30601707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393343 Affx-122965936 AX-123263699 3 86760388 ATAAGCATGGGATTAGGCAATTGTAAATTATTTGA[C/T]GTAACTCTTATAACAAATTAAGTCCATATCAGGAC Y 2 1 2 1 101000 r 74 goat snp7994-scaffold129-1416598 3 30545149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781281 Affx-122962216 AX-385268366 3 86805660 GCTGTTCATAGGAGTGCTGCTCATAATAGTTTGTG[G/T]GGTATATTCAGACAGTAGAATAACACACAACTAAA K 2 1 2 1 101000 f 74 goat snp7993-scaffold129-1371326 3 30500089 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804521 Affx-986696689 AX-385291070 3 86828983 TCAGGAACAGGTACCTTCTGCTCTTGTCTCTCAGC[G/T]TCCTGGTTCTGTTTTCTGCCTTTCCATGATGCTCT K 2 1 2 1 600010 r 74 goat 3_86828983 3 86828983 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320803542 Affx-986696104 AX-385290349 3 86829073 CATTTTGCAGCATATTATTTAGTGCCCACCATAGT[A/G]TTTAGGCTCTGTGAGTGCCAGGTTTTATCCCTTGG R 2 1 2 1 600010 r 74 goat 3_86829073 3 86829073 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804140 Affx-986696691 AX-385290790 3 86832348 TCTCAGTGCTTTTCTCTGTGTAGGAAGATGGGTAA[A/G]TCTGGAGTCACGAAAATTCTCTTTTTGAGATGCAT R 2 1 2 1 600010 f 74 goat 3_86832348 3 86832348 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320804144 Affx-986696693 AX-385290793 3 86835948 CTTCCCCTTAACAAATAAACTTTCATCTCAATTCT[A/G]TCAACTATCAATATTTTACCTTTAACCATAGCCCT R 2 1 2 1 600010 f 74 goat 3_86835948 3 86835948 Ancestral_priority_1043 ancestry 0.614 recommended IMAGE 10K 10K ancestral 320804527 Affx-986696695 AX-385291076 3 86835957 AACAAATAAACTTTCATCTCAATTCTATCAACTAT[C/G]AATATTTTACCTTTAACCATAGCCCTTGTAAGGAT S 4 1 2 1 600010 r 74 goat 3_86835957 3 86835957 Ancestral_priority_1043 ancestry 0.662 neutral IMAGE 10K 10K ancestral 320804529 Affx-986696697 AX-385291078 3 86835979 TTCTATCAACTATCAATATTTTACCTTTAACCATA[G/T]CCCTTGTAAGGATGCTGTTAACAAGTCTTGGTCTA K 2 1 2 1 600010 r 74 goat 3_86835979 3 86835979 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320804156 Affx-986696699 AX-385290805 3 86836677 AGTTTGATTTTTCCATAGGGACCAGCTAAACAACT[C/G]TTTTCAATGAGAGATCTGTAAAAATTTACCAATTT S 4 1 2 1 600010 f 74 goat 3_86836677 3 86836677 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320804533 Affx-986696701 AX-385291082 3 86836680 TTGATTTTTCCATAGGGACCAGCTAAACAACTGTT[C/T]TCAATGAGAGATCTGTAAAAATTTACCAATTTAGC Y 2 1 2 1 600010 r 74 goat 3_86836680 3 86836680 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320804500 Affx-986696667 AX-385291056 3 86836833 AGAGTGCGAAGGATGCAGCCTTCTCAGGAGCCAGG[A/T]AGCTTACTCACAAATATCGTCTAAGAGAGTAAAGG W 4 1 2 1 600010 r 74 goat 3_86836833 3 86836833 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804536 Affx-986696704 AX-385291085 3 86839224 AGGAGCCAGTGCCTTGGAGACCAGGTGTACCTTCC[C/T]TCCCGCAGAACCATCTGTCTTTTTCTTTCTCCTTC Y 2 1 2 1 600010 r 74 goat 3_86839224 3 86839224 Ancestral_priority_1043 ancestry 0.562 neutral IMAGE 10K 10K ancestral 38396761 Affx-122962776 AX-123267116 3 86842008 CGTGTTTATTGTTGGGAAGATCACTTTCAGCCCAA[C/T]GAGGTCACAGAGTTGACTTGACATGCTTCCTATCC Y 2 1 2 1 101000 r 74 goat snp7992-scaffold129-1334978 3 30464464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787190 Affx-122957534 AX-385274216 3 86873940 AACCCACTAGCTGCCAAAGCCATGAGTAAAGTGTA[A/C]TTTCAAAAACTAAACCATCTTACCACATAAAGAGC M 2 1 2 1 101000 f 74 goat snp7991-scaffold129-1303046 3 30432699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396432 Affx-122962990 AX-123266787 3 86903285 GCTCCACCCATGATGAAGCAATAGTAAGGATGTAC[A/G]TCCTGGGATGGGTGAAGAATAAAGGCTATTAATAG R 2 1 2 1 101000 f 74 goat snp7990-scaffold129-1273701 3 30401590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773758 Affx-122921831 AX-385260898 3 86953510 TACAGAGTAGTTGGTTTAACACAATGAGGTGCCGG[C/T]GAACTTTTAGGATCTAATACATAGGGTAAAGGAGT Y 2 1 2 1 101000 f 74 goat snp7989-scaffold129-1223476 3 30351336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423934 Affx-122942258 AX-123294280 3 87005453 TTAGTGACTGAACAACAGCAACAATAAAACCACCA[C/T]CTCTTGGATGACTTGTGGAAGTACTTTCCAACATT Y 2 1 2 1 101000 r 74 goat snp7988-scaffold129-1171533 3 30298877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424850 Affx-122941349 AX-123295196 3 87035443 AAAAACCTTGAAAAACTATGAGAGCATCCTTATGC[A/G]TTGCAAGCTCTGTTGCCCCAACCCCAAAATGAATA R 2 1 2 1 101000 f 74 goat snp7987-scaffold129-1141543 3 30266086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379782 Affx-122975838 AX-123250140 3 87068682 AGATAACAGTCACAATATTGCATGTTGTAACAAAA[C/T]GTAGTGGGAGCATAGATGCCGGAGCAGTAAATCAT Y 2 1 2 1 201000 f 74 goat snp7986-scaffold129-1108304 3 30233474 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781428 Affx-122923121 AX-385268513 3 87202884 CTCTTGAAATCCCTGAAAAGCAGAGTTGATAAGGA[C/T]GACTAGGTTGAGCAAATGTTGACTGAGCCTGCAGG Y 2 1 2 1 101000 f 74 goat snp7984-scaffold129-974102 3 30097401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420025 Affx-122945152 AX-123290373 3 87279428 TGCTCTGGTTGAAGACAGCCAAGTGGAGACAGGGC[A/G]TTAGCCCAGTCTGTGAGCACACCCACCATCCCCCA R 2 1 2 1 102000 f 74 goat snp7983-scaffold129-897558 3 30020133 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278000 Affx-1111836200 AX-519551492 3 87281469 TGGCAAAGGCAACATGCACACAGGCCTACTCAGTA[A/G]TCTAAGCCACGCCTGACTCTTCGTGACCCCACGGA R 2 1 2 1 101000 f 74 goat Random2.2K-363 3 87281469 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415329 Affx-122948797 AX-123285678 3 87311697 ATTTGACAACTGATTTTTTTTTTTCATTCTTATGC[A/G]TTTGTTAACTAAAAATTTCTTATGTGACTGGTTGA R 2 1 2 1 201000 r 74 goat snp7982-scaffold129-865289 3 29987691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778957 Affx-122951994 AX-385266064 3 87351208 TCAATTTGTCTAAGTCCAGGTGTGGGAAAGGGGGT[A/G]TTAGGATATTTTTAGCTGTAAGTAACAGAAGACCT R 2 1 2 1 101000 f 74 goat snp7981-scaffold129-825778 3 29947139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443930 Affx-122927032 AX-123314267 3 87410264 GCTTTATGGAGAACACTCTTGAGCTACAGGAAAAG[C/T]AGGTGCTTTTCTTCCTATAGTGCCAAAGCTTCTCC Y 2 1 2 1 101000 r 74 goat snp7980-scaffold129-766722 3 29887519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422181 Affx-122943517 AX-123292527 3 87521500 TTTATAACCCTCTAGAATTTGAAAGATAATTTCAG[A/G]CTATTTCATTTGCCATCACCTCCAACAAACCCAGG R 2 1 2 1 101000 r 74 goat snp7978-scaffold129-655486 3 29777445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804542 Affx-986696710 AX-385291090 3 87547662 TCCTCCTCAGATGCAACCAACCACCAACTTGGGGC[C/T]TTTTTCCCCTCGCCCTGATTGGCCTCTCCCTGTCT Y 2 1 2 1 600010 r 74 goat 3_87547662 3 87547662 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 320779688 Affx-122934894 AX-385266788 3 87559569 GGTTGAGTTACACTTGATCCGATAAGGCGAAAATT[A/G]CATATAATCTATATTACTCTTGACCTGATTGTTAA R 2 1 2 1 201000 r 74 goat snp7977-scaffold129-617417 3 29739458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444315 Affx-122926742 AX-123314652 3 87605552 AGTCACACACACTGACACGGTCATGTACACTCTCA[C/T]GCATAATTTAAACATTAAAAAAGGAAATAGTATCA Y 2 1 2 1 101000 f 74 goat snp7976-scaffold129-571434 3 29692751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450320 Affx-122922135 AX-123320655 3 87671218 TAAATATGGACCAAATAATAGAGAATATTAATGTA[C/T]TGTTAAATTCCTTTGGTTGAGACAATGCTATTGTG Y 2 1 2 1 101000 r 74 goat snp7975-scaffold129-505768 3 29628595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448643 Affx-122923358 AX-123318979 3 87701049 GCTTTATAAGAGATGTGACCAGAATGGGGGCAAGC[A/G]TATCAGTCTAGGTCCAAAAGAGATGCTGCCGTCTG R 2 1 2 1 101000 f 74 goat snp7974-scaffold129-475937 3 29598521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795721 Affx-122967873 AX-385282674 3 87748055 TCAGTTTTCTCATTGGGTAAATGAGGACAATAATT[A/G]CCTTTCCCAGAGTATTGTTTGTAAGTAAGAACACA R 2 1 2 1 101000 r 74 goat snp7973-scaffold129-428931 3 29550286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441548 Affx-122928699 AX-123311885 3 87798259 ACATTTAGCACACTGAGACACTGCCTCCAGCCAAC[A/G]TTTATAAGGAGCCAATTCATTCTGAATACAACATT R 2 1 2 1 201000 r 74 goat snp7972-scaffold129-378727 3 29499801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387077 Affx-122969884 AX-123257435 3 87839467 GCATTCATGTGGCTGTGCAACTATCTCCACCACCC[A/G]TCTCCTTATTCATCTGCTCAAACTGAAACTGCACC R 2 1 2 1 101000 r 74 goat snp7971-scaffold129-337519 3 29458347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443358 Affx-122927420 AX-123313695 3 87874162 GTGTAGTGAGGTTCTTTTTCTCCCCCAGAGAAAAC[A/G]CCTTGAGCTGGAGATAGGAGGCACTTGCCCCATTG R 2 1 2 1 201000 r 74 goat snp7970-scaffold129-302824 3 29423690 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779967 Affx-122949554 AX-385267066 3 87922310 TCAAAAATGAGTCATCTAGACCTGTACACTCTTAC[A/G]CAATAGCTACTAGCTTCTGGTATGCAGCTAGTCCA R 2 1 2 1 101000 f 74 goat snp7969-scaffold129-254676 3 29373546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398857 Affx-122961055 AX-123269212 3 87955222 TGCCTACCCCATCTGTTGCCCTCCCAAGAGCCCAG[A/C]GATGGAAAGGAACTTTCCTTCCTTCCCTCCGCGAG M 2 1 2 1 103000 r 74 goat snp7968-scaffold129-221764 3 29340589 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445473 Affx-122925210 AX-123315810 3 87984478 TCTGAACCTCTCCACGAGGGCTTCTTATACCTACA[A/G]CCCAGGTTTCTGGGTGGGATGGGGTATTAACTTCC R 2 1 2 1 101000 f 74 goat snp7967-scaffold129-192508 3 29310945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437206 Affx-122932046 AX-123307544 3 88018361 CACCACCACTGTGCTCCTAGGGCTTCAGATGCCCC[A/G]TAGGGTCCACAGGTTCCCAAGGTTGAAGAGCAATG R 2 1 2 1 101000 r 74 goat snp7966-scaffold129-158625 3 29278563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378084 Affx-122977166 AX-123248443 3 88067897 TGATCGGGAACCTTTCTGGGGATGCTTTACCTGAA[C/T]GAGTTGTTCATTTTCTTTCTGCTTTTGGTGAAGCA Y 2 1 2 1 101000 f 74 goat snp7965-scaffold129-109089 3 29229447 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388823 Affx-122968896 AX-123259181 3 88109119 CCTGTTAGTCTATAGTTCATTTGAGTCTATGTCTC[A/G]TTCCCCATGGTGTGCCCAAGATCTCGCCCTGGGCC R 2 1 2 1 101000 f 74 goat snp7964-scaffold129-67867 3 29188138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427574 Affx-122939477 AX-123297917 3 88167442 TAGGCTTTGTCGGGGTAAACGTGAGAATATGAGAG[C/T]TTTGCTCTGAAGAAAAGGGACAAGGCTTCTACTGG Y 2 1 2 1 101000 f 74 goat snp7963-scaffold129-9544 3 29129189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420421 Affx-122944912 AX-123290768 3 88185344 ATGTATGATCCAATTAGGGCAGCAGCTGTGCCTAA[C/T]TGGTGCCTCTGTCCTCGACATCTAACACAGTAAAC Y 2 1 2 1 101000 r 74 goat snp16958-scaffold1771-8259 3 29109416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446935 Affx-122924682 AX-123317271 3 88251876 GTCTCCCCTTTCCAACTTGGGAGCCCCTTGATGGC[C/T]GAGAGCCCATCTTCCTGATCTTTGTGCCTCTCCCA Y 2 1 2 1 201000 r 74 goat snp16959-scaffold1771-74791 3 29042366 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381933 Affx-122974130 AX-123252291 3 88289922 TGTTAATAGTAAACAGGAAACCAGCAAGAAGAGAG[C/T]TGGCTGCAGCCCAGTCCCTCTCTCAATTCCGCACC Y 2 1 2 1 101000 f 74 goat snp16960-scaffold1771-112837 3 29004122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405089 Affx-122956992 AX-123275441 3 88321211 CTGGGACAGTTAGCCCAGCCACATGTGAAGCCATC[A/G]GCTGGAACCCAGACTCCTCACTTTTTACATGGATC R 2 1 2 1 101000 r 74 goat snp16961-scaffold1771-144126 3 28972868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402297 Affx-122959096 AX-123272650 3 88360058 CCTGGCACGCACGAACCACCTGTTGGTTGATGAGC[A/G]CTCTGGGTCCCTAGGTTGGAATCCACCTTCTTCAA R 2 1 2 1 201000 f 74 goat snp16962-scaffold1771-182973 3 28933712 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272234 Affx-1111833404 AX-190537523 3 88372622 AAATGGTTGGATGGCATCACCAACTCAATGGATGT[A/G]ACTTTGAGCAAACTCAAGGAGATAGTGAAGGACAG R 2 1 2 1 103000 f 74 goat 3_88372622_AF-PAKI 3 88372622 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394276 Affx-122964713 AX-123264631 3 88444061 AAAGCAGGCTTGCGGGGAACCAGCACTGGTTTTGT[A/G]CGTCCTCTTTGAAATAGAAGGTCCGTCTCTCCCAT R 2 1 2 1 201000 r 74 goat snp16963-scaffold1771-266976 3 28849694 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278159 Affx-1111836201 AX-519551648 3 88450909 CCACAGTAGAGGTGGGCACTCTGCAACCTGAGAGA[A/G]TTAGTAAAGGAACCCATAGGCTCTAGAGTGGTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-364 3 88450909 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406764 Affx-122955724 AX-123277115 3 88475113 AGCTCCCACAGCCTTGTGTCTCCCTGTCCTGGTCG[A/G]TATGATGAATCTGTACTTTTTGGATCGTCTGTCGG R 2 1 2 1 103000 r 74 goat snp16964-scaffold1771-298028 3 28818703 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433243 Affx-122935245 AX-123303584 3 88520299 CTTGTATTCCTCCGTCCCAGTGCTGAACGAGGAAG[A/G]GAAGGGAAGAGGTGGGGAGGCTGAGGCAGGTGGGC R 2 1 2 1 101000 f 74 goat snp16965-scaffold1771-343214 3 28774213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476179 Affx-1251763683 AX-586011606 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20000 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 539476434 Affx-1251763683 AX-586011835 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 4 1 4 1 20000 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165123 Affx-1251763683 AX-606940535 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165532 Affx-1251763683 AX-606940943 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165571 Affx-1251763683 AX-606940982 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165936 Affx-1251763683 AX-606941345 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 38447561 Affx-122924034 AX-123317897 3 88562744 GTCCACAGGCTTCTGTGAGGGTGACCTGAGTCCAC[A/G]TGGAAGGAAGTACCTGGCCTGTGGTGGGGCTGGGT R 2 1 2 1 101000 f 74 goat snp16966-scaffold1771-385659 3 28731636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375449 Affx-122979169 AX-123245808 3 88592908 TGTTCATAATGCTGAACAACGTTGCTTGTACAGTC[A/G]TAAGTCCTGACTGACCGTGGTTTGAAAAACTACTG R 2 1 2 1 101000 r 74 goat snp16967-scaffold1771-415823 3 28702170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798905 Affx-122976955 AX-385285835 3 88637958 CAGAACTTCCCACACTGTATTATAACTTCTATTTG[A/C]CTATTTCCCTCAGAAGATTGTGAGTGCCTCCAGGG M 2 1 2 1 101000 f 74 goat snp16968-scaffold1771-460873 3 28657196 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803254 Affx-122955117 AX-385290107 3 88692673 TGAGAGAAAACTTGGCGATTTTAATCACACACATG[A/G]GGGTTGGCACACATGAGAATTACAGGTTTGCAGCA R 2 1 2 1 101000 r 74 goat snp16969-scaffold1771-515588 3 28601921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796723 Affx-122954448 AX-385283668 3 88744487 ATTAAGATTAAATACACTTGTTTCACACAAAAACT[A/G]CATTCTTGACAAATGTTGTGTCAAATTCTAAATGT R 2 1 2 1 101000 r 74 goat snp16970-scaffold1771-567402 3 28550061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436624 Affx-122932502 AX-123306962 3 88777985 TATCTTTGGTATTATTATATTGATCATGTTCATTA[A/G]AAACACCGAAGAGAAAGCATAGGGCAAATAAAAAT R 2 1 2 1 201000 f 74 goat snp16971-scaffold1771-600900 3 28515997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464234469 Affx-1110383484 AX-515709204 3 88788145 GAGAGGGTAGAGCCTGAAGCAGACATGCTGGCAAC[C/T]GGAGCAGGTGAGCAGGTGAAAGTGTGGGTTCTGGG Y 2 1 2 1 102000 f 74 goat GoatD01.022479 3 88788145 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38405959 Affx-122955543 AX-123276311 3 88857917 TCCTCCTAGATAAATAAGAAGACATATAGAAGGGC[A/G]TTATTCTTCATTGCCTCCTCATTGCTTGTAATTAG R 2 1 2 1 201000 r 74 goat snp16972-scaffold1771-680832 3 28436538 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447860 Affx-122923887 AX-123318196 3 88897901 TATCTTTTAAAAATTTTTTTCTAAAATTAATTCTT[A/C]ATTTCTTTATTGTGGCTGATAAGAAAGATGAAAAG M 2 1 2 1 101000 r 74 goat snp16973-scaffold1771-720816 3 28397619 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432789 Affx-122935419 AX-123303130 3 89000905 AACAGTCAGGTATCATGTTTACCAAATGATGGTCC[A/G]TACTTTGGAGAAAAAGCAGGGAAGGGAGTTAGGGG R 2 1 2 1 201000 f 74 goat snp16975-scaffold1771-823820 3 28295233 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401500 Affx-122958940 AX-123271853 3 89046550 GATGACTGACCTAAGCACACCCTCGGTGAGGTTCC[A/G]TTCAAATGAGTGGCTCTGGAAGTCAGAGCCTTAAG R 2 1 2 1 202000 f 74 goat snp16976-scaffold1771-869465 3 28250779 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414489 Affx-122949546 AX-123284838 3 89099821 CATAGAAAGTGGCTGATATTCAGGTGTAAGCTCCA[C/T]GTGGGCACTATGTCTGGTTGATGGCTCATCCCTGG Y 2 1 2 1 101000 f 74 goat snp16977-scaffold1771-922736 3 28197345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406740 Affx-122955742 AX-123277091 3 89129658 ACTCCCTGTGTAACCTTGGGTAACCCACTAAACTC[C/T]TCTGAGTCTTTGTCTGAGATGGAGTGGTCTTACCA Y 2 1 2 1 101000 r 74 goat snp16978-scaffold1771-952573 3 28167490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273499 Affx-1111833654 AX-519547115 3 89197917 CTGTCTGCAGAAAGGCCTACCAGATTCCACACCAA[A/C]TGCATGCCTAGCCCTAATGCCTGCAGCTTCTGGCT M 2 1 2 1 102000 f 74 goat GoatD01.000714 3 89197917 C A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38411086 Affx-122951930 AX-123281436 3 89217595 GGGCCCCAACTTAAAGTCCCATGGACTCCCCACCA[C/T]GATTCCTTGCTTCAGAAGAGAAACCCGGACCTCTG Y 2 1 2 1 101000 r 74 goat snp16980-scaffold1771-1040510 3 28079529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412841 Affx-122950457 AX-123283190 3 89282144 CATCACTTCAAACGTTTCCTTTAAAAGCCCTTCCC[G/T]GAAAGCTGTTGGGAGATCAGGTGTTTTGACCATGA K 2 1 2 1 101000 r 74 goat snp16981-scaffold1771-1105059 3 28015171 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410788 Affx-122952667 AX-123281138 3 89313042 TGGGCTACCTCCTCTATCTCTCTGGTTCAGGTCAC[A/G]GTCACCTGAGGTCTGGGTTTTCATATTAGCCTCCC R 2 1 2 1 201000 r 74 goat snp16982-scaffold1771-1135957 3 27984311 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447340 Affx-122924886 AX-123317676 3 89342466 TGCCTTGTTCCCTGCAGTCTCTGCTCAGCTCAGGG[C/T]TGAGAATTGTTGCTGTTGCTGTTCAGTTCCTAAGT Y 2 1 2 1 201000 f 74 goat snp16983-scaffold1771-1165381 3 27955791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406021 Affx-122955496 AX-123276373 3 89383764 GAAATATGAATGAAAAATAACCCCGAAGAAAAGAT[A/G]CTGAACCTTACAGAAAATCAGGAAAAAGTAAGTGA R 2 1 2 1 101000 r 74 goat snp44030-scaffold595-5911614 3 27914723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446591 Affx-122924818 AX-123316927 3 89418243 CTTAGGGAGAAGGATGGTGTGGCTTCCACTGCCCC[C/T]AGGAGAGCCTGAGAGCCTGCATCCTCACTGGAAGG Y 2 1 2 1 201000 r 74 goat snp44029-scaffold595-5877135 3 27880634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791183 Affx-122938267 AX-385278178 3 89459966 CATTTCCAATAGTAAATGAAACTAAGGAAATGTAC[A/G]TTCCTTCTCCTCCCTTTATTGGGCACCTTCTGTAT R 2 1 2 1 101000 r 74 goat snp44028-scaffold595-5835412 3 27839261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278005 Affx-1111836202 AX-519551497 3 89553563 AATCTCTGATTTTAGAATTGCTACAGGAAGGGATT[C/G]GAATTTTGGTAGAATGACCTAATGATCCTTTCAGG S 4 1 2 1 101000 f 74 goat Random2.2K-365 3 89553563 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413994 Affx-122950280 AX-123284343 3 89553914 CAGCTTCACTCTGTGAAATATGAGCATGAACACAA[C/T]GGTGAAGACATGGGGCCCCCTGGGACAGTGTCTCT Y 2 1 2 1 101000 f 74 goat snp44026-scaffold595-5741464 3 27745177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381865 Affx-122974181 AX-123252223 3 89593851 ACATCCTGGAGCTTCTCCTTTGGGAAGCTGTTCTC[A/G]TATCTGCTCTGTCCATCCCCACTCTCATCCCTGCA R 2 1 2 1 201000 r 74 goat snp44025-scaffold595-5701527 3 27704731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387334 Affx-122970496 AX-123257692 3 89638236 TGGGAGGCCCTGGGAGGCCCTGCTGGGCCTGTCCG[C/T]CCTGAGCCTTCCAGGACTCTTGTGAGGATAGAAAG Y 2 1 2 1 101000 r 74 goat snp44024-scaffold595-5657142 3 27660329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427367 Affx-122940098 AX-123297710 3 89714538 GAGCTGGCTGTCTCTGGATGGATAGAGAAAGTGAT[A/G]CAGTGACACTGATGGATACAGAGAGTGATAAAAGG R 2 1 2 1 101000 f 74 goat snp44023-scaffold595-5580840 3 27583839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787482 Affx-122953243 AX-385274507 3 89749391 AGTTTTCCTTGGGAGAATGAGGGATGAAACAGAAT[A/G]TCATTATTAGCTGACCAGTAATTAATGTTGTGCAT R 2 1 2 1 101000 f 74 goat snp44022-scaffold595-5545987 3 27548591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787571 Affx-122954910 AX-385274595 3 89846008 TTGGTACTCAGGAGGCCAGAGGCAGCTACAATCTC[A/G]TTTCTTGACATGCTCATTACCTCTGTGCTCCAGTG R 2 1 2 1 202000 f 74 goat snp44021-scaffold595-5449370 3 27454000 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429089 Affx-122938271 AX-123299431 3 89935530 TGAGGCACATTTGTTTTTGAAAGCAAGTCAACAGC[A/G]TTACTGGTCTGTGTCCATGCCCATGCCCATGGTTC R 2 1 2 1 101000 f 74 goat snp44020-scaffold595-5359848 3 27364230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377908 Affx-122977237 AX-123248267 3 89974384 GCACTGATCAAATAGGGTCATTCTGAATAATCTGA[C/T]GTTCGGAGCCTCCATGTCTTTGTTTTGTTCTCCCA Y 2 1 2 1 101000 f 74 goat snp44019-scaffold595-5320994 3 27327364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403751 Affx-122958008 AX-123274103 3 90015480 CTGCCCTCAGTCTTTCCCAGCATCAGGGTCTTAAT[A/G]CTCTTGCCCATATCACACAGCAAGTCAGTGACAAA R 2 1 2 1 101000 r 74 goat snp44018-scaffold595-5279898 3 27285691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454256 Affx-122919650 AX-123324589 3 90059437 TTTTTCTCACTGGAGAATTTTGGTCTTGATGGAAG[A/G]TGGTATCTGAATCAGACCTTGAAGGATAGAACTGT R 2 1 2 1 101000 r 74 goat snp44017-scaffold595-5235941 3 27242111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789912 Affx-122937762 AX-385276918 3 90088649 TGTTGTAGGAAACCTGTTTAGAAGGAATAGCATAT[A/G]TGAATGACCTAGTCCTGTCTCTTGCCTGCTTAACT R 2 1 2 1 101000 r 74 goat snp44016-scaffold595-5206729 3 27212900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406105 Affx-122956216 AX-123276457 3 90122796 TCATAAGTCAGTACAAGCACAATTAAAGGACTGAT[A/G]CATCTCTACTTTCCTCCCAGACCTACCCACTGCCT R 2 1 2 1 101000 f 74 goat snp44015-scaffold595-5172582 3 27179933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404392 Affx-122956793 AX-123274744 3 90161719 AGACCCAATTACCTCCTCCTGATTGGAAATGATTG[C/T]AAGAGACTTAAATTTGTCAGTTATTAGAATAGCTG Y 2 1 2 1 201000 r 74 goat snp44014-scaffold595-5133659 3 27139985 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439069 Affx-122930313 AX-123309406 3 90191490 AGTCACAGTGGATTACCTATCTTTCAGAGTTGTAG[A/G]TCTGTGAAATTCTAGAAGGCTAGTGGCTCTTCAGG R 2 1 2 1 101000 f 74 goat snp44013-scaffold595-5103888 3 27110185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404437 Affx-122956757 AX-123274789 3 90225952 TAAGTTCAAAAATTTTTTTTTCTGTTTTATTAACT[A/G]CTATATCCCTGGCCATGAAATTAATGTCTTGTACA R 2 1 2 1 101000 r 74 goat snp44012-scaffold595-5069426 3 27075765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273589 Affx-1111833686 AX-519547203 3 90254623 AATCTTCCTCCAAGCAGTCTCTCTCTTC[A/G]CTAGCTACAGAACACAGTGTTATCTTTTAGTGTTT R 2 1 2 1 101000 r 74 goat GoatD01.001476 3 90254623 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414175 Affx-122949675 AX-123284524 3 90268693 GGAAGTCAAAATAGTTGTTATCTCTGTGTGAGGAT[A/G]TAGATATGGACTGGAAAGGGGTACAGGGGAGCCTA R 2 1 2 1 201000 f 74 goat snp44011-scaffold595-5026685 3 27031936 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378674 Affx-122977080 AX-123249033 3 90317440 CCACTGGAACATTCTGAATAGCAGTAACACAATCT[G/T]AATAATTTTAACAGGATCATTCTGGCTGCTATGTT K 2 1 2 1 101000 f 74 goat snp44010-scaffold595-4977938 3 26982720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382986 Affx-122973343 AX-123253344 3 90376195 ACAAATCCCGTTGACTCTACATTCAAAATATATCT[G/T]CAATTTGTTTCTCATTGACTCTTTTAAATCACTAT K 2 1 2 1 202000 r 74 goat snp44009-scaffold595-4919183 3 26923433 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384221 Affx-122972380 AX-123254579 3 90458380 AACTTAAAACCGACCTTTCTACATTCTACATTCGG[C/T]ATTTGAAGCAAATTGGAAAGGTGAAAAAGCTTGAT Y 2 1 2 1 101000 f 74 goat snp44007-scaffold595-4836998 3 26841547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433695 Affx-122934540 AX-123304036 3 90542462 TGGGTAACAGAGCCGCTGGTCTTCTTTCACTAGTT[G/T]CTGAGATTACCACTTTGACTGAGACACTCCAAATC K 2 1 2 1 101000 r 74 goat snp44006-scaffold595-4752916 3 26757648 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278007 Affx-1111836203 AX-519551499 3 90568819 GTCAGTCCTCAGACACAATAGGTTTCATGCTCATC[A/C]AGTATCAATAGTTAATTTCTTCCATTTGGTGATGG M 2 1 2 1 101000 f 74 goat Random2.2K-366 3 90568819 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435266 Affx-122934056 AX-123305606 3 90576796 TCATCAGAACAGGGAGCAGAATGCTTTAGGAAGAG[A/G]GAACATCATGGACACAGTCTCTGAGGTAGGAAAGC R 2 1 2 1 101000 f 74 goat snp44005-scaffold595-4718582 3 26723318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274527 Affx-1111834275 AX-519548118 3 90624529 GTCTTCCTTTGATGGTTGGGGAAAGCCCTTAAACT[A/G]TGAATAACTCCACAATCTCACCACTTCTCAGATAG R 2 1 2 1 201000 r 74 goat GoatD01.028520 3 90624529 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320781037 Affx-122967794 AX-385268124 3 90668366 GTAACTCTCCCACTGGGGCTTGCTATAAATGCTAT[A/G]CTGCAACTTTTCCCACCATTTCTACCTCCAGTGGC R 2 1 2 1 101000 r 74 goat snp44004-scaffold595-4627012 3 26630847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801152 Affx-122956790 AX-385288066 3 90697354 AATCCCCTACCCTATTCACCATATGGGGCTATTAA[A/G]GGGCTCAAACAGGATGGTGCATGTAAAAAGGCCTT R 2 1 2 1 101000 r 74 goat snp44003-scaffold595-4598024 3 26601650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776104 Affx-122953271 AX-385263234 3 90748095 TGCTAATCCTGTTTAAATAATCTAATCTGTTTATA[C/T]GTTGACTTTTCCTTCCCATTGTAATGTATGCTCCT Y 2 1 2 1 201000 f 74 goat snp44002-scaffold595-4547283 3 26550959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405556 Affx-122955961 AX-123275908 3 90804388 AAATGTATGAAATTATTCAAAGGCTCCAGGGAACT[C/T]CAGGGATTGTAAGTCTCTGGAAGCACAGACATGAT Y 2 1 2 1 101000 f 74 goat snp44001-scaffold595-4490990 3 26497412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430964 Affx-122936819 AX-123301305 3 90838954 TCATACATGGGTTTTGAAGTCCAATGTACATGCGT[A/G]CTAAGTCGCTTCAGTCATGTCCCACTCTGTGCAAC R 2 1 2 1 102000 f 74 goat snp44000-scaffold595-4456424 3 26462960 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402208 Affx-122959162 AX-123272561 3 90878845 AAGAGAAAGGTCCTCCTGATTCAGATAAAGTGGCC[A/G]CTTCCCAACTGAGGAGTCCTAGCCAGGTTGGTGGC R 2 1 2 1 101000 f 74 goat snp43999-scaffold595-4416533 3 26422735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386841 Affx-122970085 AX-123257199 3 90914099 TCTTCCCTTCCTTTCTGAATATTTATGTCTAAAAG[C/T]CATTTGCATAAGTGGGGCTAATCGAGATAGGAACC Y 2 1 2 1 101000 r 74 goat snp43998-scaffold595-4381279 3 26387663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441275 Affx-122929475 AX-123311612 3 90978789 AAAGTATATAATTAGCTTTTTTAGTGCCATCTGCT[A/C]GCGGCGCCGCCTCCTGCTCCTCCCGCCGCCGCCCT M 2 1 2 1 103000 f 74 goat snp43997-scaffold595-4316589 3 26321728 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793213 Affx-122975676 AX-385280191 3 91072473 CTTCTGGTCCATAGTCAGATGCATTATCCATTATG[C/T]CACCAGTCCCATACTTAGATGTTATTCAGTGTAAA Y 2 1 2 1 101000 f 74 goat snp43995-scaffold595-4222905 3 26227487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771375 Affx-122963078 AX-385258533 3 91137720 AAAGAAGAGTATTTCCCTGCTTTAATGTATAATGT[A/G]TAACTGAAAATGTACATGGAAGTAAACTGAGTTGA R 2 1 2 1 101000 r 74 goat snp43994-scaffold595-4157658 3 26161467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423547 Affx-122942429 AX-123293893 3 91193337 GTTTTAGGGATGGGAAGCAGGGTACTTTTAAAGAT[A/G]AGAGTAGAGTTAAGATTTAAGGAATGTAGTAAAGA R 2 1 2 1 101000 f 74 goat snp43993-scaffold595-4102041 3 26105251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394772 Affx-122964835 AX-123265127 3 91246782 GAGCAAGACATTGAGAAAATATAAGGAATAATGCT[A/G]TATTCCAGGCTAGCAACAGTAAGGCTATTCCCAAC R 2 1 2 1 101000 r 74 goat snp43992-scaffold595-4048596 3 26051693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395632 Affx-122963796 AX-123265987 3 91320095 CGTGGAGTTACAAAGTCTATAAACCTGAAGCTTTT[A/C]GTGCTTATTTTAGTGTTATAATGGGAAAGCCTACC M 2 1 2 1 101000 f 74 goat snp43991-scaffold595-3975283 3 25978236 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273774 Affx-1111833803 AX-519547385 3 91358010 AGACTCCATCTCAGAGGCGGTGTGGACACAGACAC[A/G]TCATTAACTTTTATGCCTCTGCACCTTTGCATATT R 2 1 2 1 201000 r 74 goat GoatD01.005555 3 91358010 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402454 Affx-122958612 AX-123272807 3 91380236 AGATAATAACAAAAACAGAAAATGCAACATAGTAT[C/T]ACAGACCAAACCTGCACACACTAATGTGCATGTTT Y 2 1 2 1 103000 r 74 goat snp43990-scaffold595-3915142 3 25917969 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445870 Affx-122925989 AX-123316207 3 91415421 CACACTGTGCACGTACCCTAAAAGGGCACTGTGAC[C/T]GCAAGAGGAACAGGATGGACTGTGCAGCCCATGAA Y 2 1 2 1 101000 f 74 goat snp43989-scaffold595-3879957 3 25882478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411653 Affx-122951567 AX-123282003 3 91443952 TCACACTAAATGCACACCCGAGCAGGGGCCTAGGT[A/G]AAGTCATCTGGGTTACCACTTGCACAGGGGGAAAA R 2 1 2 1 101000 r 74 goat snp43988-scaffold595-3851426 3 25853951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438843 Affx-122930770 AX-123309180 3 91485702 GAAAGGCCTGGAGGAGATGCTCCCACCAGTTAACC[A/G]TGTTTCCTCCAGGTAGAGGAACTGTGGGGAAGGAA R 2 1 2 1 202000 f 74 goat snp43987-scaffold595-3809676 3 25812412 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778927 Affx-122970693 AX-385266034 3 91517967 AAGCACTTAAAGATTTGACATTCAACTGTAGCAGT[A/G]TCTATGTTGGTTAATTTTCTTATGAGCCCCATGAT R 2 1 2 1 101000 f 74 goat snp43986-scaffold595-3777411 3 25782931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768262 Affx-122977256 AX-385255443 3 91590481 TAACAGGAATATTCTCTAGTGTATGATAATAATAA[G/T]AGTACAGCTATGAGTATCTTGAAGATCAGGGACTA K 2 1 2 1 101000 r 74 goat snp43985-scaffold595-3704897 3 25710155 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274865 Affx-1111834462 AX-519548449 3 91602712 GTGCCTGAGCTGGGCCC[A/C]AGCCTGCAGAGATCGACTGGGTCCATCCAATCCTC M 2 1 2 1 102000 r 74 goat GoatD01.036833 3 91602712 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320801503 Affx-122962889 AX-385288412 3 91627336 GATTTTGGTGACTCATTTCTCTAAGTCTTATTCTC[A/C]GTAATATCTTTTGTGAAGTAGGGCTAATAACTACC M 2 1 2 1 101000 f 74 goat snp43984-scaffold595-3668042 3 25672936 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770610 Affx-122921949 AX-385257774 3 91687660 GAAAACAATGGGTTCAATGATATCATACCTATCTA[A/G]TTCAAGTCAGGGAGATTAAAGTGCTTATCCTAGCC R 2 1 2 1 101000 r 74 goat snp43983-scaffold595-3607718 3 25610772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427555 Affx-122939491 AX-123297898 3 91726316 CAGCAGCAAAAATAAATGTAAATAAGTTAGTCTCA[C/T]GAAAACAATTTGCACTGTGATTATTAGCACATAGA Y 2 1 2 1 101000 r 74 goat snp43982-scaffold595-3569062 3 25571613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779043 Affx-122971620 AX-385266149 3 91763684 CTTTAAGGCAAGATGTGTTGCTAAGTATAAACAGA[C/T]ATTTGATAATGTTTAAAGTATTGATTCAAAAGGAA Y 2 1 2 1 101000 f 74 goat snp43981-scaffold595-3531694 3 25533756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435999 Affx-122933498 AX-123306338 3 91820783 CCAATGGAAGAAGCATTTAGAGAAAAATCTAAATG[C/T]TTTGCGTTCTGAATGCAAAGCTTCCAGGGTCCTGG Y 2 1 2 1 201000 f 74 goat snp43980-scaffold595-3474595 3 25476546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424236 Affx-122942475 AX-123294582 3 91860533 CCTGAGAGGCATAGAGCAGTTCCCTTCATCTAGCT[A/G]CTTGTTTTTTAAGTTCTTTATATGTCACAACCCCT R 2 1 2 1 101000 f 74 goat snp43979-scaffold595-3434845 3 25436178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426450 Affx-122940805 AX-123296796 3 91928599 GAGAAATAAGATGCAGGAGAGACAATAAGGGTTAA[C/T]GGCAGCAGAAAATTTACATGTGTCCATGGAACATA Y 2 1 2 1 101000 f 74 goat snp43978-scaffold595-3366779 3 25377427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273628 Affx-1111833735 AX-519547241 3 91974436 GAACAGCTTCCAGTTTCCACACCTTTTCACATGCA[A/G]CCTTGTAGCCATGCTC R 2 1 2 1 102000 f 74 goat GoatD01.003065 3 91974436 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427263 Affx-122939547 AX-123297606 3 91992725 AGCAAGATAAGAAATGGTAAAAGAAGGCATAAACT[A/G]TTTATGGTGAAAATGGAAAAGGTGATGCACGAGAC R 2 1 2 1 101000 r 74 goat snp43976-scaffold595-3302653 3 25312991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779431 Affx-122972655 AX-385266534 3 92025455 CTTTTATCCAGAATGCATAACTTTAGGGAAATGTC[A/G]TCTTCTTAAAATAAGCCACTTTTCAGTACCCTTTA R 2 1 2 1 201000 r 74 goat snp43975-scaffold595-3269923 3 25280181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445239 Affx-122925491 AX-123315576 3 92070125 TCTTTACAGAAAATGCAACTAAGGGTAATAACTCT[A/G]CAAGTAAGAAGCAGAAGCAAAATTCAAAAGGAAAA R 2 1 2 1 201000 f 74 goat snp43974-scaffold595-3225253 3 25235510 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437657 Affx-122931791 AX-123307995 3 92106304 TATTGGTTCATTGGTTCTTCTATATCCATACACAA[G/T]CTCACACACACACACACAAAATAATAATATTTTGT K 2 1 2 1 101000 f 74 goat snp43973-scaffold595-3189074 3 25199355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434146 Affx-122934908 AX-123304487 3 92193503 CAACCAATCAAAATTACAGCAAGAAATATACATAC[A/G]TATACACAGACACACACACATACATATGACATCAT R 2 1 2 1 201000 f 74 goat snp43972-scaffold595-3101875 3 25112029 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432696 Affx-122936031 AX-123303037 3 92228035 CTGAATTGGCTTTAATATTTAGGTCTATCAGTTTG[C/T]AAAGCCTATATTCTTTCCACTAAACTAATGGTCCT Y 2 1 2 1 101000 f 74 goat snp43971-scaffold595-3067343 3 25076519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796480 Affx-122969381 AX-385283430 3 92266607 GACCCTGATCTGAGTGTTAAGTTGTTCAGAACATA[A/C]TTCTCGGATCTCCTATGGGATACAGAGATGAGATC M 2 1 2 1 101000 r 74 goat snp43970-scaffold595-3028771 3 25037442 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783904 Affx-122955325 AX-385270959 3 92297040 GAACCTTTGTTTATGTTGTTCCCACTAGTGGACCA[G/T]CCTTTCTCCCCAGTTTCACATGTTGAAAACATCCT K 2 1 2 1 101000 r 74 goat snp43969-scaffold595-2998338 3 25006938 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415648 Affx-122948571 AX-123285997 3 92358697 CCTACCTGCTCCTTGGAATTTTCACCTGGAGCCTG[A/G]CTGTACGTTAATGACATGTTTATGTGACTGTCCAC R 2 1 2 1 101000 r 74 goat snp43968-scaffold595-2936681 3 24944827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389157 Affx-122968535 AX-123259515 3 92394866 AGTAAGTCAATCTGCCTTACTGATAGACCCCTGTC[A/G]ACCCCTAAAGGAAGGTGAACTTGCCACAACCAGTT R 2 1 2 1 201000 r 74 goat snp43967-scaffold595-2900512 3 24908534 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383560 Affx-122972605 AX-123253918 3 92437208 ACGTGCTATGAATGTACGCACAAATGCTTGATATG[C/T]ATAGAGCATCTGAAAAGATACATAAGAAATATAAC Y 2 1 2 1 101000 f 74 goat snp43966-scaffold595-2858170 3 24865955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396509 Affx-122963524 AX-123266864 3 92469643 CCTCAGAGGGAAATCTAACTTCTCAGGGATGTGAG[C/T]GCTGCCAACCCGTCTCCTTCTCCAGCCTCATTTCT Y 2 1 2 1 101000 f 74 goat snp43965-scaffold595-2825735 3 24833505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449861 Affx-122922369 AX-123320196 3 92517445 GTCTTTTAAGGCAAAACCTTTGGGGTTACCATTAA[C/T]TCCATTTATTTTCCTTCTCTTCTCTAGACATTTTC Y 2 1 2 1 101000 f 74 goat snp43964-scaffold595-2777933 3 24785761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390724 Affx-122967924 AX-123261081 3 92548939 AAGAAGCACTCCCCTTCTTAGTGCTTCTTAAGAAT[A/G]CAATTGCAGTGGTCCAGCTCTTTGTTGCATGAATT R 2 1 2 1 102000 f 74 goat snp43963-scaffold595-2746439 3 24754268 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391860 Affx-122966987 AX-123262217 3 92587541 AATATAAAGTTGTAATCTTTTATTTTGCCTCATGA[C/T]GTAAATACTGATGGTGTAAACTAGGTTAAGATACA Y 2 1 2 1 101000 r 74 goat snp43962-scaffold595-2707837 3 24715682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783578 Affx-122922619 AX-385270639 3 92626068 TCTCCTTCCTGTCTTCCTTTTCAAGCTATGTACCT[A/G]TATGAAATACTTTCCACTCTCCAGAACAAACCCTG R 2 1 2 1 101000 f 74 goat snp43961-scaffold595-2669310 3 24676736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454108 Affx-122919358 AX-123324441 3 92682548 GGGGGAAGTGATCAGAGTAAACTTAAAATTTAGCA[A/G]TTTGTCCTCTAGTAACAAATAGTGTCATGCAGAGT R 2 1 2 1 101000 f 74 goat snp43960-scaffold595-2612830 3 24620121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407897 Affx-122954397 AX-123278248 3 92726151 TCTGTTTAGAGATACACACTTGGGTGATAAAACCA[C/T]AAAGAAACATATAGACGTGATTGTGTGTCCTTGGT Y 2 1 2 1 101000 f 74 goat snp43959-scaffold595-2569227 3 24581630 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431261 Affx-122937118 AX-123301602 3 92756680 CTTAGAGTAAAGGGTCTGAATCACCATTTTAAAGA[C/T]GAATAAAACTGAGTCTCATAGAAGCACTGTTACAC Y 2 1 2 1 101000 f 74 goat snp43958-scaffold595-2538698 3 24550910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449612 Affx-122923203 AX-123319947 3 92848267 AATGCCAAAACTTACCCAGATAAATTGTTACTAAT[C/T]ATTCCAGATTTAGCTCTTTGTAGCTCTGAAAAGAT Y 2 1 2 1 101000 r 74 goat snp43957-scaffold595-2447111 3 24457883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777718 Affx-122950583 AX-385264837 3 92906610 TTATTGCATTAATGAACACCATTTGGTCAAATAAT[A/G]GAAATCCATAACTTTCTATCTCCTTATTTTTATTT R 2 1 2 1 101000 r 74 goat snp43956-scaffold595-2388768 3 24399004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409533 Affx-122953614 AX-123279884 3 92946695 TTCACAATACAGCTCTATCCCCTATTATCTGTGTG[A/G]CCGTAGACTAGATATGGTGCCTCAAATATTTCAAT R 2 1 2 1 201000 r 74 goat snp43955-scaffold595-2348683 3 24358458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421394 Affx-122943986 AX-123291741 3 92999226 GAGAAAGGTCTTTCATATAGAAGGGGCAGCATGAA[C/T]AATAAATGAATCATAAAGGATTAATCTCAAATTTC Y 2 1 2 1 101000 f 74 goat snp43954-scaffold595-2296152 3 24304803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400867 Affx-122959768 AX-123271221 3 93034131 AATGGAAACAGGCATATAAGGTGTTTGTATTCCTG[C/T]TTGGTTTTAGTTCAGTTAGCTGACCATCATTAATA Y 2 1 2 1 101000 r 74 goat snp43953-scaffold595-2261247 3 24268368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381989 Affx-122974087 AX-123252347 3 93087569 AGGTTCAATCAGGCCCCCACCTGCTGTGGTACACT[A/G]AGAATCTTAATCCAACAAATTGCTTTAAAATACCC R 2 1 2 1 101000 r 74 goat snp43952-scaffold595-2207809 3 24213902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410666 Affx-122952760 AX-123281016 3 93140340 GACACTGCTTTATATATGTCATATTTTCATATTTA[C/T]ATCATATTCAAATTCACACAACTATCTTGTAAGGT Y 2 1 2 1 103000 r 74 goat snp43951-scaffold595-2155038 3 24160488 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431288 Affx-122937096 AX-123301629 3 93175103 ATTAAAATAAATAAATTTATATTTTAAAAAAATAA[G/T]AAAATTTAAAAAAAATGAAATGCTGCCTCCACTGG K 2 1 2 1 303000 f 74 goat snp43950-scaffold595-2120275 3 24125733 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405573 Affx-122955947 AX-123275925 3 93240915 GGATTCTAAGTAGAATTCAGGCATCTTAACTCCCA[A/G]TTCTGGGCTCCTTCCTACCTCTTCACTAGCCAAAC R 2 1 2 1 101000 f 74 goat snp43949-scaffold595-2054463 3 24061940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396711 Affx-122962814 AX-123267066 3 93278160 GTAAACAGATACAGTGCCCCACCAGTGGGTGCCAC[A/G]TCACTAGAAGCACTCAAACAGAAGCTGAACACCCT R 2 1 2 1 101000 r 74 goat snp43948-scaffold595-2017218 3 24024683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429053 Affx-122938302 AX-123299395 3 93308753 CTCAGGATGCTTCTCTCCCTCATGCTTTTCTGTGC[C/T]CCTCCCCTACCCTGTCAAATGCTAAGACTTGCCCT Y 2 1 2 1 201000 r 74 goat snp43947-scaffold595-1986625 3 23993976 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413985 Affx-122950287 AX-123284334 3 93358363 GCCAGTGCAGGGGAGCGATCCAGAGGTCACCTGTA[A/G]ATGGTTATCAATTTCTGGCTCTGCCTAAAATATAG R 2 1 2 1 101000 r 74 goat snp43946-scaffold595-1937015 3 23944078 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793700 Affx-122930024 AX-385280672 3 93395171 TAATTCATACCAAAGAATCTCAGAAATGGAAAGCA[C/T]TGGAAGTACTTGGGATGCCAGTCTGAGCTTGGTTC Y 2 1 2 1 101000 r 74 goat snp43945-scaffold595-1900207 3 23907313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782180 Affx-122955168 AX-385269258 3 93436125 AAAATGTCTCACCATCAGTGGAGATCCCACATCTA[C/T]TTGAGAACCTTTAAAACGTGAGTGCAATCACAAGA Y 2 1 2 1 101000 f 74 goat snp43944-scaffold595-1859253 3 23866244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464244987 Affx-1110385057 AX-515719609 3 93452848 GATAGGCTTGTACTTGGAGAGCCCTTGGGAGGATG[G/T]TCAGGAGCAAGGCTGCAGTTATTGCATAGGGCCAC K 2 1 2 1 101000 r 74 goat GoatD01.032672 3 93452848 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446988 Affx-122924642 AX-123317324 3 93481088 GGACACTAACCCAGGTTTCTCTAGACCATGTTGTA[C/T]TTCGTTTATTCATTCAACAAATGCCACACACTAGC Y 2 1 2 1 201000 f 74 goat snp43943-scaffold595-1814290 3 23821463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417762 Affx-122947405 AX-123288110 3 93510491 CATCACTGCTACCAGCACTTCCTAACCTTCTGATC[G/T]CTATCTCTTGAATTAATACCTGCATACTCTCTATG K 2 1 2 1 201000 r 74 goat snp43942-scaffold595-1784887 3 23791797 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431921 Affx-122935993 AX-123302262 3 93547920 AGGGCACAGAGTAGCAGCATAAGAAGTGAGCCAAA[C/T]GACATAGTGAGTGGGTGGGCAGATGATGTCAGTGG Y 2 1 2 1 101000 f 74 goat snp43941-scaffold595-1747458 3 23754897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441352 Affx-122928876 AX-123311689 3 93577776 AGGAGCTCACCTTCTCTTTTCCCTTTGGCAGAATT[A/G]CCTTTTGCTTCCCTTGAAAGAAATGGCAACCCACT R 2 1 2 1 201000 f 74 goat snp43940-scaffold595-1717602 3 23725233 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278164 Affx-1111836204 AX-519551653 3 93630347 GAGAGTGGGGGGCAGGCCGTCCACCTAACTTGTAA[A/C]ACCCAGCTTGACTCCTTGAATTTATATCCCAATCA M 2 1 2 1 101000 r 74 goat Random2.2K-367 3 93630347 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422088 Affx-122943585 AX-123292435 3 93645465 TAAGTTTACAAACATTGTTAGCAGCTGAGCCTATT[C/T]TTCAAACCAAGTCTATGAGGAAGGCCAGTAAGTAG Y 2 1 2 1 101000 f 74 goat snp43939-scaffold595-1649913 3 23657044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409880 Affx-122952908 AX-123280231 3 93689765 GGGGCATTGATTCATGCTCACTGGAATGCGTATTT[A/C]TTATGCATTTGAATTTGCCTTATCTATACTCAGTG M 2 1 2 1 101000 r 74 goat snp43938-scaffold595-1605613 3 23612052 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401425 Affx-122958998 AX-123271778 3 93733199 CTTTCCATTGCAACCTCCTCTATTCCCTGCCCCTA[C/T]GGGATCTAATACTCGCTTATCCTTCCCCTTTCTGG Y 2 1 2 1 101000 r 74 goat snp43937-scaffold595-1562179 3 23569065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272073 Affx-1111833405 AX-519545837 3 93740688 GGGTGTGTGGTGGAGCTTTGTACTGTTTTCTGATC[A/G]CAGAGATACTTTAGCCATTACAGGGCATCCAGAAC R 2 1 2 1 101000 r 74 goat 3_93740688_AF-PAKI 3 93740688 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403295 Affx-122957846 AX-123273648 3 93774072 CATACAAGAGGAGCTATGAACCACATTTGATATTG[C/T]GATGATGTTGTTTAATTGATGAGGAAAGTCAAGTA Y 2 1 2 1 101000 f 74 goat snp43936-scaffold595-1521306 3 23528232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401082 Affx-122959631 AX-123271435 3 93807362 AAAAACAGTAGTGAAATGTTGGAAGGGAGGGGTAT[C/T]GATAGGAGGGAAAATTCTTCCTGATAGCAATAAAC Y 2 1 2 1 101000 f 74 goat snp43935-scaffold595-1488016 3 23494804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387008 Affx-122969939 AX-123257366 3 93837698 CTCCTGCCTTCTGTCTCCCATTCCATCACACTCTG[C/T]GCTCTGACCATGAGAAGCCACTTCCAGTTCCCCAA Y 2 1 2 1 101000 r 74 goat snp43934-scaffold595-1457680 3 23463397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386795 Affx-122970914 AX-123257153 3 93866487 AAAGTCTTATCTCATTTGACACCAGGGATCACTCC[A/G]TACTTCTTGAAACTCACACAAATGGATCGCTCACA R 2 1 2 1 101000 r 74 goat snp43933-scaffold595-1428891 3 23434546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417855 Affx-122946776 AX-123288203 3 93911698 CCTTCCCTCTTGAGGTCCATCCTGGCAGCGATTCT[A/G]CCCAAATATCCATTAGTTCATGCAGCAAACCTTCC R 2 1 2 1 101000 r 74 goat snp43932-scaffold595-1383680 3 23389298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431230 Affx-122937143 AX-123301571 3 93961663 GACCAGGCTCTCCTGCCTGTGTGCAGTACGCATTA[C/T]GATATCCATTTTACAGAGGAGAAAAGAGAGGCTGA Y 2 1 2 1 101000 f 74 goat snp43931-scaffold595-1333715 3 23338982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403745 Affx-122958012 AX-123274097 3 93991763 AACCAAATTCTGGAGAGATGTGCAGACTCAGAAAT[A/G]ACCAAAGGAATTAGAATGAGGTACCAATTTTCACT R 2 1 2 1 201000 f 74 goat snp43930-scaffold595-1303615 3 23309405 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386642 Affx-122970215 AX-123257000 3 94029226 TCTCCATTCATGCACTGCTGCTGACTGTTGCTGAG[C/T]GGGATGCTTTATGCAATCAGAACAGATTCTACCAG Y 2 1 2 1 101000 r 74 goat snp43929-scaffold595-1266152 3 23271713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416917 Affx-122948051 AX-123287265 3 94070259 AGGCTCAATGTTTTCCCTCTGGTGGTTTTAGGACC[A/G]TGGGGTCCTTGCAATGGGGGAAGACACATTCAATA R 2 1 2 1 101000 f 74 goat snp43928-scaffold595-1225119 3 23231181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403373 Affx-122957788 AX-123273726 3 94107052 ATCTGTGCCTTCCCTCTTCCTCGGCCCCGCCACCC[A/G]CCTAGGATCCTGAAGAGTTCTCTCATTTGCCCCGT R 2 1 2 1 201000 r 74 goat snp43927-scaffold595-1188326 3 23194089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785326 Affx-122945599 AX-385272371 3 94150701 TCCTCTTACCTCTATGGGTAGATATTTTTGTCTTC[A/G]GGATGTTCACTGCTATTAATACAACCCCTGTGCTT R 2 1 2 1 101000 f 74 goat snp43926-scaffold595-1144677 3 23149565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385306 Affx-122971679 AX-123255664 3 94199811 AAGGTAAACAGACTGACCTCTGGGCTTGTGAACTA[A/G]TACAGAGCAAGCCCGGCACTGTTTATGGAGATTTG R 2 1 2 1 101000 r 74 goat snp43925-scaffold595-1095567 3 23100139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790361 Affx-122954281 AX-385277364 3 94254550 AAAAAATAAACATGGAAAGGGGAGGGAAAATGAAG[C/T]ACCACATTTTCCATAAGCAAGTAGAAATTAAACAC Y 2 1 2 1 101000 f 74 goat snp43924-scaffold595-1040828 3 23044316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794775 Affx-122922848 AX-385281735 3 94313884 CTACAACAGAGGCATTCAGGTTGTGCTGTAAGAGT[A/G]TTATAACAAGATAATCCAGTCAGGGAGTCAGCAAA R 2 1 2 1 101000 f 74 goat snp43923-scaffold595-981494 3 22984314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402843 Affx-122958254 AX-123273196 3 94361066 CCCCCTTTTCCCTTGGACATGTGCTTCCCTCCTTT[C/T]TACACAGTAAATTACTATCCACCTTCAGAGCTCCA Y 2 1 2 1 201000 r 74 goat snp43922-scaffold595-934312 3 22937184 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434322 Affx-122934744 AX-123304663 3 94392829 TGAAACACTAGGCTAGAGAGGTAGAACTGAAGACT[C/T]GAAGAGCCTCAAACACAGAAAAGGTCCTTATCAAG Y 2 1 2 1 101000 f 74 goat snp43921-scaffold595-902549 3 22905203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274354 Affx-1111834151 AX-519547949 3 94406262 GC[A/C]GACTGGATATAGAAATAACTGGGAGCATTATAATC M 2 1 2 1 101000 r 74 goat GoatD01.021831 3 94406262 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408046 Affx-122954282 AX-123278397 3 94487857 CTTGGTCTACCTGTAGGGCAGCCTCACACAGAGCA[C/T]GCATTGCCTCCAGATCTCAGCTCACCACTGTGTCT Y 2 1 2 1 101000 r 74 goat snp43919-scaffold595-807521 3 22793896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402050 Affx-122958728 AX-123272403 3 94527277 TTTTCTGTAAAGATAAAACTGCTTTAGAAAAAAAG[A/G]AGTAAAATTTAAAAAGTCAATGAGGATAAAAAGTA R 2 1 2 1 303000 f 74 goat snp43918-scaffold595-768101 3 22752789 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391604 Affx-122966597 AX-123261961 3 94559462 GGAAGAGGTGGTAGAATGGAGTTCAGTAGCAAAGA[C/T]ACGAACAGGATGGAACCCACATGCATGGACTAGAC Y 2 1 2 1 101000 f 74 goat snp43917-scaffold595-735916 3 22720527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791660 Affx-122957640 AX-385278651 3 94627299 AGGGCTTATCTTGCCTCAAAACCCTCTCTGACTTT[C/T]AATACTGATTTCCTAGAGGCCTAGGACCTTGGAAA Y 2 1 2 1 101000 f 74 goat snp43916-scaffold595-668079 3 22651673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417949 Affx-122946705 AX-123288297 3 94658879 GCATGCTTTTTCTCAAAGCTGTGTGCCTGGGTTCT[A/C]GACAAGACGGCTCTAGAATTAAACAGATTGAGTAC M 2 1 2 1 101000 r 74 goat snp43915-scaffold595-636499 3 22620059 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446036 Affx-122925847 AX-123316373 3 94695090 ACTGGTGTAGAGAACTGAGTTAAATGAGATAACTC[A/G]TGTGAACATGGTCCACACCCAATCGGTATGCGAGA R 2 1 2 1 101000 r 74 goat snp43914-scaffold595-600288 3 22583863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451164 Affx-122921352 AX-123321498 3 94724206 TGAGGGAGACCCTGGGAATGATCATGGATGACTCA[A/G]TGTAACCCATCTCTACAGCTGAAAAGACCACAGGA R 2 1 2 1 101000 r 74 goat snp43913-scaffold595-571172 3 22554765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433941 Affx-122934287 AX-123304282 3 94784549 CTGGTTCTACTGTTGACCTGTTTTGTGGATAAAAG[C/T]CACAGTGGCTCTGAGAAGTTAAGTAACTCAACCTT Y 2 1 2 1 101000 f 74 goat snp43912-scaffold595-510829 3 22494275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777664 Affx-122942395 AX-385264783 3 94863569 AAGTACAGAGAACCTAGCAAATGCTTGTATTTACC[A/G]CTGAGATTTAACACACATTGATCTTCTGTCATCTT R 2 1 2 1 101000 f 74 goat snp43911-scaffold595-431809 3 22415856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412774 Affx-122950504 AX-123283123 3 94901080 GTGGGTGGTGCCATGAAGGCTCTCCTACTTGGGGA[A/C]ACAAGGGCAAGAACCCCTTAGACCCCAGGTTCAAG M 2 1 2 1 201000 f 74 goat snp43910-scaffold595-394298 3 22378335 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437067 Affx-122933084 AX-123307405 3 94933191 GCTCAGCATGAACAGAGTTGTGTTAGGAAATCCTG[C/T]GGGACTGGGGGAATCCCAAAGCGGAGGTCCAGGCA Y 2 1 2 1 101000 f 74 goat snp43909-scaffold595-362187 3 22346595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381365 Affx-122974403 AX-123251723 3 94987222 AAAATGCTGGGCTGAGAGGCTCAGCTCCAGGGTCA[C/T]GTTGCTTAGGAAAAGTGAGAGTGACCACCATTAAT Y 2 1 2 1 101000 r 74 goat snp43908-scaffold595-308156 3 22293928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386070 Affx-122971457 AX-123256428 3 95067190 ATTAAAAATCTAAGCAAATAAATGAAATTGAGGTC[A/G]CACTTTCCTTATTCATAAGCATCTCATTTAAAAAT R 2 1 2 1 101000 r 74 goat snp43907-scaffold595-228188 3 22215352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445241 Affx-122925489 AX-123315578 3 95113344 GGATTGGAATTCCAGTTACTGCACTTGACTGTGTG[C/T]GGCTGTGCACAAGTTACTAATCTTTGTGTGCCTGA Y 2 1 2 1 101000 r 74 goat snp43906-scaffold595-182034 3 22169083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402460 Affx-122958607 AX-123272813 3 95144888 AACAAAATAAAGCCTTGACTGGAGGGCAGGAGGCA[C/T]GGTCCAGAGGCCCAGCTCTGTCACAGACCTGCTGT Y 2 1 2 1 101000 f 74 goat snp43905-scaffold595-150490 3 22137413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409561 Affx-122953592 AX-123279912 3 95188532 CAGTCATCAAAGTTAGAGGCTTAGAGCGGTGAGAA[G/T]CCTTGTGGTTCCAGGTTGTCCTTCCTTCTGTACAT K 2 1 2 1 101000 f 74 goat snp43904-scaffold595-106846 3 22093980 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446874 Affx-122925239 AX-123317210 3 95231027 AAATTTTATGTTGTATTTTCATTATCATTCAATGT[A/G]CATGCTTTCTTTCCACTCAGGTCTGTGCTTAACTG R 2 1 2 1 103000 r 74 goat snp43903-scaffold595-64351 3 22050912 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399224 Affx-122960594 AX-123269579 3 95311827 TTTAAAAAGTCTGGTGCCAGGGTGGGCCAGACACT[G/T]TCATACATGATCTCATTTGAATCTTATAACAACAC K 2 1 2 1 101000 f 74 goat snp5260-scaffold1181-397294 3 21970295 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388540 Affx-122969192 AX-123258898 3 95344670 TACTTAGATTTATAAAAGTGATTCGGTTAGTGTTT[C/T]AGTAATACTTCAAAATGTTTCTGTTTATTTTTTAG Y 2 1 2 1 101000 f 74 goat snp5259-scaffold1181-364451 3 21937557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384592 Affx-122972986 AX-123254950 3 95400318 TCTTAGAACTCTGCTTTTAACAAGTAACTCTCTTA[C/T]ATACAATATCTCAATGGATCTCTGTTTTCTATTAC Y 2 1 2 1 101000 r 74 goat snp5258-scaffold1181-308803 3 21881519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577586 Affx-1248697226 AX-579216003 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 4 1 2 1 500000 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG 5 indels body size 0.476 neutral SV-TF-chip candidate gene ou candidate region SPAG17 562165375 Affx-1248697226 AX-606940786 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562165770 Affx-1248697226 AX-606941179 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562165780 Affx-1248697226 AX-606941189 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562166002 Affx-1248697226 AX-606941411 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 r 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 38448146 Affx-122924279 AX-123318482 3 95555443 CATTTATTAGAAGCAGAATACATGTGAAAGAACAC[A/G]TGGGTGGGCTCAGAGAGTCGTGTTTTGGGGGTGAC R 2 1 2 1 201000 f 74 goat snp5254-scaffold1181-153678 3 21725993 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797705 Affx-122935376 AX-385284644 3 95584866 TAATAGAGCTACTATTATTAACCATGGAAACTAAA[G/T]CAATTGAAAAATGGAAGCAGTAACATGTTTATAAT K 2 1 2 1 202000 r 74 goat snp5253-scaffold1181-124255 3 21696060 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406163 Affx-122956167 AX-123276515 3 95711606 GAGGGCCCAGGAGCCAAAGAATGCAAGGATTGCAG[C/T]GCTAGATGCAGAAAAGGCACAGAGTGGGACCCTGT Y 2 1 2 1 101000 f 74 goat snp17513-scaffold181-931146 3 21492044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786702 Affx-122933100 AX-385273734 3 95776414 ATAGAATTTTCTGAGAGTTCAATAAAAGAATTTGC[A/G]TGTAGTATTAGCTCAGTATCTGAACACATCAAATG R 2 1 2 1 101000 r 74 goat snp17511-scaffold181-866338 3 21426270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415073 Affx-122949468 AX-123285422 3 95806065 AGTTCTGACCATATCTGTTGCAGCCTTGGCATTTT[A/G]TTAAGACCAAAAAATTTCTGGCCCCATATCTCACT R 2 1 2 1 201000 r 74 goat snp17510-scaffold181-836687 3 21396003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447522 Affx-122924062 AX-123317858 3 95855611 AGTATTTCTAAGGGTACTCCAGGAGCTGGAAAGGA[C/T]ACACAGATTGGTGTTTCGGACTTCCGGGGCAGGAT Y 2 1 2 1 201000 f 74 goat snp17509-scaffold181-787141 3 21346008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793338 Affx-122930439 AX-385280316 3 95928233 GTCATTCTTTGCCAGATCTTGCTAGGTAAATATAA[A/G]GAACCACCAGAGGGTACTTTGATCACATCTGATGT R 2 1 2 1 101000 r 74 goat snp17507-scaffold181-714519 3 21273172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437034 Affx-122933113 AX-123307372 3 96009785 GAAAACCCCACCATCAGAGGGAGACATTGTGTTCA[A/G]AAGAATCAGGCCAAGTCCTGGATGGTTCCCTCGTG R 2 1 2 1 201000 r 74 goat snp17505-scaffold181-632967 3 21191756 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391018 Affx-122966882 AX-123261375 3 96089956 CAGCCCCACGGGGAGCTCATCTCTCCATTTATTAA[C/T]GGGCACTGGATGCGTGCTGTGGAGTGGAGGTGGGA Y 2 1 2 1 101000 f 74 goat snp17503-scaffold181-552796 3 21111062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448161 Affx-122924267 AX-123318497 3 96132466 CTCACTCTATAGAATGAGCTTCACTCCTCCCATTT[A/G]CAAGTGAGGAAACTGAAGGGAAGTGAAATGACCTT R 2 1 2 1 101000 f 74 goat snp17502-scaffold181-510286 3 21068194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411738 Affx-122951514 AX-123282088 3 96201921 GATCTTAACCTCTGGGAAGTTCAAAAATGTATTCA[C/T]GGAGTCCAGGAACCTCCTGAAATTGAAAAGTTGTT Y 2 1 2 1 101000 f 74 goat snp17501-scaffold181-440831 3 20998727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390008 Affx-122968040 AX-123260365 3 96241073 TCTTGGCCTGGAGAATCTTTCACTAAATTGTGTTT[A/G]TAGCGCTGGCATTTTATGTGGCCAAATGTGTCTAT R 2 1 2 1 101000 f 74 goat snp17500-scaffold181-401679 3 20959314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272238 Affx-1111833406 AX-513054855 3 96245599 GTACGTAATGAGAAACGCTGGGCTGGAAGAAGCAC[A/G]AGCTGGAATCAAGATTGCCGGGAGAAATATCAATA R 2 1 2 1 303000 f 74 goat 3_96245599_AF-PAKI 3 96245599 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394052 Affx-122964985 AX-123264407 3 96270797 TCCCAGAGGTACCACCATCCTAACTATGTTCATCA[C/T]CCCTTGCTTTTTGTGATAGTTTTACCGTATGTATA Y 2 1 2 1 101000 r 74 goat snp17499-scaffold181-371955 3 20929572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403017 Affx-122958560 AX-123273370 3 96322194 TCACTCTGCAAACTTTAGCTCAGGGCAGAGAAAGA[A/G]CTAACTTAGAATGTCTTGCTTTGGAAACTAACTTT R 2 1 2 1 101000 r 74 goat snp17498-scaffold181-320558 3 20877710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408580 Affx-122953661 AX-123278931 3 96399403 AACACAAAACTGGCTTTAGCCTTTGGGGAAGGATC[A/G]CTGGACTCAATTCCCCTCTTTTTCTTCCTTTCTTA R 2 1 2 1 101000 f 74 goat snp17496-scaffold181-243349 3 20802795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411647 Affx-122951571 AX-123281997 3 96431938 CAAACTCTTGCCCACCTTCTCAAGTTTCCCTAGGG[C/T]ATACACTATGTCAGATACTTCTAAACTATCTTCTA Y 2 1 2 1 101000 r 74 goat snp17495-scaffold181-210814 3 20769991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405000 Affx-122956388 AX-123275352 3 96464065 AGGTGAAGAGACATAAAAATCAACTGGGGAGGTTA[C/T]AAATGCAGATTCCTGAACCCTACTCCATTGATTTT Y 2 1 2 1 101000 f 74 goat snp17494-scaffold181-178687 3 20737431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778366 Affx-122926066 AX-385265481 3 96493936 TTTACCATACTTCAACTAATTTGATCTGAACTTTA[C/T]GAGTGGTTGATTTTCTATTAATCAATGTAGAAGTT Y 2 1 2 1 101000 f 74 goat snp17493-scaffold181-148816 3 20707461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410188 Affx-122952584 AX-123280538 3 96528053 TTGCTGTCAGATACTGGAAGTCTTCTCGTATGTAA[C/T]AGATGCATAGCTTTTCTGTCCCCTAAAAGGCAGAC Y 2 1 2 1 101000 f 74 goat snp17492-scaffold181-114699 3 20673827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422296 Affx-122943481 AX-123292642 3 96571122 GAAAAGTGTAGTGGCAATACAAGAAATAGTCAAGA[C/T]AGTGACAAAAGTTATTGCAAGATGGCACACAATAA Y 2 1 2 1 101000 f 74 goat snp17491-scaffold181-71630 3 20630635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399513 Affx-122961162 AX-123269868 3 96603895 TGTGTGGGGGAGGGGATTTGACGCTTGTCACTGAG[A/G]AGGAACGAGGTGCTCCCTGGGACTCTGATTTGTTC R 2 1 2 1 101000 r 74 goat snp17490-scaffold181-38857 3 20598001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402826 Affx-122958266 AX-123273179 3 96647246 CACCACTCCGCTAAACCAGGTTTCTCTCAGTCCAG[C/T]GTGAGTACACAATCACTGCCTCACATCACAGCCAC Y 2 1 2 1 101000 r 74 goat snp41820-scaffold545-4395 3 20554328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787118 Affx-122922904 AX-385274144 3 96682192 TTTATGGTCCCAAAGAGTACATGAACTCATCTTAA[C/T]GGGAACATGCTTCTGTTATCATATCCTGCAAATTA Y 2 1 2 1 201000 r 74 goat snp41821-scaffold545-39341 3 20519366 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413780 Affx-122949922 AX-123284129 3 96711777 TTTAAACTGATAAGTTTATGGTAATTTATTACCCC[A/G]TAATAGAAAACTAATACACTCAGCTACTTAGTTTC R 2 1 2 1 101000 r 74 goat snp41822-scaffold545-68926 3 20489667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278011 Affx-1111836205 AX-519551503 3 96734226 CATGATTCCTTGGTGTATAACTCTCAAACACTCAC[A/G]AACCAGAGCAGAGGTGTTGTGGGAGGGATGGAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-369 3 96734226 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396196 Affx-122963366 AX-123266551 3 96756832 GCCTGGAACATGTTGACATGCTCCATTGAACTAGT[C/T]TCCTGGGGCTTCTCAGAACGACTGCTCTAGTTCAT Y 2 1 2 1 201000 f 74 goat snp41823-scaffold545-113981 3 20443840 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278168 Affx-1111836206 AX-519551657 3 96807888 CTATACTGCCTCACCAGCCAACTGACCCCACGAGT[A/G]ATTTCTTGGGACCCAGTGGGGTCCTAGACCTGTGC R 2 1 2 1 202000 r 74 goat Random2.2K-370 3 96807888 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378269 Affx-122976880 AX-123248628 3 96810078 GTGCTCAAATATTTGCTGAATAAACCAACCTTTGA[A/G]GATGCTTGAGAAAACTTCCGGATGAAGTGAAGCAT R 2 1 2 1 101000 r 74 goat snp41824-scaffold545-167227 3 20390939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799838 Affx-122924317 AX-385286764 3 96845252 CTGTTCTTAAGCCCTGCCTTTCTACTTGTTTTAGT[G/T]TTGCTGTGAATTTATAAATAGTGAAGACCAAAGAA K 2 1 2 1 102000 f 74 goat snp41825-scaffold545-202401 3 20355923 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401957 Affx-122958798 AX-123272310 3 96951426 GAGCCGGGCCTTCGTAGGTCAGCGATTCTTGAGAG[C/T]ACCACCGACAGAAGGCACACACTTCTAGACACTAG Y 2 1 2 1 201000 r 74 goat snp41827-scaffold545-308575 3 20248678 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452235 Affx-122920789 AX-123322568 3 97005899 TTGGAGGCAGACAGCCTAGGTAGTTTGGAAAGTAA[C/T]GTGCTAATCCAGGTCAGAGGAGAGTGAAGAGAATG Y 2 1 2 1 101000 f 74 goat snp41828-scaffold545-363048 3 20193851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448280 Affx-122924178 AX-123318616 3 97038848 GGTCAGTTTCACTGCAGAGTTCACAGCTATGTTTC[A/G]TTAGGAAGTAGGCTTTGCCTTGTCAGGGGACTGTG R 2 1 2 1 101000 f 74 goat snp41829-scaffold545-395997 3 20161006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409552 Affx-122953599 AX-123279903 3 97069587 TTCTTGCTGTTGTTTTCATTTTCATTGCGCTCTTA[C/T]GATGTGCCAGGCCTTTTATTTAGGTACTGCAAAAT Y 2 1 2 1 201000 r 74 goat snp41830-scaffold545-426736 3 20130107 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396929 Affx-122963195 AX-123267284 3 97104428 AGCTCTTGGTTTCACTAAGGATCATAAAGAAAATT[A/G]CTAATTACATCAAGCACACTGCTTAGAGCTTGGAT R 2 1 2 1 101000 f 74 goat snp41831-scaffold545-461577 3 20094915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450456 Affx-122922953 AX-123320790 3 97174673 CATCACATTGATGTGGGGCCTCTTGCCAGGAGCTC[A/G]TGGAAGACAGTGACATGTGTGGTAGAAAGCACATG R 2 1 2 1 101000 r 74 goat snp41833-scaffold545-531822 3 20022189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424450 Affx-122941784 AX-123294796 3 97228915 AAGGATATGGACACATAGACGCTTTCCGTACAAAG[C/T]GACAGAGCTAGGAACACTATGCTGTCTTAGCCTAA Y 2 1 2 1 101000 f 74 goat snp41834-scaffold545-586064 3 19967898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379024 Affx-122976364 AX-123249383 3 97270781 TAGAAGGAAAACAATTTTTTTTTTAATTACACAGC[A/G]CCAGAAAACATCTATTATGAAAGAGACACTGAACA R 2 1 2 1 101000 r 74 goat snp41835-scaffold545-627930 3 19925224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781772 Affx-122973682 AX-385268854 3 97327272 TGAATTAACTTATTTATAGTAAGTTATCAGGACTA[C/T]GTGTGTTTAAAGTCTTATTATGTTGAAATTATTCC Y 2 1 2 1 201000 r 74 goat snp41836-scaffold545-684421 3 19868308 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416119 Affx-122948302 AX-123286468 3 97374853 TTTTGCATTTGGAGTAGCAGACACCTCAAATATTT[A/G]CTAGTTGCCTTCAGGCAGGATATACTGTTTGTTGG R 2 1 2 1 101000 r 74 goat snp41837-scaffold545-732002 3 19819661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430262 Affx-122937301 AX-123300603 3 97404364 AGCAGAACAGAGCAGGTTGCGTCCAGGGAGCCCTA[C/T]TGCCTCACCCTGGTCGTCCTCTTCCTCTTGCTCCA Y 2 1 2 1 201000 f 74 goat snp41838-scaffold545-761513 3 19790100 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395982 Affx-122963511 AX-123266337 3 97444122 CATTAGGGAAGACACCCACTAGGATGGCTTGGCTG[C/T]GCTATTGCACGGCTTGTGGTATGTTAGTTTCCCAA Y 2 1 2 1 201000 r 74 goat snp41839-scaffold545-801271 3 19750714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438026 Affx-122931562 AX-123308364 3 97472945 AGGGCTTCTCAGTGCAAACATGAAATCTGGAGCTG[A/C]GAGGGGAAATAAGGAGTCCTCTGCCCAGAAGCAGG M 2 1 2 1 101000 f 74 goat snp41840-scaffold545-830094 3 19721842 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768536 Affx-122978499 AX-385255716 3 97513564 CAAGGGAGTTCCATAGCGGCAACATGGAGGAATAC[A/G]TGATTTTGTCTGTTGTCATTTGCTTCATGTCATGA R 2 1 2 1 101000 r 74 goat snp41841-scaffold545-870713 3 19681242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378018 Affx-122977586 AX-123248377 3 97548920 TACTTACACCTGAGATCCTTTGTAGCACTGCGTGC[A/G]CCTGTCAAGCCCTTGAGGCTGTGTCTGCTGGGTCA R 2 1 2 1 101000 f 74 goat snp41842-scaffold545-906069 3 19645276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431569 Affx-122936190 AX-123301910 3 97595579 GAAATTCTTAATGATTCTGCCCAAGTGTTTTCTCT[A/G]TAGAACCTTCCTGACTCTTTCCGTGATTCCTCACA R 2 1 2 1 101000 f 74 goat snp41843-scaffold545-952728 3 19599119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275509 Affx-1111834847 AX-519549081 3 97632732 TATGGTTATCAGCAGAACTTATCTTAATATAGTAA[A/C]CACTGCAGGCTTTCATGTTATTAAATATCCACAGC M 2 1 2 1 101000 r 74 goat GoatD01.056320 3 97632732 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437757 Affx-122931714 AX-123308095 3 97653936 AACACAGCCAACTGGAAGCACTGTCAGAGAAGTGA[C/T]AGGACTTCAGGGCCCGAGCTCCCCAGGTACCAGAG Y 2 1 2 1 201000 f 74 goat snp41844-scaffold545-1011085 3 19540309 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392514 Affx-122966119 AX-123262871 3 97691482 GCCATGGGACCAGCAACTGATTTTTCTGGAATCTT[A/C]AAAGAATGCTTAACTGACAGAAACAATTTAACTGA M 2 1 2 1 201000 r 74 goat snp41845-scaffold545-1048631 3 19502864 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423001 Affx-122942984 AX-123293347 3 97765593 CTGAGCCTCCCTAGGCTTGCTGCTGAGAAATCTGA[C/T]GTCATTCTGATTCCTGTGCCTTTGTCTGTGGCTTG Y 2 1 2 1 101000 r 74 goat snp41847-scaffold545-1122742 3 19428646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418222 Affx-122947048 AX-123288570 3 97844380 TGCCCTTGCCATCTTCCTTTCCCTCTACTCTGCTG[G/T]CAGAAACCCAGATTGGTATTGCCCGCTCCATATGG K 2 1 2 1 201000 r 74 goat snp41849-scaffold545-1201529 3 19351212 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388773 Affx-122968936 AX-123259131 3 97904157 CCGGGAAGATGGAAAGCAGAGGAAGAGAAGGGGAA[C/T]GGGTCTGGCAGGAGGTATAAGATGAATGTCATTTC Y 2 1 2 1 101000 r 74 goat snp41850-scaffold545-1261306 3 19291620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804552 Affx-986696720 AX-385291097 3 97917691 CGTGACTGATTGTCTGCAGCGGCAGCTGGACCAGC[A/G]TTTCGACTGTGGTGACAGCAAAGCCATGCTTGGTC R 2 1 2 1 600010 r 74 goat 3_97917691 3 97917691 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 38386690 Affx-122970178 AX-123257048 3 97963917 CATTGGAGAGTTGTAAGTATGCAGAAATATGAGAA[C/T]TGCATTTTAGAAAGGGCAGGATGACTGCAGGATGG Y 2 1 2 1 101000 f 74 goat snp57206-scaffold910-1289981 3 19231991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434016 Affx-122934226 AX-123304357 3 98010026 TTGGTCTCCTCACACTGACTCACCTTAGCAAGGGC[A/C]TGCTTCAAAAATAAAGTGCTAAGGAGGACACCTCA M 2 1 2 1 201000 r 74 goat snp57205-scaffold910-1243872 3 19185914 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396685 Affx-122962833 AX-123267040 3 98042831 GGTGGGGTTAGAGGAACAAGATGCTTTCACTCCCT[C/T]TTCCATTCTGCCCTACCATCCAACCCATTCCTACC Y 2 1 2 1 101000 r 74 goat snp57204-scaffold910-1211067 3 19152554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415374 Affx-122948763 AX-123285723 3 98122998 ATACTGTAAGAGTTTAGTTACCTGATTCTCCTCTT[A/G]CCAGTCGTTTTCAGGGAGATGAGAATTTTCAGGGA R 2 1 2 1 101000 r 74 goat snp57203-scaffold910-1130900 3 19072180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431183 Affx-122937179 AX-123301524 3 98154587 AGGCAGAGACGTAATGAGCTGGAGTGGATTCTAGA[A/G]GTGGTAGGAAAGGGCTTGGGAAGGAAGAAAACACA R 2 1 2 1 201000 f 74 goat snp57202-scaffold910-1099311 3 19040670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418065 Affx-122946617 AX-123288413 3 98211068 ACTGGATGGGGATCAGTCAAGCTCCCTGGACCACT[A/G]TCTCTTTCAGCACACCCTCATGACAGGAGGTGGGG R 2 1 2 1 101000 r 74 goat snp57201-scaffold910-1042830 3 18984248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453503 Affx-122919818 AX-123323836 3 98259388 GCTCTTGCTTGCCTACTAGGATGCAGGAGCTCGAT[A/G]TCTCACTCCAGGACGTGACTTCTTGCTCTAGGGTA R 2 1 2 1 101000 f 74 goat snp57200-scaffold910-994510 3 18937163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781850 Affx-122942277 AX-385268932 3 98313265 GCAGAGTGCTTCTGATTCTGCTGAAGTGTACACAC[A/G]TATTCTTTGCACATTACATTTATACAAAAGTTAAT R 2 1 2 1 101000 f 74 goat snp57199-scaffold910-940633 3 18882405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443207 Affx-122927584 AX-123313544 3 98356402 ACCTAAAGGGTTTATGGGGGCTAGTTGGGTCTCCC[A/G]TTTCCTGGATGTCTGCCTTTGATCATGCTCTGTGC R 2 1 2 1 101000 r 74 goat snp57198-scaffold910-897496 3 18838617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778992 Affx-122967938 AX-385266099 3 98411389 CTTTGTTAATTTCTTCATTTCGCTTTTCCTTTTGT[A/G]GTTTGATGATTTTCTTCTGTAATATGCTTGAGTTC R 2 1 2 1 103000 r 74 goat snp57197-scaffold910-842509 3 18783832 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451848 Affx-122921078 AX-123322181 3 98446354 ATAGTATACCCACAGTAAATAAAAGGACATTTTTG[C/T]CAGGGTGGGAAAATAGAAGGGTTTGGGGGGAAGGG Y 2 1 2 1 101000 f 74 goat snp57196-scaffold910-807544 3 18747929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417122 Affx-122947465 AX-123287470 3 98531989 CCCCAGACCTAGAAGCCTTGAGGCCTCAGGTGCAT[C/T]CTGTTTGCTCACAGGTCTCAGGCTCAGGTGTCTGG Y 2 1 2 1 201000 f 74 goat snp57194-scaffold910-721909 3 18661955 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401934 Affx-122958813 AX-123272287 3 98570686 CGTGGTGAGGCAGGTAGACACTGTGGCCTCCTACT[A/G]CTCAACAAGTCCTCTGCTGACCCACCTTGGTGGTC R 2 1 2 1 101000 f 74 goat snp57193-scaffold910-683212 3 18623326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422305 Affx-122943475 AX-123292651 3 98610351 TCTAAGCACTGAACTTGATGGGCTCCCTGAATAAG[C/T]GCAAATAACTGGGAATTTCATGTCTGTTGGTTCAC Y 2 1 2 1 101000 f 74 goat snp57192-scaffold910-643547 3 18583543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379905 Affx-122975761 AX-123250263 3 98653959 CCCTCATTAGACTGGCTGCCTGGAAACTGGGCTCT[A/G]CCCCTCTGTTCATGCCCTGTCGAGGCCCCCTCACA R 2 1 2 1 101000 f 74 goat snp57191-scaffold910-599939 3 18539528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384364 Affx-122972236 AX-123254722 3 98717449 GGGCCATGATGAGTCCCAAGAAAGGCCTCAGGCTA[G/T]ACCATGAGGGCAGTGAAGTTGGGATCGGTCCTTTT K 2 1 2 1 201000 f 74 goat snp57190-scaffold910-536449 3 18475228 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435089 Affx-122933718 AX-123305429 3 98747328 TTAATTTTTATTCATTTATGACTTAATCAAGATTA[C/T]ATATTAGGATTCCATCACGTTGGGGGAAAGAAGGG Y 2 1 2 1 202000 f 74 goat snp57189-scaffold910-506570 3 18444571 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272077 Affx-1111833407 AX-519545840 3 98783372 ACACAAGCTTAGGCCGTGTGCTAGTGGCAACACTG[A/G]CACAGTCTCATTCCAAACCTTGGCATCATGGCTAG R 2 1 2 1 101000 r 74 goat 3_98783372_AF-PAKI 3 98783372 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426535 Affx-122940192 AX-123296881 3 98798960 TTACAGAGTGGGCCTCTTCCAGGCCTCAGTTCCTC[A/G]TTCAATAGGTGTTGCCATAACCCATGTCTCCTAAA R 2 1 2 1 101000 r 74 goat snp57188-scaffold910-454938 3 18392814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771550 Affx-122943062 AX-385258708 3 98842401 CTTTTTATCACATTTGAAGTTATTATAAGTACAGC[A/G]TCTACTCTGTACTCTGGGCCTAGAGTTTGTTTCAC R 2 1 2 1 101000 r 74 goat snp57187-scaffold910-411497 3 18349415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425376 Affx-122941567 AX-123295722 3 98881711 TGTCACTCCACTGAATGCCGATGCCTCCAGGCGCC[A/G]CACCGCCCTGTTATAGGGGGTTGTCAGCTCAAATA R 2 1 2 1 201000 f 74 goat snp57186-scaffold910-372187 3 18309716 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443463 Affx-122927827 AX-123313800 3 98939077 CTGATGGATGATGAAGCTGGCACTCATTCAAACAG[C/T]AGCTGAGGATTACTAGGATATGGACCCAGTGTGAT Y 2 1 2 1 101000 r 74 goat snp57185-scaffold910-314821 3 18252067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382378 Affx-122973854 AX-123252736 3 99051697 CATGCTCTCATAAAACCACATTCTTATCCTTAGGC[A/G]CACCTAGTTTGTATTAATATAATAATTAGAGTGAT R 2 1 2 1 101000 f 74 goat snp57183-scaffold910-202201 3 18139486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380190 Affx-122975503 AX-123250548 3 99105752 CTCCCCTGTATCTGTCCTGTGCATACCGCAGCTGA[A/G]CCCTGTTCCAGCAGCTTCCTTGCCTTTGGCCCTGT R 2 1 2 1 101000 f 74 goat snp57182-scaffold910-148146 3 18085741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441187 Affx-122929541 AX-123311524 3 99142971 GGAACGGCTAAGTCAGAAGCTCAGGTCCCAGCCTC[A/G]CCACGACCTCAGAGAGCCCTCAGGCCCTGCAGGCT R 2 1 2 1 103000 f 74 goat snp57181-scaffold910-110927 3 18048402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436541 Affx-122932925 AX-123306879 3 99176284 ACGAATGAGTGACTCACACACTCTGTACTCTCAAC[G/T]CAGTTGGTTGCTCTGCCAGCCTTCTTCAACTTCAC K 2 1 2 1 201000 r 74 goat snp57180-scaffold910-77614 3 18014645 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452813 Affx-122920750 AX-123323146 3 99245848 GGTCCTGAAACATAGGTATCAGGAATGAAACTTGG[C/T]GTGAGCTAAGATTGGTGAGGTTAGCAGGACCTGAG Y 2 1 2 1 101000 f 74 goat snp57178-scaffold910-8050 3 17944887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424587 Affx-122942211 AX-123294933 3 99280469 GAGCACCTCAAATTGAAAGGTCTCTAAGACCTCTG[C/T]GTCTCCAAAATTCTGTGTCACAGTAGGTGAAATGC Y 2 1 2 1 101000 f 74 goat snp23602-scaffold238-1302314 3 17711754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403953 Affx-122957447 AX-123274305 3 99309198 ATTGAAGAGGAACACTCAGTAGAGGAGAGCTAGGC[A/G]TAATTTCTGAAGGTGCTAGACTTGATGGGGCAGTG R 2 1 2 1 201000 f 74 goat snp23601-scaffold238-1273585 3 17682727 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424019 Affx-122942091 AX-123294365 3 99350239 GGCCTTTGTCATGACACTAATGGGGTTATTAAAGA[G/T]AAACAGCCCAGAAGACAGTTTGGAAAGTGACTCCC K 2 1 2 1 101000 f 74 goat snp23600-scaffold238-1232544 3 17641832 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783386 Affx-122969043 AX-385270449 3 99382758 ATTCTTTACATATTCTAAATATGAATCTTTTGTTA[C/T]ATGTATTTCAAGTATTTCCCCCCCTTTAACTTCTT Y 2 1 2 1 101000 r 74 goat snp23599-scaffold238-1200025 3 17609732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426452 Affx-122940803 AX-123296798 3 99411427 TTAACATGCATCATGGACCTGTGTCCTTAAAATAC[A/G]CCGGTCCATGAACAAAGGTGTATATGTTGGACTGG R 2 1 2 1 201000 f 74 goat snp23598-scaffold238-1171356 3 17581336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423425 Affx-122942613 AX-123293771 3 99462841 TGGTGAATGATATGGCAGGTGAACGAGTGAATACA[G/T]GTATGTGGTCACCTGAGCCATTTTCTTTCTCCAGT K 2 1 2 1 101000 f 74 goat snp23597-scaffold238-1119942 3 17529677 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424080 Affx-122942045 AX-123294426 3 99513129 TGAGAAGCCTTGTCATGATAAGTGGTGTGTGTCAA[C/T]AGTTTGCTGTGTGCCAGGGGCAGAGCTGAGTAACT Y 2 1 2 1 101000 f 74 goat snp23596-scaffold238-1069654 3 17479639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443467 Affx-122927825 AX-123313804 3 99553060 AGCTGTCCTGACCTCCCTGCTGGTCCTTTAACACA[C/T]CAGACATGGTCCTGCCTTTGTACCTTTGGACTTGC Y 2 1 2 1 101000 r 74 goat snp23595-scaffold238-1029723 3 17439965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451520 Affx-122921104 AX-123321853 3 99603117 GATCCAGCCCTAACTGTAGCTGGTGTCCCTTCCAT[C/T]ATTGTTTGTTGTTGTTTTCCACAAAGGATGAAGAA Y 2 1 2 1 201000 f 74 goat snp23594-scaffold238-979666 3 17388892 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784794 Affx-122972718 AX-385271841 3 99636923 TACAACATAGTCACAATATTTGTTTTATCATTTCA[G/T]TTTGTGAAAAAGAGGCTGGATAGAAACACAACAAA K 2 1 2 1 201000 f 74 goat snp23593-scaffold238-945860 3 17356281 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788180 Affx-122944427 AX-385275199 3 99668575 TTCTGGAGAATGGGAATGCTAATACTAACATTAGG[A/G]GCATTTGAGAAAATCCAGTAAGGTGACTGTAATGT R 2 1 2 1 101000 f 74 goat snp23592-scaffold238-914208 3 17324839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765078 Affx-122933443 AX-385252642 3 99732458 TTTCTAGGTACATCCAAAACCCTGTTCAGTAATCA[C/T]AGGGTCAAACATTAAGTATGGAAACATTTAAATTC Y 2 1 2 1 101000 f 74 goat snp23591-scaffold238-850325 3 17261113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416599 Affx-122947641 AX-123286947 3 99775062 TTTCCACATCATCACTGCAAGAGTACTCTCAATAC[C/T]TGGCTGACATGCCAAGCAACTGAAACCCTGACGCT Y 2 1 2 1 101000 f 74 goat snp23590-scaffold238-807721 3 17217595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451944 Affx-122920966 AX-123322277 3 99804201 GAGATATGGGCAGAGTCCAGGTGTTCCACTTTGGC[A/G]TATATTGGCGTAAATGTGGTATTTTTAGATCCTGA R 2 1 2 1 201000 r 74 goat snp23589-scaffold238-778582 3 17188087 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434744 Affx-122933912 AX-123305085 3 99852658 AGAGAGATGGTTTGCTACAGCCTTTTCTCTTGTAC[A/G]CCTAAGATGAGTAATGTTCCTTGTTGCTGAGGGAT R 2 1 2 1 101000 f 74 goat snp23588-scaffold238-730125 3 17139401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429789 Affx-122938206 AX-123300130 3 99904952 GAAAAGCAGTGAGTAGTGGGCAGGCTAATGTGGCT[C/T]GGCATCTGTCTTTCAAAGGTCTTTCAATACTCTTA Y 2 1 2 1 201000 r 74 goat snp23587-scaffold238-677831 3 17086548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390103 Affx-122968018 AX-123260460 3 99956120 GTGCAAGACTGACTTGAAGAAAAACACTTGCAAAC[A/G]CAGCTTCTCTGCTTGTTCTATTTTTCTGTGTTGTT R 2 1 2 1 101000 f 74 goat snp23586-scaffold238-626663 3 17035286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274716 Affx-1111834456 AX-519548302 3 99970177 CAACATGGGGGTTTTCACTTCTGAGAAACCGCGGC[A/G]GGT R 2 1 2 1 102000 f 74 goat GoatD01.036647 3 99970177 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779372 Affx-122973597 AX-385266476 3 99986041 GATCATGTTTGGGATGACACATATTCCTCCTAGCA[C/T]GACATGGTAGTGCGCAGCACTTGATGGATTATTAT Y 2 1 2 1 101000 r 74 goat snp23585-scaffold238-596742 3 17005342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404847 Affx-122956625 AX-123275199 3 100015933 TCAGCCGGCAGATCAGTTTGAAAGTCAATTATGCA[C/T]AGTTGTTTCATTTCCATTCCTGAAATTATCTTTTA Y 2 1 2 1 101000 f 74 goat snp23584-scaffold238-566850 3 16975367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422113 Affx-122943563 AX-123292460 3 100076003 TTAACCAAAATATTAAGCTTTGGTTCTTGTTATTC[A/G]TGCACTAAAATCCATTTATGCCAATTAAGATGGTC R 2 1 2 1 101000 r 74 goat snp23583-scaffold238-506780 3 16913410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419887 Affx-122945351 AX-123290235 3 100126947 GTATAAGGTTTATAAAGTTCTCACTCCATACATAA[A/G]ATAGTATAATGAAGGTAGAGTGTGATAAGTTAAAG R 2 1 2 1 201000 r 74 goat snp23582-scaffold238-455836 3 16862712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429330 Affx-122938585 AX-123299672 3 100158401 CTGCAGTTACTTCTCCACTGAAGTCTAGAACGCCT[C/T]ACAGCCATCCATGACGGTTAGAATTAACCTCTTTC Y 2 1 2 1 201000 r 74 goat snp23581-scaffold238-424382 3 16830260 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386693 Affx-122970176 AX-123257051 3 100189953 CCTTCTCTGTGCAGCTCTCTCATCTCTAACATGCC[A/G]CCCTGTGAACTCTAGCCACCAAGTTCTCCTGACTC R 2 1 2 1 201000 r 74 goat snp23580-scaffold238-392830 3 16799006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766689 Affx-122925689 AX-385254033 3 100218950 CTAGCAATGCTAAAGAGCAACCAGTGAGCAGTTAG[C/T]ACTCCTTGATTTCATCTAACATTTTATTTCCCCAT Y 2 1 2 1 101000 f 74 goat snp23579-scaffold238-363833 3 16770910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278170 Affx-1111836207 AX-519551659 3 100234401 CCATTCTATACATTCCAGTTTGCATCAGCTAATCC[A/C]AGACTCCCAGTCCAAACCTCTGCCACCTTTATCCC M 2 1 2 1 202000 r 74 goat Random2.2K-374 3 100234401 G T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443868 Affx-122927511 AX-123314205 3 100264624 CCCAGAACCTAATTTTGCAATGAATGATGAATATC[A/G]CATAGGGTTGTCATCAGGATTAAACAGGAAAATGC R 2 1 2 1 101000 f 74 goat snp23578-scaffold238-318159 3 16725168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446233 Affx-122925698 AX-123316569 3 100296505 TGGGCCAAGGAAGGGGGAAGAGGAAGTGAATGGCA[G/T]AGCACCCTAGGTCTCCTAGCTTCACTGCAGGGACC K 2 1 2 1 101000 r 74 goat snp23577-scaffold238-286278 3 16692635 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776876 Affx-122927996 AX-385264000 3 100343353 CCCCAAAGCACCTTAAGTTTTTCTTGCCTACAAGC[A/G]TGCTTCATCCTCATCCCTCCCTTAGAATACCTTCT R 2 1 2 1 101000 r 74 goat snp23576-scaffold238-239430 3 16646444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421827 Affx-122944310 AX-123292174 3 100386251 AGGATAAGGGGATGGGGATTTATTTACTCCTCTTG[C/T]GAGTACCCCCACACATACATCAAAGCATGTACCTC Y 2 1 2 1 201000 r 74 goat snp23575-scaffold238-196532 3 16603212 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405611 Affx-122956609 AX-123275963 3 100446217 GTCACAGGCATCAGCCCAGAGGCAAATGAAAGGAC[A/G]TTAGGAACTAGGAAGATTCTCTCCACACAGAACAG R 2 1 2 1 201000 r 74 goat snp23574-scaffold238-136566 3 16543852 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785743 Affx-122946014 AX-385272783 3 100495621 AATTTTACAACTCCCACAAAGCCTAATTTCATTTG[C/T]AAAATACACCAGGGAATCCTGGCAAGTTCCTGTGG Y 2 1 2 1 202000 r 74 goat snp23573-scaffold238-87162 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383938 Affx-122972964 AX-123254296 3 100557182 TATACACATTCACAGTGGAAAGCACTGGGCTGAGA[A/G]TGAGCAGCCCTTACCTCTAGCTCTGCTTCTGCCAT R 2 1 2 1 201000 r 74 goat snp23572-scaffold238-25601 3 16457450 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433434 Affx-122935077 AX-123303775 3 100605584 GCACCTGCTGCTGCTTCTTCCTGGAACACCCTATT[A/G]CCTTTCTCTGATGGGCAAATTCCTACTGACCTTTG R 2 1 2 1 101000 r 74 goat snp28607-scaffold3068-430703 3 16409481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278171 Affx-1111836208 AX-519551660 3 100662067 TGAGTTCCCGAGGAACTGTCCCAAGGCTTCCAGAC[A/G]GACGGGAGGATGGCATCCAGACAGGTCAGCCAGGG R 2 1 2 1 202000 r 74 goat Random2.2K-375 3 100662067 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445196 Affx-122925525 AX-123315533 3 100664105 TCCCCAAGCACAACCTCACCTGCGGGCTGAGCCCC[A/G]CTTCTCAGAAGGATGTCCACCATTTATTCCTATGG R 2 1 2 1 101000 r 74 goat snp28606-scaffold3068-372182 3 16351762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411391 Affx-122952225 AX-123281741 3 100715960 TGATAGGATGTTCAAACAACTAGCTCAGAGCACAG[C/T]AAGCATCAATTTAGTCATTCCACAAACATTAATTT Y 2 1 2 1 101000 f 74 goat snp28605-scaffold3068-320327 3 16303386 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434187 Affx-122934874 AX-123304528 3 100745676 CCTGTAGGGAAGAGTGAGGATTCCCATATTATAGA[C/T]GAGGACACTGAAGCTTGGGAGAGGCAAAGGAACTT Y 2 1 2 1 101000 f 74 goat snp28604-scaffold3068-290611 3 16273852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387091 Affx-122969874 AX-123257449 3 100776702 GTTTGATACTGTGAGTGATGCAAACCAGAATTCCC[A/G]TCTCTTCCTCCCCAAATGTCCACATAACATTAAAC R 2 1 2 1 101000 f 74 goat snp28603-scaffold3068-259585 3 16243114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799056 Affx-122971788 AX-385285986 3 100849466 AGAGGAGGAGGCTTTTATTCTAAAGGAATCAATAC[A/G]ATAACTTGAGATGCTGTGCAATGAATGACTGAGGC R 2 1 2 1 101000 f 74 goat snp28601-scaffold3068-186821 3 16170284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453206 Affx-122920445 AX-123323539 3 100899487 TGCTCTTTCACTTTCTGGAAAACCAGTCACTTCCC[C/T]GTTGTCACCTGGCCCCACCAGCTCTCAGGAAGCTC Y 2 1 2 1 101000 f 74 goat snp28600-scaffold3068-136800 3 16120618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406975 Affx-122955050 AX-123277326 3 100932354 CCAGGCAGAGGTCAGGGCAGATGAGGAGGTTTGGG[A/G]CATTTGAGGGTTCTGGAGACCCATGGGGAAGAGGT R 2 1 2 1 303000 f 74 goat snp28599-scaffold3068-103933 3 16087822 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384144 Affx-122972807 AX-123254502 3 101000851 GGGTTGGGCCAATCCTGCGCACACTTGTCCGCAGG[A/C]TTCCCTAGAGAGTGGCCCTGGTCTCTCTGCACTGA M 2 1 2 1 101000 r 74 goat snp28598-scaffold3068-35436 3 16019647 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424400 Affx-122941819 AX-123294746 3 101035027 ACTGGGCCCTGAGGCACAAACTGGAGAAGCAAACT[A/G]CACAAGGTCACAGTCAGGAGATGGGAAGGCTGGAT R 2 1 2 1 101000 f 74 goat snp28597-scaffold3068-1260 3 15985686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402745 Affx-122958329 AX-123273098 3 101082059 TGGCACTGTCTACCATGCACCTGGAGACCTGTCCA[C/T]TCGTCTCTCCCATTAGATGCGGGGCATCTCCAGGA Y 2 1 2 1 101000 f 74 goat snp14497-scaffold158-544965 3 15938867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414541 Affx-122949504 AX-123284890 3 101118053 ATGATATGATGGGCAGGTAAAAATGAGAGAGAGGA[C/T]GAGGTTGGAGAGAAGTGAGGGACGTGAAGGTGTAG Y 2 1 2 1 101000 f 74 goat snp14496-scaffold158-508971 3 15902833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428621 Affx-122938682 AX-123298963 3 101159741 CTTTTTAAGTGGTTGAAAAAAGAATATGCCATGAC[A/G]TGTGAAACTTTAATGCCAATAAAGGTTTATTGGAG R 2 1 2 1 101000 r 74 goat snp14495-scaffold158-467283 3 15862332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406022 Affx-122955495 AX-123276374 3 101246268 AAGTTTCAGTACTTCTCCAATTTAGCAGTATATTG[C/T]GACAGTTTTTGCTAAAGTAATCTACTTTTGAGATT Y 2 1 2 1 101000 f 74 goat snp14494-scaffold158-380756 3 15775363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787323 Affx-122934740 AX-385274348 3 101307931 TTGAGAGCTTAGTATATGCTAGATGTTGTTCTAAT[A/C]CGTGAACTCATTTAACTCCTTACAATAATCACGTG M 2 1 2 1 101000 r 74 goat snp14493-scaffold158-319093 3 15713913 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272175 Affx-1111833371 AX-519545928 3 101341578 CTCAAACCTTGAGCTAACCAATGTGTTTTTCTTAC[A/G]GAAATGTTTTTCATTAAGCTATGCTAATGAACTAT R 2 1 2 1 103000 f 74 goat 3_101341578_AF-PAKI 3 101341578 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789858 Affx-122920419 AX-385276865 3 101350037 GTAGAGAAAAAGTGAGGGAAAATCATTGATAAATT[C/T]AAGAAAGTTTCAAGAAACCAAATGATGGAATGGGC Y 2 1 2 1 101000 r 74 goat snp14492-scaffold158-276987 3 15672032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781893 Affx-122961034 AX-385268974 3 101381542 AGGCCCTGAGACCCTTCTTCACTCAAATCTTAAGC[A/G]TAGGTCTGATTCTGGAAATGGTCAGAAGGAATTTT R 2 1 2 1 101000 r 74 goat snp14491-scaffold158-245482 3 15640013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409485 Affx-122954055 AX-123279836 3 101431782 GAGGAGTCCAGGGTGACTAGAGGCTGGCATGAGTC[A/G]TGTGGCCAGAGGGTTGTAAACTGAGGCCAGCTTGT R 2 1 2 1 101000 r 74 goat snp14490-scaffold158-195242 3 15590151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444858 Affx-122926290 AX-123315195 3 101462307 GAAGCTGGTCCAGGCGAGAGAAGCTGGTGCTTAGC[A/G]TGGGGTGCTGGCTATGGGGAAGGAGAGAGATACAT R 2 1 2 1 201000 f 74 goat snp14489-scaffold158-164717 3 15559576 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384106 Affx-122972835 AX-123254464 3 101503398 CCTGAGTGTGACTCTTTGCATCATAGACAGAATGA[C/T]AGGACTGGAAGGTCATTATGCCCCAGTGCCCTCTA Y 2 1 2 1 101000 f 74 goat snp14488-scaffold158-123626 3 15517713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274022 Affx-1111833991 AX-519547626 3 101521601 GTGACACATCTTTCAGTTTGCTTTTCATCTCAGCA[A/C]CAAATGTGACCCTTGTTTGTGGTCAGAGCAGGAAA M 2 1 2 1 101000 f 74 goat GoatD01.012998 3 101521601 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443152 Affx-122928063 AX-123313489 3 101538661 ACGACTGAGTGGCTGAACTGAACTGAACTGAAGCT[C/T]TCCCTAAGACCCTAGGTGCTGGTTGGGAAGACCTT Y 2 1 2 1 101000 r 74 goat snp14487-scaffold158-88363 3 15482609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427288 Affx-122940566 AX-123297631 3 101606209 AGCCCCTCTTCCCTCCTCATTCCCACCCTTGCTTG[A/G]TGTGTTGCTCAGTGCACTTACCTGGTGCGCCAAGT R 2 1 2 1 201000 r 74 goat snp14486-scaffold158-20815 3 15414967 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396464 Affx-122962969 AX-123266819 3 101629223 AGGGCCTTTCCCCAGCGCAGCCTTTAGTGACTAAG[A/G]CACTTTTCCGAGCCCACAGCTGTCTCAGGTGCTCT R 2 1 2 1 202000 r 74 goat snp16199-scaffold1704-2100 3 15390350 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442471 Affx-122927938 AX-123312808 3 101659763 TCAACCCAAGTAAATCCTCTCACAAACATAAGCTG[C/T]GTAAAACAACTCACAGACTGAAAAGTTAGAACAAG Y 2 1 2 1 101000 f 74 goat snp16200-scaffold1704-32640 3 15359969 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440281 Affx-122930231 AX-123310618 3 101710242 GCTGAGCCCTGAAATCCATGCTACACTCTGAGATC[C/T]ATTGCCCTTCACCCCCAGGCCTCACTTCCCACAAG Y 2 1 2 1 101000 f 74 goat snp16201-scaffold1704-83119 3 15310434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451215 Affx-122921967 AX-123321549 3 101744676 AGAGTCAGGCTTTATCTGACCCTTTTGGTTTACAC[A/G]CAGATGAGGAACCCAGGCCCAGAGAAGGTCACACA R 2 1 2 1 101000 f 74 goat snp16202-scaffold1704-117553 3 15276396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381970 Affx-122974102 AX-123252328 3 101776263 ATAGCTGGTGCCCAGTCCTGGAGAGGTGGTATAGC[A/G]ATGGCACAGAGTTAATAGGATGGGGAGGGGGAGCA R 2 1 2 1 201000 f 74 goat snp16203-scaffold1704-149140 3 15244846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768811 Affx-122924218 AX-385255988 3 101806921 CACAAATCAGGGGACAGAGTATATATGCAATTATA[A/G]CCAGTTTAATGCCTAATTATTCAATTTTTTCACAA R 2 1 2 1 101000 f 74 goat snp16204-scaffold1704-179798 3 15213013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407714 Affx-122955011 AX-123278065 3 101864247 ATGTATTATGGGGTATATAACATGTAAAGTGAAAA[G/T]CATGATGACAACACACAAAGAATGGGAAGAGTAAA K 2 1 2 1 201000 f 74 goat snp16205-scaffold1704-237124 3 15155116 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804212 Affx-986696726 AX-385290852 3 101866680 CATCTTCTGTTGAAGTTGGTCTCTGGTCCCCAATT[G/T]GTCTTCTGTCATCACCCCTGGGATCCGGTCTTTGC K 2 1 2 1 600010 f 74 goat 3_101866680 3 101866680 Ancestral_priority_1043 ancestry 0.468 neutral IMAGE 10K 10K ancestral 38412790 Affx-122950495 AX-123283139 3 101894383 TTATATCCTTCAGTTGAGTATTAGTATGAGTATAT[A/G]TGTAGAAACTTTATCTGGTTCACTTTTTCCCATCT R 2 1 2 1 101000 r 74 goat snp16206-scaffold1704-267260 3 15124939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407841 Affx-122954529 AX-123278192 3 101954280 CGATCCTTAATTTGAGTCACTTGTGTCAGATGCCT[A/G]TTCATAGACAAGGCTCAAAACCAAGTCAGAAGGCT R 2 1 2 1 201000 r 74 goat snp16207-scaffold1704-327157 3 15065070 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411377 Affx-122952236 AX-123281727 3 101990115 TTCTACCTAAAATAACTATCCAAAGCTTGCTGGGC[A/G]CTATGCTAAGCACTTCATGGCCATCAAGAGGCATG R 2 1 2 1 101000 f 74 goat snp16208-scaffold1704-362992 3 15028433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784981 Affx-122957310 AX-385272028 3 102035403 TAACCTTGTAGGAAATTATACTGAGAGAGAGCAGA[A/C]GTTGTGCGAAGAATTAGCAGAAAGAAAAAGGAACA M 2 1 2 1 101000 f 74 goat snp16209-scaffold1704-408280 3 14983536 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452472 Affx-122921001 AX-123322805 3 102067635 CCATCAAACTGTTAATTCTGATTATCTCCAGGGAA[A/C]TGTTACTAAGTAATTTTCACTTTCTACTTTACTGT M 2 1 2 1 101000 f 74 goat snp16210-scaffold1704-440512 3 14951706 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387017 Affx-122969931 AX-123257375 3 102128165 TCTTTGTCTTTTCCTTTTCTCATCAAGAGAAGAAA[C/T]AAGCCTCATAACCACATCAGACACTGAAGATGTAG Y 2 1 2 1 201000 f 74 goat snp16212-scaffold1704-501042 3 14890956 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423021 Affx-122943416 AX-123293367 3 102178799 CTGGCTACTTAAGAACTAAAAATTAAGCTGGGGGC[A/G]AGGCTGTTACGACTTTTCATCCCAAGAAATCAGGA R 2 1 2 1 101000 r 74 goat snp16213-scaffold1704-551676 3 14840121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382222 Affx-122973985 AX-123252580 3 102235114 AGGATTAAGTTGGGAACCTTTGGCATATGGCTAGT[A/C]TTTAAAGCCGTGAGACTGGACAGGATCATGTAGGG M 2 1 2 1 101000 f 74 goat snp16214-scaffold1704-607991 3 14783297 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781677 Affx-122961617 AX-385268760 3 102284739 GACATGGATTTAAAACCAGTTTTCTGACTCCAAAC[A/G]CAGTTCTCTTTCCATTACATAAAAGAATTTCAAGC R 2 1 2 1 101000 f 74 goat snp16215-scaffold1704-657616 3 14733539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278173 Affx-1111836209 AX-519551662 3 102338775 ACAGATTTAGAGAACAAACTTATGGTTGTCAAGGG[A/G]GAAGAATGGGAAGAAAGGATAGGAAGTTTTCAGTT R 2 1 2 1 102000 r 74 goat Random2.2K-376 3 102338775 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396986 Affx-122963153 AX-123267341 3 102351172 TCTGGGCTTGAGTCCACAGCCCTAACATCCTCAGC[G/T]CTAGGGGATTACACTGCATCAGACGTGATTTAGAC K 2 1 2 1 101000 r 74 goat snp16216-scaffold1704-724049 3 14665805 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382071 Affx-122974917 AX-123252429 3 102416789 GTTAGATACTTTGTGTCTTGTACAGTGCTGATGAC[A/G]TGGTAGATCTTTAACATTTGATGAAATATTTGTTG R 2 1 2 1 101000 f 74 goat snp16217-scaffold1704-789666 3 14600060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779399 Affx-122966468 AX-385266502 3 102457326 ATATGTCTATTTATTTAGCAGATGTTTATTGAGCA[C/T]TTAATTGTATTCCTGGAAAACATCTGGAAAGGGTC Y 2 1 2 1 201000 f 74 goat snp16218-scaffold1704-830203 3 14559681 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378433 Affx-122976771 AX-123248792 3 102500959 TCTTTAAAATTGCTGTCTCTTTTTCATATTCTATA[C/T]GGAGTAGGTCTTGGCAATGATAAATTTAACTTTGT Y 2 1 2 1 101000 r 74 goat snp16219-scaffold1704-873836 3 14522128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451529 Affx-122921097 AX-123321862 3 102536986 ATGTGTGTCACCTCCAGAAAGAGCTGAATGAATAG[C/T]GTGATTTAGGGCCAAGGCCAGTGTCAGTTACCTTC Y 2 1 2 1 101000 f 74 goat snp16220-scaffold1704-909863 3 14487962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381932 Affx-122974131 AX-123252290 3 102596366 TAAAATGGCTCACAGAGCCAAAGGAAAAATAGAAG[C/T]AGGTCTTTGGAAGAAATGTGTACCAAAGTGGCTCT Y 2 1 2 1 201000 r 74 goat snp16221-scaffold1704-969243 3 14428392 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390721 Affx-122967927 AX-123261078 3 102628534 AGTAAAATTGAGCCCAAAGGGCCTGAATCCAAGTA[C/T]TGGTAATCTCTCCAGGGCTCTTTTTCTCTCTGGAC Y 2 1 2 1 101000 f 74 goat snp16222-scaffold1704-1001411 3 14396587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384147 Affx-122972804 AX-123254505 3 102672345 CCCTGGGCCGGAACATAGTGTCTATTTCACTTCCT[A/G]AGATAGAAACCGCACAGGGGCCACTAAGAGGTCTC R 2 1 2 1 101000 f 74 goat snp16223-scaffold1704-1045222 3 14353235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445343 Affx-122926390 AX-123315680 3 102723661 CGCAGCTCTGAGCTTCCATTTCACTTTCACATCCA[G/T]TGGCTGAGTTGATCCTTAGTTGCTCTGCAAGGTGA K 2 1 2 1 101000 r 74 goat snp25493-scaffold2623-30425 3 14301933 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386383 Affx-122970841 AX-123256741 3 102804714 TAATGGTTGAGAAAAAAAAAGCAGGAAATACAAAA[C/T]GTTTGTTACTGCAAGCAATTTTAATACAAAAGTGT Y 2 1 2 1 101000 r 74 goat snp41712-scaffold543-13848 3 14218863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435658 Affx-122933344 AX-123305998 3 102852105 TTCTTCAGACCATGATAAATGCTCTTATATAGGCC[C/T]GTCCTTATGTCAAAACTTATTTTTCCACGAATAAA Y 2 1 2 1 201000 f 74 goat snp41713-scaffold543-61239 3 14171510 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410282 Affx-122952510 AX-123280632 3 102889434 TGCCTATATCCTTAATCGGCTATAAACATTAAAAT[A/C]AATTAGAATAGAGGAACATTCAACCCAGTTGCTCA M 2 1 2 1 101000 r 74 goat snp41714-scaffold543-98568 3 14134132 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407357 Affx-122955276 AX-123277708 3 102935430 CTTCTCCACCTCATCATTTCTTGCCTGTATTGTCA[G/T]AACAGCCTCTTAACTGCTCGCTGAGGCCTCTACTC K 2 1 2 1 101000 f 74 goat snp41715-scaffold543-144564 3 14088330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779440 Affx-122947837 AX-385266543 3 102982636 ATCCGTTCTGTACCAAGGTAAAAGCTGACTTTGAC[A/G]TTCCCTCTTATCCAATGAAACTCAGATACACCCCA R 2 1 2 1 101000 f 74 goat snp41716-scaffold543-191770 3 14041196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776017 Affx-122930889 AX-385263147 3 103021079 AAATTCTAAACTTCGAATAACCTTATTGTTACTCA[G/T]CAATAAGATCATTAACTCCCTGAGGAAAGACATCA K 2 1 2 1 101000 r 74 goat snp41717-scaffold543-230213 3 14002666 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432646 Affx-122935472 AX-123302987 3 103051923 CCTTATAGAGAAAAGAGCAGGCAGAGAAGGAACAG[C/T]CACTGGCACACAACCCCTACCCCACACTACCCTGC Y 2 1 2 1 201000 r 74 goat snp41718-scaffold543-261057 3 13971768 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765910 Affx-122962362 AX-385253342 3 103085616 GCAACCTTTCCCTTAAAAATAAACGTCACCCTCTC[A/G]TCATCAGGGTCAGTGACCCTAAATTTGCACAGTGT R 2 1 2 1 101000 f 74 goat snp41719-scaffold543-294750 3 13937948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412730 Affx-122950730 AX-123283079 3 103146486 CTCAGCCCGACATGCCTCTCCATCTGACATGTGTC[A/G]TCAGCAGGGGTCCCCCATTCACCTCTCCAGCGTGA R 2 1 2 1 303000 r 74 goat snp41720-scaffold543-355620 3 13881430 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776424 Affx-122976529 AX-385263551 3 103197258 TCTATTTTGCACTCCTTCTCTGCTCGGATACTACC[A/G]ATTCCATGTGCACACTCTATCCATTCTTTCTCAAA R 2 1 2 1 101000 f 74 goat snp41721-scaffold543-406392 3 13830093 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803548 Affx-986696107 AX-385290353 3 103253439 GGAAGTTCTATGAGGCCCTTTTGCAGATGAGAAAG[C/T]GAGGATCAGGGAATGAGAGTGACTTGTCCAAAGTC Y 2 1 2 1 600010 r 74 goat 3_103253439 3 103253439 Ancestral_priority_1043 ancestry 0.526 neutral IMAGE 10K 10K ancestral 38382546 Affx-122973782 AX-123252904 3 103270593 AGCTGGAAAGACGCGTGGTCCTTGCATTCCTATAG[C/T]GCCCAAACCCAAATCAGTCCTACCATCCTACTATG Y 2 1 2 1 101000 r 74 goat snp41722-scaffold543-479727 3 13757181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375992 Affx-122978422 AX-123246351 3 103304486 CCAAACCAGAATTGTGTCCCCCAAGTTGTGTGGTG[G/T]TGTTAAATGTTCCCTTTAAAATGTGAATTGCCAGT K 2 1 2 1 101000 r 74 goat snp41723-scaffold543-513620 3 13723042 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783068 Affx-122924803 AX-385270135 3 103348119 GCTGTTTCATGGGGGTCTCATGAATCTTCTGCTCT[C/T]GTTTATATTAGCTGGAACGAATGACTCTTTGCCAC Y 2 1 2 1 101000 f 74 goat snp41724-scaffold543-557253 3 13679300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413245 Affx-122950235 AX-123283594 3 103396911 CCAGGGGAATGTGGATGGACAGCTTTCAGCTGAAG[C/T]CATTCTTTCGCTTTCCATTTGGTCACTCATTCAAC Y 2 1 2 1 101000 r 74 goat snp41725-scaffold543-606045 3 13631059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390960 Affx-122967053 AX-123261317 3 103446745 ATTTGACTTCGGTTCTAGGTGTGTTGGGTTTCCCC[A/G]GTGGCTCAGCAGTAAAGAATCTGCATGCATTGTAG R 2 1 2 1 201000 f 74 goat snp41726-scaffold543-655879 3 13580719 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440538 Affx-122929329 AX-123310875 3 103476676 CGACCAGGTCCTGGATCTCTGGCCCAGGCTCCCTG[A/C]CCCTTCTATTGCATCGTGCCAGCATATCATCAAGC M 2 1 2 1 101000 r 74 goat snp41727-scaffold543-685810 3 13550772 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796821 Affx-122961379 AX-385283764 3 103517378 TCACGTCTTAAGCGTACACTTTGATGACTTTTGAT[A/G]TAGGTGTATACTCATGTAACTGTCACCCCCGTTAA R 2 1 2 1 101000 r 74 goat snp41728-scaffold543-726512 3 13510202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441776 Affx-122929101 AX-123312113 3 103574877 CCTGGCAAAAATACTTATTTTAGGAGTGTATTGCT[A/G]CAGTGGGTAAGTGCCACCGGACATCTGTGATGTCT R 2 1 2 1 101000 f 74 goat snp41729-scaffold543-784011 3 13452491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383228 Affx-122972763 AX-123253586 3 103668392 TTGGGCTTGGAGTTCTCAAGGGCTCCAGTGATTGC[A/G]CCCACTTTGAAGCACAGAGCGAGTGTAGGCTCAGA R 2 1 2 1 202000 f 74 goat snp41731-scaffold543-877526 3 13358478 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786106 Affx-122923364 AX-385273142 3 103699963 CCACTGAGACTAGCTGACATTTTAACAAGACTTAA[C/T]GAGTGTGTAGAATTTTCATCAATGGAGTGGGGCAC Y 2 1 2 1 101000 r 74 goat snp41732-scaffold543-909097 3 13326794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439707 Affx-122930562 AX-123310044 3 103763753 TTCCTGTCCAAGTCTTTTGTCCATTTTTAATTGTA[C/T]CTTTTAACACTGAATGCCTGATATTACAGTTTTCT Y 2 1 2 1 101000 r 74 goat snp41734-scaffold543-972887 3 13262497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424918 Affx-122941296 AX-123295264 3 103796023 ACAACTGTCTTTAAAATGAGGATAGTCTCTGCTTC[A/G]TAGGTTTGTTTTTCCTCTGTGCAAGAATTAAATAG R 2 1 2 1 101000 f 74 goat snp41735-scaffold543-1005157 3 13229834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382049 Affx-122974936 AX-123252407 3 103851374 ATCTAGGAGCTCGGAGTCCAATAGAAAAGACAAAC[A/G]CAATAGACTAAGGGCAAAAATGGCCCCAACTCTTC R 2 1 2 1 101000 f 74 goat snp41736-scaffold543-1060508 3 13177327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401510 Affx-122958933 AX-123271863 3 103896879 GCCAGGCAAGCTTCTAGGCACTTTCCATATGCTGA[A/C]TTATTTAGGTGGGTGCTATGATGAATCCCCATTTT M 2 1 2 1 101000 r 74 goat snp41737-scaffold543-1106013 3 13132448 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387641 Affx-122969853 AX-123257999 3 103995983 ATGGTCCCCTTTTCACAGATGAGAAAACTGAGGCT[C/T]AAGCAGTTAAATAACTTGTTCAAGGGCTTAGAATC Y 2 1 2 1 201000 r 74 goat snp41739-scaffold543-1205117 3 13033085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782537 Affx-122964429 AX-385269612 3 104038196 GACTGCTAAACATTACTCCTTTGGTGTTGCTCAGC[A/G]TATCTAAATCTAAATTCAGTATCTCATCAAGCCAG R 2 1 2 1 101000 f 74 goat snp41740-scaffold543-1247330 3 12990959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393884 Affx-122965123 AX-123264239 3 104097023 GGCTCTTCTGGGCTGGGAGGTGGGCAGAACATGAA[C/T]ACTCTCTCTCACTCCCCTCCTCAACAGGCTATGAG Y 2 1 2 1 101000 f 74 goat snp41741-scaffold543-1306157 3 12932089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444776 Affx-122926352 AX-123315113 3 104210916 TTTAAGATCAGGAAAGGTCTGCTGAAGAGGAATTC[G/T]ATTTGAAAGCAAGACTTTCCTTTTGTTGTGCAAGA K 2 1 2 1 101000 r 74 goat snp41743-scaffold543-1420050 3 12818174 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779494 Affx-122975913 AX-385266597 3 104249799 AAATTTACTCTAGGTATTCAAAATTAACAATTCAA[C/T]TTCTCACTCACTCTTGCCACATTTTAACTGTTCAA Y 2 1 2 1 101000 r 74 goat snp41744-scaffold543-1458933 3 12779321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410983 Affx-122952012 AX-123281333 3 104279679 GGGCATTGAGTCATTTTGTAAAACAAATGAATATA[C/T]GGGATCCTAGGACTCATGGAAATACCTTTATTGCC Y 2 1 2 1 103000 r 74 goat snp41745-scaffold543-1488813 3 12749199 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385991 Affx-122971517 AX-123256349 3 104333194 CCTATAGCTTTGGATTCCCACCGAGGTTTCCAGTC[A/G]TTTTACTCCTCCCTCCCAAACTGAAGCAGTGTGTG R 2 1 2 1 101000 r 74 goat snp41746-scaffold543-1542328 3 12695463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410342 Affx-122952463 AX-123280692 3 104364018 AACTCTTGAAGTGTTGAGATATTTCTCCTAATGAT[A/G]TCAAGATGGTTGCTGCAGCAGCAGGTGTCAGATGC R 2 1 2 1 201000 f 74 goat snp41747-scaffold543-1573152 3 12664743 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278175 Affx-1111836210 AX-519551664 3 104393730 TGGGGCAGGAGGGTGGGTGGGGGTCAGGCCGCCAC[A/G]ACTCTCAGGAGCAGCAGACTGTGACAAGGGCTCTG R 2 1 2 1 102000 r 74 goat Random2.2K-378 3 104393730 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382146 Affx-122974045 AX-123252504 3 104398672 GCATTGAAGTGCTGACCCCAGGAGAGGGTAAGTGA[C/T]ACGTGAAAGAGGAGAGAAAACCCAGCCTGGGGCTG Y 2 1 2 1 102000 f 74 goat snp41748-scaffold543-1607806 3 12630148 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451159 Affx-122921357 AX-123321493 3 104445083 GCTGGCCCCTGGTGGCCATGGCCTCTGGTAAAGAC[A/G]TGGTGTCCTGGCAAGATCACGAGCTTTGGCAGAAT R 2 1 2 1 101000 r 74 goat snp41749-scaffold543-1654217 3 12583914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411768 Affx-122951491 AX-123282118 3 104501818 CGCCATGGGTCCTCCATTGCTGCACGGTCTTCAGC[A/G]ATCTCTGCTCTGATTCCCCTGGTTCTCTCCTCCAG R 2 1 2 1 101000 r 74 goat snp41750-scaffold543-1710952 3 12526653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776720 Affx-122957165 AX-385263846 3 104611898 ACAAAAAACCACGAGCTGTAAGTATCAGCCAGACC[A/G]TTTCAGAGAGGCTGGTAAATTTTGAAAATGGTTAG R 2 1 2 1 101000 f 74 goat snp41752-scaffold543-1821032 3 12417993 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794592 Affx-122926316 AX-385281554 3 104657033 TTCCCCAGTTGTCTAGGTACACTTCTTAAAATGTC[A/G]TAAATATAATTCTCAGGCAATATAAAGTGAACACA R 2 1 2 1 101000 f 74 goat snp41753-scaffold543-1866167 3 12373067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380666 Affx-122975190 AX-123251024 3 104692180 GCCATAGTTTTAGTCCAGGGTCCAGTGCCAGCCAG[C/T]GACTCAGTCTTTACTTGAGCAGGCCACCAAAGTCT Y 2 1 2 1 101000 r 74 goat snp41754-scaffold543-1901314 3 12337511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802825 Affx-122932528 AX-385289724 3 104725260 AAAGGTTTCATCTAATATCTGGGAAGAGATGGCCC[A/G]TGTGGCATGTCCTAAATTAATTATTGTGTGTGTGT R 2 1 2 1 101000 f 74 goat snp41755-scaffold543-1934394 3 12304721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390093 Affx-122968025 AX-123260450 3 104755902 CCAGGGACCACTGTGTGGAAGCCAGCCTGGCACTG[C/T]GGCTCTGATGGAGCTGGTTCTCCCTAGAGGTAGGT Y 2 1 2 1 101000 r 74 goat snp41756-scaffold543-1965036 3 12274018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438778 Affx-122931379 AX-123309115 3 104786540 AAAGGCAACAGAACGTGGTGCCATGCATCCCCCTT[C/T]TGGGCCTCAGCATCCACATAAACGCTGGAGTGAAA Y 2 1 2 1 101000 r 74 goat snp41757-scaffold543-1995674 3 12243766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395267 Affx-122964089 AX-123265622 3 104819553 TCTACAAGTACTTTCCTGGGAAGCTGTGTCAGCCC[C/T]GCAATTAGTTCCCTCAATCAGGAAAGCAGCTCATC Y 2 1 2 1 101000 r 74 goat snp41758-scaffold543-2028687 3 12210791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385098 Affx-122971792 AX-123255456 3 104870070 CTGGCTCTTCCAACATTATCTTTCTTCCTCTTCCA[G/T]CATAAAATTCACCCATCCTACATCCTTGAGGAGAT K 2 1 2 1 101000 f 74 goat snp41759-scaffold543-2079204 3 12160476 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385210 Affx-122971711 AX-123255568 3 104911600 CATAGCAATTCTTTGCATTGTCATCACGTACAATT[A/G]TGTGTATGTTTTTGTGTGTGAAATTGTTCTGTCTC R 2 1 2 1 101000 f 74 goat snp41760-scaffold543-2120734 3 12118740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435837 Affx-122932821 AX-123306176 3 105040213 GAGAGGGACCATGGAGATGGCAGGGAGTGAACAAA[G/T]CTCTCCATTCCCCGTTTACAGGGGCCTCTAGAGAG K 2 1 2 1 101000 f 74 goat snp41763-scaffold543-2249347 3 11990400 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433398 Affx-122935104 AX-123303739 3 105135792 ACAGGCTTTGCCTTCCTCATGCCTACATGGCAGCA[C/T]CAGACATCGTGCTCCTGGGAGATCCCTTTTCTTCA Y 2 1 2 1 101000 f 74 goat snp41765-scaffold543-2344926 3 11894799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444313 Affx-122926743 AX-123314650 3 105173268 ATGAAGATGTTGGAAACCAAAATAAAACTGGGCAC[C/T]GATCTTCTGGGCAGGAGGAAGCCAGGGAGGCTGAA Y 2 1 2 1 101000 f 74 goat snp41766-scaffold543-2382402 3 11857630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448488 Affx-122923615 AX-123318824 3 105218886 CTTGTGCCCAGGGCACAGTCAGCACTGGATGTGGC[A/G]CAGCTTTAAACTCAAAGTGGGAGAGACAAAGCTCC R 2 1 2 1 101000 r 74 goat snp41767-scaffold543-2428020 3 11812358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377773 Affx-122977353 AX-123248132 3 105279820 CCATCCAAGAATTCCTTGGGGGAAGGAATGAAGCC[A/G]TATACTCGTAGCCTAGAACAGTCCTGGTACATCGT R 2 1 2 1 101000 r 74 goat snp41768-scaffold543-2488954 3 11751891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439607 Affx-122931149 AX-123309944 3 105319893 TTGAGATTTAGCACAATCGCTGTAGTTCAAGAGCC[A/G]CTCTGTGGTCTCCTCATTTGTTAGTATCAACAGCC R 2 1 2 1 101000 f 74 goat snp41769-scaffold543-2529027 3 11711587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405881 Affx-122955603 AX-123276233 3 105350666 TACCAACAGAATGCTGCTGTGTCCCCAAGGTCTTA[C/T]GGAAATTTTAGTGAAATGCTCCTTTTTATTTTTGC Y 2 1 2 1 201000 r 74 goat snp41770-scaffold543-2559800 3 11680228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383842 Affx-122973157 AX-123254200 3 105449494 TCTGTGGGCTGTCTGGGGTCACTCGACCTTGGCTG[A/G]GGCCACTTGTGGTCTATGAGGGAGCTAGGCGCTCA R 2 1 2 1 201000 r 74 goat snp41773-scaffold543-2658628 3 11583343 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804562 Affx-986696730 AX-385291103 3 105489744 GAAGCCAGCCCTGACTGTGGGCTGGCTCTGTGTGC[A/G]GCAGCAAGAGAGAGGGCAGTGCGGCTTGAAGTCTG R 2 1 2 1 600010 r 74 goat 3_105489744 3 105489744 Ancestral_priority_1043 ancestry 0.456 neutral IMAGE 10K 10K ancestral 320794650 Affx-122935637 AX-385281611 3 105496693 GAATATAATGTATAGTATTTTACAGAAGACAAGCT[G/T]GTCTGGTATGTAGGTCTGCATGGATATATCGTGTG K 2 1 2 1 101000 r 74 goat snp41774-scaffold543-2705827 3 11536117 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438336 Affx-122931339 AX-123308674 3 105537719 CTTCTCCAGGGACTCGTCTCAACCCAGAGATCAAA[C/T]CTTTGTCTCTCGCATCTCCTGCCTGACTTCTTGCT Y 2 1 2 1 101000 f 74 goat snp41775-scaffold543-2746853 3 11494754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436754 Affx-122932286 AX-123307092 3 105613279 AGAATACAGCTTGAGAGCCCAGGAGAAACTGGAGC[C/T]AGGACCAGGCCCTTGTTTCATCTTCCATGAGGGGT Y 2 1 2 1 201000 r 74 goat snp41777-scaffold543-2822413 3 11418722 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420199 Affx-122945550 AX-123290547 3 105652675 TAAACCGGAGGCCAGTCTTGCTAAGTTCAGAAGCT[A/G]TTTCTAGCTATTTCTAGAAAGGTGGGCGTCTGAAA R 2 1 2 1 101000 f 74 goat snp41778-scaffold543-2861809 3 11379086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376893 Affx-122977812 AX-123247252 3 105698672 AAAGGGCTCATCTGCTGGTGCAAGAAGCTGATTCA[C/T]GGAGGGCGTGGTTGCTGGAGAAGGAGGAGAAAGGG Y 2 1 2 1 101000 f 74 goat snp41779-scaffold543-2907806 3 11333285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407884 Affx-122954495 AX-123278235 3 105764589 AGGGTCCATGTAAGGAATGGAGAAAAACAACTCCT[C/T]GTCTTCTATTCAAATACTTTTCTGCTGTCCTCTAG Y 2 1 2 1 101000 f 74 goat snp41780-scaffold543-2973723 3 11267621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406639 Affx-122955820 AX-123276991 3 105796523 GCCACAGGAATTAAAAAGTATACAAAAAGTGTAAA[C/T]TGCCTGGCATTCAGCAGGTGACTTCACACCTTAAG Y 2 1 2 1 201000 f 74 goat snp41781-scaffold543-3005657 3 11235698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452866 Affx-122920709 AX-123323199 3 105864255 GCACAGTGTACACAACAGAGGTTCCCAAAGGGTTA[G/T]TGCTACTAACAGGATGTCCATGGGGGTGAGGCTGA K 2 1 2 1 101000 f 74 goat snp41782-scaffold543-3073389 3 11168070 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418717 Affx-122946282 AX-123289065 3 105896927 ACCAAGCCAGGCTGGAGGAAGGCTGGGAAGATGGC[A/G]TGATGAGCATGGCAGCTTGTGAGTGAATGCAGACC R 2 1 2 1 101000 r 74 goat snp41783-scaffold543-3106061 3 11135541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383502 Affx-122972648 AX-123253860 3 105946848 GAGCAGTTGGTTGATTACTGTCTGCCGAGATAACC[A/G]TCATGATTTTCTGGTACATTTGTGTACACTACCAG R 2 1 2 1 101000 f 74 goat snp41784-scaffold543-3155982 3 11087061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800342 Affx-122967853 AX-385287265 3 105999110 AAACCATGGCATTTAGATGATCACATATTAATGGT[G/T]GGTAATGCACTACCTTCCAACAAAGCTGACTGTGC K 2 1 2 1 101000 r 74 goat snp41785-scaffold543-3208244 3 11036080 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794902 Affx-122936439 AX-385281862 3 106036746 TTCATCCTTGCTAGAACTGTTCAAGGAACAGTTAT[A/G]TAAGGGAAGATACCAACTAGAAGATCGAAATGTAT R 2 1 2 1 101000 f 74 goat snp41786-scaffold543-3245880 3 10998907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386553 Affx-122970715 AX-123256911 3 106103811 TGAGTTTGAAGTCCAGCTTTGCCAACTCTAGATGA[C/T]GTTACCTTGGGCAGGACTCTTAACCACTCTAAGAC Y 2 1 2 1 101000 f 74 goat snp41787-scaffold543-3312945 3 10931633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793239 Affx-122966217 AX-385280217 3 106271692 ACACCCCTCCACTGCAGAGCAACTGTTACAAACTT[C/T]ATTGACTTAAACTTCTGATGAAAAGGAATCTGTGT Y 2 1 2 1 101000 f 74 goat snp41790-scaffold543-3480826 3 10766917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377566 Affx-122977442 AX-123247925 3 106313689 GTGTGTTCCAGAGATGCTCCAGGACATGAGCACTG[A/G]CCCTCAGAGAGCTTCCTGAAGCTGCAGTCCCTGTG R 2 1 2 1 101000 f 74 goat snp41791-scaffold543-3522823 3 10725042 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402641 Affx-122958389 AX-123272994 3 106368480 GGAGAAAGAGGTGATTCACATGACCATGCCTAGTT[A/C]GTCATTAGTTTGACACCACCCTCGCTATGCATAGG M 2 1 2 1 101000 f 74 goat snp41792-scaffold543-3577614 3 10670284 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397291 Affx-122962329 AX-123267646 3 106407377 CTGTCATTCAACCCGTAGATTCTGGATGTCTAGTA[C/T]AAAATAGGGGTTGTGTAAATACTTGTTGAGTGGAT Y 2 1 2 1 101000 f 74 goat snp41793-scaffold543-3616511 3 10631274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795647 Affx-122923079 AX-385282602 3 106436457 TAACCCTTCTTTAATTCCTGATGTTGTCAATTTGT[A/G]CTCTCTTTTTTTGTCATCAGTCACGCTAGAGCTTT R 2 1 2 1 101000 r 74 goat snp41794-scaffold543-3645591 3 10602268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419556 Affx-122945412 AX-123289904 3 106469603 TTGTACATTAGTTCTGTGGCAAGAACTGGGGATTT[A/G]CTAGTTACCAGTGTGAGAGTTGGACTGTGAAGAAG R 2 1 2 1 201000 f 74 goat snp41795-scaffold543-3678737 3 10568666 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387612 Affx-122969872 AX-123257970 3 106542261 TTCCTCTCTTTGCCCCTCTTCCTCATACATAAAAA[C/T]AGAAAAAGCACTGCAAAGAAAAGGCCAGATGATTC Y 2 1 2 1 102000 f 74 goat snp41796-scaffold543-3751395 3 10495582 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272179 Affx-1111833373 AX-519545931 3 106579784 GTATGGCCTAACATATGATGTATCCTGGAGAATGT[A/C]CTGTGTGCACTTGAGAAGAGTATGAGTTCTACTGC M 2 1 2 1 303000 f 74 goat 3_106579784_AF-PAKI 3 106579784 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397891 Affx-122961958 AX-123268246 3 106593421 AACCATTGATATTTCATTGGAATTGTATCAGAACT[A/G]TATTTTACTTTGGGAGTAACTAATTTCTTTCATTT R 2 1 2 1 101000 f 74 goat snp41797-scaffold543-3802555 3 10444299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379821 Affx-122976223 AX-123250179 3 106633729 CTGAGCCACAGAACGACAAGCATAATAAAATTGTC[A/G]TTTTAAACCACTAAGTTTATGGTGATCTGTTAAGC R 2 1 2 1 103000 f 74 goat snp41798-scaffold543-3842863 3 10403504 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380320 Affx-122975383 AX-123250678 3 106699483 GACACAGACTTTGGAGACAAGGCTAAAAGATTAGG[C/T]GAAGGCCAGGAAGTGGATGATGAGGTGGGTGAAAA Y 2 1 2 1 101000 f 74 goat snp41799-scaffold543-3908617 3 10337000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794214 Affx-122921986 AX-385281180 3 106739463 TTTGTTGTGCCAGAAACTAAGCAGTGCTCAAAGAA[C/T]GATGCAATATTCAAAAGTACACATGAGCCAGCTTG Y 2 1 2 1 101000 f 74 goat snp41800-scaffold543-3948597 3 10296943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411637 Affx-122951577 AX-123281987 3 106774246 GGTGTCTACTGCTACTTCAGAATGATTTTAGATTC[C/T]ACCCCACCCCCATGAAGTTTCTTCCTATTTTTTAT Y 2 1 2 1 201000 f 74 goat snp41801-scaffold543-3983380 3 10262086 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781233 Affx-122944926 AX-385268318 3 106852182 AAAAATTGAAACTTTTTTCACAATTCAGTTAGTGG[C/T]ATAATTACTTAACCTGAACTCTTTTAGCAACAAAA Y 2 1 2 1 101000 f 74 goat snp41803-scaffold543-4061316 3 10183400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420295 Affx-122945033 AX-123290643 3 106880741 GTATAGGGTAGTGGTTAGGAGCCTGGACTTTGGAT[C/T]CAGATGAAGTAAGTTAAATCTCCTACTTTTCTGTT Y 2 1 2 1 201000 r 74 goat snp41804-scaffold543-4089875 3 10154952 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452682 Affx-122920315 AX-123323015 3 106966316 TTTTCTAGGCAGACAATTATATCATCTGAAAATAA[C/T]GATAGCTTTATTTTTCCTCTTTAATCCTATCATGT Y 2 1 2 1 303000 f 74 goat snp41806-scaffold543-4175450 3 10068570 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378173 Affx-122976958 AX-123248532 3 107023863 TATATTCTATTATTTTTAATATATTTTTAAAAATT[A/G]TCCTTTATTAGTCTTAAAAAAAAACCTAGCTTTTG R 2 1 2 1 103000 r 74 goat snp41807-scaffold543-4232997 3 10010523 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402658 Affx-122958376 AX-123273011 3 107063659 TTCCAGGTCACTTCTGCCCCTGCTGTCTGGTTCTG[C/T]GGTGAGTGAGCGAATCACCGTGCAGAGGGGGTGAA Y 2 1 2 1 103000 r 74 goat snp41808-scaffold543-4272793 3 9970900 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384961 Affx-122971910 AX-123255319 3 107093333 ACATGCTCAGGACTCGCCTGGTGGCTGTCAGTAGG[C/T]GGCTGCAGTGCTTGGGCGGGAAGGACAGAGCTGTT Y 2 1 2 1 101000 f 74 goat snp41809-scaffold543-4302467 3 9941165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395921 Affx-122963595 AX-123266276 3 107123677 TAAACCTCACTGAACTTGCAACACTTGGCCTGTTC[C/T]GGACCCTCAGGGCTGGGGTGTGCTCAGGACTGGTT Y 2 1 2 1 101000 f 74 goat snp41810-scaffold543-4332811 3 9910480 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782298 Affx-122942166 AX-385269376 3 107212203 CTTTCGGGGTGTCCTCTAAAAATACCACAGGCAGT[C/T]TTCTCTGTGTGCTTGCTCACTCTTTTCCCTTGCGG Y 2 1 2 1 102000 f 74 goat snp41812-scaffold543-4421337 3 9822999 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391665 Affx-122966551 AX-123262022 3 107238060 ATTATACCACACATAGTATCAATATGGTGGTGCTT[A/G]TGAAGGATGCATGTTACCTTACAGCAGAACTGACT R 2 1 2 1 101000 r 74 goat snp10650-scaffold1378-5076 3 9797033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451304 Affx-122921289 AX-123321637 3 107281325 AGGTAGGCTGTTGGGCTGCCATTTCTGCTGAGTTC[A/G]TTGTGACAGTTCATCCTTTGTTGGTTTCCAACTCT R 2 1 2 1 101000 r 74 goat snp10651-scaffold1378-48341 3 9752840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433257 Affx-122935234 AX-123303598 3 107355424 TCAGGGTATTCTTGTGAGTTTGATCCAGCTTTGGC[A/G]TTGGGGTAGGGTGTCAGATCAATCATGCAAGACGC R 2 1 2 1 101000 f 74 goat snp10653-scaffold1378-122440 3 9678388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791379 Affx-122921562 AX-385278371 3 107389035 TAGCTTGTGTGAATGCTGATATTGAGAAATTTGAT[A/G]CTATCTTGTTCCTAATATTTTTGAAAATCAGTGGG R 2 1 2 1 101000 r 74 goat snp10654-scaffold1378-156051 3 9644394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386822 Affx-122970099 AX-123257180 3 107422236 CGTTTTTACACCCCGGATTTCCTTGGAAACTCAGT[C/T]GTCCCTCTCCATATGGCACTCTCTGTGGTGCTTTA Y 2 1 2 1 201000 r 74 goat snp10655-scaffold1378-189252 3 9610997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420721 Affx-122944775 AX-123291068 3 107490582 GGTCTCTGCTAGCCCAGTATGGAGCTCCTCTCTTC[A/G]TCAAGATTTTCTTCTGAGGGATACAGACGGGTGCT R 2 1 2 1 101000 r 74 goat snp10657-scaffold1378-257598 3 9542132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768563 Affx-122975896 AX-385255743 3 107551739 TACTTAAGATACTTTGTTTTATACATTAGAGAAAG[C/T]AAAGGGATATAGAGAGTGGTAAGACTTCAATACCT Y 2 1 2 1 101000 r 74 goat snp10659-scaffold1378-318755 3 9480693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444814 Affx-122926326 AX-123315151 3 107608507 TGGGGTCTCAGGAGTCACCTTTGCATCTATCCATC[A/G]TTTCCAGGAAAGCAGAAGCTAGAGTCTTGCATCTT R 2 1 2 1 201000 f 74 goat snp10660-scaffold1378-375523 3 9423534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776068 Affx-122956959 AX-385263198 3 107646845 CACACCCAGCTCTACACCATTTTTAATGACTACAT[C/T]GCAATCCTTTGGGTCAATATTCTAAAATTCATTTA Y 2 1 2 1 101000 f 74 goat snp10661-scaffold1378-413861 3 9384899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439977 Affx-122929807 AX-123310314 3 107675518 CAGTGGCCACTGCAGATGTTAACCCTCTCTCAGAC[A/G]CCACATTCCCTTCTCTCTGAGCAGCTTAATTCACG R 2 1 2 1 101000 r 74 goat snp10662-scaffold1378-442534 3 9356013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434960 Affx-122933848 AX-123305300 3 107707616 TGTGGACCACTTTTAAAGTCTTTATTTGAACGTTG[A/C]TTCTGTTTTACAGTTTGTTTCTTAGGCCACGAGGC M 2 1 2 1 101000 r 74 goat snp10663-scaffold1378-474632 3 9323556 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404580 Affx-122957363 AX-123274932 3 107779942 CCAAGCTGCTCAGCTGTTCAGCATACTGACTGCCC[A/G]CTCTCACCCTGCACACCCTTATCTAGTTTAAAAAG R 2 1 2 1 101000 r 74 goat snp10665-scaffold1378-546958 3 9254628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411329 Affx-122952272 AX-123281679 3 107811817 ATACCTGGATTGTTGTACTTGGTTCTGGTTGCTGC[A/G]CTGCCCTAAGAACCAGCAGCGTGGGCAGGAAACTG R 2 1 2 1 202000 r 74 goat snp10666-scaffold1378-578833 3 9222802 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404561 Affx-122957377 AX-123274913 3 107847070 AGACACCTGCTGAATTCCGCCTTGTCCAAGTCGTG[C/T]GTGCCCCGTGCATTTTCGCCATTCTGCCTCCTCTG Y 2 1 2 1 101000 f 74 goat snp10667-scaffold1378-614086 3 9188351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432143 Affx-122936430 AX-123302484 3 107881997 ACCTCGTCCAGGCAACCTTCCCCACTGCCCCTCAG[C/T]AGAGGCTACTGGACTATAAAGCATTTGGCGACACC Y 2 1 2 1 101000 r 74 goat snp10668-scaffold1378-649013 3 9155917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778483 Affx-122935031 AX-385265597 3 107921691 ATGGAGAGGAGCCAAATAAGAATGAAGACCCAGGC[G/T]CGAATGAATCTGGGCGGGACATAAGAAATGTGTTC K 2 1 2 1 101000 f 74 goat snp10669-scaffold1378-688707 3 9116288 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422842 Affx-122943103 AX-123293188 3 107950974 ATTCATTTACATATTTGTCTTAATCACCTCAGGTT[A/G]CTAGAACAAAAACACCTTAGACTGGGTGGCTTATA R 2 1 2 1 201000 f 74 goat snp10670-scaffold1378-717990 3 9086046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420736 Affx-122944764 AX-123291083 3 107970702 CTTCCTACAGATACCATGGGATTATGCATTAAAAC[A/G]GGAGATCGACACACTCTTTGACCCGGCAACTGCAC R 2 1 2 1 201000 f 74 goat snp32019-scaffold3595-128545 3 9066689 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380319 Affx-122975384 AX-123250677 3 108007017 TTTGGAACGGCAGTTAATTTAGATTTTCCTGTTGA[C/T]GTACACCTGACAGTTCTTATTCCCACATGTGACCC Y 2 1 2 1 101000 r 74 goat snp32018-scaffold3595-92230 3 9030422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413934 Affx-122949807 AX-123284283 3 108050024 TGCAAGCAAGGAACGTTAGGTCAGCTTGGTTCTCA[C/T]AGGGGACTTGAAGCTGGACTCAGCTGATTTCCAAA Y 2 1 2 1 201000 f 74 goat snp32017-scaffold3595-49223 3 8987512 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427922 Affx-122939223 AX-123298265 3 108081147 CAAAGAGGGTGAGGAGTGTCAGATGCCCCTGGCAC[A/G]TCTGATTTGGCCACCTTGAATGGTAACACGCATCA R 2 1 2 1 101000 r 74 goat snp32016-scaffold3595-18100 3 8956181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804566 Affx-986696734 AX-385291105 3 108102821 AGCAGGCTGTGAGCTGCATTCTGGGGAGGCCATAG[A/G]AAGCTCTTTGAGAGGAGCTTTAGGAGGACTGGATT R 2 1 2 1 600010 r 74 goat 3_108102821 3 108102821 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 38392739 Affx-122966016 AX-123263096 3 108107693 ACTCCATTAACCCTCACACTCAGTAGTATCACACC[A/G]CAAAGGTTTATTTCCTGCTTACGCTGCACGTCTGT R 2 1 2 1 101000 f 74 goat snp22160-scaffold219-8347 3 8929232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380225 Affx-122975477 AX-123250583 3 108158019 AGTTTTATGAAAATAAACTAGTTACGTGTGTGATG[C/T]ACTCTTTTCTTTTCCATTCTATACTCTTGTAACCT Y 2 1 2 1 201000 f 74 goat snp22161-scaffold219-58673 3 8878414 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435809 Affx-122932844 AX-123306148 3 108218076 AATCCTGGCTTCAGCCACACTGCGCTCCTGGATCA[C/T]AGACACAGCTGGCCCTTTAAAACCTCTGTCCAGCA Y 2 1 2 1 101000 r 74 goat snp22162-scaffold219-118730 3 8818355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439268 Affx-122930988 AX-123309605 3 108250343 AGATGATCTGGGTGCGCTGAGAGAATTAGGGATTC[A/G]GCATCTGGAGACCTGTGTCAGTCTTGGCTCAGTTT R 2 1 2 1 101000 f 74 goat snp22163-scaffold219-150997 3 8787382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428148 Affx-122939050 AX-123298491 3 108280994 CTCCCTGAGGTTAGGGAACCTTCCTCGGCCTTGTA[G/T]CCCCACAGCTGGCTTATTATGGTCTGACACCCGCT K 2 1 2 1 201000 f 74 goat snp22164-scaffold219-181648 3 8756877 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425732 Affx-122940753 AX-123296078 3 108310541 ACCAGGAACATGCCCCCCTGAGAAGGAGATAAACA[G/T]CTCTGGGCTCTAATTCATGGTGTGGCGGGCAACAC K 2 1 2 1 202000 r 74 goat snp22165-scaffold219-211195 3 8727808 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793091 Affx-122943414 AX-385280069 3 108347117 GATGGACAGTCGCAGAGCCTTCATTTACAGGGTGA[C/T]GATGACGAGAGAACAAGTCCAAGTTTACTTGGCAA Y 2 1 2 1 101000 r 74 goat snp22166-scaffold219-247771 3 8691971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446166 Affx-122925746 AX-123316502 3 108383432 CTTCCCTTCAGCAGTCTTTCCAGGAGTCCCACATG[C/T]ATCCACTTTGTTGTTCAGTTGCTAAGTCGTGTCCA Y 2 1 2 1 201000 f 74 goat snp22167-scaffold219-284086 3 8656432 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404198 Affx-122957675 AX-123274550 3 108419076 CTCTAGTCCCCTGGTTATTCGTTACTCAGTTTGGG[C/T]AGCCTGCCTCTCACTTATCCTGTCTAGTCACTGAG Y 2 1 2 1 102000 r 74 goat snp22168-scaffold219-319730 3 8620937 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451467 Affx-122921143 AX-123321800 3 108449457 CCTTTGCGCTCCTTTGGTCAGGCCTCTTTCCTGGC[C/T]GCACAGAACTTCCCCCTGAGGCTCCCTGGCAGAGG Y 2 1 2 1 101000 r 74 goat snp22169-scaffold219-350111 3 8590964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427341 Affx-122940118 AX-123297684 3 108478556 TTAACTGAGTTCCTGTTTCCAATTATTTATTTTGC[A/G]TTTGAGAAACAAATGCATTATTTGTTTTTTCACAT R 2 1 2 1 103000 f 74 goat snp22170-scaffold219-379210 3 8561839 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398692 Affx-122961861 AX-123269047 3 108524317 GGTCATCCAGGAGCAAAAGCCACCCAAAGAGACAC[A/G]AGGAAGGAAAGTAAAGGCTAGTAAAAACTAGCATT R 2 1 2 1 101000 r 74 goat snp22171-scaffold219-424971 3 8516018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415493 Affx-122948697 AX-123285842 3 108569184 TTCCTGCGTGCTGGAAGAGTGTTAATTGTTATTAG[A/C]GTAATAATCACCAGAATAATTTTAATATAAATCCA M 2 1 2 1 101000 f 74 goat snp22172-scaffold219-469838 3 8471276 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773865 Affx-122946433 AX-189247382 3 108600826 CCCTGGTTATATTGGATGCTAATATTAGGGGAAGC[C/T]GGAAGAAGGGTATACGGGAACTTTATGTACTATTT Y 2 1 2 1 101000 r 74 goat snp22173-scaffold219-501480 3 8439761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404609 Affx-122957341 AX-123274961 3 108634143 TTGTGTGATGTGGGAGGAGCTGGAAGGAGGTGGCA[C/T]GATTTCTGGCGGTTTCATCTTTGCAGAGAGCTTCC Y 2 1 2 1 101000 r 74 goat snp22174-scaffold219-534797 3 8407402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414869 Affx-122949144 AX-123285218 3 108669231 ATCCATTTCCTTGGGTCATCCTTTTCTGTGTCTCT[C/T]CTTTCTTTCTCATCCAGCCTCCTTGTTCTCATTCT Y 2 1 2 1 101000 r 74 goat snp22175-scaffold219-569885 3 8372344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414851 Affx-122949182 AX-123285200 3 108707171 TTATTTTACAGTTTTTAAAAAATTCTTTTAAATTT[A/G]TTTAGCAAATAAGTCTAACAAATTTTCATCAGGCA R 2 1 2 1 103000 r 74 goat snp22176-scaffold219-607825 3 8334419 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404302 Affx-122957027 AX-123274654 3 108767340 CAGTTTAGAATTGGGAAGATGATGTCAGACCTAAG[A/G]TTCAGTGATGGGGACTAGGAAAAACCATTGTGTTT R 2 1 2 1 101000 f 74 goat snp22177-scaffold219-667994 3 8274317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766026 Affx-122961381 AX-385253444 3 108804261 AAGGTATGCTCTCTTATTTTAAAGTTCTGAGTCCA[G/T]ATATTGTTCCCTCTTAAGTATTTGTGTTTATAGTC K 2 1 2 1 101000 f 74 goat snp22178-scaffold219-704915 3 8239694 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278177 Affx-1111836211 AX-519551666 3 108839115 AAAAGACTGTGACGTTCAGGGTGATACTTAAGCAT[C/G]AAGCATTCTCAAAGGTGAATTTCAAGCAGTGCACA S 4 1 2 1 101000 r 74 goat Random2.2K-380 3 108839115 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392322 Affx-122966698 AX-123262679 3 108871088 TTGCCAGAACAAGTTGCCTGACTTGCTTTGATAAA[C/T]GGAAAGATGACCTGATGCAGACGTCTCTGATTTGG Y 2 1 2 1 101000 f 74 goat snp22179-scaffold219-771742 3 8177011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401722 Affx-122959528 AX-123272075 3 108918605 GAAGGCAACTGGTGATTTTGTGCTCAGGGCTGTCA[C/T]GCACAGCAGCTCAGGTTGTGCACTGCCCAACACCA Y 2 1 2 1 101000 f 74 goat snp22180-scaffold219-819259 3 8129403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274005 Affx-1111833947 AX-519547610 3 108961002 CTGTGGCTTGATATTTCACAGTCTTTGCTGCAGAT[A/G]TTTCCTCTTCCTAAACTGTTTTTTTCACCAAATAT R 2 1 2 1 201000 r 74 goat GoatD01.011258 3 108961002 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38398412 Affx-122961630 AX-123268767 3 108992924 GCGAACTAGGCAGATTGCTTCCTGACTCATGAGAG[A/G]CAACATCCTAACTAGGTCAAGGCTGGGCCTGCACA R 2 1 2 1 101000 f 74 goat snp22182-scaffold219-893578 3 8054668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413577 Affx-122950584 AX-123283926 3 109034992 GGAGATGCTGAGAGAGCAGGACCCCAGGTAAGCCA[A/G]CTATGGTGTCAAGGCCTTTTAATGACCCTGCTCCA R 2 1 2 1 101000 r 74 goat snp22183-scaffold219-935646 3 8012715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797404 Affx-122948469 AX-385284343 3 109063609 ATAAAACACTCTCATAGGTTCCAGGCAGCATTGAG[A/G]CATGGGCATCTTTGAGGCGCTGTGGTTCTAGCTCC R 2 1 2 1 101000 f 74 goat snp22184-scaffold219-964263 3 7983688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422314 Affx-122943469 AX-123292660 3 109123595 CAGAAGGTAGAACAAAAGGATAAAAGGAAGAAAAA[C/T]AGGAGAGAAGAGGTTTTTAAAAATTAGAAGACCAG Y 2 1 2 1 202000 f 74 goat snp22185-scaffold219-1024249 3 7924454 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418458 Affx-122946469 AX-123288806 3 109159738 GAAACCACGGCTGCAGTTGAGATTAGAATTTCCCA[C/T]GCGGTTCCTGTTCTTCCTCGTGGCCACGTGGTGCG Y 2 1 2 1 101000 f 74 goat snp22186-scaffold219-1060392 3 7888065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427323 Affx-122940131 AX-123297666 3 109196014 TTTTCTCTTTGAACCTCACTTACTAAATATCAGCC[A/G]AAATTATAGAGGTTTGTTTGTTTGTTTGTTTAATC R 2 1 2 1 101000 f 74 goat snp22187-scaffold219-1096668 3 7853048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790803 Affx-122934010 AX-385277803 3 109232665 TAATGCCAATGGCCATCGCCTAGGAAAAAAATGAC[A/G]TTTTATCTAAGCTTGAGACTAAAGAGACGAGTATG R 2 1 2 1 101000 f 74 goat snp22188-scaffold219-1133319 3 7816460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418573 Affx-122946379 AX-123288921 3 109309203 TTCCTGAGCCTCAATTTCCATATCTGTAAAGTAGC[A/G]ACGATAGTAATAGTTCTCAGGTCTGTGAAATAGAA R 2 1 2 1 201000 r 74 goat snp22190-scaffold219-1209857 3 7739171 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448249 Affx-122924202 AX-123318585 3 109347309 TCTGTAATTCTGGTTCATGTGCTTTGTCTTGTTCT[C/T]TGGGAGTTCGGCAAAATCATTCTCTCACTGTTTCA Y 2 1 2 1 101000 r 74 goat snp22191-scaffold219-1247963 3 7700830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389008 Affx-122968643 AX-123259366 3 109376663 TTTTGCTGTGTGGCTTCTTTCAGCATTGTAAAGCT[A/G]TTACTTTGTGCGGCTGCAGGTGGACTGTTCTTGCT R 2 1 2 1 101000 f 74 goat snp22192-scaffold219-1277317 3 7671560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412731 Affx-122950729 AX-123283080 3 109405945 TATATAAGAAAGTGTCAAAGCTAGAAAAAGATGGA[C/T]GTTATCTCAGTTCATTTTTTTTTTATTGTGGTAAG Y 2 1 2 1 101000 f 74 goat snp22193-scaffold219-1306599 3 7642218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802792 Affx-122921361 AX-385289691 3 109444137 TTCAAGCCAACCAAAGTACTCCTTTAGTGAGTACA[C/T]AGAATTCTTTAAAGGATATTATGTAAACCCTAGCC Y 2 1 2 1 201000 r 74 goat snp22194-scaffold219-1344791 3 7598497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426260 Affx-122940328 AX-123296606 3 109496699 TGGGCTTTGGAGGCAGGCAAGACCTGATTTTTTTC[A/G]TCCCTGTTCCACACTACCTGTGTGACCTTGGGCGA R 2 1 2 1 101000 f 74 goat snp22195-scaffold219-1397353 3 7546305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781866 Affx-122931000 AX-385268948 3 109557440 GACTGCCCTTTCCAACAGCGTCTGTTGTAATGGTC[A/G]TGCAGTTTTCTGAATCTAGTAAGAGCCAGGAACTT R 2 1 2 1 201000 f 74 goat snp22196-scaffold219-1458094 3 7485126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436615 Affx-122932508 AX-123306953 3 109639368 TGCATTTGGAATTTTTGTTTTCATTTTAGACACAT[A/G]CCTGCTAGATTGTTGCACACAGGTTTATGACTGCT R 2 1 2 1 101000 r 74 goat snp22197-scaffold219-1540022 3 7402582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376114 Affx-122978880 AX-123246473 3 109676619 CCGCAGAACTTTATCAACTGTCTTTCTTGATATCA[C/T]GTCTTTATATCGTTTATTGACATATTTGCCCCTAA Y 2 1 2 1 101000 r 74 goat snp22198-scaffold219-1577273 3 7365026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771314 Affx-122973025 AX-385258472 3 109822076 CCATCAGCGTCACGGACAAGCGTGTCTGCCCGTCA[C/T]GGAGTGTTTGTGTGTTGTTGTCAGCTCACTGCGGT Y 2 1 2 1 102000 f 74 goat snp22201-scaffold219-1722730 3 7217267 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408970 Affx-122953914 AX-123279321 3 109929446 TCCATACATTGGTGTCAGCCACTCAGGATGATGGT[A/G]CATTCTGTGTAGAATGGTTCTGTCACAATCAGCTT R 2 1 2 1 101000 f 74 goat snp22204-scaffold219-1830100 3 7110014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437728 Affx-122931736 AX-123308066 3 109980452 CACGTGTAATTAGAAGTAGAAGCTACTGGAAGGAA[C/T]GCCTTATAGCCGCTGCCCCTGCACCTCCAGATGTC Y 2 1 2 1 101000 f 74 goat snp22205-scaffold219-1881106 3 7060467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419557 Affx-122945411 AX-123289905 3 110073101 TTTACAAGCTTCAATTATTAATTAGTTTAAATGTT[A/G]CTTCTTTCTTCTATTTTCTAGGGGTCTTTGAACTT R 2 1 2 1 303000 f 74 goat snp22207-scaffold219-1973755 3 6968262 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418809 Affx-122946167 AX-123289157 3 110108356 ACCGGGGGCAGAGCCTGACCTGGAACGCTGCCCTT[A/G]TCCTAAGCCAGACACCACTCCTCAGATAGCATGCA R 2 1 2 1 102000 r 74 goat snp22208-scaffold219-2009010 3 6932930 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444656 Affx-122926463 AX-123314993 3 110139196 TGGTCAATTAGTATTTTATTTATAGTGTGGAATAA[C/T]GGTTAGGAGAAAATTGGCATTCCCATGGTGGTACA Y 2 1 2 1 101000 r 74 goat snp22209-scaffold219-2039850 3 6901718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411480 Affx-122951794 AX-123281830 3 110172542 AACTGTCATCCCCTTCATAGATTTCAGCCCTCCCC[A/G]TGGTGAAGATGCTAACTTGACTGATAATCAGACAA R 2 1 2 1 101000 r 74 goat snp22210-scaffold219-2073196 3 6868425 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445599 Affx-122925117 AX-123315936 3 110211996 TCCTTACATGTCTCGTTCCAGACTATAGTAAGTCA[C/T]GATATGTAAGAATATCTCCATCATAACAACTGAAT Y 2 1 2 1 101000 f 74 goat snp22211-scaffold219-2112650 3 6827435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439205 Affx-122931035 AX-123309542 3 110251841 CTGTTGCTATTTAAGGTGATGTTTAGAGTTCCTAA[C/T]GATGTGCAAAGAAAAAAAAAAAGTGTACACTATAA Y 2 1 2 1 101000 f 74 goat snp22212-scaffold219-2152495 3 6787570 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429804 Affx-122938195 AX-123300145 3 110356767 TGAAGGCAGGCAGCAGTGCCGGCAAGATGAACCTC[A/G]TAGTCTTCCAGAGATAATTAAAGGAAATGACTCTG R 2 1 2 1 101000 r 74 goat snp22214-scaffold219-2257421 3 6681861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405353 Affx-122956322 AX-123275705 3 110402425 TCTCGCACTGGTTGGAAGGAAGCCAACTGCAACAA[C/T]GTGTCTTATCAATTTTGTTTTACACCCAAGAAGCC Y 2 1 2 1 101000 r 74 goat snp22215-scaffold219-2303079 3 6636375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801542 Affx-122959054 AX-385288451 3 110431911 CACTACTGAAAATATTCAAGGACAAGTTGAATGGC[G/T]CCTTGTCAGAGATGTGATAATAATCAATGCTCAGA K 2 1 2 1 101000 r 74 goat snp22216-scaffold219-2332565 3 6606730 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388588 Affx-122969158 AX-123258946 3 110505218 GGTGGCTGGTTTCACCTGATAACCTGAGGTCCTCT[A/G]CCAAGAAGATCTGTTTTAGATGGAAAGAAGGCTTT R 2 1 2 1 101000 r 74 goat snp22218-scaffold219-2405872 3 6532570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464248293 Affx-1110390475 AX-515722869 3 110532386 TCCATGGACAAACCCACAATGTACTCACGGCAAAT[A/G]GTGATAAGCTGCTGAGCCTGGAGAGAGGGGACAAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs660465535 3 110532386 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275625 Affx-1111835002 AX-519549195 3 110532565 GGCACACTGAGTAAAATGGAGCGGAACTTTTCCAC[A/G]GCCTCCTCAAACTTGCCGACTGTGGTGAGCTGGTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs639500528 3 110532565 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276130 Affx-1111835183 AX-519549680 3 110533011 AGCTCCTTCACGACCAAGTAGGGGTAACCCAGTTC[A/G]GCCCCTACAAGCAACTGTTCCTGCAGACCTATGCC R 2 1 2 1 202000 r 74 goat ilmnseq_rs661460057 3 110533011 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276243 Affx-1111835239 AX-519549792 3 110533012 GCATAGGTCTGCAGGAACAGTTGCTTGTAGGGGCC[A/G]AACTGGGTTACCCCTACTTGGTCGTGAAGGAGCTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs667085686 3 110533012 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275894 Affx-1111835063 AX-519549452 3 110533800 CAGGGCTATATTTCTCTGCTTACCTGAGTTGGGCT[A/G]GTTCCCTTGGTTGGGGGCACAAAGAACCCATCCTC R 2 1 2 1 202000 r 74 goat ilmnseq_rs646426062 3 110533800 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275931 Affx-1111835157 AX-519549489 3 110533832 GCTGGTTCCCTTGGTTGGGGGCACAAAGAACCCAT[C/G]CTCAGCTCCACCAGCTGCCCCGGAGGGTATATCCT S 4 1 2 1 101000 f 74 goat ilmnseq_rs657521433 3 110533832 C G 1 recommended Goat_IGGC_65K_v2 Illumina 468276177 Affx-1111835279 AX-519549727 3 110534680 ACCAGCTCAGGAGGAAGCTCCAGATCTTCTTCCAC[A/G]TCCCAGCCACCTCCTTCTTCTTGTCCCTTGCCAAG R 2 1 2 1 102000 f 74 goat ilmnseq_rs671093869 3 110534680 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275925 Affx-1111835154 AX-519549483 3 110534972 GAGGCGCGCTGGCTGCTGACATCGACATTGACACT[A/G]TTGGTACTGAGGGCTGGGGAGAGGATGCCGAGCTG R 2 1 2 1 202000 f 74 goat ilmnseq_rs657418381 3 110534972 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276186 Affx-1111835210 AX-519549736 3 110535000 TTTCTGTCCCTTCGCGCTGTAGGGAAGGGAGGCGC[A/G]CTGGCTGCTGACATCGACATTGACACTGTTGGTAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs663834397 3 110535000 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275584 Affx-1111834983 AX-519549154 3 110536192 GAGAGCCTGAAGGAGACATTTGACCCAGAGAAGGA[A/G]ACAGTGAGTCTTTATGTAAAGTGTCTCTGATTACA R 2 1 2 1 101000 f 74 goat ilmnseq_rs636676154 3 110536192 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276113 Affx-1111835247 AX-519549664 3 110537448 TATCAGAATGCTCTCTACCTGGGAGATGTGTCCGA[A/G]CGAGTGCGGATCCTGAAGAACTGTGGACAGAGTAA R 2 1 2 1 201000 f 74 goat ilmnseq_rs667713149 3 110537448 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275941 Affx-1111835085 AX-519549499 3 110548134 TCACGCTCTTTGATGTACAGCAGAAGCGGTAACAT[A/G]TCAGATATCCCTATGCAGACAGGTTTATAGTGGGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs649458664 3 110548134 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275911 Affx-1111835146 AX-519549469 3 110558928 CGATCATGGTCCCTGCGGAATGTCTGAACTCCAGT[C/G]CTAGGAAAGCAAAAGGTATACAAAGAAAAATATTA S 4 1 2 1 101000 f 74 goat ilmnseq_rs656488281 3 110558928 C G 1 recommended Goat_IGGC_65K_v2 Illumina 38444088 Affx-122926837 AX-123314425 3 110559650 TCACCCTGGCCTGTACTCCAGTCCCTGGAACCACC[A/G]TGCTCTCTGGCCCCACACGCTTGAGCTTGCCCTTC R 2 1 2 1 201000 f 74 goat snp22219-scaffold219-2460304 3 6477783 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395041 Affx-122964205 AX-123265396 3 110614740 AGACCACAGCCCATGGGAGAAAAGACCACGGCCTC[A/G]CCAGGGAGGCAAGACCCAGGGTCACCAGATGCCTT R 2 1 2 1 201000 f 74 goat snp52716-scaffold790-42071 3 6422063 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789841 Affx-122960001 AX-385276848 3 110659633 TCCAGCTTCTGGATGTGTAGGATTTTCTGAAATGC[A/G]TGGAGTAGACTCAAACTTTTCAGCTTCAACAAATC R 2 1 2 1 101000 f 74 goat snp52717-scaffold790-86964 3 6377130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789327 Affx-122952073 AX-385276337 3 110711320 GGGACAACACATCAAGTGCAGGCAGGGAGAAGATA[C/T]ACGTGTCTACACCCATTTTAACTTCAGTCTCGGAG Y 2 1 2 1 101000 r 74 goat snp52718-scaffold790-138651 3 6325072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376952 Affx-122977768 AX-123247311 3 110745986 CTCTGCTCTAGGCTGTGAACACACACACACATACA[C/T]GCTAGTCAAGTCAGAAAAAAGAAAGTGGTAGGTGT Y 2 1 2 1 201000 r 74 goat snp52719-scaffold790-173317 3 6290876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437884 Affx-122931672 AX-123308222 3 110779667 AGAGAATCAGACATGAATGAAGCGACTTATGCCCC[A/G]GAACCTGCTGCAATTATTCAAAACAGCCAGTCCCA R 2 1 2 1 201000 r 74 goat snp52720-scaffold790-206998 3 6258008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424569 Affx-122942224 AX-123294915 3 110825438 GACAGGGTGCCTGTGTTCAATTAAACTGTGCTTCT[G/T]CACACTGCGATCTGAATTTCATATTTTTAAAACAT K 2 1 2 1 101000 f 74 goat snp52721-scaffold790-252769 3 6212113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379967 Affx-122975634 AX-123250325 3 110872410 GAAGGGAGAGAGTGGAATTGGTTTTTAGACACAAA[G/T]AGATTTCTGCTGGAGGGCTTTCCTGGTCTTTGGTT K 2 1 2 1 201000 f 74 goat snp52722-scaffold790-299741 3 6166245 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385949 Affx-122971545 AX-123256307 3 110933251 GGTAGTGGGGGTGTATGTGTCCTCTAGGGTGGTGG[G/T]GGTCGGGTCATTGATAAAGAGAAATGGATCTTAGC K 2 1 2 1 103000 r 74 goat snp52724-scaffold790-360582 3 6104728 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434041 Affx-122934205 AX-123304382 3 110967860 AGGGGTGGAATTGCTGGGCCAGATGTTAGGTGCCC[A/G]TTAAACTTTATAAGGAACTGGAAGACTGTAAAAGT R 2 1 2 1 201000 r 74 goat snp52725-scaffold790-395191 3 6069589 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774727 Affx-122934482 AX-385261861 3 111045639 ACAGCGAGCACAAATGACCAATGAAATGGTCCTTG[A/C]TCCAAATGATCCATGTGGTATTTCTCCCCGTATGA M 2 1 2 1 101000 f 74 goat snp52727-scaffold790-472970 3 5990538 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411843 Affx-122951227 AX-123282193 3 111157014 GGCTCTCCTACAGCTCTGCCCCTTGCTTAGGAAAA[A/G]TAGCTGGTTGTTTAAACAGTCAAGGTGAAATACAA R 2 1 2 1 101000 r 74 goat snp52729-scaffold790-584345 3 5878885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278179 Affx-1111836212 AX-519551668 3 111222666 GGTGAGTCACAAGACTGTTAAAGTTTGAGAAGCAA[A/C]GTGTTAAAGGAAGGTGATTTGGGGAACAAAAGAGA M 2 1 2 1 102000 r 74 goat Random2.2K-382 3 111222666 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408972 Affx-122953913 AX-123279323 3 111252380 ATTAGCACTGAAACCTACTTCCTGGCAGCCCCATC[A/G]CTCAGATTACTTGCTAATTTTTCTGTTTGCAAAAC R 2 1 2 1 201000 r 74 goat snp52731-scaffold790-679711 3 5784974 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380962 Affx-122974991 AX-123251320 3 111331594 ATGGGGCTGGCTGTCTTCCCTTTGTCTGAAGATGA[C/T]GGTTCTGCCTCATGCCTCCTGCCACGTTCAGCTCT Y 2 1 2 1 101000 f 74 goat snp52732-scaffold790-758925 3 5705906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427737 Affx-122939261 AX-123298080 3 111371741 AGTTAGCCTGGTGCTTTCAGGTTTCATCCCTGTTG[C/T]AGCGTGTATCCGAATTCCCTCCCTTTTCACCGACG Y 2 1 2 1 201000 r 74 goat snp52733-scaffold790-799072 3 5666704 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412353 Affx-122950828 AX-123282702 3 111420666 GAAAAAAAAAAAAAAAATTGGCAGAATGGAATAAA[A/C]GCCTTAGCAAGGTATGTGGCCTTTGACCTAGCTTT M 2 1 2 1 101000 r 74 goat snp52734-scaffold790-847997 3 5618660 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415545 Affx-122948656 AX-123285894 3 111459414 CAGCCTGGGAACCAGGGAGCTGGTGACACCTTGGC[C/T]AATGAAGGCAGGAGGCTGATCACATGTCTTTCATT Y 2 1 2 1 101000 r 74 goat snp52735-scaffold790-886745 3 5580712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452333 Affx-122920656 AX-123322666 3 111506485 ATCAAGAAAAATAATAAAATACGAAGCAGTAGAAA[G/T]CCGTAGCTATGTTGCTTTTTCGGTAGTAGTGGCAG K 2 1 2 1 101000 r 74 goat snp52736-scaffold790-933816 3 5533863 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804537 Affx-986696705 AX-385291086 3 111522308 CCCATGACTTCTGTTAGTATCAGCATAATCATACA[A/T]TGTCAAGAGATTCCTAAATCTCGGAAGTCAGGTCC W 4 1 2 1 600010 r 74 goat 3_111522308 3 111522308 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38379161 Affx-122976714 AX-123249520 3 111549985 CCATAAAGTATGTGAAGCTACTGCGCCAGCAGTGC[A/G]CGGAGGCAGAAGTGAAAGAAGTTTCATCCGCTCAT R 2 1 2 1 101000 f 74 goat snp52737-scaffold790-977316 3 5490907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418714 Affx-122946283 AX-123289062 3 111598884 CCAGCATCACAGGTGAGACAGAGGCGGAAGTCCAC[A/G]GGGTTTCACAAGACCCCTTCAGAGACGGGGGAACT R 2 1 2 1 201000 f 74 goat snp52738-scaffold790-1026215 3 5441606 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381539 Affx-122974839 AX-123251897 3 111631111 GGACTCCAAGAAAACCTCCGCACCAGTGGTTTTCC[A/G]TCTTGGAGATACATCTGTTCACGTCGCTGCACACA R 2 1 2 1 201000 r 74 goat snp52739-scaffold790-1058442 3 5409301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392666 Affx-122966431 AX-123263023 3 111659662 AACTGGAAAAATCAAGAAGGGTCTGTGCATCCTGG[C/T]GGGAATAGGTTTTTTCTCCCTTTCTTTTATTTCGA Y 2 1 2 1 101000 f 74 goat snp52740-scaffold790-1086993 3 5380268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777737 Affx-122927589 AX-385264855 3 111693725 ATACCTTTAAAAAGTATATGTGAAATTGGGGTGAT[A/G]TTGAGTGCATTTCAGAGCTGTGTGTTTTATTCTGA R 2 1 2 1 101000 r 74 goat snp52741-scaffold790-1121056 3 5346420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454133 Affx-122919339 AX-123324466 3 111740812 TAGAGATACTGTTTTGTTACTGATTTTTCTCATGT[A/G]TTAAAGTTGTATTTGTGGGAGTTCCCTGGAAGTCC R 2 1 2 1 202000 f 74 goat snp52742-scaffold790-1168143 3 5299683 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464248844 Affx-1110390750 AX-515723413 3 111802936 ATCTGAGGTTATTGATATTTCTCCCTTGATTCCAG[C/T]TGGTGCTTCATCCAGCCTGGCATTTCGCTTGATAT Y 2 1 2 1 103000 f 74 goat 3_111802936_AF-PAKI 3 111802936 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379981 Affx-122975622 AX-123250339 3 111806829 AACCCTAACACGGAAGTCCCAATTCTGACAACAGA[C/T]GTCACAAGCACAGAGGACGGCAGTTTCCGCACGAG Y 2 1 2 1 101000 f 74 goat snp52743-scaffold790-1234160 3 5233653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801026 Affx-122944751 AX-385287940 3 111843331 TGTCTGCATATACTGTATTGTTCGTGCATCTACAC[A/G]CATGTACCTGTGATTTCACCACCAGTCAGCACTGG R 2 1 2 1 101000 r 74 goat snp52744-scaffold790-1270662 3 5197690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781486 Affx-122978613 AX-385268571 3 111915776 TAACACACATATTCTAAATGATCACATGAAGGTCT[A/G]TGATATTTCTGCATGTGGGTGGCCGAGTGCCCCCA R 2 1 2 1 101000 r 74 goat snp52746-scaffold790-1343107 3 5125372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419514 Affx-122945446 AX-123289862 3 111982177 CTTGACTAGGGATATTACTGTAAATAAATCATAGA[C/T]GACCAACAAATATGGAGACAAAGAAACCACAAAAC Y 2 1 2 1 101000 f 74 goat snp52748-scaffold790-1409508 3 5058744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387436 Affx-122970386 AX-123257794 3 112072099 TTCCTCAAAATGCAGAGGAACATTATCATTTTACA[A/C]AGGAGAAATAACCTGGGAATTTCTAACAAGAATAT M 2 1 2 1 101000 f 74 goat snp52750-scaffold790-1499430 3 4968078 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426665 Affx-122939926 AX-123297011 3 112126025 TTCTTGGACATGGAGTCTTACAATATAGACTCTTT[A/G]GTGTCTGGCTTCCTCCAATCAGTATTACGATCACA R 2 1 2 1 101000 f 74 goat snp52751-scaffold790-1553356 3 4914517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424200 Affx-122942506 AX-123294546 3 112173594 CTGCATGCTCTGACTCCCTACTCCAACAAAATGCT[A/G]TTGGTATTTTTATTTGGGTCGTATTATATGTATAA R 2 1 2 1 101000 f 74 goat snp52752-scaffold790-1600925 3 4866614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773380 Affx-122955796 AX-385260522 3 112226682 TCAGTGTAAGCCATTAAGACTTTACCATGGAAAAA[C/T]AGCATTTGACCATTCTCTAAGTTTCTCGTGTACTA Y 2 1 2 1 101000 r 74 goat snp52753-scaffold790-1654013 3 4814568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446863 Affx-122925248 AX-123317199 3 112257623 AGATACAGGCTGGTAGGTGCTCCATCAGGCAGCAA[C/T]AGGGGCCCCACGTTGGCCTTCACCCCATCCAGCTG Y 2 1 2 1 101000 f 74 goat snp52754-scaffold790-1684954 3 4783670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418184 Affx-122947074 AX-123288532 3 112290920 GCAAGAAATTTATAATCCCCTTTACACGTGTTTTG[G/T]GTTAGGAAGGAGTGGTGCGGCTTTCGTTCTGGGCA K 2 1 2 1 201000 r 74 goat snp52755-scaffold790-1718251 3 4757984 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444619 Affx-122926940 AX-123314956 3 112332505 GGCCTGGGCTCAGACAGAAACACTTAAGTGCGAAG[C/T]GGGATATGGATTGCACCCCCAGTTCAGCTCCGTAA Y 2 1 2 1 201000 f 74 goat snp52756-scaffold790-1759836 3 4716828 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391565 Affx-122966623 AX-123261922 3 112401794 GTTATAAGCCACCAAGGAGACGCTATGAGAGGCCC[A/C]AAATAAATTCACTTTGCATCATGGCTAACTTCACT M 2 1 2 1 201000 r 74 goat snp52758-scaffold790-1829125 3 4647929 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394171 Affx-122964930 AX-123264526 3 112431368 GTAAGATCTGTATAGAGATATCAAGTTAAAAATGA[C/T]GTCATCAGGATGACCCTATTCCAGTGCTGGTATCC Y 2 1 2 1 101000 f 74 goat snp52759-scaffold790-1858699 3 4618289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410213 Affx-122952566 AX-123280563 3 112439560 GCTGTGAGTGTGGCCTTGGTCAGCCCTTGATGTCT[C/T]CTCTTATTGGCAAACCCTCACACCAGTACCCAGTT Y 2 1 2 1 101000 r 74 goat snp12103-scaffold1447-604691 3 4610152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375887 Affx-122978495 AX-123246246 3 112502839 ACCAGGGGCCCTGGTGCTCACTCCAAGTGCAGCGT[A/C]CACTCCATGCCCAGGGCCTCAGCGGCATTTTCTGG M 2 1 2 1 201000 f 74 goat snp12102-scaffold1447-541412 3 4546390 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442139 Affx-122928328 AX-123312476 3 112568346 CCCATTTGGAATGTGGGTGCTATTCCGTGGATGGG[C/T]ATCCAAGACTGTCAAGGTCTCAGAGCTGGATCGAG Y 2 1 2 1 201000 r 74 goat snp12101-scaffold1447-475905 3 4480801 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767964 Affx-122939486 AX-385255179 3 112613336 GTGCCAAACAGGATGTAACTCACAGCTGAGTTTTC[A/G]ATGAACTTTTTACCTCTTGGACCGCCATGGGAAGC R 2 1 2 1 101000 f 74 goat snp12100-scaffold1447-430915 3 4436243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395113 Affx-122964153 AX-123265468 3 112645987 TCTACTACTCCTGAGGTCCACCCTGAGGCTGCTGT[C/T]GGCAGTTCCTAGAATAGTGACTGGTATGTATAACA Y 2 1 2 1 101000 r 74 goat snp12099-scaffold1447-398264 3 4404617 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447664 Affx-122923959 AX-123318000 3 112687676 GCTCTTTGTGGATCGTGCCAACAGCGACATAGCAG[C/T]GCTAATGTCTCTGGAGATCCCGACTGCCGTCCTCT Y 2 1 2 1 201000 f 74 goat snp12098-scaffold1447-356575 3 4363089 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442976 Affx-122928200 AX-123313313 3 112739878 TGATGGTATGTTCAACATGAGATTCCAGAACCTCA[G/T]AGGGAGGGCATCAGAGATGCTGGGTGATTTTTCTT K 2 1 2 1 101000 f 74 goat snp12097-scaffold1447-304373 3 4310331 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416400 Affx-122947855 AX-123286749 3 112777582 AAGACGGCAAATTAGGCGAATCCCACTTGGTAGGC[A/G]TCTCAGCAGGGTCCCCACGTTGTGCTCAGCCTTCT R 2 1 2 1 101000 f 74 goat snp12096-scaffold1447-266669 3 4272639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421909 Affx-122944247 AX-123292256 3 112825397 TTGTGCTGCGGTTTGCCAGGCAGCATTCTCAGCTC[A/G]TAACTCACACGGTTTTCATTTTATCCTTAACACTG R 2 1 2 1 101000 r 74 goat snp12095-scaffold1447-218854 3 4224922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784310 Affx-122975151 AX-385271361 3 112859855 ATAGGCTGCAGACCAATTGTACAAAGTGTATCACG[C/T]AATAGCTTCTTTCCCCAACAATGCATTCCACACTG Y 2 1 2 1 101000 f 74 goat snp12094-scaffold1447-184396 3 4183491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792688 Affx-122970563 AX-385279668 3 112895609 TTCTTTAGGGAAACTAAAGACCAGAAAGCCAGCAG[C/T]TATCCAGTCTGAAACTACAACAAACCAAACTGGTA Y 2 1 2 1 101000 f 74 goat snp12093-scaffold1447-148642 3 4147434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275347 Affx-1111834848 AX-519548922 3 112901970 TTTCTGCAGTGGTTGGTGTGTCAAGAGAGGCTGGT[A/G]TTGGTGAGTGGTTATGAAGGAGAAAGGATGTGAGG R 2 1 2 1 202000 f 74 goat GoatD01.056345 3 112901970 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424476 Affx-122941763 AX-123294822 3 112925091 AAGCATTAAGGTAGATCTTGGATTATTTTTGTGCC[A/G]TTCAGAAGAAAAAGAGCAACATCTGACTCTCTGAT R 2 1 2 1 101000 f 74 goat snp12092-scaffold1447-119160 3 4117968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431708 Affx-122936766 AX-123302049 3 113001783 TAACTCACATAGTCGAATTTTGTGACTGAATTTCC[A/G]TAGCTTTGCCTACACAGCCCACACGGAGATGTTCC R 2 1 2 1 101000 f 74 goat snp12090-scaffold1447-42468 3 4041443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433435 Affx-122935076 AX-123303776 3 113041653 CACAAAATCCTAACCACTGGACCACCAGGGAAGTC[C/T]CTGACCCATCTCTTTGATGTTCATGCTTCTGCCTG Y 2 1 2 1 103000 r 74 goat snp12089-scaffold1447-2598 3 4001522 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408022 Affx-122954301 AX-123278373 3 113055226 TAAAAAGCTGGTCAAACGTCTTGACGAGGAAGAGA[C/T]GGTTCACTGTGCTGACCGCATCCCCCAGCTAAACT Y 2 1 2 1 101000 f 74 goat snp15829-scaffold1661-10876 3 3989111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380609 Affx-122975247 AX-123250967 3 113091559 GCCTCCATACCAGAATCTGGCGCAGTTTTCAGTTA[C/T]GGAATCATAGTACCACTTTAATACAAACTCTCTGC Y 2 1 2 1 101000 r 74 goat snp15830-scaffold1661-47209 3 3953039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429619 Affx-122937697 AX-123299960 3 113136222 TGAGCTCAAAGTCAAGCTGCTGAGACACTTTCAAC[A/G]TACAGGCACAGCTGGGGACGTGGACCGGGAACACG R 2 1 2 1 101000 f 74 goat snp15831-scaffold1661-91872 3 3909972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408632 Affx-122953486 AX-123278983 3 113175811 AATTTGAGATGCCTTTTTCCTTTTCATAGCTGTCC[A/G]CTTGAAACTTAAAAAGACACCTCTCATTATGAAGA R 2 1 2 1 101000 r 74 goat snp15832-scaffold1661-131461 3 3871389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443155 Affx-122928061 AX-123313492 3 113236371 TCGGCAAGAGGAGGACTTCCGAAGCCGTCCTATGC[A/G]CTTTGAGTTTCAGATTCACGTGGAAGGCAGGCCAG R 2 1 2 1 101000 r 74 goat snp15833-scaffold1661-192021 3 3811056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396853 Affx-122963254 AX-123267208 3 113278981 GAAGGGGGGCCGTATAGCCTCTGATTTAGCCCCAA[G/T]CAGATATAATGTCTCCCTGAAGTTGGCTTGTGCGA K 2 1 2 1 201000 r 74 goat snp15834-scaffold1661-234631 3 3768350 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429575 Affx-122937808 AX-123299917 3 113336914 CAGGTAGACGTCTGTGTTCTCACCTGTCACCCCTG[C/T]GGGCAGCGAGCACCTGGACTTTTATGCATCCGTGT Y 2 1 2 1 102000 r 74 goat snp15835-scaffold1661-292564 3 3711110 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420165 Affx-122945578 AX-123290513 3 113399996 AGCCTTTCAAATGTTGAATCCTGTCGGGTGAGGAC[A/G]CGCCTGGCCTGTTGGTGGGTTTCACGGGCATCCTT R 2 1 2 1 101000 f 74 goat snp15836-scaffold1661-355646 3 3648388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414954 Affx-122949077 AX-123285303 3 113452924 GCTCAGAGGAATGAACTGCTGGGCCCGGAGAAGAA[C/T]GGAGTGACCATGGGGAGCAGGATCTGAGGCAGGAG Y 2 1 2 1 101000 f 74 goat snp24416-scaffold2477-1504 3 3593852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413987 Affx-122950286 AX-123284336 3 113483736 ATCTGTGTCTTTATCTAAGAAATTAACACTGATAC[G/T]ATTAGCTATACAGACTGTGAACTCAGCATTTAGCA K 2 1 2 1 101000 r 74 goat snp24417-scaffold2477-32316 3 3563255 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436926 Affx-122933194 AX-123307264 3 113534897 ATGTCAATTAAAATGGAACTCAGAAGGACGATAAA[C/T]GTATCTTACACATAACATTTTCTGTTTTCATTTAT Y 2 1 2 1 101000 f 74 goat snp24418-scaffold2477-83477 3 3512168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436908 Affx-122933208 AX-123307246 3 113587905 ATAGGCACACAGCAGTGTTCAGGTTTGAATGCCAT[A/G]ACTCAGTGAAGCTGAGTGCTCCCAAAATGCCGCTG R 2 1 2 1 101000 f 74 goat snp24419-scaffold2477-136485 3 3458938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779239 Affx-122944107 AX-385266343 3 113625758 ACGGGTTCCCAACTGTGATGAAAATGCCCCAGTAG[C/T]AAATGTGATGTTTGCTATTCGTTTGAGAGATTTTT Y 2 1 2 1 102000 f 74 goat snp24420-scaffold2477-174338 3 3425877 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278026 Affx-1111836213 AX-519551518 3 113669696 GAGTGCATCTTACTGTATTACTAACTCCTGGCCTG[A/G]CATATTTGTTAAACTTAATGAAATTGAACTGGGAG R 2 1 2 1 101000 f 74 goat Random2.2K-383 3 113669696 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777507 Affx-122960756 AX-385264626 3 113683257 GCTCTTTATTATGACTTTCCTAGGGTACTGCCCAC[C/T]GAACTCTGTTTACACAGGCTGTGCTTTTATTGTTT Y 2 1 2 1 101000 r 74 goat snp24421-scaffold2477-231837 3 3377935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418084 Affx-122946603 AX-123288432 3 113713622 ACTTTATAAGGACTTTTTTTCTTTAAAACCCCTTA[C/T]GCTTACGGTTCCTGCAATCAAGGTCAGTTTTTTTA Y 2 1 2 1 101000 r 74 goat snp24422-scaffold2477-262202 3 3347909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409888 Affx-122952903 AX-123280239 3 113760692 AACACACCTGAAACAGAAGAAAGTGTCAGCAAAGA[C/T]GAAGAGGAGCAAGACTGAAATTTTAGAACAAACAA Y 2 1 2 1 101000 f 74 goat snp24423-scaffold2477-309272 3 3303465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446547 Affx-122924851 AX-123316883 3 113805185 TCGGGAACGATTTGGGGAAGAAAATGTATGACCTT[A/G]CAGCACCCCATGCCCCAGATAGATCCCAGATGGAA R 2 1 2 1 101000 f 74 goat snp4734-scaffold1157-21395 3 3262850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453040 Affx-122920080 AX-123323373 3 113864365 AAGCTGAGCACCACTTCCCATCAATCGGCGCCTGC[A/G]TTTCTTCTGTAAACTGTCAGGATACATCCTTTGAC R 2 1 2 1 101000 r 74 goat snp4735-scaffold1157-80575 3 3209476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429110 Affx-122938019 AX-123299452 3 113914168 GGAGGTGGGCCTGTCACCACTGTTTATAGCACGGT[C/T]GCCTTGGGAACGCAGGTGACATCCCCAAGAGTGTC Y 2 1 2 1 201000 f 74 goat snp4736-scaffold1157-130378 3 3161113 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400856 Affx-122959777 AX-123271211 3 113943596 CCGGAAAACAGGCAGGCTCCAAGGCAGCTCAGCTG[C/T]ACCCTGCTCTGAAATTGCATGGTCCGACGTGGGAA Y 2 1 2 1 101000 r 74 goat snp4737-scaffold1157-159806 3 3131653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394253 Affx-122964730 AX-123264608 3 113987287 TGACTTAGCTTATGATGTGGACCTCTCTGTGCTTA[C/T]AAGCTGTGCTTAAAACTCTCAAAACTGACCCACAT Y 2 1 2 1 201000 r 74 goat snp4738-scaffold1157-203497 3 3086863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385412 Affx-122971337 AX-123255770 3 114024287 GAAAGAGAAAGAATCTTAGCATTCCTCCTCACCCC[A/G]CCTGCACTTAGAGTAAGCTGGCTCCTTAGGGCAGA R 2 1 2 1 201000 r 74 goat snp4739-scaffold1157-240497 3 3059781 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453244 Affx-122920413 AX-123323577 3 114056851 ATTCATGAAGTCCTAGGAAGTCACTGCATGTGGTT[A/G]TGACTGTATTCAACACAGATGAATAAATCTTGTTA R 2 1 2 1 201000 r 74 goat snp4740-scaffold1157-273061 3 3027003 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426848 Affx-122940497 AX-123297193 3 114105865 GTCTAGAATCTGGATTGTTTTTGGACAGGAAGGTC[A/G]CCCCGAGTTGGGATGGTTGGTATGACCCCCCGAGT R 2 1 2 1 101000 f 74 goat snp4741-scaffold1157-322075 3 2978396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378565 Affx-122976603 AX-123248924 3 114123940 TGTCCATCCAGGAGGGGTTCTGGCTGCTCAGATGG[A/G]CGGCGCCCCTCAGGCAGAGGACTTCCTCATTCCGA R 2 1 2 1 103000 r 74 goat snp24633-scaffold2509-84042 3 2960058 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388971 Affx-122968796 AX-123259329 3 114164292 CACATGGCGCTTTTGGGCCAAAATATAGAAGGGCC[A/G]GAGTGTCACTCTCCAGTGTGTCTTCTCAGCTGTAT R 2 1 2 1 101000 f 74 goat snp24632-scaffold2509-43690 3 2919887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411650 Affx-122951569 AX-123282000 3 114195412 TGTTGTTTCAGGCCATTGGTTTGTAGCGATGTGTT[A/G]CAGAAAGCCGATACACAGTAGGGGCCCAGGTAGTC R 2 1 2 1 101000 f 74 goat snp24631-scaffold2509-12570 3 2889608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272183 Affx-1111833375 AX-519545935 3 114417276 TTCATGGGGTTGTGAAGAGTCAGACACGACTGAGC[A/G]ACTGAACTGAACTGAAATCCTTTGTTCTCAGTGAA R 2 1 2 1 303000 f 74 goat 3_114417276_AF-PAKI 3 114417276 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429610 Affx-122937704 AX-123299951 3 114441716 CAGCTCACTGCAAGCCAGTCCCCATCTCAAGGTGA[C/T]GTGTAATTCTTCAATTTCCTAACAAGTAACAAACG Y 2 1 2 1 101000 r 74 goat snp29174-scaffold3130-115137 3 2644098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415007 Affx-122949034 AX-123285356 3 114495946 TTTCTTTCTGAATATTCTTTGAGGTATATATCCCG[C/T]GATGAGAAAACCTGAAGAAGATTTCAGGTGCAAGA Y 2 1 2 1 101000 f 74 goat snp29173-scaffold3130-60907 3 2594329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418874 Affx-122946117 AX-123289222 3 114554536 AGGCCACAAGACAGGCGTGGTGAGACCTGCTCACT[A/G]CAAACAGTGTTTCTGGGAGTTTCTCAGATCACCAA R 2 1 2 1 201000 f 74 goat snp29172-scaffold3130-2317 3 2545584 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433003 Affx-122935793 AX-123303344 3 114586405 CTCCTCCTGCCTTCAATCTTTACCAGCATCAGGGT[A/C]TTTTCCAATTTGGGTCTAGTTAGTGTTAATCCTGA M 2 1 2 1 201000 r 74 goat snp24076-scaffold2455-91009 3 2325911 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437018 Affx-122933125 AX-123307356 3 114638801 ATTTGCAAACAACCATGTTTGATTCTCTTCATTCT[A/G]TTAGATATTTTTTAAAAAGAATTAATTTCTGATCT R 2 1 2 1 101000 f 74 goat snp24075-scaffold2455-38613 3 2273358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777730 Affx-122955249 AX-385264848 3 114690399 CCACCCATCTGTCTGGTAGAGCCTAGATTTTTAAA[A/G]CAAGGATCGTTTGTTTCCTCAAAGGAAACTGGGTG R 2 1 2 1 101000 r 74 goat snp17455-scaffold1806-12886 3 2222124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453424 Affx-122919881 AX-123323757 3 114734749 AAATTTCAGAGTATCATAATGATCATTCAGATAAA[C/T]GTCTAAAGGGGACAAACTTTTTACCTTTCAGCGAC Y 2 1 2 1 201000 f 74 goat snp17456-scaffold1806-57236 3 2177464 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416846 Affx-122948105 AX-123287194 3 114774449 CTGAAGCTGGGATGTTCTGTTGGGACATCTGGAAG[C/T]GTCCTGGCCTCAATTTTCTACCTAAACGCTGAGCT Y 2 1 2 1 101000 r 74 goat snp17457-scaffold1806-96936 3 2149000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441708 Affx-122929154 AX-123312045 3 114821635 TTTCAGGAGACGACTGTTAACTCCAGGTGCTGCGC[A/G]TTGTCTTCCATGTCTCGACTATTTATCCTGTCTAC R 2 1 2 1 101000 r 74 goat snp17458-scaffold1806-144122 3 2102227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278183 Affx-1111836214 AX-519551672 3 114845737 ATATGTCTCTTTTTCAAAAGTTAATATTTTTTTGA[C/G]AGAAAAGGATCAGACAACTTGGTTCTTAAGTGTTT S 4 1 2 1 101000 r 74 goat Random2.2K-385 3 114845737 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394875 Affx-122964755 AX-123265230 3 114857097 ACGGGATTTTGTGTGAATATCTCATTTCTCTGGGG[C/T]AAATGCCCAGGAGTAGAGTTGCTGGGTTGCCTGGT Y 2 1 2 1 101000 f 74 goat snp17459-scaffold1806-179584 3 2068482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427452 Affx-122940034 AX-123297795 3 114891802 GAAGTTGAAGTCCTAAGCACTGGACTGCCGGGGTA[G/T]TCCTTCAAATTGGTTTTTAATACATAACAATTCAC K 2 1 2 1 101000 r 74 goat snp17460-scaffold1806-214289 3 2033691 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395502 Affx-122963885 AX-123265857 3 114927776 CAAGAGAAATGAGTTCCCCCAGTCAGAGGAATGGG[C/T]AAGGGTTGTCTAGGAGCAGGGAACTCTGGTCAGTG Y 2 1 2 1 102000 f 74 goat snp17461-scaffold1806-250263 3 1999955 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432590 Affx-122935512 AX-123302931 3 115015238 TGGGAGCCAGTGATGCCCTGGGGTGGCCAGGTCTG[C/T]GTGCCGAGGGCTCCTGCTCACACAGTGAATGCTCA Y 2 1 2 1 103000 r 74 goat snp17463-scaffold1806-337725 3 1911105 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379985 Affx-122975619 AX-123250343 3 115046839 TGCCTAAGTATATGAGTCCTTATCTCTTAGAAATA[C/T]GCGTGAAGAGGGTACAGAAGAGATTTTATGATGCC Y 2 1 2 1 201000 f 74 goat snp17464-scaffold1806-369326 3 1879688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425349 Affx-122941587 AX-123295695 3 115095779 AAACCCAACTTCAGTTACTATTCACATTCCCAATC[A/G]TCTTTTGTGTACCTGAAAAACAGCTTGGTCGGGAC R 2 1 2 1 101000 f 74 goat snp17465-scaffold1806-418266 3 1830855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387371 Affx-122970467 AX-123257729 3 115126034 CCGAAATATTTAATTAAAGAAACAGAAGGGTAATG[C/T]GCAATTTCTTTTTCCCAGAATTGGAGGCACTACCC Y 2 1 2 1 101000 r 74 goat snp17466-scaffold1806-448521 3 1801638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788395 Affx-122958812 AX-385275413 3 115163563 TTTTAAAACTAAACCTTACTCAGTTACACAGAAAT[A/G]CTGTTGTATCTAGAGTAAGTTGAGCTGTTGGTGCA R 2 1 2 1 101000 r 74 goat snp17467-scaffold1806-486050 3 1764231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446377 Affx-122925590 AX-123316713 3 115207786 AGAAGCCGCATCCTCTGAGGACCTTTCCTTGGCTG[C/T]ACTCTATCCATGTTTGACTACCTCATTAGAAACTC Y 2 1 2 1 101000 r 74 goat snp17468-scaffold1806-530273 3 1719278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769444 Affx-122931958 AX-385256614 3 115257571 TGCAACTAGTCGTCACACCATGTGAGATGCACAAA[C/T]ATTCAGAAGATGAAAGATGTTAAGTGCTGAGGGGA Y 2 1 2 1 101000 f 74 goat snp17469-scaffold1806-580058 3 1669699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445193 Affx-122925527 AX-123315530 3 115308000 TGCAGTTGGGAAGTGGGCAGTGATATGTCCAGGAT[C/T]CAGGCCCCCAGGACTCACCTGTCAGTGATGCTGAC Y 2 1 2 1 202000 r 74 goat snp15827-scaffold1659-217357 3 1507467 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441897 Affx-122928615 AX-123312234 3 115336832 GATGGCTCCTCCCAGCTGCCGCCCCTGGCCTAGGA[C/T]GCAGTGTAGCTCAATAACATGAGCTGATAAGGAGG Y 2 1 2 1 101000 r 74 goat snp15826-scaffold1659-188525 3 1479575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387694 Affx-122969815 AX-123258052 3 115389897 TTAGCCAAGAAAGAGAAGAAGGTTTTAGCCATCTG[A/G]AGGAGGCCTGTTAAACTCTTGAATGTGGCCAGCTT R 2 1 2 1 101000 r 74 goat snp15825-scaffold1659-135460 3 1425992 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402007 Affx-122958759 AX-123272360 3 115430599 AACACCTGACCACATGTCACACAACCAACCCTTCA[A/G]AGGTTGAATGAAGTGGGCTGGAAGCTTTGCCCCAT R 2 1 2 1 201000 r 74 goat snp15824-scaffold1659-94758 3 1385645 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450817 Affx-122921799 AX-123321151 3 115492211 AGGGACACGTAATAACAACCACAAGGAGATGGCGT[A/C]TCCCATGCACCAGGTGGCTGGAATGATAGACCAGC M 2 1 2 1 101000 f 74 goat snp15823-scaffold1659-33146 3 1327171 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446211 Affx-122925713 AX-123316547 3 115551240 AGGCGTATGCAGAACAGTCCACCCAGCAACAGCAG[C/T]GTACGCAGAACAGTCCACCACCACCAACAGCAGCG Y 2 1 2 1 202000 r 74 goat snp57090-scaffold9081-61950 3 1270209 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767252 Affx-122976355 AX-385254533 3 115593701 CAACATTAAAAACCCACCAGGCACTCTGTGTGAGC[A/G]TGGGAATTCTTCTATAGAACAAATGATCAGAAAAA R 2 1 2 1 101000 f 74 goat snp57089-scaffold9081-19489 3 1228606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403325 Affx-122957824 AX-123273678 3 115689389 CTTAATATGCGTTCACTTTTTGACCAAACGATCCC[A/G]CTTCCAGGAATGCATCCCAAAGGTCGTGGGTGAAA R 2 1 2 1 101000 f 74 goat snp24964-scaffold2564-76100 3 1144810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385553 Affx-122971228 AX-123255911 3 115745279 AGAGAGGGGAAGCTTGTGCGTTAAAAATGACACTC[G/T]AATATCTGGCCTTGGCAACAAGAGGAGTCATCCTC K 2 1 2 1 101000 f 74 goat snp24965-scaffold2564-131990 3 1091568 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428899 Affx-122938926 AX-123299241 3 115896763 TCATCATCTCGGTGTGGAGAAATCAGGATACATAC[A/G]CTGATTGCTCCAAAGAAGACAGAAGGACTACATGA R 2 1 2 1 101000 f 74 goat snp24968-scaffold2564-283474 3 987087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440462 Affx-122929388 AX-123310799 3 115936546 GGTGAGCCTGGCCCTGAGGTGAGGCTGGCCCCTAA[A/G]GTGAGCCTGGCCTCAGGTAAGCCTGACTCCTCAGG R 2 1 2 1 202000 f 74 goat snp24969-scaffold2564-323257 3 949425 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375844 Affx-122978528 AX-123246203 3 115986152 TGGAACTCTGAAAAGTCTTTGAAACCTGGAATGAA[C/T]ATGGTATGTTCCAAAAAAGATTTTCGTTTGCTTCA Y 2 1 2 1 201000 r 74 goat snp24970-scaffold2564-372863 3 905464 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405991 Affx-122955517 AX-123276343 3 116010625 GCTAACCAAAGCCTTTTAAATGGCCGTGAATTCCT[C/T]GGGATCTTGCTGAGAGGCTCTGTCTGTGTGTAAGG Y 2 1 2 1 101000 f 74 goat snp29140-scaffold3125-7445 3 2516863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408959 Affx-122953922 AX-123279310 3 116103520 GGGGGAGCAAAGTGAATAAGGAAGAAAGAGAAAGC[A/G]TGGAGTGAAGGTTCTGGAACATCGCCCTGACCCAG R 2 1 2 1 201000 r 74 goat snp29142-scaffold3125-100340 3 2431089 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449682 Affx-122922556 AX-123320017 3 116144614 GTGAAGAGAGTGGAAATCGTCAAAACAGAGGCCGG[C/T]GTATGGGATGACGGTTACATAGTTTTAAATGGCTT Y 2 1 2 1 201000 r 74 goat snp29143-scaffold3125-141434 3 2389860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603594 Affx-1002479413 AX-310998304 3 116167006 AGATATAACAATTATAAATATATATGCACCCAACA[C/T]GGGAGCCCCACAATATGTAAGACAAATGCTAATAA Y 2 1 2 1 303000 f 74 goat 3_116167006_RH-map 3 116167006 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378988 Affx-122976393 AX-123249347 3 116193593 AAAATTATACCTTGATAAAGTGGTTTTAAAATTAC[A/G]TAATTGTTATGCTGACATCTTAACACATCTACAGG R 2 1 2 1 101000 r 74 goat snp11602-scaffold1426-13596 3 776966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447244 Affx-122924957 AX-123317580 3 116223610 ATTACCAGCTGAAAGAAGCCTTGGTTCTCAAACAC[A/G]TCCAGCACCTGTTGAGAGAGAGAGACAAGCTGGGT R 2 1 2 1 101000 f 74 goat snp11603-scaffold1426-43613 3 753303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436445 Affx-122932998 AX-123306783 3 116260679 AAACCGCCTGGAGGCTGGCCGTGCTATGGAACACC[C/T]GAACTGATAAGACATGGGGCTTATGAACATAGTAA Y 2 1 2 1 101000 r 74 goat snp11604-scaffold1426-80682 3 714754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603136 Affx-1002479414 AX-185909890 3 116287414 TGTTTCTTGACTTCCTACTTTTGCATTCCAGTCCC[A/C]TATATTGAAAAGGACATCTTTTCTGGGTGTTAGTT M 2 1 2 1 103000 f 74 goat 3_116287414_RH-map 3 116287414 C A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603138 Affx-1002479415 AX-413837331 3 116306750 GAAATTAGAACACTTCCTAACACCATACACAAAGA[G/T]AAACTCAAAATGGATTAAAGACCTAAATATAAGAC K 2 1 2 1 103000 f 74 goat 3_116306750_RH-map 3 116306750 T G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38393842 Affx-122965157 AX-123264197 3 116329221 AAGATCCCTCCCCAAATTAAAAAAAATTAAGCTCT[A/G]GAAGCAAGGTCCAAAATCAGATACCCTCAGCAAAC R 2 1 2 1 101000 r 74 goat snp11605-scaffold1426-149224 3 650730 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603229 Affx-1002479416 AX-413837410 3 116365210 CTAGAGGGGAGAAGGCCCATCAGGCAGTGGGAGAA[A/G]TAATCCACAGCTTCTGGGAGAGGAAATAAGACAGT R 2 1 2 1 101000 r 74 goat 3_116365210_RH-map 3 116365210 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38417632 Affx-122946856 AX-123287980 3 116390536 CGGGGAGTTAGCAGTTGGTCTGTGCAGAAGCCTGC[C/T]GTTGTGGCAGGCTTGGCGTGTTTCCTGTGACTGCG Y 2 1 2 1 101000 f 74 goat snp11606-scaffold1426-210539 3 590753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603142 Affx-1002479417 AX-413837335 3 116437755 CCAGAAGAGACACACAGGAAGTACATTTGGTCATT[A/G]TTACTGTCACTGAAACATATTGCTATCCAGACTAC R 2 1 2 1 101000 f 74 goat 3_116437755_RH-map 3 116437755 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425350 Affx-122941586 AX-123295696 3 116443446 AGGTGGGTCTTGTCCACAGTTGGCAACACAAGTGT[G/T]GAAGCATCTTTATTGTTGTTTGGTTGTTAAGTTGT K 2 1 2 1 201000 f 74 goat snp11607-scaffold1426-263449 3 537332 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603144 Affx-1002479418 AX-413837337 3 116479323 TATTAGCCACAAACACGCCTGTCCCAGAGACAGAA[A/G]AAAGAACACTAGCAGGACTTCTATCCCCAGGTCAT R 2 1 2 1 102000 f 74 goat 3_116479323_RH-map 3 116479323 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38407840 Affx-122954530 AX-123278191 3 116482810 ATGATTCCGTAGTTGCTTGTGTATTCGTGAGGTTG[C/T]ACCACATCGCCACTAATTCCAGGACATTTCCATTC Y 2 1 2 1 101000 f 74 goat snp11608-scaffold1426-302813 3 498081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603235 Affx-1002479419 AX-413837416 3 116528611 GCACACTCCAGCCAAATGCATGCAAGGAAGGGTCC[C/T]CTGGGACGCTCTAACCCTTTAGATTTCCAAAGTCT Y 2 1 2 1 101000 r 74 goat 3_116528611_RH-map 3 116528611 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603148 Affx-1002479420 AX-413837340 3 116547139 TCAGGTCGCATATGGATACTATCAATATTGAAATG[A/G]AATTTCAATTATATACAGGAAACAAAAAAGCAAAT R 2 1 2 1 101000 f 74 goat 3_116547139_RH-map 3 116547139 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378509 Affx-122976646 AX-123248868 3 116554711 ATCGAAACATTTCAACACAGAAAATCAACTGGACA[C/T]GGAAGATAGTATGCAGGAAACGAAGGACAAAAAGG Y 2 1 2 1 201000 r 74 goat snp11609-scaffold1426-374714 3 427607 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408311 Affx-122953770 AX-123278662 3 116566088 GGAAAAGCAGATAAAGTCTAAGAACAGACACGTAA[C/T]GTAAGAAGAGAGAGGGAACGTGGACAAAGCATGAA Y 2 1 2 1 201000 f 74 goat snp36346-scaffold4353-5630 3 412873 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420706 Affx-122944787 AX-123291053 3 116630641 TAAAGTATTTTTTGGAACAAACATTTGAGAACCCA[G/T]CCTTTCTGGAAATAAGACTTCAGTGTCGTGTCGAG K 2 1 2 1 201000 f 74 goat snp36347-scaffold4353-70183 3 349076 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603150 Affx-1002479421 AX-413837341 3 116740369 TTTGTACATACTACAAGCAGGTTTGTTACTTCTAG[C/T]ACTTTTATGCTCTAACAGTTACAAAAAGTTCACCT Y 2 1 2 1 101000 f 74 goat 3_116740369_RH-map 3 116740369 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38400979 Affx-122960100 AX-123271332 3 116743421 TCTCTTCCCAAGTTGACAGCCCCTCAAACCCTCAC[C/T]TGCATTTCCGGGTCCAAACAGCTCTGAAAAGCACA Y 2 1 2 1 101000 r 74 goat snp36349-scaffold4353-182963 NW_017189534.1 37978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603240 Affx-1002479422 AX-413837421 3 116765506 CCTTTTAAAGAGCCCCTACCATCACCCCTCAAGTA[A/G]CTAATGGATATAAACTCACACTAGAGCATTAGTGA R 2 1 2 1 201000 r 74 goat 3_116765506_RH-map 3 116765506 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452179 Affx-122921232 AX-123322512 3 116773477 CAGGGAAAGACACACTGGGCTGACACTAACCAAAC[A/G]GAACCTGGACTTGCTCTGTCGACATCAGACTCTAC R 2 1 2 1 101000 f 74 goat snp36350-scaffold4353-213019 NW_017189534.1 64315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603155 Affx-1002479423 AX-413837344 3 116827349 TATAGCCTGTTTAAGTACCACTTGATATAATCATT[A/G]ATGACTAAGAATTTTGATAATAATTTGGTAATGTC R 2 1 2 1 101000 f 74 goat 3_116827349_RH-map 3 116827349 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603654 Affx-1002479424 AX-413837792 3 116867220 AGGGAGTGAGAAATGCTAAAGAGAAAAAGGAAATT[A/G]TAGAGGACAAATAAGGAGTTCAGATGGAGGTCAGT R 2 1 2 1 400000 r 74 goat 3_116867220_RH-map 3 116867220 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603656 Affx-1002479425 AX-413837794 3 116908666 AGACACTGAGTAATTTTCTTGAGGACACACAGCTA[A/G]GAGTATGAGATCCAGGTTCTAAACCCAGACAATTT R 2 1 2 1 201000 r 74 goat 3_116908666_RH-map 3 116908666 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603157 Affx-1002479426 AX-413837346 3 116953479 TTCCATGGACAGAGGAACCTGGAGGACTGCAGTCC[A/C]TGGGATCACAAAGAGTCAGATAAGACTGAGTGACT M 2 1 2 1 303000 f 74 goat 3_116953479_RH-map 3 116953479 C A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603159 Affx-1002479427 AX-413837348 3 116998730 TCGGGTTGTAATTCAATAAATGCTCACTGACCTTC[A/G]CACTGTATGGCAGGTTCATCTATATATATTTTCTC R 2 1 2 1 101000 f 74 goat 3_116998730_RH-map 3 116998730 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468278030 Affx-1111836215 AX-519551522 3 117344700 AGCAGGTTTTCAGGGAGGGGGCATGAAATAAACAC[A/C]TCAACTTGCAAAGAGAACCTGGGCATTTACAAGGA M 2 1 2 1 101000 f 74 goat Random2.2K-390 3 117344700 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804180 Affx-986696711 AX-385290828 3 117776320 CCCCTTGCAAAGGTAAAACCTTTGTTGAGGCAGAC[C/T]TTTCTATGAATCTTAATTTTCTGACATGGGTAACA Y 2 1 2 1 600010 f 74 goat 3_117776320 3 117776320 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320802979 Affx-986696110 AX-385289864 3 118818403 AAGAGTAAGGCTCTAGCAAACCAGTATAAATTAAG[A/G]CCGAGCAGAGTGGGTTTCCATCCATCGCCATGTGC R 2 1 2 1 600010 f 74 goat 3_118818403 3 118818403 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 468278186 Affx-1111836216 AX-519551675 3 118955088 CACGTACTCACTGTGTTCACTGCAGACGACCGTGC[A/G]ATAGCAGGGATCTGCCCTACAATGCCCAGGTGGAT R 2 1 2 1 202000 r 74 goat Random2.2K-392 3 118955088 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272016 Affx-1111833376 AX-519545782 3 119768649 CTGTTGGGCTTCCCTGCCTCTTTCCTGGACCCCTC[A/G]CCAGGCCATTTCCCTCAGAACTGTGGAGTCACTCA R 2 1 2 1 102000 r 74 goat 3_119768649_AF-PAKI 3 119768649 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278188 Affx-1111836217 AX-519551677 3 119986641 GGGATGACTACTGTCTGGTTGTGATGTGAAGGGGC[A/G]CTTTTTCTAGTTTTGATGTGCATGAGGCTACTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-393 3 119986641 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804545 Affx-986696713 AX-385291093 3 120027299 TTTTCCATTATATTAATTATATTTGATACTTTTGG[A/G]GCTTGCTACTTTTTAGCATCTAGAATCATTTATTT R 2 1 2 1 600010 r 74 goat 3_120027299 3 120027299 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38426974 Affx-122940397 AX-123297319 3 CCATAAACCTCTGCTTTGCAGAGGGGACTCTATTA[A/C]AATTCATTTATTTCACAACAGTTCTAAATTTCTGA M 2 1 2 1 201000 r 74 goat snp35512-scaffold428-358707 NW_017189517.1 21270534 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789306 Affx-122941634 AX-385276316 4 15471 TTTATCCTCCCTTGTGACACTGGAATACAGAAAAG[C/T]ACTGGTCTTACCATCTCAGTTGGAGGAGAACAGAT Y 2 1 2 1 101000 f 74 goat snp46390-scaffold641-15471 4 119118717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272120 Affx-1111833430 AX-519545878 4 50909 AAGGTTCATCCACCAAGACTGGCCACAGGCTGGCC[A/G]CATGGGCTTCGGTACAACCAGATGGCAGATTCTTG R 2 1 2 1 101000 r 74 goat 4_50909_AF-PAKI 4 50909 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381662 Affx-122974745 AX-123252020 4 86784 TTTACAAAGTGTGGCTATGAATACGGCTTTAAACT[A/G]ATTTTAGTTGAAATATTGACTGATTTGTTAAAATG R 2 1 2 1 101000 f 74 goat snp46391-scaffold641-86784 4 119047514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785183 Affx-122949165 AX-385272229 4 122901 AATAACTACTGCTTGCATGTGATAATAATGTTGTT[A/G]CTGTTTTATTACTCTTAGAGATGCAAAAGTAGATA R 2 1 2 1 101000 f 74 goat snp46392-scaffold641-122901 4 119011329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781215 Affx-122929161 AX-385268300 4 193748 ATGAAAAGGACGTGCAGTAACATACCCAGCAGGGT[A/G]TTTGCCATTGACATCATCAGTAAATGATGGGAAAT R 2 1 2 1 101000 f 74 goat snp46393-scaffold641-193748 4 118939982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801521 Affx-122938520 AX-385288430 4 274857 AGTGAAAAACTAAGGAATAAAAAGCAAATGAACCA[C/T]TTTAGCAACAGAACTGATTCTTTGTTGCCAACTCC Y 2 1 2 1 201000 f 74 goat snp46395-scaffold641-274857 4 118858148 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779350 Affx-122979026 AX-385266454 4 330180 AATATTGTGTTATGGTTACATAGCACAAAAAGATG[C/T]AATTTTGTATATTAACAAAATATATTGTGGAGAGG Y 2 1 2 1 201000 r 74 goat snp46396-scaffold641-330180 4 118807086 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796869 Affx-122975656 AX-385283812 4 378530 CTACAGTAAAGCACATACACTGGAATCTGGGTCTT[A/C]AAGTTGGCTTCTGCAGAAATCTAAAACAAATATAT M 2 1 2 1 101000 f 74 goat snp46397-scaffold641-378530 4 118757652 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388033 Affx-122969552 AX-123258391 4 427227 ACCAAAGGTAACTACTGGTTTACAGTGGTGATACT[G/T]GTAGAACGGGACATCAATGACAAAAACACCAGAGT K 2 1 2 1 101000 r 74 goat snp46398-scaffold641-427227 4 118708961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422735 Affx-122943254 AX-123293081 4 461272 TAGTCTGAAATTCACAAATTTATTCTCTTTAAAAA[C/T]AAGGTCTTGAAATATGAAAATACATTAGGTTAGTT Y 2 1 2 1 103000 r 74 goat snp46399-scaffold641-461272 4 118674240 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431295 Affx-122937092 AX-123301636 4 519686 AAATGCAGAGCAGAATCTCCCCTGGAGGCGGTGGA[G/T]GGAGAAAGCAGTGCTAACCTCCAGCTGTGGGCTGG K 2 1 2 1 201000 r 74 goat snp46400-scaffold641-519686 4 118615150 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438295 Affx-122931392 AX-123308633 4 563098 TCTAGATTTTATCCACTACAGTTTCTAAATTCTTT[C/T]TTCCATAGTAAATTATGCCCTTTCAGCCCAAATCG Y 2 1 2 1 101000 r 74 goat snp46401-scaffold641-563098 4 118572114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278035 Affx-1111836218 AX-519551527 4 578015 CTGTGTTGCTTGTCCAGTTTATTGAGGGCTCTCCC[A/G]GGGTGATGGTGAGGGGTCTGGCCTGGCTCTCCTGA R 2 1 2 1 101000 f 74 goat Random2.2K-394 4 578015 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408767 Affx-122953387 AX-123279118 4 657922 GGCAGAAAAGCTGGGTACTTACTGCTGGTACCACC[C/T]ACACTGCAGCTGCCAGAAGCTGTCAGGCATCTGGA Y 2 1 2 1 201000 f 74 goat snp46403-scaffold641-657922 4 118479343 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792471 Affx-122919951 AX-385279452 4 694292 AGAGTAGATATAAGTATATTGGAGGAAAGTACAGG[A/G]ACACACTCCTAAAATCTCAGGGTGCAAATAAGAAA R 2 1 2 1 101000 r 74 goat snp46404-scaffold641-694292 4 118440178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405860 Affx-122955854 AX-123276212 4 778594 AGAATATCTTCTTTAAAATAAATTAAACCCTGCTA[C/T]AACTAAAGCTGTCAAATTACTGTCAAATTTTTACT Y 2 1 2 1 101000 r 74 goat snp46406-scaffold641-778594 NW_017211816.1 6897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413829 Affx-122949885 AX-123284178 4 808989 TAATAAATATGCTATAAAACACTACCATAGTCAGA[A/G]CTCAAAAGTTTCACTTTAAAAAATTAAAAACTATT R 2 1 2 1 101000 f 74 goat snp46407-scaffold641-808989 4 118324857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434221 Affx-122934846 AX-123304562 4 842556 GTGAAGTATATTATCTATAATTATATACTTTCAAG[A/C]TTAAAAATTGCCTGTCAACCCTACAATGTTGACCA M 2 1 2 1 101000 r 74 goat snp46408-scaffold641-842556 4 118291067 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425109 Affx-122941228 AX-123295455 4 905679 TCATTTTGTAAATATCATGGTGCTTAATATTAGAC[A/G]TCTGACCACATCCCACATCTTGGGGAGAATGTAAA R 2 1 2 1 201000 f 74 goat snp46409-scaffold641-905679 4 118226600 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772718 Affx-122950419 AX-385259864 4 958268 CTGCAGGCAAGCAGATACAGGATAAGCCTTTAGAA[C/T]ATCTGCTACAAACTCATTTATATATTTAAGCTTTT Y 2 1 2 1 201000 r 74 goat snp46410-scaffold641-958268 4 118173742 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420235 Affx-122945076 AX-123290583 4 1006943 GTTAAAGTTGTTCACTGATATTCCATTGCAAAATG[A/C]ATTTAACATATTCTCTGAGATGACAGCATATAGGT M 2 1 2 1 101000 r 74 goat snp46411-scaffold641-1006943 4 118124568 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786012 Affx-122935940 AX-385273048 4 1063698 CTAGTGATAACATTCTATCTCCTCAACTCAAGTGT[A/G]TTGCTCCAAACATAAATAACTTTCTCTCTTTTTTC R 2 1 2 1 101000 f 74 goat snp46412-scaffold641-1063698 4 118063801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794750 Affx-122975873 AX-385281710 4 1098932 TATTTGTTGTCTGTATAGACTCAACTGAGTTGCCT[A/G]TTTATATTATTTGTCCATTTTCTGAATCGAATCAT R 2 1 2 1 101000 f 74 goat snp46413-scaffold641-1098932 4 118028473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797111 Affx-122921959 AX-385284051 4 1128987 GTCTGCAGAGTGTCCTACCTGAGGCAAGTCTTCAT[A/G]TGTTAGCATTATGTCATCAGTGTAATGGGCCCACT R 2 1 2 1 101000 f 74 goat snp46414-scaffold641-1128987 4 117998522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426449 Affx-122940806 AX-123296795 4 1168871 TTGACTTTCTACTAATAGGCATCCTCACAAATAAC[A/C]TTTGATATTAAATAAGTAAAATAAATGAAGAAATG M 2 1 2 1 101000 f 74 goat snp46415-scaffold641-1168871 4 117958301 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416205 Affx-122948239 AX-123286554 4 1278697 ACCACAACTCAATGTTTTTACAGTATTTCTGCCAA[C/T]GGTGAGATTTTTTTCAAAATGATAACCAATATTTT Y 2 1 2 1 101000 f 74 goat snp46417-scaffold641-1278697 4 117851568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771680 Affx-122967090 AX-385258839 4 1327116 GGGGGAAAGAACTTCAATGAATCACTAATGCAGGA[A/G]CTCAAGCTCTAAGTCATTTTCCATTCTGTGCTGGC R 2 1 2 1 101000 r 74 goat snp46418-scaffold641-1327116 4 117803520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387714 Affx-122969801 AX-123258072 4 1390123 GTTTTTTGCTTTCTTTCTTTCTCCCTTGGTATCTT[A/G]TTTGACTTAATGTACTCTGTGCACATTTACAGGTT R 2 1 2 1 201000 r 74 goat snp46419-scaffold641-1390123 4 117740580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425538 Affx-122941453 AX-123295884 4 1426922 CGGTATCTAGGCATACACTCTGTGCCCCATTTCAA[C/T]GACCACCCATGCTGCAGGGTTAACTACTATCATGA Y 2 1 2 1 101000 r 74 goat snp46420-scaffold641-1426922 4 117703610 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445158 Affx-122925553 AX-123315495 4 1467834 TTGTTTTACTGTAGTACATATGCTGTCACTCAGCA[C/T]GATAGTTGTTTGTTTTTCTTTTCTTCCTCTTTCTT Y 2 1 2 1 103000 f 74 goat snp15036-scaffold1609-17621 4 117028084 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415905 Affx-122948465 AX-123286254 4 1533006 GTAATCCCACTTACATGAGAAAGAATACTATAAAA[C/T]GTGGTGCTGGAGACAGAGAGGAAGGACTCATATTT Y 2 1 2 1 201000 f 74 goat snp15037-scaffold1609-82793 4 116962964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392440 Affx-122966177 AX-123262797 4 1573618 CTCTAGGAAGACAGAATATAAACTATAACCAAGAT[C/T]ATCTATTTACTTATCTACCATCTGTCTGTGCATGA Y 2 1 2 1 201000 r 74 goat snp15038-scaffold1609-123405 4 116921321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452823 Affx-122920742 AX-123323156 4 1606230 CACACTGCTGCAGAGAAATAAGTTCTGCATTTTCC[A/G]TAATACTCCAACTTAAACTGAGCAAAAGTTATGGC R 2 1 2 1 101000 r 74 goat snp15039-scaffold1609-156017 4 116887995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387790 Affx-122969701 AX-123258148 4 1656659 GCAACACATTTTCTCAGATGCTGCCTTCATACCAC[A/G]TAAATGATGACCATTGAAAAGGAGTATTCACTCGC R 2 1 2 1 201000 r 74 goat snp15040-scaffold1609-206446 4 116837253 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384832 Affx-122971973 AX-123255190 4 1700668 AGGTATCTGCCATAGCATCTGCAAAGTACATTCAG[C/T]ATAAACCTCAGCCACCCCTAGCTCTCTTCCCTTAA Y 2 1 2 1 101000 f 74 goat snp15041-scaffold1609-250455 4 116792793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438828 Affx-122930782 AX-123309165 4 1746324 CCCAAGAGAGCAGCCCAGCTGAGTCCTTGTGATCA[A/G]ACCTCCATCTGTGACTCTGACGCACATCAACTGCT R 2 1 2 1 101000 r 74 goat snp15042-scaffold1609-296111 4 116747580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409649 Affx-122953523 AX-123280000 4 1829476 AAGACTGGAAAACAGGTAACAAAATGGTAATAAGT[A/G]CAAACATATCAATAATAACTGTATATGTGAATGGA R 2 1 2 1 101000 f 74 goat snp15044-scaffold1609-379263 4 116662996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795186 Affx-122940926 AX-385282144 4 1858062 AATCATTTTCACCTAGTATCAAAAAAATACAGCTC[A/G]AGTGTGCTAGATTTCCCAGCCATTTTATTTCCACT R 2 1 2 1 101000 r 74 goat snp15045-scaffold1609-407849 4 116633694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801305 Affx-122922534 AX-385288217 4 1892217 GCAAATAATATTTCTTCATAGTCTAATTAGTCTTC[A/G]CAGTCTAAAAACCAAAATTTTTATCAGTGTCTACC R 2 1 2 1 101000 r 74 goat snp15046-scaffold1609-442004 4 116599659 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275469 Affx-1111834916 AX-519549042 4 1924240 CAGTGAGATTTCGAAAAATGAGGAAATTAATACAG[A/G]CTGCGGTGGCCAGATAAGACCTTCCAGAAGGGTAG R 2 1 2 1 101000 f 74 goat GoatD01.058735 4 1924240 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38378550 Affx-122976612 AX-123248909 4 1934427 GAGACTCAGAGGTTTCCGGTGAAGCAGGTTGTTTC[A/G]TGGCAGTCTCACAGACTAGAAATCTGTCACAAAAA R 2 1 2 1 201000 r 74 goat snp15047-scaffold1609-484214 4 116557293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450197 Affx-122922295 AX-123320532 4 1966172 TATCAAGTAAAAAAAAAAAAAAAACAGGAACTTCT[A/G]ACAGCTTAATGATATTCTCTGAAAAGTCTGCACCA R 2 1 2 1 101000 r 74 goat snp15048-scaffold1609-515959 4 116524972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378583 Affx-122976589 AX-123248942 4 1995442 AAATATACTGTAAAATGAAAGAATTAATTCAAGAA[A/G]CTACAAATTAGAAAAAGTAGAAATTACTATACTAG R 2 1 2 1 201000 f 74 goat snp15049-scaffold1609-545229 4 116495305 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390450 Affx-122967620 AX-123260807 4 2050994 CCGTTAAGAACAGAAACAGCTACGAATATTGAACT[A/G]TGCTTGAGAAAGCCTAAGTTGAGCTAGGAAATACA R 2 1 2 1 101000 f 74 goat snp15050-scaffold1609-600781 4 116440306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780473 Affx-122934955 AX-385267564 4 2098633 AACTGGACTTGAGGCATTAAAAGCAATTTATCCCT[C/T]GTCCATTAATTTTTGAGATTAGGAATGAAAGGCCC Y 2 1 2 1 101000 f 74 goat snp15051-scaffold1609-648420 4 116393666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415263 Affx-122948847 AX-123285612 4 2128311 CATTCTATGCAAAACAAAGAAATCCTTCAAAAAGA[C/T]TGGCATTTCATTCTGTAAATCTAAATAATAGCTCT Y 2 1 2 1 101000 r 74 goat snp15052-scaffold1609-678098 4 116363592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421176 Affx-122944165 AX-123291523 4 2173921 AAATCACAAAGTTTTTCTATTGAGAGTGAATGGCC[G/T]AGGCTACATCTTCTGGAGACGGATTGCCTGTTTTC K 2 1 2 1 101000 f 74 goat snp15053-scaffold1609-723708 4 116317336 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411416 Affx-122951839 AX-123281766 4 2179520 TATAGTAACATTAGGTCACTGATGATGATGCTGAG[A/C]TTAAGCTCTGAGCTAAACTGATGACAGACAGATTC M 2 1 2 1 101000 r 74 goat snp34376-scaffold404-1637 4 116311562 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397296 Affx-122962325 AX-123267651 4 2239943 TAAAGAGAAAACAAATCACAATTTTTAAGGACTCA[C/T]AAAATCCAAAACTGAAATTAGAGGACAGAGGAATC Y 2 1 2 1 101000 f 74 goat snp34377-scaffold404-62060 4 116252427 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792527 Affx-122919836 AX-385279508 4 2305591 ACAAAGTAGATCTGGAAAACTTAGGCCAACAGGAA[C/T]GGAGTTACATATATGGAAGGAAACCAGTGTGCACT Y 2 1 2 1 101000 r 74 goat snp34379-scaffold404-127708 4 116185963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382396 Affx-122973840 AX-123252754 4 2335774 TCTCTACACAGGCTTCTTTTTATCTTTAAATGTTT[A/G]TTACTCGTTATTTATTCATTTTTGGCTGCCTCAGC R 2 1 2 1 102000 r 74 goat snp34380-scaffold404-157891 4 116155635 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413362 Affx-122950145 AX-123283711 4 2411378 CCACATGTGCTGGATGAATTGGACATCACTTCCCC[A/G]CTTTTAAGTAATTTTACCTTCAGGGTCTACATCAG R 2 1 2 1 201000 r 74 goat snp34382-scaffold404-233495 4 116079409 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422377 Affx-122943403 AX-123292723 4 2492788 TTTCTTGATGATTCTATCTATTCTCTGCTTTCTTT[A/C]GCCCTAGAAGGAGCTCCTTGTGAGTCTGGGCCCTT M 2 1 2 1 101000 f 74 goat snp34384-scaffold404-314905 4 115997831 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781175 Affx-122957648 AX-385268260 4 2541387 GAAAAGTTGGCCATAATGTCTATCTCAGTATCTGT[A/G]CAGTCTGTAGTGATGTTACACTCTTATCCTGATGA R 2 1 2 1 101000 f 74 goat snp34385-scaffold404-363504 4 115949358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453539 Affx-122919790 AX-123323872 4 2575720 TGCAGATTCTCTGGGTGGCAGTCCTTGGCCACATC[A/G]TCTCTGTGGCCCTGCAGGAAGAAAGTGGCCCGTGG R 2 1 2 1 101000 f 74 goat snp34386-scaffold404-397837 4 115914847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796364 Affx-122939463 AX-385283314 4 2618688 CCTGTCGTTGGGGCACTGGTCAATTTCAGCTCTGT[A/G]TTCTCACCATGAGGTCCTGCCGAAAATGGTCCTAA R 2 1 2 1 101000 f 74 goat snp34387-scaffold404-440805 4 115871625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774378 Affx-122959214 AX-385261514 4 2663695 TATTGGAATTCCCTCTTTTTGACCTGTGGTTAGAA[C/T]ATCTTATATTTTTTTTGCCATTGTGAATTGTACTG Y 2 1 2 1 101000 r 74 goat snp34388-scaffold404-485812 4 115826699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383834 Affx-122973162 AX-123254192 4 2746459 GGCTTGTGATGGAACATTTAAATGCAGCCCAGATA[C/T]GGGCTACCAGGTATGTACGTTACACACACTGACAA Y 2 1 2 1 101000 r 74 goat snp34390-scaffold404-568576 4 115747461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775581 Affx-122953787 AX-385262712 4 2778708 TCTCTTAGTATTTTTATTAATAGTCTGATAAAGAG[C/T]ATGAAGTGTAAGACTCTATTAGTTACTAGAAGAGT Y 2 1 2 1 201000 f 74 goat snp34391-scaffold404-600825 4 115715353 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396140 Affx-122963394 AX-123266495 4 2821408 TTCGAGGTGGGTGGAATGAATTCAGGCCTCCAGAG[C/T]GAGTTACAACTCTGGGCATCGGTTCCTTCTGCTCC Y 2 1 2 1 102000 f 74 goat snp34392-scaffold404-643525 4 115672795 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379864 Affx-122975792 AX-123250222 4 2852086 AGCTTTTTAGTGCTGACCTGCAATTTCCTCTTTGA[C/T]ACCAAAGTTTAGGACTTTTCCTTCCCAAATATTTT Y 2 1 2 1 101000 f 74 goat snp34393-scaffold404-674203 4 115643531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416548 Affx-122947678 AX-123286896 4 2882774 TATCTTGTTAATAGATTCTGCCTTGGTGGCTCAGA[C/T]GGAGAATCTGTGTGTCATGCAGGAGACCCAGGTTC Y 2 1 2 1 101000 f 74 goat snp34394-scaffold404-704891 4 115612333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452641 Affx-122920345 AX-123322974 4 2913169 GCATGGGGCATCTCGGGCTCACAGTTCCCAAGGAA[C/T]GGCCCAAGGGCCTGCCTGCCTTGGACAGCTTTGTA Y 2 1 2 1 303000 f 74 goat snp34395-scaffold404-735286 4 115581983 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414267 Affx-122949610 AX-123284616 4 2947419 ACTCTTTATTCCCATCTTCTCCATAACAGCCAAGC[A/G]TTAGCTTGGTGTCTCCCTTTGCCTGGCAAAGCAAT R 2 1 2 1 103000 f 74 goat snp34396-scaffold404-769536 4 115547484 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272102 Affx-1111833421 AX-519545862 4 2961725 TTTTAGCAACTCTATTCTCATAAAACATTTTATTC[A/G]GCTGGAAGATGGAGACCATTCTTGAGAAAATACTA R 2 1 2 1 101000 r 74 goat 4_2961725_AF-PAKI 4 2961725 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450066 Affx-122922809 AX-123320401 4 2977990 CTTTTAAATTCAAAATAATATCAGAATTACAGAAA[C/T]GGTGTACTAGTCCAAACAATTCTCATAAGTCCTTT Y 2 1 2 1 101000 r 74 goat snp34397-scaffold404-800107 4 115516473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791019 Affx-122974484 AX-385278015 4 3027631 AATTCCAGCTCTACAATTTCCTGATTATTCACCAA[A/G]TGGAAGATAGTCTCTGTTTTTCAGCTTTGGATTCC R 2 1 2 1 101000 r 74 goat snp34398-scaffold404-849748 4 115466499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398008 Affx-122961787 AX-123268363 4 3063464 AATGAGTTCAGTTTATTGTTTTTGGTCAACACACA[C/T]AATCAAATTGTTTAAAACCGATGAAAAAGAAATCC Y 2 1 2 1 101000 f 74 goat snp34399-scaffold404-885581 NW_017202663.1 15472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452894 Affx-122920216 AX-123323227 4 3136703 GGGGTCCTTGGCATCCTGGATGAGCCTCTGCAGTA[C/T]GGGGAACACATTTGACCCAAGTCAGGCTCACCTGA Y 2 1 2 1 201000 f 74 goat snp34401-scaffold404-958820 4 115357440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450929 Affx-122921774 AX-123321263 4 3207022 GTGTCCCCTGCATTGCCAGGGAGATCCTTAACCAG[C/T]GGACCACCAGGGACATCCCTGTTGGAGAGTTTAAG Y 2 1 2 1 201000 f 74 goat snp34402-scaffold404-1029139 4 115286722 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273896 Affx-1111833879 AX-519547504 4 3239273 AGTAGCATGCGGAGGAGTCTGGGGCCTCCCTGCAG[A/G]GGAGCAGGCCATCAGTCTAAGGCGAGTGCCAGGGA R 2 1 2 1 202000 r 74 goat GoatD01.008900 4 3239273 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386622 Affx-122970230 AX-123256980 4 3264319 CCACGAGGAATAGCACTTGTACAGAAGTAGAATAG[C/T]GGTGAGCCCCACATGCCCCCCACCCAGACCCCACA Y 2 1 2 1 101000 f 74 goat snp34403-scaffold404-1086436 4 115229760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391682 Affx-122966540 AX-123262039 4 3300526 TCCAGACCCCATAATCCTCCTCCACCTATTTGATG[C/T]GGTTGGAACAGCCAAAGAACACACTCTAATTAATA Y 2 1 2 1 101000 r 74 goat snp34404-scaffold404-1122643 4 115193529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428948 Affx-122938887 AX-123299290 4 3353363 TAGGATGAAAGCGTGGCATCTTTTATTTTCCCAAA[C/T]AAAACCAGTGCGGGTCAGCGTCACGGAGAGAGGGA Y 2 1 2 1 202000 r 74 goat snp34405-scaffold404-1175480 4 115142465 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428630 Affx-122938675 AX-123298972 4 3399134 TTACCTTGAAACAACTTACGTTTGCATTGTGTTTT[A/G]CTTAGAAATGTGTGAAACAATACCTTAGATTACTT R 2 1 2 1 201000 r 74 goat snp34406-scaffold404-1221251 4 115096853 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445365 Affx-122925415 AX-123315702 4 3469297 GCTGCACCCTGTCTCACCCCTGGAGACAGGCACTC[A/G]CCACTGACGGAAAACTGGATGTTTCAAGTCAGCGC R 2 1 2 1 101000 r 74 goat snp34408-scaffold404-1291414 4 115023051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776657 Affx-122935662 AX-385263784 4 3608380 TAGATAACTCAGTTATTTCTTTAATAGGTTGTTGA[A/G]AAGATGGCCCAAGATGCCATTTAAATAAAGATGTT R 2 1 2 1 102000 r 74 goat snp34411-scaffold404-1430497 4 114884142 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418681 Affx-122946307 AX-123289029 4 3659583 CATGTTTCTGTACTTCTGAAATGTGTGCATTCTGA[C/T]GGCCCAAGGAAGCCACGGGGAAATCATTGCACTCA Y 2 1 2 1 101000 f 74 goat snp34412-scaffold404-1481700 4 114833710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392039 Affx-122966465 AX-123262396 4 3761348 CTAACTCATCTGCTCTCCTTTTCTGTGATGCTGTA[C/T]GCTTATCTCATCCTCTCTCTCTGACCATTTCCTTT Y 2 1 2 1 101000 f 74 goat snp34414-scaffold404-1583465 4 114730585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773293 Affx-122952479 AX-385260436 4 3861340 ACATATTTGTTTTTATCTGAGGTTTATAAATCTGA[A/G]TGTCCATTCCCTCTGCAGATTTCTTTGGCATTATT R 2 1 2 1 101000 r 74 goat snp34416-scaffold404-1683457 4 114632106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387971 Affx-122969599 AX-123258329 4 3907846 TGTGTATCACATTCCCACCTCCAACATGTATAGTG[G/T]GTGACCATAACACATTTTCATCCCATTCCACAGCA K 2 1 2 1 201000 r 74 goat snp34417-scaffold404-1729963 4 114585621 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426802 Affx-122940534 AX-123297148 4 4002182 TAGTCTGTCTAAATTAAATTTGATGACTTGATGCT[A/G]TATTGGTTAAATGTGGGAACAGAATCCCAGATTTT R 2 1 2 1 101000 r 74 goat snp34419-scaffold404-1824299 4 114490887 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447053 Affx-122924520 AX-123317389 4 4038636 ACACACACACCATTTGATGCTGTGCAACTCACTAC[A/G]TGCGGTTTAATTATGATCTTATCCTGCTGTCTGAA R 2 1 2 1 101000 f 74 goat snp34420-scaffold404-1860753 4 114454701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428696 Affx-122938628 AX-123299038 4 4073559 CATTCCAGACCCCCAGACCACAGACATATGGACCC[A/G]TATAGAAGTTTCCAAAACAATCCTAAAGGGACCAG R 2 1 2 1 101000 r 74 goat snp34421-scaffold404-1895676 4 114419798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800268 Affx-122920174 AX-385287191 4 4144055 TATTACTCATTTAAAGCAGTCACTTGAAAGGCTGT[A/G]CATATTCATTATAATATGGCAAATGTTCTTTGGAA R 2 1 2 1 101000 f 74 goat snp34423-scaffold404-1966172 4 114340663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386062 Affx-122971462 AX-123256420 4 4231116 TATAGGATGTAATAACAAGGCCGGTCCTCTGCCAC[G/T]TGCTTCTCCAGCTACAGCCCAAGACTCTGGTTCAT K 2 1 2 1 201000 f 74 goat snp34425-scaffold404-2053233 4 114254639 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275234 Affx-1111834782 AX-519548813 4 4252831 TTCATGCAGGAAAAAAATCCTGCCAACTCTCACCA[A/G]AGCTCACTGCAGGACAGG R 2 1 2 1 101000 f 74 goat GoatD01.052699 4 4252831 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797874 Affx-122947474 AX-385284812 4 4306277 AAAGGATTTTCCACTCCCAATGAGATGCCTCTGGG[C/T]GCTCTTCCTGCTGTCCCGTGAACCTGCCTTGGAAT Y 2 1 2 1 202000 r 74 goat snp34426-scaffold404-2128394 4 114179121 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802526 Affx-122936312 AX-385289430 4 4337782 TGGAGCTTTTCAAAAAACTAACTAGTTAATTGTCA[A/G]TTGGTTACATTGAGTCTGATTTGTGACATGGGGGA R 2 1 2 1 101000 r 74 goat snp34427-scaffold404-2159899 4 114148116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278192 Affx-1111836219 AX-519551681 4 4386566 GTTCACTGAATGAATAGATTTTGAGCACCTTTTAT[A/G]TGCTGGACGCTGTTCTTGATGTGGATAACAGCGGG R 2 1 2 1 101000 r 74 goat Random2.2K-396 4 4386566 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414359 Affx-122950014 AX-123284708 4 4399943 AGTCCTGCTCACTAAGGACCCAATAGTGGTTGGAA[A/C]GTAGTAAAATCAAGAAATCAAAATCAAAAAAGAAA M 2 1 2 1 101000 f 74 goat snp34428-scaffold404-2222060 4 114084740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414933 Affx-122949097 AX-123285282 4 4470729 AGCGACTTCACTTTCACTTTCAAGATAATCTTACC[A/G]CCTCAGTGTCAGTGGTTTTAATCACATCTTTTTGT R 2 1 2 1 201000 r 74 goat snp34429-scaffold404-2292846 4 114019607 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787746 Affx-122926281 AX-385274769 4 4501539 CCCCAAAGAAGGGTGTTTATCACATTTCATTCATA[C/T]GATTTCAGTATAATTCATTATGATATTTGGCCCTG Y 2 1 2 1 101000 f 74 goat snp34430-scaffold404-2323656 4 113988367 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384582 Affx-122972993 AX-123254940 4 4549023 TAAATAGTGGAGTGTGTGCTGGAAAGAAAGCTGGC[G/T]TTAGGTTTCAATAAACTAGAATTGGAATCCCTGTT K 2 1 2 1 201000 r 74 goat snp34431-scaffold404-2371140 4 113940912 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427495 Affx-122940002 AX-123297838 4 4596695 TGTGCTTGCTCTACCGTGGGAGGTCCTCTAAGAGA[C/T]GTCTTGACACTTGGGGGCCCTGGTTTCTTGTGCAT Y 2 1 2 1 101000 f 74 goat snp34432-scaffold404-2418812 4 113894320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792769 Affx-122933797 AX-385279748 4 4620400 ACAACACATTTAACCACTTGTTTTCAGCCAGATTT[A/C]TGAAAAGCAAAAGGTGGCTTTGGTTTTATTGATCA M 2 1 2 1 201000 r 74 goat snp14556-scaffold1588-32651 4 113863730 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787528 Affx-122954881 AX-385274552 4 4650578 GCATAAATGCAATCTCAAGTAACATGAAAATTAAC[A/G]TGAGAAACTCAGAATCAGCCAAGAAACACTGCTTG R 2 1 2 1 101000 r 74 goat snp14555-scaffold1588-2473 4 113833627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417188 Affx-122947319 AX-123287536 4 4654902 ATGAGATGAAGCGACAGAGTTGCCTGGCCTAGTTC[A/G]CTCTTGCATTATCAAGATCTTCATGATCTAAGTCA R 2 1 2 1 201000 r 74 goat snp56732-scaffold898-750442 4 113829449 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772748 Affx-122933043 AX-385259893 4 4684127 TCTGTAAACTAGGATATTTACACCTCTGGCAAAAA[C/T]GGTGAACATTTCCTAGCTAATTTGCATGTAATCTT Y 2 1 2 1 201000 r 74 goat snp56731-scaffold898-721217 4 113802221 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779623 Affx-122943380 AX-385266725 4 4717296 AGTTTCTTTGGAGAAAGACTAAAGGAATAATTACT[A/G]CATAATTTTGTGGTGGTGTTGCTGAACTCTTACTA R 2 1 2 1 101000 r 74 goat snp56730-scaffold898-688048 4 113767771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787275 Affx-122976935 AX-385274300 4 4752731 TGCTTTTATTTATTCATTGACTTATTTAACAGATG[G/T]ACTTGAGTACATACCTTAGGCTAGAATCTGTCTGG K 2 1 2 1 101000 r 74 goat snp56729-scaffold898-652613 4 113731685 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399221 Affx-122960597 AX-123269576 4 4786480 TTCAAGTGCATGAACTGTTCCCTGTGAAATTCTAT[A/G]CTCTGAACAGTCTCCAAGTTCTTTTTCTGAACTCC R 2 1 2 1 101000 r 74 goat snp56728-scaffold898-618864 4 113697525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386859 Affx-122970069 AX-123257217 4 4823556 TCCTAGGAACCAAGTAACCAGGAGTAGGCTAAAAT[C/T]GAGCACAGGCACTTAGTCATCTTGTAAGTTAGTTA Y 2 1 2 1 101000 f 74 goat snp56727-scaffold898-581788 4 113658702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793180 Affx-122942140 AX-385280158 4 4909528 AAAGAGCATGATCTTTCAACATGATTCTTAGTGAC[A/G]AGAAGGGAGAGAGATTAGGTTAAAGCCTCTGCCTG R 2 1 2 1 101000 r 74 goat snp56725-scaffold898-495816 4 113568350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792136 Affx-122951584 AX-385279120 4 4962488 ATCCCATGTAACATACCTTCTTCAATCATCCAACA[C/T]GTTCATGTCAAAATGTGATTGGAACATGATATAGT Y 2 1 2 1 101000 f 74 goat snp56724-scaffold898-442856 4 113515130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274429 Affx-1111834280 AX-519548020 4 4977137 CAGGTCCAGCAGCCAGATGAAAATCCTGAGACCAA[A/C]GCCCAGCGCTGAGGA M 2 1 2 1 101000 f 74 goat GoatD01.028657 4 4977137 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409021 Affx-122953872 AX-123279372 4 4994037 GTGGAGTATATGGAAAATCTCTGGACAATTTTCTC[A/G]TTTTTTTCTGTAAATCTAACACTGCTTAAAAAAAT R 2 1 2 1 202000 r 74 goat snp56723-scaffold898-411307 4 113483145 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427986 Affx-122939178 AX-123298329 4 5024049 CCACGAGAAGAACTTCTCTTTTTGATTGTTGATTC[A/G]TCTTGGCACAGAAAACATCTCCTTTCTGTGCAAAT R 2 1 2 1 101000 r 74 goat snp56722-scaffold898-381295 4 113452873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278194 Affx-1111836220 AX-519551683 4 5042272 TGGTGGTGGGTGTGTGTTCGGGAGAGCCTCAGAGC[A/G]GTAGGAGAAGTTGCAAGAAAGAACGTTAATGCTCA R 2 1 2 1 101000 r 74 goat Random2.2K-397 4 5042272 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800574 Affx-122932112 AX-385287493 4 5052638 GCAATTTCAACAACAAGGTGCACTTTCTGCCCTCA[A/C]ATAAAATCCAGGAAGTTTATGAAAGCATTGGTGTG M 2 1 2 1 101000 f 74 goat snp56721-scaffold898-352706 4 113424299 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392676 Affx-122966425 AX-123263033 4 5107625 CCACATGCCCAGGAGGGCCCAGCCTCAGCTGAAAC[A/G]TGGCAGTGGGCCTCCTCATTTCATTCTCTGTTCTG R 2 1 2 1 101000 r 74 goat snp56720-scaffold898-297719 4 113365857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401614 Affx-122959607 AX-123271967 4 5151423 CATCTTCAGTGTTGAGTTGACTCAGTAGCTGTGTC[C/T]GCATCCCAGCTTATGGGAAGTGGAAAGATCCAAAA Y 2 1 2 1 201000 r 74 goat snp56719-scaffold898-253921 4 113321775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411064 Affx-122951945 AX-123281414 4 5214219 CCATTCTCCCCACCACCCCCAGCAATCCTAAATTC[A/G]TTCTCTAAGTCTCTGAGTCTGTTTTGTAGATATGT R 2 1 2 1 103000 f 74 goat snp56717-scaffold898-191125 4 113258575 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779603 Affx-122973537 AX-385266706 4 5256908 GTTACAGTGTACACAGGTGACTTACTGGTAGTGGC[A/G]TTTGCTGCTTTGCTGTATAGAAACATTACTTGAAC R 2 1 2 1 101000 f 74 goat snp56716-scaffold898-148436 4 113214996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442710 Affx-122927867 AX-123313047 4 5294482 GAGCCAAGGGAGGCTACCATGATGTCTGTCCTTGT[G/T]TTTGATGTTGTGAGATGCCCTGTGTGTGAAACTTC K 2 1 2 1 102000 r 74 goat "GoatD01.031682;snp56715-scaffold898-110862" 4 113177481 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796213 Affx-122930109 AX-385283164 4 5351694 GCTAATATTAAGGTGAGGAATACCAGATAAGACTT[A/G]TTTGTATATGATAAAAAATGTGGAAGTAACATTAA R 2 1 2 1 201000 r 74 goat snp56714-scaffold898-53650 4 113120666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782434 Affx-122973849 AX-385269510 4 5383118 TAGCAGATTTTGCATGGAATAGAACTGGACTGTTA[C/T]GAGTACTTTTCTCATGAGGGAGCTTATTTGCATAA Y 2 1 2 1 101000 f 74 goat snp56713-scaffold898-22226 4 113088818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401086 Affx-122959628 AX-123271439 4 5423819 AACCTAAAATGGCAGAAAATTAAAGCTAATTTAGG[C/T]GAGATAAAACACCAGGAACAATGTTGGTTGAATAC Y 2 1 2 1 101000 r 74 goat snp18882-scaffold1903-18376 4 113047435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415791 Affx-122948907 AX-123286140 4 5465713 GTGAATGAACTTCACATGAAGTTTCTCTAATACAA[C/T]ACCATTAAAACATGTATGTTCTTGTTGGAATGAAC Y 2 1 2 1 101000 f 74 goat snp18883-scaffold1903-60270 4 113005525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788665 Affx-122945818 AX-385275681 4 5508328 AGTCTGACTTGTTAGTTTCTGACCTTCAAAATTCT[A/G]CACAAATTTCCAACTGAAATCATTTTCATCCTGAA R 2 1 2 1 201000 r 74 goat snp18884-scaffold1903-102885 4 112963187 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802451 Affx-122974971 AX-385289355 4 5556863 ATTCTAAACCATTATCTCACACAGAAACCCTTCGC[C/T]GTGCCACTCAGGATAGTCAGTTAATTTTTTAACCG Y 2 1 2 1 101000 f 74 goat snp18885-scaffold1903-151420 4 112914344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407018 Affx-122955018 AX-123277369 4 5594982 TGGAACCAGCTGTCCAAAATGCATGGCAGTCAGGG[C/T]CTAACACAGGACCAGCTCCTGGCAGGTGTAGTGGG Y 2 1 2 1 101000 f 74 goat snp18886-scaffold1903-189539 4 112875088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770259 Affx-122920880 AX-385257425 4 5628233 ATGGGAGCGAATCTATTTATAGATCAGAATGCTGG[A/C]TCAGAACAATTAAGGGAATTTCTGTGTGTGCCTAA M 2 1 2 1 201000 r 74 goat snp18887-scaffold1903-222790 4 112841086 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411527 Affx-122951665 AX-123281877 4 5673207 ACCAATTGTTCCCTTTTCACCTCTAAAAATATGAT[A/G]GCATATCAAAGAGGGAGAAGTATTTAAAATCTCTC R 2 1 2 1 101000 f 74 goat snp18888-scaffold1903-267764 4 112798683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401611 Affx-122959617 AX-123271964 4 5713736 AGCAGGGACTTATTTCTTCTTCTGAAATGACTATC[A/G]TTTTTCCTTCTGTCCTTATCTTGTCAGTTTATGAG R 2 1 2 1 102000 f 74 goat snp18889-scaffold1903-308293 4 112757144 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396336 Affx-122963065 AX-123266691 4 5757228 GGAATAGATGGTTTCTTTTCTGCCAAGTCGAACCT[C/T]TTCTGGGAATATTTGTGCTGAGTGAGCTCCCTGAC Y 2 1 2 1 101000 f 74 goat snp18890-scaffold1903-351785 4 112713071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780222 Affx-122921941 AX-385267318 4 5788006 AAGGAATATCTTGCTTGAAGGGCAATCTTGTTATC[A/G]GAAGGATTTTTACCTGTTATGTAACTTGTTGTTCA R 2 1 2 1 101000 r 74 goat snp18891-scaffold1903-382563 4 112681992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272125 Affx-1111833433 AX-519545883 4 5792170 AGCCTTCCAAGGTCTCCCCAGAAAGCAGCTGTGGA[A/G]TTAAACCGGTGAGCATCCTGGCTGGCCTGCTCAGG R 2 1 2 1 102000 r 74 goat 4_5792170_AF-PAKI 4 5792170 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780142 Affx-122934474 AX-385267239 4 5829345 ATCGCCGTTGAGATAAAGTCAGATCTGAGGGGCAA[C/T]TTAGTTATATCTGTTTGAGAAGTTGCCCATGCACA Y 2 1 2 1 201000 f 74 goat snp18892-scaffold1903-423902 4 112640532 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802747 Affx-122953710 AX-385289646 4 5868831 TAGTTAAAGTAGAAAATCTGCTTCAACATGTAATT[A/G]TAGACTCAGCCTACGTTGTATCAGGTAGAGTATTT R 2 1 2 1 101000 r 74 goat snp18893-scaffold1903-463388 4 112602700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795882 Affx-122939234 AX-385282834 4 5923414 GCTCTGTGTTGTTTTGACCCTATAGACTTAGGATC[A/G]TTCAGTCCAACTCTTTCATTTCACGGAGGAAAGAA R 2 1 2 1 202000 r 74 goat snp18894-scaffold1903-517971 4 112548209 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429974 Affx-122938058 AX-123300315 4 6021603 GGTGAGAGTGGGGTGGGAGTTGACCGCAGCAAGAG[C/T]GGTGAGACCACTTGCTCTTAGCACTTTTGTAGTCA Y 2 1 2 1 101000 r 74 goat snp18896-scaffold1903-616160 4 112448782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410486 Affx-122952199 AX-123280836 4 6053872 TTTTCTCCACACCATAGTGAGGGAGCTGCAGGCAC[A/G]TAATTTAATCATGCTCTCTCTTTTCTGAAGAGTCC R 2 1 2 1 101000 r 74 goat snp18897-scaffold1903-648429 4 112416475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418129 Affx-122947117 AX-123288477 4 6086036 TAGGATTCATGAGAAGCTGTTTGATTTCCCGATTT[A/G]TTTTTGTAGGTGGTGCAGCCAAAAAATTGAATCTC R 2 1 2 1 101000 f 74 goat snp18898-scaffold1903-680593 4 112383547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795272 Affx-122966167 AX-385282230 4 6126119 TATCTTCCAGCCTCTCTGTTGAAAGGACTGAAACA[C/T]GCTAACATCGTGCTACTTCACGACATCATCCACAC Y 2 1 2 1 101000 f 74 goat snp18899-scaffold1903-720676 4 112343638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435367 Affx-122933584 AX-123305707 4 6162680 GTAGGAACTCTGCAAGACATTCTTTTTAAAATAAA[G/T]ACTAGAATCAGTATGGTACTTGAAGTATTTGTTGA K 2 1 2 1 303000 r 74 goat snp18900-scaffold1903-757237 4 112307004 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396955 Affx-122963174 AX-123267310 4 6198643 GAGTTAACAATGAGCTGAGCATATAAACCCTATGC[A/G]GTCTAAAGATGTATAAAGGGTTTGGTGATGATGAT R 2 1 2 1 101000 r 74 goat snp18901-scaffold1903-793200 4 112271030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414816 Affx-122949207 AX-123285165 4 6247416 ATGGAGGATGGGGTGGCAGAAAGGGTTAGTTAAGG[A/C]GTTTGGGATGGACATGTACACACTGTTATATTGAA M 2 1 2 1 101000 f 74 goat snp18902-scaffold1903-841973 4 112222208 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394233 Affx-122964883 AX-123264588 4 6286491 AACGCTTTTTTCCGAGTTTAGATAATTGCCACAGT[A/G]TCATCCTTCCTTGGAGACAGTAGTCAGCCCCAGAC R 2 1 2 1 101000 f 74 goat snp18903-scaffold1903-881048 4 112183721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416262 Affx-122947960 AX-123286611 4 6356431 GTTACTGGAACTAGCTTCAGAGATTTGAGCTTATC[C/T]TGTCTTCATTTGGAAAAGAAAACAGATGCGGTTAG Y 2 1 2 1 101000 f 74 goat snp18904-scaffold1903-950988 4 112113336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403846 Affx-122957937 AX-123274198 4 6385362 TGGGCTTTAAGACTGGGCTCCCATGCACAAAGCCC[A/G]TTCCCTGCCATTTTAAGATGGGTTGACCTCCTGTT R 2 1 2 1 101000 r 74 goat snp18905-scaffold1903-979919 4 112084538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378414 Affx-122976784 AX-123248773 4 6420272 TTTCCTAAAGTAGGCTGCCAGGTAAACAGTAGGAT[A/G]CAGAAACTGCTCAAAAATTTTGGCTAAATAAGACA R 2 1 2 1 101000 f 74 goat snp18906-scaffold1903-1014829 4 112049442 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792846 Affx-122923074 AX-385279824 4 6471199 TGGTCAGCAAGTGCATATTTTCTGAGCAAACTAAC[A/G]TATAATGTGAAAAGACTAGTTTTCCCTGTTTCCCA R 2 1 2 1 101000 f 74 goat snp18907-scaffold1903-1065756 4 111998068 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436941 Affx-122933183 AX-123307279 4 6526465 AGAGTGCCAGTGCTGGAGTGAAATGTACCAGTCAG[C/T]GGCTCTGCCACTTCCTTTCCACTCAGCCCCAAGGA Y 2 1 2 1 101000 f 74 goat snp18908-scaffold1903-1121022 4 111942425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781779 Affx-122967441 AX-385268861 4 6572545 AATACACATAAATTTTCACTGCCTTTGTTGCTGAA[C/T]CAAAAGACTATTCTTGCTATCTTTGAATTAAACTC Y 2 1 2 1 101000 f 74 goat snp18909-scaffold1903-1167102 4 111896405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797127 Affx-122957166 AX-385284067 4 6576842 CACCCCATTTCAGATTAATTTGATCTGTATTTCTA[A/G]CTGTGACTAAAGATTTTAATCCTTTATGAAGTTAC R 2 1 2 1 101000 f 74 goat snp38586-scaffold49-2395 4 111892173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398432 Affx-122961618 AX-123268787 4 6623456 AACCTCAGAATGACTTTCACTGATATTACCCAGAG[C/T]GGTGATAAATTAATCTCTTAGGCATAGAGAAGAAT Y 2 1 2 1 101000 r 74 goat snp38587-scaffold49-49009 4 111845720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418166 Affx-122947088 AX-123288514 4 6684779 TTGTCATACAGTCCTTAAGGAAGAAGAAAAGGAGA[A/G]AGAAATGTATCGAAATTCATCAGGTTTTTCAGGCA R 2 1 2 1 201000 r 74 goat snp38588-scaffold49-110332 4 111784472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278197 Affx-1111836222 AX-519551686 4 6692653 GCCTGCCCCACTGGCACAGAGCTTTAAAAGCCATC[A/G]TGCCTGCCCTCTTAACAGTCAAGGACACAGCCCAA R 2 1 2 1 102000 r 74 goat Random2.2K-400 4 6692653 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411094 Affx-122951923 AX-123281444 4 6717765 TTTTTTGCAGCCCTAGAATGTCAGAGCTAAGGGTT[A/G]CTGACAGAACTGGAATTAGTCCTGGGCTATTACCT R 2 1 2 1 101000 f 74 goat snp38589-scaffold49-143318 4 111751334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387202 Affx-122970599 AX-123257560 4 6764072 CTAGATATGGGTCCCTGAAAATCAAGACCAAAATG[A/G]TCTGGCTTTCTCTGTCCAGAGGATATCTATGACTT R 2 1 2 1 101000 f 74 goat snp38590-scaffold49-189625 4 111705085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433256 Affx-122935235 AX-123303597 4 6796192 GGAGAGAAAATCAAGGAGATTATTCATTTACTTAC[A/G]TTTATTCTGAGACTTGGCAAAAGGCATTTTAGTCA R 2 1 2 1 101000 r 74 goat snp38591-scaffold49-221745 4 111673121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278199 Affx-1111836223 AX-519551688 4 6868190 TTGCATCCTGAACCACCAGCTGAGCACCCACACAT[C/G]AGTCAGTCTGGCTGAGATTAGCCTGGTGGGTCCAG S 4 1 2 1 202000 r 74 goat Random2.2K-401 4 6868190 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426556 Affx-122940176 AX-123296902 4 6875674 CAGAAAATCTCAGAGTCTTTACTTAAGGGAGGAGA[C/T]GGGATGATCGTCTATGCAGGCATGTTCTTCTAACA Y 2 1 2 1 101000 f 74 goat snp38593-scaffold49-301227 4 111592239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430083 Affx-122937539 AX-123300424 4 6933637 AACACTGAATTCCTACATCTACCCCTTTCCCACTG[A/C]TGCCCCCTAGCAAAGGAACAAAGCTAGAGACCAGA M 2 1 2 1 201000 r 74 goat snp38594-scaffold49-359190 4 111534248 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433666 Affx-122934562 AX-123304007 4 6990443 CTAAAGCCACTCTCGACAGGCTGAAGGAGCCAGGC[A/G]GATGGCTGCCCTTGCTAAAGCGACGTGGGAAGGCC R 2 1 2 1 201000 r 74 goat snp38595-scaffold49-415996 4 111477173 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406801 Affx-122955695 AX-123277152 4 7033112 ACATGTACTCCTTCAGTTACTGATGAGTTAATTTC[A/G]TTCTATTCTCAATGACAGACTTATTCTCTGATCCA R 2 1 2 1 101000 r 74 goat snp38596-scaffold49-458665 4 111433737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406323 Affx-122955454 AX-123276675 4 7074160 CGCAATAAATGATGGCATGAATCACCCCTTTCAAA[C/T]ACAGGACAACATCCTGAAGCTCCTTACTTGCAGTA Y 2 1 2 1 201000 f 74 goat snp38597-scaffold49-499713 4 111392557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795298 Affx-122941748 AX-385282256 4 7125345 GATAATGGTAAAGAACTATCATGTCTAAAAATAGA[C/T]ACTTGGAGCTTAGAATCTGTCAGACCATATGTTGT Y 2 1 2 1 101000 r 74 goat snp38598-scaffold49-550898 4 111340901 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390435 Affx-122967633 AX-123260792 4 7193967 CAGAGACCTATTCTGTCAACTTTCTTCCTCCTACC[A/G]CAAAATGTCGGTGATAGAGGCATTTGTATTATGGA R 2 1 2 1 101000 r 74 goat snp38599-scaffold49-619520 4 111269808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449830 Affx-122922394 AX-123320165 4 7239847 CTCACATGCCATTTTTTATCCTAAAAAACAAAATT[A/G]TACATGTCAGTTTATTCCTTCACTGTTCAGACATG R 2 1 2 1 101000 r 74 goat snp38600-scaffold49-665400 4 111223958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476438 Affx-1251763688 AX-586011839 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 4 1 4 1 20000 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 560378490 Affx-1251763688 AX-605230905 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20000 f 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166096 Affx-1251763688 AX-606941505 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166133 Affx-1251763688 AX-606941541 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166287 Affx-1251763688 AX-606941695 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 f 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 38389645 Affx-122968734 AX-123260003 4 7303861 GTACGTGCCAGGTACTATATTGGGTTCTGAGGCTA[C/T]GATGAACAAATCTGATAAGGATCTTGCCCTTATGT Y 2 1 2 1 101000 f 74 goat snp38601-scaffold49-729414 4 111159034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782071 Affx-122940733 AX-385269149 4 7335957 TCATAGTACTTTCTTTTTATCTGTATTATGACTCA[C/T]GTCACACTCTTAAGTATTCAAACATTCATGTGAAT Y 2 1 2 1 101000 f 74 goat snp38602-scaffold49-761510 4 111126804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278047 Affx-1111836224 AX-370982909 4 7352975 TGTGAATCAAAGAAGAGCTCGTTGGTGAGGAAGGC[A/G]CGCTAGTGCTCCCGCTCCAGCCCCTCGATCACAGC R 2 1 2 1 101000 f 74 goat Random2.2K-403 4 7352975 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381973 Affx-122974100 AX-123252331 4 7368047 CTTTTTAAGGATTAATGCCTGACTTTAAGTCTTTC[A/G]TGTAACTCTTAAGGAACCTCCACAGCTAGGGACCA R 2 1 2 1 201000 f 74 goat snp38603-scaffold49-793600 4 111094130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785082 Affx-122943854 AX-385272129 4 7407900 GTTAAGTTCTGTTATTTCTCTGAAACAGTTCACCA[A/G]CTACCTCCTATATATTCCCACTATAATTTACCATT R 2 1 2 1 101000 f 74 goat snp38604-scaffold49-833453 4 111053817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402833 Affx-122958261 AX-123273186 4 7441644 TTCCAGTTTGAGCAGCAGCTTCTGTTTCTTCTTCC[A/G]TCAACCATGGCTCTGCTTCTTTAGTTGAGGATCAA R 2 1 2 1 201000 r 74 goat snp38605-scaffold49-867197 4 111020164 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802883 Affx-122934274 AX-385289781 4 7486400 TACTTAACCTAGGTAATCTTGACAATTCTGCAGGG[C/T]AGGTGGCCTTATCCCTTTTTTATGTAAGAAAAAAT Y 2 1 2 1 101000 f 74 goat snp38606-scaffold49-911953 4 110974470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278203 Affx-1111836225 AX-519551691 4 7516291 GTCACCTGATAAAAGAAATTCATTTATTTATTCTC[A/G]ATTCAATGTTTGGCAGGAAGCATGAAAATACTGGT R 2 1 2 1 201000 r 74 goat Random2.2K-404 4 7516291 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784277 Affx-122941977 AX-385271328 4 7533989 AGAATGGGCCTTTGGTAAATAACTGACTCTGTGTT[A/G]CTTTTGACCTGTGCTTTATTGAGCTGCACTGGAAA R 2 1 2 1 101000 r 74 goat snp38607-scaffold49-959542 4 110926942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788740 Affx-122919366 AX-385275756 4 7581831 AAGAAAATGCTGGTCTTAGTTGTAATTAAGATACA[A/G]TGGTACAGTGTGTAATTAAAACTAGAATAAACTGT R 2 1 2 1 101000 f 74 goat snp38608-scaffold49-1007384 4 110879395 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434432 Affx-122934663 AX-123304773 4 7611108 AATGTCTTGGAAAACTTGGGGAGCTGTCTGTTCTT[A/G]CATATATCATGTTTCATGGTAAAGCATGATGGGAA R 2 1 2 1 201000 r 74 goat snp38609-scaffold49-1036661 4 110850682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451958 Affx-122920954 AX-123322291 4 7650476 GCAAAAATGTGAGATGCATACAACGTTCTCAAAAT[C/T]GGCCAAGGTTCAGTTCAGTCCAGTCCAGTCACTCA Y 2 1 2 1 101000 f 74 goat snp38610-scaffold49-1076029 4 110810925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441936 Affx-122928583 AX-123312273 4 7679220 ACCCATCTCCTAGTCGTGTCTTCCTGGTCAGATTA[C/T]ATCACCTTGAATTTCCACTTACTCACCTGTAAAAC Y 2 1 2 1 101000 r 74 goat snp38611-scaffold49-1104773 4 110781983 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414640 Affx-122949327 AX-123284989 4 7715452 CTCTAGCTTCTGTGGGTTGGAGAATTTCCCCGAGC[A/G]TCTTGCCCGCTCCCCAGTTGTTCCCCTCGGCGCCT R 2 1 2 1 101000 f 74 goat snp38612-scaffold49-1141005 4 110745862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793294 Affx-122955142 AX-385280272 4 7747711 AGGAAGGAATGCAACTTCTTTTTTTCTAGACAGCT[A/G]TATCTTCTTTGTAGAAGACTATATGGGATATAGGT R 2 1 2 1 101000 f 74 goat snp38613-scaffold49-1173264 4 110713855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418011 Affx-122946657 AX-123288359 4 7784360 ACAGCAGCCTGGAATGTGCTTTATATTCTTGGGTT[A/C]GTTTTTCTATTTGCACCACAGCCGAAACGGAATGC M 2 1 2 1 201000 r 74 goat snp38614-scaffold49-1209913 4 110677395 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411705 Affx-122951537 AX-123282055 4 7891659 TCATGGACAAAATACACGTGGGTGAAATACGGATA[C/T]ATGTGTATTTCTCCCAGATGGTCTTGGTATCACAT Y 2 1 2 1 101000 f 74 goat snp38616-scaffold49-1317212 4 110570371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775275 Affx-122924849 AX-385262406 4 7935339 CTCACCTCTTCGGTTCTGAGGTCATTCTGTCTCAT[A/C]GTCTATGCGAAGATTAACCTCAATGAGTGCAAATG M 2 1 2 1 101000 f 74 goat snp38617-scaffold49-1360892 4 110525936 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388213 Affx-122969413 AX-123258571 4 7973287 CCACAGTTAAGTAGATCAAAAAACATTCTGAACGA[C/T]AAAGAGGAAAATAAGATACAGCAATGATCGGCCTA Y 2 1 2 1 201000 f 74 goat snp38618-scaffold49-1398840 4 110488027 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795394 Affx-122924354 AX-385282350 4 8002859 AACATAAGGTCCAGAATCTATTAACTTGTGATCCA[C/T]AGCCTTCAAAGCAATTTACGTGCAGTATACATTTC Y 2 1 2 1 101000 f 74 goat snp38619-scaffold49-1428412 4 110458569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435037 Affx-122933755 AX-123305377 4 8042267 TCTGCAGCTCGTGAGGATGATGACATCATCGATGA[C/T]TGTCTCAAGTGTCATTGAACTTCATGGCATATAAC Y 2 1 2 1 101000 r 74 goat snp38620-scaffold49-1467820 4 110419145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792105 Affx-122924736 AX-385279091 4 8124777 GAAAGTCCTTGTCATTTATCTTAGAGTTAAGAACC[A/G]TAGCTTGGAGTCTTAGAAATTAGAGATCATTATAT R 2 1 2 1 101000 f 74 goat snp38622-scaffold49-1550330 4 110335944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383334 Affx-122972684 AX-123253692 4 8156285 GGGGGTGAAGGTGAGGAGACAGAAGCCAGATTACA[A/G]TGGATTGGCATGTGAATATTTGTTCAAGTCCTGTG R 2 1 2 1 101000 r 74 goat snp38623-scaffold49-1581838 4 110304399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787421 Affx-122964955 AX-385274446 4 8194109 TCTGAAATAGATACTGATACTTCTCTAAGACATCA[A/G]GAATTATTTACCCCTTTTTTTTGACTAGTGCAGTA R 2 1 2 1 101000 f 74 goat snp38624-scaffold49-1619662 4 110266145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377055 Affx-122978296 AX-123247414 4 8230472 TATCACAGACCCTTTTGAGAAACCGGAGGATGCTG[C/T]AGACAAACTCTTTAGGGAAATGCATATACACATTT Y 2 1 2 1 101000 f 74 goat snp38625-scaffold49-1656025 4 110229528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447919 Affx-122923797 AX-123318255 4 8267578 ATCTGTGCCTTTAACTTTTAATATACTGAGAAGTG[A/G]CTTCAAGAGTTCATTCCAATTTTCATATCTATTGG R 2 1 2 1 101000 f 74 goat snp38626-scaffold49-1693131 4 110192077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272141 Affx-1111833441 AX-519545898 4 8293720 CTCATGTGGTTTTAATGTGCATTTCTCTAACTATT[A/C]ATGATGCTGATGGCATTTGGGTGCTTATTGCCATC M 2 1 2 1 201000 r 74 goat 4_8293720_AF-PAKI 4 8293720 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377654 Affx-122977858 AX-123248013 4 8298732 GTAACAAATGGCATTACTATTTGGTATACAAATGG[C/T]AAGCTGCTATTTGGAAAATCATTGGCAATCTGGGT Y 2 1 2 1 101000 f 74 goat snp38627-scaffold49-1724285 4 110160466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418600 Affx-122946358 AX-123288948 4 8330032 TAAATCTGGTACAGCTCTCTGTCGCTCCTCGCCCA[C/T]GGCATCTGCTCCTGCTTCCAGCACTTCCCTTGTTT Y 2 1 2 1 101000 f 74 goat snp38628-scaffold49-1755585 4 110129300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800609 Affx-122979206 AX-385287528 4 8369249 ATCTGATCTGGAACAGGAACACAGCGAAGCAGCAG[C/T]AGCTTATTGTAGTTAGACTCTTGGTGCTGGAGAGG Y 2 1 2 1 101000 f 74 goat snp38629-scaffold49-1794802 4 110089204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393625 Affx-122965310 AX-123263980 4 8402887 TTATGAGTGGAAGAGGCTAAAGGAAAGTGAGTGCT[A/G]TGGAGAGATAGGAATGGGGTGCTGAAGGTGCACAG R 2 1 2 1 101000 f 74 goat snp38630-scaffold49-1828440 4 110055580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791408 Affx-122950804 AX-385278400 4 8437686 AACAGACGTGTGTGAAGGCAGTCGTGGTGATACAC[A/G]TTTCAGAGGAATAGAGGATAGAGAGTTCTGGGAGT R 2 1 2 1 101000 r 74 goat snp38631-scaffold49-1863239 4 110020159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800073 Affx-122959479 AX-385286996 4 8480609 TGTGCATTGCTCCAGGCATCTGGATATAAGCCCTC[A/G]TGTATCTTACCTTCTAGTTCAGAAGACAGAAATTA R 2 1 2 1 101000 f 74 goat snp38632-scaffold49-1906162 4 109976926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419466 Affx-122945483 AX-123289814 4 8527941 GGAATTAAGCCGGTCGAATATTTTTGAAATAATGT[A/G]TCCCTCTGTACTAGTGATTTGTTCATTTTAATCTC R 2 1 2 1 101000 r 74 goat snp38633-scaffold49-1953494 4 109926139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387417 Affx-122970403 AX-123257775 4 8579711 GAACTCTTTCAACAGGTATGTTAGAACTGTGAGTG[C/T]ACTACCTTTGATCGTTTTCTCCATGTTTTTCCAGT Y 2 1 2 1 101000 f 74 goat snp38634-scaffold49-2005264 4 109874497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794189 Affx-122955525 AX-385281155 4 8609855 TGGAAGTGTTCATTACAATCGTAAGGTGTTGAACC[A/G]TAACCTAGCCAATGAAAGAACTACTATTTTAGACC R 2 1 2 1 101000 f 74 goat snp38635-scaffold49-2035408 4 109843682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434114 Affx-122934933 AX-123304455 4 8641462 GTGCTGCGCTTTTAAACACCCATCTTTAGTGGTTT[A/C]ACAGAGAAATAATTACTGAAAGAACATCCTTACTT M 2 1 2 1 101000 f 74 goat snp38636-scaffold49-2067015 4 109812035 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785741 Affx-122970741 AX-385272781 4 8673781 ACTGAAGAGTTTTTTTCCTATCACACAACATTTAT[C/T]GTAGTGCTAGGCATAAAGCCAAAACTCTGAAAATG Y 2 1 2 1 101000 r 74 goat snp38637-scaffold49-2099334 4 109779996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376573 Affx-122979079 AX-123246932 4 8702520 ACAAGATTCTAGAGTAGATAAGTGAGAAGAAACTT[A/G]TTGTCATTTCTGTTTTTGTTAACTTGTTCAAGACA R 2 1 2 1 101000 f 74 goat snp38638-scaffold49-2128073 4 109751119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378624 Affx-122977117 AX-123248983 4 8740302 GACAGGAAAGATGATGACGTAACCATGGTAGAGAA[C/T]GCATGAGCTGGGAGAAGAGTAGGAGAAAATATTTA Y 2 1 2 1 101000 f 74 goat snp38639-scaffold49-2165855 4 109713390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278051 Affx-1111836226 AX-519551541 4 8826678 GCTAACTTCAGTAAAACATGCTGTGTAGCCATCCT[A/G]CCATGAGAGCCTTGGGGTCCTTTAAGGTTGGGGGT R 2 1 2 1 201000 f 74 goat Random2.2K-405 4 8826678 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382330 Affx-122973892 AX-123252688 4 8833627 GAAACTAGAAAGTTGGATGACCTTGAGGCAGACAT[A/G]CAAGCAGAGCCTCCCTCCCTGATGGTACAACTTGG R 2 1 2 1 101000 f 74 goat snp38641-scaffold49-2259180 4 109619940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799479 Affx-122929213 AX-385286409 4 8870175 TCTTACCAGAGCAAACAGAGAGATAGTTTAAAATA[C/T]GAATTGCATCTTTTATCTTGCCACTTTCCTCCTGA Y 2 1 2 1 101000 r 74 goat snp38642-scaffold49-2295728 4 109582324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785704 Affx-122959861 AX-385272745 4 8924550 TTTTATGGAAGAATAGCGAGAGGTTCTCTAAGCTC[G/T]CTTGAGTTCCTTGATTTGCTGAAGGTCATGGCTAG K 2 1 2 1 101000 r 74 goat snp38643-scaffold49-2350103 4 109527372 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278207 Affx-1111836227 AX-519551695 4 8938494 CAGTTAGGCCCAGCTAACTGCCCTCTGCTCTCACC[A/G]AGACCCTTTACCCTCCGCTTCCAAAACACGCCCCA R 2 1 2 1 201000 r 74 goat Random2.2K-406 4 8938494 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802562 Affx-122975989 AX-385289464 4 8960292 TTCAATACTACCACTGGACTTTGCATATAGCAGAC[A/G]TTTGGTTAATGTTCCTTGAACTAAATTTTTAATTA R 2 1 2 1 101000 f 74 goat snp38644-scaffold49-2385845 4 109491040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381642 Affx-122974759 AX-123252000 4 9009396 AGATCAAGTGTGCTCACCCCTACTGTAGGAAAATA[C/T]GAATTCTGCAGTTTGGGGCAGTGTTCTATATTCTC Y 2 1 2 1 102000 f 74 goat snp38645-scaffold49-2434949 4 109441705 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431466 Affx-122936487 AX-123301807 4 9035931 TAAGTATTCTGATGTTGATGTATTCAAAAACAGCA[C/T]TGTAAATGTGAGTTAGCAACAACAACAAAAAAAAC Y 2 1 2 1 101000 f 74 goat snp2240-scaffold1069-433050 4 109391748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418934 Affx-122946507 AX-123289282 4 9084076 TAACATTTTCAGAACATTTTAAAAAATATTTATTT[A/C]TTTGGGTGTGCTGGATCTTACAAGCCCCTTGAGGT M 2 1 2 1 103000 r 74 goat snp2239-scaffold1069-384905 4 109343657 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396166 Affx-122963376 AX-123266521 4 9182607 CAACCAAAGATTGTATGACAGTGTCATGGTGTCCC[A/G]CTTCCTAAGGCCAACTGAACCCATTTCACTAAGAT R 2 1 2 1 101000 f 74 goat snp2237-scaffold1069-286374 4 109244119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394306 Affx-122964690 AX-123264661 4 9222695 AATCATATTCTCTTTAGGAATGAATTTTTTAGGAA[C/T]GATATCCACAATCACAGGGCAGGGGTAGATATGCA Y 2 1 2 1 101000 f 74 goat snp2236-scaffold1069-246286 4 109204415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436532 Affx-122932933 AX-123306870 4 9290744 GAAAGTAGTCCAGATGCTCACTGGTATGAATTCAA[C/T]GGTATCATTTATTTGGTAATTATGAGAGGTACCAA Y 2 1 2 1 101000 r 74 goat snp2235-scaffold1069-178237 4 109136736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769653 Affx-122962583 AX-385256823 4 9325842 TTTATACTCTTGGGAGATTAGATATCAGGTTTTAT[A/G]TTTCCACGTAGTTAAATCACCATGCCCCTTATTCC R 2 1 2 1 101000 r 74 goat snp2234-scaffold1069-143139 4 109101618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394817 Affx-122964799 AX-123265172 4 9376675 GCAATATACATATTTATCAAAACTTTACAATAAAA[C/T]ATCCTTAAAGATGGATTTTAAAATTAGGAGCAAGA Y 2 1 2 1 303000 f 74 goat snp2233-scaffold1069-92306 4 109050057 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437591 Affx-122931867 AX-123307929 4 9436126 GAGATTTCCCATGTACCCTTTGCTTCCCTGCATGC[A/G]TGACTTCCCCCATCATAAACACACCCCTCCTCCAC R 2 1 2 1 101000 r 74 goat snp2232-scaffold1069-32855 4 108990425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381523 Affx-122974852 AX-123251881 4 9482233 GGAAAGTCTCCTAGGGGAGATCCAGAGGGAGGAGG[G/T]CAAAGCCAAGGTCGTGGGGTAGGTGCTGCGATTGG K 2 1 2 1 303000 f 74 goat snp44424-scaffold603-6640725 4 108943158 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769028 Affx-122937385 AX-385256203 4 9512423 AGTTTTCACCTCCCACCTTTCTTCTTTAAGGGTCA[C/T]GCCACTTTTAATGACTAGAAATAGTTGCAAATGAA Y 2 1 2 1 101000 f 74 goat snp44423-scaffold603-6610535 4 108912533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402672 Affx-122958364 AX-123273025 4 9544634 ATCAATCGTATAGGGTGACTGTTCAAGCCACATCT[A/G]TCATTTATCACTGGAGAGATCTGTTAGGGCCAAGT R 2 1 2 1 101000 f 74 goat snp44422-scaffold603-6578324 4 108880366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797366 Affx-122948453 AX-385284305 4 9575034 CCCCCTTACCTAAGCTTAGATTTTTATAGATTTGA[A/C]TACAAAAATAGCTACTGCTTTTATCTGATCTGAGT M 2 1 2 1 201000 r 74 goat snp44421-scaffold603-6547924 4 108849963 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433443 Affx-122935068 AX-123303784 4 9605962 AGATGACTTTATAGCAGGAGGCAAATATTACAATC[A/G]CAATTATGTTCTGCAACAGGAAGTAAGTTCTAAAT R 2 1 2 1 101000 f 74 goat snp44420-scaffold603-6516996 4 108819032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378967 Affx-122976410 AX-123249326 4 9635059 GCTCCTTTGGGCTTGCCATTTATGGAAACTCTTAA[C/T]GGAAAGTGAATTCATGTGTGGATGGGATTTAGGTA Y 2 1 2 1 101000 f 74 goat snp44419-scaffold603-6487899 4 108789915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787606 Affx-122925587 AX-385274629 4 9676896 ATTTTGATAAAAACTGTTCCTGCTCTACTGTGTCC[A/G]TTTTGTTGGGATTTTAAAATTTGGGTATAATTGGC R 2 1 2 1 101000 f 74 goat snp44418-scaffold603-6446062 4 108746887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447814 Affx-122923920 AX-123318150 4 9709013 TTCCTTAGAGTATATGAAAACTCTTACATATTCAG[C/T]GAGGTGATGGAAAGTCAAATTATTTCTAGATCTAT Y 2 1 2 1 101000 f 74 goat snp44417-scaffold603-6413945 4 108714604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791707 Affx-122931897 AX-385278698 4 9743196 CATTTTTAGTGTAAGAAAATGAACCAGAATAAATA[C/T]GTTGCCAGATACATTTCTCTGAATCTCAGCTATCC Y 2 1 2 1 101000 r 74 goat snp44416-scaffold603-6379762 4 108680532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444987 Affx-122926657 AX-123315324 4 9799836 GAAAAAAATTTTAGGAAGTAAGTCAAGAGAGTGTC[C/T]GTACACTAAAACACTCAGTAAATATTGGTTGAATA Y 2 1 2 1 101000 f 74 goat snp44415-scaffold603-6323122 4 108623866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437776 Affx-122931702 AX-123308114 4 9849958 AAACCTGCACAGAAAAGAAACCACAGCAGAAAAAC[C/T]GCAGGAGGGCGGGGCTGTGCAGCCAGGCTCAGGCA Y 2 1 2 1 103000 f 74 goat snp44414-scaffold603-6273000 4 108573551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768771 Affx-122965727 AX-385255948 4 9897210 CATCCTCCTCAGAATTATATATAAATCAAATACAA[G/T]TCCAATCAGAATTCCAAAGATATTTAATTTGATAC K 2 1 2 1 103000 f 74 goat snp44413-scaffold603-6225748 4 108526018 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792065 Affx-122959217 AX-385279052 4 9943987 AATGCCATTTCTGTTAGATCTATATTAGTGTTACT[A/G]TAGTATGTTGTCAAGAGTTTAATGTATTTTAAATA R 2 1 2 1 101000 f 74 goat snp44412-scaffold603-6178971 4 108478905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428318 Affx-122939009 AX-123298661 4 9978362 CCCCACATCAAGTAGAACTTATTCTTTTTGTACAA[A/G]CATAATTAAAAGTTCAGAATCTATGTTTACAAACT R 2 1 2 1 101000 r 74 goat snp44411-scaffold603-6144596 4 108444453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603161 Affx-1002479428 AX-413837350 4 10047285 CATGGTGGAAAAACTTTCTGAGAGTAGCTATTTCT[G/T]ACCCATCTCACTTGTCAGTGGCTGATGTTGTTTTT K 2 1 2 1 101000 f 74 goat 4_10047285_RH-map 4 10047285 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414767 Affx-122949245 AX-123285116 4 10067567 TGGGAGCTGGTTCCCCTTACTTTAAATTATTCCTA[C/T]AAAAATTTATATAAAGATTAAGGGATCTCACCAAA Y 2 1 2 1 303000 r 74 goat snp44409-scaffold603-6055391 4 108355223 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793271 Affx-122939030 AX-385280249 4 10116756 TGCAAGGAACCCTGAAAATAGATTAATCTCTATAA[C/T]ATGTCCCCAGTCTCAGCCTCTTCCTAGTTTGCTAG Y 2 1 2 1 101000 r 74 goat snp44408-scaffold603-6006202 4 108305526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430194 Affx-122937350 AX-123300535 4 10145777 AGTCCTCAAGGCACTGAGAGATTTTGCCTAAGGTG[A/C]CCCTGCTGGTGTGGCCAGCCATTCACAGGACAACA M 2 1 2 1 101000 f 74 goat snp44407-scaffold603-5977181 4 108276743 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784832 Affx-122926357 AX-385271879 4 10185729 GCTGTAGTAACTGAGAGAAGCCATGATCTCACTAC[A/G]TGAGTACAAAGTATGTTCCTAACTTAGAAAGGTCT R 2 1 2 1 101000 f 74 goat snp44406-scaffold603-5937229 4 108236346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603250 Affx-1002479429 AX-413837430 4 10199787 TTTGAGATGCCATGTGACCCACTGACAGGTGGAGA[C/T]AGAGAAAAGTAAAGTGGACAGTAAATATGTATAAC Y 2 1 2 1 201000 r 74 goat 4_10199787_RH-map 4 10199787 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38402024 Affx-122958746 AX-123272377 4 10223838 TTGGTGAGGCAGTGTGTAACACAAGAAAGGGAGAG[A/G]GATATGCCCAAAAGGAACATGAGAGAGAAACAAAC R 2 1 2 1 101000 r 74 goat snp44405-scaffold603-5899120 4 108197423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603166 Affx-1002479430 AX-413837355 4 10232070 ATGAGACCTAATTAAACATACCAGGTTTTACACAG[A/G]AAAGGAAACCATAAATAAAATGAAAAGACAACCTA R 2 1 2 1 101000 f 74 goat 4_10232070_RH-map 4 10232070 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38390911 Affx-122967094 AX-123261268 4 10277772 GCAATTGCAGAACAACAGGTATATTCATTTTAAGT[A/G]TTAAAAAACCAGCAACATAAAATACATTTTCTAAC R 2 1 2 1 101000 f 74 goat snp44404-scaffold603-5845186 4 108143041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414884 Affx-122949134 AX-123285233 4 10318838 TTCTCTGACTTGATAAAAGGAAGAAGTTTGTTGAC[A/G]TCAATGACTGGATATAGGAGGAAGCCCGTAATTGA R 2 1 2 1 101000 r 74 goat snp44403-scaffold603-5804120 4 108101424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794187 Affx-122938807 AX-385281153 4 10400731 TAAAAATACTACTACTACCTTATCAAAGGCCCAGT[A/G]TCCATGAGCTTTGTGCTGAGTCCTTTGGAAACACT R 2 1 2 1 101000 r 74 goat snp44402-scaffold603-5722227 4 108018875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603167 Affx-1002479431 AX-413837356 4 10411948 CTAGAGAATCCACAGAGGGAAAAAATGTGGTATTA[A/G]AAGTATGAAAAATAAATCAACTGAACATCTTCAAA R 2 1 2 1 102000 f 74 goat 4_10411948_RH-map 4 10411948 A G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603169 Affx-1002479432 AX-413837358 4 10429139 ATCTGAGACAGAGAAGACAGTTTAACAGTAAACAG[A/G]TCTAGAAAACTAAAGTTTTGTTGATATAAAAAGAA R 2 1 2 1 101000 f 74 goat 4_10429139_RH-map 4 10429139 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603172 Affx-1002479433 AX-413837360 4 10458331 GTTCTTGCCATAACGTAATATTTGAAATATGTTCC[C/T]TATGCAAAATAATAAAAAAGCTATATTTGACAGAG Y 2 1 2 1 101000 f 74 goat 4_10458331_RH-map 4 10458331 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603600 Affx-1002479434 AX-413837750 4 10494906 CAAATTCGTGCATCAGCAGGAGGATTCTTTATAGT[A/T]GTACCACCTGGGAAGTCCTATACAATGCCTATAGG W 4 1 2 1 103000 f 74 goat 4_10494906_RH-map 4 10494906 T A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38385399 Affx-122971345 AX-123255757 4 10504647 CCCACAGAATGCATGAAAGCTGTTTGTGCCGGAGT[A/G]CTACTGGGCATAACACACAATCTCTGGCTTCCTAC R 2 1 2 1 101000 r 74 goat snp44400-scaffold603-5618311 4 107914144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603260 Affx-1002479435 AX-413837439 4 10516519 ACATCTAGCAAAAATACCCTTCAAACATGAAAGCA[A/G]CATAAGGATACTTAGGACAAATGCTGAGAAAATTC R 2 1 2 1 400000 r 74 goat 4_10516519_RH-map 4 10516519 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401678 Affx-122959561 AX-123272031 4 10538527 CTGGCATTAAAGCCATATCTTACTTTGGCTTGCCC[A/G]CTGAAAATGAGCATGTGTCCTGCGGTCTCTGGATC R 2 1 2 1 101000 f 74 goat snp44399-scaffold603-5584431 4 107880246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768429 Affx-122955059 AX-385255609 4 10573012 GGTCTGCACTCTATTATTTGATAAAATACTGTGGC[A/G]TAAATGTCACTGGGAAGTGGTTAGTCTCATTTCTA R 2 1 2 1 101000 f 74 goat snp44398-scaffold603-5549946 4 107844964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429132 Affx-122938003 AX-123299474 4 10601740 CTCCAGCTATTGTTTTTGGGCAAAAGTCACAAAAC[G/T]GGTTTTTCCCACCTTTACAAGTCCTTCTTAGGTGG K 2 1 2 1 101000 r 74 goat snp44397-scaffold603-5521218 4 107818046 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446015 Affx-122925862 AX-123316352 4 10638467 AAGGCCCCTAACTATAGTAAGCCCTCCTTGTCTGT[A/G]CCAGTTAGGAATACTTTCAATTGCAAATAACAACA R 2 1 2 1 101000 f 74 goat snp44396-scaffold603-5484491 4 107781881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603176 Affx-1002479436 AX-413837363 4 10666100 CCCAGGGTCATCCCAGTGCACTAGCCCCGAGCACC[C/G]TGTCTCATGCATAGAACCTGGACTGGTGATCTGTT S 4 1 2 1 303000 f 74 goat 4_10666100_RH-map 4 10666100 G C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320789537 Affx-122919655 AX-385276546 4 10696439 ACACAGATGTGCACCTCTGTCAAAACTCTAAGAAT[G/T]TACCCTTAAAAGGATCACATTTTATTGTATATGAA K 2 1 2 1 101000 f 74 goat snp44395-scaffold603-5426519 4 107723838 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603178 Affx-1002479437 AX-413837365 4 10709598 CAAATGAAAAGGCCACACTTGCTCAAAGATACAGC[C/T]ATTTTAACTAGAATAGAGGGAGAAATACAGGGCTA Y 2 1 2 1 101000 f 74 goat 4_10709598_RH-map 4 10709598 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38438776 Affx-122931380 AX-123309113 4 10732937 AGTCCTCTTTTTCCTTATTAGGAAGTCAATGTTGC[A/G]CTGTGCTTAGTCGCTTAGTCGTGTCTGACTCTTTG R 2 1 2 1 101000 f 74 goat snp44394-scaffold603-5390021 4 107686736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278209 Affx-1111836228 AX-519551697 4 10739260 AATAAGGTGTATAGAAAGCCTCATTTTGGAAACTA[A/T]CATAATGTACTTCACTTCTACATTGCAGAAGGGAG W 4 1 2 1 101000 r 74 goat Random2.2K-409 4 10739260 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400570 Affx-122960415 AX-123270925 4 10772367 AGTGCTTTTAGTTGTCAATTAGAGATAAGTCACTA[C/T]CAGAAATTTATAAAGCATGGAAAGCTTATCTTTTC Y 2 1 2 1 101000 f 74 goat snp44393-scaffold603-5350591 4 107646727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603181 Affx-1002479438 AX-413837367 4 10809126 CCTCAAGTGGCAACAAGAGAAACCCATGAGTTACA[A/G]ATACTGAGCTCTGTGCCACAACTAGAGGGTCCAGT R 2 1 2 1 102000 f 74 goat 4_10809126_RH-map 4 10809126 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38428073 Affx-122939108 AX-123298416 4 10817225 ATTCTTTGGGCCCCAAAGAACTGCCAAAGACAAAA[C/T]GAACTAAACTAATGTCTGAAGGTCCTACACAGCTT Y 2 1 2 1 201000 r 74 goat snp44392-scaffold603-5305733 4 107600681 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603183 Affx-1002479439 AX-413837369 4 10850488 TTGCTGTTTTGTTTTTAGCTGAGGTCTATAACCTT[A/C]TCAAGAACTTAGTAAATAAATGAATTTGTTGATGG M 2 1 2 1 101000 f 74 goat 4_10850488_RH-map 4 10850488 A C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404648 Affx-122957307 AX-123275000 4 10853480 CTAAATCAAAAGACAGTAAGACTGACATAACTCCC[A/G]CTGCTCCCCTCTAACTTGCTTGCCTGAGTACTCAC R 2 1 2 1 101000 f 74 goat snp44391-scaffold603-5269478 4 107561917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272520 Affx-1111833410 AX-519546238 4 10869594 TATATATTCTTGAATTCTTATATTCTTAGCCACCT[A/G]TAATTTAAAAAACCAAAAAGCCAACAGCAACAACA R 2 1 2 1 201000 f 74 goat 4_10869594_AF-PAKI 4 10869594 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350603185 Affx-1002479440 AX-413837371 4 10888468 GGGGCAAGTCAAACATAAGAAAATGTCATTGTAAG[C/T]AGGGTCCCAGAGGAGGTGACCCTGCCTAACTGCAT Y 2 1 2 1 101000 f 74 goat 4_10888468_RH-map 4 10888468 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38421545 Affx-122943867 AX-123291892 4 10890231 GGCTTTATGCAGGTTAGGGGAGAACAAATCTTCTA[C/T]GGTTGTGTTTAACCAGTGTTCACACTGCAGCAAAA Y 2 1 2 1 201000 f 74 goat snp44390-scaffold603-5232727 4 107525200 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603187 Affx-1002479441 AX-413837373 4 10987779 GGCAATATTAGAAATTTTCAAATTTTATTCTAGGT[C/T]CATCACTTCTCCTTTCTCCATCCTTTTCAAATTAC Y 2 1 2 1 303000 f 74 goat 4_10987779_RH-map 4 10987779 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38402137 Affx-122958666 AX-123272490 4 10990241 ACCAGGGCAGTGTGAGAGTTCCTGTTTCACCACGA[C/T]GCCTCAACTTGTTCAAGTTCCTGAGTGGCTGGGGC Y 2 1 2 1 201000 r 74 goat snp44388-scaffold603-5132717 4 107425852 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799812 Affx-122929621 AX-385286738 4 11125402 CTACCAATGGGAATAAAGAAATCTCAAGGAGGTAT[A/C]TTTAGTGAAGCACCTTCTGACATTATATTCATCGA M 2 1 2 1 101000 f 74 goat snp44385-scaffold603-4997556 4 107291145 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278059 Affx-1111836230 AX-519551549 4 11206800 GTTAATAAACATATGTGCCTTCTAAATCAGAACTT[A/G]AGATACTTTAAGGCTATAAGAGACTTTGTCGTTGT R 2 1 2 1 101000 f 74 goat Random2.2K-411 4 11206800 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783594 Affx-122978871 AX-385270653 4 11226696 GGGCCACTGTATGCAGCCTGTAGTTCAGGTTGCAC[A/G]TATCTGGCCCACACTGTAATGACCAGGGGAAAGGT R 2 1 2 1 102000 r 74 goat snp44383-scaffold603-4896262 4 107190130 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397351 Affx-122962295 AX-123267706 4 11267629 GAATGCCTTCTCACTCATCTTGTGTCCTTACTGTT[A/G]CTAGGACAAACTTGGAACCTGATTGGTAAAAATAT R 2 1 2 1 101000 r 74 goat snp44382-scaffold603-4855329 4 107149249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437746 Affx-122931723 AX-123308084 4 11296443 AAAAGAGCATGGCCATACTCAAGCTAGCAAGAGCA[C/T]AGGGGAACGTTCCGTAAGAGTTCGTGAGGGAGAAG Y 2 1 2 1 101000 f 74 goat snp44381-scaffold603-4826515 4 107119712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778803 Affx-122949414 AX-385265912 4 11348100 TGGAACTATTTGCTTTTTTAAAGAGGGACTTTGAA[C/T]GAGTAGACATATGTCAGTTAAGACTTTTCCAGTAT Y 2 1 2 1 101000 f 74 goat snp44380-scaffold603-4774858 4 107068009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379185 Affx-122976309 AX-123249544 4 11390115 AAACATTGATACTTTCAATATCTGTGTCAATTTCA[G/T]ATTTATTAATTTATTTAATGAATATTTATTGATAC K 2 1 2 1 103000 f 74 goat snp44379-scaffold603-4732843 4 107025741 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387076 Affx-122969885 AX-123257434 4 11437185 GCAGGGAACTGCTAGATTCTGTCCCAGGCTATGCT[A/G]CTTTCATTCAATCCTGATTCTCTCTCATTCTCTCT R 2 1 2 1 101000 r 74 goat snp44378-scaffold603-4685773 4 106979258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785711 Affx-122935149 AX-385272752 4 11469364 GTAAGCCATAAAATTTCAGAGTAGGAAAAGAACTT[A/G]AAGAGCTTGATTCACTGATTCTCTCCATTAAAAAG R 2 1 2 1 201000 f 74 goat snp44377-scaffold603-4653594 4 106948974 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418745 Affx-122946213 AX-123289093 4 11506800 ATTGCAACAAATCTGTTTCAAGGGTAATAATCTTC[A/G]TTTGGACAGAATTGAATTCAAGACCTCAGCCTTGC R 2 1 2 1 201000 f 74 goat snp44376-scaffold603-4616158 4 106912214 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382988 Affx-122973341 AX-123253346 4 11535647 CTGCATGGAACTTTATAACTGAAAGAGTGTTTTCC[A/G]CCTGTGGTCTTCACAACAACCCTGTGAGATAGTTA R 2 1 2 1 201000 f 74 goat snp44375-scaffold603-4587311 4 106883445 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397430 Affx-122962236 AX-123267785 4 11568840 TTTTCTTTCCGTCCAATTTCTCAGTGAATTCTGCC[A/G]GTTGTGTGGATAGCTTTAGTCTATCTGCTTCTTTT R 2 1 2 1 201000 r 74 goat snp44374-scaffold603-4554118 4 106849796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390000 Affx-122968046 AX-123260357 4 11615439 TAATTTCCACTGTACAAAATTCAAAACCTGAGGGA[C/T]GCAGTTTGGTAATTTAGCATTTTTGCTTCATGTGA Y 2 1 2 1 201000 r 74 goat snp44373-scaffold603-4507519 4 106803408 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765173 Affx-122971495 AX-385252724 4 11666429 AGGTAGTTAGGGAAGGCTTTCATTCCTGGGTTCCA[C/T]GGGACTGTGGCAGTATGAAAGATAGTTCTTTGCAG Y 2 1 2 1 101000 f 74 goat snp44372-scaffold603-4456529 4 106750812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406308 Affx-122955466 AX-123276660 4 11709027 GATGGTCTCAACTAAATTATCATTCTGCTTAAGTT[A/G]TCTGGGTTTTGTTTGTATTTTACTCTCTAGCTTCT R 2 1 2 1 101000 f 74 goat snp44371-scaffold603-4413931 4 106707873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389984 Affx-122968059 AX-123260341 4 11787687 CTATATATAACAGCCCTGATTTGAATTTTTGGTTG[C/T]GTGCAACAGAGATTAACCCTAAATATCTTAAGCCA Y 2 1 2 1 101000 r 74 goat snp44369-scaffold603-4335271 4 106629236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438151 Affx-122931467 AX-123308489 4 11838720 CCTCCAGCCACACTAGCTTCCTTCCTGCTACTCAG[A/G]CACACCAAGTTTGCTGCAACCTTCCTCCTGTGCTT R 2 1 2 1 101000 r 74 goat snp44368-scaffold603-4284238 4 106577825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424256 Affx-122942460 AX-123294602 4 11900239 CCTTGCAGGTATTTAGCACACTGTGTAACCTCACT[A/G]CTCCTGGAGGAAGCTTACTGAGCAGCACTACTTCT R 2 1 2 1 101000 f 74 goat snp44367-scaffold603-4222719 4 106516034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388821 Affx-122968898 AX-123259179 4 11965939 GAAAGTGACATTAATCATCTACAGTCATTTAGATC[A/G]TAGGGAAAGTCAAGGAAGAGGAATAAACCACAGAT R 2 1 2 1 201000 f 74 goat snp44366-scaffold603-4157019 4 106450121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441186 Affx-122929542 AX-123311523 4 12007678 ATCTATAGCATTTATCAATGGTTCTCATTCAGCTT[G/T]CTTTCTTTTTGTTTTAGTCCAAAAGTTTCATGGAA K 2 1 2 1 101000 f 74 goat snp44365-scaffold603-4115280 4 106408620 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408250 Affx-122953818 AX-123278601 4 12057510 GAAAAGATTCCATCATTGTTTTCCTAATGAAAGAC[G/T]ACCACAAAAAAAATTGCCAAATCTTTATAAAAGGT K 2 1 2 1 101000 f 74 goat snp44364-scaffold603-4065448 4 106358246 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788543 Affx-122923330 AX-385275560 4 12087312 GTTGAGGATTTAGGCATCCAAAACAAATAGATGCT[A/C]TCATTTTTATATCCTTGAACATACTAAAAAGATTA M 2 1 2 1 101000 f 74 goat snp44363-scaffold603-4035646 4 106328568 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793522 Affx-122943910 AX-385280499 4 12136028 CAGATTAAAACCCAAACGCGTTGAATATACATACA[C/T]AGGCATACACTGCATAAGCCACCCACTGTACATGG Y 2 1 2 1 101000 r 74 goat snp44362-scaffold603-3986930 4 106280166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783515 Affx-122927607 AX-385270578 4 12202170 CAGGGGACATTTATTTCTTAATGAGGACTTCTTAA[C/T]GAGAAACTCTCTAAGAGGACTTGAACCTCCAGATT Y 2 1 2 1 201000 f 74 goat snp44360-scaffold603-3920788 4 106213256 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450833 Affx-122921786 AX-123321167 4 12239582 AATGAGGATTATATCTGGTGACTTTTTTAAATACT[A/G]CGAATTATTAATGTTGAGGGCAGTATATGAAACAC R 2 1 2 1 101000 f 74 goat snp44359-scaffold603-3883376 4 106175767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415887 Affx-122948480 AX-123286236 4 12286375 TGAGGCCATAGTGATTACCTGGGTAACAAAGTTTA[A/G]TCCCTTTTAGTTCTTGCTGTTACTCTTACTTGAGC R 2 1 2 1 101000 f 74 goat snp44358-scaffold603-3836583 4 106128146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397031 Affx-122963115 AX-123267386 4 12347417 ATATGAGTAGAAAGAATAAAGTCTAAACTGGAGGC[A/G]TGTAAAGAACTTAAAAGAAGCTCTTCTCTCCAGAG R 2 1 2 1 101000 r 74 goat snp44357-scaffold603-3775541 4 106065896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432180 Affx-122936403 AX-123302521 4 12379084 GACAATCCAAGTGTAACATACTCTTAATTATATCA[C/T]TGGACTTCAGCCCTTCGGATGTTGTCATGGAAATT Y 2 1 2 1 101000 r 74 goat snp44356-scaffold603-3743874 4 106033189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436170 Affx-122932617 AX-123306509 4 12436935 AAAGGCTATAAAATTGACTTAATTCTTCACTGTCT[A/G]TTTAGCTGAAATGTTTATTTAATTTCTAAGTTCCA R 2 1 2 1 101000 f 74 goat snp44355-scaffold603-3686023 4 105967172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789922 Affx-122977052 AX-385276928 4 12485615 ACATTTGCATAGAGTGTTGCCTGAAGGTTTGAGGA[G/T]AGAGCCCATGGCATCTAAATGTTCCCTTTAACATG K 2 1 2 1 101000 r 74 goat snp44354-scaffold603-3637343 4 105918380 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798074 Affx-122934963 AX-385285010 4 12528962 TCACTACCTCTGTGGCCTTGGGTGAACTTACTTAA[C/T]ATCTCTTTGCTCTTGCTTCCTCATCAATAAAACAG Y 2 1 2 1 101000 f 74 goat snp44353-scaffold603-3593996 4 105873295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424391 Affx-122941826 AX-123294737 4 12590559 GTGTTTTCTTTTGCAAAAAGTTTTGGGAAGATCAT[A/G]CTGTTGGATAAGCAGGAAGAAAAATACTTGTGTTG R 2 1 2 1 101000 r 74 goat snp44351-scaffold603-3532399 4 105812736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769850 Affx-122966911 AX-385257020 4 12663607 TTCTGTGGTACTATAGTATGATGGCAATTTGCTGT[C/T]TAATCTGACAGTATATCTTGGAGCTATTCAAACTA Y 2 1 2 1 101000 f 74 goat snp44349-scaffold603-3459351 4 105739757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422283 Affx-122943489 AX-123292629 4 12810373 GTTATGTTTCATACCAGGGGATGGATAAAAAATGG[C/T]GAAGATGCTTAGTAATTCTTAGGAGAAAAACAACA Y 2 1 2 1 201000 r 74 goat snp44346-scaffold603-3312585 4 105590883 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278061 Affx-1111836231 AX-519551551 4 12876984 AACAACACGGAGAATAGCTCCTATTGTTTTTGTTT[A/T]GTTTTAACCTCAAAACCCCCAGGATCTACAGACTT W 4 1 2 1 102000 f 74 goat Random2.2K-412 4 12876984 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439356 Affx-122930283 AX-123309693 4 12924629 AAGGAGCTGAAAGTGGGTGAGGAACAGAAGGTCAG[C/T]CAGCAACACTGAAATCCAGGAAGTAAGGAGGAAGA Y 2 1 2 1 101000 r 74 goat snp44344-scaffold603-3198329 4 105476408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770323 Affx-122974163 AX-385257489 4 12965640 ACTTGGGCTCCTAATTCTCAGTCCTATGTCTACAA[C/T]ATGATTTAAAGAGCTTATCACATAATATTCAGTGG Y 2 1 2 1 101000 f 74 goat snp44343-scaffold603-3157318 4 105436151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784619 Affx-122971936 AX-385271667 4 13001863 ATAGTGGAGCCTACCTAGCACAATCTAGGTATTTG[A/C]TTATTTGTTGTTTTGAATGAGTAAACAACTGAATG M 2 1 2 1 101000 f 74 goat snp44342-scaffold603-3121095 4 105399928 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772101 Affx-122930675 AX-385259256 4 13051054 TTCAGGTGGCCCTCAGTTAAACTTTTGTTCAGTTA[C/T]ATAATTCTCATAGATTTCTGAGCTGGCATGAGAGC Y 2 1 2 1 101000 f 74 goat snp44341-scaffold603-3071904 4 105350869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453548 Affx-122919783 AX-123323881 4 13079789 GGTTAACTATTCAAGCAAATCCCTCTTTGCTACCA[G/T]CATGTCATCATCTTGCATCAAGAACTATCCCACAA K 2 1 2 1 101000 r 74 goat snp44340-scaffold603-3043169 4 105322215 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804567 Affx-986696735 AX-385291106 4 13105755 CAGCCCCTCTTGCTCCAGCACTGCTCCCCTCTGGG[G/T]CAAGGAGTTGTTGGGTACAGGAAGAGCACACACCC K 2 1 2 1 600010 r 74 goat 4_13105755 4 13105755 Ancestral_priority_1043 ancestry 0.598 neutral IMAGE 10K 10K ancestral 38376447 Affx-122978060 AX-123246806 4 13124008 AATAGTGGGGGTGATCAGCCCTCTCACACACCCCC[A/G]CTCCATGACCTCTGCTCCCTGACTGCTAAGGAGGT R 2 1 2 1 101000 r 74 goat snp44339-scaffold603-2998950 4 105277656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796823 Affx-122947295 AX-385283766 4 13154792 GACTTCTTTTCCTACTAATAGGCAAGACTACATTA[A/G]CTGGACAAACCTCCCTGCTGGAAACAATGAACTTG R 2 1 2 1 101000 r 74 goat snp44338-scaffold603-2968166 4 105247008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804234 Affx-986696737 AX-385290867 4 13178272 GTAAGAACTGAGGAAGAATGGCAAAGACGTCTGTA[C/T]TCAAGAGACTCTTGAAATAAAACTCTAAGTGATAA Y 2 1 2 1 600010 f 74 goat 4_13178272 4 13178272 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 38437752 Affx-122931718 AX-123308090 4 13204056 ACTATTCTGTCTTTTGCCCTGTCTGGGGAATCCTA[C/T]GGACAGAGAAGCCTGGAGAGCTACAGGGCATGGGG Y 2 1 2 1 101000 f 74 goat snp44337-scaffold603-2918902 4 105197965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786748 Affx-122937052 AX-385273779 4 13236140 CTCACTCATAAGAAGTCAGGGATAGGTTCAATGTA[C/T]ACTAAGTTGCAAATACCTGGGACATCGCCCACAGC Y 2 1 2 1 101000 r 74 goat snp44336-scaffold603-2886818 4 105165564 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38404851 Affx-122956623 AX-123275203 4 13272654 GGGCTCCCAGGACAGCCAGGAGTACCAGGAGAAGA[C/T]GGAGCTGCAGGGAAGAAGGTAACACTGTTTTCCAT Y 2 1 2 1 103000 r 74 goat snp44335-scaffold603-2850304 4 105128268 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780011 Affx-122945417 AX-385267110 4 13304993 TTCATCTGGGAGACTGGTGCCTCATGGTTATAAGA[C/T]GAGCTATTACCTCTCCAAGGAACAAAAGAAGCAGA Y 2 1 2 1 101000 f 74 goat snp44334-scaffold603-2817965 4 105095520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397511 Affx-122962057 AX-123267866 4 13360516 AAATATCTTCAAATGGATAATGGACTTAATTTTCA[C/T]GTTCAAAATTTGGACTATCAGTAGCATATTTGCAA Y 2 1 2 1 101000 r 74 goat snp44333-scaffold603-2762442 4 105039822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786253 Affx-122967542 AX-385273288 4 13390617 TCTTTTCCCATTTTGTGATAAAGAACCTATTTAGT[A/G]ATGTGGTCATAAGTGGTTAAAGCAGGAGAGAGAGG R 2 1 2 1 101000 r 74 goat snp44332-scaffold603-2732341 4 105009572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379262 Affx-122976251 AX-123249621 4 13433683 GGAGCATCCTTCGCAGGTATTTTTATGAGCACTCA[C/T]TCTGGAATATCCCTGGCAAGGCAGGTACCAAATCC Y 2 1 2 1 101000 f 74 goat snp44331-scaffold603-2689275 4 104966481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769266 Affx-122962079 AX-385256439 4 13474626 AATTAACTATATTCCAAATAATCTATCCTGACTTT[C/T]ACTGGTCAATTCTCAGTTAAGGCTTTAACTGCGGA Y 2 1 2 1 201000 f 74 goat snp44330-scaffold603-2648332 4 104927339 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421839 Affx-122944301 AX-123292186 4 13511263 GACTCTTTTAACTCAGCCACACCTAAGTTGACAGT[A/C]TCTTTTTTTTTATTTTAGCAATTAAACTATAATGA M 2 1 2 1 101000 f 74 goat snp44329-scaffold603-2611695 4 104890875 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783454 Affx-122967977 AX-385270517 4 13542446 AACGAATGGAATCACCATACACGTCCCAACTTGGA[C/T]GAACCTTGAAAAGTAGAAGCAAAGGAACCAACCAT Y 2 1 2 1 102000 r 74 goat snp44328-scaffold603-2580512 4 104858747 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434233 Affx-122934836 AX-123304574 4 13573217 AGCGCAGATCAGCCACCATCTTCTGTGCACGCCCA[A/G]CTCAATCCTGACACAGAGATGGAACTCAAGACATG R 2 1 2 1 101000 r 74 goat snp44327-scaffold603-2549741 4 104828125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443763 Affx-122927113 AX-123314100 4 13620685 GTACCAATTTAAACTGCCTTCAATACCAATTCCCA[C/T]TGTACCTGTATTTGGATTATGAATATCTTGTGAGA Y 2 1 2 1 101000 f 74 goat snp44326-scaffold603-2502273 4 104780775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449666 Affx-122922571 AX-123320001 4 13650037 CTGCATAAGGAAGGACCACGGCTGTCATGTCCATG[C/T]GTATATTGTTAGGCGGCTCCATAAATATGCGTTGA Y 2 1 2 1 101000 r 74 goat snp44325-scaffold603-2472921 4 104751421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444585 Affx-122926961 AX-123314922 4 13717914 TTTTTCAGAACTGCCTGATCATTCCTGATAGTTTT[A/C]TGCTGCTTGTTCAGGCTTCTGATTCTATGCTTTAT M 2 1 2 1 101000 r 74 goat snp44324-scaffold603-2405044 4 104684434 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382547 Affx-122973781 AX-123252905 4 13774147 AGAAGATATGATAAATATAGATTGGAATAAATCTG[C/T]ATTTTCAAAACCTGATGAATTTTTAAAAAACTGAA Y 2 1 2 1 101000 f 74 goat snp44323-scaffold603-2348811 4 104628190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405166 Affx-122956939 AX-123275518 4 13847341 ATACCAACTCCTGGCTATAGCTTTAAGATTATATT[C/T]ACCTGTGAGATAAAAGAGCAAATTTACTTTTTATT Y 2 1 2 1 101000 f 74 goat snp44321-scaffold603-2275617 4 104553325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451127 Affx-122921379 AX-123321461 4 13911880 CAGGTTTATACAGTTTGCTTGGGGCAGGGAGTTCT[C/T]TTCAGTTTTTCTTGATGAGGTAGTTCAAGAAGTTT Y 2 1 2 1 201000 r 74 goat snp44319-scaffold603-2211078 4 104487560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378719 Affx-122977047 AX-123249078 4 13942682 CCTGGCTTAAGGTCCTCATTCATAATTGGCTCTAT[A/C]AGATCTAATGAGGAGGACTCAGGCATCTGTCTGTA M 2 1 2 1 101000 f 74 goat snp44318-scaffold603-2180276 4 104456591 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398451 Affx-122961604 AX-123268806 4 13989924 TGAAGAGTATATGGGGACATCAGCTTCAAAGAACC[A/G]TAGGAAAACAACGGGGAAAAAATTGTCCTCTTACC R 2 1 2 1 101000 f 74 goat snp44317-scaffold603-2133034 4 104409559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798735 Affx-122923140 AX-385285666 4 14044412 TGGTACAGTTCTACGTAAATTGGACAAGCTGGCTT[A/G]CCTTACTCTTCACAAGCTTACATTAATACCGTCAT R 2 1 2 1 101000 f 74 goat snp44316-scaffold603-2078546 4 104354088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430257 Affx-122937305 AX-123300598 4 14083052 CTTTATAGTTACTGCTTTTTGTGTGTGATGAGTGC[G/T]CATGAAGAGTAATGCTCCCCTCCTAGCCTGTTTGC K 2 1 2 1 101000 r 74 goat snp44315-scaffold603-2039906 4 104315554 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785654 Affx-122949260 AX-385272695 4 14143426 TGGATCAAACTAAGAAAACTAATACCAACAGTCTG[C/T]AGGAGCTAGAACACTATTTCAGGTATCAGATTAGA Y 2 1 2 1 101000 f 74 goat snp44314-scaffold603-1979532 4 104254985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452395 Affx-122920609 AX-123322728 4 14175395 GACTGCACCACTCCCTGGCTTCCATTATCACCTGC[A/G]CTTCTGACTAGCTATAGACTGAAGGAAGGTTTCAG R 2 1 2 1 101000 r 74 goat snp44313-scaffold603-1947563 4 104223190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802105 Affx-122972252 AX-385289009 4 14224353 AAATTTCTAAGCAAGAATAGCATAATGTGTACTGT[A/G]CTTTCAGAGATAATTACCATCTTTTTAGAATGAAT R 2 1 2 1 101000 f 74 goat snp44312-scaffold603-1898605 4 104174246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393637 Affx-122965301 AX-123263992 4 14282839 CCCTATTAATTTAAATGGTGAGGACTCGTTAAGGT[A/C]TTGGAATGAGATCTGAAGCTCTTAAAGCACAGAGT M 2 1 2 1 101000 f 74 goat snp44311-scaffold603-1840119 4 104115306 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391596 Affx-122966602 AX-123261953 4 14319573 AGCAAATAACACGAGTAGTCTTCTACCCTTTTAAC[A/G]TGAGATCCACAAGGTGAGGTTTCATTGAGGAAGTA R 2 1 2 1 101000 f 74 goat snp44310-scaffold603-1803385 4 104078353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792756 Affx-122967092 AX-385279735 4 14348657 CAGTCAGATCCTAAAGCCTGTGTGTAACATCCTGC[A/G]TCTTCCCAGTTCAACAAACTTCAAAACTTTCCAAT R 2 1 2 1 101000 f 74 goat snp44309-scaffold603-1774301 4 104049548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389546 Affx-122968272 AX-123259904 4 14381942 CACCACAGCTTCTCTCTCAGTACATCAGTTATTGC[A/G]CTTTGGGAGCTGGGTCAAAGGGCCACCCTTTCCAG R 2 1 2 1 101000 f 74 goat snp44308-scaffold603-1741016 4 104016156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412297 Affx-122950868 AX-123282646 4 14437984 TCCGTGTACTTCAACTCTTTAAAAAAAGGCTTATA[C/T]GCTTTGTATTCATTTTAACAAATTCTAAACATGAA Y 2 1 2 1 101000 f 74 goat snp44307-scaffold603-1684974 4 103958557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776788 Affx-122967819 AX-385263912 4 14478923 AAAAATGTCACAGTGGGAAGTGTTTTAATATTGAG[C/T]GGTAAATCCCCAGAGGCAAATGCAAAATATATCCA Y 2 1 2 1 101000 r 74 goat snp44306-scaffold603-1644035 4 103915656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446554 Affx-122924847 AX-123316890 4 14528279 TTGTTGGAATTTCCAAATCATTTTCAAAAGAAAGC[A/G]CAGCCCAGTGAATTTTTACATGGAAGGCTGATATG R 2 1 2 1 101000 r 74 goat snp44305-scaffold603-1594679 4 103866505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764624 Affx-122925097 AX-385252266 4 14567440 CAAATAAGTATCTTAAAGGAAGCCGACTGAGAGTC[A/G]TCAGTTTATTAAACCTTTGCGTGAAAAGGTTTAAG R 2 1 2 1 101000 f 74 goat snp44304-scaffold603-1555518 4 103827008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449141 Affx-122923558 AX-123319476 4 14610615 ATTCACTTCAATTAACTATTCCCATATACTGCCCC[A/G]CACTGGTAGTCTGTTGTATTCTGATAACAAGTCTG R 2 1 2 1 101000 r 74 goat snp44303-scaffold603-1512343 4 103782098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441836 Affx-122929053 AX-123312173 4 14642251 TTCTTGCATTTTAATAAATTACTTTGTCCTTCAAT[A/G]TAGGTTTTAATCTCTATATTAAAATGTGTTTGATT R 2 1 2 1 101000 f 74 goat snp44302-scaffold603-1480707 4 103750713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379433 Affx-122976104 AX-123249791 4 14698846 AATCTAAAGATTATTTGGGAATGTTGGTTCTTATC[A/G]TAATGACTTGCAATTACTAGAAGTAGAGATTATAC R 2 1 2 1 101000 r 74 goat snp44301-scaffold603-1424112 4 103693324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784521 Affx-122939010 AX-385271570 4 14731947 AAAAATCAAATTGCATCTCAGTAACTGTTTGATTT[A/C]TAAAACACTTAATCAATAGATGAGGCTTATCCATT M 2 1 2 1 201000 f 74 goat snp44300-scaffold603-1391011 4 103659734 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804535 Affx-986696703 AX-385291084 4 14786986 CCTCCTGTTCCCTGATTGGAGCATTTGCCTATGAC[A/G]TCACTGCTCTGTGCCTCTGCAGGCTGCCCTGTCCA R 2 1 2 1 600010 r 74 goat 4_14786986 4 14786986 Ancestral_priority_1043 ancestry 0.416 neutral IMAGE 10K 10K ancestral 320786094 Affx-122942498 AX-385273130 4 14841149 ATTCAAATAGTTTCACTTTTAGGTTAAGCACAATC[A/G]CAGCAATGTCTGACACAGTAAAGAAAGGGCTGTGC R 2 1 2 1 101000 r 74 goat snp44298-scaffold603-1281809 4 103551211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381734 Affx-122974330 AX-123252092 4 14912777 CCAACAGAAGTCTATAAATAATTATGTATGTCTAT[C/T]TGTTAAAATGTAAACATAAATGTATAGAAAATACT Y 2 1 2 1 103000 f 74 goat snp44297-scaffold603-1210181 4 103478895 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804240 Affx-986696740 AX-385290871 4 14931156 TAAACAGCTTCATCTCTTCATGACCCTCCCTGTTA[A/G]CCAGCGTCACCTTCCTCCCATCCTGAAAACATTAC R 2 1 2 1 600010 f 74 goat 4_14931156 4 14931156 Ancestral_priority_1043 ancestry 0.556 neutral IMAGE 10K 10K ancestral 320797039 Affx-122948590 AX-385283980 4 14955328 TTACTACTTGCCATTTATAAGCTAACTATCATTTG[C/T]ACAATAGCACTATGACATGATAAAATTGGTTTTTG Y 2 1 2 1 101000 f 74 goat snp44296-scaffold603-1167630 4 103436922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404271 Affx-122957049 AX-123274623 4 15028401 GGATAGCAGGAATTGTGTTATACTTTTCCATTTCC[G/T]AGAACACTGAGAGCTCTGACTTTATGACACCCAGC K 2 1 2 1 101000 r 74 goat snp44294-scaffold603-1094557 4 103360894 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379186 Affx-122976308 AX-123249545 4 15057396 TCCCAGCAGTGTTTCCCCAATAAAATCCTGGCATG[C/T]AAATCTCAGAATCTGTTCCTGAAAATCTAACCTAT Y 2 1 2 1 201000 r 74 goat snp44293-scaffold603-1065562 4 103331918 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778474 Affx-122955139 AX-385265588 4 15090046 AACACAAGACTCAGGTAAAGTGTGCAAACTCATAA[C/T]CTTTTAAGAAGAAAAGGAGACATTGTTTTGGCAGA Y 2 1 2 1 202000 r 74 goat snp44292-scaffold603-1032912 4 103299289 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775370 Affx-122936200 AX-385262501 4 15120226 TCACATAATACCCAATACTCTTGGTCCTAAAGAAT[C/T]CCGTGCCCATATGCACATTAAGTCACAATAGAAGA Y 2 1 2 1 101000 r 74 goat snp44291-scaffold603-1002732 4 103268626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804243 Affx-986696742 AX-385290874 4 15121246 TAGCCCCCACGGACATGAAGATTAATGTGGTCAAG[A/G]GGCGCTGGCAAGGACTTCCACTCACCCGTCGACTG R 2 1 2 1 600010 f 74 goat 4_15121246 4 15121246 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320804575 Affx-986696744 AX-385291114 4 15121252 CCACGGACATGAAGATTAATGTGGTCAAGAGGCGC[C/T]GGCAAGGACTTCCACTCACCCGTCGACTGAATGTC Y 2 1 2 1 600010 r 74 goat 4_15121252 4 15121252 Ancestral_priority_1043 ancestry 0.502 neutral IMAGE 10K 10K ancestral 38377211 Affx-122978178 AX-123247570 4 15188775 CAAATGTTTGAATTTCTGCAATAGTCTAAAGATTT[A/G]TGAGAATAATGAGGTCTTTTTAGGAATACGAATTA R 2 1 2 1 101000 r 74 goat snp44290-scaffold603-934183 4 103199656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386960 Affx-122969974 AX-123257318 4 15232656 GTCACTCAGTAGGACATTTAAAACACCCTCAGTTC[A/G]TAGCTGCTGCAGTGTCACCATCAACTAGTCAATAA R 2 1 2 1 101000 f 74 goat snp44289-scaffold603-890302 4 103154955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408168 Affx-122954210 AX-123278519 4 15287123 TCAATGTTTCCACTGAAAAAATTTAAGGCAGTGAT[A/G]CTAATTATGGAATAATAATGTTCAACATGTCATAC R 2 1 2 1 201000 r 74 goat snp44288-scaffold603-835835 4 103099867 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390128 Affx-122968001 AX-123260485 4 15327171 ATTAACAGATTTATTCTCTAATTTTATATGATTGG[C/T]ACAATCAAATTAAAAGGTGAAAACAAATGGTGATA Y 2 1 2 1 103000 r 74 goat snp44287-scaffold603-795787 4 103059400 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788458 Affx-122965025 AX-385275475 4 15371792 GTTATGAGGGAATGCAAACAATACAATGACATGTA[C/T]GTTCAGGAAAAATCCACTAATTAGGGAAAAATTTT Y 2 1 2 1 201000 f 74 goat snp44286-scaffold603-751166 4 103013741 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405446 Affx-122956047 AX-123275798 4 15437030 AATCACTCAATTAGATTTTTTAGCTTGCTTATCAA[G/T]AAAATAGAGAATACATCCATGATTGTGAAAGGTTT K 2 1 2 1 101000 f 74 goat snp44285-scaffold603-685928 4 102947467 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792639 Affx-122939703 AX-385279619 4 15466256 AAAATTAACTTAACCCAGGGGTAAGATTATTAGTG[C/T]ATAATGCTGATCTATTGTCTTGGGGATGTAGTCAG Y 2 1 2 1 102000 r 74 goat snp44284-scaffold603-656702 4 102918076 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445061 Affx-122926226 AX-123315398 4 15504497 TAAAGTGTACAAAGGGTTTTGACATTTGCATGTAC[C/T]TGGGCAGTTATGGTAAACATCAAGATAAGAACATG Y 2 1 2 1 101000 r 74 goat snp44283-scaffold603-618461 4 102879937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440723 Affx-122929890 AX-123311060 4 15551691 ACCTTGGCTAAACCAACAGTTTTCCTTCAGTGCCT[A/G]ATTTTGAATGATGCTTACAGTTGGCATTCAATAAA R 2 1 2 1 101000 r 74 goat snp44282-scaffold603-571267 4 102832608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379599 Affx-122976023 AX-123249957 4 15603284 ACTGAACCAGTGAACCAGAGGGCCAGAATGACGGA[C/T]GGAAGAGACAACTTACATTTTAGTTATATCTCATA Y 2 1 2 1 201000 r 74 goat snp44281-scaffold603-519674 4 102783799 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423382 Affx-122943134 AX-123293728 4 15632383 GGCATACAGTCCCAGCTTCTCAGTATAATTTAATA[C/T]TACTGAAAATGGTTTATTCATAAAAAATTACCATT Y 2 1 2 1 201000 r 74 goat snp44280-scaffold603-490575 4 102754551 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375687 Affx-122978658 AX-123246046 4 15666907 CCTGGCTGGTTTGACCCTTGATAGCTACCTTGTTT[A/G]CAGTGCTGCCTCCTGAAGCACACTGGGCTCTAATG R 2 1 2 1 101000 f 74 goat snp44279-scaffold603-456051 4 102719412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273515 Affx-1111833663 AX-519547130 4 15682830 GCAAAGCATTACCATCCTTGCAGATGGGTCTCCTA[A/G]CCCCCAATACATCAGCATACATTTCTGCAGCAGCT R 2 1 2 1 201000 f 74 goat GoatD01.000958 4 15682830 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278063 Affx-1111836232 AX-519551553 4 15708549 GGGGGCTGGGAGTCTCTTTTACTCCCTCTTGCTTC[A/C]CAGGGGCAGCTCCAGAGGCACTGCCGTGGCACATG M 2 1 2 1 102000 f 74 goat Random2.2K-415 4 15708549 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399809 Affx-122960277 AX-123270164 4 15712343 CCAAGGGCCTCTTCAAACAATCAGCCTTTAGCAAT[G/T]CACATCTACTTTACAGAGAAACTTGGTCTGCATGG K 2 1 2 1 101000 f 74 goat snp44278-scaffold603-410615 4 102673403 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423043 Affx-122942968 AX-123293389 4 15766945 CAAGACAATTATGCTTGAAAATCACAAACCTGATC[A/G]TTTTTGTTTTCTCTTAAATCAAGCCTCTTCTCATT R 2 1 2 1 101000 f 74 goat snp44277-scaffold603-356013 4 102620010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781310 Affx-122948865 AX-385268395 4 15798371 ATTTTTTGTATTTAGTTTGAAATCTCACCCTGCAC[C/T]ACTTTTGGAATTTCAAGTCAGTTCCCTTTTCCTGG Y 2 1 2 1 101000 r 74 goat snp44276-scaffold603-324587 4 102588036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791644 Affx-122968186 AX-385278635 4 15856059 GACCCTTCCACATATTAAATACTTGACTGAAGTCC[C/T]CACTTTCTGTAGCTTTGGGAATAGTAATATCTAAG Y 2 1 2 1 101000 f 74 goat snp44275-scaffold603-266899 4 102529834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765905 Affx-122954410 AX-385253337 4 15900923 AAATTTCTTTTATGTTGGCTTCTGCACCCTTTTAG[C/T]ATATCCCCATTTTTTGAATGTCTTTACTATTTTCT Y 2 1 2 1 101000 f 74 goat snp44274-scaffold603-222035 4 102484704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451941 Affx-122920968 AX-123322274 4 15949360 AAGTAAAGGAATTTTCTCCTTTACTCTGTTAAAAA[C/T]ATGAATTATATTATTAAATTTTCTAAGTTTAAATA Y 2 1 2 1 103000 f 74 goat snp44273-scaffold603-173598 4 102435822 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778272 Affx-122953043 AX-385265387 4 15991964 GATATTAAAAGAACAGATTAGGAGAACAACTAAAT[A/G]TATAAATTATTTATATTCTAGGAACTTTGCTGTAC R 2 1 2 1 303000 r 74 goat snp44272-scaffold603-130994 4 102393001 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272255 Affx-1111833415 AX-519545996 4 16021218 TTTATCTCAGTAACACTAGAAGAAAAAATAAAAAA[A/C]CAAAAAATAAAAGCAATTCACAAGACGACTACATG M 2 1 2 1 303000 f 74 goat 4_16021218_AF-PAKI 4 16021218 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771274 Affx-122923424 AX-385258432 4 16035598 TTGCAACTTTAGAAATATTAAGGCCAGATTAATTG[C/T]AATCTATCAAGAAAGCTCTGTTAACATCTTTGGAT Y 2 1 2 1 101000 r 74 goat snp44271-scaffold603-87360 4 102348308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426667 Affx-122939924 AX-123297013 4 16064415 AGTGAATGTGTTCATTCCCACTCAGACTTCTCATA[A/G]GAAACAAGTTGGAACAGATAGGAGACATTTAAAGA R 2 1 2 1 101000 f 74 goat snp44270-scaffold603-58543 4 102319752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391401 Affx-122966778 AX-123261758 4 16102679 CACTCACTTATTCACCTCTTTGAAATTTTGGGTGC[A/G]TTTTGTCTCTTTCATTGGCCTGGCCTTGAATTTTC R 2 1 2 1 201000 f 74 goat snp44269-scaffold603-20279 4 102281199 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403656 Affx-122957519 AX-123274008 4 16182006 TAGTTCATGGAAGCAAGAAGATCTTGCCACATACA[G/T]ACTCCTATACAAAATACTTCCGCCTCAACTGCCAT K 2 1 2 1 101000 r 74 goat snp47971-scaffold676-58949 4 102236845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791226 Affx-122921988 AX-385278220 4 16237885 AAGATGGATAAAATCAAAGCCAGTCATTCATAATG[C/T]ATTTGCAGTTACACTGCAGCTCATTTTTATTGAAT Y 2 1 2 1 201000 f 74 goat snp47972-scaffold676-114828 4 102179755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393133 Affx-122965555 AX-123263490 4 16282467 AACTTTACTCTGGAAGATGATACTCACTGCCAGCA[C/T]AATCCTTTGGGCTTCTTCTTGGCAGATGCAGGGGC Y 2 1 2 1 101000 f 74 goat snp47973-scaffold676-159410 4 102134856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774086 Affx-122975011 AX-385261224 4 16323475 AAGTATAAATGCTGTGCCTGTTTACTGGTAAATGA[A/G]AATTAAGAGTCATTGAACTTGCTAAATAAGATTCT R 2 1 2 1 101000 f 74 goat snp47974-scaffold676-200418 4 102093391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278218 Affx-1111836233 AX-519551706 4 16333343 AAATTCCTTGAGCTTGAAAGTGATGTTCCTCAGGG[A/G]CTATGAGAAGTTAAAGGTGAACATAGCTGCCTCTG R 2 1 2 1 201000 r 74 goat Random2.2K-416 4 16333343 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384940 Affx-122972322 AX-123255298 4 16371546 GTCCCACTTATTTACTGCTTTGTTCCCCATTCCTC[A/G]TGCCTAGAGAAGTACAGTCAGCCCTCCCTACCCAT R 2 1 2 1 202000 r 74 goat snp47975-scaffold676-248489 4 102045063 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424659 Affx-122942155 AX-123295005 4 16401531 CGATGCTGAGGTTTAATTCTCCCTATCCCCTCTAT[A/C]TAGGAGGCATTTCAGAAACAGGGTATGGGGGGAAA M 2 1 2 1 303000 f 74 goat snp47976-scaffold676-278474 4 102014010 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448895 Affx-122923255 AX-123319230 4 16440626 ACATTAGACATTATAAAATTGCTCCCCTAAAAAGA[C/T]AATACTAATTTATCACCTATCACCAGCATTGTATG Y 2 1 2 1 101000 r 74 goat snp47977-scaffold676-317569 4 101974567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378342 Affx-122976838 AX-123248701 4 16481627 GACCAGAAGAGAAGATGTGTTTTTATCTTGGTTTT[A/C]TTTCTTTCTAACTAGTTTACCTTGGGTAGGTCACT M 2 1 2 1 101000 r 74 goat snp47978-scaffold676-358570 4 101934031 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398814 Affx-122961402 AX-123269169 4 16528540 TTTGCATAAAAATCATTCTTCCCTTGGTTCTTCGC[A/G]TGGCTACTTCCATCTCACCCTTCAAGACTCACTTC R 2 1 2 1 101000 f 74 goat snp47979-scaffold676-405483 4 101886905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274931 Affx-1111834499 AX-519548513 4 16552808 AATGGTCAAGCCCTGTTTCCTTCAGTAACAGGGTT[A/G]ATCTGTTTTCTGGGACAGCTTGTATGGAGAAAACT R 2 1 2 1 101000 r 74 goat GoatD01.038482 4 16552808 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434964 Affx-122933845 AX-123305304 4 16572983 CCTCAGTGTCAAGGAATTGGAGGAGGAGTGATGAG[C/T]AAGAGATGTCTCCCCATGCCATTCCCCACTTCAAG Y 2 1 2 1 202000 r 74 goat snp47980-scaffold676-449926 4 101842219 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420415 Affx-122944916 AX-123290762 4 16603759 TGTTATGTTATGACAGGAGATCCTGGTAAGAAACA[C/T]GAAACTAACAAACCATCACCAAGTGGAAGAATTTA Y 2 1 2 1 303000 r 74 goat snp47981-scaffold676-480702 4 101810839 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445821 Affx-122926026 AX-123316158 4 16644306 CCTATTAATTAATCTAACAGCACAGTTAAAAGTTT[A/G]CCTTAATCACTCATTCCACTGATATCTACTGAAGT R 2 1 2 1 101000 r 74 goat snp47982-scaffold676-521249 4 101770307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397278 Affx-122962340 AX-123267633 4 16677274 CCCAGGCCCTCAAAACCCCTACAATGTACAATGTT[C/T]GCTGCTGATCGTGGTATCTCCTGGGTGGAGTCCTT Y 2 1 2 1 202000 r 74 goat snp47983-scaffold676-554217 4 101740644 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416875 Affx-122948084 AX-123287223 4 16711852 TTGAGTTCAGTTCACCCTGGAATCTTTTCTCGACT[A/G]CAGTAGTGTATTACTGATTAAAATCTGTCCTGACC R 2 1 2 1 101000 f 74 goat snp47984-scaffold676-588795 4 101705619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772334 Affx-122939570 AX-385259487 4 16761218 ATTCTACATATGGCAATTATTTCGAATGTGTGAAA[C/T]ACTGTGGTATATGAAGTATTTTTTCCATCCTTGTG Y 2 1 2 1 101000 r 74 goat snp47985-scaffold676-638161 4 101656681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443517 Affx-122927787 AX-123313854 4 16857236 GATCCTTTAAAGTCGCCCTAACTCAAACACAAAGC[A/G]TCAGCAACTACAGAGTTTGAAATGCAAAAGTGAGT R 2 1 2 1 101000 f 74 goat snp47986-scaffold676-734179 4 101559771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772446 Affx-122976144 AX-385259597 4 16890852 TTCCATTTCCACTTCAGTGTCTTTAACAGCAATAA[C/T]TGGATGTAGTTTCTTCAAGACATGTCTCATACCAA Y 2 1 2 1 101000 f 74 goat snp55520-scaffold860-11629 4 101526731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410010 Affx-122953262 AX-123280360 4 16979457 TATGTTTCATTTTGAAATTCCTCTGGAGTTTCTAC[G/T]ACTTGTCTGTAATTCCGACCCCTCGTTATCTTCAT K 2 1 2 1 101000 r 74 goat snp55522-scaffold860-100234 4 101437464 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780890 Affx-122926926 AX-385267977 4 17110413 GCATTTCTTGTAAGTTCATTTCAGTATCTTTATCA[C/T]GGCCCACTAAAGTTGGGATTCAGTTGTAAAATGGT Y 2 1 2 1 201000 f 74 goat snp55526-scaffold860-231190 4 101305967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389525 Affx-122968288 AX-123259883 4 17194402 CCATGAACCTGGGGAAATGGGGATTGTTTCAGGAT[G/T]TTTTCAGTACTTTACATTTATTGTACACTTTATTT K 2 1 2 1 101000 f 74 goat snp55528-scaffold860-315179 4 101222466 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437301 Affx-122931977 AX-123307639 4 17266126 TTCCATTGAGGTCTGCCTGAAGCTTTCATAAGATG[C/T]ATTTGAACTGCTCCCTTTGGAACTGGCTTTTCAAT Y 2 1 2 1 101000 f 74 goat snp55530-scaffold860-386903 4 101152249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431076 Affx-122936629 AX-123301417 4 17296380 CGAAGTTGAACACAGCACCTGCCTGCGAGTGCTGT[G/T]TCCAACTGACCTCTCTTACCTTAACCCCGGCACAT K 2 1 2 1 101000 r 74 goat snp55531-scaffold860-417157 4 101120685 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396675 Affx-122962839 AX-123267030 4 17359559 TTTTCATATGAAAGAAAGCAGCCAAGCTAGATATC[A/G]TTTTACTGTGCCATTCCCAGGGCTACATCTGTGAA R 2 1 2 1 101000 r 74 goat snp55532-scaffold860-480336 4 101056685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426035 Affx-122941115 AX-123296381 4 17408877 TCCATGGGCTAAGACGGTGATGTTTCCTGGTTCCA[C/T]GGGGCGACAGCATGGATGCCCTGTGTTTGGGACCC Y 2 1 2 1 101000 f 74 goat snp55533-scaffold860-529654 4 101007463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770884 Affx-122936797 AX-385258047 4 17453664 CACAAATGATATCCATCAAATTGAAAGTCTTAATT[A/G]TAGGTTTCAAAGTGGTGCTCATTTCAGTGAATTAG R 2 1 2 1 201000 f 74 goat snp55534-scaffold860-574441 4 100962814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780508 Affx-122931866 AX-385267599 4 17575017 ATCAGCAACACTTCCATCAGCTTTCTAGGAATTAT[A/G]CTGATAACCTCCTCATGGGCAAGGCCTCTTCCTGT R 2 1 2 1 101000 r 74 goat snp55536-scaffold860-695794 4 100851080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433998 Affx-122934243 AX-123304339 4 17604118 TAGAGTTGCCGCCATTGGCTTTCTAGTTCTGTTAA[A/G]TGCTGCTATCAGCGTTTCTACTGGGAAGCCCAAAA R 2 1 2 1 201000 f 74 goat snp55537-scaffold860-724895 4 100821533 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409501 Affx-122953638 AX-123279852 4 17643280 TCTCTGCATTGGCCAAATCTTCTCTATCAATTATC[A/G]TTTGGGACTGTGATTATTTCCTATTGTCATAAAAA R 2 1 2 1 101000 f 74 goat snp55538-scaffold860-764057 4 100781800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402308 Affx-122959088 AX-123272661 4 17703890 TCATGGGATAATTAAAGGGAAACTGATTCAATAAC[A/G]TAGTCTCCTTTTCTACAACAGTAGTGCAAAACATA R 2 1 2 1 101000 r 74 goat snp55539-scaffold860-824667 4 100720169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800432 Affx-122937639 AX-385287353 4 17740983 CTCAATATTGCTTTTATTCTTCTGGAACCAAAATC[A/G]TAAAAGAAAGCCATCATTTTTCTTGATACTTACAG R 2 1 2 1 201000 r 74 goat snp55540-scaffold860-861760 4 100681764 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380565 Affx-122975278 AX-123250923 4 17780775 TGGTACTAGCTACACAATAATGTGAACGTACTTAC[G/T]CCACAGAAATGTACACTTAAAAATGGTGAAAATGG K 2 1 2 1 101000 f 74 goat snp55541-scaffold860-901552 4 100641968 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446226 Affx-122925703 AX-123316562 4 17872419 CCAAGTTTGTGTTTCAACAAAGATAACTTCAGAGC[A/G]CCAAGCTATCTTGGCATTTCCAGGATACTGGTTAC R 2 1 2 1 202000 r 74 goat snp55543-scaffold860-993196 4 100550756 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274953 Affx-1111834511 AX-519548535 4 17910852 CAGTTGGCCCCACTGGCTAATCCCTGGGCTGCCAC[A/G]TGTGCAAGGAGAGTGGGCCACTGGGGAACCAGGAA R 2 1 2 1 303000 r 74 goat GoatD01.039036 4 17910852 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320766318 Affx-122925063 AX-385253704 4 17937215 ATTCTCCTTGGTCTGTACCCTCTCAATCAAAATCA[C/T]ATTTCTTAATTCTTTGCTCTTCAACCTCAGTCTTG Y 2 1 2 1 101000 f 74 goat snp24932-scaffold255-963671 4 100489210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408525 Affx-122953700 AX-123278876 4 18011955 GATGATTAACATAACATGACACGACATAAAGAGTA[C/T]GAGTCATTCATTTATATGCTTCTGAAATTCAAAGA Y 2 1 2 1 101000 f 74 goat snp24930-scaffold255-888931 4 100413822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423524 Affx-122942448 AX-123293870 4 18040961 CTTTATCAGTTGATAGAGTAACTGAGCATGGAGCC[C/T]GGATGCATGCTGCCTTTTAATATTGATCTCCTGTT Y 2 1 2 1 101000 f 74 goat snp24929-scaffold255-859925 4 100384330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424053 Affx-122942066 AX-123294399 4 18071161 TTGAACTCCTGCTCCTTTAGAGGGGACTCTGCCCT[C/T]ATACCTCCCTTTTGCTTGTGGGTTGCTACACTGGG Y 2 1 2 1 101000 r 74 goat snp24928-scaffold255-829725 4 100354304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774082 Affx-122937296 AX-385261220 4 18101192 AGAGTTGGATTTGACTGTTTTAAAATTACATGCTC[A/C]TTAACTTGTAATCAGTGCTGTTGGTTTATCACAAA M 2 1 2 1 101000 f 74 goat snp24927-scaffold255-799694 4 100324340 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780557 Affx-122934122 AX-385267648 4 18156621 GCTCATAGTTTACTGTGAAAAGCTAGGTTCTAACG[C/T]ACAACCTCAATTTTGCACATAAGAGCTTCTTGATA Y 2 1 2 1 101000 f 74 goat snp24926-scaffold255-744265 4 100269334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398057 Affx-122961748 AX-123268412 4 18196040 GTAGATAACTGATAAAATTCTCATGAACCATAGAT[A/G]CTGTTTGGTATGTAGAATTGGATGAAATCACTTAA R 2 1 2 1 101000 r 74 goat snp24925-scaffold255-704846 4 100229568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417274 Affx-122947253 AX-123287622 4 18251934 GGGTTCTCTGGCAGTTACTTAACCCTCTGTGAAAA[C/T]AGTCACAAGCGATCTTTATTTCTCTACTACTTTCT Y 2 1 2 1 101000 f 74 goat snp24924-scaffold255-648952 4 100173543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401770 Affx-122959494 AX-123272123 4 18302674 TATCTGACATATCCAGATATAAAGTGTTAATGCAA[A/G]ATTAGGAACTCTCAGGACTGTTGCAAGAGCCTTGG R 2 1 2 1 101000 f 74 goat snp24923-scaffold255-598212 4 100122224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405746 Affx-122956508 AX-123276098 4 18339291 GCTGGAATATTAATGTAGGTTTTTACTTTCATATC[A/G]CAAATACTAATAGAGAAAAGCCTTTCTCAAGTTTA R 2 1 2 1 101000 f 74 goat snp24922-scaffold255-561595 4 100088066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409241 Affx-122953146 AX-123279592 4 18389808 CTTGTGTAGCAATGCCAGGTCTCTCAGCAGGGGGT[A/G]CAGAAGTTACTGGGTCTTCTGAGACCAACAATGAA R 2 1 2 1 201000 r 74 goat snp24921-scaffold255-511078 4 100039076 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449168 Affx-122923538 AX-123319503 4 18420685 CAGGTACCAGCATGTGAACTGATATGAACGTGTCC[C/T]ACTGCTTTCCAGAGTCCAAATCAGATTCCCTTCTA Y 2 1 2 1 101000 f 74 goat snp24920-scaffold255-480201 4 100008197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410672 Affx-122952755 AX-123281022 4 18451665 CATGTTGTTTTCATGTTGGGTGCTTCTGAATCTGG[C/T]TAATGTGACTTCAACACTGACCCACCTACTCACTA Y 2 1 2 1 101000 r 74 goat snp24919-scaffold255-449221 4 99977178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417144 Affx-122947354 AX-123287492 4 18558933 GACTGTTTTTCTATTTTAGGTTCATAGGAGGCCTG[C/T]GACCTGAAAGAAATTATCTCCTTGTGCTGCTTTTG Y 2 1 2 1 201000 f 74 goat snp24917-scaffold255-341953 4 99869914 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401928 Affx-122958817 AX-123272281 4 18596248 CTTTTTTCTCCAACACTTTCTTCTAAGTTTGTGTT[C/T]GTTTTAGTGCTAGACTATGGAATGATTTGCCCCTA Y 2 1 2 1 101000 r 74 goat snp24916-scaffold255-304638 4 99832666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450886 Affx-122922209 AX-123321220 4 18627050 TAGAGCAGTCAGCCCAGAGGTTTTTCGAAAAGTTA[C/T]CAGAATCACTTGGGGAGGTTTGTCAGTCTGCTTAT Y 2 1 2 1 101000 f 74 goat snp24915-scaffold255-273836 4 99801262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388385 Affx-122969307 AX-123258743 4 18691254 TGAAGGCTGTGCCTAGCATGTGGCAATGGTAAGAA[C/T]GGTTGTCGTGTGATGAAAACTCAATATTCACTGGT Y 2 1 2 1 101000 f 74 goat snp24914-scaffold255-209632 4 99736996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797781 Affx-122929481 AX-385284720 4 18773625 TTTTCATCTCTGTAGACCTTTTATCAACACATCCT[A/C]TGTCAAGACTAACTGTCATACCTATAGAGAGAATT M 2 1 2 1 101000 f 74 goat snp24912-scaffold255-127261 4 99654238 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419523 Affx-122945439 AX-123289871 4 18803080 CATTTTGTTTCCTTTGTTTATTTAGGATGGCTCAG[A/G]AGAGGCTGGTGGACACTAATCTGGCCTCCCATCCC R 2 1 2 1 201000 r 74 goat snp24911-scaffold255-97806 4 99624997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800642 Affx-122946642 AX-385287561 4 18862978 GGTTAGGAAAGCAAAGCAAAATACTATGCAAAAAT[A/G]CAGTCATTCTCGGTATATTTTGCTTTCTCCATTAA R 2 1 2 1 101000 f 74 goat snp24910-scaffold255-37908 4 99564736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272093 Affx-1111833416 AX-519545853 4 18867752 GATTCCCAACCAGTCACTCCACAGTGGAGGTGAAC[A/G]AGCTGATGAATCACAAACGTAACCACATGGTGCTT R 2 1 2 1 101000 r 74 goat 4_18867752_AF-PAKI 4 18867752 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444789 Affx-122926345 AX-123315126 4 18924688 GGATTGAGAGAAATTTTATTCCATATACTGTTGCT[G/T]GATATGGCAGTCAACCTCCCTGCCTCCGCATACAG K 2 1 2 1 102000 r 74 goat snp20329-scaffold2013-22977 4 99500206 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405613 Affx-122956607 AX-123275965 4 18965980 TTACAGAAGCTCTATTCCAGGTGCTCTTCCCTGTT[C/T]ACTGCAGTCAGAAGAGATGGGTGCCCTCTTGGCTG Y 2 1 2 1 101000 f 74 goat snp20330-scaffold2013-64269 4 99458739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775287 Affx-122919814 AX-385262418 4 19020368 GGAAACAAAAGAAGAATAACAGGAAAGTCACTAAT[A/G]TTTGCCATCACATGAGTTTTGCAAATGGTTGACTT R 2 1 2 1 101000 r 74 goat snp20331-scaffold2013-118657 4 99403473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426493 Affx-122940222 AX-123296839 4 19051989 AGGACAAAAATTGGCTAGGAAATAAGATAGGGGTC[A/G]TCAGTTAGAAGCTATGTTTAGAATGAATTGTCTAG R 2 1 2 1 101000 f 74 goat snp20332-scaffold2013-150278 4 99372160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450765 Affx-122921841 AX-123321099 4 19100984 AATGCTACTTTATTTTATTTATTTTAGCTAATACT[A/G]TAAAGTACTTATTATAATAGCAAGTTTCGAACAGC R 2 1 2 1 103000 r 74 goat snp20333-scaffold2013-199273 4 99329918 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777550 Affx-122949225 AX-385264669 4 19130087 AGTATGTGCAGCACTACTGTAGAAGTCGGGTGGTT[A/G]TCAGCAGATGCACTCTAAAGGACACAATTCTAAAT R 2 1 2 1 101000 f 74 goat snp20334-scaffold2013-228376 4 99299509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765294 Affx-122942869 AX-385252821 4 19182780 GGGTTGCCATTTAGCTTACTAAATTTATAACTGAC[A/G]TTAAGAAAGGATTTAGTCATGGAAACTACTAATCA R 2 1 2 1 101000 f 74 goat snp20335-scaffold2013-281069 4 99247159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443878 Affx-122927503 AX-123314215 4 19247099 TCCTCGGGTACTGGTCCCACCCAGGTATCCTTAGC[A/G]TGCAGGGAAGTACACAGTGCTCCATCAGTCTGGAA R 2 1 2 1 101000 r 74 goat snp49477-scaffold706-40859 4 99176119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448772 Affx-122923310 AX-123319108 4 19292133 GTGCTGTCAATCCTTTTTCATTTTAACCACTCTGG[C/T]AAATATGTATATCGTATCTCACTGAGGTTTTAATT Y 2 1 2 1 201000 r 74 goat snp49478-scaffold706-85893 4 99129856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781068 Affx-122925684 AX-385268155 4 19320690 AAAAAGTATTTCTTTCATTTGACCTTATATCTCTT[C/T]CCACCTGCATACTTTCAGTTTTCTCCCCATTTTTG Y 2 1 2 1 101000 r 74 goat snp49479-scaffold706-114450 4 99100909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791618 Affx-122979209 AX-385278609 4 19358552 GTAATTGGCATCCTTTTACCAAAAGACATTTAACT[A/G]TTCTTCTACTGCCATTATATAGATCAATGCTTACA R 2 1 2 1 101000 f 74 goat snp49480-scaffold706-152312 4 99063151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792984 Affx-122970682 AX-385279962 4 19434591 TCAGCCATGGAGAAAGCTTTGACTTTATTATTTAC[A/G]TTATGTGTAAATAGAAAACGCTGTGGATTTATTTA R 2 1 2 1 101000 f 74 goat snp49481-scaffold706-228351 4 98988160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780903 Affx-122947417 AX-385267990 4 19496220 GCATAGCAGGAAATGCAGATAATTTAATGTTCCCA[C/T]GGTCAAAATATTACCAGAAAGGGATAGGAAACAGG Y 2 1 2 1 101000 f 74 goat snp49482-scaffold706-289980 4 98925794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433563 Affx-122934979 AX-123303904 4 19551214 CATGTTCCTTGCCATACTTCAGGCCTAGCACAGTC[A/G]GTAAAGTATCTGCCTGCAATGCATGAGATCCAGGT R 2 1 2 1 201000 f 74 goat snp49483-scaffold706-344974 4 98870393 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785793 Affx-122929335 AX-385272833 4 19598220 TCATTTCTATAACACATGTTTGAAGACATATTTTT[A/C]TTTTCCTCAATTTCCATAATAGTTTGTTGCTTTTT M 2 1 2 1 202000 f 74 goat snp49484-scaffold706-391980 4 98823422 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778764 Affx-122927887 AX-385265874 4 19630123 GACATTAAACCCATCAACCCTCCATTAGGTATATG[C/T]GGGTTTTCTTGTTTGTTGGACTTGTATATCAAACT Y 2 1 2 1 201000 r 74 goat snp49485-scaffold706-423883 4 98790604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431394 Affx-122936546 AX-123301735 4 19809518 CCCAATTTAAAAAAAAAAAATCACAGTATGTCTTA[C/T]ACTGCTGTGGATTAGTTCATTTCCAAAAGATATGC Y 2 1 2 1 101000 r 74 goat snp49487-scaffold706-603278 4 98609124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791441 Affx-122942943 AX-385278432 4 19852393 ACCTTATTCTTGCATAAGGATACTTTAGTCTTATC[A/G]TAAATCCCACATCTGGTTTACCCCGGGTACATCTT R 2 1 2 1 101000 r 74 goat snp49488-scaffold706-646153 4 98566016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453036 Affx-122920084 AX-123323369 4 19890084 TTAAACACTTGTTTTCGTGGCTCCCTTTCCACAAA[A/G]CTCTGAACTCCCTCTGCTTCTTGAAGACCAGATGC R 2 1 2 1 101000 r 74 goat snp49489-scaffold706-683844 4 98528350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375460 Affx-122979161 AX-123245819 4 19918794 TTTGGTCTAAGCAATTCAGAATACAACTTTATTTC[A/G]CTTATAATTCCAGCTTGAATCAAAGCATCTTCTAC R 2 1 2 1 101000 r 74 goat snp49490-scaffold706-712554 4 98498900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767213 Affx-122965363 AX-385254494 4 19951660 CTATTTCACCTCTGATCAGACACTGTCATTATCCA[C/T]AGGTTTTGCTCAATAAATTCTAAAGGGAGATTTTC Y 2 1 2 1 101000 f 74 goat snp49491-scaffold706-745420 4 98465997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404571 Affx-122957370 AX-123274923 4 19997123 TTCAAACAGATGAGAATTACTGACATTTATATTGC[A/G]TTATGATCCTGATGAACTGAAACAAATACAGTTTA R 2 1 2 1 101000 r 74 goat snp49492-scaffold706-790883 4 98420571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776269 Affx-122938093 AX-385263397 4 20030046 CCTCAACCACATTTCCATGCAAACTTTTATGACCT[A/G]CAACTCCTCCGGACAATCAGATTTTTAGGAGGAGA R 2 1 2 1 101000 f 74 goat snp49493-scaffold706-823806 4 98387749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420657 Affx-122944823 AX-123291004 4 20076216 GGGACACCGAAGCCATGTGTATCGAGTCACCAGTT[A/G]TCCTAACTGGTGTGTTTGGTCCACTATCCGGCTGA R 2 1 2 1 101000 r 74 goat snp49494-scaffold706-869976 4 98341650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411789 Affx-122951474 AX-123282139 4 20107026 GAATAGAAAGAGAAGACGGTGTGTTATTTTTGTCT[A/G]TAAGAAATGAAAAATCTAATAGGGGGACATAATAG R 2 1 2 1 101000 f 74 goat snp49495-scaffold706-900786 4 98313318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391282 Affx-122967351 AX-123261639 4 20171345 AACTGGGTTATCACAAAAACTATTTCTCCTAAATT[A/G]AGCACATTTGTGTGTGAGTGTGTGTTAGTTGCTCA R 2 1 2 1 201000 f 74 goat snp49496-scaffold706-965105 4 98247331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790130 Affx-122935777 AX-385277136 4 20206066 AAAATTTGGGACTACTGCAGAAGTAGGAACTATAT[G/T]TGTCCCATGTCATACAAATCAACAGATACTTTTGA K 2 1 2 1 101000 f 74 goat snp49497-scaffold706-999826 4 98211672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399841 Affx-122960252 AX-123270196 4 20245413 GTGACTTCATCATGACTGATTTCCTGAGGTTCCTC[A/G]CTGGTGATGGGGAAAAAGCAAGCAGCAGGCATACG R 2 1 2 1 101000 f 74 goat snp49498-scaffold706-1039173 4 98172374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784016 Affx-122921516 AX-385271070 4 20281396 TGAAAATAGAACAATATCTCGCTAAGTGCTCTTGA[C/T]ACAGTAGGACCCTTAATCCATGCTACTGACTACTT Y 2 1 2 1 101000 r 74 goat snp49499-scaffold706-1075156 4 98136101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421075 Affx-122944238 AX-123291422 4 20350156 TGGGAGACAATGAAAGTTTTAAGACAAATTTTTTG[C/T]AAGAGTAAAATATGGATAATATAGTAAAAGCACTT Y 2 1 2 1 101000 f 74 goat snp49500-scaffold706-1143916 4 98067654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427077 Affx-122939798 AX-123297420 4 20389131 ATATTGTAATTCTGATGAAAGAAAATCATGGTTAC[C/T]GAGTTTCCAAAGGGGAAAAAAATTTAGTTGATATG Y 2 1 2 1 101000 f 74 goat snp49501-scaffold706-1182891 4 98027566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416734 Affx-122947541 AX-123287082 4 20425882 TCACTCCTTTAATGTTTAAACATCCACAACTGAAA[A/G]CACTTTTTTCTCTGACCCGTTACTGTCTCTATATA R 2 1 2 1 101000 r 74 goat snp49502-scaffold706-1219642 4 97991067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799848 Affx-122946472 AX-385286774 4 20477723 ATGATATTGGGACTATCCTGATCAAGACAGATATG[C/T]AATTGTAAATGACATGAACTTTGTACCTCTCACTT Y 2 1 2 1 101000 r 74 goat snp49503-scaffold706-1271483 4 97939188 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394121 Affx-122965337 AX-123264476 4 20518887 ACTATCTATATTCTCTGGCCCTTTTGATTTACAGC[A/G]CGGAGCAGAAGAGGCAAGGAGAGCAAGATAGTTCT R 2 1 2 1 101000 f 74 goat snp49504-scaffold706-1312647 4 97897298 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409175 Affx-122953194 AX-123279526 4 20570314 AGGTCAACAGAACTACCAATAAGGACAGATAGAAT[A/G]AACAGAATTAGGAATTAAATTTCAAAGATTAAACC R 2 1 2 1 101000 f 74 goat snp49505-scaffold706-1364074 4 97845632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409403 Affx-122954137 AX-123279754 4 20621111 TATACTGTTCTTCAAAGTGTTTCTATCAACATAAA[C/T]ATGATAGGCAGTGTTTAAGATCTGCCTTTGCTTCT Y 2 1 2 1 201000 f 74 goat snp49506-scaffold706-1414871 4 97794389 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780753 Affx-122954561 AX-385267843 4 20658229 GAAAGATTCCATGTACACATAGAATCTATAATAAT[A/G]AGCAGAAATTCTTTTTAAGTTGCCTTCTGTTTAAA R 2 1 2 1 101000 r 74 goat snp49507-scaffold706-1451989 4 97757468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380789 Affx-122975099 AX-123251147 4 20706677 TTGCAGTGTGTTGGACCGTTCGTTAGTTGCAGCAT[A/G]TGAATTCTTAGTTGCAGCATGTGGGATATAGATCC R 2 1 2 1 103000 f 74 goat snp49508-scaffold706-1500437 4 97709367 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387158 Affx-122970634 AX-123257516 4 20775814 TTCACCAAAGCCCCCACCCAATCCACGGGCAAGCT[A/G]TATCAGCCTATCCCTGAAAATGGCAGTGTGTCCAC R 2 1 2 1 101000 r 74 goat snp49510-scaffold706-1569574 4 97639751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448541 Affx-122923434 AX-123318877 4 20806121 AGGATAAAATAAGAGGCACTCATTCTCCAGTGCCT[A/C]TCCATGATATATGAGAAGTAGCTGGCAGTAGGCTA M 2 1 2 1 101000 r 74 goat snp49511-scaffold706-1599881 4 97609391 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383609 Affx-122972558 AX-123253967 4 20849470 TTGCACATGAGAAAAAACAGCCCCTTCATCTGGTA[C/T]GGGCTCTTTGACAAATAAACAACTAAGTGTATAAA Y 2 1 2 1 201000 r 74 goat snp49512-scaffold706-1643230 4 97565862 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406827 Affx-122955678 AX-123277178 4 20881677 ATATTAATAATAATGCTTCCTAACCACTTTTTCCT[A/G]TTCCTAGTCAAGACATAAACCACCAGATTTGAAGC R 2 1 2 1 101000 r 74 goat snp49513-scaffold706-1675437 4 97533685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427560 Affx-122939487 AX-123297903 4 20939726 TGGGGGAGGCATTTGCTTCCTGTGGTTGTACCTCC[A/G]CATGCCTCAGTGTTCATCTTTGCATTTCAAACTCT R 2 1 2 1 201000 f 74 goat snp49514-scaffold706-1733486 4 97474219 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407020 Affx-122955017 AX-123277371 4 20972432 GATAATAACACTGGACTCATATGGACAGTATTCAA[C/T]GAACTAATAAACACAAAATGTTTATATAAAATATA Y 2 1 2 1 101000 f 74 goat snp49515-scaffold706-1766192 4 97441582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801468 Affx-122967521 AX-385288377 4 21010865 GTACTGTATTTATTGATGATATGGCTATAGGTCTT[A/C]TAGGTCTTCTATAAAGTTCCTAATGAGTCTCTGGA M 2 1 2 1 101000 f 74 goat snp49516-scaffold706-1804625 4 97403556 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452924 Affx-122920193 AX-123323257 4 21079806 CAGAAGGAGGTGGAAATGATGGCAACATTTCCTTA[C/T]AGTCTCTGCCTCTGTATAAATGTATACAAAGAAAA Y 2 1 2 1 103000 f 74 goat snp49517-scaffold706-1873566 4 97333214 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407055 Affx-122954926 AX-123277406 4 21111874 TCACCTGCATTTCTGAATTTCCTGTACAGCTGGTG[C/T]GCAAGATGAACTGCAGGATGCTGTACAGTGTCATT Y 2 1 2 1 101000 f 74 goat snp49518-scaffold706-1905634 4 97300876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409153 Affx-122953212 AX-123279504 4 21143037 GAGAAAGACCAATCTTAAAATATTGTTTGGCGTTA[C/T]GCCCATAACATTTTCATTTTATTCCTTGTTAGTAT Y 2 1 2 1 101000 r 74 goat snp49519-scaffold706-1936797 4 97269729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448012 Affx-122923728 AX-123318348 4 21201441 AATGCCTTTGAGCCATCTGTAGTGGAGGCCAGTCC[G/T]CTGATGCCACAAACCCTCTATTTGGCAAAATTTAA K 2 1 2 1 201000 r 74 goat snp49520-scaffold706-1995201 4 97211189 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765497 Affx-122960399 AX-385252983 4 21248642 CAAATAAGAGCACCCTAAAAGTGCTTACAAGCTAC[A/G]TTTCTTGATAAACTCAAACAACATATTTTCAGCAA R 2 1 2 1 101000 f 74 goat snp49521-scaffold706-2042402 4 97163384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396106 Affx-122963418 AX-123266461 4 21296683 TCAGGTTTTTTTCTATTCCTTTTGGAAAACATATT[G/T]AAATGCCAAAAATAAATACTAATAAAATAATACCT K 2 1 2 1 101000 f 74 goat snp49522-scaffold706-2090443 4 97114891 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769166 Affx-122932631 AX-385256341 4 21359607 AGGTGTAATGTAACATTATCTTACCTAAAACCAAA[C/T]AGTCTCCTTAAAACTGCATTTTATCATTTCCCTCA Y 2 1 2 1 101000 r 74 goat snp49523-scaffold706-2153367 4 97050876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796728 Affx-122971755 AX-385283673 4 21410352 AGCATTCTAATCTTCTCTCTTCTTGGTGGCGTGTG[C/T]GTGTATGTGTTCAGCCATGACCAACCCTTGGTGAC Y 2 1 2 1 102000 f 74 goat snp49524-scaffold706-2204112 4 96999642 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272095 Affx-1111833417 AX-519545854 4 21421330 AAAGGCCTCCTAACAATTCACTTTTTAAAACATTA[A/G]GCATCTACCAGTCACACATGATTCCTATCTCAGGA R 2 1 2 1 101000 r 74 goat 4_21421330_AF-PAKI 4 21421330 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407349 Affx-122955283 AX-123277700 4 21445118 AGCAAAAATTCAGGGTAAAATTTATTTTATTTTTA[C/T]ATCCCAAGAAATCCCAATTATGCCCAAGATCATAT Y 2 1 2 1 101000 r 74 goat snp49525-scaffold706-2238878 4 96964924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445721 Affx-122926103 AX-123316058 4 21473938 TAATTCAACTGAACTCCAAAACCAGAAAAATTAGG[C/T]ATTTTATTATTTTTCTCTTCAGTGGGGGGGCAAAG Y 2 1 2 1 303000 f 74 goat snp49526-scaffold706-2267698 4 96936265 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786267 Affx-122968782 AX-385273302 4 21504644 ATTTACCAAATAGATTATAATGTGACTCTTCCAAC[A/G]TGAGGCTCATAATTTCCTATCTCAAAGGAGACTTA R 2 1 2 1 101000 r 74 goat snp49527-scaffold706-2298404 4 96905039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443971 Affx-122926999 AX-123314308 4 21558580 TGTTAGAGGGGAGGAGAGGGGGGAAACACGAAAAA[C/T]AGGCGAAGAAGATTAAGAAGTACAAACTTCCAAGT Y 2 1 2 1 103000 f 74 goat snp49528-scaffold706-2352340 4 96850105 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406625 Affx-122955829 AX-123276977 4 21589563 ATTATTCAATGGATAGTACCATTTAATAATTTCCA[C/T]GGGAAGGGATTCAGCAAGGTTTCCCTTTTTGTTAT Y 2 1 2 1 201000 f 74 goat snp49529-scaffold706-2383323 4 96818744 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433800 Affx-122934463 AX-123304141 4 21619251 CTTTGAAAAGTTCCCTTCCACATCTGTTCTTTTGC[A/G]ATGCAATTCCTCTCCCCAAAGCATTCTAATGTTGG R 2 1 2 1 101000 r 74 goat snp49530-scaffold706-2413011 4 96788691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789468 Affx-122971987 AX-385276478 4 21648311 TAATACAGAATTCTTGAAACTCAAATTATGACATG[C/T]ATAAAATAGGTATGTGTATTTAAAATAAAGTTGAG Y 2 1 2 1 101000 r 74 goat snp49531-scaffold706-2442071 4 96759522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402425 Affx-122958633 AX-123272778 4 21707545 CTACCATGAAGACTTCTACCAGTCAAAAGTGTATA[C/T]GCAAAAAAACCCACGAGTGGATGCACTTCTCAAAA Y 2 1 2 1 101000 f 74 goat snp49532-scaffold706-2501305 4 96700230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414931 Affx-122949098 AX-123285280 4 21743094 CCCTAGCTTCAGTCATATCTAAACATTCCACTTTG[C/T]AAAATATGAACCATTAACCTTGCTTTCCTTAATTT Y 2 1 2 1 101000 f 74 goat snp49533-scaffold706-2536854 4 96664971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797905 Affx-122953401 AX-385284843 4 21842146 ACAACCACTTAGCAATAATGTAGGTTATTAAAGAA[A/G]TGACTTAAATGCATGCAAAAAGAAAATTTTAAATA R 2 1 2 1 201000 r 74 goat snp49535-scaffold706-2635906 4 96565193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438804 Affx-122930799 AX-123309141 4 22020690 TGTGGCACATTTTAGTTTTACTTCTAAAAGTTTCT[A/G]TTTCCATATTTACTTTTCCACACTTGCAACCCTAG R 2 1 2 1 101000 r 74 goat snp55987-scaffold87-2297972 4 96385701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452034 Affx-122920898 AX-123322367 4 22078034 TATTCATCAAGTTCAGAAAATACAACTATGAATTC[A/G]TGAATTTAAGTCTTAATCTTATATCCACCCAAACC R 2 1 2 1 101000 r 74 goat snp55986-scaffold87-2240628 4 96327571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405853 Affx-122955860 AX-123276205 4 22115162 TAAGAACTTGAGAATCTATTTGATACAGTCTTCTA[C/T]AATTGGTACATGCTTTACATCACTTAATGATATTT Y 2 1 2 1 101000 f 74 goat snp55985-scaffold87-2203500 4 96290247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785127 Affx-122924575 AX-385272173 4 22213996 ATATATATGTAGAGCCAGCATATGTGTGTATGCAC[A/G]TAAATACGCTGGCTCTCATGTAGCTAACTCTCCAT R 2 1 2 1 202000 f 74 goat snp55983-scaffold87-2104666 4 96192027 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442345 Affx-122928038 AX-123312682 4 22314248 GGCAAGGAATTTGAGGGTGGTATTAGGACAAACCA[C/T]GGATCCTACTTTTGGAGGGAAGAATATAAGCATAG Y 2 1 2 1 101000 f 74 goat snp55981-scaffold87-2004414 4 96091931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765880 Affx-122962909 AX-385253318 4 22514508 GATTAAGTAGAGCTATTGTAACTCATGGATTCTCT[A/G]TTACAGAGATATTTCGATGCACATATGCCCATTTT R 2 1 2 1 101000 f 74 goat snp55976-scaffold87-1804154 4 95890757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429173 Affx-122937968 AX-123299515 4 22584481 GATGCATCCTATTTCTTCATGCTCAAATTTTGTCA[A/G]CCTGAAAATCACTGCTGATGGTGACTGCAGCCATG R 2 1 2 1 201000 f 74 goat snp55974-scaffold87-1734181 4 95819430 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796493 Affx-122958943 AX-385283443 4 22663017 TCTTATACAGTTGCAGTTCTGCTAGTGACTGTTTT[A/C]CACTGTTCATCAATAATTTTGTTCATGTCTCTCTA M 2 1 2 1 101000 f 74 goat snp55972-scaffold87-1655645 4 95740576 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797235 Affx-122936711 AX-385284174 4 22770741 GAATAAAGACAACTCAGCTAACTGAAATGGTAATT[A/G]CCTAGTCAGGGTTTCTGTTGTAGAGTGTCATAATT R 2 1 2 1 101000 r 74 goat snp55970-scaffold87-1547921 4 95630908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441043 Affx-122928932 AX-123311380 4 22807495 GCAGGAGTCAATCATAAGCCCTGGGTCAAGTGGAG[C/T]AGAGGTCAGGAGGAAGATTTCCAGGAGGTGGGTGT Y 2 1 2 1 101000 f 74 goat snp55969-scaffold87-1511167 4 95593474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775551 Affx-122977204 AX-385262682 4 22854689 ACTTTAAATATACCAAGATAAACTGTTTATGAAGA[C/T]GGTATGAATTCTCACCTAGAAGCTCATATGTGTAA Y 2 1 2 1 101000 r 74 goat snp55968-scaffold87-1463973 4 95545781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379705 Affx-122975897 AX-123250063 4 22954261 TAGAATTTCTGTCAAAAATGGATTTGTCCTAACTA[C/T]GTTATATGTGAACATCCTGTCATAATCAATTTGTA Y 2 1 2 1 101000 f 74 goat snp55966-scaffold87-1364401 4 95448750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779259 Affx-122936438 AX-385266363 4 22987971 TTACATGTTGCCTGCAATATATTTGCTTGATTGTC[A/G]TTTTCCTCCCTTCTTGAAAAGTATGTAGGTAGAAA R 2 1 2 1 102000 f 74 goat snp55965-scaffold87-1330691 4 95414563 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438799 Affx-122930803 AX-123309136 4 23018211 TGCCCAACAGTAATGTCAGTTTTAGACAAAACAAA[C/T]GTATCACTGAGTAGCTCTGGTGAGGAGTGATGATA Y 2 1 2 1 101000 r 74 goat snp55964-scaffold87-1300451 4 95382322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393479 Affx-122965831 AX-123263835 4 23047211 ACTAAAGTAGGAAAATAATAAACGACGCACATGCA[C/T]GGCTAGATGGCTCACAACTGATGGCTCACGGGGGG Y 2 1 2 1 101000 f 74 goat snp55963-scaffold87-1271451 4 95353271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430386 Affx-122937771 AX-123300727 4 23096542 TCTTCACCAGTAAGCAGGCTTTGCTGCACAGAGGG[C/T]AAGTGGACCCAAGTTTGGTTCAGTAGCAATGTCAG Y 2 1 2 1 101000 f 74 goat snp55962-scaffold87-1222120 4 95304711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780680 Affx-122939177 AX-385267770 4 23129459 CTTCTTTGCTTATTACCTATCCTCCCCTTCAAATG[C/T]AAGATCCATGAAGGTAGGACATTTTGGTTTGTTTT Y 2 1 2 1 202000 f 74 goat snp55961-scaffold87-1189203 4 95271808 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429384 Affx-122938545 AX-123299726 4 23173385 TCTAGACTTGACTCTCTGGCAGTCATGAAGGCCTG[C/T]GGTTCTGACTTGGAAACAGTCTTACTATTGGTCAC Y 2 1 2 1 101000 f 74 goat snp55960-scaffold87-1145277 4 95227994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396283 Affx-122963301 AX-123266638 4 23260010 CAATGACTGACTCAAAAGATAGAAAACCTGAAAAA[C/T]ATTACACCAATTAAACAAAACTGATTTTGTAATTA Y 2 1 2 1 101000 f 74 goat snp55958-scaffold87-1058652 4 95140568 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396284 Affx-122963301 AX-123266639 4 23260010 CAATGACTGACTCAAAAGATAGAAAACCTGAAAAA[C/T]ATTACACCAATTAAACAAAACTGATTTTGTAATTA Y 2 1 2 1 600000 r 74 goat snp55958-scaffold87-1058652 4 23260010 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381683 Affx-122974728 AX-123252041 4 23292639 AAAAAGAAAACATTACTATAACTATAAAATTAAAA[C/T]GTCTGGTCATCAGACTCCAACTCACTATGTTTATG Y 2 1 2 1 102000 r 74 goat snp55957-scaffold87-1026023 4 95108186 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789550 Affx-122942553 AX-385276559 4 23332258 AAAATTAGTAATACTACTATTGGAATTGTCAGTCC[A/G]TCTTCCCAGGTTGGTCTCAGAAGCATTTTGCTAAA R 2 1 2 1 101000 r 74 goat snp55956-scaffold87-986404 4 95069962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436367 Affx-122933057 AX-123306706 4 23365053 ATTACATTAGCCTCTCAGGCCTCAGAATTGATTCC[A/G]CTCCTTCATGATTTTTCAGCCCAAGGGTCCTGCAC R 2 1 2 1 101000 f 74 goat snp55955-scaffold87-953609 4 95038785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790209 Affx-122931191 AX-385277213 4 23454536 CAGTTTTTTCTATTTGGTAACGAAAAAGCAGAAGA[C/T]AGATACTTTGTTTTTGTAGACCACAGAAAACTACT Y 2 1 2 1 101000 r 74 goat snp55953-scaffold87-864126 4 94948823 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780346 Affx-122967669 AX-385267441 4 23497673 TTTTAAATATGATTGTGCTGAGCCCATAATCTGAT[A/G]TTTTATTACATAAAGATTCCACTGAGAGACATAAA R 2 1 2 1 201000 r 74 goat snp55952-scaffold87-820989 4 94905212 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791698 Affx-122922043 AX-385278689 4 23553756 AAGAACACATAGATCCCATTTTTTCTGAGTTTCAC[A/G]TGTATATATCCATGCCATTCTGATCTGCTTGTTTG R 2 1 2 1 201000 f 74 goat snp55951-scaffold87-764906 4 94849293 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383825 Affx-122973170 AX-123254183 4 23600891 CATCTTCTCTATTTCTCAGTATAATCACTTTACAC[A/G]TTTTCTGTATTACCCATTCACACATGAGTTCAGCC R 2 1 2 1 101000 r 74 goat snp55950-scaffold87-717771 4 94801564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379204 Affx-122976294 AX-123249563 4 23680822 ACCTTAGGTTCCTATAGAGGAAACTGAAATAATAA[C/T]AAAACCTTTTCATAGTACTACTATAAAAATGAAAT Y 2 1 2 1 202000 r 74 goat snp55948-scaffold87-637840 4 94721323 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798102 Affx-122961905 AX-385285037 4 23836709 GAAAGGTAGGATGAAGCTGTAGGTTTATTAGTATC[A/G]CTTCTGCTCCATTGCTCTTACCCTCATCATAGGTA R 2 1 2 1 201000 f 74 goat snp55944-scaffold87-481953 4 94565266 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418007 Affx-122946660 AX-123288355 4 23911510 GAATAGAAAAAGCTTTTTGGAGGTACAGTTCTGGT[A/G]CTCTTGTCTATAAGAGACTGGAATGTTTATGGGAG R 2 1 2 1 101000 r 74 goat snp55942-scaffold87-407152 4 94490451 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427991 Affx-122939173 AX-123298334 4 23948928 CTCTCTATAAATTTGGTTTTGGACATTTCATAAAT[C/T]CAGTTGTCTGCTGTGCAGTCTTTTGTATCTGGCTT Y 2 1 2 1 101000 r 74 goat snp55941-scaffold87-369734 4 94452603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272262 Affx-1111833418 AX-519546001 4 23952911 ATGACAACAACAGGCTGCAAGATGGGGATTATAAC[A/G]CCGAAGCAAGTGAGAAACAGGAGGTGGTGGTGAGA R 2 1 2 1 101000 f 74 goat 4_23952911_AF-PAKI 4 23952911 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387171 Affx-122970625 AX-123257529 4 23994900 CATTATTGAGCAAATCTTATTTTTGAAAAGGTTCA[A/G]GATGCATTTAGATTACTCAACTTAAATTAATAGAG R 2 1 2 1 101000 r 74 goat snp55940-scaffold87-323762 4 94405984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764557 Affx-122920464 AX-385252212 4 24033953 ATCATGTCTCCAAGGGGTGCCTATAGTCTGCTTTT[A/C]AATTCTTTCTCCATTTTGCTAAGATTTGATCTAAA M 2 1 2 1 101000 f 74 goat snp55939-scaffold87-284709 4 94366434 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418370 Affx-122946574 AX-123288718 4 24108960 AACAACACAAGAAATCACACAGTGAAAGATGACTT[A/G]CAACTTCATAAAAACATGACATTTTAACATTCCCA R 2 1 2 1 201000 r 74 goat snp55937-scaffold87-209702 4 94291163 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799429 Affx-122932375 AX-385286359 4 24141130 TATGGTTGACAAAAATTTTGAGTGCTTTCTAGATG[C/T]GTGAATGTGTGAAAGCTCTTAAACATAAGTATCAT Y 2 1 2 1 201000 r 74 goat snp55936-scaffold87-177532 4 94259033 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777472 Affx-122963694 AX-385264592 4 24173147 ATTCATGTAAGAGTCTACTGTGTACATGTGAAAAT[A/G]CATTTCTAGATAATGTGAGGAACGCTGGCCATCAA R 2 1 2 1 101000 r 74 goat snp55935-scaffold87-145515 4 94227172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430165 Affx-122937371 AX-123300506 4 24201960 TAAGAGGACTCACAGACCCCAGCATAGCTATACTC[A/G]CAGCTAAAACTTATTATAGTAGAAGGATATAAAGC R 2 1 2 1 201000 r 74 goat snp55934-scaffold87-116702 4 94198220 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278220 Affx-1111836234 AX-519551708 4 24226142 CATTGCCATGGCTGAGCGGTGAAAGGTGAGGGGGA[A/C]GGTTCTTGCATCAGAATGATCAGAATGACCGTGGG M 2 1 2 1 102000 r 74 goat Random2.2K-425 4 24226142 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408236 Affx-122953830 AX-123278587 4 24279418 GTGACCCAGGTTGGCACTGAAGTAACATCAGCTTT[A/G]TGAGTCTCAGCCCTGTCTGGCTGGCTGCCCTATGC R 2 1 2 1 101000 f 74 goat snp55932-scaffold87-39244 4 94119902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379743 Affx-122975868 AX-123250101 4 24317444 GGAAGAAATTTTAATGGGCAGTGGGAAGTATTCCT[A/G]CTTGGACTGATAGAGAGAAATGTGTGTAGATGAGT R 2 1 2 1 201000 f 74 goat snp55931-scaffold87-1218 4 94081893 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382326 Affx-122973896 AX-123252684 4 24319537 TTTTCCGAAATGCCTTCGTATCCCCTTAAAAGAGA[C/T]GGAAGGATTCTGCATGTCAAATTTGAAAACTTGTC Y 2 1 2 1 201000 r 74 goat snp59163-scaffold970-900354 4 94079574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386043 Affx-122971477 AX-123256401 4 24353668 GGGAGGGAGATAGTCAGGGAGTTAGGGGTTGACCT[A/G]TACACACTGCTAAATTTAAAATAAAAAACCAACCA R 2 1 2 1 201000 f 74 goat snp59162-scaffold970-866223 4 94044962 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790543 Affx-122954888 AX-385277546 4 24395421 TAAAGGAAGCTATCACATGCTCTGAATTTCTCTAA[C/T]CACTAGTCACCATCAAATTGATTTATGGTTTGCCC Y 2 1 2 1 101000 r 74 goat snp59161-scaffold970-824470 4 94003030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386310 Affx-122970895 AX-123256668 4 24432352 GCTCTGAAAAATCTTTGTATTCCCTCTCAGTGGTT[A/G]TGATCCTTTTCTCTGCCAGATGAGTAAGGTTTTGA R 2 1 2 1 201000 r 74 goat snp59160-scaffold970-787539 4 93962664 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434435 Affx-122934661 AX-123304776 4 24485240 CTCCTATATGGCCTGTTCTCCACTCCTGCAGTCTT[C/T]GGGTACAGCTTACACATTTGATTTAGAATTCAGGA Y 2 1 2 1 101000 r 74 goat snp59159-scaffold970-734651 4 93908494 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786581 Affx-122923135 AX-385273613 4 24613072 CCAAGATGAATGACACATTTCTCCTCAAGGAACAA[A/G]AAGTGTTTCAGAAATTGTCTAAATATGTATATATA R 2 1 2 1 101000 f 74 goat snp59157-scaffold970-606819 4 93779941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786294 Affx-122946595 AX-385273329 4 24678502 ATCTCAATTGACATAGCTTTAAGTTCACTATTTTT[C/T]CCTTCTGCCAGCTCAATCTGATGTTAACCTCCTCT Y 2 1 2 1 101000 r 74 goat snp59156-scaffold970-541389 4 93713834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433876 Affx-122934419 AX-123304217 4 24749655 ACAGGTGAACAGTGATTAAAGCTGCTAAATCTACA[G/T]AAAGGCTGAGATGATTTTATGTTACAGATGATTTA K 2 1 2 1 101000 f 74 goat snp59155-scaffold970-470236 4 93641786 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401763 Affx-122959499 AX-123272116 4 24829633 TTTTGGATTACTTTCATCTATCCATCCTTTATTTT[A/C]TTGATTTCTTCCCTTTCATGCTAAGAAGATCTACA M 2 1 2 1 202000 f 74 goat snp59153-scaffold970-390258 4 93560613 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416336 Affx-122947900 AX-123286685 4 24868014 TATAAGTACTGAGGTAAAAATTGAGTTGCATAGTC[A/G]TTATGGAATAAAGAATAAAAAGGAACTACAAAGAT R 2 1 2 1 101000 f 74 goat snp59152-scaffold970-351877 4 93521730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441529 Affx-122928711 AX-123311866 4 24897176 TCAAGTCTGCTGTTTGCTACAGCAGATGATGCCTC[C/T]GTACTGCAGGTGGATTCCACAGCCAAATTGCCTGA Y 2 1 2 1 101000 f 74 goat snp59151-scaffold970-322715 4 93492517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436082 Affx-122932689 AX-123306421 4 24943529 CCTGGGAGCTGACTCATAGTGTTCTCCAGAAGAGG[G/T]TCTTCCCTGAACCAGAGCAGCCTAATTTTCATCTG K 2 1 2 1 101000 r 74 goat snp59150-scaffold970-276362 4 93446261 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772046 Affx-122940939 AX-385259201 4 24981573 ACACTATGTGAATCAAAAGTACCCTGAGAAAGCAA[C/T]AGCATACAAATATACATGGTGAGGCAGTGTGGTGA Y 2 1 2 1 101000 r 74 goat snp59149-scaffold970-238318 4 93408298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387347 Affx-122970486 AX-123257705 4 25027177 AAATAAGGGAACCTAATTAAAGAGCTAGGAGAACA[C/T]CTGGAAATTCAGTAAATATTACTTAAGATAATAAT Y 2 1 2 1 101000 f 74 goat snp59148-scaffold970-192714 4 93361008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800517 Affx-122932816 AX-385287437 4 25057624 GGAGTTGCAGAGGTTCCTCTTCAAGAAGCAAAGCA[G/T]GATTTTTGCCAGGATTCTTTTTACTTACTCTAGGT K 2 1 2 1 101000 f 74 goat snp59147-scaffold970-162267 4 93330492 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392198 Affx-122966286 AX-123262555 4 25133579 AGCACATGATAAAGATCCCCTTTTTCTTACTATCA[G/T]AAAGATGATTAGACTTTTGCCCATGAGGTTTTGTT K 2 1 2 1 101000 r 74 goat snp59146-scaffold970-86312 4 93253652 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777356 Affx-122936465 AX-385264478 4 25175768 ATTAAATGATATATGTAAATTGCTAGGCCAGGTGA[C/T]AGGCATTTAATTAATTCTCAAACATACTACCTTTC Y 2 1 2 1 101000 f 74 goat snp59145-scaffold970-44123 4 93211468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774770 Affx-122927538 AX-385261904 4 25208004 AAATCTTAAGGAGAGCTGACAAGCAGTATAAATAT[A/G]GCTACTTAAGACACATGAATTAGACGGATTTATCT R 2 1 2 1 101000 r 74 goat snp59144-scaffold970-11887 4 93179239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439703 Affx-122930565 AX-123310040 4 25256495 ATCTTGTTAGCAGATTATTTTTCAAGTGTGTGATT[A/G]AGCGTTCAGCCTAGTGAGGTTGTGGGAGAATGAGA R 2 1 2 1 101000 r 74 goat snp1953-scaffold1055-36505 4 93129454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793566 Affx-122957185 AX-385280541 4 25314267 GGAAGAACAGCTTTTTTAGTCCTTAGCTCAATGCA[C/T]GTTGAGTTACAGAAATTTGTAGGATCATTCAAGTC Y 2 1 2 1 101000 r 74 goat snp1954-scaffold1055-94277 4 93071607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789175 Affx-122945245 AX-385276187 4 25353038 CTTTACATTTAGAAGGTATTGATGAAATAGCAAAT[A/G]TCTCATTTGGCACGCACTGAAGACAAGCTAAGAGA R 2 1 2 1 101000 r 74 goat snp1955-scaffold1055-133048 4 93032403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793227 Affx-122976437 AX-385280205 4 25401552 CATATCTCAATTGGAAGGCCTCTTACATTTGTTGG[C/T]ATTTCATTGTTGTATTGGCAGTGTTTTTTTTCTAA Y 2 1 2 1 101000 f 74 goat snp1956-scaffold1055-181562 4 92983834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391958 Affx-122966532 AX-123262315 4 25464130 TTGCCTACTAGATAACATATTTTGCATATCCACCT[A/G]TATTCTAAAATTACTTATTTCATTTTAGATATAGA R 2 1 2 1 101000 f 74 goat snp1957-scaffold1055-244140 4 92920851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278069 Affx-1111836235 AX-519551559 4 25466137 GCAGGCTCTCCTCTCCCTTGGAATTAAAGCCTCAG[A/G]AGTGAGGCAGCCTCAGTGTGACTGTTGCCCCTGAT R 2 1 2 1 102000 f 74 goat Random2.2K-426 4 25466137 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384297 Affx-122972288 AX-123254655 4 25496972 CATGAGTGACATGAACACTGAAGACACAGTGTTAC[C/T]GAATCAGGAGCAGTAAAATGTAGTCATCATGAAAA Y 2 1 2 1 201000 r 74 goat snp1958-scaffold1055-276982 4 92887868 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424651 Affx-122942162 AX-123294997 4 25536438 TTGGGGGTAGTCTTTCAAGGGTCTTAGATTAATTG[C/T]AAACATGGTGTAAAAGATAGCTTTCATAGTTCCAA Y 2 1 2 1 101000 f 74 goat snp1959-scaffold1055-316448 4 92847933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797608 Affx-122957854 AX-385284547 4 25571694 AAATTGAATATTTTCCTAAGCATCCAGCACATAAA[C/T]AATTCATGTTTCAGCAATGGCCAATCAATAAAAGG Y 2 1 2 1 101000 f 74 goat snp1960-scaffold1055-351704 4 92812560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796885 Affx-122949561 AX-385283827 4 25682062 CATTGAGCCAAACAAATCTTAAGTGAAAGATTTTC[A/G]CTTAATCTGAAAGCTTTTTTACCCCTAGTAGGAGG R 2 1 2 1 101000 r 74 goat snp1963-scaffold1055-462072 4 92702047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425819 Affx-122940687 AX-123296165 4 25718176 AATGTGAGCCTATCCTGTTTCCCTCTTTTAGAGCC[A/G]TGCTGGCTCACCCACATGCATTAACTTAGAGGATC R 2 1 2 1 201000 r 74 goat snp1964-scaffold1055-498186 4 92665560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417266 Affx-122947259 AX-123287614 4 25798828 TTTCCTAATATACATTGACAGCGAGGATTTATTAA[C/T]GAACCTGGAGTAACTTAAAACATAAATCACCTTAA Y 2 1 2 1 101000 f 74 goat snp1966-scaffold1055-578838 4 92584790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422746 Affx-122943246 AX-123293092 4 25850430 GAGAGAAAATTTTACAAAACATGTCCCACAATGAT[A/G]TATGCCCAGCATGGGGTGGGATATGAAGACGGAAA R 2 1 2 1 201000 f 74 goat snp1967-scaffold1055-630440 4 92533001 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804579 Affx-986696748 AX-385291118 4 25850949 GCCTCCCCCATTTTCTTCTCTGACTAGACCTAAGA[A/C]GGTCCCTGTTTTCGCCCCCTGGTTCCTTGTGTGGA M 2 1 2 1 600010 r 74 goat 4_25850949 4 25850949 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320804259 Affx-986696750 AX-385290888 4 25856966 AGGTTACTCCTCTTCATTTCAGACCTGTGACACCG[C/T]CCCCCTGGGGAGCCTTGCCCCCCCAAGTCTCCCTG Y 2 1 2 1 600010 f 74 goat 4_25856966 4 25856966 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320804263 Affx-986696752 AX-385290891 4 25865271 AGGGAGAGCATCAGCCTCTCCTCTAGGCCCATCGT[C/G]TCCTCTCCGTACTCCCTGATGCCTGTCGTCACTGC S 4 1 2 1 600010 f 74 goat 4_25865271 4 25865271 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 320804587 Affx-986696756 AX-385291125 4 25869497 GCCACTGCTCCCACCCACTGCTAGCCCCCCACTTT[C/T]GTTCCACGCCTCCCTCCACAATCCTCAGCCCGCAC Y 2 1 2 1 600010 r 74 goat 4_25869497 4 25869497 Ancestral_priority_1043 ancestry 0.484 neutral IMAGE 10K 10K ancestral 320804276 Affx-986696758 AX-385290898 4 25869700 CCCTGGGTGCCTCCCATCACCTGGTCTGTCTCTGC[C/T]AGGTGACCCTCCTGTCCTGCCACATCAAGAACCTG Y 2 1 2 1 600010 f 74 goat 4_25869700 4 25869700 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 320778914 Affx-122930516 AX-385266021 4 25879180 CAAGCACCCTCAAATAAACTGTCTTCTTAATGTTC[A/G]TTATATTTTTCATGACAAAAGTTAAGTACAAATGA R 2 1 2 1 101000 f 74 goat snp1968-scaffold1055-659190 4 92504253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781265 Affx-122932541 AX-385268350 4 26035188 GATAATTTCTTTTTTAACCCTTGAATTACTAAAGT[A/G]TATTCGTAAGGCACAATAAAGCTTCTAGTAATATT R 2 1 2 1 101000 r 74 goat snp1971-scaffold1055-815198 4 92349061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415301 Affx-122948819 AX-123285650 4 26081495 TGCCCTTGTGGAAGTGGTATAAACTGGGATACTTT[A/C]TAGAATGAGAAGAGACACTATTAAAAATTGGATAA M 2 1 2 1 101000 f 74 goat snp1972-scaffold1055-861505 4 92302579 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423610 Affx-122942381 AX-123293956 4 26147614 CCACTTAAATTTCACACTTGCCTTGTGAAATTTCT[A/G]TGCACCCATGGAAAAAATCCTTTTTGGATTTTTAC R 2 1 2 1 101000 r 74 goat snp1973-scaffold1055-927624 4 92235689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453399 Affx-122919913 AX-123323732 4 26179462 AAGATGAGGAAACAGACATTCAGAGTTAAGTAATC[A/G]AACCAAATATTTGGACCTAAGTCTGCCAGGGTTCA R 2 1 2 1 201000 f 74 goat snp1974-scaffold1055-959472 4 92205975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402810 Affx-122958278 AX-123273163 4 26254854 GAGAAGGAGAGAACAGTCAGCACTGTTTCCTAACT[A/C]ATGATCCACAGGTAGGGCTACGGTTCAAAGAGGGC M 2 1 2 1 101000 r 74 goat snp14140-scaffold1566-46818 4 92129521 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376106 Affx-122978888 AX-123246465 4 26291208 TTTGGGTTATCAGAAAGTGGTAAACTGCCTAGTTC[A/G]TAGAGAAACGTTTAGGGCCATTTGTGCATACTTTT R 2 1 2 1 101000 r 74 goat snp14141-scaffold1566-83172 4 92092771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417778 Affx-122947392 AX-123288126 4 26341629 ATAAGCATTGCCTTAGCTTCACAACAACTTCACAG[C/T]AACCCAATAATAGGTACTGTTATTTCTCTCCCTGA Y 2 1 2 1 101000 f 74 goat snp14142-scaffold1566-133593 4 92042268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383408 Affx-122973491 AX-123253766 4 26398407 TACCCTTTTAAAAATGTCAATATGTTTTTTAAAGC[A/G]CCTATTACCAAGCTCATGGACTGAAGAAAAGGAAA R 2 1 2 1 101000 r 74 goat snp14143-scaffold1566-190371 4 91985736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445244 Affx-122925486 AX-123315581 4 26447945 GAATTGTTCTCCTAGGAAACTCTTGTATCTCCTTG[A/C]TTCCTCACTGCTCCCTGCAATCCCCAAATTAAAGT M 2 1 2 1 102000 f 74 goat snp14144-scaffold1566-239909 4 91935431 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272263 Affx-1111833419 AX-519546002 4 26467662 TCAGCTGTACAGGACTCCCAGTACAAGGATGTGCA[A/G]CATCTCCCCAGCCCCTTGTTGATGGGGTTGAACTT R 2 1 2 1 201000 f 74 goat 4_26467662_AF-PAKI 4 26467662 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403076 Affx-122958513 AX-123273429 4 26485346 AATTTTATTTTATTTTGGTTTGTTTGGGGAGACTA[C/T]CAATCACTAAGTCTCAGTTTTAAAAGGTTTTAGAT Y 2 1 2 1 101000 r 74 goat snp14145-scaffold1566-277310 4 91898238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798837 Affx-122923843 AX-385285767 4 26520163 ACATGATAATTTTGATATATCATGGGTTGCTGAGT[A/G]TGAACTAGCTTGAGAGTGAGAAGCTCTTAGGGCTA R 2 1 2 1 101000 r 74 goat snp14146-scaffold1566-312127 4 91863410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382674 Affx-122973656 AX-123253032 4 26549188 ATGCCGTGAGCTGGAATGACTTTTACTCTCTGCTG[C/T]GTCAGCCAAAGACGGTGTTGCTTCACTGAGCTCTA Y 2 1 2 1 101000 r 74 goat snp14147-scaffold1566-341152 4 91834082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780600 Affx-122947729 AX-385267690 4 26593196 GGAAAAATGAATAACATTGATCAAGTACTATCAAG[C/T]GTTGCTCCTTAAAGGGATGGCTTTACCCTTTAGGG Y 2 1 2 1 101000 r 74 goat snp14148-scaffold1566-385160 4 91789356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409393 Affx-122954145 AX-123279744 4 26622502 CATCTCAGTTTCTTAGTGCAGGCAGTTTGGTATAC[A/G]TAGGGGTTACCATCTTGGACCAGCACAAAGGATAA R 2 1 2 1 101000 r 74 goat snp14149-scaffold1566-414466 4 91759869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777143 Affx-122961362 AX-385264266 4 26653213 GAATGGAAGAAAATTATCAGTTAAACCATACTGAT[A/G]TGGTCTTGATGCAGCAACAGAAATCACACCATATT R 2 1 2 1 101000 r 74 goat snp14150-scaffold1566-445177 4 91728911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425870 Affx-122940649 AX-123296216 4 26697358 TCACTAATAAGAAATGCTGAGTCCTACTCAAAGGC[A/G]TGAATAACAGGAAAACACAGCTGCCTGAATGAATG R 2 1 2 1 101000 f 74 goat snp14151-scaffold1566-489322 4 91684215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431160 Affx-122936565 AX-123301501 4 26732659 GTTCTGGCCAGTTCTGATGGCTCTCCAGAATTCCA[A/G]TTCCAAGTGATTAACAACTCAGTTTCCCTTTCCAC R 2 1 2 1 101000 r 74 goat snp14152-scaffold1566-524623 4 91649103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771196 Affx-122958421 AX-385258354 4 26766765 GAACAGAAAGTTAGTGGTCTCTAAAACTATTTTTC[A/G]TCTCCCTGGAGTAAAGACTGAACTCAAGATTGAGA R 2 1 2 1 101000 r 74 goat snp14153-scaffold1566-558729 4 91615082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375717 Affx-122978636 AX-123246076 4 26830272 TTCTCATCCCTCTCATCTCTTAATTCTGTCCTTCT[A/C]TGCTCCCTTGTAGTCAAACAACCTTATCTCTATAT M 2 1 2 1 201000 r 74 goat snp14154-scaffold1566-622236 4 91552063 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430161 Affx-122937375 AX-123300502 4 26900341 ATTCATGGTGTTTTATTTCTTCTTTTACATTTTCC[A/G]TCATCTGAGCATGAATTGCCTTGTGTTTTGTTATT R 2 1 2 1 102000 r 74 goat snp14155-scaffold1566-692305 4 91481688 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419292 Affx-122946239 AX-123289640 4 26959284 CCAGTCTCTGTTAACAGTAAAATATTAAAAATCAA[C/T]GTACTGGTCCTTCTACATGACTATGATAACTACTG Y 2 1 2 1 101000 r 74 goat snp14156-scaffold1566-751248 4 91422529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436362 Affx-122933060 AX-123306701 4 26990652 ACAGTTTCCTCCTCCACAAACACCAAATATTTTCA[A/G]TTTTTTGAGTAGGAGAAAGTAGACCAAAAAGAATG R 2 1 2 1 101000 f 74 goat snp14157-scaffold1566-782616 4 91391045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801000 Affx-122953803 AX-385287914 4 27021957 TGAAAGAGCAAGATAAAATCCCTAAAAAAATAAAA[C/T]AAATAATTTACCAAATAAAGCTTTAAAACATTACT Y 2 1 2 1 303000 r 74 goat snp14158-scaffold1566-813921 4 91358799 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439774 Affx-122930511 AX-123310111 4 27117949 GGCTGTCTGTACCTACCAGTGAATATCCATGTATC[C/T]CTCAGGCTTCCTTTATAGAGTTGGGGCTGTTGATT Y 2 1 2 1 101000 f 74 goat snp14160-scaffold1566-909913 4 91261102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417787 Affx-122947386 AX-123288135 4 27148091 TAACTATTCTATATTTTACTCAGTAGCAGGGAAAA[C/T]AAAAACATCAAAAAGCAGGCTGTCAGGGCCAAGTG Y 2 1 2 1 103000 r 74 goat snp14161-scaffold1566-940055 4 91231604 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786299 Affx-122924986 AX-385273334 4 27197446 TGATTTCTAGTTCCAGACTATCATGGTCCAAAAGA[C/T]ACTTGGCATTTCAGTCTGCTTAAATTTGCTAAGAC Y 2 1 2 1 101000 f 74 goat snp14162-scaffold1566-989410 4 91181688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796725 Affx-122944816 AX-385283670 4 27262362 AGTTTTTTGTTAGGGCACATTAACATAAGTGGTAG[C/T]GATTAGGCTCTAGCTATCTTCATTCTGCCTTGTTC Y 2 1 2 1 101000 r 74 goat snp14163-scaffold1566-1054326 4 91118129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782791 Affx-122923640 AX-385269863 4 27291231 TACTAAAAAATTTTTGAAGACTATTTCATGACCCA[C/T]GAAAAAGCTTGCAGTGTAATATAAAGGGATAAAAG Y 2 1 2 1 201000 f 74 goat snp14164-scaffold1566-1083195 4 91089624 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769931 Affx-122969018 AX-385257100 4 27332228 AGAAATTAGAACAAAAAGTCATACATAAGGATGTT[C/T]AATCATTTGGGAACAACTAGATGCCCAGTATTAGG Y 2 1 2 1 101000 r 74 goat snp14165-scaffold1566-1124192 4 91046022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771060 Affx-122932200 AX-385258220 4 27361501 CCTTATACTTAATATTCAGTCATTAGCATTATTCT[C/T]TCTTCTATGGAAAGTCAACTTCTAACTGCATGAAA Y 2 1 2 1 101000 r 74 goat snp14166-scaffold1566-1153465 4 91016806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430811 Affx-122937456 AX-123301152 4 27395182 GTGAGAAATATTTTGGCAGTTCTTTAAAAATGTGA[A/G]CATTCTCCTCCCATGCAATCCAAAATGACACTCCT R 2 1 2 1 101000 r 74 goat snp14167-scaffold1566-1187146 4 90982874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777514 Affx-122927282 AX-385264633 4 27475171 TTGGTAAGAATCAAGACAAAGGACTTCTATCACTC[A/C]TATCTTAATTCTCCTTCAAGATTTCTTGAACTGCT M 2 1 2 1 101000 f 74 goat snp14168-scaffold1566-1267135 4 90904763 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378947 Affx-122976426 AX-123249306 4 27529509 GTTAACCCTGCTAACAAGCTACTATTCTGTCTCTT[C/T]ACACCACAAAATACCATGTGAAGAGGTGATGGCAG Y 2 1 2 1 101000 r 74 goat snp14169-scaffold1566-1321473 4 90851566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452461 Affx-122920559 AX-123322794 4 27680846 GGTTGGTGGTACAATTATTGGAAAAACAATTTCCA[C/T]TACAGACTAGAAGTTTCCCCTAGAATGTTCCTTCA Y 2 1 2 1 101000 r 74 goat snp14171-scaffold1566-1472810 4 90701889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435883 Affx-122932784 AX-123306222 4 27716020 CATGAAGCGTAGCACCTTTCTAAGCTCAGGTTCCT[A/C]TGTGACTGCTCTGGTCACAATCCTGTGAAACCTCC M 2 1 2 1 101000 f 74 goat snp14172-scaffold1566-1507984 4 90665806 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451083 Affx-122921412 AX-123321417 4 27754242 ACATTATGTACCAGCCCTTATCCCTTTTGGCCTTG[C/T]AATAGGGTTATTTATGTGTGTGTCTAATCTCTACT Y 2 1 2 1 101000 r 74 goat snp14173-scaffold1566-1546206 4 90628349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426773 Affx-122940555 AX-123297119 4 27810202 TATGTATATTTTAAATTAATATATGTAAATAATTT[A/G]GAAAAATTCATGAGTGACAACCAAGATTGTTGAAG R 2 1 2 1 103000 r 74 goat snp14174-scaffold1566-1602166 4 90572098 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394044 Affx-122964990 AX-123264399 4 27852726 CAAAGGTTATGTATGTTTTTATCTTAATAGATATT[A/G]CAAACCAAGTTCCTTAGGTGTTACACCAATTTATA R 2 1 2 1 201000 f 74 goat snp14175-scaffold1566-1644690 4 90528269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418260 Affx-122947020 AX-123288608 4 27897201 AGGGAATCCTTCTCTGACAGGTAATATTTGAGAAA[A/G]TGTAGGAAGACAGATAACCATTATGAAAATATGTC R 2 1 2 1 101000 r 74 goat snp14176-scaffold1566-1689165 4 90483232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395420 Affx-122963945 AX-123265775 4 27949204 AGGCTCACAGTCAGATACAGCTGACCAACTAAATA[A/G]TAAAGCAATAGCAGCACTGGAAAATTCTGTGGTTT R 2 1 2 1 101000 r 74 goat snp14177-scaffold1566-1741168 4 90431756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435131 Affx-122933684 AX-123305471 4 27966272 TAAAACAAGGCATTGTGGTATATCAGAAAAAGGCT[A/G]TGAAGTCAGACAAATCCAAGTATAATCCTATTTAT R 2 1 2 1 201000 r 74 goat snp15440-scaffold1637-10670 4 90407622 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388563 Affx-122969175 AX-123258921 4 28010585 TAATAAATAAGTTCATAGCAAGGCTTTTGTGTGCT[A/G]CTGTTCTTTATCCTGCAGTATCATCAGTCAAATTC R 2 1 2 1 101000 r 74 goat snp15441-scaffold1637-54983 4 90363722 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274488 Affx-1111834322 AX-519548079 4 28023348 CTGACAGCCCCAGCTGCTGTGCTCTGAAACCCATC[A/G]CT R 2 1 2 1 103000 f 74 goat GoatD01.029976 4 28023348 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397021 Affx-122963123 AX-123267376 4 28093990 TCACTATCTCCTGGAGTTTGCTCAAATTCATGTCC[A/G]TTGAACTGGTGATAGTATCTCAACAGAGATCGTCC R 2 1 2 1 201000 r 74 goat snp15442-scaffold1637-138388 4 90279740 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776608 Affx-122960701 AX-385263735 4 28123552 GTTTTATTTTCAGTTCTTAGCAGAATCAGGACTTT[A/C]GCACAGTTCTTTTATTCCCAGTCACCTGGTCTTTG M 2 1 2 1 101000 r 74 goat snp15443-scaffold1637-167950 4 90249752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402435 Affx-122958624 AX-123272788 4 28175880 GTGAAAGAAAGTGATTAGAGAAAATTGAGTTATAC[A/G]CAGAGCACCAGTGTGACAAGGCAGGGCTGGCTAGA R 2 1 2 1 101000 f 74 goat snp15444-scaffold1637-220278 4 90196868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420430 Affx-122944905 AX-123290777 4 28206627 GGTGCAGCCACATACACACAAAAAAACAACCCAAC[A/G]TTTATTATGGAAATAAAAGGTAATATTGAAAAAAA R 2 1 2 1 303000 r 74 goat snp15445-scaffold1637-251025 4 90166278 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450480 Affx-122922934 AX-123320814 4 28263751 TTTACCTTCTTTCCTTATCTCTTTAAAAAGTCCAT[A/G]TTTCTCTTTGATACCCCCAGTGTTTAATGTGGAAG R 2 1 2 1 101000 r 74 goat snp15446-scaffold1637-308149 4 90108709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403197 Affx-122958063 AX-123273550 4 28320845 GTGAGAAATTCTTGACTGTCCCTAGACTCTAGTAC[A/G]AGGAAGATAAAGAAGGACTTATTGACGGGTTCCGG R 2 1 2 1 101000 f 74 goat snp42201-scaffold552-21764 4 90051034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788727 Affx-122945089 AX-385275743 4 28354323 TGTGCTTGTGTTGCAGCTTGGCTTTTGGGTTTGGT[A/G]TGTGGAGCAGGGGTAAATCCTTTGCCCTGCTTGGC R 2 1 2 1 202000 r 74 goat snp42202-scaffold552-55242 4 90017067 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382193 Affx-122974008 AX-123252551 4 28440536 AGTGACTGTTTTACAAGAAGAATTTGAAGAGCAAA[C/T]GGTAAAGGGAACTCAGTGGAGATGCTGAGGCTACA Y 2 1 2 1 201000 f 74 goat snp42204-scaffold552-141455 4 89930327 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446575 Affx-122924829 AX-123316911 4 28490723 ACCATTCAGAAACCTGTTAGAAGTTTAGAACATTG[C/T]ATCTTACCCACATCACCTGTGAAGAGTTGTCACAA Y 2 1 2 1 101000 r 74 goat snp42205-scaffold552-191642 4 89880401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402923 Affx-122958191 AX-123273276 4 28538038 AGTTTAAGCAGAAATGGTGACTGGACACAGGCGAA[C/T]AGGGAAGGAAAAATAACTAGAAAATGACACCCAGG Y 2 1 2 1 201000 f 74 goat snp42206-scaffold552-238957 4 89832795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775090 Affx-122945957 AX-385262222 4 28569884 TACTACAGTTCTTATAGTGGTATGTTATATACTGA[C/T]GTAGTGGTTTATTATGGTAAATAAGAAATTCCAGG Y 2 1 2 1 101000 r 74 goat snp42207-scaffold552-270803 4 89800935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783433 Affx-122950887 AX-385270496 4 28623135 TGAAGAGTCTGCAACATGTCGATCCTCTGTTCTAG[C/T]GTTTCAGTTTGGCTTGGATTTTTGCAAGCAGCTGA Y 2 1 2 1 101000 f 74 goat snp42208-scaffold552-324054 4 89747274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453383 Affx-122919927 AX-123323716 4 28659466 TGAGCTGGAGAGGAAGGTGAAAGCCTGAAGACAGA[C/T]AGCGCAATGAAGGATAAACACCAAACAGCATTTGA Y 2 1 2 1 101000 r 74 goat snp42209-scaffold552-360385 4 89711942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787167 Affx-122942733 AX-385274193 4 28710269 GTAACAAACTCATGTTCGAAAGTGTGTCGTAACTC[A/G]TAGTCAGAACTTTGCAAACGCTAACCTGCACAGGG R 2 1 2 1 101000 f 74 goat snp42210-scaffold552-411188 4 89671995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383032 Affx-122973304 AX-123253390 4 28753818 ATTCCCCCATAATACCCTGCACAGATGTGCAAACA[C/T]AGAGTGATCAATACAGATTTCCTAAATATATTACA Y 2 1 2 1 201000 r 74 goat snp42211-scaffold552-454737 4 89629231 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380287 Affx-122975411 AX-123250645 4 28789230 AATTCTGTCTCATTTCATATTTATTTCTGGGATTT[A/G]GGGGAAGGACTGACAGCCAAACAGCAGCCTTAAGT R 2 1 2 1 102000 r 74 goat snp42212-scaffold552-490149 4 89593811 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476185 Affx-1251763690 AX-586011611 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 4 1 4 1 20000 f 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 539476440 Affx-1251763690 AX-586011841 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 4 1 4 1 20000 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562165816 Affx-1251763690 AX-606941225 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562165867 Affx-1251763690 AX-606941276 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166222 Affx-1251763690 AX-606941630 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 f 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166402 Affx-1251763690 AX-606941810 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166541 Affx-1251763690 AX-606941949 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 38385474 Affx-122971291 AX-123255832 4 28832474 TTAGAAATCATCCCATGTAGAGAGAAATTTGATGG[C/T]GTGGGCCAAAGAGATGGCATTTTTAGGAGACATGT Y 2 1 2 1 201000 f 74 goat snp42213-scaffold552-533393 4 89550707 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429028 Affx-122938321 AX-123299370 4 28876546 CATCTAAGACCCCTTCCAACCAGGAAGTCTATCTA[C/T]AAAAACTGCGAATGTGGGAGGACATCCTGGAAGAA Y 2 1 2 1 202000 r 74 goat snp42214-scaffold552-577465 4 89506781 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444693 Affx-122926435 AX-123315030 4 28916317 CTAAGATAATAGCTATGTAACTACCTATTCTAGTT[A/G]TTTTTGCTATTGGACCATTTAGGCTATTAGGCTAT R 2 1 2 1 202000 f 74 goat snp42215-scaffold552-617236 4 89466870 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448459 Affx-122923637 AX-123318795 4 28956694 GCTTACTGAATGGGAGTACGTAAATTAGTTGCAAA[C/T]GATATACCCAACAAGGAGCTGATCTAAAATATGCA Y 2 1 2 1 101000 f 74 goat snp42216-scaffold552-657613 4 89426527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272264 Affx-1111833420 AX-519546003 4 28994988 ATGCACCTATTGAAATTCCATATGAAATCTCAGAA[A/G]TGGCCTAAATAAATCATTCTGGAATTTCTGCTATT R 2 1 2 1 101000 f 74 goat 4_28994988_AF-PAKI 4 28994988 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454141 Affx-122919334 AX-123324474 4 29001121 AAACCATCAAGGGAACCAGGACAGTCCTGGGAGTC[A/G]CCTGCATCCTTGAGGTCCTCCCCCAGTGTGGACCA R 2 1 2 1 102000 f 74 goat snp42217-scaffold552-702040 4 89381772 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408810 Affx-122954039 AX-123279161 4 29036708 CCGGCCAGATATTCTCAAGAAACCTGGAGACAGCC[A/G]TGTCCTCCTGCTTACAGGTGATGACCTCATTCAAA R 2 1 2 1 101000 r 74 goat snp42218-scaffold552-737627 4 89346410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769210 Affx-122932380 AX-385256385 4 29065224 CTATTTTATTGCTCACTTTAAAGGAGAAATACTTA[C/T]AGGAATCCCATTATTTTTCAGACAGCATGTTGAAG Y 2 1 2 1 101000 r 74 goat snp42219-scaffold552-766143 4 89317844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399507 Affx-122961167 AX-123269862 4 29138814 TCAGCAGAAGATGGTGGAGTATGTCTCCTAGCAAC[A/C]GGGATAGTTTACCATTTAACAGTAGGACTGTCTCA M 2 1 2 1 101000 r 74 goat snp42220-scaffold552-839733 4 89244086 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388566 Affx-122969173 AX-123258924 4 29180153 TGAAAGTAAGGTCTTTATTGTCTATTATCTCTCAC[C/T]CTGTGAGACTGCAAGCTCCAAGACAGCAGGCACTT Y 2 1 2 1 101000 f 74 goat snp42221-scaffold552-881072 4 89202682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418450 Affx-122946475 AX-123288798 4 29235278 AGGCATAGCACTGGAATTAGGACAGACGAGGACAA[C/T]GCAATGGGAGGTGTCCCCAGCAGACAGGAAGGAGG Y 2 1 2 1 101000 f 74 goat snp42222-scaffold552-936197 4 89147630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426093 Affx-122941072 AX-123296439 4 29289578 GAAAACAGAAAAGGAAGGATTCTATTATTACTAAC[A/G]CAAGAGTAAATGGATAGAGGGAGGTAGCCAACACG R 2 1 2 1 101000 f 74 goat snp42223-scaffold552-990497 4 89093482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444228 Affx-122927236 AX-123314565 4 29324529 TTGTAACAGCGCTACCGACACCCGTGAGACAACAG[C/T]AGCAAACAGCGTCACGAATCTGCACAAAAGGAGAC Y 2 1 2 1 201000 r 74 goat snp42224-scaffold552-1025448 4 89058317 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778857 Affx-122933132 AX-385265965 4 29405212 CTGATCTCTTATTTGGGCCGGCTCATGTGTCCTCA[A/G]ACTAATGTTTCCCAAAATCCTTCTACAACATTTCC R 2 1 2 1 101000 f 74 goat snp42226-scaffold552-1106131 4 88976703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430464 Affx-122937258 AX-123300805 4 29439437 AAGCAAGCACTGGGGAGGGATATTGTGTTACAGAA[C/T]AGACCTGTCCAATATAATCACACCAACAACAATAC Y 2 1 2 1 101000 f 74 goat snp42227-scaffold552-1140356 4 88941418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436568 Affx-122932903 AX-123306906 4 29480271 GAATGTTTACACATTTATATGAGAAGTCAACTAAC[A/G]TTCATCTGCTACTCAAAAGACTCTCTGTTCCAGAA R 2 1 2 1 101000 r 74 goat snp42228-scaffold552-1181190 4 88900328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407191 Affx-122954818 AX-123277542 4 29552432 AAATAAGAAGAGCCTATGTTGAGGGATCATGAGAA[C/T]AATTTTTCCTTTTTAATTTATGTTCTTCCTCTGTA Y 2 1 2 1 101000 f 74 goat snp42229-scaffold552-1253351 4 88827571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396818 Affx-122963280 AX-123267173 4 29565668 AGGGAGTTGTCAATGGGCGTTGTTATGAAAATTCA[A/G]TGAGAAAAGCCTGTAAAACACTTTGCAGAATGGCT R 2 1 2 1 101000 f 74 goat snp3301-scaffold1100-649710 4 88815675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779982 Affx-122940628 AX-385267081 4 29604610 CAAATTATTCATAATTCCTACCTGACCAGGTTGAA[C/T]AGCAGAGAAATACAGTTTTATTAATGTTATATTTA Y 2 1 2 1 202000 r 74 goat snp3300-scaffold1100-610768 4 88776733 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780084 Affx-122941813 AX-385267182 4 29635896 CAATGACCTTTTTCCAGTTATAAAGTTACTTCTCC[A/G]TTACTTGAAAAAAGCCTAGAAAAGATGCATCTTGA R 2 1 2 1 101000 f 74 goat snp3299-scaffold1100-579482 4 88745519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278224 Affx-1111836236 AX-519551712 4 29658726 TTATTATTATTATTATTATTTTCGTTTAAAAGATG[A/G]ATTGAGGAGGAAAGTAATAAAACCGCATGAGAGAG R 2 1 2 1 101000 r 74 goat Random2.2K-429 4 29658726 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274778 Affx-1111834416 AX-519548364 4 29682721 TT[A/G]GATGTTGGGGTCATCATGCCTGCAGCTTACTCTCA R 2 1 2 1 102000 r 74 goat GoatD01.034617 4 29682721 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399987 Affx-122960816 AX-123270342 4 29718629 CCCCCTTGGCTAGCGTTCACATGTTTCAAGTAAAC[A/G]TTCATTTGCTTTGTTCTTAATTCATTCTTTCTACA R 2 1 2 1 101000 f 74 goat snp3297-scaffold1100-496749 4 88662934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450344 Affx-122922116 AX-123320679 4 29764892 AGGGAGAACAGAGCTGGGAAGTGCCGTCTTGTGCC[A/G]TGGGAAGCTGGCTGTTGATTTAGGTGTTTCCAGTT R 2 1 2 1 101000 r 74 goat snp3296-scaffold1100-450486 4 88616629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402589 Affx-122958432 AX-123272942 4 29814425 TTTCTGTTCTCCCATCGGACTCTTAACTTAGGGAC[C/T]AGGGGCTGTGTCTTCTGTTTTGTCATCAAAGACAC Y 2 1 2 1 101000 f 74 goat snp3295-scaffold1100-400953 4 88566789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454270 Affx-122919640 AX-123324603 4 29850880 CCTTGTAAAAGGGTGATTGGTGTGTGGTGTCCAGC[A/G]TACAGTCTCACATAATTCGTATTGCTTCCGTCTTT R 2 1 2 1 201000 r 74 goat snp3294-scaffold1100-364498 4 88530471 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404526 Affx-122956690 AX-123274878 4 29880984 ACAGAAATAAGAAAAAGTTGTCTTCTGTTCTGGGA[C/T]GTGTGCTCATAAACGTAGAAATCTTTGGGTGGTGT Y 2 1 2 1 101000 r 74 goat snp3293-scaffold1100-334394 4 88500144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413033 Affx-122950993 AX-123283382 4 29931485 GATTAAAAAGTAGTACATGGTTATAATATTTTTAC[A/G]CATAGATAATTCTTAGATTGAGTACATGGTCATGG R 2 1 2 1 101000 r 74 goat snp3292-scaffold1100-283893 4 88449459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791044 Affx-122944292 AX-385278039 4 30025751 AGTCTTAACTGTATCAGTAATAGAATAGACAATGA[C/T]AGATTAAAGAAGAGATTCTACAAATAGTTTTCATT Y 2 1 2 1 101000 f 74 goat snp3290-scaffold1100-189627 4 88354741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390337 Affx-122967697 AX-123260694 4 30087869 CGAATTGGTCGGATGTTGGGGGAGAGAGGAGATGA[C/T]GGGCCATGGCTGTGAAGTGCAGCATTTCAGTCCTT Y 2 1 2 1 101000 r 74 goat snp3289-scaffold1100-127509 4 88292444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415475 Affx-122948709 AX-123285824 4 30117900 CATAAAAGTCTGCATTGTGTGTGATGTGTGAAGTC[A/G]CTCAGTCATGTCCGACTCTTTGTGACCCCGTGGAC R 2 1 2 1 103000 f 74 goat snp3288-scaffold1100-97478 4 88262904 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791610 Affx-122950444 AX-385278601 4 30154093 ATCCACCTATTCTTTCATCTACCTGAATACCTGTC[A/G]TTCATTCTGTCTCCCTGATACACATTCAACAGAGT R 2 1 2 1 101000 f 74 goat snp3287-scaffold1100-61285 4 88226637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768506 Affx-122958219 AX-385255686 4 30182606 ACTCTGAGATTATTGCTTTCAGTGTAGAATAATTT[C/T]TCTCTTCTTTACAAGAATGCTCAATGGTTATGATT Y 2 1 2 1 201000 f 74 goat snp3286-scaffold1100-32772 4 88198440 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376331 Affx-122978346 AX-123246690 4 30228638 ATGGCACATTGAGAATGCCCAGGTCTCATTGCCTC[A/G]TGGAATTCTGTGCCCTGTGAGGATTATGGTAACAG R 2 1 2 1 201000 f 74 goat snp19229-scaffold1934-283568 NW_017189707.1 14769 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772207 Affx-122948919 AX-385259362 4 30309881 AGGCGGGCAGAATCAAGCCAATCATGCTCTCATCT[A/G]CTTTCTTGATAGGCGGAAGTGTTGTGAAGATACTA R 2 1 2 1 101000 f 74 goat snp19228-scaffold1934-202325 NW_017189707.1 104113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403654 Affx-122957520 AX-123274006 4 30354781 TGTGAATTTCTGTTGCTTTTCTCACTTTCAGAATT[A/G]CCAGAACCTGGGTATCTCACCCACATCTGTTAATT R 2 1 2 1 201000 f 74 goat snp19227-scaffold1934-157425 NW_017189707.1 149604 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426461 Affx-122940797 AX-123296807 4 30443000 ACTTAAGTATGTATAAACACAGAGCCATTTATAAT[A/G]CTGACAAAACTGTTCTGCCAACAAAATAAATAAAA R 2 1 2 1 101000 f 74 goat "snp19226-scaffold1934-69206;snp22340-scaffold2208-51495" 4 87557203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788767 Affx-122928065 AX-385275782 4 30483955 TAATACCATGAAACTTTTCATTAAACAATGACACC[A/G]TGATCCCTAACACAAGCTCTGCAAATCAGCAAGAT R 2 1 2 1 101000 r 74 goat snp19225-scaffold1934-28251 NW_017189707.1 279588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768342 Affx-122921262 AX-385255522 4 30518639 TTTAGGTAAGGAGTTTGTAAAAGGGTGATATGTCC[A/G]TCTACATAACAGAAATATCAAAGAAGTTAAATCTG R 2 1 2 1 201000 r 74 goat snp10824-scaffold1385-957875 4 87479143 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392786 Affx-122965981 AX-123263143 4 30553925 AAAGTGTCTTCAGTTGTGTTTGACTCTTTGTGACC[A/G]TATGGACTGTAGCCCTCATACCACAAAAGAATAAG R 2 1 2 1 303000 r 74 goat snp10823-scaffold1385-922589 4 87444643 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784254 Affx-122974010 AX-385271305 4 30587319 GGAAGGGTGTTGGTTTGGTGGTTGAGGTCCAGGTA[C/T]GCCTTCTCTTTCGTGGGATGCTTATAGCTCCAGTT Y 2 1 2 1 101000 f 74 goat snp10822-scaffold1385-889195 4 87410994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789572 Affx-122957224 AX-385276581 4 30620298 TATGAGGGAAGGAAAGGCCAAGCACTCTGTATTCT[C/T]TATTGCTGTGTAACGAATTACCCAATATCTTAGTA Y 2 1 2 1 101000 f 74 goat snp10821-scaffold1385-856216 4 87378071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394907 Affx-122964324 AX-123265262 4 30659535 AAGGGCAAGAATTATATTGGCTTAAAGCAGTCTCT[A/G]CCACACCATTATTATTATTATTTTTTAAAATAATG R 2 1 2 1 101000 f 74 goat snp10820-scaffold1385-816979 4 87338972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405750 Affx-122956505 AX-123276102 4 30706837 TCCTATTAATTAAATATCTATCTCTGGTCTCAAGT[A/G]TTCCTTTCATATTCAGACTCCAAATTACCTGATTT R 2 1 2 1 101000 r 74 goat snp10819-scaffold1385-769677 4 87291024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421302 Affx-122944098 AX-123291649 4 30740061 GGTGCTTGGGGCCACACCCCAGGCCAATAATATCA[G/T]AATCTCTGGCGACAACACTCAGCAACAGTATTTTT K 2 1 2 1 101000 r 74 goat snp10818-scaffold1385-736453 4 87260109 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423444 Affx-122942598 AX-123293790 4 30801141 CTACTTCAGACTTTGTTTTCCTGCCACTAATTCCT[A/G]TCTTTGCAGTTTACTTTCTCTAATACTTCTGCAGT R 2 1 2 1 101000 f 74 goat snp10817-scaffold1385-675373 4 87199259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427293 Affx-122940156 AX-123297636 4 30871858 ATAGGATTAGGGGCCCACCACACTCCAATATGACC[G/T]CATCTTATTTTAAGTAGTTCCATCTACAATCACCC K 2 1 2 1 101000 r 74 goat snp10816-scaffold1385-604656 4 87127859 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767066 Affx-122936376 AX-385254355 4 30925186 AACAACTCTGCAACTTTCAGAGTTAAAAGTGGCAG[C/T]ACATGGTTCTACAGATATCAAACATCTTCTTGGAT Y 2 1 2 1 101000 f 74 goat snp10815-scaffold1385-551328 4 87074552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395151 Affx-122964121 AX-123265506 4 30956659 AAACAAGTTTGCAAATAAACCCTGTGCCTGATGCT[A/G]TACCAAACAAAATAATAAAGGACAGAATATTTCCT R 2 1 2 1 101000 f 74 goat snp10814-scaffold1385-519855 4 87043385 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797646 Affx-122957006 AX-385284585 4 30994302 TGAGCTTAATAAAAACAAACTAGTTATTTGAGTTC[A/G]TTTGAACTCAATTGAACCTATAAGAATCTCTCAAA R 2 1 2 1 101000 f 74 goat snp10813-scaffold1385-482212 4 87005252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375507 Affx-122979126 AX-123245866 4 31042999 CAAGCAGAGCACAGTGGTCTCACTGAGGGATGAAT[A/G]TCTGGAGGAAGCTGAAATAACCAGAATTTACAGGC R 2 1 2 1 201000 r 74 goat snp10812-scaffold1385-433515 4 86956656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412315 Affx-122950854 AX-123282664 4 31082340 TAAGTTCACACTTGAAAGAGAATGCTAAGCCTAGA[A/C]ATTTACCTCTGAAAGCCACTCTTTCACTTACCACC M 2 1 2 1 101000 r 74 goat snp10811-scaffold1385-394174 4 86917197 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801695 Affx-122935340 AX-385288603 4 31114727 CATTCATAGTTTCCTATTCAGATACTAATATAAAT[A/G]TACATTTAATATAAATGTGATAGTCTACAGTCGCT R 2 1 2 1 101000 r 74 goat snp10810-scaffold1385-361787 4 86884466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793199 Affx-122968802 AX-385280177 4 31171548 TTACATTCATTCCAATTGCTACCTTAATAATGTTC[G/T]TGCTTATTGCTTTTGCTTCAAATGAGTTATCATAT K 2 1 2 1 101000 r 74 goat snp10809-scaffold1385-304966 4 86827831 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426225 Affx-122940353 AX-123296571 4 31208968 ATTACTCCTTGGTATGCAAATATACAAATATATCC[A/G]CTCATTAACAGCTAATAGAATGAAAATTCTTGGAT R 2 1 2 1 101000 r 74 goat snp10808-scaffold1385-267546 4 86789684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278074 Affx-1111836238 AX-519551564 4 31211039 TTTGATCACCTGGCAAGGTGTTATTTTGTTTCTCC[A/C]CTGGAGAGGTACACTGGATTGTCCCCTTGGCATTC M 2 1 2 1 201000 f 74 goat Random2.2K-430 4 31211039 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402320 Affx-122959080 AX-123272673 4 31247080 GTAGATTCGTGCCTTAGATCAATGTTTTGACATTC[A/G]CTATTATATTTTAAACTTTTCTATTTCCGTTGGTC R 2 1 2 1 103000 f 74 goat snp10807-scaffold1385-229434 4 86751624 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420122 Affx-122945079 AX-123290470 4 31289988 GTAGGCATCTGCACATGTGAGCCAAATGAGATCAT[G/T]CAAGAGAAACACTCTGCATTATAACCCAGTTGGCC K 2 1 2 1 101000 f 74 goat snp10806-scaffold1385-186526 4 86708973 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781152 Affx-122951329 AX-385268236 4 31322694 GTAACGTAAACACTCAAAAGAGTACTAAAAGAATG[C/T]AAAAGTTAAAATCTTAAAGGAATTACAAAATGGAT Y 2 1 2 1 202000 r 74 goat snp10805-scaffold1385-153820 4 86676892 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781292 Affx-122969731 AX-385268377 4 31369127 AGAAAGGTCACAGTTTTATATCTGGACATCTTTTC[G/T]AAATATTTAAGACACATCCTTAGGTCATTCATGTG K 2 1 2 1 101000 f 74 goat snp10804-scaffold1385-107387 4 86630518 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781909 Affx-122968778 AX-385268990 4 31401836 GTAATATTTTCGCAGGAAGACATATATATTACATC[A/C]TACCAAATAGTATACTTCGATATGGACAATTTATT M 2 1 2 1 101000 f 74 goat snp10803-scaffold1385-74678 4 86597901 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414942 Affx-122949089 AX-123285291 4 31434472 GCAATTTAATCTCAATCCCACCATGTCAAGCTCTA[A/G]CTGGAAATTCAGAAACCTAAAGTAAAGGCTTATTG R 2 1 2 1 101000 r 74 goat snp10802-scaffold1385-42042 4 86564681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442115 Affx-122928347 AX-123312452 4 31473409 TGGTACTTTCAATCAATAATATTGGGAAAATGGCT[A/G]TATAAAAGAAAAATAAACATTGACTCTTTTCTCAT R 2 1 2 1 103000 f 74 goat snp10801-scaffold1385-3105 4 86525132 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406713 Affx-122955762 AX-123277064 4 31486949 GAGAAGCTTTCTGTCTTCTAGAGCATGTACCATGT[A/G]GTTAGTGGGACCTGATAATGTTGCTGCATGATAGA R 2 1 2 1 101000 f 74 goat snp49381-scaffold704-10336 4 86511557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428223 Affx-122939438 AX-123298566 4 31539164 AGATAGGACATCATGTGAGCAGTGACTTGAAGAAA[G/T]CAAGGGAGGACATTTATATGAATTTGGGGAAGGGG K 2 1 2 1 101000 f 74 goat snp49382-scaffold704-62551 4 86459227 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395249 Affx-122964100 AX-123265604 4 31576628 GATATTTGGTCAATAAAAATGAAATTTAACAGGAT[G/T]GCCAAGTCAGAATGTAAGAGAACATAAATATTAAG K 2 1 2 1 201000 r 74 goat snp49383-scaffold704-100015 4 86421019 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377395 Affx-122977625 AX-123247754 4 31615809 GACAGTCATCCACATACAAAGCTAGTAGAGAGGTT[A/G]AAAAACAAAAGTAGTAACATCATTTATATAATTTA R 2 1 2 1 102000 f 74 goat snp49384-scaffold704-139196 4 86381468 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416125 Affx-122948297 AX-123286474 4 31663504 AAGAGCCTACAATGAGGTAGAGAGACCTTTTCAAC[A/G]TTAACTACTATTACTAATATTTAATAAGGAAAAAA R 2 1 2 1 101000 f 74 goat snp49385-scaffold704-186891 4 86334401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443535 Affx-122927771 AX-123313872 4 31730360 AATGAAATGCAAGAGGGATTCTTCAAAAAGCAATG[C/T]GTCTTTGCTTTTAAGGAAAAATCAGCATTGGTTCA Y 2 1 2 1 101000 f 74 goat snp49386-scaffold704-253747 4 86266862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435878 Affx-122932789 AX-123306217 4 31763519 CAAAGAGCTTCTCAAAATCACACACATTTCAGAGA[C/T]ACCAACTGAAGCTACATTGCCTAAACATGCATGGC Y 2 1 2 1 101000 r 74 goat snp49387-scaffold704-286906 4 86233773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385915 Affx-122971572 AX-123256273 4 31804844 TATATTCAGTTTATAAAATGTATCCTGTGTATCTG[C/T]CTGCCCCCTTAATCTTCTCTATTGCTGTCAAAGGA Y 2 1 2 1 201000 f 74 goat snp49388-scaffold704-328231 4 86193863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415069 Affx-122949471 AX-123285418 4 31865464 TATTGGAAACTTTCTTACATAGAGTTAGTAGCACC[A/G]TCCTTTTCCACGTAAATCAAACATTACTGAACTCT R 2 1 2 1 101000 r 74 goat snp49389-scaffold704-388851 4 86132620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798882 Affx-122950661 AX-385285812 4 31899451 ACAATCACCTTGATAAAGGTTTGGTAGATTATTAA[C/T]AATTATATTAGTTACAATCATCACTCAGAACAAGA Y 2 1 2 1 101000 r 74 goat snp49390-scaffold704-422838 4 86097965 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272266 Affx-1111833422 AX-519546005 4 31916163 GTTCCAGATAGTGGAGAACACTTAGGGAACTGTTT[A/G]CTGGCTGGATCTGTCTCTCTCCTTTTCATTTCCCT R 2 1 2 1 103000 f 74 goat 4_31916163_AF-PAKI 4 31916163 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387968 Affx-122969602 AX-123258326 4 31974506 TTTAAATATTGACAATAATATTTAAAAAGAAAAAA[C/T]GGTACAGATAGCTTGACAGGAATGTGAAGTGAGCT Y 2 1 2 1 103000 r 74 goat snp49391-scaffold704-497893 4 86018173 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405979 Affx-122955527 AX-123276331 4 32023040 TTATATGCTGTTTATTCCTTTTCAAACTGAATGCC[A/G]TAAGAACATTCATTTTATCCATATTTTTTCTAGCC R 2 1 2 1 101000 f 74 goat snp49392-scaffold704-546427 4 85968441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445876 Affx-122925986 AX-123316213 4 32058212 AGGTACCTTAGAGTAATGATATTTTAAAACAGTGG[C/T]CTTATTCTCACAGGTATTAAGTTTTCATTCTTTAA Y 2 1 2 1 201000 r 74 goat snp49393-scaffold704-581599 4 85931997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434762 Affx-122933898 AX-123305103 4 32116288 AAAAATATCACTGTCATGTAAACAAATGGCTACTT[A/C]TGTGTGTGCAATACCAGAGTGGGTAGCCTTTCCTT M 2 1 2 1 201000 f 74 goat snp49394-scaffold704-639675 4 85875708 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781416 Affx-122951209 AX-385268501 4 32154042 CTTATATCTAACTATTCATTAACAGTTCTGGTGCT[A/G]CATTATGTCTCTATGTCAAAAAAAGTATTTACTGC R 2 1 2 1 101000 f 74 goat snp49395-scaffold704-677429 4 85838794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783069 Affx-122942699 AX-385270136 4 32261815 ATCCCGAACGCTGTGTCTACTACATTGCTTAAATT[G/T]CTTAAAATTCAGAAAGCATGCAAAAAACCCGTAAG K 2 1 2 1 201000 r 74 goat snp49397-scaffold704-785202 4 85730667 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399530 Affx-122961149 AX-123269885 4 32300443 ACTGTTATGGTATAGTTTTGATCTTCAAGCTCAAA[C/T]GTCTGTTAAAGCCCAGCTGTGAGAAATGATAGAAA Y 2 1 2 1 101000 r 74 goat snp49398-scaffold704-823830 4 85691768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792037 Affx-122925366 AX-385279025 4 32367344 TACAGTGAGTATTTATTATTCTGATAAGAATCAAC[A/G]TGTGGGTCTCCAGAAATTCTTATGGTAATTTTTTT R 2 1 2 1 101000 r 74 goat snp49399-scaffold704-890731 4 85622669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779409 Affx-122977945 AX-385266512 4 32395918 GATTGTAGTCTGTTGATCTCATTGTCATATAGATA[C/T]GTCTCAAGCAGAATTAGGTTTTGAAATCTGTTGTT Y 2 1 2 1 101000 r 74 goat snp49400-scaffold704-919305 4 85593094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795922 Affx-122930964 AX-385282874 4 32429998 AGATCAGGTTCTGTTTACATGTCATAGCATAGCTC[A/G]CCAGCTATCTAGTGGACTGGCTAACTTGATAGTTT R 2 1 2 1 101000 f 74 goat snp49401-scaffold704-953385 4 85558996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428865 Affx-122938346 AX-123299207 4 32462367 TCAGTTATGATAAGTGTGCAGATGTGTGCATGTGT[A/G]TATGAAAGAGAGAGATGAATGGAGGGAAATTAAAA R 2 1 2 1 303000 r 74 goat snp49402-scaffold704-985754 4 85526698 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779665 Affx-122933482 AX-385266767 4 32515150 TAAACTGTGTTTCCTACCTTAATAACTGAAGAGAA[C/T]GCTGAATTTAATTACAGATTAGTGAATATAAATAC Y 2 1 2 1 101000 f 74 goat snp49403-scaffold704-1038537 4 85473914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429816 Affx-122938186 AX-123300157 4 32566445 CTGAGAAAATGGAAAAAGCGATGCAGGGAAGGTAT[A/G]CGATTTTTAGTGGACTTCATATTACACACCATTTT R 2 1 2 1 101000 f 74 goat snp49404-scaffold704-1089832 4 85415707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377966 Affx-122977624 AX-123248325 4 32604848 CTCCGTTCTAGTTTAGAATGGAGTTTCCCCATTAG[G/T]AGGTTAAAAACCAAGTGTAAAAGGTAAAATTAATT K 2 1 2 1 202000 r 74 goat snp49405-scaffold704-1128235 4 85377003 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413423 Affx-122950698 AX-123283772 4 32654716 ACACAGTTGAATTGAAAAATAGTAAAAGGTAAAAA[C/T]ATAAGCAAATAAACAGAACTAGAATGTGTTGATCA Y 2 1 2 1 201000 f 74 goat snp49406-scaffold704-1178103 4 85326894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417473 Affx-122947179 AX-123287821 4 32689113 TTCAAGTCTCAGAGGAACCAGTGAACCAAGTAAAG[C/T]AGATTATCAAGGCAAGAACTGGCATTATAGAATTA Y 2 1 2 1 101000 f 74 goat snp49407-scaffold704-1212500 4 85292043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449594 Affx-122923215 AX-123319929 4 32718759 ATCATCTGTATTATAGTTAGGTCAAAATAAGAGAC[A/G]CTTTAGAATGATGTTGGAAACTTAAACAAAGGTTT R 2 1 2 1 101000 f 74 goat snp49408-scaffold704-1242146 4 85261912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778048 Affx-122920845 AX-385265164 4 32761998 TGAGCTATAAATTAAGATATGAATTATGGAATGGT[A/G]TTTGAGAGATGACTGGCAGGATCAAGACTAAGAAA R 2 1 2 1 101000 r 74 goat snp49409-scaffold704-1285385 4 85217679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787997 Affx-122929484 AX-385275018 4 32809343 GTTCTTCACAATAAGCTTTTCATTGTGGCACAGAA[C/T]ATATTTGTACTAATAAGCCCGAATACCTTTAGTCC Y 2 1 2 1 201000 f 74 goat snp49410-scaffold704-1332730 4 85170259 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791519 Affx-122968475 AX-385278510 4 32850546 AGGTTGAACTTCAGTTGATGGCTGCCAAGAGTTCT[C/T]ATTTTAATGTCACACCCAAACCCTAATACAATGAC Y 2 1 2 1 101000 f 74 goat snp49411-scaffold704-1373933 4 85128182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785596 Affx-122959821 AX-385272640 4 32922975 CATAATTAATTGTGTTAGGACACAGAAGTTTGAGG[A/G]TTACCTAAGATATCATCATTATGCTAACAAGTACA R 2 1 2 1 101000 f 74 goat snp49413-scaffold704-1446362 4 85053541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396025 Affx-122963477 AX-123266380 4 32959499 GGCTTGAGATGTCATTTTTCTCTGAAACTTGTTCT[C/T]ATGGGACTCAGCTAAAAGGACATAGCTAAGAATGT Y 2 1 2 1 201000 r 74 goat snp49414-scaffold704-1482886 4 85006985 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789249 Affx-122971393 AX-385276260 4 32995172 ATGTTTCCCTGTTATATAGTCAAAGCATTATTATT[A/G]TAAAGTGAACTTTGCTCTCAGCCTGACTCAAACTA R 2 1 2 1 201000 f 74 goat snp49415-scaffold704-1518559 4 84970958 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414015 Affx-122950265 AX-123284364 4 33048497 GAGGTTAGTTATTGAGGATGCTGAGAGATTATATC[G/T]AAAGAAAATTCTGTATTTATTTTCAAGTATTTATT K 2 1 2 1 101000 f 74 goat snp49416-scaffold704-1571884 4 84917507 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427132 Affx-122939651 AX-123297475 4 33079199 AGAGCTGTGTTATTTGGCTTGCTAATGAAGACAGA[A/G]AGGAAACTCTTTCTATTTTACTGTTAAAAGTATTT R 2 1 2 1 101000 f 74 goat snp49417-scaffold704-1602586 4 84886966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776062 Affx-122974749 AX-385263192 4 33109036 GTAAAAAACGTCCTTTCCTAGTTTTCCTATTAGGT[A/G]TTTAGACTTTTATAGGCACATCTCTCAATTTTTTT R 2 1 2 1 101000 f 74 goat snp49418-scaffold704-1632423 4 84855944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433311 Affx-122935188 AX-123303652 4 33138271 CTAGGGTTAATGAGTCCTGTCTATGTTCTTTTCCT[A/G]TATATGAAATGGTAATCTATGGCAGTGACTCTTAA R 2 1 2 1 201000 r 74 goat snp49419-scaffold704-1661658 4 84826707 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797674 Affx-122958221 AX-385284613 4 33192690 TTGAATCCATCTAATTGAATTTCTCCCAAGCCCTT[A/G]CCCTGTCACCTAACAATCAGCCTGCATCCTCCCTG R 2 1 2 1 101000 f 74 goat snp49420-scaffold704-1716077 4 84764297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406009 Affx-122955504 AX-123276361 4 33227687 TCTTTATCAATGGCATCTAAATTCATGAGAAATGA[C/T]AAGAATAGAAATGATTTTAATATATTTTGCTTTGA Y 2 1 2 1 101000 f 74 goat snp49421-scaffold704-1751074 4 84729070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388468 Affx-122969243 AX-123258826 4 33265517 AATTTTTCTCCTTTGAGTTTATAGTAGTATTTGTT[A/G]TTTTAATTTACACATATGTGATTACTTGTGAATTT R 2 1 2 1 201000 r 74 goat snp49422-scaffold704-1788904 4 84690571 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441100 Affx-122928891 AX-123311437 4 33300951 GCCTGCATATAGTACTTTTTAAAAGTTAACACATA[C/T]GCTGTGGAAAGGAAACTATGCTCACCTATTTTGTC Y 2 1 2 1 101000 r 74 goat snp49423-scaffold704-1824338 4 84654397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408704 Affx-122953434 AX-123279055 4 33331743 GATAGATGTTATTTTTAGGTAAATGTTTAGAAGGT[A/G]CAGAATGCAAGTAAGAATTATCAGTGATTTAAGTA R 2 1 2 1 201000 f 74 goat snp49424-scaffold704-1855130 4 84623821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795344 Affx-122935122 AX-385282300 4 33410643 ACAATATTTTCTCTTCCAGTCTTTGAACCATTAAA[C/T]AGCTCTTCAGTTATTTAGGCCATCTTTAATTTTTC Y 2 1 2 1 101000 r 74 goat snp49426-scaffold704-1934030 4 84544071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275048 Affx-1111834562 AX-519548630 4 33455915 CTGGAAGGCACCCTGAACAGTAAGACCTATGACAC[A/C]CTACACAGACGTTTAACAGTAGAGGAGGCTACAGC M 2 1 2 1 201000 r 74 goat GoatD01.041646 4 33455915 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422847 Affx-122943100 AX-123293193 4 33461191 GACTTCCAAGAATAGAAAATGTCTTATGTCAAGTC[G/T]AAAATATTTACATTTTTCTTAAATTTATAGCTGAG K 2 1 2 1 103000 f 74 goat snp49427-scaffold704-1984578 4 84493728 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767808 Affx-122947504 AX-385255032 4 33509657 TATCTTCTGAGTATTAACCTAGAGCTAGCTACCAA[C/T]GCAAACTTCTAATTTAGCACATCTCGATATAGAAA Y 2 1 2 1 101000 f 74 goat snp49428-scaffold704-2033044 4 84445203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442923 Affx-122927625 AX-123313260 4 33544664 TATTAGTATATCAGTTACCTATTGCATAAGAAACT[A/G]TCCCAACCCTTAGTGACTTAAAACAACTATAGCCT R 2 1 2 1 201000 f 74 goat snp49429-scaffold704-2068051 4 84409417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788576 Affx-122919480 AX-385275593 4 33576902 AGTAAACACAAAGAAATCATGGCTTGTTGCAGCCG[C/T]ATATTGATTTCAATGCTCTAGGTTATGTGCAAAAC Y 2 1 2 1 101000 f 74 goat snp49430-scaffold704-2100289 4 84377259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445926 Affx-122925924 AX-123316263 4 33646673 AGAGCACACTATCTAATGGCTCTCATATGTCCACC[A/G]TGCCCACGGACAATTTGTCTTCCGAGTGGAGTGTT R 2 1 2 1 101000 f 74 goat snp49431-scaffold704-2170060 4 84307415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769531 Affx-122957013 AX-385256701 4 33685152 TGTCATTTAATTACACTACCTCAATATTTTCAACT[A/G]TAAAACAAAAAGTTTGAAATAGATGATGTACATAG R 2 1 2 1 303000 r 74 goat snp49432-scaffold704-2208539 4 84268958 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791140 Affx-122946050 AX-385278135 4 33725251 AGAAAAAGTTCAAGATCCTCTTCACCTTAAATATA[C/T]GTGGACAGAATTGAGGTAAACTTTAGAAAGAATTA Y 2 1 2 1 101000 r 74 goat snp49433-scaffold704-2248638 4 84228554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411601 Affx-122951606 AX-123281951 4 33761457 TTGTCTGTCTTAGCTAGTCTATCCTGGTTATTGTA[G/T]AAGTTGGCAATAGAAGTGAGAGGATGTCTTTAAAA K 2 1 2 1 101000 f 74 goat snp49434-scaffold704-2284844 4 84192001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274757 Affx-1111834405 AX-519548343 4 33785474 CATCTGAGCCACCAGGGAAATGAAAAAGGGAGAGA[A/G]GCAAAAGATGACTCCCAAGATCCTGACTGGAGCAC R 2 1 2 1 101000 r 74 goat GoatD01.033795 4 33785474 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443048 Affx-122928144 AX-123313385 4 33792207 GCAGATGTCTATAGACTGACTCTCCCATTGCTACC[A/G]TGTTTGGCCTGTGAGGCAGCTCGGTGATCTGTCAG R 2 1 2 1 101000 f 74 goat snp49435-scaffold704-2315594 4 84160491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435426 Affx-122933488 AX-123305766 4 33855827 ATAAATATCAGTTTATTTGAAAATGCTATCTGGCT[A/G]TTTCAAAGTGGGAGCCCCAAGACCTTTTTTTTTTT R 2 1 2 1 103000 r 74 goat snp49437-scaffold704-2379214 4 84097096 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783581 Affx-122942580 AX-385270641 4 33940541 GTTGGCTGCTATATTAATAACTACTGATATACTTA[C/T]ACAGATTGGCCAATAGATAAATGATACATGGAAAT Y 2 1 2 1 201000 r 74 goat snp49439-scaffold704-2463928 4 84011886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430337 Affx-122938215 AX-123300678 4 33984008 CATGGTTGGTCTGGTTACAGTTTAATGTATATGCT[A/G]TTTTTTAATGAGGATTTTAAAGAAAATATTTGTTC R 2 1 2 1 103000 f 74 goat snp49440-scaffold704-2507395 4 83968387 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409992 Affx-122953275 AX-123280342 4 34033515 GATTTTTTTAAAGAAGTAATTTCTTCTCACTGAGC[A/G]CTTAGAAATGATAAAGCAACAGCTATATTTGGGAA R 2 1 2 1 101000 r 74 goat snp49441-scaffold704-2556902 4 83919057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379174 Affx-122976705 AX-123249533 4 34091284 TCTCAGTCCTTCCTATCTTAGCATCCTTTTCTGGG[C/T]CACACTCCTCTTACCTTGTCCTAGCACCCTGGAGT Y 2 1 2 1 101000 f 74 goat snp49442-scaffold704-2614671 4 83861101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441999 Affx-122928427 AX-123312336 4 34123201 AGAAATTGATAAGCATAGTTTCAGGTACCTTCCAC[C/T]TTTCAAGGTGACTAATTTAAAAATGCTTGAGAAGC Y 2 1 2 1 101000 f 74 goat snp49443-scaffold704-2646588 4 83828133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772345 Affx-122920886 AX-385259498 4 34165484 GTATAAAAAGGACAAGGAAGGGTCAAAGTAACTAG[C/T]ACCTTTTATTTTCGCTTACTGTTTGTGCTCATCTT Y 2 1 2 1 101000 f 74 goat snp49444-scaffold704-2688871 4 83785029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452362 Affx-122920633 AX-123322695 4 34251505 TTTATCCGAATGACATCTTAGCCAGATGTTGAGCT[G/T]TTTGAAAGGAAAAAATCATGTCCTATGTATCTTTA K 2 1 2 1 101000 f 74 goat snp49446-scaffold704-2774892 4 83698823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452044 Affx-122920890 AX-123322377 4 34315774 TGATTAGCTTCCTTTCTAGTTTGATCTGGGTTGCA[A/G]ATTGCTCAGACCCATTCACTATTGTAAGCATTAAA R 2 1 2 1 201000 r 74 goat snp49448-scaffold704-2839161 4 83633153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418781 Affx-122946186 AX-123289129 4 34350867 TTTCTATTCTCACAACAGTTTTATGAAGTAGAAAT[A/G]TCATGATCCCCCAAGGAGTACAGGGGGCTTTGACT R 2 1 2 1 101000 f 74 goat snp49449-scaffold704-2874254 4 83597893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404881 Affx-122956474 AX-123275233 4 34385049 AACTAATTTTGATACAGTGTAAAATCTGAATGATA[C/T]ATGATAACTAAATAAGGTGTTTCCAAGGGCCAAAG Y 2 1 2 1 101000 r 74 goat snp49450-scaffold704-2908436 4 83564236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431854 Affx-122936077 AX-123302195 4 34417236 AAAACCTTACATAAGATAAGGAAAAACAGAGATAC[A/G]TGGCAAAGGGGTATTTGTATCCTTTTCTCCTGCAA R 2 1 2 1 201000 f 74 goat snp49451-scaffold704-2940623 4 83531942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423618 Affx-122942375 AX-123293964 4 34475790 TAACATAAAATGAACACATTAATCTGTTTTCCTAG[C/T]GATGGAACTTAGAACTTATCCTGAAAAAATTAAGA Y 2 1 2 1 101000 r 74 goat snp49452-scaffold704-2999177 4 83471885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272107 Affx-1111833423 AX-519545865 4 34543491 CTCAAATTGGTTTTTAACCTGAATTTGTCTGAATT[A/G]TATAGATAACCTAGTATTGCGAGGCGGAACTGAAA R 2 1 2 1 101000 r 74 goat 4_34543491_AF-PAKI 4 34543491 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436620 Affx-122932504 AX-123306958 4 34553691 AATGCAGAGGGCACATCCTTCTTCATTAATTCTTA[A/C]ATGTCTTTGGTTGCAAAGAGGATGTAATGGCTGGA M 2 1 2 1 201000 f 74 goat snp49454-scaffold704-3077078 4 83393354 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424958 Affx-122941927 AX-123295304 4 34584887 AACAGCAGCTATTTACCCCCAATTGAACCTAATGA[C/T]AAAAATTATAAAAGCATAGCTTTGGAAAGGCCCTT Y 2 1 2 1 202000 r 74 goat snp49455-scaffold704-3108274 4 83362371 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411232 Affx-122952344 AX-123281582 4 34627174 TTCCTCTAAAAGTAAGGTTGTTAAGAATGAGAAAT[C/T]GACTTGTCTACTATCAAAAATCTATAAAGTGCTGA Y 2 1 2 1 101000 f 74 goat snp49456-scaffold704-3150561 4 83320160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779535 Affx-122922478 AX-385266638 4 34666328 AAGGGGCAAAATTCAGTCTAAAGCAATGTGTAATT[A/C]TGCATAAAATAGAAACTAAATACCGGATATTTTCA M 2 1 2 1 201000 r 74 goat snp49457-scaffold704-3189715 4 83280697 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375672 Affx-122978671 AX-123246031 4 34743305 CTAACTAATTAAAGAAGTAGGAGGTCAGATCCTCA[C/T]GAAGCAGTGAGTTCTGCCATGTGGGCTGTTTCCCA Y 2 1 2 1 101000 f 74 goat snp49458-scaffold704-3266692 4 83203377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453834 Affx-122919548 AX-123324167 4 34791632 CAGAATGATATGGGAGGACAGAGGATACTGGTGAA[C/T]AAGTGGAGCTCTTTCCTGAAAGCTAGACTGGTTTG Y 2 1 2 1 101000 r 74 goat snp49459-scaffold704-3315019 4 83154754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445756 Affx-122926078 AX-123316093 4 34830716 AAGGGAATGGACTTTGAAGAGTTAAATGGTACTCA[C/T]GGACAGAGGAGCCTGGTGGGCTATAGTCCATGGGG Y 2 1 2 1 101000 f 74 goat snp49460-scaffold704-3354103 4 83115872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785492 Affx-122961058 AX-385272537 4 34860149 GGTTGCCACCTAGACTTATTTGTTATTCTGTGAAA[C/T]GTATAAAACATATCTAGCTTGATTTCAAGCTATGA Y 2 1 2 1 101000 f 74 goat snp49461-scaffold704-3383536 4 83086778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420841 Affx-122944655 AX-123291188 4 34899804 AGGGTATATTAAATTTAAATATGAATATGATATTT[A/G]CAAAATCCTCTGATGATAAATGCAAGACTCTCCAA R 2 1 2 1 103000 r 74 goat snp49462-scaffold704-3423191 4 83046541 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444139 Affx-122926799 AX-123314476 4 34928305 CAAACACAAAACATTGTGAACATGATATTACCATA[A/C]GCTAACCTTTATATCACTAAAGTTATTTTTATTAT M 2 1 2 1 101000 f 74 goat snp49463-scaffold704-3451692 4 83018019 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411422 Affx-122951835 AX-123281772 4 34958431 GCCCCCATACACAGTGCAATGCAAGTCTGACGGCA[C/T]TTGTGCCTGCAATGTGGTTTGCATCACCTCAAATT Y 2 1 2 1 201000 f 74 goat snp49464-scaffold704-3481818 4 82987664 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787795 Affx-122930451 AX-385274818 4 35018104 TCCAGTTAGACTTTACATATTGCTATTGAAATTTC[C/T]CTCTTCTTTCTCTCCTTGTATACCGACAAGGGCAA Y 2 1 2 1 101000 r 74 goat snp49465-scaffold704-3541491 4 82926525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435218 Affx-122933624 AX-123305558 4 35062720 TAACTCTACCAATAATCAGTTTTTAAAGAACTCCA[C/T]GACAGAGATAAATACACATTCTGTGTAAAAATTTC Y 2 1 2 1 201000 f 74 goat snp49466-scaffold704-3586107 4 82881691 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444329 Affx-122926731 AX-123314666 4 35121637 TAATTCATAAGTAAGGAACCAGGAAGCTATGCTCC[A/G]TGATGAAATGGTTGAGTCGAACACAACTCCTGAAT R 2 1 2 1 101000 f 74 goat snp49467-scaffold704-3645024 4 82823670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425595 Affx-122940928 AX-123295941 4 35144237 ATGCCGTCTATTCATAAGATTCATAAAAGAAAACT[A/G]TATATAACTTGTTCCTTAACATGTTGCTGGTTTGC R 2 1 2 1 201000 r 74 goat snp31934-scaffold357-289602 4 82801189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400104 Affx-122960731 AX-123270459 4 35186024 AACAAAGGAAACAAGGATCAAACCAACAAAACAGC[A/G]TTAAAGAGCTATCAATTCACTGGTCCATGGCTTAC R 2 1 2 1 101000 r 74 goat snp31933-scaffold357-247815 4 82758576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453477 Affx-122919840 AX-123323810 4 35217169 GGTGCGCTGGCTGGTAAATCTTCCATCTCCATCCG[C/T]GGTTGTTTCTTTTCTTCCACTGCTTCCGGAGGCAC Y 2 1 2 1 201000 f 74 goat snp31932-scaffold357-216670 4 82727473 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395006 Affx-122964232 AX-123265361 4 35247859 GCTTCCTTCAAATTAAATTAAATTAACAAAATTTC[C/T]TTGGAAAGTAGGACCATGGTCCTTCTGTACAAACT Y 2 1 2 1 103000 r 74 goat snp31931-scaffold357-185980 4 82696647 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780688 Affx-122923168 AX-385267778 4 35276755 TGTGCTGGGGTGACTGAAGGTTTTCAGAACCGTTG[C/T]ACAGTTGTTGATCAGCACCTATATCTTTGAAGTTT Y 2 1 2 1 101000 f 74 goat snp31930-scaffold357-157084 4 82668154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379010 Affx-122976374 AX-123249369 4 35335970 AAAAAGGAAACCAGAATCTTCAATAACCATCCCCT[A/G]ATTTTTTTAACTATACCTCCAATTGTTGATTACTT R 2 1 2 1 201000 r 74 goat snp31928-scaffold357-97869 4 82608605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453254 Affx-122920407 AX-123323587 4 35371691 TGTTATGATGAGTTGTATAGATCTTTTGGTGAGAA[A/G]GGAAATTTTGAATTGAATAACTTAAAATAATATTG R 2 1 2 1 101000 f 74 goat snp31927-scaffold357-62148 4 82572963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442838 Affx-122927694 AX-123313175 4 35402527 TAAGTACAGTATAGATGAAAATTTAAAAATAGGAA[C/T]GGTATGAGTTACCTGAAGAGAATGTCCAGCAGGAC Y 2 1 2 1 101000 r 74 goat snp31926-scaffold357-31312 4 82542219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420369 Affx-122944949 AX-123290716 4 35445234 TGATAAAAGTAGGAAATGAAAGAAGTGGAAAGAGA[C/T]GTAAATACAAGTTAAATGCTGGGTAACTAGGGTTA Y 2 1 2 1 101000 r 74 goat snp31520-scaffold350-11088 4 82495191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800218 Affx-122955206 AX-385287141 4 35499259 GCTGCACACCATGGAAAACTCAGAACTGGGCATTG[C/T]GAATACTAAATTGTAGTCATTAGTATACAAAGGAA Y 2 1 2 1 102000 f 74 goat snp31521-scaffold350-65113 4 82440854 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445764 Affx-122926071 AX-123316101 4 35539531 CTAAACCAGTGTTAGCCTGTACTAATGGGAAACAA[C/T]GGTCAAGGAATCCTAACATATACCAAACACAATCT Y 2 1 2 1 101000 f 74 goat snp31522-scaffold350-105385 4 82400049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453158 Affx-122920479 AX-123323491 4 35597659 TTGACTGAATAACTGCAGAACACGTGCTGAAAAAT[A/G]CAGCTAAGTGATCTCAAAACGCAAGTCAGGTAATG R 2 1 2 1 101000 r 74 goat snp31523-scaffold350-163513 4 82341679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795476 Affx-122963112 AX-385282431 4 35652486 AGTGTTGGGGAAATCATTGATTTCCTTAGCAACTG[C/T]AATTTCAATGAGATTATTGATAGGAAGAAGCCAGA Y 2 1 2 1 101000 f 74 goat snp31524-scaffold350-218340 4 82286598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425209 Affx-122941025 AX-123295555 4 35717882 GTTTCAATAGAAAGTGCAACTTATTTCATCTGAAT[A/C]TTTTAGCCATTGTCACTGGAATTGAAGAGCCATAG M 2 1 2 1 101000 r 74 goat snp31525-scaffold350-283736 4 82227122 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769486 Affx-122972955 AX-385256656 4 35762203 TTTCTGTCTTTTCTTGCAGTCCTTCTGAGTAATAT[A/C]TTTCTCTATACACTTATTCCTGAACAGTTGTCTCA M 2 1 2 1 101000 f 74 goat snp31526-scaffold350-328057 4 82182448 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407767 Affx-122954971 AX-123278118 4 35794926 AGAATTACTGCCCTTTGCTTTTTTTGTAGGCTGTC[A/G]TTTTATTGTATTTGAATCTTTCACCACTGAGCTTG R 2 1 2 1 201000 r 74 goat snp31527-scaffold350-360780 4 82149528 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802344 Affx-122930973 AX-385289248 4 35850307 TGTGAATATTTTCCCTTGTGATCAATGAAATCTTC[A/G]CTTATATCCTAGCCATTATTATTTTCTCATTCCAG R 2 1 2 1 101000 f 74 goat snp31528-scaffold350-416161 4 82094163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476186 Affx-1251763691 AX-586011612 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 539476441 Affx-1251763691 AX-586011842 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 560378492 Affx-1251763691 AX-605230907 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165472 Affx-1251763691 AX-606940883 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165577 Affx-1251763691 AX-606940988 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165876 Affx-1251763691 AX-606941285 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165880 Affx-1251763691 AX-606941289 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562166399 Affx-1251763691 AX-606941807 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 38410792 Affx-122952663 AX-123281142 4 35910395 ATCCTTAGAATTTGTGTTGTATAGAATGAACTGAA[C/T]GATGCTGAAAGACACAGATTGGTGAAGACCAAGCT Y 2 1 2 1 201000 f 74 goat snp31529-scaffold350-476249 4 82035959 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405646 Affx-122956582 AX-123275998 4 35939396 AAAAGAAGCCAAAAGGACCTATTACAAATGGGATT[C/T]GGGGATGTTGTTGAATGAAATCCAAATGTATTCAT Y 2 1 2 1 201000 f 74 goat snp31530-scaffold350-505250 4 82007699 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430830 Affx-122937442 AX-123301171 4 35990480 ATGGTCAAAGACATTATAAAGAAAAAGAAAGTAGC[A/G]CTTTTAAAGTAGGTGACTGCAAAATAATTCTCCAC R 2 1 2 1 103000 r 74 goat snp31531-scaffold350-556334 4 81956310 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789376 Affx-122920253 AX-385276386 4 36030853 GTGCTGTTTTTCTTGTAGTCTTTAGCAAATTCTAA[A/G]AAGTACTGGGCGTTTTTCCATTAACCTTAAATAGT R 2 1 2 1 101000 r 74 goat snp31532-scaffold350-596707 4 81916319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804599 Affx-986696768 AX-385291134 4 36042918 GAAATTATGGCATTTAAAATACATAGTGTAGGGAA[A/T]ATTACAATTACTCCTGGGTATGAATATAAGCTCTG W 4 1 2 1 600010 r 74 goat 4_36042918 4 36042918 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320804301 Affx-986696770 AX-385290918 4 36042973 ATGAATATAAGCTCTGCCTATTAAAATTCATGACA[C/T]TGAAAGGGATTTCCTTCCCCTTTTTTAAACTTCAG Y 2 1 2 1 600010 f 74 goat 4_36042973 4 36042973 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 38443084 Affx-122928116 AX-123313421 4 36104166 GCCAGAGTCACTCTGACAAAGTTTTTTCTTGTCTG[C/T]GCAGTAAATGTTGTCCTGTGTATGTTACAAAGTGA Y 2 1 2 1 201000 r 74 goat snp31534-scaffold350-670020 4 81843329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425969 Affx-122941166 AX-123296315 4 36133138 GGAAATAAATTTATAATGAAAATGAAAGATTAATC[A/G]CTAGTACATACTGAGAATCTATTGAAAAGACTTTA R 2 1 2 1 101000 r 74 goat snp31535-scaffold350-698992 4 81814167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436083 Affx-122932688 AX-123306422 4 36184470 AGGCTAATCCTTCTCACTGTTGTTCAGTGCATTCC[A/G]TCGTTCCAGTTATGTTCCACCCCGCCTCCAGATGC R 2 1 2 1 101000 f 74 goat snp31536-scaffold350-750324 4 81762161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414289 Affx-122949595 AX-123284638 4 36216955 GACTTCGTAACTGGGAAGGGTTTATTAATCAGTGA[G/T]TTATATGAAAGTTATAAAATTCCATACATTAAAGA K 2 1 2 1 102000 f 74 goat snp31537-scaffold350-782809 4 81729813 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392008 Affx-122966490 AX-123262365 4 36253783 TTTTAAAAATGATACATTATTAAATATTTGATTTA[G/T]CCAGTTTCCTGGTTCATTAAGATGACCACAGAGTG K 2 1 2 1 101000 r 74 goat snp31538-scaffold350-819637 4 81692957 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453357 Affx-122919946 AX-123323690 4 36322323 CCCATCTCTTTAAAAGACTCACACATAAAAATAAA[C/T]GAGAATATATTAAAAGTTTCTAAAGACACTTTTTT Y 2 1 2 1 101000 f 74 goat snp31539-scaffold350-888177 4 81624409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378023 Affx-122977583 AX-123248382 4 36356997 CCATATGTGGTGCTCCAGGTTTTAGGATTCTTACC[C/T]AGAGACAATTCTCCAAATCAAATACCTAAGAAAGC Y 2 1 2 1 101000 f 74 goat snp31540-scaffold350-922851 4 81589129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416577 Affx-122947658 AX-123286925 4 36398208 TTCCCAACCACATGGCATAACCATATAGATTAGCT[A/G]CAGGGAATCTAGCCAGAGTATTTTTTTAAAACCTA R 2 1 2 1 101000 f 74 goat snp31541-scaffold350-964062 4 81550193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396719 Affx-122962807 AX-123267074 4 36447101 TAGTTCAATGGTGAGTTCAGTGGTAAATCCACAAA[C/T]ACAAAATAACAAACTAGGAACGGGGGCCCAATTCT Y 2 1 2 1 201000 f 74 goat snp31542-scaffold350-1012955 4 81500074 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406718 Affx-122955757 AX-123277069 4 36484917 ACTCATTCTGCTCCTTCATCATCTAATTACGATCT[A/G]TCCCCAAGAGTTATCATACCTTCATCTTTGCCTCC R 2 1 2 1 101000 r 74 goat snp31543-scaffold350-1050771 4 81462199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383645 Affx-122972529 AX-123254003 4 36530756 TCCCTAAATTCATACATTTTACTAATATACTAGTG[C/T]CCAACATCCCAGGTGTGGAATGCTTAGGGTTTATA Y 2 1 2 1 201000 f 74 goat snp31544-scaffold350-1096610 4 81415710 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386855 Affx-122970072 AX-123257213 4 36592696 GCCAGCAGGCTTGGCATATAGAGGGGCTGATTCCT[A/G]GTTCATAGATGGCTAACTCTTCCTTGTGTCTTCAT R 2 1 2 1 101000 r 74 goat snp31545-scaffold350-1158550 4 81353677 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785998 Affx-122968234 AX-385273034 4 36632032 TTTTGAGTTTTAGGAAAATGCCCTATTTACGGAGC[A/G]TAAATTTGTATTGAAGTACATATGTTATGAATATA R 2 1 2 1 201000 r 74 goat snp31546-scaffold350-1197886 4 81313502 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379452 Affx-122976092 AX-123249810 4 36690519 TTATGGCACATCACCGCAAGTAGTTCAGTCCCATG[C/T]GGTGCCCCAGGCAATACTAGCTGATAGCTGAAACC Y 2 1 2 1 101000 f 74 goat snp31547-scaffold350-1256373 4 81254161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429456 Affx-122938489 AX-123299798 4 36723993 GTCTTTTTTAACAGTGTTTAGTAAATATAAAAATG[C/T]AGGGTCATAATACAATTTATTAGTTCATTAAGCAC Y 2 1 2 1 101000 r 74 goat snp31548-scaffold350-1289847 4 81221306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776916 Affx-122938162 AX-385264040 4 36767099 CTCTGGAAATTCCCTTGCTCATTTGGAGCTCAGGA[C/T]ATTTGGCTCCTTAGCAAGTATACTAATCACTCTCC Y 2 1 2 1 101000 f 74 goat snp31549-scaffold350-1332953 4 81178463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397801 Affx-122962496 AX-123268156 4 36802568 TATTTTAATATTTATTTTTTAATCCTCAAACATGT[A/G]TAAAGTGTTTCAGATTCTTTCTAAGCCACACAAAA R 2 1 2 1 101000 r 74 goat snp31550-scaffold350-1368422 4 81142808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780269 Affx-122963800 AX-385267364 4 36834548 AGTAGATACCATTAACTCTAAATTTATCTTAAATC[A/G]TTGAATAGTGATGTTCACCAGGGTACTGGTGATAG R 2 1 2 1 201000 f 74 goat snp31551-scaffold350-1400402 4 81111247 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427496 Affx-122940001 AX-123297839 4 36930030 CTCCTGCATTGACAGTCGGCTTCTTCACCACTAGC[G/T]CCACCTGGGAAATCCCTGCATCACAGTAAAAGTGC K 2 1 2 1 201000 f 74 goat snp31553-scaffold350-1495884 4 81015149 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417095 Affx-122947486 AX-123287443 4 36958798 ATGTGTAAAATAATTATATTTAAACAGTTTGAATT[A/G]AAGAACAATACCTAAAATGTCCAGGTATATTATAT R 2 1 2 1 101000 r 74 goat snp31554-scaffold350-1524652 4 80986381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792464 Affx-122948998 AX-385279445 4 36997125 GCACAATAGTTTGAATAGCTATTTTCATATACAAA[C/T]GTTTTCAAATTATTGCAAGTAATGTGAAACTCCCT Y 2 1 2 1 101000 r 74 goat snp31555-scaffold350-1562979 4 80948222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390884 Affx-122967115 AX-123261241 4 37027746 ACGTGCCTTTGACGACTATTCAACCTCTAGTTACC[A/G]TCAACAGTTCTAATTTATATTTCACCCACAAAGGC R 2 1 2 1 101000 f 74 goat snp31556-scaffold350-1593600 4 80917506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777260 Affx-122934929 AX-385264382 4 37084088 TGCAAGGCAGCATAAAGAACACTGGGACAAAATTC[A/G]CTTTCAATTCCCAAACTGTCATTTCCAGTACCCAA R 2 1 2 1 101000 f 74 goat snp31557-scaffold350-1649942 4 80860809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395892 Affx-122963617 AX-123266247 4 37188218 CCCATGAACTGCTATACATCCAAAGACCATCACAG[C/T]GGGGTAAAAGGAATCCAGTATATTTCATTAGTATA Y 2 1 2 1 101000 f 74 goat snp31559-scaffold350-1754072 4 80755115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785754 Affx-122922129 AX-385272794 4 37238147 CCACTAGAACTAATCATAAACCCAAAATTTATATA[C/T]AAGCTAACAATAGAGATATATGGCATGTGAAAGTA Y 2 1 2 1 101000 r 74 goat snp31560-scaffold350-1804001 4 80705407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413957 Affx-122950306 AX-123284306 4 37272651 TTTCACATCTGAGATGCAGATGTCACGATAATGAT[A/G]TTCTCTGTGACTTTTACTGAAAACACTGCTATATT R 2 1 2 1 101000 f 74 goat snp31561-scaffold350-1838505 4 80670888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776439 Affx-122927178 AX-385263566 4 37354466 GTCAAGAGAGCTGTGTAATAGGTGGAGGAACAATA[G/T]AGTAAAAACAAGTGATAAGTTAAAATGAGACTTAT K 2 1 2 1 201000 r 74 goat snp31563-scaffold350-1920320 4 80588062 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412630 Affx-122951268 AX-123282979 4 37408503 CGCACACGCTTGGCCTGGTTCTTAGACCAACAGTC[A/G]CCCCTCCTTGCCTGAATAAAGGTAACCTGTCTCCA R 2 1 2 1 201000 f 74 goat snp31564-scaffold350-1974357 4 80533894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406805 Affx-122955692 AX-123277156 4 37444987 AAATGTTATCTAATTTATGGTTGCAGTCACTGTCC[A/G]CAGTGATTTTGAAGCCCAGAAGATAAAACCTGTCA R 2 1 2 1 103000 f 74 goat snp31565-scaffold350-2010841 4 80497173 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272268 Affx-1111833424 AX-519546007 4 37453124 TTTCTGTTTTTCCTCTTTTAGATTGTGTAGTTGTC[A/G]CAGAGAATTAAGAACATACAATTTTATGTTGTAAA R 2 1 2 1 101000 f 74 goat 4_37453124_AF-PAKI 4 37453124 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320785687 Affx-122953049 AX-385272728 4 37487049 AATAAAGCATTGTCTTGGACAAAATTACCCTACAA[C/T]GTCTCCAAATGGTTGCCTAGTCTTACTCTAGTGAC Y 2 1 2 1 101000 r 74 goat snp31566-scaffold350-2052903 4 80455037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405173 Affx-122956934 AX-123275525 4 37515285 TTTCATATTGGAAACCAGTGAGTATTCCAAAAACT[A/G]TCAACCATGTGATTTCAAGCCAGACATTGCATTTT R 2 1 2 1 101000 r 74 goat snp58422-scaffold950-12337 4 80424657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780939 Affx-122937550 AX-385268026 4 37593101 GGTGTTCTTGCAGGGAGAGTGAAATTGACCTAGAC[A/G]TGCAGCTAAGTCTGAAGACTGTGGTTTAAAACTTA R 2 1 2 1 101000 f 74 goat snp58424-scaffold950-90153 4 80346808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386880 Affx-122970055 AX-123257238 4 37644410 CCAGGTTGAAAAATATATGTAATTCCTTTTTGTCC[A/G]TCTAAATAAATATCTTTTCCCTTCCCCTTGTATGT R 2 1 2 1 101000 r 74 goat snp58425-scaffold950-141462 4 80295102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450278 Affx-122922171 AX-123320613 4 37678372 ATGTAAATGCAAAGTGATTGGAACTCTTAAACACT[A/G]TAACTTAGGAATTCCTGACTGGGTGAAAATTTCCT R 2 1 2 1 101000 r 74 goat snp58426-scaffold950-175424 4 80260491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400410 Affx-122959989 AX-123270765 4 37708551 TTTTTCCTCTGAAGAAAACCACCCCCCTTGGTCCC[A/G]CAGTGCCTCATAAGACTCTTCACCCAATGGCAGCT R 2 1 2 1 201000 r 74 goat snp58427-scaffold950-205603 4 80230550 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801737 Affx-122958588 AX-385288645 4 37740118 CAAAATTATAAATTCACACCCTAAAGTACATGCTC[A/G]TACTTTAAGAGAGTGATGACTTGATATTCACAAAG R 2 1 2 1 201000 r 74 goat snp58428-scaffold950-237170 4 80198934 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783140 Affx-122934628 AX-385270207 4 37769154 AATTGTGTATTTCTCAGGGCTATTATGTTGCCATG[C/T]GTGAGCGTTACTTAGATAAAGTGCTATTGAAGAAT Y 2 1 2 1 101000 f 74 goat snp58429-scaffold950-266206 4 80169911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773053 Affx-122936499 AX-385260197 4 37812407 TTTACTTTATGCACTTCTGTTCAATGAATTCATTC[A/G]CTTCCATGGCTTTAATTAGAGCTCTGACTCCATCT R 2 1 2 1 101000 r 74 goat snp58430-scaffold950-309459 4 80126106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785799 Affx-122975646 AX-385272838 4 37858698 ATGTAGGGTACACATTGTGATTTTGTACTGTGATT[A/G]TAGCATGTTTTATGCTATAATCCTTTATATTAATG R 2 1 2 1 101000 f 74 goat snp58431-scaffold950-355750 4 80079256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439221 Affx-122931024 AX-123309558 4 37894661 TATTCCTAATATTACAATAAAGTTAGTGTTTTTGG[C/T]ACCTCTGCCCCTCCTTTTCTTACTTTGATAGTTAG Y 2 1 2 1 102000 r 74 goat snp58432-scaffold950-391713 4 80042867 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783843 Affx-122959277 AX-385270899 4 37946977 CTCCAGCTCTAAATATGGTCAGTGTATAGTTCAGA[C/T]GTTGATAATGGGTTATGATAGACAGATTAATACAT Y 2 1 2 1 101000 f 74 goat snp58433-scaffold950-444029 4 79989673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403106 Affx-122958131 AX-123273459 4 37983778 TTTTAAAATCTAATAAACATATTTTACACAAGTAG[A/G]AATGATTATTTGCAAAACACGTGAGACTACCATAA R 2 1 2 1 101000 r 74 goat snp58434-scaffold950-480830 4 79953041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773767 Affx-122978663 AX-385260907 4 38017256 ACATATAGGTAATTCTGTTACTATATGCAGAAAAT[C/T]ATAATGAATAGTCATTAATTAAGTGGAGTGGTTAT Y 2 1 2 1 101000 r 74 goat snp58435-scaffold950-514308 4 79910740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796604 Affx-122950673 AX-385283550 4 38046146 ATAGATAAGTATTATGGCTATTCTAAATGTAAAGG[A/C]GTTTACTGTAAATGATGAGGGTTTTGAAGCTGAAG M 2 1 2 1 101000 r 74 goat snp58436-scaffold950-543198 4 79881872 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433589 Affx-122934962 AX-123303930 4 38091052 AACTTGCCTTTAGGAGTGCGTCTGCTGCAGAACGG[A/C]TCACAGCAGCTCTCTGGGATTTGGTCATGTCTAAA M 2 1 2 1 101000 r 74 goat snp58437-scaffold950-588104 4 79836857 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768818 Affx-122976049 AX-385255995 4 38123063 TAGAAGGTTAATAGGAGTGAATGCTTATTGCAATG[C/T]ATCTTCTTTTGTTTGGGTCATCATACAAAGTTTCC Y 2 1 2 1 101000 f 74 goat snp58438-scaffold950-620115 4 79804879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449721 Affx-122922526 AX-123320056 4 38162721 AGCTGTAATGTAGATGTGTTATTTTTATTCAAACA[C/T]GTCAACACAACATAAAACACATAGTAGGTATCTAT Y 2 1 2 1 201000 f 74 goat snp58439-scaffold950-659773 4 79764951 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378101 Affx-122977152 AX-123248460 4 38254272 ATATGCAGTTCTTCTGATGGACTCCCAACAGAACA[C/T]ACTAGATGTACTTAAAAAATAAAACAGTTAAGGTT Y 2 1 2 1 103000 f 74 goat snp58441-scaffold950-751324 4 79677329 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780838 Affx-122968870 AX-385267926 4 38292409 AGTAAGTAATGTATACAAAGCACACAGCATAGTGC[A/G]CGGGGAATATCCAACAGATAATGGCTAGCTGTTAT R 2 1 2 1 102000 r 74 goat snp58442-scaffold950-789461 4 79639197 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422041 Affx-122943616 AX-123292388 4 38335478 AGTATGAGCACTGCATTTAGTATTTTAGTAAGATA[C/T]CTAATTCTTTTATTAATAAAATGGACTGACTTCAG Y 2 1 2 1 101000 f 74 goat snp58443-scaffold950-832530 4 79595353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426736 Affx-122939872 AX-123297082 4 38396504 GGAAAGGTGAGGGAGGAAGAGAAGAAAAAGAAGAA[G/T]AAGCAGGAGAATGAAAAAGTAGAGAAACTAATATA K 2 1 2 1 303000 r 74 goat snp58444-scaffold950-893556 4 79534172 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770709 Affx-122974573 AX-385257873 4 38453077 CTCTGGGCCACAAGAAGGGACAAAGAGCTATTGCT[A/G]TAATGCAGGTTAGATGAGTGAGAAAAAAACATAAT R 2 1 2 1 101000 f 74 goat snp58445-scaffold950-950129 4 79473106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449502 Affx-122922624 AX-123319837 4 38483738 CATGAAATATAATCCTTTGATATTCTGTTACCTTC[A/G]TGATGTTCAGACCCATTATCATTCACATAGGGGCT R 2 1 2 1 101000 r 74 goat snp58446-scaffold950-980790 4 79442519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448655 Affx-122923346 AX-123318991 4 38521484 TTATTTTAAAATAATCTCAACACAGATAACAAAAC[G/T]AAATAGCTAATTAAAAGTAAACAAATCATGAACAA K 2 1 2 1 101000 f 74 goat snp58447-scaffold950-1018536 4 79405041 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435116 Affx-122933696 AX-123305456 4 38559452 ATACTTGTCCTTTTCCCCATCTCCTTCCTTCTTCC[A/G]CTAGAGGTAAGGGAAGCTTTCCTCTTTAGCTCTTT R 2 1 2 1 101000 r 74 goat snp58448-scaffold950-1056504 4 79365758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450389 Affx-122922082 AX-123320724 4 38594941 TTTGGTAAAGAATGACTGACTGAGGGAAGGAGTGG[C/T]GGAAGATGACATTAGTTTCTAACGTAATAGAACTG Y 2 1 2 1 201000 r 74 goat snp58449-scaffold950-1091993 4 79329692 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410054 Affx-122953229 AX-123280404 4 38633665 TTTATGTGAAAGTTAAAGAAAGAAATCACAGGAAA[C/T]GATAATGTGAAATCTGGTCCATAGAAGTCATTTTC Y 2 1 2 1 101000 r 74 goat snp58450-scaffold950-1130717 4 79290789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779796 Affx-122975865 AX-385266896 4 38690681 ACAGAAGCTTACTGAAAATAGGCTTGTGCAATAGT[A/G]TTTATTTTATTATAACTGTTACAAAAACAAAAGCA R 2 1 2 1 202000 r 74 goat snp58451-scaffold950-1187733 4 79234297 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769659 Affx-122976675 AX-385256829 4 38744179 TGACCTCAGATGACGCATTTTTGTTGACTGATTCT[A/C]TTACTGATGAAAACATCAAGAAGGCTCTTAACTGG M 2 1 2 1 101000 f 74 goat snp58452-scaffold950-1241231 4 79179764 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772260 Affx-122978362 AX-385259415 4 38779015 ATATAAAGAAGCAAATTGTAGATAACGTAGTTAGA[C/T]GGAAGGATCAGTGCCTTGGAATCATTCAGGCTGCA Y 2 1 2 1 101000 r 74 goat snp58453-scaffold950-1276067 4 79144583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781577 Affx-122979095 AX-385268661 4 38824695 AAAAAAAAAAAAGTAACTATAGGGTTTCCCAAAGT[A/G]TGTTTTGCATTCCCATGATTTCAGGTAAAATGACT R 2 1 2 1 101000 r 74 goat snp58454-scaffold950-1321747 4 79098662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789765 Affx-122975064 AX-385276773 4 38866860 AACACGGCCAAACTATTAGAGGTCCATTTCAAGTG[A/G]TAAATTTTCCTCGCACTGTTTGAAGGGAGAAAAGG R 2 1 2 1 201000 f 74 goat snp58455-scaffold950-1363912 4 79056354 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423705 Affx-122942887 AX-123294051 4 38912730 TATCTGTATCATTTTCTGTTTTTTTGTTGCCTGTC[C/T]ACTTCCCAAGCCTGACTAGTCATGAGATTTGGGAC Y 2 1 2 1 101000 r 74 goat snp58456-scaffold950-1409782 4 79010351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797664 Affx-122931230 AX-385284603 4 38954717 CCTGTAACCAACAGAGGAAGAGTTGTTAAGCAGCT[A/G]CTATTCCCAGGACATGGTGTGAAGCAACAGACCAA R 2 1 2 1 101000 f 74 goat snp58457-scaffold950-1451769 4 78967601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433422 Affx-122935086 AX-123303763 4 39018957 GGAAGGAGAACTGGAGGCTAAGCGTACAAAGGCCC[C/T]GTGGAAGGCCATCATCCAAATAATCGGTATAAAAT Y 2 1 2 1 101000 r 74 goat snp58458-scaffold950-1516009 4 78902954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787082 Affx-122964224 AX-385274109 4 39056277 AATCAGGTCATTTGAAATATAGTATAGCACAACTG[A/C]TATTCCTATGAAAATATTCATAGGAATTCATCAAT M 2 1 2 1 201000 r 74 goat snp58459-scaffold950-1553329 4 78864954 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440740 Affx-122929876 AX-123311077 4 39098862 TTTCAAGTGCAAGAGTAGAAAATATTCTAACTCAG[C/T]AACTGATCTTTTCTTCTTTTTAAACTTTACTTAAC Y 2 1 2 1 103000 f 74 goat snp58460-scaffold950-1595914 4 78822367 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783955 Affx-122977785 AX-385271009 4 39132929 TTATATCATAAGTAATTACTTTGCTAAACTGTAAT[A/G]TTTTGCAACACCCTTGAAGACCATATTTTGTCTTG R 2 1 2 1 202000 f 74 goat snp58461-scaffold950-1629981 4 78787917 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449409 Affx-122922697 AX-123319744 4 39164797 AAATAGTCCATTATTTGGGTTCTGTACCCAATTCT[A/G]CTTCTCCGTGGAGAGGGAGGTTTCAAGCAATGCTC R 2 1 2 1 202000 r 74 goat snp58462-scaffold950-1661849 4 78755419 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395809 Affx-122963645 AX-123266164 4 39200153 GAATGACAAAGATAAATAGTCTTTATTCTTTTCAC[G/T]CAGTGACTTATCTGGAAGACGACATTTATGGTGGG K 2 1 2 1 101000 r 74 goat snp58463-scaffold950-1697205 4 78719143 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278076 Affx-1111836239 AX-519551566 4 39247022 ACTTGTTCTTGTCTCTGAGAGCCAAACTACTGTTA[A/G]TGATCTTCTTTTCAATTCTAAGCATGTTTCCATTG R 2 1 2 1 101000 f 74 goat Random2.2K-433 4 39247022 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781196 Affx-122929360 AX-385268281 4 39254131 GTTGGCATATAGACAACCACCCAATAAGCACTTAC[A/G]CCAACTTAATAGCTAACTCCATGAGCAGGTATGAT R 2 1 2 1 101000 f 74 goat snp58464-scaffold950-1751183 4 78665117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432542 Affx-122935548 AX-123302883 4 39283632 AAGGTGCCAAATCCTCTGTTCCCCCTTCTGCCCAA[C/T]ACATAGTATTACTAGATCTAAAGTGCTGTACTGTC Y 2 1 2 1 101000 r 74 goat snp58465-scaffold950-1780684 4 78635024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773860 Affx-122939657 AX-385261000 4 39313833 GAGATAGGAACTATAACAGTGAATGACACAGTCTA[C/T]AGCAATATAAATATTAACGGTTGATTTAACCAAAA Y 2 1 2 1 101000 f 74 goat snp58466-scaffold950-1810885 4 78604184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425094 Affx-122941238 AX-123295440 4 39400880 AACTTGTCTTCTTCCCCTTCTCAAATGCTAATTAG[C/T]ACTGTTTCTGACCAAACTGGATTTTTAGATGGTGG Y 2 1 2 1 101000 r 74 goat snp58468-scaffold950-1897932 4 78516587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388705 Affx-122968985 AX-123259063 4 39439529 GCATATCAGACAGTTATAATACCCAAATGTTGTGT[A/C]ACTTTTCTAGTTCTATTTTCCTTTCCAAAGCCTCA M 2 1 2 1 101000 f 74 goat snp58469-scaffold950-1936581 4 78477943 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375946 Affx-122978453 AX-123246305 4 39511812 CTAAAGTCAGATATTAGTGTCCTCTGAGTTCATGA[C/T]AATTGAATGAAAAACAGAACTAAATATTGGTGAGT Y 2 1 2 1 101000 r 74 goat snp58471-scaffold950-2008864 4 78405265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773879 Affx-122940871 AX-385261018 4 39558619 ATGGTGCAAAGAAGTGAAATGCAGGTTGAAAACAC[A/G]GCATAAAACACTGCTCTGAGAAAAGTAAATTATGC R 2 1 2 1 101000 f 74 goat snp58472-scaffold950-2055671 4 78358504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377577 Affx-122977435 AX-123247936 4 39596023 ATAAGTAGGCTGTCTAGGGCTCCTGTGGTAATTCC[A/G]CAGTTTTATCATGGCTCATATTTTCTTCTTTGCCA R 2 1 2 1 101000 f 74 goat snp58473-scaffold950-2093075 4 78319690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398506 Affx-122961555 AX-123268861 4 39680249 TGTTCAGAAAGAGAGTGTGGGGTCACCAGGGAACA[G/T]AGAACACAGAATATGACAAACCTTGAAAACTAGAT K 2 1 2 1 201000 f 74 goat snp58475-scaffold950-2177301 4 78234643 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389808 Affx-122968199 AX-123260165 4 39712193 CTCAAGCTATTGGTGGCCAAGTTGGTACAGATCTC[A/G]TATACCATGATTTCAGTAGTCTTTCCTCTGCTATC R 2 1 2 1 201000 r 74 goat snp58476-scaffold950-2209245 4 78202207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404767 Affx-122957214 AX-123275119 4 39761273 AGGATATAATTCTAGAATTGGGGTTACTATAATCC[A/G]TAATGGTAGATTGTGGTTACTATAAATAAATCTAT R 2 1 2 1 101000 f 74 goat snp58477-scaffold950-2258325 4 78153202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406694 Affx-122955776 AX-123277046 4 39807929 TTCCTTTTAGAAAAATTTTTGCTGGCCTCTTCTCT[A/C]GTGCTATCCCTTGTAATCACTAAACTATAATATAT M 2 1 2 1 201000 r 74 goat snp58478-scaffold950-2304981 4 78105758 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764655 Affx-122950740 AX-385252291 4 39844058 GGTGTTTGTGTTGCATATATGGTGGTCATGGTGGT[A/G]CAAAGAGATTGTTAATGAACTGTAATTTTGAGAGT R 2 1 2 1 101000 f 74 goat snp58479-scaffold950-2341110 4 78069596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787862 Affx-122921463 AX-385274885 4 39921290 ATTTGTTGGTATTTACTTCCTTTATATGGAATCAC[A/G]TTCCATAAAAGATTCAGGATCATAAAGAGGCTTTA R 2 1 2 1 101000 r 74 goat snp58481-scaffold950-2418342 4 77987318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402592 Affx-122958430 AX-123272945 4 39970616 CACAACTGAATCAGGCAACTAGAAAGAGTTGTTTA[C/T]AGAACTGAGAGGACAAAAGACAGAGAGGCTTTCTT Y 2 1 2 1 201000 f 74 goat snp58482-scaffold950-2467668 4 77936288 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272269 Affx-1111833425 AX-519546008 4 40037513 TGAAAGGCTTGAAAACGTAGTTCTATGTGTTCTAA[A/G]GGCTAAAAAGTGGCACAGAGGAAGAGTGCAAATGG R 2 1 2 1 101000 f 74 goat 4_40037513_AF-PAKI 4 40037513 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766005 Affx-122934409 AX-385253425 4 40040863 TAGATATGACATAAAACACATTATATATTCAAGTC[A/G]CTATCATTCTTAATTGACAGTAATTCTAGGAATTC R 2 1 2 1 201000 f 74 goat snp58483-scaffold950-2537915 4 77865169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790721 Affx-122948032 AX-385277722 4 40089283 TGTATGTTTTAGTTATGATTTAAAGAAACTGATTC[G/T]CTTGTCTACATCACAGGAGTATAATGTGTGTTTAT K 2 1 2 1 101000 r 74 goat snp58484-scaffold950-2586335 4 77817220 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275431 Affx-1111834892 AX-519549004 4 40121270 GCATATAAGAAGCCTGCAGTTAGCTTTTGTCACTG[A/G]CTCAAAAAGCTATGTAAATATACATGAGTAAA R 2 1 2 1 101000 f 74 goat GoatD01.057647 4 40121270 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795340 Affx-122943170 AX-385282297 4 40136612 TGTACTTTGTTTGTGAGTTCAATCTGAGAGTAGGT[A/G]TATAAATTTAACATCAAAATAAATGCTGCTGCATC R 2 1 2 1 201000 r 74 goat snp58485-scaffold950-2633664 4 77769613 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774538 Affx-122935186 AX-385261672 4 40178635 GTTTGGTGGTTAATAGCACATTCCCAACCTGGTCC[C/T]ACTAACCTCTAAGTATTATAAGTATTCTTTCTTGT Y 2 1 2 1 101000 f 74 goat snp58486-scaffold950-2675687 4 77727667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437887 Affx-122931670 AX-123308225 4 40213097 GTGGAGGGAGGTCTGTATGCTTACTGTTCATTGCC[A/G]TATGGGAGATGCTGCCCTGAAGGCTGTTTCAGATG R 2 1 2 1 201000 f 74 goat snp58487-scaffold950-2710149 4 77692775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443089 Affx-122928112 AX-123313426 4 40248973 TGCACCTAGACAATAATTTTATTTAATTTATCAAG[C/T]GAGATTATCCATGGTCATGTTCCAGAGCAGCAGTT Y 2 1 2 1 101000 r 74 goat snp58488-scaffold950-2746025 4 77655844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441617 Affx-122928647 AX-123311954 4 40281296 GTTAAGTGCATAGAAATAACCCTTTTAGAAATCAA[C/T]GGCATGGCCTCTTGGGATGAGCCCTGCCCTAGTAG Y 2 1 2 1 201000 f 74 goat snp58489-scaffold950-2778348 4 77623505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394539 Affx-122964519 AX-123264894 4 40375527 CATAGATTTGACACATATGAGATCTGTGTTAAGGC[A/G]CATTTGCACACATAGAATTTTAAGCTAAACTTCAT R 2 1 2 1 101000 f 74 goat snp58491-scaffold950-2872579 4 77529107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796719 Affx-122967744 AX-385283664 4 40407710 TTTAGTTTCACATGCAAGAAGCACAGAGTTTATTG[C/T]ACCATAGGTTCTAAATTGCTTCTTCACTTTCTTTC Y 2 1 2 1 101000 r 74 goat snp58492-scaffold950-2904762 4 77497120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399361 Affx-122961346 AX-123269716 4 40460628 AGGAAAAAAATGAGAACAGCAGGTTGCATTTTCCA[C/T]GAGGTCAAACTGAAGGGCAGGACTTGAACTTTGAC Y 2 1 2 1 201000 f 74 goat snp58493-scaffold950-2957680 4 77443505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405274 Affx-122956861 AX-123275626 4 40508729 CCCTCCAGAGCTACCTGTGTACTTTGTCTGCACGT[A/G]CCACTGCTGTTGAATGGTTTGGATTTTTACATGTA R 2 1 2 1 201000 f 74 goat snp58494-scaffold950-3005781 4 77395795 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770922 Affx-122934928 AX-385258085 4 40537236 CAACAGCATTATCTTAACAATGTTTTTCTCCTTTA[G/T]GCCTTTGAGTAGTTCTCTAAATATTCCAAGAAAAC K 2 1 2 1 101000 f 74 goat snp58495-scaffold950-3034288 4 77367320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788931 Affx-122955434 AX-385275945 4 40590286 GAAGTTATATTATGAAATTAAGAAGGCAGACTAAC[A/G]TAGCATGTTCTATAAAAGTAGCTTATGTCTTGGCC R 2 1 2 1 101000 r 74 goat snp36588-scaffold440-2102239 4 77314256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444461 Affx-122926542 AX-123314798 4 40658080 GACCTCAGTCCTCAGAATGTTTCTGTTCTTTCCTC[A/G]TACTCAAGCCCTAGGTGTTCTCATTCAGTATCCAG R 2 1 2 1 101000 r 74 goat snp36587-scaffold440-2034445 4 77246996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797276 Affx-122978082 AX-385284215 4 40714641 ATGCTTAACCAGAACCTGCCATCTAATTGTAGATA[C/T]TCTCATTTTTGCATCGCTGCTGAGTATGGTGAGAA Y 2 1 2 1 101000 f 74 goat snp36586-scaffold440-1977884 4 77189779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453048 Affx-122920074 AX-123323381 4 40758119 TTCACTAAGAGGAGAAAACAGGAAAGGAAAGAAAT[A/G]CTTACTTATATGGGAATTATCCAGCTGATGAAGAA R 2 1 2 1 101000 r 74 goat snp36585-scaffold440-1934406 4 77146832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778503 Affx-122975184 AX-385265617 4 40802861 TATGTTATCTCTGTTCAGTCTTGCATTGTTATTGA[C/T]GTGAGGCCACCTAGTCATTTGACAAATATGAGCCA Y 2 1 2 1 101000 r 74 goat snp36584-scaffold440-1889664 4 77101816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389107 Affx-122968570 AX-123259465 4 40853766 GACTCCGCTATGCATACTCAAAGCAACTGTGAGTA[C/T]GGAAGACACGGGTCCTAAATGGCTCCTTCTGATCT Y 2 1 2 1 101000 r 74 goat snp36583-scaffold440-1838759 4 77050844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416871 Affx-122948087 AX-123287219 4 40884181 TGGAGTGGGATGCCATTGACTTCTTCAGAAGGGTA[A/G]TGGGGAAGAAGTAATAATACACCAGCTCTTGGGTG R 2 1 2 1 202000 f 74 goat snp36582-scaffold440-1808344 4 77022157 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781293 Affx-122929831 AX-385268378 4 40929723 GTGGACAATGACCATTTAATTTATCTATCAAGGGA[C/T]GTTTGAAGCTCTGAATAGTGTACTGTCAGGAGAAC Y 2 1 2 1 101000 r 74 goat snp36581-scaffold440-1762802 4 76976566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775808 Affx-122944177 AX-385262939 4 40973672 CTGTGGTTTAACACTCTTTCCATTCAGCTTATCAT[A/G]CTTGTTCCAGGCTTTTTGGTTTCATCATTTTTCAT R 2 1 2 1 101000 r 74 goat snp36580-scaffold440-1718853 4 76932726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401443 Affx-122958985 AX-123271796 4 41003565 TTATAGGGGTTAAGGAATAAACCAAAGAAAACAGC[C/T]CATGTGAAACCAGACCTCATAGATGTTGATCTTGT Y 2 1 2 1 101000 r 74 goat snp36579-scaffold440-1688960 4 76904752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379593 Affx-122976027 AX-123249951 4 41037380 AAAATAATAGGTAAATTCATTGCACAGGGCTCTCC[A/G]TATCCTCAGGTTGTGTATCCTCAAGTTAAGCCAAA R 2 1 2 1 101000 r 74 goat snp36578-scaffold440-1655145 4 76870891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793678 Affx-122938140 AX-385280650 4 41073778 TAATTTCTTCTGTGTTTATTAGGTGACTTTCTGCT[A/G]CAGAAAATACTTCATTCTCTTATTTATTTGCCCAT R 2 1 2 1 201000 r 74 goat snp36577-scaffold440-1618747 4 76834337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410326 Affx-122952476 AX-123280676 4 41125187 AAAACATCTATGGAGAATATAAAAAAAGATCTAAG[C/T]GGATGTTTAGATCTGTACTCTGGATTGAATGCAAG Y 2 1 2 1 103000 r 74 goat snp36576-scaffold440-1567338 4 76781636 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407692 Affx-122954580 AX-123278043 4 41171684 CTTAGATTTTTAAAATTATGAATAAGCAAGTTTTG[A/C]TGTATAAAGAGGTAATCCACTAAAGAGTTCACAGC M 2 1 2 1 101000 r 74 goat snp36575-scaffold440-1520841 4 76735131 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792944 Affx-122948452 AX-385279922 4 41241440 TTTGGTTAGGCAGTGATATAGGGGTTGTATACCCT[A/C]GTGGAGTAGGCATTCTATGTTGACAGAAGGATGGT M 2 1 2 1 101000 f 74 goat snp36574-scaffold440-1451085 4 76665327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379514 Affx-122976078 AX-123249872 4 41281956 ATTTGCTTCTGCAAAGATGAAAATATGAATTGTGC[A/G]TCCACACTATTAATTTGAAGGGTCTCTATTTTTCA R 2 1 2 1 201000 r 74 goat snp36573-scaffold440-1410569 4 76624786 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451436 Affx-122921167 AX-123321769 4 41312444 ATTAGGACCACTGTGAATCTCAGGCGCTCTTTCAC[C/T]AGGTTTTAGACTGATTTGCAAAAAAGCAAAAAGTC Y 2 1 2 1 101000 r 74 goat snp36572-scaffold440-1380081 4 76594239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434061 Affx-122934190 AX-123304402 4 41396081 TAATGAATGATTTCATAGGGACAATAAAGGAAGAC[A/G]TTATTTTAATCTATATTCATATACACAGAACTTAA R 2 1 2 1 101000 f 74 goat snp36570-scaffold440-1296444 4 76510474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375559 Affx-122979086 AX-123245918 4 41487123 GATATATGGGAAAATAGAAATAAAATCTAGTATTT[A/G]TTTAGAACTCAAATGTCCTGGGTTTCATTAACATA R 2 1 2 1 102000 r 74 goat snp36568-scaffold440-1205402 4 76418979 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409360 Affx-122954169 AX-123279711 4 41516890 GTCCCAACCTTGTTTTCCAAGACAAGTCTAACAAC[A/G]CTATGAAAATATTAGTTTGTGTCTCTATGAATAAA R 2 1 2 1 101000 f 74 goat snp36567-scaffold440-1175635 4 76390642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403803 Affx-122957968 AX-123274155 4 41555779 TAAAACCCAAGCCCCACCAGTACCGATGCTGAGAG[A/G]TTTAGGTCAGTTCAGAGGGTGAGGGTTGAATCCCA R 2 1 2 1 303000 r 74 goat snp36566-scaffold440-1136746 4 76351718 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768047 Affx-122937374 AX-338229914 4 41608886 CAAAGACTTGGTGACATTTTTACAGTTGATCTGCA[C/T]GTGAACTTTATGATGTAGGTAGTATTACTAATCTG Y 2 1 2 1 101000 f 74 goat snp36565-scaffold440-1083639 4 76297940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782728 Affx-122924672 AX-385269800 4 41641590 TATCATCAGAGTAGGAATAACATAGACATAATAGG[C/T]AATATGTGCTCAACAAAACCTTAAAATTACATAGG Y 2 1 2 1 201000 r 74 goat snp36564-scaffold440-1050935 4 76265035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386480 Affx-122970764 AX-123256838 4 41672806 AAAAATGCAAATGTGTGGCATTCAATGAGGTAAGA[A/G]ACTATTGCTTGAAAAGTTTACTTATTTATTCCCTA R 2 1 2 1 101000 f 74 goat snp36563-scaffold440-1019719 4 76233536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411324 Affx-122952276 AX-123281674 4 41715603 GATCTGCAGTTTGTTCAGTCTACAGCTGTGGAACC[A/G]CTAATAGGGAGGACTGACTGAAAAGCTACAGGTGG R 2 1 2 1 101000 f 74 goat snp36562-scaffold440-976922 4 76188377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445915 Affx-122925934 AX-123316252 4 41757641 GGATGTTTAACTGCATCCTTGCCCTCTATCCAGTA[C/T]ATGTCAGTAGCACCTAGTCCCCCCACCATACCTCC Y 2 1 2 1 101000 r 74 goat snp36561-scaffold440-934884 4 76146324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382448 Affx-122974226 AX-123252806 4 41814327 AAGAGGAATTCAACAAATGTTTTCCTGAGCTTTAC[C/T]GGGAAGTCTTTGAAATCATCTAACAGGACATTTTT Y 2 1 2 1 201000 r 74 goat snp36560-scaffold440-878198 4 76089621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379325 Affx-122976184 AX-123249684 4 41855400 ATTAAATATGGAGAAAGCAAACATTGACAAGAAAT[A/G]TTATCCAATTTATATAATGCTATTATTTATCCTAT R 2 1 2 1 101000 f 74 goat snp36559-scaffold440-837125 4 76047990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765059 Affx-122930743 AX-385252628 4 41890323 ATTATAATGTAGTGACCTTCTTTATCAGATAAACT[C/T]TAAAAATCCACCTAAAGTACAATGCTGAACAAGAT Y 2 1 2 1 201000 f 74 goat snp36558-scaffold440-802202 4 76012763 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443309 Affx-122927457 AX-123313646 4 41941219 AGTAATGGAAAATTCTGTGCAATGACTCTGTTGCC[A/G]TTTACAATGGATTTTTTTAAAGAGTAAAGGTAAAC R 2 1 2 1 101000 f 74 goat snp36557-scaffold440-751306 4 75962116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776611 Affx-122951438 AX-385263739 4 41990230 ATCCTTTTAAAAAACGGCATTTCTTTAGCTTAAAA[G/T]CATGTATTTTCATAGGATGCTCCTGTCTTTCCAAG K 2 1 2 1 101000 r 74 goat snp36556-scaffold440-702295 4 75913071 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394451 Affx-122964585 AX-123264806 4 42021443 TTTCTAGGCTTCCGCCACGGTTTAATTTTTATCAA[C/T]ATTAGCATTCTTTCCACTTTGGCATTTTGTTCCTT Y 2 1 2 1 101000 f 74 goat snp36555-scaffold440-671082 4 75880763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801781 Affx-122940220 AX-385288689 4 42069211 AGGCTTGTTTAGAGAGTTCATGAAAAGTACTGCTC[C/T]GTATATTGTGCTGTTGTATGGCTGAAGTAACTAAT Y 2 1 2 1 101000 f 74 goat snp36554-scaffold440-623314 4 75833254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796543 Affx-122920347 AX-385283489 4 42151788 AATCTCATCTATGAATGTATTGAATAATACCAAAA[A/C]CAAACAAAAACAGTTAATAGCAAAATGAATTCAAC M 2 1 2 1 303000 r 74 goat snp36553-scaffold440-540737 4 75750403 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386682 Affx-122970183 AX-123257040 4 42180327 GGATTCCAATGAAAAGAAATGTTTTTGCAAACACT[A/G]CCAGGGCTCAGTTGTATGTCATATAGCGGGGAGTA R 2 1 2 1 201000 r 74 goat snp36552-scaffold440-512198 4 75722151 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430729 Affx-122936890 AX-123301070 4 42331724 ATTGAAAACATACTGAAGATTCTCCATGTGCAAAA[C/T]AGAATTGTTTGAAGGTGTCACAAGATGAAAAATAG Y 2 1 2 1 101000 r 74 goat snp36549-scaffold440-360801 4 75570000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401228 Affx-122959315 AX-123271581 4 42363585 GCATTCTGCTTTAGTTAGGATACAGGTCTAGCTAC[G/T]ATAAAAGCAAAATAAATTCAAATGCTTAACAAGGC K 2 1 2 1 101000 f 74 goat snp36548-scaffold440-328940 4 75538181 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404282 Affx-122957040 AX-123274634 4 42410306 TCAGCAATAATGTGTAGTGATGGATAACACAAAAC[A/G]ATTTCCTAATTGATCAGTAGAAATCCCTTCAGAGC R 2 1 2 1 201000 f 74 goat snp36547-scaffold440-282219 4 75491504 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445424 Affx-122925369 AX-123315761 4 42482322 TAAATGCAGATCACTAGGAGATAGGTGCTGTTCTG[C/T]GTATTTTTTATTTTTAAGAAATCTTCCCACTCTGA Y 2 1 2 1 101000 f 74 goat snp36546-scaffold440-210203 4 75419596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386379 Affx-122970843 AX-123256737 4 42514434 TTAATCATTGTGTTCCAGCAGGATTATGGTGCCAA[A/G]TGCTTTTAGATTTAGAAAAGAGTAAGTCTTAACAC R 2 1 2 1 101000 f 74 goat snp36545-scaffold440-178091 4 75387315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415786 Affx-122948911 AX-123286135 4 42560242 TGAAGCCAGGGAAGTTAACTTGACAAACTGTATAC[C/T]GCTTATATTGGCATGTGTTGTGCTGTGTGCCATGT Y 2 1 2 1 101000 r 74 goat snp36544-scaffold440-132283 4 75333392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272113 Affx-1111833426 AX-519545871 4 42577276 CATAGTGTCCAGATGGAATTGAACATGGATAAGTG[A/G]AAAAGAGCAGATCAAGAGCCCATGTCTCTATCAAT R 2 1 2 1 101000 r 74 goat 4_42577276_AF-PAKI 4 42577276 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378357 Affx-122976828 AX-123248716 4 42597109 ACTCAATTTCCTTTGCGTGGTTAGGGAATCCATGC[A/G]CTTTGTGACTTGACTTTGAACTTTCGTGTTTTACC R 2 1 2 1 101000 f 74 goat snp36543-scaffold440-95416 4 75296608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780918 Affx-122924923 AX-385268005 4 42631404 TATATCCCATCCATTGTCACAAGGGGAATCATATA[C/T]AGGGAGAGAATGTGTGAATTAAAGGCAAAATTGAA Y 2 1 2 1 101000 r 74 goat snp36542-scaffold440-61121 4 75262403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425252 Affx-122940989 AX-123295598 4 42682337 GTGCTCTTATCCACTATGTAAGATGCTGCTGCTGA[C/T]GACAATGGTAGTGATAATGGTGATGATAAGGCAAG Y 2 1 2 1 101000 f 74 goat snp36541-scaffold440-10188 4 75211380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388905 Affx-122968849 AX-123259263 4 42706406 CTTATACAGCACAGTGGCAACTTTTACTAGAATCT[A/G]CTCTAAAAATATGACTTTACCAATGTTTTTATTTG R 2 1 2 1 101000 f 74 goat snp49148-scaffold701-13782 4 75185096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778401 Affx-122975682 AX-385265516 4 42748621 ATCCATAGTGATCTGCACATTAAAGAAAAGCATGA[C/T]TGCAGTGCATTAGGCTTTTGATGAAATTCTCAACA Y 2 1 2 1 201000 f 74 goat snp49149-scaffold701-55997 4 75142909 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428894 Affx-122938929 AX-123299236 4 42785895 AGGCTAAGGAGCTGGGGTGAAGAAGAGGGATTATC[A/G]GGGGAAAGAAAAGGTGCAGACATCAACTCAATCTT R 2 1 2 1 101000 f 74 goat snp49150-scaffold701-93271 4 75105253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439603 Affx-122930058 AX-123309940 4 42819993 TGGAAGCAGGAACAGGAACTCAGGCAGTGACACTG[C/T]GGGGCAGTTTTCAATTATAATATACAAATGGTCCA Y 2 1 2 1 201000 f 74 goat snp49151-scaffold701-127369 4 75071013 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426200 Affx-122940374 AX-123296546 4 42887471 GACGTTTCTCCTTATAGATTTGGTGCCAAACTGTT[A/G]AAACTGATTTTTTTCACTGGTCTTTATCTTCCTTA R 2 1 2 1 101000 r 74 goat snp49152-scaffold701-194847 4 75001538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453420 Affx-122919885 AX-123323753 4 42930436 AATTTAACAAATAGGTTTCTTTCCTAATAACCAAC[C/T]AGTTTACTTAAAACTCACTGTATTTTATTTGAAAA Y 2 1 2 1 101000 f 74 goat snp49153-scaffold701-237812 4 74958656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426497 Affx-122940219 AX-123296843 4 42977739 AATGGCCTAACTACTGTGGCGGGATGCATGATCAC[C/T]ATTACTAGGCACAGAGGAAAATAAGGGAGTAAGTT Y 2 1 2 1 101000 f 74 goat snp49154-scaffold701-285115 4 74911591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424367 Affx-122941845 AX-123294713 4 43008687 CAAGTTTGTGCAAAGAAGCATGTAGGACTGAATGA[C/T]CCAGCTGCCTCTGGAAATGTCCGCCCCTTCCTAGA Y 2 1 2 1 101000 f 74 goat snp49155-scaffold701-316063 4 74880894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799953 Affx-122941529 AX-385286879 4 43044637 AATATGCTTTATTCGCAGATTGTAAGCAGGTAAAT[G/T]GGTATTCACACCACACACCTAAATAGAAGCCTGTG K 2 1 2 1 101000 r 74 goat snp49156-scaffold701-352013 4 74844740 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446644 Affx-122924780 AX-123316980 4 43094745 AAGGATTTCTTTTTAAGTAAGTGTCTACAGTTGTG[C/T]AATAATCATCATAATCCAATTTTAGAACATTTAAG Y 2 1 2 1 101000 f 74 goat snp49157-scaffold701-402121 4 74793732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405651 Affx-122956578 AX-123276003 4 43179323 GAGGGTGTCTTGTGAATCCTGGAATCATGGTGGAC[A/G]TGAGTACTATTCACTTCACTTTTCCTTTTCCATCT R 2 1 2 1 101000 f 74 goat snp49159-scaffold701-486699 4 74707779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451983 Affx-122920934 AX-123322316 4 43232217 CTTGTCATGTTCCGCATTCTCTAGAGATGATCCCA[C/T]CTCCTTTAAAGACTTCAGTTACCACTTACATGTTG Y 2 1 2 1 101000 f 74 goat snp49160-scaffold701-539593 4 74653854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775673 Affx-122973877 AX-385262804 4 43267276 TAAACGAAACTAAGATTTTATCCTTTGTGGACCTA[G/T]AGGCAGTGAAATGGAGAACTGTTTTCAAAGAAATG K 2 1 2 1 101000 r 74 goat snp49161-scaffold701-574652 4 74618762 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384098 Affx-122972841 AX-123254456 4 43296575 ACCAAGGGGAAAAAAAGACAATCAATAGGTGCCAA[C/T]ATCAAAATTACAGAGATATTAGAATTATTTGATCA Y 2 1 2 1 101000 f 74 goat snp49162-scaffold701-603951 4 74589339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382394 Affx-122973841 AX-123252752 4 43347743 AGAGGACACAAAGCCTTTTTTCTGACCTCTTTCCC[A/G]CTGGTCATTCCATGGCCCTGAAAGTCTCACCTTTC R 2 1 2 1 201000 r 74 goat snp49163-scaffold701-655119 4 74537886 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427426 Affx-122940054 AX-123297769 4 43409242 ACACACTGGGGACAGGAGGTGGGAGATACTGCTGT[A/G]TTATATGGGGCATTTGGGGGAAGACCTCACTGAAT R 2 1 2 1 303000 f 74 goat snp49164-scaffold701-716618 4 74475613 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448990 Affx-122923109 AX-123319325 4 43440881 GCAAAGAAGTAGTGTATTCAAAAGCCTTGAGGAAT[G/T]ACAGAGCATGGAGAGTTTGCAGGGTCCAAGGGACA K 2 1 2 1 201000 r 74 goat snp49165-scaffold701-748257 4 74443741 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406326 Affx-122955452 AX-123276678 4 43492640 AGTAAATGCCAGGTTACTTCTTTTAGGACTTATTT[A/C]TTTTTGGCTGTGCTGTGTCTTCATTGCTGTGTGCA M 2 1 2 1 202000 f 74 goat snp49166-scaffold701-800016 4 74391333 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409423 Affx-122954122 AX-123279774 4 43522645 GAGAGGAAGTGCCACTAAAGAGGAACAGAATAGAC[A/G]TCAGGTACAGTCAGTTCGAAAATTTTGTTATCCAG R 2 1 2 1 101000 r 74 goat snp49167-scaffold701-830021 4 74361310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453234 Affx-122920421 AX-123323567 4 43620341 TGGTGTCTAGCTCTTTGTGACCCCATGGACTGCAG[C/T]ATGTCAGGCTTTTTGATCACTTTCAGGATTTGATC Y 2 1 2 1 101000 r 74 goat snp49169-scaffold701-927717 4 74263204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767909 Affx-122945177 AX-385255127 4 43659547 GAGCAGCAAAGGAAAATTCAAAAAGAAGCCACAAA[C/T]AGTGTCGAATTTTAAACTCTGTGTTCAGAAGGAGT Y 2 1 2 1 101000 f 74 goat snp49170-scaffold701-966923 4 74224181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787076 Affx-122956479 AX-385274103 4 43722181 ATGTGTATTGGAGGAGGTCAAAAGTATAATAAATA[A/G]TTTCCTTTCCCCTCACTCTGAGTTTAGCAACAGTG R 2 1 2 1 101000 f 74 goat snp49172-scaffold701-1029557 4 74160816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391806 Affx-122967030 AX-123262163 4 43772543 ACACTTGAACTGAAGGATGCATTCACAAGGGGTAG[A/C]GTAGGAATATTCCATGAAGAGATGATACAAAAGAA M 2 1 2 1 201000 r 74 goat snp49173-scaffold701-1079919 4 74110658 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788922 Affx-122925247 AX-385275935 4 43802533 AATGAGGTGCCCAGAGTTTCATAGGTAGTAACTTC[A/G]CAATAGATTTTGATCAACTAGTATTCTTTTTTTAT R 2 1 2 1 101000 f 74 goat snp49174-scaffold701-1109909 4 74080662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767541 Affx-122970964 AX-385254796 4 43835598 CTTATTTTTCTTCATTTTTGCTTCTACAAACGCAG[C/T]ATGCCCTCATAGTAGTATAGTAATACCTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp49175-scaffold701-1142974 4 74047602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767257 Affx-122925338 AX-385254538 4 43874883 TACAAAACCAGATTCCCATTGGGAGGGAACAGTTA[C/T]TGTATCAGAAGCTGAGAATGGTGTCCACCTGAAAA Y 2 1 2 1 101000 f 74 goat snp49176-scaffold701-1182259 4 74008248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435536 Affx-122933399 AX-123305876 4 43916112 ATGAATACACACTTTTCACAAGACATGCTATAATG[C/T]AAAATTCTTCCAATCTTCCTGTGTAGACAGACATT Y 2 1 2 1 101000 f 74 goat snp49177-scaffold701-1223488 4 73967107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782483 Affx-122942011 AX-385269559 4 43970228 GAAACTGAAAAGGCATTTGGAATAATTTTTTTATA[C/T]AGTCCACTTCTGAAAGTTTAGCTGTAAAATTATAA Y 2 1 2 1 201000 f 74 goat snp49178-scaffold701-1277604 4 73913208 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784805 Affx-122941833 AX-385271852 4 44018110 AACAAGAAATGGTCCTTTTAGTATCCATTTCCTGA[A/G]TCCCCTGAAAAGGAAATGGATTTCCTACAAGGCAC R 2 1 2 1 103000 r 74 goat snp49179-scaffold701-1325486 4 73865462 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409785 Affx-122952977 AX-123280136 4 44066046 TTGACTTGTGAAACTATAAACTAGCAACACCTTCC[A/G]AAGATCAATATGAAAATAAATTTCAAAGCATATAT R 2 1 2 1 101000 f 74 goat snp49180-scaffold701-1373422 4 73817109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398993 Affx-122960950 AX-123269348 4 44098574 GGCATCATGCTAAATATGTCACATGAACTCTCATT[C/T]AACTTTCAGAGTAGCCCCAGGAGATACAAATCTAT Y 2 1 2 1 101000 f 74 goat snp49181-scaffold701-1405950 4 73784301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796444 Affx-122967426 AX-385283394 4 44185014 GCCATTTAAATTGCTACCCATCTTCTGCTATTACT[A/G]TAAAGTACTCTCTAACAAACATCCTCATACAGACG R 2 1 2 1 101000 r 74 goat snp49183-scaffold701-1492390 4 73696976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409621 Affx-122953542 AX-123279972 4 44217641 TAGCAATTCCCTAATGAAATACTGGCCCTGGGCAA[C/T]GACATCAATGGCCACTAACATCACAAAAAAGAGAC Y 2 1 2 1 101000 f 74 goat snp49184-scaffold701-1525017 4 73664231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396067 Affx-122963443 AX-123266422 4 44286312 GCCTTGCTGCTCAGCTTGTGGCCAGCACACCAGTG[C/T]AGCAGCACTGCCTGGTGTCTTTTAGAAATGCAGAC Y 2 1 2 1 202000 f 74 goat snp49185-scaffold701-1593688 4 73594381 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395308 Affx-122964060 AX-123265663 4 44339136 AAAAAAGGGAAGATATAGGATGGCTCTGGTTTTGT[C/T]AAGGTTGTTTTTTAAATCCACACAAGATAAAGAAA Y 2 1 2 1 101000 f 74 goat snp49186-scaffold701-1646512 4 73541571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804574 Affx-986696743 AX-385291113 4 44354376 ATAGGGGTGTTCGACTGGTTGTCCTCCAATTCATG[G/T]GAGTGTTAGTAGGTCTGCTACTAGGATTCAGAATA K 2 1 2 1 600010 r 74 goat 4_44354376 4 44354376 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 320804253 Affx-986696747 AX-385290883 4 44361573 CTGAGCATTGACCATAGAATAGGCCTGGAAGAGTT[A/G]ACATAAGGGTTGTTTGATTTAAACGACCTGGAATT R 2 1 2 1 600010 f 74 goat 4_44361573 4 44361573 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320804580 Affx-986696749 AX-385291119 4 44363618 CGAATCCTCCAATCATAATAGGCATTACTATAAAG[A/G]AAATTATGACGAATGCATGTGCGGTTACAACTACA R 2 1 2 1 600010 r 74 goat 4_44363618 4 44363618 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 38452769 Affx-122920254 AX-123323102 4 44391219 ATGCACCCTCACTATTTGCTGATGGATGGAGTTAA[A/G]CCAGAGCTGGTGATGACAAGGCTACCTTTTTCAGG R 2 1 2 1 101000 f 74 goat snp49187-scaffold701-1698595 4 73488864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420035 Affx-122945145 AX-123290383 4 44423087 CTGTTGGCTTCTGCTGAAGCACTGATTTGATTAGT[A/G]GCATTCAGTGGAACTACAGACATGAGATGTTGAGC R 2 1 2 1 101000 f 74 goat snp49188-scaffold701-1730463 4 73456635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770826 Affx-122978894 AX-385257990 4 44490242 CCTTCTTCAACACTGACCAAAATTGTAGACTTCAT[A/G]CAAATGATCAAAATGCACTTACCAAAGTAAGACTA R 2 1 2 1 101000 f 74 goat snp49190-scaffold701-1797618 4 73389477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438805 Affx-122930798 AX-123309142 4 44529063 ATTTTTATCAGAATCGGTGGCTTGGGGTCTCCTCC[A/G]CCCACAGTGAGGGAAGGCTGAGCCGAACCTGAATC R 2 1 2 1 101000 f 74 goat snp49191-scaffold701-1836439 4 73350397 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413874 Affx-122949853 AX-123284223 4 44568872 ACTCGACACTCTGTCCAATCCCAAAGAAGAAGAAA[C/T]GGTTCACGTGGCCAAATGTGCATTCTTCAGACAGC Y 2 1 2 1 201000 r 74 goat snp49192-scaffold701-1876248 4 73310800 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797527 Affx-122971381 AX-385284466 4 44602696 TTTGGACATTCAGTTGAGGCTGTAAACAATGAGCC[C/T]GACCTTAATTCAAACACTAGGTGATTATGTTTGAC Y 2 1 2 1 101000 f 74 goat snp49193-scaffold701-1910072 4 73276829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414517 Affx-122949525 AX-123284866 4 44663471 GGAGCGTAGGGAGGCCAGGGCAGAAGGACAATGAA[C/T]GAGAAGAGTTAGTAGATGAGCTCAGACAGGTAAGG Y 2 1 2 1 101000 r 74 goat snp49194-scaffold701-1970847 4 73216548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393199 Affx-122965507 AX-123263556 4 44738239 TCCTCTTTAAAAAATGTATATCAAAGAGAAAAGAA[C/T]AGAAACATTAAGTATTTTGCACTGTGGGAGTACAC Y 2 1 2 1 103000 r 74 goat snp49196-scaffold701-2045615 4 73141882 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436914 Affx-122933204 AX-123307252 4 44777377 CTACTTAAGAAGAAAAGGGTTTATCAGAAAATAAG[C/T]TCCATGAGCACAGAGGCCAGCTTGTTCTCTGCTGC Y 2 1 2 1 201000 f 74 goat snp49197-scaffold701-2084753 4 73102420 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415861 Affx-122948857 AX-123286210 4 44811194 TTGTATGGAGAGTTTGTCCGTTGGGTGAACATGCC[A/G]TCCATCCTGTCCCCCAAGGCGTTGAGTGAGCTCAT R 2 1 2 1 101000 f 74 goat snp49198-scaffold701-2118570 4 73068203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795459 Affx-122962736 AX-385282415 4 44852368 TTAAGCTGGCGGGATGTATTAACATTATTCAACAG[C/T]ACCCTGTTTGTGGACTTCCTCTTTGCTACCAGTGT Y 2 1 2 1 101000 r 74 goat snp49199-scaffold701-2159744 4 73027129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390872 Affx-122967810 AX-123261229 4 44909240 AACTTAATGAAAAATATAACAATCAAAACATCTAA[A/G]ATAAGTACACTCACTACCCATTCCACTAATTCATT R 2 1 2 1 101000 r 74 goat snp49200-scaffold701-2216616 4 72969700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430545 Affx-122937025 AX-123300886 4 44949544 CAAAAAAAAACAAATCAACAATTTAGTTTGTTTTG[C/T]TCTGTTCCACCAATACAACCAAAGCTGCTAGCTCC Y 2 1 2 1 101000 r 74 goat snp49201-scaffold701-2256920 4 72931108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453582 Affx-122919760 AX-123323915 4 45016894 CTGCCTGCTAGTTTCTCTAATTCCTAAACCGCACA[C/T]GCATGAGACAGATTCAAGGCATCTTAGCTAATGAC Y 2 1 2 1 201000 r 74 goat snp49202-scaffold701-2324270 4 72864751 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776343 Affx-122968074 AX-385263471 4 45091720 GCACTTACTCAGTGTTTCTAGGCCATGGTTCCTTC[A/G]CTTATAAAATGGGGAGAAGAGTCCCAACCAGTAAA R 2 1 2 1 102000 r 74 goat snp49204-scaffold701-2399096 4 72789884 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272271 Affx-1111833427 AX-519546010 4 45095773 TCTAAACTGGGTGAGACCAATGGTGTTGAAGGGTC[A/C]GAGGAAGGAGTTAATTTTCTGGTTATGTCTTAAAG M 2 1 2 1 101000 f 74 goat 4_45095773_AF-PAKI 4 45095773 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432971 Affx-122935273 AX-123303312 4 45130748 GTAAATGTCTGGAAATGTCTACTGCAAAACAGTTG[C/T]GAGAAAGAGAGTGAGAGAAACATTTTTTAGCAACT Y 2 1 2 1 201000 f 74 goat snp49205-scaffold701-2438124 4 72749905 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392169 Affx-122966308 AX-123262526 4 45199232 AAATGCCTGGTGGTTATGCTTATTGCCACCCAAGA[C/T]TGCCTCTGGGGAACTTACACACTCTATCAATGATG Y 2 1 2 1 101000 f 74 goat snp49206-scaffold701-2506608 4 72680277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774199 Affx-122960195 AX-385261336 4 45258389 AAGGGCTGAATTCAAAAGCTTTCTGTTCAAAAAGC[G/T]AAGTTTCTCCTCTTCTTATCTTACTGCTGTACTGT K 2 1 2 1 101000 r 74 goat snp49207-scaffold701-2565765 4 72619696 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394682 Affx-122964361 AX-123265037 4 45292967 TGACACCACAATTCTAGTTCTAGGAAAATTTCCAA[C/T]AGATGAAAGGCATATTTGTTCAAAAACTTACTAGA Y 2 1 2 1 101000 r 74 goat snp49208-scaffold701-2600343 4 72585446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396226 Affx-122963346 AX-123266581 4 45326121 ATCACCCCCCAGACAATGCTCCATCTCCCACTCTA[A/C]ACTTCACCAATATCCTGGTTTTCAACATCATAGGT M 2 1 2 1 101000 r 74 goat snp49209-scaffold701-2633497 4 72541454 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801507 Affx-122954587 AX-385288416 4 45360621 GCTAACTCTGACTTTGTTTTATACTTTAGTACTAA[C/T]AAAATCTGACATCTATTAACTCAAACCTAGCCAAG Y 2 1 2 1 101000 r 74 goat snp49210-scaffold701-2667997 4 72507000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790916 Affx-122921732 AX-385277913 4 45378364 GAGTATACTGAATTTACGAAACTGTATCAAGCTGA[G/T]CTCATACTTTTCATACATCCACTTTTTAGTATGTG K 2 1 2 1 101000 f 74 goat snp4987-scaffold117-1975 4 72488465 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795915 Affx-122946484 AX-385282867 4 45413074 CCTGAAATTTTTGTTAACTTTGAGCATTGGTTATA[A/G]CATTGGTTTTCAGTGACAGGACATAGACTCTCCTA R 2 1 2 1 101000 r 74 goat snp4988-scaffold117-36685 4 72453299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432394 Affx-122935849 AX-123302735 4 45441758 TTGCCAGAATGAATTTTATTATCTGTAATTGAACC[A/G]TGACTAATACAATAAATGAAATCAGCAGTGTGGTT R 2 1 2 1 101000 f 74 goat snp4989-scaffold117-65369 4 72424614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405758 Affx-122956500 AX-123276110 4 45522178 CTTCTTAAAGTCATGGATTTTATATCAGAAATGGA[C/T]ATTAGAGATCAGCCTCGTCATCAAAGTGGAAAAGA Y 2 1 2 1 101000 r 74 goat snp4990-scaffold117-145789 4 72342981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793629 Affx-122924816 AX-385280603 4 45560486 GGTAAATCTTGGCACTGGTGGCAAATAGACTGATA[C/T]GGCAATTTAACTATAGTAATCATAGAATTTTCAAA Y 2 1 2 1 101000 f 74 goat snp4991-scaffold117-184097 4 72304947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414649 Affx-122949320 AX-123284998 4 45639441 TCTCAGAGTCTCGCCCCTTTCTGCCGTCATCTGCT[A/C]TAGAAGCTGTGCTGCATTTTCAAGCTCTACTTGAA M 2 1 2 1 101000 r 74 goat snp4993-scaffold117-263052 4 72226163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386817 Affx-122970103 AX-123257175 4 45698905 GAAAATAGGTCATTTTGATTTATGACCCAGCTATC[A/G]CTAGAAATTCCAGGTGCTTTAGAGACATTTTCTCA R 2 1 2 1 101000 r 74 goat snp4994-scaffold117-322516 4 72166692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440460 Affx-122929390 AX-123310797 4 45740281 TACTTCCAGCTTGGTGTCAATTCTTGTTAAAAGGG[C/T]AACCTTTAGGTGTTAGAATGATAGTGGCATATTGT Y 2 1 2 1 101000 r 74 goat snp4995-scaffold117-363892 4 72125389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421244 Affx-122944112 AX-123291591 4 45800002 GCATAGGTATTCACTAAGCTCCTGACCTCTGTGCC[A/G]GGTCCTTAGGTGAACAAGATGGAAGGTCCTCATTT R 2 1 2 1 201000 r 74 goat snp4996-scaffold117-423613 4 72065859 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787260 Affx-122969222 AX-385274286 4 45844814 AAATGGTATAAAACATCTTATGCAATTTTAAAATC[C/T]TTTATATTTTTGCAATAAAATACCTTTTGATTTCT Y 2 1 2 1 303000 r 74 goat snp4997-scaffold117-468425 4 72020600 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777394 Affx-122978088 AX-385264516 4 45875914 GGATTAACAATTGTGAGAATAGCAAAAAAGTTAAT[A/G]TTTGGAATGACTTGAATAAAGCGATTTTTTCCTGA R 2 1 2 1 101000 r 74 goat snp4998-scaffold117-499525 4 71989455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800142 Affx-122924174 AX-385287065 4 45920848 TCAATTAATGCAAACTTTCTAGATTTTACATGACA[C/T]GATACAATATTAACTCTAAAAGACTGTGGGAAGTT Y 2 1 2 1 101000 r 74 goat snp4999-scaffold117-544459 4 71944424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423447 Affx-122942596 AX-123293793 4 45949887 ACTATAAGAGTAACACTGTAAAATCTTATTAATTC[C/T]AATGGGGCCATGTCTTCACTTAGCCTGTTTCTACA Y 2 1 2 1 201000 f 74 goat snp5000-scaffold117-573498 4 71915245 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446045 Affx-122925840 AX-123316382 4 45987619 AAGAGTCAGACACAACTGAAGCAACTTAGGACAGA[C/T]GGACAGATGAACTAGATGAGAGGGAACCAGGTGTA Y 2 1 2 1 201000 r 74 goat snp5001-scaffold117-611230 4 71877286 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395224 Affx-122964483 AX-123265579 4 46018879 AATACAAAAATGGGAAGAGGAGAAAACTTTTTTAA[C/T]AGGCATTAAAAAACACTCTGGGGAATTTTTTCAAT Y 2 1 2 1 101000 f 74 goat snp5002-scaffold117-642490 4 71845463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770263 Affx-122927749 AX-385257429 4 46101273 ACTTGTCAAAGGTTACAACAAGTGAAAGGCTAACA[C/T]AAGTTCTGAAAATTGTTAGCTTTTATAATTTGTTA Y 2 1 2 1 101000 f 74 goat snp5003-scaffold117-724884 4 71762650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776668 Affx-122952592 AX-385263795 4 46130264 ACTCTAGAAGTATAACTATGATCATAAAAATACAA[C/T]GAACCTCTAAATTCACCTATAACCAATCTCAATTT Y 2 1 2 1 101000 r 74 goat snp5004-scaffold117-753875 4 71733694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394581 Affx-122964439 AX-123264936 4 46162620 AGTGACTGAAAAACAACAAAACCACAGAAATTAAA[C/T]GACAGAACAATTGTAACCACAGTTAACATATTTTG Y 2 1 2 1 303000 r 74 goat snp5005-scaffold117-786231 4 71701451 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423454 Affx-122942590 AX-123293800 4 46234541 TTATGATCCTGGCCTGGTCAGCAAGTCAAGTCTAA[C/T]GACAGAATAGCATACAGAAAAACAGAAATTACACC Y 2 1 2 1 101000 f 74 goat snp5007-scaffold117-858152 4 71629534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794352 Affx-122964450 AX-385281316 4 46267940 GAAGGAAGTATGTTAGCCTAGACTACATGTAAATG[A/G]TTTTTCTGCTCTTGCCTCTCCCTCCCCATTTGAAA R 2 1 2 1 101000 r 74 goat snp5008-scaffold117-891551 4 71596049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788765 Affx-122978643 AX-385275780 4 46302695 TGTTCATGGACAATTGATCTTATTATTTTTACAGG[C/T]AGTCACCCGCTTCACGGTACCTGATGAATTAGCAT Y 2 1 2 1 101000 r 74 goat snp5009-scaffold117-926306 4 71561084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387660 Affx-122969841 AX-123258018 4 46334541 TGGTCTAATTGCAGGGAGGGCATAGAAAGAGAGGA[A/C]AGGAAGGGGAGCCAGGGAGACTGCTCTTTCTAGAA M 2 1 2 1 101000 f 74 goat snp5010-scaffold117-958152 4 71529210 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395640 Affx-122963789 AX-123265995 4 46368965 AAACATCTTCCTTGGCTCCCTCCATTACCTCTCCA[G/T]TAATCTTTGAGGAATTACTTCTATTCTTGGAAGAA K 2 1 2 1 201000 r 74 goat snp5011-scaffold117-992576 4 71494659 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791235 Affx-122945200 AX-385278229 4 46415107 TAAAGATGGAATTTTTTGTTATTGATAGATTTAGA[G/T]AAGAGGAGAAACTATAAGAACCTTTTACCTTTTGT K 2 1 2 1 101000 r 74 goat snp5012-scaffold117-1038718 4 71448582 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435155 Affx-122933666 AX-123305495 4 46472632 GAAATCTTGGGCAGCAAGACGAGAGGGTGCAGAGA[C/T]GAGCAGGAGGATGGAGGGTGCAAGGGAAAATGCAG Y 2 1 2 1 101000 f 74 goat snp5013-scaffold117-1096243 4 71390889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382289 Affx-122973920 AX-123252647 4 46530584 AAAAAGTCTCTCTCCCCCCAGTACACATCAAAACA[C/T]GATAAACCTTATCATGTAGCTCTTATATTCATTCA Y 2 1 2 1 102000 f 74 goat snp5014-scaffold117-1154195 4 71332892 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378037 Affx-122977572 AX-123248396 4 46582345 GGAAAACAGTATAGGAACAGTCTACTAAAATCTTC[A/G]CCAAGAATGCTTTTAGTTTAAGATCTGAAAAATAA R 2 1 2 1 101000 f 74 goat snp5015-scaffold117-1205956 4 71280968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774560 Affx-122956761 AX-385261694 4 46612646 AAGCAGTTTCCTCGAACCACCATATCATAAACCGC[A/G]TAATAATACTTTTCTCTGATTTCCATTCTGGAATC R 2 1 2 1 201000 r 74 goat snp5016-scaffold117-1236257 4 71250672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389057 Affx-122968608 AX-123259415 4 46678254 TCTTGGGGCACTAGAGTCCTTTTCTTCTCTTCCTT[A/G]CCATCATATCTTTTTAACGTGATATATATATATTT R 2 1 2 1 201000 r 74 goat snp5017-scaffold117-1301865 4 71185023 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776055 Affx-122960099 AX-385263185 4 46734106 TTACTTATGTCCGGATGTTAGGGTAGCGAATGTCA[C/T]GGAAAGATAAGTCTGAATCAGGTCTTAAGGGATGA Y 2 1 2 1 101000 f 74 goat snp5018-scaffold117-1357717 4 71127942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438869 Affx-122930750 AX-123309206 4 46767316 ATGACCTCACTGTGGTGAACTGGGATATAGCTTAG[C/T]GTGCTAGGGTGAATGGCTTGGGGAAAGGTTTGTTG Y 2 1 2 1 101000 f 74 goat snp5019-scaffold117-1390927 4 71094464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430768 Affx-122937488 AX-123301109 4 46819395 CAAAGTACCATTTTATAATTCCACCAACGATGTAG[A/C]GTCCATTTTCCCTAGATATGTTATCGTTGTATTTT M 2 1 2 1 101000 f 74 goat snp5020-scaffold117-1443006 4 71042384 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777520 Affx-122939737 AX-385264639 4 46877379 TGTGTTTTTTCAACCAGAGTAAAAAGTTACCTCAC[C/T]ATGAACATGGAAGACAGCTCAACTCACAAAGCCAC Y 2 1 2 1 101000 r 74 goat snp5021-scaffold117-1500990 4 70984442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804261 Affx-986696751 AX-385290889 4 46890119 ACCTTATGACTACTTGACAGTGGTTGCTGAACATC[A/T]TGGCTAATCAATATTGAATTATATATTGCAATTAA W 4 1 2 1 600010 f 74 goat 4_46890119 4 46890119 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 320790999 Affx-122972518 AX-385277996 4 46950271 TAACTATACAGATTCCAATGTAGGAACAAAATGTC[A/G]TCAGCAGTAGTAACAGATGCAATCTTCAAATGCAA R 2 1 2 1 101000 r 74 goat snp5022-scaffold117-1573882 4 70911492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784350 Affx-122978771 AX-385271401 4 47001393 AGTTCCAGATCACTGACCAAAGTCAAGATCAAATA[C/T]GAAGCTGTCCATTTAAAAAGAGGTCATCTTTAATG Y 2 1 2 1 101000 r 74 goat snp5023-scaffold117-1625004 4 70860114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795064 Affx-122927543 AX-385282023 4 47041199 CAAAGGCAGGATTATCCCATCAGGAAAAAGATGCC[A/G]TGAGATGAAATAGGTGCCCTAATAAAAGCAAAACT R 2 1 2 1 101000 f 74 goat snp5024-scaffold117-1664810 4 70820532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796953 Affx-122922103 AX-385283894 4 47071258 AGTGATTGAACAAGAGGCACATACACTGATTTCAT[A/G]TCTCCTCACTTGTTGAAGAGAACACTCCTCAGATT R 2 1 2 1 101000 r 74 goat snp5025-scaffold117-1694869 4 70790492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766013 Affx-122975497 AX-385253433 4 47106610 TAGCTCTATTCTGAAGTAGGGCATGATAAGATCCA[C/T]GTATCATATGCCTTATGAAATAATTCAAGAAAAAA Y 2 1 2 1 101000 f 74 goat snp5026-scaffold117-1730221 4 70755209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802024 Affx-122922192 AX-385288928 4 47159063 TCTTTTCATTTTTCTTGACAAATCTAAACATGGTA[A/C]AGGATTTATATGGCAGATAGATAACACAACAAAGA M 2 1 2 1 101000 f 74 goat snp5027-scaffold117-1782674 4 70702058 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396070 Affx-122963442 AX-123266425 4 47187873 CCCCATCACTTCATGGCAAACAGACAGGCAAACAA[C/T]GGAAATAGTGCAAGACTTTATTTACCTGGGTGTGG Y 2 1 2 1 102000 r 74 goat snp5028-scaffold117-1811484 4 70673267 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377246 Affx-122978151 AX-123247605 4 47225853 TGCGTTAAAGGTTATAGAGTTTGGGGCCTTTTAAA[C/T]ACCTGTAGCTGAACATGAGTAATATGATTTGGGGC Y 2 1 2 1 101000 r 74 goat snp5029-scaffold117-1849464 4 70634699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416755 Affx-122948187 AX-123287103 4 47254994 TTTAAAGGTTTTGTTTTAAAGCATTTTCCATATAG[C/T]ATATATGCATTATTCCTGATAGTCTCCACATCCCA Y 2 1 2 1 303000 r 74 goat snp5030-scaffold117-1878605 4 70605754 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791335 Affx-122963054 AX-385278328 4 47288022 CTCAATACAATAAGCCTATTTGACCAGCTTTCTTA[C/T]ACCTTCCATACCAAAGGGCATACCTACCACTATGG Y 2 1 2 1 101000 r 74 goat snp5031-scaffold117-1911633 4 70572499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449048 Affx-122923065 AX-123319383 4 47323189 TTGGATGCTGCTCATTCTGGAAGGGAAGGCTCTCA[C/T]AGACTTCTTGTTATAAGGTATCCAATAGGTAATAT Y 2 1 2 1 201000 r 74 goat snp5032-scaffold117-1946800 4 70537123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451192 Affx-122921330 AX-123321526 4 47362294 AGATTTAATTGGAAGCCGGTGGGTCTGATGCTCAG[A/C]GAGTGATGCTTCTAAGGTACCTATTGTGGAAGAGA M 2 1 2 1 101000 f 74 goat snp5033-scaffold117-1985905 4 70498581 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430588 Affx-122936993 AX-123300929 4 47407342 TATTAGCCATGGTACTGCCATATTTCAACTTTCCA[C/T]GGTATAACAAGAAAATCATTGCTTTTACTCTGTAC Y 2 1 2 1 101000 f 74 goat snp5034-scaffold117-2030953 4 70454847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445777 Affx-122926061 AX-123316114 4 47495564 ATGTGCACTAAATATAAGACTATGGGAGGCATTTA[C/T]GCTTCTTATCATGATATCACTATGTTTTGAAAAAT Y 2 1 2 1 101000 r 74 goat snp5036-scaffold117-2119175 4 70364733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399075 Affx-122960887 AX-123269430 4 47538256 TGAATTATTAAACATTTACATCTGACTGGTCACAT[A/G]GTATTGTTTCTCTAAAAGTACACACCATTGATTTG R 2 1 2 1 101000 f 74 goat snp5037-scaffold117-2161867 4 70320842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803161 Affx-122971501 AX-385290024 4 47605452 TAGAGCTGCTTTTCTAGACATTGTATTTAACTTGG[A/C]GTATATAAGACATAAAGTAAGCCAGGGCTGTTTTG M 2 1 2 1 101000 r 74 goat snp5038-scaffold117-2229063 4 70262476 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272272 Affx-1111833428 AX-519546011 4 47628976 CCCTGTTGTTTTGTTTACTCAGGTTCTCCTCTGCA[A/G]GAACCATCTCACCTTGACCCCAACTAACAAGGAAA R 2 1 2 1 101000 f 74 goat 4_47628976_AF-PAKI 4 47628976 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795318 Affx-122976574 AX-385282276 4 47639969 ATTTATTTTATCCAACCAAGTGTCATGGACTTTAG[G/T]CACAGAGGTCCTATTACCAGATGGAAAGTCAGTGT K 2 1 2 1 101000 r 74 goat snp5039-scaffold117-2263580 4 70228051 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777552 Affx-122933764 AX-385264671 4 47678708 ACAAACAAAATCTACACAACTGGGTGAAGCCCACT[A/G]TGGAAATAATTTAGAGCCTATCAGTGCATCCTCTC R 2 1 2 1 101000 f 74 goat snp5040-scaffold117-2302319 4 70131233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772569 Affx-122974495 AX-385259717 4 47769513 GTATGATCTTAGGCAGGTCAGTTAAGGTCTGGTCC[A/G]TCCTTCCTCTGCTCATGCATAAATGGAGATGATTA R 2 1 2 1 101000 f 74 goat snp31311-scaffold345-7623023 4 70030303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375540 Affx-122979101 AX-123245899 4 47802445 AACACAAAAGTATAGCATTTTGAGGGGGACAGTAT[A/G]CTAGTGATCAAAGTCAACATCTTAAACTCCATGAT R 2 1 2 1 101000 f 74 goat snp31310-scaffold345-7590091 4 69997263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385426 Affx-122971327 AX-123255784 4 47837380 CACTAAATTCACAATGGACTTGGATCTTTCAAAAA[C/T]GTTTTTAACTGAACAACTCTTTACTGGCAAACAGA Y 2 1 2 1 101000 r 74 goat snp31309-scaffold345-7555156 4 69962352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802304 Affx-122950626 AX-385289208 4 47900653 AATTTATTTGCCAGGTGTTGAACTCATTAGGTTTA[C/T]ACAATTTAAAGGTGGTAAGTTTTCAACTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp31308-scaffold345-7491883 4 69898188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444287 Affx-122926762 AX-123314624 4 47929698 CGAAAACAAGACAAAAACAAACACACCAAGCACTG[C/T]GGGCCTGCACAGTTCTTTTCTTTTTAGTGCCAAGC Y 2 1 2 1 101000 f 74 goat snp31307-scaffold345-7462838 4 69868879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278232 Affx-1111836240 AX-519551720 4 47961346 GACTAAACAACAACAAAAATTACCATTTGTGAAGT[C/G]CCCACTCCATAAAAGATAGCTGAATGGCAGAAGTA S 4 1 2 1 102000 r 74 goat Random2.2K-437 4 47961346 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391073 Affx-122966840 AX-123261430 4 47984758 ATGTCGATTTTCACTCCTTTTCTTACACTTTATGA[C/T]GGAGAATTGCATTTTCCCGTAAGTGACAGATAGCA Y 2 1 2 1 101000 r 74 goat snp31306-scaffold345-7407778 4 69812824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784372 Affx-122944794 AX-385271422 4 48028845 AGAGCAAAACCATTACAACTGCTTTTTAACTGAGT[G/T]TTTAACTCAATGGAAAGACCAGGTTTTCAAAAAGG K 2 1 2 1 101000 f 74 goat snp31305-scaffold345-7363691 4 69769412 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278235 Affx-1111836241 AX-519551722 4 48031805 TTTGTCCTGGTGAGAGGCTGAAGACTAAGAAAACC[A/G]GGTTAATACAGTTCAAGCAGAGAGACCTGAAAAAT R 2 1 2 1 101000 r 74 goat Random2.2K-438 4 48031805 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452509 Affx-122920972 AX-123322842 4 48080751 CCTGAAAACTTTCAAAGAAAACTTTCACAGAAATA[C/T]AAGCAATCTAGAACAGACAAGACAATTCTCATAAA Y 2 1 2 1 201000 f 74 goat snp31304-scaffold345-7311785 4 69717464 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440997 Affx-122928965 AX-123311334 4 48114220 AGTCAGGCAGATCAGTAGGCAATAATCTAAGCAGT[A/G]GCTTTCTCTATAAGGAAGCGCAGAATGTCAGAAAG R 2 1 2 1 101000 r 74 goat snp31303-scaffold345-7278316 4 69683931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385828 Affx-122971016 AX-123256186 4 48147408 AATTGCTGGGTAGAAATCTTCTCACCAAGAATGGA[C/T]AGTTTCGCACTAGTGAAACAGATTTTCAAGGGTTA Y 2 1 2 1 101000 f 74 goat snp31302-scaffold345-7245128 4 69651699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378816 Affx-122976552 AX-123249175 4 48179781 ACATTTATTATTATATATTCTATGGATGATTTAAA[C/T]ACGTATTTATGTAAACATGGGCTTTTCTGTTTAAG Y 2 1 2 1 202000 f 74 goat snp31301-scaffold345-7212755 4 69619376 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793203 Affx-122952927 AX-385280181 4 48210870 AGCAGTTTCGATTTAATACTGGCACTTTTTTTCAC[C/T]GCGATCTTGCAGATCCTGTCAGCTTAACTGGGCTT Y 2 1 2 1 101000 r 74 goat snp31300-scaffold345-7181666 4 69588270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800302 Affx-122960744 AX-385287225 4 48270818 TTAACATGAGTACAGGTACTTATTTCCCAGTATAA[C/T]AGCTGTGTTTTCTAAGTATAATTTTGGAATTTCAT Y 2 1 2 1 101000 r 74 goat snp31299-scaffold345-7121718 4 69527205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393382 Affx-122965906 AX-123263738 4 48304297 CGGGGAGTGAGTAATTCATAATATTATCTGGCCAC[A/G]TCGTCCGTTCACTATTTCAGTGGCTGAAAACCTAA R 2 1 2 1 101000 r 74 goat snp31298-scaffold345-7088239 4 69493551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442192 Affx-122928797 AX-123312529 4 48341174 ACAGCAGAGTGCCACCTCTGGAATCAAACTGACCT[A/G]GCTGTGAATTTTAATTCTGTGTTCTTAACACTATT R 2 1 2 1 101000 f 74 goat snp31297-scaffold345-7051362 4 69456648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451318 Affx-122921279 AX-123321651 4 48374020 CATGACACAAGGCATGTGTCTCGAAGCCAGTTCTT[A/G]TTAGTGAGTGCTGTGGAAACAAGGTGGGTTTTGGC R 2 1 2 1 201000 f 74 goat snp31296-scaffold345-7018516 4 69423953 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438759 Affx-122930815 AX-123309096 4 48412389 AAATTGAGATACACATCAGTAAAACTTGGGTCAAA[A/C]TACTTTTTTCATTTAAATCTCTTAAGCCCCAGAAG M 2 1 2 1 101000 f 74 goat snp31295-scaffold345-6980147 4 69385636 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388827 Affx-122968893 AX-123259185 4 48475270 AGGTGGCACTCATGAAGGAATTCTTTTTTCCTAAT[A/C]TATTAATATTAGCTGACTATGGAGTAGGAAATGGC M 2 1 2 1 101000 f 74 goat snp31294-scaffold345-6917266 4 69322970 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430543 Affx-122937027 AX-123300884 4 48523382 CGTGGACTTACTGCTATAACACTGGAATGTGGGGA[A/G]ACTTTCCACATGAAAATAAAATTTTAGCACCGTTC R 2 1 2 1 101000 f 74 goat snp31293-scaffold345-6869154 4 69274572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785505 Affx-122931960 AX-385272550 4 48558787 AGATCTCAAAGTTTGGGATAAGAGGCAGACCTACT[A/G]TTATAACCAAATTATTCACAGGGACATATGAAAAA R 2 1 2 1 101000 f 74 goat snp31292-scaffold345-6833749 4 69239490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414307 Affx-122949581 AX-123284656 4 48588819 CTCAGCGCATCTCCCAGAAGAGGGGAGTTAGAAAT[A/G]CATGGAGTGTGACTGTCAGCTTAGAGGCCTTTCCT R 2 1 2 1 101000 f 74 goat snp31291-scaffold345-6803717 4 69209489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400538 Affx-122960440 AX-123270893 4 48619228 AGATTTCTCCACATAATATCAAACACCCTAAATCA[C/T]ATTTTCACTAAAACAGTCATCTGACGGTCAACAGA Y 2 1 2 1 101000 f 74 goat snp31290-scaffold345-6773308 4 69179248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800130 Affx-122971759 AX-385287053 4 48651867 AAATATGATTCTCAGTTACATGCTAATATTAATGT[A/G]TCTCAAGACAACCAGCTCTCAGGGACCATTAGGCA R 2 1 2 1 101000 r 74 goat snp31289-scaffold345-6740669 4 69148668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452269 Affx-122920761 AX-123322602 4 48689037 AAAAAGATTCTCAGCAGTTCCCCCCAAAATGCCTG[C/T]GTTCTAAAAGAATTACATGAAGAATTAAGGAAATC Y 2 1 2 1 201000 r 74 goat snp31288-scaffold345-6703499 4 69111475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451642 Affx-122921607 AX-123321975 4 48721716 TTGGGCAATTGAGTCCTAGATTCTGAGACAAAAAC[C/T]TGGGTTCCAGTTCTGGCTCTGTCATTTACTAATCA Y 2 1 2 1 201000 f 74 goat snp31287-scaffold345-6670820 4 69078372 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425248 Affx-122940993 AX-123295594 4 48765436 GCAAATAATAGATTTATTGGTTATTACCTTGTTGC[A/G]TCAGTAGTGATGAAGCACAGTTTCATCAGCATTAT R 2 1 2 1 101000 r 74 goat snp31286-scaffold345-6627100 4 69033701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278237 Affx-1111836242 AX-519551725 4 48793857 CCAGTCTGCAGTCCCAGCTCAGAATTCTGCTCCAG[A/G]ATCTCTGCAGACCTTGGGAAGAAGGGCTGAAGGAA R 2 1 2 1 202000 r 74 goat Random2.2K-439 4 48793857 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795589 Affx-122951358 AX-385282544 4 48806815 TAGAGTATATCTTGAGGAGTCAAACACTCTTTAAG[C/T]GTTTCGTGTTCAGTGTGTTTTCCAGGAGTGTAACT Y 2 1 2 1 101000 r 74 goat snp31285-scaffold345-6585721 4 68993561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449916 Affx-122922925 AX-123320251 4 48837832 CACATTTTAGCCCAAATGTCATTTTCTGAAATGAT[A/G]CCTTCTATAGCTTCCCAACCTAAGCCCTCTTGTTT R 2 1 2 1 101000 r 74 goat snp31284-scaffold345-6554704 4 68962432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422521 Affx-122943285 AX-123292867 4 48870093 CAGGAGAGATTTTAGCTGTCTTCACTGTTATGGTT[A/G]TCAGACCCTTTCTCTTCACATTAACTTGATTATTT R 2 1 2 1 201000 r 74 goat snp31283-scaffold345-6522443 4 68929920 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433658 Affx-122934568 AX-123303999 4 48901926 CCTATAACATGAGGATAATACCTCACAGGGTTATC[A/G]TATGGGTTAGGTAAGTTATTAATGCATGATTCAGA R 2 1 2 1 101000 r 74 goat snp31282-scaffold345-6490610 4 68898194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409492 Affx-122954050 AX-123279843 4 48985097 TAGTTATTTGTATTTTTTTGTTGTTGTAATTGTTG[C/T]TTATGTATCCTGATACAAGTCGTGTCAGATACATG Y 2 1 2 1 103000 r 74 goat snp31281-scaffold345-6407439 4 68813339 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404324 Affx-122957011 AX-123274676 4 49081017 AAAAGGCATTAGGGAGGTGTGTAGTAAACAAAGAG[C/T]CCATGGTTTTTCATTGTCTGAGTCCTTGCCAGAAC Y 2 1 2 1 101000 f 74 goat snp31279-scaffold345-6311519 4 68717040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440610 Affx-122929975 AX-123310947 4 49116518 TTTGAGACTCCAATACAATTATTCAGAGGAACCTA[C/T]GTACATGCCATGAAGGAGAAAAGCAGAGAGGTGGG Y 2 1 2 1 101000 f 74 goat snp31278-scaffold345-6276018 4 68684141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278084 Affx-1111836243 AX-519551574 4 49148629 AGGTTGATGGTGAGCTAACAGGGTGTCATCACAGC[A/G]GTTAACATTATCGATCCTTAGTAGCTAGTAGGTCT R 2 1 2 1 101000 f 74 goat Random2.2K-440 4 49148629 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767936 Affx-122968130 AX-385255152 4 49154243 AAACACACAAAATGAGAATTACAGTCCTAAGGGCA[G/T]AACTCTAGTGCAGGCAGATAACTCCTGAAGTGTAC K 2 1 2 1 101000 f 74 goat snp31277-scaffold345-6238293 4 68646628 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421566 Affx-122943851 AX-123291913 4 49206464 CCGGCTTCCTCTCCGTGTCTCCCTTCAGTGGTTCA[C/T]ATTCAGACCATTCAGTCAGGTTCATCCTAATCAAA Y 2 1 2 1 201000 r 74 goat snp31276-scaffold345-6186072 4 68594388 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767752 Affx-122970476 AX-385254979 4 49237253 TGAAGGCTCTCTCTTGAGAGCACATCTCCAATGCT[A/C]GCTATGCCTTCAGAGAAGTCTACAGAGGATATAGT M 2 1 2 1 101000 f 74 goat snp31275-scaffold345-6155283 4 68563612 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447107 Affx-122924478 AX-123317443 4 49352353 CATAGTAAGATTCTTCCCTGGGGGACTTTAACCTT[A/C]AGTTATGCTTTTATTTCCATACACCTGTTGGAATT M 2 1 2 1 101000 f 74 goat snp31273-scaffold345-6040183 4 68448334 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431256 Affx-122937122 AX-123301597 4 49384144 CCTATTCCACTGGTGATAATGACATAAGTTAGACT[A/G]CAATTTAGTTCCAATAAAACTTGTTTCTTCTTTCA R 2 1 2 1 101000 f 74 goat snp31272-scaffold345-6008392 4 68416324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392530 Affx-122966108 AX-123262887 4 49422061 CCCTTTGCTCTTGAGTCCCAGATGACTCTCTCAAG[C/T]ATTAAAGGTCACCTAACAGACACCAAAACAGTAAT Y 2 1 2 1 101000 r 74 goat snp31271-scaffold345-5970475 4 68379011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451873 Affx-122921060 AX-123322206 4 49458643 ACTCTTCCCCTTACTCCATTGTAGTCTCACAGGTC[C/T]TATTTTGCCAACTCATCAAACATGACCAAGGTTCT Y 2 1 2 1 201000 r 74 goat snp31270-scaffold345-5933893 4 68342480 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781602 Affx-122923202 AX-385268686 4 49495337 TCTGGCAGGATAGCAACTAATCAGAAAGTAGAAAC[A/G]CATAAATGCCGTTAAAATGAGAAACCACTTAAGGT R 2 1 2 1 101000 r 74 goat snp31269-scaffold345-5897199 4 68306024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425074 Affx-122941253 AX-123295420 4 49528341 ATGTTACAGCCTAGATGCTTCCTGAGGCCTCAGGA[C/T]GTTGAAGGCCCCATCAGTTTTCATTTCTGGCTCTT Y 2 1 2 1 101000 r 74 goat snp31268-scaffold345-5864195 4 68272735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441988 Affx-122928436 AX-123312325 4 49613256 ATTAACCCATTTATGTATGCAACAAATGGATGGAT[G/T]GCAGAGTTGTTCCTGACCTTAGGTCGACCTGACCT K 2 1 2 1 101000 f 74 goat snp31267-scaffold345-5779280 4 68186738 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441624 Affx-122928642 AX-123311961 4 49650828 GGGAACACTTTCCCACCACTTGTCATCACCTGTTT[A/G]TATTACATAAAGAAAATGGATTTACTTATCAGCAA R 2 1 2 1 201000 r 74 goat snp31266-scaffold345-5741708 4 68148435 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413525 Affx-122950622 AX-123283874 4 49688177 GCTCTGCCCTCTGCTGGGCACAGTTCTTGCTTTGC[A/G]GTCTCACATCATGCTCTTTTTAGTTTGACTATGCA R 2 1 2 1 101000 r 74 goat snp31265-scaffold345-5704359 4 68110711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775234 Affx-122945566 AX-385262365 4 49731300 TTTCAAGTAATACACTTTTGCTCTGTTTTGTGGAC[A/G]CATCTTTCTGATGTACTGTAGGGAAGTTATTCTGC R 2 1 2 1 201000 f 74 goat snp31264-scaffold345-5661236 4 68066673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786710 Affx-122950797 AX-385273741 4 49822899 AAAATAACTGTGTAGAAAAAGTAGATATAATCTAG[C/T]TCAAGGATGTCTAGAAGAAACTGTTCAGCAACTGT Y 2 1 2 1 101000 r 74 goat snp31262-scaffold345-5569637 4 67974500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454081 Affx-122919376 AX-123324414 4 49857413 AAGATTGGCACAACTGGACCTCTACTTCAGGAATG[C/T]AATGTGTCACAATATGCAAGATAATGGAAGAGGGT Y 2 1 2 1 101000 f 74 goat snp31261-scaffold345-5535123 4 67939402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417745 Affx-122947420 AX-123288093 4 49890290 TATGACTATTTGAGATGTTGTACTTTAAAAATGTC[A/G]TGAGAGGTCACCAGTGGGTTCACTCGTGCCCTGAC R 2 1 2 1 201000 f 74 goat snp31260-scaffold345-5502246 4 67906406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788102 Affx-122933907 AX-385275122 4 49929967 TTTTCATTATGAAATTGTGAATATTCTTTCAAGGA[C/T]GCCGAAAATAAACCAGAAACAAGACTGATTTCTTT Y 2 1 2 1 201000 f 74 goat snp31259-scaffold345-5462569 4 67865656 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448861 Affx-122923281 AX-123319196 4 50021594 CTATTATTATTTTCCTCATTTTTAAAATGTAAAAG[A/C]TAGAACTAATTCTTTACTGTGTATGCCTTCATGTA M 2 1 2 1 101000 r 74 goat snp31257-scaffold345-5370942 4 67773321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273694 Affx-1111833744 AX-519547306 4 50052309 TATGGTAGAGTTTTCTG[A/G]ACAAAGAAGTTCCTCTCTGGTCCCTTTAAGTGCAT R 2 1 2 1 102000 r 74 goat GoatD01.003392 4 50052309 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408763 Affx-122953391 AX-123279114 4 50057717 AAAAAATGACATAAGAGAAAAAAAAAAAAACCTCT[A/G]CTGCCTAGGGGAGAAAAAAAAGCATAACTGGTTTG R 2 1 2 1 102000 r 74 goat snp31256-scaffold345-5334819 4 67735504 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801728 Affx-122924845 AX-385288636 4 50086553 CCCCTTGAAAAACCAGTTCTATTAGTTATGATTTG[A/G]CATTGCTTTGCTATCACTGTTCATTTGAAATATTA R 2 1 2 1 101000 r 74 goat snp31255-scaffold345-5305983 4 67706784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781930 Affx-122933079 AX-385269011 4 50128905 AAATGTGAGATTTGATGTTGATGGGAGACATGTGA[C/T]GTATGATGGAGAAGATTCAATGAAGACTCCGTAGA Y 2 1 2 1 101000 r 74 goat snp31254-scaffold345-5263631 4 67660907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433541 Affx-122934997 AX-123303882 4 50162188 TTGCCCTGCCAGTGAAGGCTTCCAGGCATTCGCCT[A/C]TTCTGGATCCATGTCACCTTGCCACCTGCCTTTAT M 2 1 2 1 101000 r 74 goat snp31253-scaffold345-5230348 4 67626996 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411104 Affx-122951915 AX-123281454 4 50204462 CATCTTTACCATCCTTGAATACTAGTGACCCCCCA[A/G]CTGTCAATGACCATAAGACCCTTCATGCAGGGGAA R 2 1 2 1 201000 r 74 goat snp31252-scaffold345-5188074 4 67585003 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409632 Affx-122953534 AX-123279983 4 50257096 AACAAATTCTAATAATGTTTTTCTTTTAATTCTGA[C/T]ACCAGTTTATTCATGACACTCTGAGATTCAATTCT Y 2 1 2 1 101000 r 74 goat snp31251-scaffold345-5135440 4 67532413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389301 Affx-122968509 AX-123259659 4 50285969 AAACAGCAAAGTATTATTCTATCTAGGCATTCAAC[A/G]TAGGTTTATAATATTACAGCAGCAGATAAAACTTC R 2 1 2 1 101000 r 74 goat snp31250-scaffold345-5106567 4 67503659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802401 Affx-122939735 AX-385289305 4 50330501 GGTAATCATCCTTAATTCTTAAAACTGTTTCATAG[C/T]ATATTTGTAGACATCAGATTACCATTTTCTGGATA Y 2 1 2 1 101000 f 74 goat snp31249-scaffold345-5062035 4 67457742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801288 Affx-122948012 AX-385288200 4 50361272 TAGACTAACAGTTAACCATGCTTGGACTCTTGCCC[A/G]TTTGTCAAAAGGGAGAATTCAAATAAGGAAGTAAG R 2 1 2 1 101000 f 74 goat snp31248-scaffold345-5031264 4 67426357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405883 Affx-122955602 AX-123276235 4 50391488 TTAATACATAATTGGGAAAAAGAAACTGTCTTCCA[C/T]GGTTTTAGGGTTCTACCCCCAAATCTTTTCACAAA Y 2 1 2 1 101000 r 74 goat snp31247-scaffold345-5001048 4 67395710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384535 Affx-122973029 AX-123254893 4 50423589 GAAAAAGTCGCCAATAACTTGGCATATATCTATAC[A/G]GACTTCTTATCTCACCCCACAAAGTAACCAACCCC R 2 1 2 1 101000 r 74 goat snp31246-scaffold345-4968947 4 67363482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441508 Affx-122928726 AX-123311845 4 50463066 GGGAGAGGAAACTGGAACAAAGGGAAAATAATGAT[A/G]CGATATCAGCAAAGCTATAGGCTAGACTAGTATGA R 2 1 2 1 101000 r 74 goat snp31245-scaffold345-4929470 4 67323989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414016 Affx-122950264 AX-123284365 4 50521166 CCAGAGCAAGCTCTGGACCCCTACATTATTATGCA[C/T]ATGTACTTACTGGATAAAATTGCTTGCTAAAGCAA Y 2 1 2 1 201000 r 74 goat snp31244-scaffold345-4871370 4 67265580 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787615 Affx-122936196 AX-385274638 4 50565236 TTTCATGAGGTATCTTATATTTCAAGAGTCTAAGA[C/T]AATACTGAGCACAGAACAGGCCATCACAAAATAGT Y 2 1 2 1 101000 r 74 goat snp31243-scaffold345-4827300 4 67220858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272118 Affx-1111833429 AX-519545876 4 50595219 TTGAGTGATTTGCAGATATGTTCTTCCAGTCTGCA[A/G]TTTGTCTTTGCAGCCTCTTTGCAGGAGGTACAGAG R 2 1 2 1 101000 r 74 goat 4_50595219_AF-PAKI 4 50595219 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413623 Affx-122950553 AX-123283972 4 50601008 ATGTTCACATCCTGCTCTACTAGAACCTGCAAAAA[C/T]GTTTACACAGCAAGGGGCTTAAGATGGCTAATCAG Y 2 1 2 1 201000 f 74 goat snp31242-scaffold345-4791528 4 67185296 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405280 Affx-122956857 AX-123275632 4 50653289 ATAACCATTGAGCCTTTGTCTATGAATCATATAAA[C/T]ATAATGTTATGAAATGTTTTAAACTTCAGGAAATA Y 2 1 2 1 101000 f 74 goat snp31241-scaffold345-4739247 4 67134435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786684 Affx-122923148 AX-385273716 4 50699275 GGTACCCAGAAAGAAGCAATGAACTTAGATTTTGA[G/T]AAGCAGCAGTTTGTCAAAAACACAAATTAATTTCA K 2 1 2 1 101000 f 74 goat snp31240-scaffold345-4693261 4 67088139 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418579 Affx-122946375 AX-123288927 4 50732553 TTCCCTTGCTTAGGCCTCTAGAACCCTGTCATTTC[C/T]GGTATCTTCTCACTGTTTTAATAGGTAATAAGATC Y 2 1 2 1 101000 f 74 goat snp31239-scaffold345-4659983 4 67054856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798963 Affx-122976157 AX-385285893 4 50817390 TTTCTCTACAAGAAATTTCTAGAGGCTTAATGGAA[C/T]GTAAAATGACACAGCCACTACGAAAACAGTTTGGT Y 2 1 2 1 103000 r 74 goat snp31237-scaffold345-4575146 4 66972505 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273488 Affx-1111833649 AX-519547105 4 50854217 CTGTGTCGCTCAGCGTGTGTTAGATGATTTGAGCC[A/G]AAGCAGCTGCTGTCGTCTGTCCTGCCCTCTGTTCT R 2 1 2 1 201000 f 74 goat GoatD01.000523 4 50854217 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774857 Affx-122964542 AX-385261991 4 50857141 GCAATGTTTCTGCCCACCTGGATTTAGGTACTGTC[A/G]TGAGCTTTGAAATTCTGAGATTTTTACCCTATTTG R 2 1 2 1 101000 f 74 goat snp31236-scaffold345-4535395 4 66932452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447421 Affx-122924391 AX-123317757 4 50994247 TTACATCATTTTTATACAAATATATATTTTCTTAT[A/G]CTTTTTTTTTGTCCTATAAATAGATAATATTGTGA R 2 1 2 1 103000 r 74 goat snp31232-scaffold345-4398289 4 66794118 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396548 Affx-122962939 AX-123266903 4 51027961 CCAGAGAGCCTTATCATATTTGTTGTTGTTCAGTT[A/C]CTAAGTTGTGTCCTCATGGACTGTAGCATGCCAGG M 2 1 2 1 103000 r 74 goat snp31231-scaffold345-4364575 4 66760380 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415477 Affx-122948708 AX-123285826 4 51071852 AGAGATTATTGAAGGCCTCAATGTTCTCAGAAAAA[G/T]AGATGTAACATTTGCTGAGAGCAAGTTGGGGTTAG K 2 1 2 1 201000 f 74 goat snp31230-scaffold345-4320684 4 66717172 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799130 Affx-122974501 AX-385286060 4 51106681 GTATGCTATCCATTTGGTAGAGAATATGACTACTC[A/G]CAGATTTAGTCATATTCTTATGTTAGTGAATCATG R 2 1 2 1 101000 f 74 goat snp31229-scaffold345-4285855 4 66682547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452353 Affx-122920640 AX-123322686 4 51136366 GTGATACAGAGTTAATATTATGTTATAAAAGTTGA[A/G]CTCAAACTATATTTTCTTTCAGTGGGCCAGCTTGC R 2 1 2 1 101000 r 74 goat snp31228-scaffold345-4256170 4 66652913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783660 Affx-122945223 AX-385270719 4 51169549 CAAAACTAGAAGTATTCATAACATACCTTCCTACA[C/T]GGAGTTCCAGATAATATCTGTTTCAGGGTTTCTGG Y 2 1 2 1 201000 f 74 goat snp31227-scaffold345-4222987 4 66619559 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377015 Affx-122977721 AX-123247374 4 51228091 GTGTACACCTATTGTAAAGTTAAAGGAGTTGTACA[C/T]GAGAATCATTCTGCTCAGTTTTGCCTTAACATGGT Y 2 1 2 1 101000 r 74 goat snp31225-scaffold345-4164445 4 66561442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453693 Affx-122919696 AX-123324026 4 51277417 TGACCACCCACCCAGTAAATGAAAGCTTTCATGAC[G/T]ATCAGTAGGGCTTCCTTCTTTCCTCTTTTCAAGGA K 2 1 2 1 103000 f 74 goat snp31224-scaffold345-4115119 4 66511959 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775613 Affx-122941671 AX-385262743 4 51327657 TTAATTAGAAATGGTTTGATTTCAAGAAGTAATCC[A/G]TCCAAAAGTATAATCCAGGATTCTCTCAAAACTCT R 2 1 2 1 101000 f 74 goat snp31223-scaffold345-4064879 4 66461708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772290 Affx-122959286 AX-385259445 4 51366784 ATAAAGTATAATAATGTCCTTTATGTTGAGTTAGG[A/G]CTCTGCTGAAGTTCTTCTTTGGCGTCAGTGTTCAG R 2 1 2 1 101000 r 74 goat snp31222-scaffold345-4025752 4 66422056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788656 Affx-122933800 AX-385275672 4 51407578 TATTAACATTCTTCCCCAAAAATAGAAAGCCATGC[A/G]ATTGTAATATTGAAGACAATATGAAATCACTTCAT R 2 1 2 1 102000 f 74 goat snp31221-scaffold345-3984958 4 66380720 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397962 Affx-122961904 AX-123268317 4 51444895 TCTCTTTTATCTCCAAGGATAGATTAATGACAGTA[G/T]CATTTTTATTTGCTGTATTTTTATCTCCAGCAACA K 2 1 2 1 101000 f 74 goat snp31220-scaffold345-3947641 4 66342837 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391000 Affx-122966898 AX-123261357 4 51480502 AGTAACACAAAGGAGAAAATCCATTTCACTATTCC[A/G]CCTCCTTCCCATAGAGCCAAGCATGTAATAGACAT R 2 1 2 1 201000 f 74 goat snp31219-scaffold345-3912034 4 66306893 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434682 Affx-122933962 AX-123305023 4 51592322 GTCACTTCAGTTGTGTCCAACTCTGTGCGACCCCA[G/T]AGACGGCAGTTTCTTAGCAGTTTCACATTATTTAG K 2 1 2 1 101000 r 74 goat snp31217-scaffold345-3800214 4 66214478 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406882 Affx-122955639 AX-123277233 4 51640751 CCTCTTTACACACTAGGTGATATTATCTCTTACTT[A/G]ACTCAGATCCAGGGATGGAGTAGATACAATGCTAA R 2 1 2 1 201000 f 74 goat snp31216-scaffold345-3751785 4 66166018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406194 Affx-122956142 AX-123276546 4 51686073 GTGAAATAGAAATTTCATTATTTATATTTCACTGA[A/G]TATCACTGAGTGACCAAATCATACAGACTTTTATA R 2 1 2 1 101000 r 74 goat snp31215-scaffold345-3706463 4 66120648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423110 Affx-122942915 AX-123293456 4 51742523 GCCATAAGGAAAAATAAGGCTGGAACCAAGGATAG[A/C]GACTGATGTTGAGAGCTATTTCATATAAAGTGGTC M 2 1 2 1 101000 f 74 goat snp31214-scaffold345-3650013 4 66064013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382822 Affx-122973554 AX-123253180 4 51784276 CCTACAAGCTAATGGTGATGAAGAATCATTGTCAA[C/T]GATAAATAACATAAGAGATATCTGTCAGATATACA Y 2 1 2 1 101000 f 74 goat snp31213-scaffold345-3608260 4 66021890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415737 Affx-122948502 AX-123286086 4 51830904 TGTTTAGGGCTTTGGTCTATAGTTTGTTTATTAAA[C/T]AGAACTTTTCTTACTGAGTTATTAGGGTGGGAGTT Y 2 1 2 1 101000 f 74 goat snp31212-scaffold345-3561632 4 65974801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381595 Affx-122974795 AX-123251953 4 51890875 TTATTCCAAACACTAATGCAGTGAATGTATCTGTA[G/T]ATTTCTTTTTGTGTACATGTTTGAGAGTTTTGTTA K 2 1 2 1 101000 r 74 goat snp31211-scaffold345-3501661 4 65914251 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769570 Affx-122937977 AX-385256740 4 51942782 TGTCTTTAACCTAAGAGTGATAGTAAACCATCAAA[A/G]CATTTGGAACTAGGAGATGGCATGATCCAAGTTAT R 2 1 2 1 101000 r 74 goat snp31210-scaffold345-3449754 4 65860149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381053 Affx-122974626 AX-123251411 4 51972298 CAAATGTACAATAATAGAGAATATATGGTAACAAG[C/T]TATGAATAAATAAACAATAAAATATTTAATGCTTA Y 2 1 2 1 101000 f 74 goat snp31209-scaffold345-3420238 4 65830619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445221 Affx-122925506 AX-123315558 4 52020449 CCACTAGGTGGCACCAAATAGCCATAATTCATAGA[C/T]TGTATCCTAAACCTATACACAAGCCATTAAAAGAT Y 2 1 2 1 101000 f 74 goat snp31208-scaffold345-3372087 4 65782529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436199 Affx-122932595 AX-123306538 4 52071569 GCAGGCGAACAGCTCATTAGCTAAGGAGAAATTAT[C/T]TGAAAATTTCAAAAAGAAATGTTGCCTTCCTTTGG Y 2 1 2 1 101000 f 74 goat snp31207-scaffold345-3320967 4 65730803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388142 Affx-122969467 AX-123258500 4 52108056 GAGGATACTCGGTTGATTCCAGTACCGCTTTCTGT[A/G]CTTGAAGTTGTTGCATAAGATCTTCTTTTGAAGAA R 2 1 2 1 201000 r 74 goat snp31206-scaffold345-3284480 4 65694126 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450781 Affx-122921829 AX-123321115 4 52147510 AAATTCATTCTGAAGCAATGCTTGTGGAACTTTTC[A/G]TTTAAATTTCCAGCTCTGAATAGTAGTTGACGTCA R 2 1 2 1 202000 r 74 goat snp31205-scaffold345-3245026 4 65654700 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795985 Affx-122969474 AX-385282937 4 52207691 AAGAGGGAAAAGCAAAGTATTACAAAGAGAACAAC[A/G]TAAGTGAAGACAGGGAGATAGTAATCTCACGACCC R 2 1 2 1 101000 r 74 goat snp31204-scaffold345-3184845 4 65594529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439030 Affx-122930344 AX-123309367 4 52242468 TTATTGATTTGTTTTAAATAATGTTGTTGTATTTC[A/G]TTTTCACTCCTTGGCATATATTTCTCCCTTTCCAT R 2 1 2 1 101000 r 74 goat snp31203-scaffold345-3150068 4 65559524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407488 Affx-122954758 AX-123277839 4 52299811 ATTTGCTGCATTGATGCATTTGGTTTAATCAATCC[A/G]TACATAGCTTCATATAGTGGCTTCAAGCAATGAAT R 2 1 2 1 101000 f 74 goat snp31202-scaffold345-3092725 4 65501354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419777 Affx-122945862 AX-123290125 4 52328554 TTTATACATTGAAGATTTAACTTTTTAATCAAATG[C/T]ATTTATGAGAACAGCATGTGACATCTGAAACTTTG Y 2 1 2 1 101000 r 74 goat snp31201-scaffold345-3063982 4 65471772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406988 Affx-122955041 AX-123277339 4 52369485 CTCCTTCACACTTCACTGAGTGAGATGGAGCCACA[C/T]GCTCTCAGAGCACTTATTAAGCTCTCCTAAGTTCT Y 2 1 2 1 201000 r 74 goat snp31200-scaffold345-3023051 4 65430079 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796325 Affx-122976123 AX-385283275 4 52416094 AATATTTAATTGTTCACCTGTACAGTTAAAATGTG[C/T]ATTATGTTTTGATGAGCACATTTTCCAACTTAACA Y 2 1 2 1 201000 r 74 goat snp31199-scaffold345-2976442 4 65382971 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377686 Affx-122977420 AX-123248045 4 52483432 ATAACAATACAAATTTTGAAAGCGGCAAGGACAAA[A/G]TCAGCAAACCTAGAAACTGCTCATATTGGTATTGG R 2 1 2 1 201000 f 74 goat snp31198-scaffold345-2909104 4 65314160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378437 Affx-122976702 AX-123248796 4 52578951 ATGTATGTTTCTATGTATCTAAGAATGGGCCATTA[C/T]ACTATCTTCAATCTTCCAAAACTGATAGTCTTAAA Y 2 1 2 1 101000 f 74 goat snp31197-scaffold345-2813585 4 65217527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390548 Affx-122967218 AX-123260905 4 52642617 GAGAGGGAATTTCTCTGTGACTAAGATGCAGCCTT[C/T]AAGAAGAATATGAGTGATTCTCTGACCGTCCCCTC Y 2 1 2 1 101000 f 74 goat snp31196-scaffold345-2749919 4 65152637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771511 Affx-122934060 AX-385258669 4 52679191 TTTTTTTCCTTTTTAATATGGTAGGACGTGACCTA[C/T]TGAATATAATAAAAGCCTGGCTGATCCCCTTTTAT Y 2 1 2 1 101000 r 74 goat snp31195-scaffold345-2713345 4 65115872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406760 Affx-122955727 AX-123277111 4 52740187 GAATTATTTTACTTGTAAAAGATATTTTGTTTTAT[A/G]ATGTTAGGAGGCTTTGTCATTCAACACTTGAGGAG R 2 1 2 1 101000 r 74 goat snp31194-scaffold345-2652349 4 65054473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793123 Affx-122978259 AX-385280101 4 52787479 ACTGGCTGGTTCCTGTCTTAGAGGTGAGAACAGTT[A/C]CAAATTCCAAACTATATAGCCTAGGAGTTAACTAG M 2 1 2 1 101000 f 74 goat snp31193-scaffold345-2605057 4 65011823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786065 Affx-122935829 AX-385273101 4 52839133 ACCAGACCTTGCGTTGTTCTCTGGGTTCTTGATAG[C/T]CTCTTCAACTAGACATTATCAATCTTGAAAATTGT Y 2 1 2 1 102000 f 74 goat snp31192-scaffold345-2553403 4 64958628 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441104 Affx-122928887 AX-123311441 4 52880649 TGCTGGAACTTGAAGCATGTGAGATTTTTGAGTGC[C/T]TGAAAGCTCTCATTTCCAACAGCCCTCTATGGCTC Y 2 1 2 1 101000 r 74 goat snp31191-scaffold345-2511887 4 64915908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775710 Affx-122927347 AX-385262841 4 52944171 AATAAAATTCACATAGCCTTTCTGATTATGTAGGA[C/T]ATTTGTTTGAAATTCATCACAAGGAAATCAAGTGA Y 2 1 2 1 101000 f 74 goat snp31190-scaffold345-2448365 4 64852573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783305 Affx-122978322 AX-385270370 4 53003276 TCCAGTGCCTTGAACATGGCAGGATAGAGAAGGAT[A/G]CTGAATTGAATATAAGTATACTGTTTTTCTTTAAG R 2 1 2 1 101000 f 74 goat snp31189-scaffold345-2389260 4 64792607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440792 Affx-122929838 AX-123311129 4 53049545 GTCTCCATGGGATTGTCCTCTTCCTTTTCCAAGTA[C/T]GCTTGCTTCTCAGAGGGACAGGTATTCATTGCTCT Y 2 1 2 1 201000 r 74 goat snp31188-scaffold345-2342991 4 64746286 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272122 Affx-1111833431 AX-519545880 4 53098624 CCCACCTATTGATACTGCCAAACTCATAAAAATGA[A/G]TCTATAAGAAATTTAACATGTTCTCTGTTGTGCTT R 2 1 2 1 101000 r 74 goat 4_53098624_AF-PAKI 4 53098624 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402894 Affx-122958213 AX-123273247 4 53110509 ACACTGTATTAGTTCTATTCCTCTGGAGAACACTA[A/G]TACACACTTCCCAATAGAATCCTATGTATCTGGTG R 2 1 2 1 101000 r 74 goat snp31186-scaffold345-2282027 4 64685331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775062 Affx-122960462 AX-385262194 4 53143088 AAAAGGTACCTTTCTATAATATCTTAGTGCTAAAT[A/G]CTAAGTAACAGTGGTTTCTGCTAGGACAGGAGTCA R 2 1 2 1 101000 r 74 goat snp31185-scaffold345-2249448 4 64651751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401461 Affx-122958971 AX-123271814 4 53200250 TCCACAAATACGTGTATCTGCACAATAGTGAAATT[A/G]CCAGAGGTGGACTTACCTGCAAGAGCCCACTCTCC R 2 1 2 1 101000 f 74 goat snp31184-scaffold345-2192286 4 64594484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778788 Affx-122947633 AX-385265897 4 53245037 GTCCACAAAACCCTAAAGTTAAAAAGTCCAAAGGT[A/G]TAGCCTATGAAAGGTAAATGAGACCTCTACTCACA R 2 1 2 1 101000 r 74 goat snp31183-scaffold345-2147499 4 64549385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464297519 Affx-1110411635 AX-515771707 4 53279359 ATGCTTCTGCAGAAAACCCCCAAAGAAGTGGGAGG[C/T]AGGCATGGTATACACTGTAACATCTGACTGAGTCT Y 2 1 2 1 101000 r 74 goat GoatD01.000108 4 53279359 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409663 Affx-122953513 AX-123280014 4 53313784 GTAAGTATCAGTAGCAGTGGATATTGCTATGCTTT[A/G]TTTTGTCTTACTTGTTTTTAAATTTTATTTTGTTT R 2 1 2 1 101000 f 74 goat snp31181-scaffold345-2078752 4 64479872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379609 Affx-122976014 AX-123249967 4 53353974 GGGCTTTACTTAAAAGGGATGTTAACCGGCATATC[A/G]TTACAGTCAAAGTCATGTTCTATTCAACTTTAGTA R 2 1 2 1 101000 f 74 goat snp31180-scaffold345-2038562 4 64439198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771088 Affx-122951490 AX-385258248 4 53408111 TGGATCTTTGCTTCTCTTTATATAAGTAGGTAAAA[G/T]CATAATCAGTCTTTTCTTCTCTAGAAGTGACATAA K 2 1 2 1 102000 r 74 goat snp31179-scaffold345-1984425 4 64383958 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386138 Affx-122971406 AX-123256496 4 53453189 GTTCATTTCTTTCCTTTCAGTCCGTGGTAACCCCA[C/T]GGACTGTAGCCTGCCAGGCTTCTCTGTCCATGGGA Y 2 1 2 1 103000 f 74 goat snp31178-scaffold345-1939347 4 64339146 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784275 Affx-122953504 AX-385271326 4 53501320 TAGGTGAGATCACCTGGGAGCCAAGTTACAGATGA[C/T]GTGTAATCATTTATCTTTAGACTCCCAGCTTTGAT Y 2 1 2 1 101000 f 74 goat snp31177-scaffold345-1891216 4 64290577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768191 Affx-122928191 AX-385255381 4 53579065 AGACTGCAGAATGCATACAGAGTAAATGATAAAAA[C/T]GAGATACAAGCTGTGAACAACTGAAATGTTTTAAC Y 2 1 2 1 101000 f 74 goat snp31175-scaffold345-1813471 4 64212344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432459 Affx-122935800 AX-123302800 4 53613242 CTTCACTATAGCTCAGAAGGTGAAAGAGGCTGCCT[A/G]TGATGCAGGAGACCAGAGTTCAGTCTCCCGGTTGG R 2 1 2 1 103000 f 74 goat snp31174-scaffold345-1779294 4 64178396 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394667 Affx-122964371 AX-123265022 4 53739951 CACTGACCAAATAAAATTCAAAGCAAATATTCCAG[C/T]AAGTTTCTGGTGCTGTGTATCTCAGGATTCTTCAT Y 2 1 2 1 101000 r 74 goat snp31172-scaffold345-1652585 4 64051781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388362 Affx-122969338 AX-123258720 4 53777571 CTCTCAAGAGAAAATCAAAGCTAATCTTCATGGTT[A/G]TAATGAAGGATACAAGTAGAAGATTAGTTGGAATA R 2 1 2 1 101000 r 74 goat snp31171-scaffold345-1614965 4 64014176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278085 Affx-1111836244 AX-519551576 4 53827669 CACCCACCCTGGACTGTCTATATACATTTGGACTA[A/G]GAGAGAGAAATAAAGGTGCCTTTTTTTAAACCACA R 2 1 2 1 101000 f 74 goat Random2.2K-442 4 53827669 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413827 Affx-122949886 AX-123284176 4 53829673 ATCCCATGGTGATGGGGCACACGGCATCATGCTCA[C/T]AGGTGCATCCTCGAAGGGGACATAGACTTGAGTTA Y 2 1 2 1 201000 f 74 goat snp31170-scaffold345-1562863 4 63961885 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776298 Affx-122975834 AX-385263426 4 53861993 AAGGGTAACACAGGACTACAAAGACTTTTTAGTTA[C/T]GGTTCCTGTGCTGCTATTAACTCTCATTTTGGCAA Y 2 1 2 1 101000 r 74 goat snp31169-scaffold345-1530543 4 63929133 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792801 Affx-122928048 AX-385279780 4 53893327 CCTTGGTTTTAATGTTGCAAAGGCACTTTCCTAAG[C/T]GGCTACAAGAACAACTGAAGGTCAAACAGTAGAAT Y 2 1 2 1 101000 r 74 goat snp31168-scaffold345-1499209 4 63897877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410135 Affx-122952807 AX-123280485 4 53959158 CTAACTAGGCCCATATAAAAAGGGGAAATGTGGTT[A/C]CAGAAACAGACACACACACCTGAAGAAAGTCATGT M 2 1 2 1 202000 f 74 goat snp31166-scaffold345-1433378 4 63832362 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386788 Affx-122970919 AX-123257146 4 53988154 ACACATGCATCTCTGATAGTAGCAGTTGGGCAAAG[C/T]CCTACACCCATGGGCAGTGGGGTATGTCAGCTTCC Y 2 1 2 1 101000 f 74 goat snp31165-scaffold345-1404382 4 63803539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405190 Affx-122956920 AX-123275542 4 54020875 TGGCATTCAGGATGCTTTCCAGAAGCCTTACATGG[C/T]GACCATGAAGAATTCAAAAATATTTATTTTACTTC Y 2 1 2 1 101000 f 74 goat snp31164-scaffold345-1371661 4 63770347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410375 Affx-122952443 AX-123280725 4 54072832 GAGCTCATATTCATCAAGAATACAAAAAAACAAAC[A/G]CACATGTTCTCACAGAGAGGGACTGTGGTCTGTGA R 2 1 2 1 101000 r 74 goat snp31163-scaffold345-1319704 4 63718409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767262 Affx-122972374 AX-385254542 4 54184069 AGGTTACTCAACTACTTTTGACTGGGATTCTGTAG[C/T]AGTCAAGTACTCAGGGTTCAAATGAACCCCAGGCT Y 2 1 2 1 101000 f 74 goat snp31161-scaffold345-1208467 4 63606705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388916 Affx-122968840 AX-123259274 4 54233057 CACAGGAGAGGGGGTACCCAATAGACGCTGCTGTC[A/G]TCTTCGGGAGAGGAAAGCAGATACTGCCACAGTGA R 2 1 2 1 101000 r 74 goat snp31160-scaffold345-1159479 4 63556935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453151 Affx-122919991 AX-123323484 4 54292215 CTTAAGTAATTTGTGTAATAATTGTTGCATCTATT[A/G]CAGTAACAATAGAAGTTAAGGGCCAGGCTCTGGAG R 2 1 2 1 201000 f 74 goat snp31159-scaffold345-1100321 4 63497280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441941 Affx-122928579 AX-123312278 4 54340099 GTAAAATGTAAAACTGGAAATGTCGCAAAATCAAC[A/G]TGACCTTTAAAGTGTAACATTTCCCACAATCATTT R 2 1 2 1 101000 f 74 goat snp31158-scaffold345-1052437 4 63448933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445937 Affx-122925916 AX-123316274 4 54369482 TACACAGCAGCACTCAGGTACTATGCAACGAATGA[C/T]GCTCAAGACTGGTTGTTGTTGTTGTTCGGTCACTA Y 2 1 2 1 101000 f 74 goat snp31157-scaffold345-1023054 4 63419480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439789 Affx-122930501 AX-123310126 4 54403819 TGATTGCTCCATTTGAAGAGAAGAAATAATCTCAA[A/G]TCAACCAGGAAAATACCACAGTAAACAGTAAAGAG R 2 1 2 1 101000 r 74 goat snp31156-scaffold345-988717 4 63384618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396485 Affx-122963543 AX-123266840 4 54433095 GTAAAGGGTTATGTCCCAAAAATGTGTATTACCAA[C/T]ATATTAGCATATGAAAAAAAATGTGCCTGGATACT Y 2 1 2 1 101000 f 74 goat snp31155-scaffold345-959441 4 63355062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445366 Affx-122925414 AX-123315703 4 54468984 AGAGAATTACTGTAAACAAATACAAAAAACATCTA[C/T]GATCTTGTCTACTGTATCAATATGTTCATACAGAT Y 2 1 2 1 201000 r 74 goat snp31154-scaffold345-923552 4 63319200 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398778 Affx-122961429 AX-123269133 4 54515737 TACGCCTACCTTTCAGTGAAGAAGTGTTCATCTAA[G/T]AGAGCCGTCTAGGACACTCATCTTTGCCAGTAGAA K 2 1 2 1 101000 f 74 goat snp31153-scaffold345-876799 4 63272143 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789399 Affx-122970324 AX-385276409 4 54560891 TCAAGTTCAAACTCATTAGCACAGCTTACAAGGTC[A/G]TTTATGATCTCTTTACTCTCAAGCCTCCTCTCTTA R 2 1 2 1 101000 f 74 goat snp31152-scaffold345-831645 4 63226713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377524 Affx-122977474 AX-123247883 4 54592938 TATTATTTACCTTTGTGAAACAACCATCCAAATCA[C/T]TGTGAGCTACTTTCACAGCACAATGGCCAAAGTCA Y 2 1 2 1 201000 f 74 goat snp31151-scaffold345-799598 4 63194138 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434337 Affx-122934731 AX-123304678 4 54640076 TATGGGCTATTAGAAATATGCCAGTGAAAAAAATT[A/C]TCAGTCAAGGATAAACTCAGATTTGACAAACAGAT M 2 1 2 1 101000 f 74 goat snp31150-scaffold345-752460 4 63146475 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439582 Affx-122930073 AX-123309919 4 54673627 TATTCCTGTCATCACAAAATACAGGTGCTTTACTA[C/T]ACTCAATGGTTAAATAAAATGATGGTAAAACTCAA Y 2 1 2 1 101000 f 74 goat snp31149-scaffold345-718909 4 63112987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766836 Affx-122959089 AX-385254159 4 54737922 TAACTTTCAAGAAAATTTAAAATCCCATCCAGGAC[A/G]TGGAAAAGATACAAGACAATGAACTCTTTTCAGGG R 2 1 2 1 102000 f 74 goat snp31148-scaffold345-654614 4 63049788 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428506 Affx-122938766 AX-123298848 4 54781502 TTTAATGTAGCCATAGCAACCACCTATCTTTAACA[A/G]TTTTTGAACTTAAGCATCCAAATGTTTTGCTTCTT R 2 1 2 1 101000 f 74 goat snp31147-scaffold345-611034 4 63006638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452622 Affx-122920362 AX-123322955 4 54816810 GCATTCCCTTTTAAAAATAGTATTTCTATTTTTAG[C/T]ATCCCTTGTTGCTAACTACATTTAATTGGTTGACT Y 2 1 2 1 103000 r 74 goat snp31146-scaffold345-575726 4 62971267 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767822 Affx-122977401 AX-385255045 4 54850822 ACTCCCAATATATCTCAAGTCCACGGGCTTGGGAC[A/C]CACCATATTCACTGCCACCTCAATATTCAAGCCAC M 2 1 2 1 101000 f 74 goat snp31145-scaffold345-541714 4 62936952 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773514 Affx-122946964 AX-385260655 4 54883509 CTGATAACTACAATGTACACAATAGGAGAGTCTGC[A/G]TTAGTAATATGAATGTAACTTTGATCTCATATCTT R 2 1 2 1 101000 f 74 goat snp31144-scaffold345-509027 4 62903046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768661 Affx-122931306 AX-385255839 4 54918796 ATCTGGTAAAAAACTGTAATTGCAAGAATTTCATT[A/C]ATACTATAATAGCAAATCAAATTAATTTCAGATTA M 2 1 2 1 201000 r 74 goat snp31143-scaffold345-473740 4 62867220 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421989 Affx-122943790 AX-123292336 4 54948124 TTCCATTGTATTTATTCTACTGCCTGTATCTGTGC[A/G]TTACCATCTCTAGCTACTGTGGTGACATGCATTAT R 2 1 2 1 101000 r 74 goat snp31142-scaffold345-444412 4 62837823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408331 Affx-122953756 AX-123278682 4 55039965 GCATGGCTTCCTAGCAAACCAATTTAAACAGAACA[A/G]TGAACTTGTAATGCTTAATTTTATTTTTCAGAAAA R 2 1 2 1 101000 f 74 goat snp31140-scaffold345-352571 4 62744258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438572 Affx-122931162 AX-123308910 4 55118975 ATGACGGTGAACAGGTCCCCTTCCCCCACAAAAGT[A/G]CCATAAAGCAATTTAGAATTGTTCATAGGAATTCT R 2 1 2 1 103000 f 74 goat snp31139-scaffold345-273561 4 62665300 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766134 Affx-122978900 AX-385253540 4 55167467 TAGTCTTTTCAAGATAATATCCTTCGGCAGAAATG[C/T]AGATACACCAATGACAGAAATGCATATTTATCAAT Y 2 1 2 1 101000 f 74 goat snp31138-scaffold345-225069 4 62616471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413754 Affx-122949942 AX-123284103 4 55199627 ATTAACATTAGCATCATTACGATGCCATCAGCATT[C/T]CCTGTTTTTCTTGTGCTAAATATTTATTTTGCAAG Y 2 1 2 1 101000 f 74 goat snp31137-scaffold345-192909 4 62586289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423054 Affx-122942958 AX-123293400 4 55237686 ATGACAGGTCTGTGACTGTGGGTGCAGGAGAATAG[C/T]AAAACTCCAAGACCCTCAGGGTAGACAGAGAAAAT Y 2 1 2 1 201000 f 74 goat snp31136-scaffold345-154850 4 62547278 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432495 Affx-122935585 AX-123302836 4 55286255 GTGTGAGACTGGGTAAGGTGCTTCCACAGACAGTA[C/T]ACAGAACAATGTGAATTTAGTGCTTACGGAGAGAG Y 2 1 2 1 101000 r 74 goat snp31135-scaffold345-106281 4 62496493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771709 Affx-122921960 AX-385258866 4 55333773 AATTTTTGAAACCATATAAAATGTAGATAGGTGAT[A/G]CATAGATACATGATTGCACCAAATAAGATCTACTC R 2 1 2 1 101000 r 74 goat snp31134-scaffold345-58763 4 62447821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788979 Affx-122951920 AX-385275992 4 55388550 AAATGTGTTTGGTAGGGAAAAAATAGTAGCTGCGC[G/T]GTCCAAATCACTCTTAAAAGATACCAAGTTGGCTG K 2 1 2 1 101000 f 74 goat snp31133-scaffold345-3986 4 62392796 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777080 Affx-122951766 AX-385264203 4 55411677 TCATATATTATCAGAGTTACTGCTACTACCAGAAT[A/G]CATTATATTATAAACCTTTCTTCTGTTTCCAGGGA R 2 1 2 1 101000 f 74 goat snp45595-scaffold624-263438 4 62369937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770898 Affx-122968848 AX-385258061 4 55454105 TTCAGAACATTTACCATAGTTACTCATATCTTTTC[A/G]TTCAAGCCTTGAGCTCTTTCCCTTACCTCAAGCAG R 2 1 2 1 101000 r 74 goat snp45594-scaffold624-221010 4 62328365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436446 Affx-122932997 AX-123306784 4 55500867 TTTGATTAAAAAAAAAGTGTCAAAACAGGTACATA[C/T]AACCAAATATCCTCATCTATTTAATCCAACCTGTG Y 2 1 2 1 101000 r 74 goat snp45593-scaffold624-174248 4 62280326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429824 Affx-122938179 AX-123300165 4 55547203 GCACATCAGGACTTGTCCCCATTTTTCTCACGTTC[A/G]TATTCCTTATCCTCACGAAAGCCTACACCAGAAAC R 2 1 2 1 101000 r 74 goat snp45592-scaffold624-127912 4 62233783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784739 Affx-122968438 AX-385271787 4 55607592 ATATCGCCAGAGCTATGAAGAACACTCAGATGCCA[G/T]CTTCTCCTCCAGCTTATGGTGGGATAGATATCTCA K 2 1 2 1 101000 f 74 goat snp45591-scaffold624-67523 4 62173242 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439433 Affx-122930192 AX-123309770 4 55650441 TGAAATATCAACAATGCTTTAAAGCAGGAGTTCCC[A/G]ACTTCCAGGATCTAATGCCTGATGATCTGTGGTAG R 2 1 2 1 303000 f 74 goat snp45590-scaffold624-24674 4 62131896 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411435 Affx-122951826 AX-123281785 4 55678598 GAGGAGGGGAGAGAAAGAGAGAAAACTTTGCCTGC[G/T]AGTGGCCTTATTGTAACCCAAACCTTCTTTATACC K 2 1 2 1 201000 r 74 goat snp37245-scaffold453-2289668 4 62103172 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410948 Affx-122952036 AX-123281298 4 55752806 ATTTTAGAGCAGAGAGAAAGAAAACAAAGAATCCC[A/G]TAGAGACAAGATGAGTCAACCAGGATGATGACATA R 2 1 2 1 201000 r 74 goat snp37244-scaffold453-2215460 4 62028713 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385648 Affx-122971165 AX-123256006 4 55786087 GTACTTCCAGTGAGAAAATAAGTTGTAATTACTGA[A/G]ATATGCCCAAGGATGAAATTGTGATGTGAATGTTT R 2 1 2 1 101000 r 74 goat snp37243-scaffold453-2182179 4 61994934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398082 Affx-122961726 AX-123268437 4 55849554 GAATCTGAAGATGTGACTGGGTTGATATAATCTTA[C/T]GATAAAACTAACAGAGAGGGCACTTTTTATGAATG Y 2 1 2 1 101000 f 74 goat snp37242-scaffold453-2118712 4 61930477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380361 Affx-122975351 AX-123250719 4 55883500 CTCATTGAAAGTAAGATGGATAGTTCAAATACTAA[C/T]GTTCAATGGAAAGTTTATAAGATTATTCTTTTGCA Y 2 1 2 1 101000 f 74 goat snp37241-scaffold453-2084766 4 61896241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793965 Affx-122968842 AX-385280934 4 55931412 AAGTGATCTCCAAGTTAACAGAGTCCAAAATGGTA[C/T]GAAAAATTATCAGCAATTCCACAGGGAATTCTCTA Y 2 1 2 1 101000 r 74 goat snp37240-scaffold453-2036854 4 61848069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409795 Affx-122952970 AX-123280146 4 55989658 TATATTTAAAAATAAAATTAAAGATAAGCTGAAAT[A/G]TTCAAATACTATCTCTGAATGCCACAGTAAATTGA R 2 1 2 1 103000 r 74 goat snp37239-scaffold453-1978608 4 61789027 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272124 Affx-1111833432 AX-519545882 4 56022252 GCAAGCAGATTCTGAGCCACTGGACCACCAGGGAA[A/G]TCCAACTAAGTATCTTTTAAACCCTCACCTGGGCC R 2 1 2 1 101000 r 74 goat 4_56022252_AF-PAKI 4 56022252 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278087 Affx-1111836245 AX-519551577 4 56061967 GTTAGCAACACCTCACAGGCCTAGAATTTTCCACA[A/C]CACCACCAGGTTCATTTGTGGAGGAAGCAGCTTCT M 2 1 2 1 101000 f 74 goat Random2.2K-443 4 56061967 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395064 Affx-122964189 AX-123265419 4 56112700 AGTAGTTGAAGTCTCTTGAGTTCTTAGTATGTGTT[A/G]CTACATACACATTTAAATGCAGAGTTCCAAAGAAT R 2 1 2 1 303000 f 74 goat snp37236-scaffold453-1855566 4 61667263 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379649 Affx-122975944 AX-123250007 4 56164592 TCATTTATTAGCACTGATCACTTGTGTATAGGGAA[G/T]CACTGGGAGGTTCTATTTTTAAACATGTTTGTTAG K 2 1 2 1 101000 f 74 goat snp37235-scaffold453-1803674 4 61614823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790473 Affx-122945253 AX-385277476 4 56206956 AGCAAAGTGTCAGGTTTTCTCAGGTAGCTGATGGT[A/G]TAAAATCATCCATGCCCTGTGACTTAACAAAAGCC R 2 1 2 1 101000 f 74 goat snp37234-scaffold453-1761310 4 61572239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796911 Affx-122942100 AX-385283854 4 56329054 CTAATGTCTACCAAAATACACACCAAAAAATGGAG[A/C]TTAATCAGTGTCCAAGAGTGAACCCCCATCTGATT M 2 1 2 1 101000 f 74 goat snp37232-scaffold453-1639212 4 61449077 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396767 Affx-122962771 AX-123267122 4 56369778 CTAATAGACATAAACTATCAAATATTTTAAAGAAA[A/C]TTTTCCCTTCTGCTAAGAACAGTGGCGATTCATTA M 2 1 2 1 103000 r 74 goat snp37231-scaffold453-1598488 4 61408302 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400522 Affx-122961264 AX-123270877 4 56411222 TTATGGCCAACATTTATTGGTCTATAAACAGTTGG[A/G]TGATCAAACAGCTAGTCAGTCAGTCAGTTGAGTTG R 2 1 2 1 101000 f 74 goat snp37230-scaffold453-1557044 4 61366093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795262 Affx-122940060 AX-385282220 4 56454325 CTGAAGGTACATGTAAAAGTCACAACTTTTATCAC[A/G]TGTTATCCCTGATTTTTAAGTAATAGCCATCAGAA R 2 1 2 1 201000 r 74 goat snp37229-scaffold453-1513941 4 61323008 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397827 Affx-122962479 AX-123268182 4 56490224 ATGTTCATCTGTGAAGTCCCTTTTGCCATGTAATA[A/G]GATAACATATTCATAGGTTCCAAGGGTCAGGGTAT R 2 1 2 1 101000 r 74 goat snp37228-scaffold453-1478042 4 61286314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410775 Affx-122952677 AX-123281125 4 56530541 TCCAATATGTGCATTTTGTCAGATGCTAGATCTAC[A/G]TTACTACCAAAAAGTAACAAAATAATAAGAAGCTG R 2 1 2 1 101000 f 74 goat snp37227-scaffold453-1437725 4 61245180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411598 Affx-122951609 AX-123281948 4 56580174 CTACTCCAGGGCTTTTACACATTTCATTTCCTATA[C/T]TTGGACTGTTTCTTCTCCCTTCTTAATACCCTCCT Y 2 1 2 1 201000 f 74 goat snp37226-scaffold453-1388092 4 61195349 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803157 Affx-122953762 AX-385290020 4 56630089 ACCTAAATTAAATTGGTTATGAATGTCAGTGATAC[A/G]CTAGTGAAGATTAACAAAGAGCTCAGAAGATACTG R 2 1 2 1 101000 r 74 goat snp37225-scaffold453-1338177 4 61145044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452155 Affx-122921658 AX-123322488 4 56671490 ATGGTTATTAAAAAAAGTGGGCATGTGGAAATTTT[A/C]TAGCATGTTCAAGAGTTAATAGAATAGTATAATGT M 2 1 2 1 101000 f 74 goat snp37224-scaffold453-1296776 4 61103045 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797403 Affx-122937093 AX-385284342 4 56715554 GAGAAATAAGTTTATTAAAGGCAAGAAAATCCAGC[A/G]TGAATGGCACTTTACTTAAGACTAAAGGTTACCAA R 2 1 2 1 101000 r 74 goat snp37223-scaffold453-1252712 4 61057609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799941 Affx-122964481 AX-385286867 4 56751769 AAAATAATAAATCAACTTATATGATGAAATCAAAG[C/T]ATTAACTTGGATTGAGAGGCCAAAGCAGATTTTGA Y 2 1 2 1 101000 r 74 goat snp37222-scaffold453-1216497 4 61021395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405432 Affx-122956059 AX-123275784 4 56786645 TTCTACTCCTTTGGCTATTTCTTTTTCCCTTTTTG[C/T]ACTTCATTCTGAAACCCCAAGACTTATCTCTTAGT Y 2 1 2 1 201000 r 74 goat snp37221-scaffold453-1181621 4 60986663 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442253 Affx-122928284 AX-123312590 4 56826533 ACCTTAGATTTCTCAGACACAAAATGTGGATCTCT[A/G]TTGGGCATGAAGTTTTGTTTTGTTTTTCCCTAACT R 2 1 2 1 101000 f 74 goat snp37220-scaffold453-1141733 4 60944652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779309 Affx-122973145 AX-385266413 4 56881254 ATCAAGTCTCTGTGAGGGTGAAATGGGATAATACA[C/T]GCAAAATGCTCTCTTCCATGCCTGGTACATGGTAT Y 2 1 2 1 101000 f 74 goat snp37219-scaffold453-1087012 4 60888772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415059 Affx-122949479 AX-123285408 4 56923762 ACAGCTCTGAATATCCAGAGATTCACATAGTTGGG[C/T]AGAGAAGAGAAGGGGGAGGGAGGAGATAGAGATGA Y 2 1 2 1 101000 f 74 goat snp37218-scaffold453-1044504 4 60847725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418759 Affx-122946202 AX-123289107 4 56955520 TCTTGAAAATTGTAGCAGCCTCAGTCACTTTGTTT[A/G]CATATTATGGAGTGGTCCCTCCTACCCTCCTTTCC R 2 1 2 1 101000 r 74 goat snp37217-scaffold453-1012746 4 60815642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377596 Affx-122978309 AX-123247955 4 56986417 GTAGTAGCATTCTACATATTGCAGTTGGGGAAGAC[A/G]CCCTGGAGACCTAAAAAAGGGGCAAGTGAGCCATA R 2 1 2 1 201000 f 74 goat snp37216-scaffold453-981849 4 60784687 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434154 Affx-122934901 AX-123304495 4 57025345 AAGGTACATGTCCTATTGGTTTCAAAGAGAATAAA[C/T]GACATGATATACTATCTTAGATTTTTCATTTAATT Y 2 1 2 1 202000 r 74 goat snp37215-scaffold453-942921 4 60745821 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440322 Affx-122930203 AX-123310659 4 57062555 CTTGGCACATGAGCCCTTGCATATATGAGGGATGT[A/G]GGAAAATAAATTAATATAAACTTATTAACATCTAG R 2 1 2 1 101000 f 74 goat snp37214-scaffold453-905711 4 60708843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422749 Affx-122943244 AX-123293095 4 57092454 GATCTTGGATCCAGGATCCAGAAAGGACTTACCAA[G/T]CATTTCCAGAGACAGTGAAATCAGGGGCTCACGCA K 2 1 2 1 102000 f 74 goat snp37213-scaffold453-875812 4 60678669 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428599 Affx-122938697 AX-123298941 4 57123986 CCCACATTGCAGGCAGATTCCTTACCATCTGAGCC[A/G]CCAGAGAAGCCCCAACACTTGTATAATAATATAAA R 2 1 2 1 303000 r 74 goat snp37212-scaffold453-844280 4 60646730 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407952 Affx-122954354 AX-123278303 4 57155269 AAGTTTGTATATATTTGAAGGTTTTGTTGGAGATG[A/C]GAGGTAAAGTGGGATGTATATGTAAATGTAGTGAG M 2 1 2 1 101000 r 74 goat snp37211-scaffold453-812997 4 60614370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273791 Affx-1111833816 AX-519547402 4 57168749 GGGTCCACAACCGCACTTTGAGTAGCATCATGGTA[A/G]CACATACAACACAGGAGGCTGCAGTAAGTAATTTG R 2 1 2 1 201000 r 74 goat GoatD01.005801 4 57168749 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443011 Affx-122928174 AX-123313348 4 57241362 ACATATCTTTTTTCATTTTTAGAATATACATTACT[C/T]ATTCAAGGAAAATCTGAGAGAGGTAAACTTTCTGA Y 2 1 2 1 201000 f 74 goat snp37210-scaffold453-726904 4 60527825 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406934 Affx-122955078 AX-123277285 4 57297429 AGAACAAAGCGTCCTTTCAAGATTATAACTGGCTA[C/T]AATTTGCCATCAATCAGACTAATTAATCTCCTGAG Y 2 1 2 1 101000 r 74 goat snp37209-scaffold453-670837 4 60470712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423276 Affx-122942658 AX-123293622 4 57330726 GGGTGTGATTTGAGCATGAAAAATTTCTTGAATTC[A/G]CTGAATACATGCTGAACTAGAAATGGAAGAATAAC R 2 1 2 1 101000 r 74 goat snp37208-scaffold453-637540 4 60436733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424917 Affx-122941297 AX-123295263 4 57360890 GACCCAGACTTAGAAGTCATGCAGTGTCATTTGTA[C/T]GTGTTAGAACTTGAGCCCACACTCAGGGGTAGGGG Y 2 1 2 1 101000 f 74 goat snp37207-scaffold453-607376 4 60406329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376463 Affx-122978048 AX-123246822 4 57395923 CGTTAGAGGTCATTCACTATGATCGAATAACTATA[C/T]GTGAAGTTGCAACATTATTGTATAAATAAAGGCTA Y 2 1 2 1 101000 f 74 goat snp37206-scaffold453-572343 4 60371367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784852 Affx-122977313 AX-385271899 4 57445297 TCAAAGCACAGACTTGGAGAAGTAGTTTTCACTTG[A/G]CACATTTCTCTCCTACACCCATACTTCATGGCAAT R 2 1 2 1 101000 f 74 goat snp37205-scaffold453-522969 4 60321840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439322 Affx-122930948 AX-123309659 4 57487928 GATACTTCTTGGACTCAGTCCCCCAAAAGAAGTGA[C/T]AAACAGGTCTGTGACCTCTGTGTGTGTCCCTTGAT Y 2 1 2 1 102000 f 74 goat snp37204-scaffold453-480338 4 60278944 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793557 Affx-122936225 AX-385280532 4 57521644 TAATTCTAAAAGCCAAAATTTTGATCTCAGTGATC[A/G]TAAAAATTCAAACCTAATGTAAAGACACAGAAAAA R 2 1 2 1 101000 f 74 goat snp37203-scaffold453-446622 4 60245129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778550 Affx-122976698 AX-385265662 4 57553322 TTAAACTCCTGTGTCATGCACCAAAACTTCAATGC[A/G]CTTTATGCAATGAGTGAGCCATTAAAAGGTCTTGG R 2 1 2 1 101000 f 74 goat snp37202-scaffold453-414944 4 60213189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767996 Affx-122933294 AX-385255210 4 57584999 TGAATGAAGACACTAATCTCCAACACTGGGGTGAA[G/T]ATTATTTCAGGCAAGCACCCAAGGTCTCTTCCAGC K 2 1 2 1 101000 f 74 goat snp37201-scaffold453-383267 4 60181503 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435308 Affx-122934021 AX-123305648 4 57621576 CCTAACTGGCATACTCTAATAGTCTTTACCAGTAG[C/T]ACCTGACCATATAGAAATGAGCAGTTTCCTGTGGA Y 2 1 2 1 101000 f 74 goat snp37200-scaffold453-346690 4 60144983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405053 Affx-122956348 AX-123275405 4 57685728 TCCATTCCACTCCTATTACAGAAAGAGATAAGAAA[G/T]ACCTAGAAGCTGACCTCCTATTATTTAGGACCCAT K 2 1 2 1 101000 f 74 goat snp37198-scaffold453-282538 4 60080633 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785795 Affx-122954373 AX-385272835 4 57727617 TCTGCCCCTTTACCCATCATGTCAGGAAGAACAGA[C/T]CTGTTGTATTCATCACAATCCAAGCCCTGAGAAAG Y 2 1 2 1 101000 f 74 goat snp37197-scaffold453-240649 4 60039029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790083 Affx-122928124 AX-385277089 4 57757026 CTCAAACCATCAGCCCAACTCTTTCTGGGGAAATG[C/T]AGGAATATGAGCACGTAGTGAAGTCTGCTACTTGT Y 2 1 2 1 101000 f 74 goat snp37196-scaffold453-211240 4 60010119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384838 Affx-122971967 AX-123255196 4 57797726 ATTAAATACTATCCTATATAGGCCTTTGGCCACTC[A/G]ATAATGAGAAGAATGTCTCCCAAAGTGGTTCAAAC R 2 1 2 1 101000 r 74 goat snp37195-scaffold453-170540 4 59968183 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774964 Affx-122940423 AX-385262097 4 57846816 TTAAAGCGCTATCACCATACAAAAACTTATTAATC[A/G]CATTATCACAGTACCTTTTTCAGGACTGGTGTGAT R 2 1 2 1 201000 r 74 goat snp37194-scaffold453-121450 4 59919054 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443497 Affx-122927802 AX-123313834 4 57895285 GGATAGAATGCTTACATTTTCATGTCTTGATCCCC[A/G]CATACTGCCTGTGTTAGTATTTCATTTTTTTTTTC R 2 1 2 1 201000 r 74 goat snp37193-scaffold453-72981 4 59870732 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419894 Affx-122945346 AX-123290242 4 57935056 TTTGGCAGAGTATTTAGAAAAGTGTAAAAGGTCGC[A/G]CTATTTTATATCAAACTAAAAAATGAGGGGACCAG R 2 1 2 1 202000 f 74 goat snp37192-scaffold453-33210 4 59830587 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449180 Affx-122923528 AX-123319515 4 57965462 ACAATGTAAAAGGCCCTAAGACTGAATGTGCTTGC[A/G]TGGAATGAGCTCCTGGCCTGGGAAAGGGAAAGATT R 2 1 2 1 101000 f 74 goat snp37191-scaffold453-2804 4 59800230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440751 Affx-122929868 AX-123311088 4 57986383 AGATGGGCAAGCTGAATAATACCTACCATTGTTGA[G/T]CAGGAAATGTGGTTTGTAAAGTGAGGCACAGGCCA K 2 1 2 1 101000 f 74 goat snp15778-scaffold1654-1545221 4 59779839 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387460 Affx-122970365 AX-123257818 4 58044496 TGAAGTATGGATAATTGTTGTGATTTCAGTCCCTG[C/T]GAAAAGAGACAGGCATTTCAAAGGTAGTAGGAGGA Y 2 1 2 1 201000 f 74 goat snp15777-scaffold1654-1487108 4 59721313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400958 Affx-122960115 AX-123271311 4 58082927 TTGTGGCCTCATCCTCTTTATCCCTCAGTTCTCCA[C/T]GCACTGTGTTGCTTCGCATTAGTCTATAGATGGGA Y 2 1 2 1 101000 r 74 goat snp15776-scaffold1654-1448677 4 59682790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424289 Affx-122941980 AX-123294635 4 58141816 GAGCAATTTAAAAATTGACACCAGGTGTTCTTTGA[C/T]ACACTTGCGGTGTTGCCTGAAAGGCAGAGAACAAT Y 2 1 2 1 201000 f 74 goat snp15775-scaffold1654-1389788 4 59624355 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796796 Affx-122946372 AX-385283739 4 58173550 CTCTTTAACATCACAGAACCTGAGAAGGACCAGTC[G/T]GTGACTGTGTCCTGTCTAATTCATACTCCTGAAAT K 2 1 2 1 101000 f 74 goat snp15774-scaffold1654-1358054 4 59592409 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420285 Affx-122945040 AX-123290633 4 58207250 GAACCTCTGTCTGTGCAGAAGGTTGGAGAAAGGTC[A/G]CACAGCTTCATTTTTAAAGACAGCTTTCAGTTGTT R 2 1 2 1 201000 f 74 goat snp15773-scaffold1654-1324354 4 59558357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399880 Affx-122960222 AX-123270235 4 58258865 GTAAGATGGTGGCTTTAGAGACTAGAATTCAAAAG[C/T]GGGACAGTATGGCCTGGTGGGGGGACTGGACAGAC Y 2 1 2 1 101000 f 74 goat snp15772-scaffold1654-1272739 4 59506815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769499 Affx-122945315 AX-385256669 4 58291326 GAGAAAGAGAGAAAGAATCTCTATCCAGTGTTAAG[C/T]AATTCCTGGTCCATGTTAGGCAATGGGAAGCAAGC Y 2 1 2 1 101000 r 74 goat snp15771-scaffold1654-1240278 4 59474502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384454 Affx-122973093 AX-123254812 4 58347455 AAATTCTTGTCTTTTTTTTTCATATCCATATATGA[C/T]GGTGTCTAGCAACCCATTATGAAAATCACTTGAAA Y 2 1 2 1 101000 r 74 goat snp15770-scaffold1654-1184149 4 59417362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782308 Affx-122934659 AX-385269386 4 58437880 AAACAGGGCATCTGCTAAAGACAAATGGAATCATG[C/T]GGCTTCATGGAGCCTACAGATTTTCAACCAGTGAT Y 2 1 2 1 101000 f 74 goat snp15768-scaffold1654-1093724 4 59327642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380064 Affx-122975562 AX-123250422 4 58528448 CCAGCAGGAAATTGGACCCTCTGGAAATACATTTC[A/G]TTGCTGGATTCCTAGAGTCGATAAATTCTGCATGC R 2 1 2 1 101000 r 74 goat snp15766-scaffold1654-1003156 4 59237778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278089 Affx-1111836246 AX-519551579 4 58548723 GGTCAGTTTGCAAAGAAAATTGAGTCCCAAGATAG[A/G]TCTTAGGCTGCTAAAGGAGTAAACAGATGGAAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-444 4 58548723 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431605 Affx-122936164 AX-123301946 4 58567775 GAAGCCTAATGAATGGAAAGGGAAGATAGGAAAAC[A/G]TGACAAGATCGCCCCGGAGACCCCTCTCATGGTTC R 2 1 2 1 101000 f 74 goat snp15765-scaffold1654-963829 4 59198823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391472 Affx-122966722 AX-123261829 4 58623491 ATTATGCAGAAATGCCCTGCTCTGCTTGCAGGCTT[A/G]TAGTTCTCAACAGAGATTTAGGAACCTAGATACTT R 2 1 2 1 201000 r 74 goat snp15764-scaffold1654-908113 4 59142988 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272127 Affx-1111833434 AX-519545885 4 58626247 ATACCTTGCAGTACCTTTCTACAGGCCCCTTATTC[A/G]TCTTTTCTTTCCATTCATCCTTGAGACATCATATT R 2 1 2 1 201000 r 74 goat 4_58626247_AF-PAKI 4 58626247 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422015 Affx-122943635 AX-123292362 4 58653245 AGAATGGGCTGCTTGAAATTTTAGACAAGTGGCTT[A/G]TGAAGGCCTGCAGGACCTGAGGAAACCAGCCCAGA R 2 1 2 1 101000 f 74 goat snp15763-scaffold1654-878359 4 59113195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448997 Affx-122923104 AX-123319332 4 58683183 AACTAGCCCCACACATCTAGGAGGGACAAATGAAA[C/T]GGTTCTTTACTGAGTGCCTCTTATGTGCCAGTCAC Y 2 1 2 1 102000 f 74 goat snp15762-scaffold1654-848421 4 59084037 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392007 Affx-122966491 AX-123262364 4 58737852 TAGGCTCTGAAGACAGGAGTGCAAACCAGATACAT[A/C]TTGAGGCTCAGTATGACTCAGTTTATGTACTGAAA M 2 1 2 1 101000 f 74 goat snp15761-scaffold1654-793752 4 59029362 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444266 Affx-122927206 AX-123314603 4 58775346 TTTCTGACATGTTCTTAGTAATGTGTTTGCTATCA[G/T]CAGGAAGATGTTACTTCAAATTTGATTCATATTTG K 2 1 2 1 10000 f 74 goat "snp15760-scaffold1654-756258;SV_290" 4 58992122 T G SV_290 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420470 Affx-122944876 AX-123290817 4 58827198 GTTGGAAAAACAATAGCCAACAAAAATCAGCACCT[A/G]TATGTCAGGCAGTATTTCAAGTACATAAAGTATTG R 2 1 2 1 10000 f 74 goat "snp15759-scaffold1654-704406;SV_288" 4 58939928 G A SV_288 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405552 Affx-122955965 AX-123275904 4 58866353 GTCAGACAGACATGCAGTCAAATCCTGGCTTTGCC[A/G]CTTACTAGATGTATAAGTCAATGATAGGTTTAGGT R 2 1 2 1 201000 r 74 goat snp15758-scaffold1654-665251 4 58900427 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798370 Affx-122957498 AX-385285305 4 58895279 TGTACATTCTTAATCTTTAAACTGTGAATTTTAGT[A/G]TTGTTCACCCTGCATATAACACCCCTCCACTGCTC R 2 1 2 1 101000 r 74 goat snp15757-scaffold1654-636325 4 58871508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797347 Affx-122950160 AX-385284286 4 58941218 TAACCTTTTAGTCCATTGTTTCTTAAGATTTTTGC[A/G]TTCATAAACACTAGTTATATCATCTTTTAGGGATA R 2 1 2 1 101000 f 74 goat snp15756-scaffold1654-590386 4 58825379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435832 Affx-122932825 AX-123306171 4 58975013 AATAATTTCCTCTAGAACTCCAAAGGGGCATTCTG[C/T]GCTTAGCTGTTTCTACTCACAGGCCAAATTAGGTA Y 2 1 2 1 101000 f 74 goat snp15755-scaffold1654-556591 4 58792399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427585 Affx-122939469 AX-123297928 4 59008164 GGTTTCTATTAATTATATAAATTAACACATAATGA[C/T]AGCCTTTCTCCATGTACCCTCTGTGAGGAATGATA Y 2 1 2 1 101000 r 74 goat snp15754-scaffold1654-523440 4 58759336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436053 Affx-122932714 AX-123306392 4 59045815 TGTTGAAGATCATGTTTTTCATCATACATTACTCA[C/T]TTACCATTTTGGCTTCTATCCAGCTCTCAGTGCTA Y 2 1 2 1 101000 r 74 goat snp15753-scaffold1654-485789 4 58720509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792581 Affx-122951252 AX-385279562 4 59088312 ATCCAAACATTAAAAACCCCAAAATGATGCTTATC[A/G]TTCTGAATTCTCTTGGCTCACTCTTTGCCTTGCCT R 2 1 2 1 202000 f 74 goat snp15752-scaffold1654-443292 4 58677252 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434841 Affx-122934380 AX-123305182 4 59124243 GTAAGCCTGGAGGACAAGCAAAGGAGGCACTTGGA[C/T]GAAGCCATGGAGATGGAGCCAACTTTCCACAAGCA Y 2 1 2 1 102000 r 74 goat snp15751-scaffold1654-407361 4 58641070 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415115 Affx-122949437 AX-123285464 4 59154921 GCCAGCAGGGGCACAGAGGCCAAAGGAAGCAAAGC[A/G]TGTGAGGACAGCAGGAAGGAGACCAATTTAGTTCA R 2 1 2 1 101000 r 74 goat snp15750-scaffold1654-376683 4 58610546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778020 Affx-122969894 AX-385265136 4 59188425 TTCTGTGTTAGAACAATGAGTGAAAGTGCAGGGCC[A/G]CTGCCAAACTTAGAATTGAAACTATTCAATTGCAG R 2 1 2 1 101000 f 74 goat snp15749-scaffold1654-343179 4 58577268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431286 Affx-122937097 AX-123301627 4 59220918 CAGATGAGTCCCTTGTGGCTGCAGGCTTCTACTTG[C/T]AGGCCCAGCTGTGTTCTGTTTCGGGGTCTCTCCTG Y 2 1 2 1 101000 f 74 goat snp15748-scaffold1654-310686 4 58544519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779874 Affx-122928439 AX-385266973 4 59274558 TGCCACTTTGCTTTTATGAAAGACCTTCATCAGTA[C/T]CTGTTTTTGCTATTCGAAAGGAATTTTCTCTTTTA Y 2 1 2 1 101000 f 74 goat snp15747-scaffold1654-257046 4 58490818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770406 Affx-122973995 AX-385257572 4 59369054 TAACTCCATGCCTCAATTCTTTTGGCTATGAAATG[C/T]AACATAAAAATACTGTTGTTCCTATCTCAAGATAT Y 2 1 2 1 101000 f 74 goat snp15745-scaffold1654-162550 4 58395689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403176 Affx-122958079 AX-123273529 4 59426047 TTGTAGATTTCTCCATCCTTCTTCCCATTCCAGGC[A/G]TCTAAATCAGAACTGAGGCGTGCTTTTGTTTATCT R 2 1 2 1 201000 r 74 goat snp15744-scaffold1654-105557 4 58338592 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410917 Affx-122952058 AX-123281267 4 59474151 GGGATGTTTTATGTATGAAAACTCTTCTGAGGAGG[C/T]AGATGGTGTGGGAAAGGTACATTCCATGCAAGTGT Y 2 1 2 1 101000 r 74 goat snp15743-scaffold1654-57453 4 58289189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440630 Affx-122929956 AX-123310967 4 59523695 ATTTGACTCTCTTAAGGTTAAGTCATCTATAAGAA[C/T]AGGAATTTAGAAAAATATTTGCAAACTCCATCTAG Y 2 1 2 1 101000 f 74 goat snp15742-scaffold1654-7909 4 58238652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403797 Affx-122957972 AX-123274149 4 59533870 TCTTCACCAGGAAGATACGAATGAGGTCAAACTCA[C/T]GGGGCTATTTAAATTTATGTTACTGCTCGGCTGGC Y 2 1 2 1 101000 f 74 goat snp56814-scaffold9-2636987 4 58226021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775028 Affx-122956198 AX-385262160 4 59698912 TCACCTATGGATTCCCATTACACTGGAATAAAATC[A/G]TACTTTTTCCCATGTCTTACAGTGTGTGTGATCTG R 2 1 2 1 101000 f 74 goat snp56810-scaffold9-2471945 4 58060412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408256 Affx-122953814 AX-123278607 4 59732173 AAGCAGAGGAAGTTCTGACACGCAGACAGAAGGGG[C/T]GCTGTAACCATGGGCTCAAAGATGGTATCGGTGTG Y 2 1 2 1 101000 r 74 goat snp56809-scaffold9-2438684 4 58027103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424774 Affx-122941404 AX-123295120 4 59779404 GCCTGAACAGAATGGGTGCCTGAAAGACATCTGCT[A/C]GAGGAATGAAAAGAGGAAAGGAAGAAAGGAGGAAA M 2 1 2 1 101000 f 74 goat snp56808-scaffold9-2391453 4 57979092 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399567 Affx-122961123 AX-123269922 4 59831556 TGCCTCCTGGTTGACTGCCTTACTGGTTGTTGACC[A/G]CTTGGCAGTGCTTCCTTAGCAGCAGGTGGGGCGAG R 2 1 2 1 101000 f 74 goat snp56807-scaffold9-2339301 4 57926964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767696 Affx-122947944 AX-385254932 4 59885872 AATAATACAGTTAATCAGCAAAGATTGGTATGATG[C/T]GTCCACATCATCGCTAACACACAAATTAAGTTGGC Y 2 1 2 1 201000 f 74 goat snp56806-scaffold9-2284985 4 57872703 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392592 Affx-122966058 AX-123262949 4 59916366 ATTTACACTCACAGCAATCTGTCATTTGGCTGTGA[C/T]GAGTTCTCTCATGAAAAGAGTTCTATGGACTTTTT Y 2 1 2 1 101000 r 74 goat snp56805-scaffold9-2254491 4 57841241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424529 Affx-122941724 AX-123294875 4 59950455 AGAATTGGAAGGTGCAAGAGCAATCCTTCTTTCCA[C/T]AGGAAGTGGCTTTCAGCCTTAGTCTCCATCTGTGC Y 2 1 2 1 101000 r 74 goat snp56804-scaffold9-2220402 4 57806533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379971 Affx-122975630 AX-123250329 4 59990147 AGTACTGCTTTCTTAGGGTGATGCAGAAAGACAAA[C/T]AAACCAACAGAACAGAAAAGAGAATTTGCACAAAT Y 2 1 2 1 101000 f 74 goat snp56803-scaffold9-2180710 4 57766722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450484 Affx-122922931 AX-123320818 4 60019692 TCATTTTCCCATTTGTGGGTCGACTCCCTGGGGGT[A/G]TGGATCTTGACTGCCGCATCTCCACCCCTCCTACT R 2 1 2 1 202000 r 74 goat snp56802-scaffold9-2151165 4 57737126 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426022 Affx-122941126 AX-123296368 4 60055190 CTCACTGGTCAGGTTCCCTAGGAAACAAACTCTGC[A/G]TCAGAGATTTGCATGCAGGAAGCTTACTGGGGAGT R 2 1 2 1 201000 r 74 goat snp56801-scaffold9-2115667 4 57701884 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385649 Affx-122971164 AX-123256007 4 60148472 GTTGGTTCACTGGGGCTTTCTCATGTTCCGAAGCA[C/T]AAGAAGAGAAGTTCTGAGGAGCTGCCTCTGCATGA Y 2 1 2 1 101000 f 74 goat snp56798-scaffold9-2022385 4 57607633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400077 Affx-122960752 AX-123270432 4 60181098 GACCAGATTCAGACTGCCAGGTCCACAGTGGATTC[A/G]CAAATATCTCAAACACCAGATGATTCTTTTCTGAG R 2 1 2 1 101000 r 74 goat snp56797-scaffold9-1989759 4 57575307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376042 Affx-122978938 AX-123246401 4 60217785 CCTGAATGTTTCCTTCAGTTTAAAAATGAACATCA[G/T]AAACACCATCGTAATGTCTGTAGAATATTTCATTG K 2 1 2 1 101000 r 74 goat snp56796-scaffold9-1953072 4 57538282 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385536 Affx-122971239 AX-123255894 4 60277285 GTGACTCATAGGGGTTCACAGAGGCCCACATTCTT[A/G]TCTGTGAGATGTTGCCTAAGAGAGACATCTTAGAA R 2 1 2 1 201000 r 74 goat snp56795-scaffold9-1893572 4 57477826 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441673 Affx-122929183 AX-123312010 4 60335356 ACTTTGGAAGTATCCATTTAATCCCCTTAATGTAT[C/T]GATTTCCCCAGGTGACACAGAAGAAACAGTGGCTT Y 2 1 2 1 101000 r 74 goat snp56794-scaffold9-1835501 4 57419971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400733 Affx-122959907 AX-123271088 4 60425892 CATTTTCCTTCTTATTTCAAGAAATGTGTGTTGCC[A/G]TTTCATAGTCTAGAAATACAGCATCTGCCAGCTGA R 2 1 2 1 201000 r 74 goat snp56792-scaffold9-1744965 4 57329454 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781187 Affx-122972405 AX-385268272 4 60459899 GAAGCCTCACGATCAGGAAGCCAGAGGAACTCTGT[G/T]TAAATGGGCTATGCCATTAACTAGTTGTGTGACCT K 2 1 2 1 202000 f 74 goat snp56791-scaffold9-1710958 4 57295461 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439532 Affx-122930116 AX-123309869 4 60559920 AAATTTAAAATTCAGTTTCTCAGTTGTATTAGTCA[C/T]GTCTTGAGTGCTCGCTAGCCATCTGTTGCAAGTAG Y 2 1 2 1 101000 r 74 goat snp56789-scaffold9-1610937 4 57197903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425294 Affx-122940957 AX-123295640 4 60593605 TCAGAACATTTTCACCCGTATCCTCTCATGTTGCC[A/G]TGGAAGGCAAGTAGAAGGAAGGACAAAAGAAAAAT R 2 1 2 1 101000 f 74 goat snp56788-scaffold9-1577252 4 57163734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429473 Affx-122938478 AX-123299815 4 60657779 GCGTGGCTGACGTCACCTTCTCAGCACAAGGAGCC[A/G]AACTGTCTCAATGTCTGTGGCTCCTTTCTGGAACC R 2 1 2 1 102000 f 74 goat snp56786-scaffold9-1513078 4 57098818 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440912 Affx-122929214 AX-123311249 4 60689489 GCTTTCCTCATGTGATAAAACAAATCCCTAAGAGA[G/T]CCTTTATTTATTACTATTTTTGAATGCGAAGACTT K 2 1 2 1 101000 f 74 goat snp56785-scaffold9-1481368 4 57067302 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387085 Affx-122969877 AX-123257443 4 60781741 ACCCTGGGAGAAGTGGTAGGTGAGTTCTCCACCAG[A/G]CCCCCTCCCTTCCCCCGTTTCCCATTGGTCAGAAT R 2 1 2 1 101000 f 74 goat snp56783-scaffold9-1389116 4 56974507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415356 Affx-122948777 AX-123285705 4 60814365 CAAGAATTTGTGTTCTAGTCAACCACTTACTTGCC[A/C]TGTGACTTTGAACAAGTAATTAATCCTTCTGAGAC M 2 1 2 1 101000 f 74 goat snp56782-scaffold9-1356492 4 56941761 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412622 Affx-122951273 AX-123282971 4 60848391 GAATCTCCCTGTTTGGCAGAGCCTGTGGAGCCACC[A/G]TGCTTGGTCAATGACTAATAGGGTTGGGAGATTAA R 2 1 2 1 101000 r 74 goat snp56781-scaffold9-1322466 4 56907298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278247 Affx-1111836247 AX-519551735 4 60852311 AAAATGTCAAAGTTGTGAAGTAGTCTTAGTTTAGC[A/G]GATCCTTCCTTTCTTATCATCTCTCTTCTTGCATG R 2 1 2 1 101000 r 74 goat Random2.2K-445 4 60852311 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774590 Affx-122972202 AX-385261724 4 60888665 TAAATAGTTGAGTTGCCTATTAGATTTGTCAAATT[A/G]CTTGCCCCAAAGTTAAACTGAAGTGCATGATAACA R 2 1 2 1 101000 r 74 goat snp56780-scaffold9-1282192 4 56866673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400022 Affx-122960793 AX-123270377 4 60919646 CGATATTTATGCTAAATATTATTTAAAACAATACA[G/T]GTTTACTGTTTCATGTAGACAGAGTAAATTATGCA K 2 1 2 1 101000 r 74 goat snp56779-scaffold9-1251211 4 56835576 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432144 Affx-122936429 AX-123302485 4 61028178 TAGGTAATTTATCATTAATTGGACATCTCAATAAT[C/T]ATAGGCATTATTATACTTTTTATCTTTGTTACTCC Y 2 1 2 1 101000 f 74 goat snp56777-scaffold9-1142679 4 56726750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400562 Affx-122960420 AX-123270917 4 61074240 TTTAACTGGATGCTTCTGCTAAGGTATCTAACCAT[A/G]AGATTTTGTTGTTCACTAAAGCCTTTGACTGTGTG R 2 1 2 1 101000 f 74 goat snp56776-scaffold9-1096617 4 56680674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397938 Affx-122961923 AX-123268293 4 61119589 TTATATACACACAGATGACATTTGCCTCTCTGACT[A/C]GTCCCATTTAGATTTCATACCTTCTTCAGATACTT M 2 1 2 1 201000 r 74 goat snp56775-scaffold9-1051268 4 56634833 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464303591 Affx-1110414694 AX-515777733 4 61162441 TACACAAATTAGTCTAATTAATTATAGAATATATT[A/G]TAGTCACTTGGACCAAAATATGTATATCTCAATCT R 2 1 2 1 101000 r 74 goat 4_61162441_AF-PAKI 4 61162441 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784244 Affx-122972133 AX-385271295 4 61174663 GAGATTTGCTGTGCTTGGCTTCTTCACATGATCTT[A/C]GTTTGTGGGAGAATTTTGACCTTATTTGATGCATG M 2 1 2 1 101000 f 74 goat snp56774-scaffold9-996194 4 56579650 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450340 Affx-122922119 AX-123320675 4 61213935 CACAAATGCTCACATATAAATCTGTATACACATAC[A/G]TACAGACTGACATATATATGTAGATTGTTTTAATT R 2 1 2 1 101000 f 74 goat snp56773-scaffold9-956922 4 56539290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409780 Affx-122952981 AX-123280131 4 61315316 TATATTCCTTTTTTTTCATTCATTAACACCCATTC[A/G]TTTTATAAATACTTACCATGTGTCTACTTTGTGTC R 2 1 2 1 202000 r 74 goat snp56771-scaffold9-855541 4 56437824 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379647 Affx-122975946 AX-123250005 4 61359074 TATTTTATAGCTGGTGTGATCCCCCCAGATTCAGT[A/G]CTTCATTTTGATGTACTTCTGATGGATATTTGGAA R 2 1 2 1 201000 r 74 goat snp56770-scaffold9-811783 4 56394562 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452774 Affx-122920251 AX-123323107 4 61401989 GAGCAGTCATCGTGATGCAGGATGCCCCTGGAAAT[A/G]AGGTACGGCCTTGGATAGGATGGCTGGCTTCAAGA R 2 1 2 1 201000 r 74 goat snp56769-scaffold9-768868 4 56351284 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400150 Affx-122960697 AX-123270505 4 61484405 AAACGAATATATTCAAGGAGAAATGAAGCTTTGCA[A/G]TGAGCTTTCACACCTGGGATACCTGCCACCCTGCA R 2 1 2 1 201000 f 74 goat snp56767-scaffold9-686452 4 56268590 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794837 Affx-122943895 AX-385281797 4 61521711 TTGGTTGAGATGACATCAGATTAAAAACTGTTTTC[A/G]TCCTAGGATATTTTTAGAGGCTGTTATTTAAGTTG R 2 1 2 1 101000 f 74 goat snp56766-scaffold9-649146 4 56230892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769911 Affx-122968467 AX-385257080 4 61553901 AAAATGTTTCTTCTCAAAAGTGCCCTCACTTAATT[C/T]GTTATGCCTTAAGAGATAATTCATAGAGTGGCTGT Y 2 1 2 1 101000 r 74 goat snp56765-scaffold9-616956 4 56198839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416854 Affx-122948098 AX-123287202 4 61614821 AGCTAGCATATTTTAGAGATTTCTTCTCCTTCTAA[C/T]GTATCTACTATGTTTGAGGCTCTATAGATCTAAAG Y 2 1 2 1 101000 r 74 goat snp56764-scaffold9-556036 4 56138054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773025 Affx-122977374 AX-385260169 4 61649062 GCTGGGAAAAGAGGGCACTAAAGTCCTCTTTACTC[A/G]TAACTGATGGGAATTAATTGGGAATGACTTGAAGA R 2 1 2 1 101000 f 74 goat snp56763-scaffold9-521795 4 56104111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407515 Affx-122954736 AX-123277866 4 61678711 TCAATACATATCATGTTATTTTTAACATCATCATC[A/G]TCACTAGGACTCTAGGTCCCTTTTGTGTGTTATTC R 2 1 2 1 101000 r 74 goat snp56762-scaffold9-492146 4 56073958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445701 Affx-122926118 AX-123316038 4 61711111 AGCCTGGCATGGATGGGAACACTCAGCAGGTGCGG[A/C]GAAAAGAAGATGGGCTTAGACCCAAACCAGGGGCA M 2 1 2 1 101000 r 74 goat snp56761-scaffold9-459746 4 56041179 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375988 Affx-122978424 AX-123246347 4 61747996 GAATAGGCTTTTGAAGAACAAGGAGGATTTCACCA[C/T]GCCCAGAAGAGACAAACACTATATTTCCTGCTGAG Y 2 1 2 1 101000 f 74 goat snp56760-scaffold9-422861 4 56008260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420402 Affx-122944923 AX-123290749 4 61785332 TCACTCCCTCTTTAACTCTCAGCAACCACTAATCT[A/G]TTCTCCGTTTATAATTTTATCATTTCAAGAAAGCT R 2 1 2 1 103000 f 74 goat snp56759-scaffold9-385525 4 55970667 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414593 Affx-122949362 AX-123284942 4 61829790 ACTGAAGATTTTTAAATGTGGGATGGGTCAGATGC[A/G]GTGATTCTAAAAGCAAAGAGGCCAGTTGGGAGGCT R 2 1 2 1 201000 f 74 goat snp56758-scaffold9-341067 4 55926118 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402962 Affx-122958162 AX-123273315 4 61867626 TTTGGCATTCCGACTTGCTGCTTGGCACTGTGGTG[C/T]TCTGACTGCCCCAAATCCCAGATTTACTGGGATCT Y 2 1 2 1 202000 f 74 goat snp56757-scaffold9-303231 4 55887719 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440743 Affx-122929874 AX-123311080 4 61896526 GGAAGTCACGAGACAGTGTGTTCACTCTAAGCTCC[G/T]AAGACTTTTTCATATGTTTCCCACCTGAGCCTGGC K 2 1 2 1 101000 r 74 goat snp56756-scaffold9-274331 4 55858986 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444777 Affx-122926351 AX-123315114 4 61936314 CAGCAGAATCCGTTCAGAAGGTGACTTCTCAAAAC[G/T]CATCCTTAACTGAGATCAGCTGACAACTCTAAGAC K 2 1 2 1 101000 f 74 goat snp56755-scaffold9-234543 4 55819338 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421131 Affx-122944199 AX-123291478 4 61983364 CTAAGCACGTGGCCCGATGCTAGGCCCCAGAGACA[G/T]AGCAACGAAAACGCCAACACACAGCCTGACCTGAC K 2 1 2 1 101000 r 74 goat snp56754-scaffold9-187493 4 55772367 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770047 Affx-122933081 AX-385257214 4 62013650 TTAAACTTCTCAATCTTGCCGATTATACTCGGATT[A/G]TGTTAGAAAATGTCACTGTCCTTAGGGAATGCACA R 2 1 2 1 101000 r 74 goat snp56753-scaffold9-157207 4 55742198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782220 Affx-122958047 AX-385269298 4 62045038 ACTATAATAAAATATTTTGGGTAAAGAGCTCTAAG[A/C]TCCATAACCTTAGTTCACTAACAATGTCTTTATTG M 2 1 2 1 101000 r 74 goat snp56752-scaffold9-125819 4 55713981 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413051 Affx-122950980 AX-123283400 4 62111736 TATGATGCATGCTGAAGTTTGAGAACCACTGCTCT[A/G]TTTGAAGCTCCCTCAAATGACTGCTATTTCACAGA R 2 1 2 1 201000 r 74 goat snp56751-scaffold9-59121 4 55647254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789368 Affx-122923737 AX-385276378 4 62150404 TTGCTTTTGTGCTAAAACAGGTCTCTGTTAAATAG[C/T]TGCAACAGAGACCAAATGGCAGCAACGCATAACAT Y 2 1 2 1 103000 r 74 goat snp56750-scaffold9-20453 4 55608373 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434783 Affx-122933884 AX-123305124 4 62215463 CTAGAAATAATAACTTATATTTATTGAGTCCTTAC[C/T]ATACACTCAGCCTTATGTTATGCTGAGGCAGATAC Y 2 1 2 1 101000 r 74 goat snp11840-scaffold1439-516798 4 55535489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377176 Affx-122978205 AX-123247535 4 62246227 ATAGAACACGTAGAATGTGAGGCACTAAGTGGGAG[C/T]AGCGTATTAGAAGGAAGCTCCACATTTCTTCCCTC Y 2 1 2 1 201000 r 74 goat snp11839-scaffold1439-486034 4 55504934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452974 Affx-122920153 AX-123323307 4 62301859 TCATCCTTAATTCCAATGTGACAACTTCAGAGTCA[A/G]TTTCTTGATGGGAGAGCTGAGTTTTGATCTTCCTG R 2 1 2 1 101000 f 74 goat snp11838-scaffold1439-430402 4 55449572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388066 Affx-122969525 AX-123258424 4 62334810 CCCAAAGCAAGAAACAGCATGAGAATCAGCACATG[C/T]GAATGAGACAAAAACCACAAGTCCAAAAAGGTTTC Y 2 1 2 1 101000 f 74 goat snp11837-scaffold1439-397451 4 55416651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278249 Affx-1111836248 AX-519551737 4 62374615 CTTTAATCCCTTCTAATCCTCGCAGCATCCCTGTT[C/G]TGTCAATGTTTTTCTTCCCTTTTGGTGCAAAGCAC S 4 1 2 1 102000 r 74 goat Random2.2K-447 4 62374615 G C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794760 Affx-122929961 AX-385281720 4 62376552 AGTTATGCATATTCAACTAAATATAAAAGGTATTC[A/G]CTTTCCCTATAACACAGTGACACTTTGTTATATAG R 2 1 2 1 101000 r 74 goat snp11836-scaffold1439-355709 4 55374209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441668 Affx-122929186 AX-123312005 4 62414941 GACTAAATATCATGGATACAAAAATGAGTAAGTCA[C/T]GGTCTTTGTTTCCCAGAAGTCCATTTATCTGAGTG Y 2 1 2 1 101000 r 74 goat snp11835-scaffold1439-317320 4 55335847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418984 Affx-122946066 AX-123289332 4 62444096 GTGAAAAGCAGGTAACATCCAGAGCTAGCAAGTGC[C/T]TGGGTAATGAGATCTCTCCTGAACCACTGGTGAAA Y 2 1 2 1 101000 f 74 goat snp11834-scaffold1439-288165 4 55307713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378693 Affx-122977067 AX-123249052 4 62475826 CAAGATGTGACAAGATGTAGAATATTCAGAACTGG[C/T]AGGAAATCTGTGCTTAGAGCAGCAGAGGCAGGGAA Y 2 1 2 1 201000 r 74 goat snp11833-scaffold1439-256435 4 55275337 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441625 Affx-122928641 AX-123311962 4 62538371 CTGTGTGGATAGCTAGAAACAGAACCTCCTGAGTG[A/C]GAATATCATGGGGGTGGGACTGGGAAGGAAAGAGA M 2 1 2 1 101000 f 74 goat snp11832-scaffold1439-193890 4 55212034 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778128 Affx-122933697 AX-385265243 4 62579161 GTGCTGTTAATATGCATTCATAACATACACCGTAA[C/T]GGCTGTTCTACTCTCTGCTAAGAAAGCATGTTAAC Y 2 1 2 1 101000 r 74 goat snp11831-scaffold1439-153100 4 55171183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386645 Affx-122970212 AX-123257003 4 62615698 TTTCTTTCCTAACGGAAGAGATGGTGACTAACACC[A/G]CTTAAACATGGTTTTGTTTTAGAGTTCTGTTTTGA R 2 1 2 1 101000 f 74 goat snp11830-scaffold1439-116563 4 55135460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397147 Affx-122962441 AX-123267502 4 62660355 CTATTGATGGACTAGATATTTTCAAAGGAATATTT[A/G]TCTTATTCAGTAAAAATAAAACACAACATTTATTG R 2 1 2 1 101000 r 74 goat snp11829-scaffold1439-71906 4 55091041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793692 Affx-122966338 AX-385280664 4 62693133 AGAACCAAAGAAGTTGGCTATCAATTATTCATAAA[C/T]AGCCATTAATTACCTTTTGGCTTTTGAGGTTTGAT Y 2 1 2 1 202000 r 74 goat snp11828-scaffold1439-39128 4 55058514 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408627 Affx-122953490 AX-123278978 4 62729836 AAATGGCTTCTGAAGGATTTTGTGCAGGTGAGAAA[C/T]ATCTTAAAAGAGATATTAAAACAAAAATTGGTCTG Y 2 1 2 1 102000 f 74 goat snp11827-scaffold1439-2425 4 55021882 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278251 Affx-1111836249 AX-519551739 4 62783676 AAAACACAGAGACGATTCCAGCCCCAACTTTCCAC[A/C]CAAAATGGCTAATGCCAGGTAGTAGAGAAATGCAG M 2 1 2 1 201000 r 74 goat Random2.2K-448 4 62783676 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438535 Affx-122931193 AX-123308873 4 62803109 GGGACAGAGGACCCTCCATGTGGTCCAGATGTATA[C/T]GCGGTTTGGGGCAGGTATAAGACTAAGCTCTAAGC Y 2 1 2 1 201000 f 74 goat snp9657-scaffold1345-298316 4 54953272 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450900 Affx-122922200 AX-123321234 4 62831882 GCTGTCTGCATTTCAGTGAAAGGTGATGGGTGATC[A/G]TGGCAAAGTTAACTTTCAGCAACCTGCTGGGATAC R 2 1 2 1 101000 r 74 goat snp9656-scaffold1345-269543 4 54923274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381654 Affx-122974751 AX-123252012 4 62866744 AGAGAACTCAGCCCTTATTTATGATGCTGTTTCTG[C/T]AGTAAACATGTGCAAGGCCTCCCAGGAGAGGCCTA Y 2 1 2 1 101000 f 74 goat snp9655-scaffold1345-234681 4 54887711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449398 Affx-122922705 AX-123319733 4 62897557 CACCTCACTCATGGAAAGAAAAAAAAGCCACTGAA[C/T]GGCTGCATTGTTGAGCTGACCACCCCTGTACCATC Y 2 1 2 1 201000 r 74 goat snp9654-scaffold1345-203868 4 54856951 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418958 Affx-122946085 AX-123289306 4 62946408 GGCCTGCCAAGGCAGGAGCAGCCACCTAGCCCCAG[A/C]GTCTCCTGCAAACCCCATTTCCTATGCCCCTTCCC M 2 1 2 1 101000 r 74 goat snp9653-scaffold1345-155017 4 54808295 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431343 Affx-122937056 AX-123301684 4 62976586 CTCTCCCCGAGCAGCTTTCAGGTTCTGCTGGGCTT[C/T]CTCATCACAGAGACCTAGAAAGGGAACTTGGGTTA Y 2 1 2 1 101000 r 74 goat snp9652-scaffold1345-124839 4 54778358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445492 Affx-122925197 AX-123315829 4 63041887 TCCCTTGGGAGTTCAACCCATGGCAGTGGCCGCAG[C/T]AGCAGTGTCTAGCTTCTGAAAGATAGAGATCAGAA Y 2 1 2 1 101000 r 74 goat snp9651-scaffold1345-59538 4 54713052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445548 Affx-122925156 AX-123315885 4 63081766 CCCCATGGAACCAAGCAGGACCCTATGGGGCCTTC[C/T]GGGCACAGATCACTCTCCCATATCCTCTGCTTAAT Y 2 1 2 1 101000 r 74 goat snp9650-scaffold1345-19659 4 54672870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409123 Affx-122953307 AX-123279474 4 63132548 GAGCCTTGGAGGAAGAGGCTTGGAGCAGTCAGGGA[C/T]AGAGGGATTTGAGAAGGCCCTGGCACAATGGGCAG Y 2 1 2 1 101000 r 74 goat snp3271-scaffold11-503068 4 54622882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771926 Affx-122975366 AX-385259082 4 63166547 TTTTTCTTTTGCGCTTACGTTTGAATCACAATACA[A/C]AGCTAATTAAAATAAATGGTTCACAGAGCACAGAG M 2 1 2 1 101000 r 74 goat snp3270-scaffold11-469069 4 54588884 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435955 Affx-122933531 AX-123306294 4 63195275 TTGGGGTACCCAAGGGAGCTGGCAGGGCTTCTGGG[A/C]TGGAGGAAGAGCAGGATCCCAGCCTGGGAGGGAGG M 2 1 2 1 103000 r 74 goat snp3269-scaffold11-440341 4 54560136 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798379 Affx-122957261 AX-385285313 4 63254641 TTTGCCCAAGTCTACTCCTCTGGTAAATACCAGAA[C/T]GTATCATAGTTCAAATGCAATGGAAACTCACTTTT Y 2 1 2 1 101000 f 74 goat snp3268-scaffold11-380975 4 54479524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377728 Affx-122977388 AX-123248087 4 63296308 TTTTTTCACTCTTTTCAGAGCAGTTTTAGGTTCAG[A/C]GCAAAACTGAGAGCAAGGTACAATTCATCTCTTTT M 2 1 2 1 101000 r 74 goat snp3267-scaffold11-339308 4 54437828 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440671 Affx-122929928 AX-123311008 4 63351609 AGGCACGAACTGGCAACCAAAGAAACCAGGGGTCA[A/C]CCAAGCTCACTAGACTACCCCCAGAGTGCACCACA M 2 1 2 1 201000 r 74 goat snp3266-scaffold11-284007 4 54382115 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414511 Affx-122949529 AX-123284860 4 63417536 AGGAGTGAAGAAACAATGAGTATCTATAAATAATT[A/G]GAAGAGGGCCTAGAATCTTGAGAGCTTTCTGTAGG R 2 1 2 1 101000 r 74 goat snp3265-scaffold11-218080 4 54315182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452209 Affx-122920810 AX-123322542 4 63460404 TGATTTAGTCACTGAGGTGTGTATGTGTTCCAGAC[A/G]TTGTATTAGGCTGCTGTATAGAAAACTCAAATGAA R 2 1 2 1 201000 r 74 goat snp3264-scaffold11-175212 4 54272546 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774858 Affx-122949790 AX-385261992 4 63530344 AACCTGCTAAGATAAATACCACTGACACTTTGGTA[C/T]ATCTCTTTATACATGTATGTTCACACCAATTTTTT Y 2 1 2 1 201000 r 74 goat snp3263-scaffold11-105272 4 54202090 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384976 Affx-122971898 AX-123255334 4 63562367 GGGCAGGCATGAAGAAATAGAGCAAAATTTATTAG[C/T]AGTATGACGTGTCTTAAAAGACCTTACTCCTTAGA Y 2 1 2 1 201000 r 74 goat snp3262-scaffold11-73249 4 54170279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772376 Affx-122921874 AX-385259528 4 63592365 CTTCACTTCAACTGAATTGAGCCCTATAATTATAA[C/T]CTGTAAAATGAACAACTTGAACTCGACTCTCATCC Y 2 1 2 1 101000 r 74 goat snp3261-scaffold11-43251 4 54140599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412015 Affx-122951746 AX-123282365 4 63622777 TTCAATCGAGAGCTCTGCATTGGGGTCCACATGTC[A/G]CATTTTAAAGCTCTGAGGTCTCCAGAGAGGTCTCC R 2 1 2 1 101000 r 74 goat snp3260-scaffold11-12839 4 54110432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414082 Affx-122949753 AX-123284431 4 63660999 AGTGTGTCTGATATGCCAGATGGATGCTTAATGAA[C/T]GGTCTAATGACGAAATCTGACACACCGTATCCGAG Y 2 1 2 1 101000 r 74 goat snp51107-scaffold743-322922 4 54075905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444916 Affx-122926244 AX-123315253 4 63710702 GTCAGAGATCTGAGGTTCCCCAGAGCTTAGAACTT[A/C]TCTCTTTAAGAGCCTCAATGTCTCACCTGTAAAAT M 2 1 2 1 201000 r 74 goat snp51106-scaffold743-273219 4 54027689 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414894 Affx-122949124 AX-123285243 4 63796760 GCAACTGCAGCGGACTTTGCTTTCTGTGCACTTTT[A/G]TATCTGCCCTCAGTCCCTCATATCCCCTCAGGTCC R 2 1 2 1 101000 f 74 goat snp51104-scaffold743-187161 4 53940976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400550 Affx-122960429 AX-123270905 4 63868157 GTTTGGTCTTAAAGATCAGGGTTCTGGGAATGTAA[C/T]GATTATGGAGATAAATGAAAAAGACTGTTTTTTAA Y 2 1 2 1 101000 f 74 goat snp51103-scaffold743-115764 4 53870305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429010 Affx-122938840 AX-123299352 4 63911575 GTCTCTGGGCCATTTTGTTCTCTAACTCACAGCAA[C/T]GGGTGCTTCTGATCAATCCTGAGCTTTCCTGTTAT Y 2 1 2 1 101000 f 74 goat snp51102-scaffold743-72346 4 53826837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278253 Affx-1111836250 AX-519551741 4 63932917 GGAGGATACCATTTAAAAGATGAGAGAATATATGT[A/C]AATTGCCATTTGGCACCAAAAAATGTATATTAAAA M 2 1 2 1 201000 r 74 goat Random2.2K-450 4 63932917 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431432 Affx-122936514 AX-123301773 4 63959179 GACCTGCCATACCCTCCAGCTGATTTGGAAGATGT[C/T]ATCAACAAGTCTGTCATGTGGAATTGACAAGAATG Y 2 1 2 1 101000 r 74 goat snp51101-scaffold743-24742 4 53779937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451566 Affx-122921696 AX-123321899 4 64011999 GTCCTCTATCTCGTCTGCTGCTGGCTAGCTTCAGT[C/T]GGTGACATGATCTCACACTCACAATTATATGAAAA Y 2 1 2 1 101000 r 74 goat snp28338-scaffold3021-27979 4 53728093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767208 Affx-122938209 AX-385254489 4 64043533 CAGATATAGTCCTGTTCAGACTGAAGGAAGAATAG[G/T]TCTAAACCCCATCTCTCAATAGCTTTAGAAAGATC K 2 1 2 1 101000 f 74 goat snp28339-scaffold3021-59513 4 53695996 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391203 Affx-122967414 AX-123261560 4 64076886 AGCTTGATGGGCTATCGGGTCGCAACGAGTTAGAC[A/G]CAACTGCGCGACTCAGCACTCACACAGCTGCTAAG R 2 1 2 1 201000 f 74 goat snp28340-scaffold3021-92866 4 53662255 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404099 Affx-122957124 AX-123274451 4 64112177 TTTTGTATACACTTAGGACGTTCTGGTTTATTTAA[C/T]ACTTAGAAATAATTTTTTCTGCTTTGAAATATAAT Y 2 1 2 1 101000 f 74 goat snp53984-scaffold820-3002875 4 53626971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452001 Affx-122920921 AX-123322334 4 64150995 CCTTGGGTTCACTCTGCAGAGCCAGGCAGGAGGAA[G/T]ACCAGACCCCGAGGTCTCCACTGCCACACAAGCAA K 2 1 2 1 201000 r 74 goat snp53983-scaffold820-2964057 4 53588334 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801776 Affx-122947171 AX-385288684 4 64195214 TGCTGCTGTGCACTCCTTACAAACATCATTTTTGA[C/T]TGTTGCATGAGCCTCATATTTAGTTATTTCCTAAG Y 2 1 2 1 101000 f 74 goat snp53982-scaffold820-2919838 4 53544039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411962 Affx-122951136 AX-123282312 4 64235944 TCCCTATATCCTGTTGTTCCCTCTTCCTCTAAATC[A/G]CTGGATCTCAGAGTGTAATCCAAGGACCCTAAAGT R 2 1 2 1 101000 f 74 goat snp53981-scaffold820-2879108 4 53505037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386452 Affx-122970784 AX-123256810 4 64295610 TAAATAGTACTGCCAGAAATATTGGGGTGTGTGCA[A/G]TTTTTCAAATGAGTCTCTCTCTCTACTTCTGTTTC R 2 1 2 1 101000 f 74 goat snp53980-scaffold820-2819442 4 53445995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449501 Affx-122922625 AX-123319836 4 64327460 GATATCTGATTTCTCTGGGGAAAGCATGGGGCCTG[C/T]GCAGGTGACAAGTGTTAGAACACATTTCTGTATAT Y 2 1 2 1 101000 r 74 goat snp53979-scaffold820-2787592 4 53413938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387800 Affx-122969692 AX-123258158 4 64363409 GCACCTCATTTAAGTGACCAACACGCTCTGGGAAA[A/G]CAGCAGATTTAGAGAAGTGCTGTCTTGAGGACCGT R 2 1 2 1 101000 f 74 goat snp53978-scaffold820-2751643 4 53378044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427271 Affx-122939541 AX-123297614 4 64393515 AGAAGAGGAAGAAGAATAGCAGGTGGTAGACATCC[G/T]AAGTGGCAGAGGAAATTAAACCCAAATAGTGAGTG K 2 1 2 1 201000 f 74 goat snp53977-scaffold820-2721537 4 53347943 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401850 Affx-122959428 AX-123272203 4 64439114 AACCTTATTCTCTGTTTCTCAGTTTACTGTGGTAA[C/T]GTTATCCCCAAGTCACATGATCCTTCTGTACTCAT Y 2 1 2 1 101000 r 74 goat snp53976-scaffold820-2675938 4 53302348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403501 Affx-122957637 AX-123273854 4 64473148 ATTATGTGTAAGCCAAATATCTTTACCTTTGTTTT[A/C]GTGTTAATTGCTGGTAATTTAATCTCAATTACCTA M 2 1 2 1 101000 r 74 goat snp53975-scaffold820-2641904 4 53267709 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377212 Affx-122978177 AX-123247571 4 64514438 ATTTGAAAATCACGCATGTACTTAGAATTGACATC[A/G]AGATCTTTTCTTTCTCTTACCCTACCACACTAGTC R 2 1 2 1 101000 f 74 goat snp53974-scaffold820-2600614 4 53226407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779826 Affx-122959804 AX-385266926 4 64545366 AGAAAATAAAATTTTTGCCACAAGGTAAATGAGGA[C/T]GAGGGAACATTCTTCCCTAAAGGTTTCAGAGGGAA Y 2 1 2 1 101000 r 74 goat snp53973-scaffold820-2569686 4 53195156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802871 Affx-122965214 AX-385289769 4 64580087 TTTTGAGCCACGTCATCCTCATCTATCGCATATCC[A/G]TGGACATGGTCGGTAAAACTGAAACCTGTGCCCAC R 2 1 2 1 101000 f 74 goat snp53972-scaffold820-2534965 4 53160648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801199 Affx-122966682 AX-385288113 4 64608759 CTGATACTCTCAGAGCCAATATCCAATTAGCAAAT[A/G]CTGGATTTTCCTTTTTGTAACTAGTATTTGGCCAT R 2 1 2 1 201000 r 74 goat snp53971-scaffold820-2506293 4 53131795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795453 Affx-122962794 AX-385282409 4 64639810 ATGGAAACAGGCCTTGGGAATCTATATTTGCTAGC[A/G]TTGAGACACACTGGATTAGGAAACCGTAATGGAAA R 2 1 2 1 202000 f 74 goat snp53970-scaffold820-2475242 4 53101393 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390827 Affx-122967842 AX-123261184 4 64674355 TACCCTAGCACAGGCATTACAGTTTTTCCAGAAAG[A/G]GCCATTCCCAAAGCAGACGGAAGGAAAGGAAGCTG R 2 1 2 1 101000 f 74 goat snp53969-scaffold820-2440697 4 53066432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443513 Affx-122927789 AX-123313850 4 64728531 AGCACCAGGGTGGAGAGAGAGATCCAAATGGCACC[A/G]TCTGGCCCTGGGGTTGCCGAGCATCTCTGGGAGAA R 2 1 2 1 101000 f 74 goat snp53968-scaffold820-2386521 4 53011787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433090 Affx-122935725 AX-123303431 4 64859479 CATCACTCAGATGACTTTTTCCTGTTCTGAGCATC[G/T]TCCCACCTCTATATTTCATTACAATTGATGGGCAT K 2 1 2 1 101000 r 74 goat snp53966-scaffold820-2255573 4 52880506 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804307 Affx-986696773 AX-385290923 4 64893969 GGAACAAAGCCATCTCTCAGATACATTTAAACTAG[C/T]GACTTCTAACATTTTTGAAGGAGGGAATCTTTTGA Y 2 1 2 1 600010 f 74 goat 4_64893969 4 64893969 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320803565 Affx-986696116 AX-385290366 4 64893971 AACAAAGCCATCTCTCAGATACATTTAAACTAGCG[A/G]CTTCTAACATTTTTGAAGGAGGGAATCTTTTGACA R 2 1 2 1 600010 r 74 goat 4_64893971 4 64893971 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 320804238 Affx-986696739 AX-385290869 4 64894227 GTGCAGTGTATGGTACACTTTAGAGACTTCTCACT[C/T]GCGTTTGTGATACCCACCCTAAATATCCCCAAATA Y 2 1 2 1 600010 f 74 goat 4_64894227 4 64894227 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320804607 Affx-986696776 AX-385291139 4 64894244 CTTTAGAGACTTCTCACTCGCGTTTGTGATACCCA[C/T]CCTAAATATCCCCAAATATGGAAAGTTGTAAATTG Y 2 1 2 1 600010 r 74 goat 4_64894244 4 64894244 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38395171 Affx-122964108 AX-123265526 4 64906788 TGCACAGTGTTTGGAGGGTTTAAGAAATCTCCTTA[C/T]GCTTTCTGATTTTCATAGTTATTTGACTTATTTAT Y 2 1 2 1 101000 f 74 goat snp53965-scaffold820-2208264 4 52833314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439282 Affx-122930977 AX-123309619 4 64946758 TCTGCAATGGAAGCTCAGTGTCTTAACCACTGGAC[C/T]GCTGGGGAAGTCTCTGAAGTTTATAATTTTTAAAC Y 2 1 2 1 303000 r 74 goat snp53964-scaffold820-2168294 4 52793337 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380145 Affx-122975979 AX-123250503 4 64993214 TTGGTAAACAGTTGATCAGATATCTTTCAAAGCAA[C/T]AGCAACCATGCAGAAATAGCAATTTCAGCAACTAC Y 2 1 2 1 201000 f 74 goat snp53963-scaffold820-2121838 4 52746709 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412874 Affx-122950432 AX-123283223 4 65039738 AGAGTATCAGGTCCCTAGACAACTAGGTGTCTCAC[A/G]CAATGAAAACATCCTTGCTTAGTCCTAAGAACGAG R 2 1 2 1 101000 f 74 goat snp53962-scaffold820-2075314 4 52699515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771222 Affx-122940966 AX-385258380 4 65074920 CCTCTCTCTGATTTTATGCCAGTTTTAGTCTTGGC[A/G]CATGTATGTTTGTAGGTATATTAGCTGTTTCATCA R 2 1 2 1 101000 f 74 goat snp53961-scaffold820-2040132 4 52664349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782282 Affx-122968071 AX-385269360 4 65114818 AATTGCTGTAAACCTTTAGAAGTAACGTCTTTACC[A/G]TCATATCACAATATTCTGAGTTTATGATAAAAATT R 2 1 2 1 101000 f 74 goat snp53960-scaffold820-2000234 4 52624427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780109 Affx-122957631 AX-385267206 4 65152340 AGGATCTTATGAGACCTAGAGTCTAGAGAATATGT[A/G]CATAATATTAAGACACAAATAGTGGTTTCAGATCC R 2 1 2 1 101000 f 74 goat snp53959-scaffold820-1962712 4 52586776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278098 Affx-1111836251 AX-519551589 4 65195283 CAAAGGGTAAAAGGAGAGTATTGAGATGAATAGGA[A/G]AAACAGAGAGATGGCCATGCCAAGGGAAAAAATAA R 2 1 2 1 201000 f 74 goat Random2.2K-451 4 65195283 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429806 Affx-122938193 AX-123300147 4 65227413 GGATTCTTAGGGGCATGGCTAAAGACTTGTTACTA[C/T]TGTTTGTTATTCATCAATTAATCTGATCAGTGCCT Y 2 1 2 1 101000 f 74 goat snp53958-scaffold820-1887639 4 52511545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428324 Affx-122939005 AX-123298667 4 65272001 TAACTGCAATTTCCTTTTATTTGTAAAACAGGACC[A/G]TAATTCTCGGATGCTATTGATTCTTTTTATTTTGG R 2 1 2 1 101000 r 74 goat snp53957-scaffold820-1843051 4 52466287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447989 Affx-122923746 AX-123318325 4 65310203 CACTCTGGCATTTAACTAGAGAATGGATAAACACG[C/T]TGATTATTTACCCAAGCTAGCCCACCAAAGATAAG Y 2 1 2 1 201000 r 74 goat snp53956-scaffold820-1804849 4 52427941 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389398 Affx-122968380 AX-123259756 4 65354642 TCAGGAGCCCTGGGAGCTGGTTCTAGCTCTGACAT[A/G]CCTGCTCAGCGTGATCTTGGGTAAGTTACAACACC R 2 1 2 1 201000 f 74 goat snp53955-scaffold820-1760410 4 52383433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768179 Affx-122975924 AX-385255372 4 65387527 AAGTGAGGGTTTTGAACTGAAGGATCTTTTAAGGT[C/T]TCTTCAGACTCCAATATTGTCTAGATGTCAGTGGT Y 2 1 2 1 101000 f 74 goat snp53954-scaffold820-1727525 4 52350950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433548 Affx-122934991 AX-123303889 4 65425460 ATTTCCTCAGTTTCTTGATCTAGCATAGTCTCTTC[A/G]CACTTCTCATCCATGTTAACTTTGAGGAGGCCAAG R 2 1 2 1 101000 f 74 goat snp53953-scaffold820-1689592 4 52312640 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780089 Affx-122934991 AX-180660633 4 65425460 ATTTCCTCAGTTTCTTGATCTAGCATAGTCTCTTC[A/G]CACTTCTCATCCATGTTAACTTTGAGGAGGCCAAG R 2 1 2 1 600000 r 74 goat snp53953-scaffold820-1689592 4 65425460 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402743 Affx-122958331 AX-123273096 4 65464897 GGAGGGATGGATATGAATTATAATACTGATTATGC[A/G]TAAGTATAATATATAAATAGAAAGTCTGTGAATCA R 2 1 2 1 101000 f 74 goat snp53952-scaffold820-1650155 4 52272959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417210 Affx-122947304 AX-123287558 4 65515137 TCTCTTTACCCCATGCCCCTCTTTCTGCCAACATA[C/T]CCACTAAAATCTATTCAAGATTTCACAAAGCTCCA Y 2 1 2 1 201000 r 74 goat snp53951-scaffold820-1599915 4 52222985 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409705 Affx-122953045 AX-123280056 4 65572221 AAGGATCAGATGCAAGGGGAAACTGTTTTAAGGAC[G/T]ACACACAAGCACGCTCATGATTCATTCTGCCAAAC K 2 1 2 1 101000 f 74 goat snp53950-scaffold820-1542831 4 52165876 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441285 Affx-122929468 AX-123311622 4 65601501 GAGGAAAGACTGGACAAATACATATTTAGAGCTTT[C/T]TAATAGATGTACAATAGGAAAAATTTCCCAGGTAG Y 2 1 2 1 101000 r 74 goat snp53949-scaffold820-1513551 4 52136614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384062 Affx-122972870 AX-123254420 4 65650258 CAACCCCTTATTCCCTTTCCCTGGAAGTTCTGAGT[A/G]AGGAAGAGAAAGGAAATTAAACTTTCAGTGTAGAT R 2 1 2 1 101000 f 74 goat snp53948-scaffold820-1464794 4 52087927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800345 Affx-122928375 AX-385287267 4 65691813 ACGAAGAAATACAAGCAAAGAATTCTTGGCATGTA[A/G]AATAAACAGGGATTAATCCATGTGGCAGCACTGTT R 2 1 2 1 101000 f 74 goat snp53947-scaffold820-1423239 4 52046492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793085 Affx-122979236 AX-385280063 4 65747139 GATATTCCATAAGTTAAAATGTCCTTCCTCAGGTC[C/T]TGTAATTGGGTTAACAGGATCTGTCTGAAAGACTT Y 2 1 2 1 201000 f 74 goat snp53946-scaffold820-1367913 4 51990934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435196 Affx-122933640 AX-123305536 4 65800902 CAACGTCATCAGAACCCAAGCAACCTGCACACTGC[A/C]TTTATGAGAGGCCCTTTCAGAAGGCTTCAGAGGCA M 2 1 2 1 101000 r 74 goat snp53945-scaffold820-1314150 4 51937071 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449935 Affx-122922911 AX-123320270 4 65829794 TCTGGATCACCCTTTAACACAAGGGTAACACTGTA[C/T]GTTCAGGACCAAGACTACTCTTAAGAGATCTGAGG Y 2 1 2 1 101000 f 74 goat snp53944-scaffold820-1285258 4 51907992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385593 Affx-122971207 AX-123255951 4 65872114 TTTCTCCAAAGAGCCTGATTTTTTTTTTTCACATT[C/T]GAGAAAGGTATTTCGAAACCAAGAACTGAATCCTT Y 2 1 2 1 101000 r 74 goat snp53943-scaffold820-1242938 4 51865806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452499 Affx-122920980 AX-123322832 4 65904779 ACATACTGAAACAAATTTTCATCAAGCAATACTTG[A/G]CTTTCATGCACTCTGATGCTTTCTAATTCTTTCTA R 2 1 2 1 101000 f 74 goat snp53942-scaffold820-1210273 4 51833070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392911 Affx-122965719 AX-123263268 4 66009352 AAGGGAAAACTGTAACTGTTTTGTTCTAGGCTATA[A/C]TACCCATACCCAGCACAAAGTATTCAAGAAACATC M 2 1 2 1 101000 f 74 goat snp53940-scaffold820-1105700 4 51728372 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783090 Affx-122957763 AX-385270157 4 66042343 TTTGACCCTTACCCTGCCTCTAAAATATTAATATT[C/T]TCCACACTATAACTATGTGATCCTTTAGAAATCCA Y 2 1 2 1 201000 f 74 goat snp53939-scaffold820-1072709 4 51695098 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397517 Affx-122962052 AX-123267872 4 66074526 ATATATTCAGTATCATATTTTAATGTAAGTCACTG[C/T]ACTTCCTCTGAACTGATAAATGGAGCTTTGTATCA Y 2 1 2 1 101000 r 74 goat snp53938-scaffold820-1040526 4 51662901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412900 Affx-122950415 AX-123283249 4 66108283 GCCACTGACGAGAGATGATTCCCCGTGTGCACTGG[C/T]GCGATAGACATGCTGGTTTATGGGCCTGACACCTT Y 2 1 2 1 101000 r 74 goat snp53937-scaffold820-1006769 4 51628577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454093 Affx-122919368 AX-123324426 4 66148682 ACTGTGAAGTCGGTAAGAAGGACTTCTCCACTCAA[C/T]GGATAAATGGAAGGCAAGGATCACTTTCCAGAGAA Y 2 1 2 1 101000 r 74 goat snp53936-scaffold820-966370 4 51588107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413393 Affx-122950123 AX-123283742 4 66193991 AGTGAAGGTGGGGTGGTTATGGAGATCTGATGGCT[C/T]CTCCTCTCTCTTTTAGGACTTGGAGTCCCTAAAAA Y 2 1 2 1 101000 r 74 goat snp53935-scaffold820-921061 4 51542800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422187 Affx-122943512 AX-123292533 4 66227651 CCACGCATGTCTCACGCCATGTAGCCAGCTCTGGT[A/G]ACTATCTTCTTCAAAGTGACAACAAATTCTCTATC R 2 1 2 1 101000 r 74 goat snp53934-scaffold820-887401 4 51509340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423565 Affx-122942414 AX-123293911 4 66258173 CTACCCAACTTAGAAGCATTCTTGAAAATAATAAA[C/T]GGAAATTTAAAAGCACTTTTCATGCTTGACTATGT Y 2 1 2 1 201000 f 74 goat snp53933-scaffold820-856879 4 51478942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438098 Affx-122931510 AX-123308436 4 66300334 GGTATATATGCCCCACAATTGGGCTTCCCAGTGGG[A/G]CCATACATTTCTGAGAGAAACAATTAGCTTTGAGT R 2 1 2 1 201000 r 74 goat snp53932-scaffold820-814718 4 51436671 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798518 Affx-122969864 AX-385285451 4 66337369 ACCTCATGTCATCCCTTAGATCTAATGTCCTGCAG[C/T]GTTGGTCTGCACAGGGTCATTGGAATAAGTGCCAG Y 2 1 2 1 101000 r 74 goat snp53931-scaffold820-777683 4 51399660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375592 Affx-122978729 AX-123245951 4 66404911 AGCATGTAGAAACTAAAATGTCCGCATTTCAAAAA[C/T]GGAGAAAACCATGAATCTATGCATCCCGGAGAATG Y 2 1 2 1 201000 f 74 goat snp53930-scaffold820-710141 4 51331639 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427499 Affx-122940000 AX-123297842 4 66441917 CGCTTCACAGCAGCCCTTGCAGCCTCCCTGCTACT[A/G]TCAAGGAGTCAGAACACACTCTCTTCCTTCTCCCT R 2 1 2 1 101000 r 74 goat snp53929-scaffold820-673135 4 51294412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272129 Affx-1111833435 AX-519545887 4 66517672 TAAATTACAAGAGCTGTTTTTAAATACACTTTTCC[A/G]AGGGCATTCATATGTTTCAAGGAATTCTAATGTGC R 2 1 2 1 101000 r 74 goat 4_66517672_AF-PAKI 4 66517672 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428710 Affx-122938467 AX-123299052 4 66546117 AACATACAAATAACAGATTTATTACTATCATGGGG[C/T]AAATTACTTCTTACACAAGAACTACTGACTTTGCT Y 2 1 2 1 101000 r 74 goat snp53927-scaffold820-568935 4 51190030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783121 Affx-122956401 AX-385270188 4 66576167 GAACATTTAAGTAATAAACCTCATCTTATACACAA[C/T]GCATTACTGTGAGGCTCACTACTTACATAAACTAG Y 2 1 2 1 101000 r 74 goat snp53926-scaffold820-538885 4 51160407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440254 Affx-122930659 AX-123310591 4 66632271 GGGAAATAACCTGTTTTGCAAGCTAATGGGGAAAT[A/G]TTTGATTGTTATCTAAACTCATTTAATCTTGGAGG R 2 1 2 1 101000 f 74 goat snp53925-scaffold820-482781 4 51103312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772585 Affx-122978136 AX-385259734 4 66674506 CTAACATCCCTTTAATATTTCTAACAAACGACACG[A/C]GTAGTCTTTTTAGAACAGCTGAATTATACTTTAAG M 2 1 2 1 101000 f 74 goat snp53924-scaffold820-440546 4 51060496 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437127 Affx-122932160 AX-123307465 4 66716423 TAATCCCTTTCCCCCTGAGTGCAAGTCAACTTCAA[C/T]GTTTCCTTTCTAATGAGTGAAATGTAGCTGAAGTG Y 2 1 2 1 201000 r 74 goat snp53923-scaffold820-398629 4 51018189 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428165 Affx-122939039 AX-123298508 4 66770064 AGCGGTTTCTGTATGCAGCCATACACCTTCAACCA[C/T]AGCAATAAACCTGATTAAAAAAACAGTGCAATATG Y 2 1 2 1 101000 f 74 goat snp53922-scaffold820-344988 4 50964160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417392 Affx-122947692 AX-123287740 4 66800168 TTTTCAAGAATCCAAGAAAGAAAAATCACAGGCCT[A/G]TAAGAGGAACCATCACCCAGTTGACTTATTGGTTC R 2 1 2 1 101000 r 74 goat snp53921-scaffold820-314884 4 50934057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431064 Affx-122936638 AX-123301405 4 66878104 ATCAGCCGAGGGAAAGTGAGGGAGGAGATTGGGAG[C/T]GAGGCTGGCATAGCTGAGGCCTGAACAACAAGACT Y 2 1 2 1 101000 r 74 goat snp53919-scaffold820-236948 4 50856371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785543 Affx-122923714 AX-385272587 4 66909104 TCCATAAAATTCACCTCCAGTGAACAAAAGTATGT[A/G]TTCCTCTCATTGACTTGTTATGGGGTTCCCTTGCA R 2 1 2 1 201000 r 74 goat snp53918-scaffold820-205948 4 50825330 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786511 Affx-122941194 AX-385273545 4 67014931 AACAATTGCCCTTTGAGGGTGAAGAGAAGGAAAAG[A/C]TGGGAGGCTCTCTGAATGACCTTGTACTATTCAGT M 2 1 2 1 101000 f 74 goat snp53916-scaffold820-100121 4 50719500 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407471 Affx-122954773 AX-123277822 4 67060883 AATATTGGAACTGAGAGTAATAAAATGAATACAGC[A/G]GGCTCCTCGTGTATGAATGACACTTTCTTCACATA R 2 1 2 1 101000 r 74 goat snp53915-scaffold820-54169 4 50673574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438557 Affx-122931174 AX-123308895 4 67144463 TAAACTGGAAAGTCCTTCAACTGAAAAGGAAAATA[C/T]CCGTAAGGAGAAAGAGGTATAATGTCTAGAAATTT Y 2 1 2 1 101000 r 74 goat snp27698-scaffold295-6418257 4 50588675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422032 Affx-122943622 AX-123292379 4 67191055 GCCAACTTAACTTGCTTTGAATAAACCTCAGAATG[C/T]AACTGGATCTCAGTTTCATTATAAGAAGTTCAATC Y 2 1 2 1 101000 f 74 goat snp27697-scaffold295-6371665 4 50542016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773427 Affx-122927302 AX-385260569 4 67255864 TCTTTTCTGACCAAGGTATAAAATGACTTTTATGA[C/T]TGACGGTGTCTAAAGCACATATTTTAACATAGCTG Y 2 1 2 1 101000 r 74 goat snp27696-scaffold295-6306856 4 50476893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451728 Affx-122921543 AX-123322061 4 67285333 ACTTCATAGCCAAAATTCTTGAAAGAATGGTCTGT[A/G]TACTGTTCCCAATTTGTTATCTCCCATTTACTCTT R 2 1 2 1 201000 r 74 goat snp27695-scaffold295-6277387 4 50447388 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775784 Affx-122958632 AX-385262915 4 67322759 TTTCTATCCTCTTAAAAGTGTGGAGGCTTATTTCA[C/T]GACCTGGTATGTGGTCTAACCTAGAGAGTGTGTAT Y 2 1 2 1 101000 r 74 goat snp27694-scaffold295-6239961 4 50409964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376654 Affx-122979016 AX-123247013 4 67353943 AAAAATCGGAGCAAGACATCAGTGACATGGGCTTG[C/T]GCTAGCACCATTTTACTGTCGTTTCTACAGCCCAG Y 2 1 2 1 201000 r 74 goat snp27693-scaffold295-6208777 4 50378802 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275519 Affx-1111834948 AX-519549091 4 67355663 AGCACCAGGTAATTGTATTGTGAACTTCTGGAATA[A/G]TGATATCACACACAAATTTCTTTGTAGAGTTATGG R 2 1 2 1 101000 f 74 goat GoatD01.059651 4 67355663 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399863 Affx-122960234 AX-123270218 4 67415791 GAAAGTAATCATCCTCAAGAAAACATTCATTTCCT[A/G]CTTTTGCCTAATGGCTTTATTTTGGGGAATCAATA R 2 1 2 1 101000 f 74 goat snp27692-scaffold295-6146929 4 50317057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395657 Affx-122963764 AX-123266012 4 67465789 TAGTTTTTTTGTTTGGTTGGTTTTTCCCTATTAAA[C/T]GGTAAAGAGGCATGTCTGAGGAGCAAAGCAGACAA Y 2 1 2 1 103000 r 74 goat snp27691-scaffold295-6096931 4 50266798 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788032 Affx-122941965 AX-385275053 4 67511329 GGACTTTGAAAAGGATAAAGCATTAGACAATGTGA[C/T]GCCATAAAAGAAGTATCACAAGGAGTGTCATGTCA Y 2 1 2 1 101000 r 74 goat snp27690-scaffold295-6051391 4 50220900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397678 Affx-122962587 AX-123268033 4 67563516 TTCAGCTCTCTGGCCAGAGGCTACGCTAACTTTAA[C/T]GGCTAGCCCACCTCACCACAATGTGGACCAAGAGG Y 2 1 2 1 102000 f 74 goat snp27689-scaffold295-5999204 4 50168587 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422471 Affx-122943328 AX-123292817 4 67607748 TACAGGAGGCAACAGAACATTGTAGAGAAGATGTG[C/T]AATTTCGAGTTAGAAATGGATTTGAATTCTGAAAC Y 2 1 2 1 101000 f 74 goat snp27688-scaffold295-5954972 4 50123947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420407 Affx-122944921 AX-123290754 4 67691101 TCGAATTATTAGTTGAGAAAACAACAACATGGATG[C/T]ATCGCATCATCAGGGTATTTCTGTTTGAAAAACAA Y 2 1 2 1 101000 r 74 goat snp27686-scaffold295-5871619 4 50051879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379874 Affx-122975786 AX-123250232 4 67734864 ATAACTGGGAACATTCCTATGCACAAGAACGTCAT[A/G]CCTTGGCTGGTACCTCCTCCTCCTCTGGTCCTTCT R 2 1 2 1 101000 f 74 goat snp27685-scaffold295-5827856 4 50008124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799503 Affx-122936370 AX-385286433 4 67796842 AGAATTCTTCATATAAATTTCCAATGTAGTTAATA[C/T]GTATAGCCAGATAAGCTCAGGTCATCAGTAATTTT Y 2 1 2 1 101000 r 74 goat snp27684-scaffold295-5765878 4 49946225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394834 Affx-122964787 AX-123265189 4 67828621 TCAATAAAAGACTGTATGTTGTGGTGTTTCTATTC[G/T]CAGAAGAAAAAGGAAATCTTTTCCCTAAGCCCTCC K 2 1 2 1 201000 f 74 goat snp27683-scaffold295-5734099 4 49913962 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439645 Affx-122930609 AX-123309982 4 67896381 GCTCTCTCCTCAGGAGAACTCCCAAGTTGGGAAAG[C/T]GTTTCTCAAACTATTGGCTGAAGATCCTTTGTGTA Y 2 1 2 1 101000 r 74 goat snp27681-scaffold295-5666339 4 49845893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384016 Affx-122972903 AX-123254374 4 67925936 TTGTTTCATATATATCATCTTTTTTTGGAGGAAAG[C/T]AAGTTTTAGGCAGAGTGTCAATCCAGCCCCCTGTT Y 2 1 2 1 101000 r 74 goat snp27680-scaffold295-5636784 4 49816148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790644 Affx-122966299 AX-385277646 4 67979885 CCACTAACTTTGTTTGATTGGTACAAGGGAGAGAA[C/T]ACTGATATTAATAAGGAAGCCCTTAAAGAAACACT Y 2 1 2 1 101000 f 74 goat snp27679-scaffold295-5582835 4 49762293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448484 Affx-122923618 AX-123318820 4 68008652 TGTAGGGCAAAGATTGCAAGGAAGCCTCTGGCCCT[G/T]GGAGACCCTTGCATGGAGGGGCACCATGGGGTGGC K 2 1 2 1 101000 f 74 goat snp27678-scaffold295-5554068 4 49733591 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772995 Affx-122950116 AX-385260139 4 68045796 ACAGCAGAGTGGAAATATGGGTCTAGAACCATGTA[C/T]ACTTAGACTAGAATTCCTATTTCCTCACTTTTTAA Y 2 1 2 1 101000 f 74 goat snp27677-scaffold295-5516924 4 49696207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426623 Affx-122939959 AX-123296969 4 68074621 CACAGAAAGCTAAAAAGAATTGCCTGCACCAAATT[A/G]TTTGGTATGCTCAAGTTAGGATTTAGATGCAGGGA R 2 1 2 1 101000 r 74 goat snp27676-scaffold295-5488099 4 49667369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448537 Affx-122923436 AX-123318873 4 68111937 GTGGTTAAACGGTGGCCTGCCACTAAGGCATATAT[A/G]TCCACCTGGAACCTGTGGAATTGACCTTATGTGGA R 2 1 2 1 201000 f 74 goat snp27675-scaffold295-5450783 4 49630142 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436373 Affx-122933053 AX-123306712 4 68171610 CTCCTTTCTTCTTTCATGTTCCTCCCAAATCTCAG[C/T]GGCAGGTTGGCTGCAGAGGGTGGCATTTTGTTGAC Y 2 1 2 1 101000 f 74 goat snp27674-scaffold295-5391110 4 49570420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777216 Affx-122970142 AX-385264339 4 68215895 TTTAAGACCTGAAAGCTGTGGACTCTGCGTTTCTT[A/G]AGTCGAGGTATATTATGGAATTTCATTTAATATCT R 2 1 2 1 101000 f 74 goat snp27673-scaffold295-5346825 4 49524873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779570 Affx-122927486 AX-385266673 4 68266941 GGATACACTAAACAAGACGATCATTTGTTTTGAAC[A/G]TTAAGGCCCTTTACAGACATGCCAGTTACAGGGTC R 2 1 2 1 101000 r 74 goat snp27672-scaffold295-5295779 4 49472631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446708 Affx-122924731 AX-123317044 4 68304700 CATTATGAAAATTGGTGTGATAGGTGGTACTTCTG[A/C]GTGGAGGCTCAGGGGAGGCTGGAAGGCATAAATGA M 2 1 2 1 101000 f 74 goat snp27671-scaffold295-5258020 4 49435164 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438277 Affx-122931403 AX-123308615 4 68334554 CGCAACCCTGAGAACGAGATGAGCGTCTGCATGCT[C/T]TTACTGCTCACCTATATCTTCATTTCCTTAAAACT Y 2 1 2 1 201000 r 74 goat snp27670-scaffold295-5228166 4 49404596 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414531 Affx-122949512 AX-123284880 4 68391720 TCAGGTTAAACACCAAGTAGAAGAGATAATAATAA[G/T]AAATCTTTACTCAGTCTTCCCAGCATGGACGGATA K 2 1 2 1 201000 f 74 goat snp27669-scaffold295-5171000 4 49347262 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278257 Affx-1111836252 AX-519551745 4 68434947 GTGACTATGTTGTCTTTCCTGGCAGAGGCACAGGG[A/G]GATGCAGAGTAAGGCAGAGCATCATTTCCAGTTGC R 2 1 2 1 202000 r 74 goat Random2.2K-453 4 68434947 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381152 Affx-122974554 AX-123251510 4 68459529 CACTCTCACACTCTAGGCCAGCACACTTACACAGT[A/G]CTGTATGTCAATCATGTCTCATTAAAATTAAAGGG R 2 1 2 1 101000 r 74 goat snp27668-scaffold295-5103191 4 49279373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409528 Affx-122953617 AX-123279879 4 68605660 AAACACTTTTGCAAAGTACATCAAGGGTTAAAAAA[C/T]GGTAGGAGACACATGGACAAAAGTTATAAACAATT Y 2 1 2 1 202000 f 74 goat snp27665-scaffold295-4957060 4 49132543 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273795 Affx-1111833846 AX-519547406 4 68690678 CTGTAATTAGTATCACTCTATACACTTCCGAAATA[A/G]TAATATTTGAATTGGAATATCTCTGCAGTACAATT R 2 1 2 1 201000 f 74 goat GoatD01.007131 4 68690678 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434399 Affx-122934687 AX-123304740 4 68736961 TTTTTTATCATGAAAAGGTATTTGATTTTGTCAAA[C/T]GCTTTTTCTTTGCCTGTTGAGATACCATGTGGTTT Y 2 1 2 1 101000 r 74 goat snp27663-scaffold295-4825759 4 49000376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770315 Affx-122948959 AX-385257481 4 68788205 GGGCTGATTCATGTGTTTTCACTGTTAAGTCTTGT[A/G]CACATATTCCCATTTTACTAATTGAACATCCTTAG R 2 1 2 1 101000 f 74 goat snp27662-scaffold295-4774515 4 48949114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434174 Affx-122934884 AX-123304515 4 68854464 CGTTGACCTCAAAGAGCTTACACCATATTGACAAG[C/T]GAAATGTATACATACATACACACCCACAAGGCGGT Y 2 1 2 1 201000 f 74 goat snp27661-scaffold295-4708256 4 48882300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278102 Affx-1111836253 AX-519551592 4 68898772 CCATAAAAATTTGATATCCTTTTTTCCTGGTAATT[A/G]AAATGTGCAAATGGCTAAAACATTATGATTGTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-454 4 68898772 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781251 Affx-122920319 AX-385268336 4 68903053 TTTTAATGTGAAGGAAAGTAACAAGCTATAAGCAA[C/T]AAGAAACCACATGCGCTATATTGGATTCCCGTCTC Y 2 1 2 1 101000 r 74 goat snp27660-scaffold295-4659667 4 48833544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443013 Affx-122928173 AX-123313350 4 68996754 TGGGCTTTATGTACAAAAAAGGTGATGTGTACATG[C/T]GGGGTGGAAAAGTACAGCAGACCATCAAAGTGAAA Y 2 1 2 1 101000 f 74 goat snp27658-scaffold295-4565966 4 48739971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798993 Affx-122935027 AX-385285923 4 69030962 AGAAAACAGCAAATGTTTATTCATTATCTAATGTC[A/G]TTCACTAATTCTTATTGAAGATGTCATACATTTTG R 2 1 2 1 101000 f 74 goat snp27657-scaffold295-4531758 4 48706340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766920 Affx-122977910 AX-385254233 4 69066817 AGTGTGCAGATTTCTGAAACCTGAGACTAGAAAGG[A/C]TGTTTAGAGGGAGACAGTCCTTCAAATTAAGGTCA M 2 1 2 1 101000 f 74 goat snp27656-scaffold295-4495903 4 48669830 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382675 Affx-122973655 AX-123253033 4 69119055 CATGGAAAATATAGGACTCAGAATCTGTTGGTAGC[G/T]GTGAGAATGGATGCATTTCAGCAGCAGTAATGTGC K 2 1 2 1 101000 f 74 goat snp27655-scaffold295-4443665 4 48616005 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417504 Affx-122947154 AX-123287852 4 69153720 GAAGTGGTCAGCATGATCTTTTACAAATGTAAATC[A/G]TATCTCAGTTCTCAAAACTTTCCAACTTCCTATCA R 2 1 2 1 201000 r 74 goat snp27654-scaffold295-4409000 4 48581073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396768 Affx-122962770 AX-123267123 4 69188362 TGTATGCTTGTCTTCTCACTGTCTTCTCTTGCCCA[C/T]GGGGTGTAAGCTCCCTGCAACTATGTCCTCTCCTG Y 2 1 2 1 101000 f 74 goat snp27653-scaffold295-4374358 4 48545999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411862 Affx-122951214 AX-123282212 4 69238525 TTGTTTGAAAGCATCTGTTACCATAACATAGTAAA[C/T]AGTTTTTAAGCCATTTTAGGAACAGCCATCTGTGA Y 2 1 2 1 201000 f 74 goat snp27652-scaffold295-4324195 4 48495521 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391300 Affx-122967337 AX-123261657 4 69284961 TCCTCTCCAGGGGTTTGGAGGTGGAGAGGCTGTGC[A/G]TTCTTAAGGAGGAGGGATGAGGCATGTGGCCCTTT R 2 1 2 1 202000 r 74 goat snp27651-scaffold295-4277759 4 48449330 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393262 Affx-122965458 AX-123263619 4 69324584 AGGGAGCTGGAAATTAGTCCTCTAATGACTTTAAA[C/T]GTCTCTCCTTTCCAATCTGCCTTTCTCAGACTCCC Y 2 1 2 1 201000 f 74 goat snp27650-scaffold295-4238136 4 48409700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278261 Affx-1111836254 AX-519551749 4 69328818 TCTTCTTTTTTTTTTTTTGGTAAACAATAGCTGGG[A/C]AATAAAAAGGAGTCAATCACAAACCCAAATTTGCA M 2 1 2 1 101000 r 74 goat Random2.2K-455 4 69328818 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272132 Affx-1111833436 AX-519545890 4 69345149 CAGAAAACGGAACTGAGACACAGAAAGGTTAAGTA[A/G]CTTACCCAAGGCCACGCAGCTAAGAAAGCAGTGGT R 2 1 2 1 103000 r 74 goat 4_69345149_AF-PAKI 4 69345149 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389598 Affx-122968771 AX-123259956 4 69354810 CTTAGAATCTGTTTTCCTTGGGGCTCAGAAACAGA[C/T]AATTGCAGAAGAAATCAAACACAACACAGTCTCAT Y 2 1 2 1 101000 r 74 goat snp27649-scaffold295-4207910 4 48378207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795174 Affx-122927592 AX-385282132 4 69388125 CTGTGAACCTGGTGAATTCTTTATCTTGTGAACTG[C/T]AGCACCAAAGAAGTTCATTCTGGGAAGTCAGGGAG Y 2 1 2 1 101000 r 74 goat snp27648-scaffold295-4174595 4 48344811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765610 Affx-122959629 AX-385253089 4 69439815 AATGGCTATTCAAGACCATAGACAGCAACACGCAG[A/G]TTGTGCACTTTACTCCCATTTCCATGTGACACTCT R 2 1 2 1 101000 f 74 goat snp27647-scaffold295-4122905 4 48293024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391045 Affx-122966860 AX-123261402 4 69486169 CACATCACATATCCAGCCTTGGAGGTACAGCCTTC[A/G]CTGAAGCCAGTTGATGAACAGTTGCAGAAGGGGCT R 2 1 2 1 101000 f 74 goat snp27646-scaffold295-4076551 4 48245355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450001 Affx-122922860 AX-123320336 4 69534303 CAGATTTCATTTTTACATGCTATAATTCCTCAGGA[C/T]ACCTTTATATTTAGTTAGGACCAAAATGGTCAACA Y 2 1 2 1 101000 f 74 goat snp27645-scaffold295-4028417 4 48196078 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766751 Affx-122954078 AX-385254087 4 69569538 AAGATCCAGAATTCAAGTGATTTGGGCCAAATAGT[A/G]TAGTGGGCATATAACAGATTACCTATATTTGAAAA R 2 1 2 1 101000 f 74 goat snp27644-scaffold295-3993182 4 48160839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776009 Affx-122978909 AX-385263139 4 69629097 TAGAATCAGAAATTTGACACAAGGAGAAAGACAGG[C/T]AGTTGGATTTTTAATTAAGCCAACCTAAATAATGA Y 2 1 2 1 101000 f 74 goat snp27643-scaffold295-3933623 4 48101126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453260 Affx-122920402 AX-123323593 4 69680676 ATCTCTGGAAGGTTCTGGTAAACAGTGGTTTTTGC[A/G]CTGGGGTACTGGGTGATGGGGCAGGAGAGAAAGAT R 2 1 2 1 101000 f 74 goat snp27642-scaffold295-3882044 4 48049615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415835 Affx-122948876 AX-123286184 4 69714826 GCCTCTAACTTTGAAATGATCTTTGCTTTAGCTTT[A/C]TATCAAAGAGTTTTGATTTGCTACTATACCATGCC M 2 1 2 1 201000 r 74 goat snp27641-scaffold295-3847894 4 48015387 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789607 Affx-122943724 AX-385276617 4 69788637 AGGTAACCACAAAGCACATCCCTGTGTTAAAAAAG[C/T]ACCAAGTATTTACGTCTTCCTTCAAAGATACAGCA Y 2 1 2 1 101000 f 74 goat snp27639-scaffold295-3774083 4 47941467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404158 Affx-122957078 AX-123274510 4 69865770 AATTTGGAGCTACAAATATAAAAAGATAGAGTTTA[C/T]GCCATGGAGAGAATTTTTCTTCTCAAACAAAAGCT Y 2 1 2 1 101000 r 74 goat snp27638-scaffold295-3696950 4 47864010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453809 Affx-122919566 AX-123324142 4 69908689 ATGACAGCAAAGCCAAGCAAAGAGTGATGGATGTC[A/G]TTCGTAGTCTTGGACTTACTCCATTGGATAAAGGA R 2 1 2 1 201000 r 74 goat snp27637-scaffold295-3654031 4 47820573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424622 Affx-122942186 AX-123294968 4 69953055 ACAACTGAATGACTAAACACCAGAAAAATAAAAAT[A/G]TCTCTCTGACCTAAAGTTCTTCTCCAGGCATGACT R 2 1 2 1 101000 r 74 goat snp27636-scaffold295-3609665 4 47776311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784150 Affx-122950486 AX-385271202 4 70012554 GTATGATTGTATTTTTTATGACATCACATTTTTTG[C/T]GATTCCTTAAAATGCTTTCTAAAAATTACACTAGT Y 2 1 2 1 201000 r 74 goat snp27635-scaffold295-3550166 4 47714548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396168 Affx-122963778 AX-123266523 4 70083553 CTAACAGTATTTTCTGCTAAACTGAATGTGGGATA[C/T]GAAGAGAAAGAAGAGTGAAAGATGATTTCTCCGGT Y 2 1 2 1 201000 f 74 goat snp27634-scaffold295-3479167 4 47643673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804609 Affx-986696778 AX-385291140 4 70115564 ATACAGAAACATCAGCTCATGTGTATATGGTCTCT[A/G]TGTATTGGTTCCTCCAAATTTGTACCAGTGTCTGA R 2 1 2 1 600010 r 74 goat 4_70115564 4 70115564 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38434457 Affx-122934645 AX-123304798 4 70126584 TGATGAAAATGTGGATATATAGAAAAAATTATTGT[A/G]CTGCTTACAGAAATAAATCCTATGATCCTATTTAG R 2 1 2 1 101000 r 74 goat snp27633-scaffold295-3436136 4 47600308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420089 Affx-122945104 AX-123290437 4 70155961 TCATAGCTGAGTGAAGAATGGATTGAAAAGGGAAA[G/T]TAAAGGGTCAGAGAAATCAGTGAAAAGGCCACTCG K 2 1 2 1 101000 f 74 goat snp27632-scaffold295-3406759 4 47571575 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402181 Affx-122959183 AX-123272534 4 70196244 TGCATTATCTATCTTTAGCAGTAGGGTCTCATTTA[C/T]AACACCTGAAGACAAGCAGATAATTGTTAATAAAT Y 2 1 2 1 101000 f 74 goat snp27631-scaffold295-3366476 4 47531544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786846 Affx-122954385 AX-385273875 4 70228188 TCATTTGAAGCCAACCTTCATATTTTCCCATTAAG[A/C]TATCTAAAGACCAGAGAGGTAAATTTACTTTCACA M 2 1 2 1 101000 f 74 goat snp27630-scaffold295-3334532 4 47503772 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788716 Affx-122975081 AX-385275732 4 70267035 AACATTTCATCAATACATATTTTCATTAATGTATT[A/G]ATATAAAATTGCCAAGTATGCAAAGATAGATGCTT R 2 1 2 1 201000 f 74 goat snp27629-scaffold295-3295685 4 47465673 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789850 Affx-122974253 AX-385276857 4 70300583 TCATGTGTTGAACCACAAGTGTGTAAAGTAGGTTA[A/G]TTCATTCTTGGTAAGATATAAAAAACAATTCAGTA R 2 1 2 1 101000 f 74 goat snp27628-scaffold295-3262137 4 47431819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413433 Affx-122950692 AX-123283782 4 70372389 TCAAAGAGCTCATTTCTTCCTCAAAGTGAATATTC[A/G]TTCTTGGGGAGCAGCTTTTATATGAGGAGGCTCCA R 2 1 2 1 102000 r 74 goat snp27626-scaffold295-3190331 4 47358899 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435711 Affx-122933307 AX-123306050 4 70418737 GAACTGAAAAACTGTGTCAGACAGTTTGTCAGTCA[C/T]GGGGGCTCAGGGGTGCAATGTAATCACAAGCAAAT Y 2 1 2 1 303000 f 74 goat snp27625-scaffold295-3143983 4 47312823 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417501 Affx-122947156 AX-123287849 4 70481098 AATGTCATTGCTGGTTCTGGATTAAGGACTAAGTG[A/G]TTCTTCGCAAAACTCAAATGACTTGATTTGTTGCA R 2 1 2 1 101000 f 74 goat snp27624-scaffold295-3081622 4 47249641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789415 Affx-122962754 AX-385276425 4 70528220 ATTCAAGAAGCCTAGACTCATTTGGGGTCAGGAAT[A/G]CATTGAGAATGAGTAGTGAAATAAGATTCAGCTAA R 2 1 2 1 101000 f 74 goat snp27623-scaffold295-3034500 4 47202226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437259 Affx-122932008 AX-123307597 4 70565552 TCACATGAAGTTTTTCTTGTATCAGATCTCCATAC[G/T]ATGCTATATAATATTAATATTTCCTATTTTAAAAT K 2 1 2 1 101000 f 74 goat snp27622-scaffold295-2997168 4 47165506 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376925 Affx-122977787 AX-123247284 4 70594748 GTGGTAACCTGGTCTAATGGATGAGGTTTCCGTTT[C/T]AAGATTTTGGCCCAGAAAACCCATTTCTTTCTGGG Y 2 1 2 1 101000 f 74 goat snp27621-scaffold295-2967972 4 47135957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396206 Affx-122963360 AX-123266561 4 70650010 ATTGCTTTTCTCAAAGCCCAGCAGCAAGACCCTCT[A/G]CTTGATATATTACACAGATGTCCTAGCATGTAAAT R 2 1 2 1 201000 r 74 goat snp27620-scaffold295-2912710 4 47080341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428697 Affx-122938627 AX-123299039 4 70680625 AATGAGAACAATGTGGTAAAACATGAGGCTGAAAT[A/G]AGTATTAGTGGATTTATTTATCTTTCCTCTTTTCT R 2 1 2 1 101000 f 74 goat snp27619-scaffold295-2882095 4 47049886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392267 Affx-122967551 AX-123262624 4 70720720 AAGGAGGCAGATCCTGTTATTGCCATCAATCTATA[C/T]GTGCAGAAACCATGGTTTAAGAGAGGCTAGTTAAC Y 2 1 2 1 101000 f 74 goat snp27618-scaffold295-2842000 4 47009127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789932 Affx-122952832 AX-385276938 4 70756571 CATTTCAATTCAGCAACCTACACAGAACTCACAGG[A/C]GATGAGTTCTGGTTACCTCCTGAGTACAGGTTACC M 2 1 2 1 101000 f 74 goat snp27617-scaffold295-2806149 4 46973425 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769967 Affx-122958839 AX-385257135 4 70788711 ACACAACCCAATAGTGTAGAGGATTAATAAACATA[A/G]AGGTGTTAGTACAGTTCCTCAAATGTAATAAGGAC R 2 1 2 1 101000 f 74 goat snp27616-scaffold295-2774009 4 46941252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792857 Affx-122970330 AX-385279835 4 70827981 AATTGATGTTATTGAATTACATATGAGAAAAATGG[C/T]ATTAAAATAGGAGAAATAGCACACATCTAGAAAGA Y 2 1 2 1 101000 f 74 goat snp27615-scaffold295-2734739 4 46902113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390308 Affx-122967716 AX-123260665 4 70868698 CGACTTAAAATAATGAAGCACATTTAAGAATAAGG[C/T]AGTTTCTAACTCCAGCAATAAAATAAGTGCAAAAG Y 2 1 2 1 101000 f 74 goat snp27614-scaffold295-2694022 4 46861447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440812 Affx-122929824 AX-123311149 4 70915580 AGTTTCCAGGTAACATGCAAAGTCAGAGTCAATAA[A/G]AGAGCTTCACAGCAATCCAAAGAGTGAATCACTGA R 2 1 2 1 101000 r 74 goat snp27613-scaffold295-2647140 4 46813903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410542 Affx-122952155 AX-123280892 4 70955177 ATCATGGGGATATGCTTCTCTTATAAAACTTTGTG[C/T]ATTTCTGCTAACTCTTTCTGTTTTATCTAACGATT Y 2 1 2 1 101000 f 74 goat snp27612-scaffold295-2607543 4 46773796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385460 Affx-122971303 AX-123255818 4 70991232 TAATTTCAGAGCTGAGACTTGATGATAAAATTAGA[G/T]ACCGAAAAAATAAATTCAGCATCAACTGAGTTCAA K 2 1 2 1 201000 f 74 goat snp27611-scaffold295-2571488 4 46737780 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278106 Affx-1111836255 AX-519551596 4 71027931 CCAAGCCAAGAACATTTTATTTACCAAAACCCTGT[A/G]CATTAACACACTGCCTCCAGGGCTGTGATATTTCT R 2 1 2 1 201000 f 74 goat Random2.2K-456 4 71027931 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415538 Affx-122948661 AX-123285887 4 71044891 TAAAAAAAAAAAAGCCTTATATTCTATTCTGTGCT[A/G]ATCAGCATATTAACTTATCTGTTTCCCCTTCTAGC R 2 1 2 1 101000 r 74 goat snp27610-scaffold295-2517829 4 46683123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799737 Affx-122954498 AX-385286664 4 71081028 TGGTGTTCATAAACAAAGAATGGGATGCTTTTACA[G/T]ACAAAGCAGGGTTATCAGCAATGTGATGATATTCT K 2 1 2 1 101000 f 74 goat snp27609-scaffold295-2481692 4 46646473 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389341 Affx-122968478 AX-123259699 4 71115479 CTCTTCCCCACTTTCCTTCATCAGCAATCCTTCTA[C/T]ATATATAAAAACTTCCTGTATTTGTTTACTTTTGA Y 2 1 2 1 201000 r 74 goat snp27608-scaffold295-2447241 4 46612156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800652 Affx-122971116 AX-385287571 4 71153360 CAGAAGAAGTTCAATACGGAGGTACCTTAAAAAAC[G/T]AAATATAGACCTCCCAGATGATTATGCAATCCCAT K 2 1 2 1 303000 f 74 goat snp27607-scaffold295-2409360 4 46574145 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781962 Affx-122941914 AX-385269042 4 71226412 GTATAGACTGTCTGGAGATAAAGCAATCATATAAT[A/G]CCCAAATATATGCTGCCTAGTAAACTCATGTCAGC R 2 1 2 1 101000 r 74 goat snp27605-scaffold295-2336308 4 46511788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439885 Affx-122930037 AX-123310222 4 71300115 GACTTTCAATTAATAAGGTCATTTTGTGGCCTGAC[A/G]TGGTAGTCCAGTCAAACTGATGTCTGTTGTGTGAG R 2 1 2 1 101000 f 74 goat snp27604-scaffold295-2262605 4 46438516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779481 Affx-122931724 AX-385266584 4 71356827 GACGTATATGCATTGTCAAAGTCTATATTCTTATA[G/T]CCCATGCTTTCTTATCATATTCTATGGCAAAGTTA K 2 1 2 1 101000 r 74 goat snp27603-scaffold295-2205893 4 46381552 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278266 Affx-1111836256 AX-519551754 4 71390598 AAAAAGGCAGAAGGCAAAATAATTATCTTGTTATT[A/T]TTGGTACAATCACCTATTACATGTATCCTTTACTA W 4 1 2 1 101000 r 74 goat Random2.2K-457 4 71390598 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438632 Affx-122930914 AX-123308969 4 71418271 TCTCATTCTAGAACTCTGCCATAACCAGTTACATG[C/T]GGCTTCCGCTCTATAGTGGGGAAAGCCTGTACCTT Y 2 1 2 1 101000 f 74 goat snp27601-scaffold295-2144449 4 46319909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411662 Affx-122951561 AX-123282012 4 71462197 CTAGACAGTTCAGTTTCTTAAAAGATGAGCCCTAT[A/G]TTTTCAGACTTAGATTTAAATACTTGTTGCCCTTA R 2 1 2 1 201000 r 74 goat snp27600-scaffold295-2100523 4 46276168 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378373 Affx-122976815 AX-123248732 4 71493822 TAATTAAAATGGAATCTTATCAAATGTAATGGTTC[A/G]GAGGTTGATTTTATTAAAAAATAATGTATTATGGG R 2 1 2 1 201000 f 74 goat snp27599-scaffold295-2068898 4 46244278 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375880 Affx-122978501 AX-123246239 4 71553340 AAATTAGAGTAGCTTGACAAAATTGCTTACTTCTT[A/G]CAGCAACTTCTTACTTCTTACTACTCTGTTTTGGT R 2 1 2 1 101000 f 74 goat snp27598-scaffold295-2009380 4 46182284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452459 Affx-122920561 AX-123322792 4 71581996 CTGCAGAATTCTCCTTGCTCTATTCACATATGTTT[A/G]TCATCTATTTTATATCATTAACTTCAGAATGTTTT R 2 1 2 1 101000 f 74 goat snp27597-scaffold295-1980724 4 46152931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405407 Affx-122956286 AX-123275759 4 71627518 TCGTGGGATCAAATATTTATTGTCCATAAGCAAGA[C/T]GTACTGTCAGGCTTTTATCTGTGTGTACTTTTCCC Y 2 1 2 1 101000 f 74 goat snp27596-scaffold295-1935202 4 46106953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786736 Affx-122923584 AX-385273767 4 71659547 AAATTAATCATTGGAGGCATATCACTAAAATTTAG[A/G]TACAGTTGAAGGGAGCAGATTTTATTTACAAATTA R 2 1 2 1 101000 r 74 goat snp27595-scaffold295-1903173 4 46073970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422541 Affx-122943269 AX-123292887 4 71716471 ATGGTTCAGCTGGCTTCCTTTAGGACTTCTGTCCT[A/G]TGGATCAATGGAATTCTCTCTTATGTGTATAATAA R 2 1 2 1 201000 r 74 goat snp27594-scaffold295-1846249 4 46015763 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422210 Affx-122944442 AX-123292556 4 71766496 CAGCATGAGACTTTTAAAAGGTTATGCTTTCAAAA[C/T]GGTTTCAAAGAGATTAGAAATGAGGAAAACCTGCA Y 2 1 2 1 103000 f 74 goat snp27593-scaffold295-1796224 4 45965576 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442462 Affx-122927946 AX-123312799 4 71817680 CTGCTTTTAATTGTGTCTACATGGGCCAATTAGAA[C/T]AGAAATCAACACTTTTGCTATGGATTTGATCAATA Y 2 1 2 1 101000 f 74 goat snp27592-scaffold295-1745040 4 45914871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450679 Affx-122921907 AX-123321013 4 71857030 GGGACTTTGAAACTGCAGAAATTGAGGGCCTGTTT[A/C]GTACCTTCAAAGATTACAGTATTTATTTAGGAGAA M 2 1 2 1 201000 r 74 goat snp27591-scaffold295-1705690 4 45875777 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379632 Affx-122975956 AX-123249990 4 71888880 AGAACAGAACAGGAACAGAACTCTTTTAGATAGGA[C/T]GGTTAGGGAAAATCACTTGGAGGAGATGCCATCTG Y 2 1 2 1 101000 f 74 goat snp27590-scaffold295-1673840 4 45843682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272281 Affx-1111833437 AX-519546020 4 71901429 TGGAAGCTTTAGATGGAAAATCTGACCAAAGCCTG[A/G]AACATTAAGCTCTGAATGAAGAAACTGAGTTTAAA R 2 1 2 1 101000 f 74 goat 4_71901429_AF-PAKI 4 71901429 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431606 Affx-122936163 AX-123301947 4 71921816 TCCTTGAAATTTCAAGGTCACAGTTTTCCTGAGTG[A/G]ACCTTTGACTTGATGCATGCATTTAATCCCTGAAG R 2 1 2 1 201000 r 74 goat snp27589-scaffold295-1640904 4 45810414 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407340 Affx-122955290 AX-123277691 4 71989868 TCAAGTTTGGTTATCCTAAGTAAACTCATCAATAA[C/T]GTGAATGTTTTTGCCTAGCCCCTTTTTTCAATATC Y 2 1 2 1 101000 r 74 goat snp27587-scaffold295-1572852 4 45739206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404162 Affx-122957074 AX-123274514 4 72050524 AGCCTTTACATTCTAAAAATTGCAACACACAAGCA[C/T]AGTAAATGTCCTTTTAAAATCTTTCTTAATACTTA Y 2 1 2 1 101000 f 74 goat snp27586-scaffold295-1512196 4 45678400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450857 Affx-122922231 AX-123321191 4 72095051 TAACTACCGACCATTCATGGGATAGTGATGAAACG[C/T]GCTGGGAATCTAACATAAATTATCTCAACTGATAA Y 2 1 2 1 101000 f 74 goat snp27585-scaffold295-1467669 4 45633080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448006 Affx-122923733 AX-123318342 4 72137279 TACACAGCCCTTCCCACTGCTTTACTCAGTTTGAG[C/T]GTGTGCATGTGCCTGTGTATATTTTTTCCTGCCTA Y 2 1 2 1 303000 r 74 goat snp27584-scaffold295-1425441 4 45590227 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438013 Affx-122931573 AX-123308351 4 72234223 TCGACCCATGGCTCCCTCCTCTGAAAACTTTCCTC[A/G]CTGGGCTTATTAAAGGATTAGCTCACCACCATTAG R 2 1 2 1 101000 r 74 goat snp27582-scaffold295-1328497 4 45493140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411540 Affx-122951655 AX-123281890 4 72265907 TAGTTTATTGAGCACTAATTTCAGTGCTGCCTCTA[C/T]GTTGCCTAACTCTAGGCCCCATGGCCCCACTGAGG Y 2 1 2 1 101000 f 74 goat snp27581-scaffold295-1296813 4 45460953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382616 Affx-122973703 AX-123252974 4 72306264 CCAGCCCTCAGCTGAGCCATGCCAGTTCCAGAAAT[A/G]CTCTTCTTCTAGATCACCATAAACTAAAATCATCT R 2 1 2 1 101000 r 74 goat snp27580-scaffold295-1256456 4 45420559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390201 Affx-122967795 AX-123260558 4 72356656 TGCAAAGCGCCGAGCAGACACCAACTCCCCACGTG[C/T]GACGTGACCACACAGATGCACCCACCATCAAAACA Y 2 1 2 1 101000 r 74 goat snp27579-scaffold295-1206064 4 45370007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375542 Affx-122979099 AX-123245901 4 72391477 GGCTCGTAGCTGTTGTTTGTGTACTACTCCTAATA[C/T]ATGAGTCTCTCTCCTAATTCTGAAAAAAATTCAAA Y 2 1 2 1 101000 f 74 goat snp27578-scaffold295-1171243 4 45335889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429691 Affx-122937637 AX-123300032 4 72445428 GCCACTGCATTCCAGCGGCGACTGGGCCTGGAGCC[A/G]CTCTGAAGGACCCAGCTCTAGCCCTGATGCACTTC R 2 1 2 1 101000 r 74 goat snp27577-scaffold295-1117292 4 45282360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379695 Affx-122975906 AX-123250053 4 72482470 AAGGCTGAATAACATTCCATTGTATGGATGAATCA[C/T]GATATGTTTATCCTTTGCCCGTGGAGGGACACTTG Y 2 1 2 1 103000 r 74 goat snp27576-scaffold295-1080250 4 45245412 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388764 Affx-122968941 AX-123259122 4 72511096 ACAGAGCAAGCCTGAGTCTCAAACTAATCATGTCC[C/T]ACCCCTCAAGACCTTCCTCCCCAGAAAGGCTGTAT Y 2 1 2 1 201000 f 74 goat snp27575-scaffold295-1051624 4 45216744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435519 Affx-122933411 AX-123305859 4 72542697 ACTAGGGAACCAAGGCCTCTGCTCCCCACTGACAA[C/T]TGATGAGGAGATGGCACCCTCGTGCCACAAGAAGA Y 2 1 2 1 201000 r 74 goat snp27574-scaffold295-1020023 4 45185184 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418124 Affx-122947121 AX-123288472 4 72588505 GTGGGTGCTGAATGAGTGGGCTGCTTGGATCAGAC[A/G]ATTTTAGTTAAGAGGTTTGAGTTGACTGGGGGGCT R 2 1 2 1 101000 r 74 goat snp27573-scaffold295-974215 4 45138617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780424 Affx-122935364 AX-385267516 4 72620422 GTTGTTGAAGTCTTGAAGTGAGACTGCCAATATCC[A/G]TCTCTATGCCCTAGAACCAAACAGATGCTGGACTC R 2 1 2 1 101000 f 74 goat snp27572-scaffold295-942298 4 45106216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397588 Affx-122961997 AX-123267943 4 72653769 GTTTCAGGTGTACAGCATTATAGTTTGACATCTGT[A/G]TACACTACATTGTGAGTATCATCACAGGTCTTGTT R 2 1 2 1 101000 r 74 goat snp27571-scaffold295-908951 4 45072641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412294 Affx-122950871 AX-123282643 4 72696361 CCTCGACATACAAGCCACATCTTATCTCCTTACCA[C/T]CACCTACCACTTTTCTTCTGACTGTACAACCCTTA Y 2 1 2 1 101000 r 74 goat snp27570-scaffold295-866359 4 45029756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423687 Affx-122942320 AX-123294033 4 72726252 GGAGCCAGTTATAACATTAGACAAACCAAGAGCCC[A/G]AGGAGAACAGAATAATAAAAAGTGCATTTCTAGCC R 2 1 2 1 101000 f 74 goat snp27569-scaffold295-836468 4 45000196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787634 Affx-122965306 AX-385274657 4 72759494 TTATGAGATATGTATTTTTACCTCCTGAAAATTAT[A/G]CTTTGACATGACATTTGATCATAAAGTACTTTACT R 2 1 2 1 101000 r 74 goat snp27568-scaffold295-803226 4 44966778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442011 Affx-122928418 AX-123312348 4 72790931 TCAAACTTCATGAAGAAGGCATTGTACAGACTAAA[C/T]GCTTCTTCTATACTTTGCTGAATGTGGTGATCATG Y 2 1 2 1 101000 f 74 goat snp27567-scaffold295-771789 4 44935670 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443388 Affx-122927397 AX-123313725 4 72877276 AAACAAAAGTACTGTGTATACTTCTAGGAAGGCAG[A/C]TTATAAAGAGTGTATTTTATATCAGAAAACCTTTT M 2 1 2 1 101000 f 74 goat snp27566-scaffold295-685444 4 44848584 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790717 Affx-122923144 AX-385277718 4 72907561 GTCAGTGAGTTGACTTTCTCTTTAGAATTTCAAGG[C/T]AGAGGTACAACACTCCTTCTTTCCAAGGATCACTG Y 2 1 2 1 101000 r 74 goat snp27565-scaffold295-655159 4 44818257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435252 Affx-122934067 AX-123305592 4 72971000 AAAGAGGACCATGACTTTATAATTGGGCAACTATA[C/T]GGAAATAAGAAACAAGATTGTATTTCTAGACTAAA Y 2 1 2 1 101000 f 74 goat snp27564-scaffold295-591720 4 44750738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789547 Affx-122929300 AX-385276556 4 73008376 ATCTGTTGATAGATTGCTAACAAAGTACTATAGAC[C/T]GAGTGGTTCATAAGCAACATTTATTTCCCACAGTC Y 2 1 2 1 101000 r 74 goat snp27563-scaffold295-554344 4 44713239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796341 Affx-122940691 AX-385283291 4 73037765 AGGTGTATGTCTAATAATTCACATGATGCCTTCAA[A/C]TCTCCAGAAAACCAATAAAAGCAGTGAAAAATCCT M 2 1 2 1 101000 r 74 goat snp27562-scaffold295-524955 4 44686025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804325 Affx-986696782 AX-385290936 4 73044581 ACAGGCCTGGACAACACGATGTGGTACAAACACAC[A/G]AGGGAAAGGCACAAGCCATCCAAAAAGGAGGAAAG R 2 1 2 1 600010 f 74 goat 4_73044581 4 73044581 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38430948 Affx-122936831 AX-123301289 4 73082098 ACCAGCAAATATTAAATATCTCTGATACTATCTTA[C/T]GCTTCCCTTGATAGAATAAATATTTGCTCCTGATG Y 2 1 2 1 101000 r 74 goat snp27561-scaffold295-480622 4 44641055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450517 Affx-122922499 AX-123320851 4 73116462 CCAAAGTACTTTGAGTCCACTGAAATTGCTGAAAT[A/G]TTTTCCCAAGTGTTTCTGGACTGGAGAATCCAGAA R 2 1 2 1 201000 f 74 goat snp27560-scaffold295-446258 4 44606707 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414868 Affx-122949145 AX-123285217 4 73185754 CAAATGCTGTTATGAACCTCCACATCGTGATATCT[A/G]TCTGTTCCACACTGGCTACATTTCCCACAAGCAGG R 2 1 2 1 101000 r 74 goat snp27558-scaffold295-376966 4 44536990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381808 Affx-122974278 AX-123252166 4 73249176 ATAATATGTGCTTTCCAGTGGGAGCTTTTAAAGAC[A/G]CAGACCTCACCACAGAACCTCACTTGGAAGGTACC R 2 1 2 1 201000 f 74 goat snp27557-scaffold295-313544 4 44471910 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400141 Affx-122960703 AX-123270496 4 73294186 GTCAGGGATGGGCTGACTCTGGGCACTATGACTAA[C/T]TGCAATTTTCAATGGATGGGGTGCACGTACCCATG Y 2 1 2 1 201000 f 74 goat snp27556-scaffold295-268534 4 44425927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464310275 Affx-1110418092 AX-515784361 4 73378247 CTGGAAGCATCACCCACTGCAGTGCACACAGGACC[C/T]CATTGCCCTACCATTTACATGTCAGTATTCCATTT Y 2 1 2 1 201000 r 74 goat GoatD01.053408 4 73378247 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448019 Affx-122923724 AX-123318355 4 73389390 CTCCAGCCTACCTTCCACACTTTCTATAGCCTGAC[A/G]GTTCTCTCCAATACACCCTTGGTGCTGCCTCTGTT R 2 1 2 1 101000 r 74 goat snp27554-scaffold295-173330 4 44328744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780173 Affx-122932832 AX-385267270 4 73434324 AATTGTTTCAAAAGTGAGGGAGAATGTAGATCTTA[C/T]GATGCTGTTTGCAACTGCTTATTAAATATTGATGG Y 2 1 2 1 101000 f 74 goat snp27553-scaffold295-128396 4 44284387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441845 Affx-122929046 AX-123312182 4 73466481 TTTGGCTCACAACACCTTCCAACATCAGCTGTCAG[C/T]GTATTTATCTGAATTTACTCTCACGTAGCCTCTGG Y 2 1 2 1 101000 r 74 goat snp27552-scaffold295-96239 4 44252069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800489 Affx-122923903 AX-385287409 4 73510016 TTCTAGGACATTTTAGACTTTAGATAGCTCTTCTT[A/G]CATAATGTTGGCATCTCCCACAAATATTTGGCCAT R 2 1 2 1 101000 r 74 goat snp27551-scaffold295-52704 4 44208838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450977 Affx-122921737 AX-123321311 4 73540653 GAGGACATGAGATGCCAAGTCTGGAGAGGGGATGT[A/G]CGAGGAAACATGATCACCATCCCCCAACTTATAGG R 2 1 2 1 101000 f 74 goat snp27550-scaffold295-22067 4 44177937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387598 Affx-122970254 AX-123257956 4 73581028 AATGGTAAGTTAGGTAGACACACAGGTTATATCCT[A/G]CCTGATGCCCCAGGACACCCTCATTCACCACCACT R 2 1 2 1 101000 f 74 goat snp16190-scaffold17019-299 4 44136425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442178 Affx-122928806 AX-123312515 4 73587173 ACAGGAGGGACAATTGTGTCCCTATTTTTGGGAGA[C/T]AGCCTCTGAGAAGAAGTGACCTATTATCTTAGACT Y 2 1 2 1 201000 f 74 goat snp39041-scaffold494-6776236 4 44130443 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802797 Affx-122929930 AX-385289696 4 73621110 GCTCACAGTCTGCATTAAAAGTGGGTGCTTGCCTT[A/G]TATTCTACCCCGTAATATATCTTTTTATTTTAGGT R 2 1 2 1 101000 f 74 goat snp39040-scaffold494-6742299 4 44095826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418758 Affx-122946203 AX-123289106 4 73690220 GAGAGCTAAAAGTCATTTGGTTACACATCAGAATC[A/G]CTTTGCATCAGACACAGGCTTTGGAAACAGTTCTC R 2 1 2 1 201000 f 74 goat snp39039-scaffold494-6673189 4 44026632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423724 Affx-122942873 AX-123294070 4 73755727 TCGCTCCCTTTTTGTTTTAATTTATTTATTTTATT[A/C]GAATATAGTCGCTACACAGTGTGTTAGTTGCTGCT M 2 1 2 1 103000 r 74 goat snp39038-scaffold494-6607682 4 43972323 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431172 Affx-122937188 AX-123301513 4 73799389 TCAGTCATCCTCCTTGGTGGTTTCATCTATTGCTG[A/C]GGAGCTGAGCACATGGAATGTGGAAGTGAGTGAGG M 2 1 2 1 10000 f 74 goat "snp39037-scaffold494-6564020;SV_250" 4 43928380 C A SV_250 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386812 Affx-122970900 AX-123257170 4 73844054 CTTTCTGTCCTCCTGGTATGGGAAGATGTGGGAGA[C/T]GTATTTCCTGCTTTCAGAGGAAAGGAGTGGAAGGA Y 2 1 2 1 303000 f 74 goat snp39036-scaffold494-6519355 4 43883834 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387081 Affx-122969880 AX-123257439 4 73874494 GTGACTTACAAGGGAAGAAACTGAGGCACGAAGCA[C/T]GCAGACCTGCTCTGTGGCTTCCACAGTCCGAGGCG Y 2 1 2 1 101000 f 74 goat snp39035-scaffold494-6488915 4 43853450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400321 Affx-122960057 AX-123270676 4 73909145 AAATGACTGTTTTAGGATGTGTGCATTTTCAACTA[C/T]ACCAAGTCAGCACTTGGGGCTATAAATATCCACTT Y 2 1 2 1 201000 f 74 goat snp39034-scaffold494-6454264 4 43818423 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415224 Affx-122948967 AX-123285573 4 73940178 AGCCTTGTGAGTCAAATCCTCACATGTGCACTTTT[A/C]AACACATCCATAATCATACCTGCAGGACACATTGT M 2 1 2 1 101000 r 74 goat snp39033-scaffold494-6423231 4 43787391 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410547 Affx-122952152 AX-123280897 4 73979274 AGAACAAAGTAAGACCAGGGACAAGGTCCTTGTGA[C/T]GGTCAGGCCTGGGCATCAAAGCCACCCAGAGGCCC Y 2 1 2 1 202000 r 74 goat snp39032-scaffold494-6384135 4 43748046 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418467 Affx-122946461 AX-123288815 4 74022276 AATGAGAAGCGTATGTTGGCCATGCTGCCCCGCTG[C/T]GGCAAGACCTTCGCCGAAAAGATGATGAAGGTAGA Y 2 1 2 1 101000 r 74 goat snp39031-scaffold494-6341133 4 43705022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453937 Affx-122919486 AX-123324270 4 74064444 CCAAAATTAATATAGATGAAACTTTAAAACATTAT[A/G]TTATGTGAAAGAAGTGTGAATGCTGTATCAGTGAA R 2 1 2 1 101000 r 74 goat snp39030-scaffold494-6298965 4 43662694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447895 Affx-122923815 AX-123318231 4 74097615 GTCTTTCCTACCAGGTCAGTTTTTGGAAAGAGCGC[A/G]AGGTGGCCAAGGCCTGAGCGTGGGGCTGCTCTAGC R 2 1 2 1 101000 f 74 goat snp39029-scaffold494-6265794 4 43629058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386272 Affx-122970945 AX-123256630 4 74130955 CAGACAGACTTTCCGACAGGGTATCCCATGGAGAA[C/T]GAGGTAGGTGCAAACCCAGTGTGGAGAGAGCCATC Y 2 1 2 1 101000 f 74 goat snp39028-scaffold494-6232454 4 43595687 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410821 Affx-122952639 AX-123281171 4 74160985 CAAACTCCGCTGCACCTTCACCAGGTGCATCAATG[C/T]GGCCAAGCCACCACCTCAGTTCCCACTTCCTCATC Y 2 1 2 1 102000 r 74 goat snp39027-scaffold494-6202424 4 43566505 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780558 Affx-122937522 AX-385267649 4 74221663 TGTATAATAAAGACTTTTTGAGCCGGCTTGATCTT[A/G]TAATATAGAGCAAGGAATGGGGATGAGAGTTTAAG R 2 1 2 1 202000 r 74 goat snp39026-scaffold494-6141746 4 43505240 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379381 Affx-122976143 AX-123249740 4 74289424 TACTTATTTGCTCTTTTACTTACTTACTTGGCTGC[A/G]CTGCGTCTTGGTTGTGGCGTGCAGATCTTCAGTCT R 2 1 2 1 101000 r 74 goat snp39025-scaffold494-6073985 4 43437880 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413658 Affx-122950118 AX-123284007 4 74338320 CTGGCATTAGAGCCTGGACATGTGCATCTTTACAA[C/T]TCTCCCAGATTCCCCAGAGATTTGGATACACAGCT Y 2 1 2 1 101000 f 74 goat snp39024-scaffold494-6025089 4 43389000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382269 Affx-122973935 AX-123252627 4 74369157 GCTTACACATGATTGGAAGTGGTTCAAGACCCTCC[A/G]CTGCAGCTGCTTAGTCACTTCATTCATGTCCAACT R 2 1 2 1 101000 f 74 goat snp39023-scaffold494-5994252 4 43358121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395255 Affx-122964097 AX-123265610 4 74414071 ACTGTCTCCATTCTTTGCCAGAGGCTCCGTTGAGG[C/T]AAATCACCCCAGGTGAGAAGTACGGCCCTATGCAG Y 2 1 2 1 201000 r 74 goat snp39022-scaffold494-5949338 4 43313592 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377627 Affx-122977879 AX-123247986 4 74472414 GTGTGCATGAGACTAAAGGGAATGGAGAAAGGCAA[C/T]GAACTGAGTAGGAGGCTTCAAGCCCCAGTCTGCGT Y 2 1 2 1 101000 f 74 goat snp39021-scaffold494-5890995 4 43256275 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434168 Affx-122934890 AX-123304509 4 74514101 GCCTCACTACCTGTGCCTCCTGCCTCCACAGAACA[C/T]GTCTGCATGGGCACTCTGCACACCCAGCAGGCATT Y 2 1 2 1 101000 r 74 goat snp39020-scaffold494-5849308 4 43214354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393309 Affx-122965961 AX-123263665 4 74551969 AGATTGAGAATAAGCTGAGATTTACAGCTGAAGAC[A/G]CTGGCAAAGAAAAACAACCCCGAGAAAGGCAAAGG R 2 1 2 1 101000 f 74 goat snp39019-scaffold494-5811440 4 43176771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275049 Affx-1111834656 AX-519548631 4 74607493 AGGCAGAGGATTTAAGGCCCCTCATACATGGTTGG[A/G]GG R 2 1 2 1 102000 f 74 goat GoatD01.044572 4 74607493 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443933 Affx-122927029 AX-123314270 4 74610604 TACTCACTGAATAGAAACTCCAGAGAGCCCAGGTG[G/T]AGGCGGCCAACCTCCCGGACAGTCGGGTACAACAT K 2 1 2 1 101000 f 74 goat snp39018-scaffold494-5752805 4 43118812 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464303820 Affx-1110418528 AX-515777961 4 74704481 AGCCTTGGACAGCAGTAGCATTAAACAATTGCTAA[C/T]GATTATCTTTTACACACGTCTAGAGGACAGTGATT Y 2 1 2 1 101000 f 74 goat 4_74704481_AF-PAKI 4 74704481 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790995 Affx-122955160 AX-385277992 4 74708960 ATTCATAGGCTATACCTATAACCTACCTCCACTGA[G/T]AATTTTAAACAATCAATACAGGGCCCTGAATCATA K 2 1 2 1 101000 f 74 goat snp39016-scaffold494-5654449 4 43021705 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421782 Affx-122944344 AX-123292129 4 74757465 GAGAAGAATCCCTGACTCCCTCCCCCTATGGGGAA[C/T]TGGCCTGAGAATGATGGAGAAGAGACGTCCTTAAA Y 2 1 2 1 101000 r 74 goat snp39015-scaffold494-5605944 4 42973768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789727 Affx-122950666 AX-385276735 4 74818968 TCAGATATGTTTTCCTTAGTATCTTTGAAAACCTT[A/C]TTTGAAGTCACCCAGATAGTAAACAGCAGAACCAG M 2 1 2 1 101000 r 74 goat snp39014-scaffold494-5544441 4 42912013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410379 Affx-122952439 AX-123280729 4 74850129 ATGTGTTCTTAATCTCGGAATCCCATCATCTATTC[G/T]CGAGCTCCAGACACTTAGCTTCTCTGCATCCAAGA K 2 1 2 1 101000 f 74 goat snp39013-scaffold494-5513280 4 42880995 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418496 Affx-122946438 AX-123288844 4 74889090 ATTATGATTACGGGGTGGACATCTCCTCCAAACAA[C/T]TAAAGAAACAGTGGTAGAGAAGTCCAGGTTTCCAA Y 2 1 2 1 101000 f 74 goat snp39012-scaffold494-5474319 4 42841551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770044 Affx-122941876 AX-385257211 4 74928898 TTTGAAGCACCTGAAGGGCAAGGGAAACTTAACTT[A/C]TACCTCTTTAGTGTACCCCACTAAACAAAAATCAA M 2 1 2 1 101000 f 74 goat snp39011-scaffold494-5434511 4 42801228 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425449 Affx-122941517 AX-123295795 4 74963390 TCTACCTCGTCTGGTTTACACACTAGGTCAAAGCA[C/T]GAAAACACTGTGGCAACATCAGCATAACTAGTTAA Y 2 1 2 1 101000 f 74 goat snp39010-scaffold494-5400019 4 42765978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401952 Affx-122958800 AX-123272305 4 75000172 GAGGTAGTGAACATTGAGAGGGGTGCCCAGAGCTT[C/T]CAGTGCCTCAGGGTGGCTGTGCAGCTGCTCCAGGG Y 2 1 2 1 101000 f 74 goat snp39009-scaffold494-5363237 4 42729190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400398 Affx-122959999 AX-123270753 4 75030393 TAGAAATGGAGCTTCAGCAATATTTCTGGGTGGGT[A/G]CAGGCTTCCTGGTGGAGACAGGGCTTGAAATGCTG R 2 1 2 1 101000 f 74 goat snp39008-scaffold494-5333016 4 42699064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379222 Affx-122976279 AX-123249581 4 75080784 GGTAGATCTAGATCACTGTGGTCAAACATGTTTAA[C/T]GCAGAGAGAGGGTCCCTTTACACCCCAACCTAGTT Y 2 1 2 1 101000 f 74 goat snp39007-scaffold494-5282625 4 42648376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274213 Affx-1111834071 AX-519547813 4 75098832 CTTCAGTTCCCAGGAAGTCCCCCTCTTCACTCTGT[A/G]AGTAGTAACCTCTTGTGAATCTCTTGGACAGAGAG R 2 1 2 1 101000 r 74 goat GoatD01.017031 4 75098832 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388480 Affx-122969235 AX-123258838 4 75127513 GGATGTTTTCCTGTGAGCCGTTCTGCACCCCAGGG[C/T]AAATGGTTTTACCAAGAAAAGTGAGGGCACCCAAG Y 2 1 2 1 201000 r 74 goat snp39006-scaffold494-5235896 4 42602091 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409273 Affx-122953120 AX-123279624 4 75177435 AGAGAGGGTGGAGAACAGCAGCAAATTACCTGGTA[C/T]ATCATGGAAAGGAGCCTGGATCTACCTCAGCAGGC Y 2 1 2 1 101000 f 74 goat snp39005-scaffold494-5185974 4 42552375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788024 Affx-122968358 AX-385275045 4 75212686 TTGGAAAACAAACATTTTCTATCTTGTCATTTAAC[A/G]TGTTATAATTGTAATTGCATATTTAGTATAATCAT R 2 1 2 1 101000 f 74 goat snp39004-scaffold494-5150723 4 42517344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409316 Affx-122953089 AX-123279667 4 75243838 GTAACCCTCCGCCTCATCCCAACCAGCCTGAGGAG[C/T]GCCTGAAGTCCAAACCAGAAAAGGTCAACAGTCCT Y 2 1 2 1 101000 r 74 goat snp39003-scaffold494-5119571 4 42486023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798755 Affx-122935018 AX-385285686 4 75281476 ATGCTTAAAATGCAGACATCTGGAAACACTCTGAC[A/G]TGTTACTGTTCTGTTATCTTCTCCAAGGTGACTTT R 2 1 2 1 101000 f 74 goat snp39002-scaffold494-5081933 4 42447965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436971 Affx-122933159 AX-123307309 4 75343556 CTGGTGACATTCCTACTGCTCCTTCCAAAGACAGC[A/G]TCACTGTTCCCCCGCCTGGAAAGTCCTTCCCAGCA R 2 1 2 1 101000 f 74 goat snp39001-scaffold494-5019853 4 42384515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383899 Affx-122973114 AX-123254257 4 75376457 CGCAAAGAGTCAGACACTGAGTGACTAACACTTTC[A/G]CTTTCAACCTTAGTCTAAACATTTTAGTATAATTG R 2 1 2 1 201000 r 74 goat snp39000-scaffold494-4986952 4 42351583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439500 Affx-122930143 AX-123309837 4 75405885 AAAATATTAATATTTGGAGAATTCCTTGTAAGATT[A/C]TTGTAACTTTTCCAAAAGTTGGAGCAGAAAGTGGC M 2 1 2 1 101000 r 74 goat snp38999-scaffold494-4957524 4 42322041 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390976 Affx-122966918 AX-123261333 4 75451889 GATCAAACATAAATATAAGTCTTTAGCAAGGAAAA[C/T]GTAAAATTTCATTAGAATTGTATCTCTTAGTGAGT Y 2 1 2 1 202000 f 74 goat snp38998-scaffold494-4911520 4 42274608 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787352 Affx-122946882 AX-385274377 4 75494751 TTGCACTTCTTTGGGGTTTTTAATCCATAGACAAA[C/T]GTTGTAAGTCTAATTTGTTTACTGAGCTTTTTCTG Y 2 1 2 1 101000 r 74 goat snp38997-scaffold494-4868658 4 42231756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273514 Affx-1111833662 AX-519547129 4 75520084 TTGTGTCTCTGATACCATCAGTTCTAAAACAAGAT[A/G]ATGAATCCTTGGG R 2 1 2 1 101000 f 74 goat GoatD01.000935 4 75520084 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447041 Affx-122924530 AX-123317377 4 75527550 CAGTGGGTAGTAGATCGACATTCCAGAAGTATCTC[A/G]CTTGAAGCTCTTTTTCTTGGAAGACTATCTTTCAG R 2 1 2 1 101000 f 74 goat snp38996-scaffold494-4835859 4 42198767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446914 Affx-122924698 AX-123317250 4 75569078 CCAAATTCTACATAATTATTTTGTTTCAGTGCTTA[C/T]GGGTCATCCTATATTTCTTCCTTTTCACTTACACC Y 2 1 2 1 101000 r 74 goat snp38995-scaffold494-4794331 4 42157173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421959 Affx-122943811 AX-123292306 4 75621496 GGTGCTGAGAACAGCAGAATGAGGACAGGACCATT[A/G]CGATGTAAGATCATTCAAAGAAGAGGAAGAAGAAC R 2 1 2 1 101000 r 74 goat snp38994-scaffold494-4741913 4 42104624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403767 Affx-122957995 AX-123274119 4 75709942 CAAAGAGGGAGACTCTTGGAGACTCTTGGAAACCC[A/G]CTGGTCTCTGGTGCTCTTCCATCTGAACATGGCAT R 2 1 2 1 101000 r 74 goat snp38992-scaffold494-4653467 4 42017506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453398 Affx-122919914 AX-123323731 4 75741057 AAAAGCATAAAAGTGAGAAAGAGCAAAGCAAGCAC[A/G]TTTAGACCACGAGGCCAGATATTTGATTGACCCTG R 2 1 2 1 101000 r 74 goat snp38991-scaffold494-4622352 4 41986300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381812 Affx-122974274 AX-123252170 4 75793887 ACCAAGAACGTGTACATACCTTTGCTCCATCAAAT[G/T]AGTCCATTAAAATAATGTCATTGTTGCATTAGAAT K 2 1 2 1 101000 f 74 goat snp38990-scaffold494-4569522 4 41933245 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804615 Affx-986696784 AX-385291142 4 75805073 AGTCCTGCCCCAAGGCCACAGAAGAGCCCAGTACC[C/T]AAGGTCATCTTGGAAGCTGATGGAGTCCCATTATA Y 2 1 2 1 600010 r 74 goat 4_75805073 4 75805073 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320804616 Affx-986696785 AX-385291143 4 75805269 TATAAAAATTGGCTACTAACCCACAAGAAAGTGTC[A/G]AATTTGCACTGACAGTGCACCTGGGACACTAGCAG R 2 1 2 1 600010 r 74 goat 4_75805269 4 75805269 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38434373 Affx-122934705 AX-123304714 4 75823148 ATGGCAAGGAGTCTCCTCCTTCCCATGGTGGCTCC[C/T]ACTCGCCCTGCCCACTTAGTGCAACATCACAAGCC Y 2 1 2 1 201000 r 74 goat snp38989-scaffold494-4540261 4 41904084 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778767 Affx-122942071 AX-385265877 4 75858585 AAAATGAACAAAACGGTCAGGCATATCTGTTTAAC[A/G]TCTTTTAGAAACAGAGACAGTTATTTTGTTAAAGA R 2 1 2 1 201000 r 74 goat snp38988-scaffold494-4504824 4 41868638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382880 Affx-122973422 AX-123253238 4 75926298 GAGAGTAGTGAAAATAAATGAACTACGGCTTGATA[C/T]ACAGAAGAATCACAAAAACATAATGATAAGCAATA Y 2 1 2 1 101000 f 74 goat snp38987-scaffold494-4437111 4 41799543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392255 Affx-122967561 AX-123262612 4 75958386 TGTTGTCTGAGAAGCAGACAACCAAGATGGAATCA[A/G]GCATGCAAGAGATTTATGGAGGTGGGGAATGCTGG R 2 1 2 1 101000 f 74 goat snp38986-scaffold494-4405023 4 41767359 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442553 Affx-122928522 AX-123312890 4 76005925 CATTTTTAGACTCTGAGCTCTTAATAAATGTTTTG[C/T]AATAAAGGAGTCAATGATCAACTCTCAATGGAATA Y 2 1 2 1 101000 r 74 goat snp38985-scaffold494-4357484 4 41720117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797405 Affx-122927345 AX-385284344 4 76061807 ATTCATTAAATGCCTGCAATATACAGGTTGCTAGG[C/T]TAGATGCAGTAAATAAGAAGAAAGTAAGACCCCAT Y 2 1 2 1 101000 r 74 goat snp38984-scaffold494-4301602 4 41664551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413864 Affx-122949859 AX-123284213 4 76092798 TAAAAATTGATTCTTTGGTGTTGAAATTAATAAAA[C/T]TAACCATTCCACTGCTTCCTCAAGGAAGCATTCTT Y 2 1 2 1 201000 f 74 goat snp38983-scaffold494-4270611 4 41633263 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391650 Affx-122966562 AX-123262007 4 76147486 AACAGGAAGTTCTCTCTTAGAGCTGGATAATGCTC[A/G]GAAGTTGCAAATAGGAAAAGTTCAGCAAAAGGAGA R 2 1 2 1 201000 f 74 goat snp38982-scaffold494-4215923 4 41578265 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410454 Affx-122952381 AX-123280804 4 76181187 TTTGAATACACAAACTGATATATTCAACATAAACA[C/T]TGATTTTTTCCAAACACCACATTTTATTTATATTG Y 2 1 2 1 101000 f 74 goat snp38981-scaffold494-4182222 4 41543765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427368 Affx-122940097 AX-123297711 4 76215949 CAGCATGTGCAATGGAGCTGGCTCTGCTGGTTTTG[C/T]AGTGTTTGTTTTCTTATTCACAGGGAATTTTGTGT Y 2 1 2 1 101000 f 74 goat snp38980-scaffold494-4147460 4 41509053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768969 Affx-122942967 AX-385256144 4 76247905 TGATGATGGTCAATGGTCAGGCACTGAGGAAATCC[A/G]TTACATAATATGAAATAAGCAAATGCCCAGTGAAT R 2 1 2 1 101000 f 74 goat snp38979-scaffold494-4115504 4 41476685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381081 Affx-122974605 AX-123251439 4 76292305 GAATTGGGATATTTCAAGAAAAGATGAGAAGTAGT[A/G]GTCATATGCTTGGGAAGTATTGTACTCACAGAAAG R 2 1 2 1 101000 r 74 goat snp38978-scaffold494-4071104 4 41432653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407896 Affx-122954398 AX-123278247 4 76351821 GAATTCTTGTGAAGATGCTAAAAAATAAAAAACTT[C/T]CTGACAATCCTCAAGAAGACCTTTTTGAACAGAGA Y 2 1 2 1 101000 r 74 goat snp38977-scaffold494-4011588 4 41373062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419916 Affx-122945329 AX-123290264 4 76387423 CTATAAGTGCTTGCTAGGCTATTTTTACACATATT[A/C]GTAACACCTTACAATGATACTGGGCTTTATGTAAA M 2 1 2 1 101000 f 74 goat snp38976-scaffold494-3975986 4 41337446 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440968 Affx-122928990 AX-123311305 4 76456676 CCAGATACTAGGGACCCGGCCCACATGGAGCAGGT[C/T]CCAGCTTGTGTGGCAGGGTGAACCCAGCTGGATCC Y 2 1 2 1 201000 r 74 goat snp38975-scaffold494-3906733 4 41268254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404891 Affx-122956465 AX-123275243 4 76498946 GAGTTGTCATTTCATGACCTCTGCATCTTGGCTTA[C/T]GCATATAGGACCCCAGCCTGCCCACCCAGGGATAG Y 2 1 2 1 101000 f 74 goat snp38974-scaffold494-3864463 4 41225913 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392129 Affx-122966337 AX-123262486 4 76530226 TCTACCCATTAAAACTGGTTCTGGAAGATCTTGTT[G/T]TATATAATACCTGAGAGGAAGCATGCATGCCACTG K 2 1 2 1 102000 f 74 goat snp38973-scaffold494-3833183 4 41196651 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388923 Affx-122968834 AX-123259281 4 76559359 TATCTCTCTTCACTGGTTCTATCAAACACTATCAA[C/T]GAGGCACGTTTGAAGAATCTATTTCTGCTTGATCC Y 2 1 2 1 101000 f 74 goat snp38972-scaffold494-3804050 4 41167355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438263 Affx-122931414 AX-123308601 4 76614331 GGGAGCTTCTCAAAAGCCTGTCACCTCTGCTACAG[C/T]ACACCCACAAGAGATTCCCAAATTCACTCTCCAAC Y 2 1 2 1 101000 r 74 goat snp38971-scaffold494-3749078 4 41112927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787035 Affx-122960461 AX-385274062 4 76648666 ACCTGTGGCCATGAGTCCTGAGGCACTCACGTTAG[C/T]TTTTGGTAAAAGAAAGTTTCTCTCTGAGACCACGC Y 2 1 2 1 202000 f 74 goat snp38970-scaffold494-3714743 4 41078489 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779715 Affx-122978278 AX-385266815 4 76681079 TCGAATGTTCCCGTGCTTTTCTTCTGCTCTGCCTC[A/G]TAGCAGAGCTTGGACAAGGGAACTATAGATAAGAA R 2 1 2 1 102000 f 74 goat snp38969-scaffold494-3682330 4 41045755 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437889 Affx-122931669 AX-123308227 4 76768976 CTTGCATTGGCGGGTGGGTTCTTTACCACAGTGCC[A/G]CCTGAGAAGTCCCAGGTGCACAGCAGGGAAGAGTA R 2 1 2 1 103000 r 74 goat snp38968-scaffold494-3594433 4 40951470 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426478 Affx-122940786 AX-123296824 4 76823842 GTGAGTTTTACACCAATCCTTCCCCTATCACCACC[A/G]CTCTCAGGAAGTGAGTGGGTCCTAGTGTTGTCCTC R 2 1 2 1 202000 f 74 goat snp38967-scaffold494-3539567 4 40896334 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780454 Affx-122974588 AX-385267545 4 76876869 TACTAAACTCAAGGGGAAGGTATAATTATCTAAAC[A/G]TATTTAAAAAGGAATGAGACTTAAAGAGGTTAGCA R 2 1 2 1 101000 r 74 goat snp38966-scaffold494-3486540 4 40843833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402499 Affx-122958578 AX-123272852 4 76911121 TTAGCAAGACCTTTCTTGTGCTTTACTTTAGTATT[G/T]TCTCAAGTTTTACCCATCCCTACTGCCATTAATTT K 2 1 2 1 101000 r 74 goat snp38965-scaffold494-3452288 4 40809927 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768266 Affx-122973159 AX-385255447 4 76952701 TTGTAGGCCATTTCTTTAACTCTGAACCATATTAC[A/G]TTCCCTTATTTTGCATTAATTAAGTGATTTTCAAA R 2 1 2 1 101000 f 74 goat snp38964-scaffold494-3410708 4 40768445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415044 Affx-122949491 AX-123285393 4 77029207 GTATGACAAAGGAATGAAGCAAGGGGAAAATCAGA[G/T]AGGGAGGAAGAGAGGAAAGGTTAAATGGGTGAAGA K 2 1 2 1 101000 f 74 goat snp38963-scaffold494-3334202 4 40691646 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406788 Affx-122955705 AX-123277139 4 77082001 TAGATCTTTATGATAGGTAGAACTCTATTTGAGTC[A/G]CTGTGTTTTATATACCACAGGTTACAGAAATGAAG R 2 1 2 1 101000 f 74 goat snp38962-scaffold494-3281408 4 40638433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450889 Affx-122922206 AX-123321223 4 77113436 GTTCTTTCTCAATTTCCATTCCCATGAGGTTATCC[A/G]CAGCAAGTCGCTGTTAGTACAGGGTCAGTGTGATG R 2 1 2 1 101000 f 74 goat snp38961-scaffold494-3249973 4 40606649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385617 Affx-122971189 AX-123255975 4 77148821 GGTCTAGACCGGTCTCAGACTTTGCTGTGTGAAGA[A/G]TTCCAGAAACCTATGGCTTTACACTGAGTCTTTCT R 2 1 2 1 101000 r 74 goat snp38960-scaffold494-3214588 4 40571163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788169 Affx-122954290 AX-385275188 4 77200482 CAAAAAGAGACAGTTCCTAGAGAAAAAGATGAGGA[G/T]CAAATGTACTAACTGTTGGCAAAATAACTGGTCCA K 2 1 2 1 101000 r 74 goat snp38959-scaffold494-3162927 4 40519018 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409599 Affx-122953560 AX-123279950 4 77229070 AAATCAGTTTTCACAAAAGGATGTCACGTCTGATG[C/T]CAGCACGAGTGATCATGTATCTGTCATGAATCAGG Y 2 1 2 1 101000 f 74 goat snp38958-scaffold494-3134339 4 40490605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272282 Affx-1111833438 AX-519546021 4 77244863 GCATCAGGGTCTTTTCAATGAGTCAGTTTTTTTGT[A/G]TTAGGTGGCCAAAGTATTGGAGTTTCAGCTTCAAC R 2 1 2 1 303000 f 74 goat 4_77244863_AF-PAKI 4 77244863 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448528 Affx-122923443 AX-123318864 4 77264208 TGTCCCTAAATGGAGGAGGGAGTCACTAGTTCCCA[C/T]CAGTACTCAACAAGAGAACAATTGGAGTGCTTCCC Y 2 1 2 1 101000 r 74 goat snp38957-scaffold494-3099201 4 40455396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414520 Affx-122949523 AX-123284869 4 77300666 AATGATTGCCAGGCAGAGAACTACTTTCCTACAAG[A/G]TAGGAAGCGCTTACTTAACCTGCTTCTCTTAGTGC R 2 1 2 1 101000 f 74 goat snp38956-scaffold494-3062743 4 40418982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781800 Affx-122935841 AX-385268882 4 77363605 CTGTATTCTTATATTTTATGTAACTCCACTGACCA[C/T]AGTTCTGCTCTTAATGCAGTTGTTTCAGGTAATTT Y 2 1 2 1 101000 r 74 goat snp38955-scaffold494-2999804 4 40356136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394025 Affx-122965006 AX-123264380 4 77407337 TAGCAGCAAAATTTCCTAATTCAGGTCATTCTCTC[A/G]CCTTGCTTCCTCACCCACCAGACACATACCACAAT R 2 1 2 1 201000 f 74 goat snp38954-scaffold494-2956072 4 40312383 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797422 Affx-122956487 AX-385284361 4 77475175 CTAGGGCTTCTATTAGACAGCAAAATTGTATACAT[C/T]AAGTCATTCTACCTGTTTAAATTCAGAGTGCTAAC Y 2 1 2 1 101000 r 74 goat snp38953-scaffold494-2888234 4 40244807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447849 Affx-122923895 AX-123318185 4 77523228 GACATTTGGCCTAAGATACTATGCATCTAAAAAGA[C/T]AGTTATATAATATTTACATTAATATCTGACTGCCT Y 2 1 2 1 101000 f 74 goat snp38952-scaffold494-2840181 4 40197135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425780 Affx-122940715 AX-123296126 4 77568572 CACATTGCATCCCAACTACACCTACAGCAGGGCAC[C/T]CTGTCCTCTCATCCAGGAACCTCTGCCCTCTCCTT Y 2 1 2 1 101000 f 74 goat snp38951-scaffold494-2794837 4 40152146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413420 Affx-122950701 AX-123283769 4 77630671 TCACAGAGGGGTTGCCCACGGGGCAAGCCAGGCCG[C/T]GCTCACTCTCCAGGCTCCTTTGACTCTGGCATCAG Y 2 1 2 1 103000 r 74 goat snp38950-scaffold494-2732738 4 40090080 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428802 Affx-122938398 AX-123299144 4 77667910 CGCCTGCCTCCTACTCAGCTCTGAGGGCATCGGGC[A/G]TGGGGTGGAGATGTCATCTTCCTGGGAGGGTAGGA R 2 1 2 1 201000 f 74 goat snp38949-scaffold494-2695499 4 40052806 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386586 Affx-122970692 AX-123256944 4 77698314 AGAACATCACCAGAACTGAACAGACTGGTCAGATC[A/G]TCTGCATCTGCTCTGATGGCTCATACGGCAAAGGA R 2 1 2 1 101000 f 74 goat snp38948-scaffold494-2665095 4 40022618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379219 Affx-122976281 AX-123249578 4 77740456 ACAAACACGCTCTACACCTGTAAGACCTAGTATTA[C/T]GGGTAGGTAACTAGGGAATATCCACTACACTAGGA Y 2 1 2 1 101000 r 74 goat snp38947-scaffold494-2622953 4 39980481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384336 Affx-122972256 AX-123254694 4 77814308 ATCCTAGAATCATACTCACAAGCATGTTTGCTAAG[G/T]CTATAGACTTGTGTCTTCACTCTGATTGTCTGGGT K 2 1 2 1 201000 f 74 goat snp38946-scaffold494-2549101 4 39905588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380696 Affx-122975166 AX-123251054 4 77846065 TGAGAACAGGATAGAAGAGAAGCTGAGGCTCCATG[A/G]CACTTTCCTTATGGTCGAGTGGTTAAGATTCCAGG R 2 1 2 1 201000 f 74 goat snp38945-scaffold494-2517344 4 39873814 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396334 Affx-122963067 AX-123266689 4 77943964 TTGAAAATAATAAACTTTCTATACATGATACATCC[G/T]ATTTGCAGAATCTGACTCTTTGCAGAAAGGCAGGC K 2 1 2 1 303000 f 74 goat snp38944-scaffold494-2419445 4 39775343 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411780 Affx-122951481 AX-123282130 4 77995040 CAATGGCTAATGGGGAAGATTTGGGACTCACCAGC[A/G]TGAGCCTGAGGAACCAGTGAGAATGCCACGAAGAG R 2 1 2 1 201000 f 74 goat snp38943-scaffold494-2368369 4 39724427 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421629 Affx-122944467 AX-123291976 4 78034765 AAGGCCAGGTGCTGGACAAGTGCTGACAGCTGTCC[G/T]GAATGTGGCATCTTATTTCCTGCAGGCCCAGGTCT K 2 1 2 1 101000 r 74 goat snp38942-scaffold494-2328644 4 39684084 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437175 Affx-122932126 AX-123307513 4 78096158 GTCTATTTCCTCCACTGGAAGAACTGTGATTTCAA[A/G]GACAAAAAGATATCTTAGATTTTTTTTTTAGCCTA R 2 1 2 1 103000 f 74 goat snp38941-scaffold494-2267251 4 39622270 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782680 Affx-122968220 AX-385269752 4 78139181 TATAACACTCTGTTTATTAACACTTAAGTAATTGA[C/T]ACCCTGATTGGAAAGGTTCAGGTTCAAAGTACCAC Y 2 1 2 1 101000 r 74 goat snp38940-scaffold494-2224228 4 39579268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779773 Affx-122946805 AX-385266873 4 78201553 GAAATAGTTGAAATATTGATACTTCAATTCTCTTG[C/T]AGTTCAGCATGACTCTCTCTGCTGAACAAGGCTAA Y 2 1 2 1 101000 r 74 goat snp38939-scaffold494-2161856 4 39516068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773144 Affx-122947140 AX-385260287 4 78262442 ACAAAATATCAAAATATTTTGCAAAGATTCTTTTG[C/T]AAAAGTAAGACTTTGGTAGAATTACTGAACAGATA Y 2 1 2 1 202000 f 74 goat snp38938-scaffold494-2100967 4 39453690 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382050 Affx-122974935 AX-123252408 4 78343941 GCTGCAAAAGATGGATGTTTCATAGGGCCACAGAC[A/G]TGAACCTCAAGACTCCATTTCTCACATACTGGTGA R 2 1 2 1 101000 f 74 goat snp38936-scaffold494-2019468 4 39371023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408796 Affx-122953365 AX-123279147 4 78382172 ATGAGAAATGAAAATTAAATGAAATAGGTAAACTT[A/G]TAGGATAGAGAAAGTCCTCACGAGTTCCTCTGTTT R 2 1 2 1 101000 r 74 goat snp38935-scaffold494-1981237 4 39332591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388438 Affx-122969265 AX-123258796 4 78435296 AGCAGAAACTTTATTCTTTCCTGCCCTACCTCTGT[A/G]AACCTGCACTTCTAACTCATTTTCCTTGCTCACGG R 2 1 2 1 201000 r 74 goat snp38934-scaffold494-1928113 4 39278791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426579 Affx-122939993 AX-123296925 4 78489142 CCTGATCATTCTCTGGACTCTATGGCTACCAGTAA[C/T]GTTACCCCTACAAGTCTCAATTTGAGCACTCTGTT Y 2 1 2 1 101000 r 74 goat snp38933-scaffold494-1874267 4 39225005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391353 Affx-122967293 AX-123261710 4 78523093 ATAGTCCTAACTGTGGTAATGCTGTGATGTCTAGA[G/T]CAATGCCTTATAGTATAAGTGTTTAAATTATTTGG K 2 1 2 1 101000 r 74 goat snp38932-scaffold494-1840316 4 39191049 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444880 Affx-122926272 AX-123315217 4 78553000 AAATGTGCTCGAACTTAGAATATCATAAAAAGGAA[A/G]GAAACTAAGAAAAGTACCACTTTCAGAACTCAGGA R 2 1 2 1 201000 f 74 goat snp38931-scaffold494-1810409 4 39161475 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377438 Affx-122977536 AX-123247797 4 78584520 ACTGGTCAGACTTCACTCTCCCACATCTACCAGTG[A/G]TGTATCTTTAGTGACTGCTTCTATTTTCTTGAGAC R 2 1 2 1 201000 r 74 goat snp38930-scaffold494-1778889 4 39129943 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392450 Affx-122966168 AX-123262807 4 78636488 TAAGCAGAAGTCTCAGTATATTGCAGTTTGGTGCT[A/G]TTTTCCAAAACTTGTCTATTAATTATAGCCACCCT R 2 1 2 1 201000 r 74 goat snp38929-scaffold494-1726921 4 39077068 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448065 Affx-122924343 AX-123318401 4 78679775 GCTATATTTGTTCTTCTTTTGCCAGGTTCAGTAAA[C/T]GTCTGTTGTTTTGGTACAGATGTTGGACATGATTT Y 2 1 2 1 101000 f 74 goat snp38928-scaffold494-1683634 4 39033583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777498 Affx-122972519 AX-385264617 4 78731696 TCTTGAAAATTCAGATGGAAGATTAGGTTATATTA[C/T]GTAAGCAGATTTTACCCAAAAGTGTAATTCAGAAA Y 2 1 2 1 201000 f 74 goat snp38927-scaffold494-1631713 4 38980560 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412717 Affx-122950739 AX-123283066 4 78776661 CTGAATCTAGGGAAAACTGCCCTACATTCATAGTC[A/G]CCTCTGGGAACAGGGTAATAGTTGATCATTATGAT R 2 1 2 1 101000 f 74 goat snp38926-scaffold494-1586748 4 38936038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768454 Affx-122942754 AX-385255634 4 78819948 ATAGGCTTGAAAGCCTTTGGAAACTGAAGCTTAAG[C/T]TACATATGAAGGATGTACCCCTGACAGCAGCCTTC Y 2 1 2 1 202000 f 74 goat snp38925-scaffold494-1543461 4 38891971 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414166 Affx-122949681 AX-123284515 4 78860043 GACCAGTCAGTGCAACATGTAAGACAAATGCCACA[C/T]GGAACAGTCCCAACTGGACAAGCCATGGACATGAG Y 2 1 2 1 101000 f 74 goat snp38924-scaffold494-1503366 4 38852307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804333 Affx-986696786 AX-385290942 4 78873976 GGACTAGATGATTTCTAAAAATAGGTCTTTCTAGA[G/T]GTGCTTAAAAATAACTGAGATTTATTTTTAATTTA K 2 1 2 1 600010 f 74 goat 4_78873976 4 78873976 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 320762304 Affx-986696835 AX-385250486 4 78874059 TACAACAAAATTGTATATGATTCTACAAAATGATG[G/T]TCAAAATTTGTCTAAACAGAACTCCCCACTGTGTT K 2 1 2 1 600010 f 74 goat 4_78874059 4 78874059 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320764455 Affx-986696837 AX-385252146 4 78874071 GTATATGATTCTACAAAATGATGTTCAAAATTTGT[C/T]TAAACAGAACTCCCCACTGTGTTCTTTCTCCATGT Y 2 1 2 1 600010 r 74 goat 4_78874071 4 78874071 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320774451 Affx-122932775 AX-385261587 4 78890413 CTGGCCGTCTGCTAAAATAAGTGCTCCCTCATCAG[C/T]AGGCTGTTGGGCTGAGATCGATCTACTCAGTCAGG Y 2 1 2 1 101000 r 74 goat snp38923-scaffold494-1472996 4 38821523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775854 Affx-122958577 AX-385262985 4 78921391 GATTCAGACTTGGCACCTTCTTTATATTAGATATG[C/T]GTTTCTTCTGTAACAATCCCACAAGCAGAGAGTGT Y 2 1 2 1 101000 r 74 goat snp38922-scaffold494-1442018 4 38790521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430235 Affx-122937319 AX-123300576 4 78959622 GTCATAGTGCTGGGAAGAACATTTTGCTTCCTTCT[A/G]TTTCCATGCAAGTGGGAAAGGTAGGCAATAGAAAG R 2 1 2 1 202000 r 74 goat snp38921-scaffold494-1403787 4 38752433 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392635 Affx-122966456 AX-123262992 4 79018460 CCTACTCCTTCCACATAGCACCCACACTTGCCCAA[C/T]GCTCAATAATTGTTCTGTTCTCTGAACTCACATGA Y 2 1 2 1 101000 r 74 goat snp38920-scaffold494-1344949 4 38692876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278268 Affx-1111836257 AX-519551755 4 79039928 GCAGGGAGTGTTTGTAGACTTTTGAGGATGTCCCT[A/G]CAAACCGGTTCAAGGTCAGTCTCATGGGACTTTAG R 2 1 2 1 102000 r 74 goat Random2.2K-459 4 79039928 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768713 Affx-122926839 AX-385255891 4 79072762 TCAATGACAAATGCCTACCCAGTTGTTTTCTAAAA[C/T]GGATTCAACTAAAAACAAGTTCAACTTAAAGTACC Y 2 1 2 1 101000 r 74 goat snp38919-scaffold494-1290647 4 38638627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783627 Affx-122957979 AX-385270686 4 79110699 AAAGAGCTTAAAGTGAGTTTTCTGAGTTGGCTGCC[A/G]CTGGAAGTAGTTTACAAGGATGGAGTAACACTGGA R 2 1 2 1 101000 f 74 goat snp38918-scaffold494-1252710 4 38601870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392244 Affx-122967569 AX-123262601 4 79145056 TGTAATTAACACCATCTTTTTTTGTCCCTCACTTT[A/G]TAAATATCTGTTGCTCTCCTGCTTACTTCTCCTGG R 2 1 2 1 101000 r 74 goat snp38917-scaffold494-1218353 4 38567548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404032 Affx-122957174 AX-123274384 4 79231806 CTGATGAAGAGAGACTGGGAGAAAGCAGGAGAGAG[A/G]AGTCCAGGAGGAATCAGACTCTCAGGGAGGCATTC R 2 1 2 1 101000 r 74 goat snp38916-scaffold494-1131603 4 38480991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429067 Affx-122938291 AX-123299409 4 79271636 CATTGTGTGGTTATAGGCTGACTGAAGGTGACCAC[A/G]TGAAGAGTGCATAAGTACCACTTACCAGAAAAAAA R 2 1 2 1 101000 r 74 goat snp38915-scaffold494-1091773 4 38440240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375584 Affx-122978735 AX-123245943 4 79337291 GACAATGAAATGCTTCAAGATATTTTGAGAAAATT[G/T]TATCTAGTGAAGAAGCAGAATGTAGCATTTTTATT K 2 1 2 1 101000 f 74 goat snp38913-scaffold494-1026118 4 38374461 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376208 Affx-122978809 AX-123246567 4 79397667 AAGACTTCATTGTTAAAAGTGAGAGGCAAATATTG[C/T]ACCAATGCAGAGGCATGGGTACCAGAAGCCCTAAT Y 2 1 2 1 201000 f 74 goat snp38912-scaffold494-965742 4 38314124 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443599 Affx-122927315 AX-123313936 4 79436770 GGAGGCAGTTTTTGGCTGAGTACCAACCTGTGACC[A/G]TGTCTGAGGAAACTACTGACCTTGGGGAAAGGATC R 2 1 2 1 201000 f 74 goat snp38911-scaffold494-926639 4 38274979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394230 Affx-122964886 AX-123264585 4 79504324 CAGCCAGACTTCGGGCAGAATGTCTCTCACAAGCA[C/T]GGTATGGGCAAATAGTGTCAGACATCTGTGATTAC Y 2 1 2 1 101000 f 74 goat snp38910-scaffold494-859085 4 38207596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454062 Affx-122919389 AX-123324395 4 79548820 AGACTTTAGCAGATGAGGAAAATCAGACCTGAGCT[A/G]CAGAACTGATATTTTCCACAGAGCATTCTGGCAAC R 2 1 2 1 201000 f 74 goat snp38909-scaffold494-814589 4 38163017 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793761 Affx-122951457 AX-385280733 4 79580514 CTTTAAAAGCTGAAGAGAAGCTGATGGCTTACATA[C/T]AGCAGTCACTTCCTCGTGGTACCTACTATATTTCA Y 2 1 2 1 201000 f 74 goat snp38908-scaffold494-782895 4 38130864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799113 Affx-122922873 AX-385286043 4 79612954 CATCTACTCTGAACAGGGAGGTCTAGTGCAAGGTT[A/G]TCACCATTTGCTAAATGTTGGACTCTTCAAACTTG R 2 1 2 1 101000 f 74 goat snp38907-scaffold494-750455 4 38098358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446469 Affx-122925065 AX-123316805 4 79657309 AGAGCATTCTAGTTGACCAACATGAAAGATTTATT[A/G]CAAAAAATGCTTTTATCCTCTTTATGTTACTGATC R 2 1 2 1 101000 f 74 goat snp38906-scaffold494-706100 4 38053557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278113 Affx-1111836259 AX-519551603 4 79681707 TAGATGACTGTTAGGCCACAAATTTTAACTGGCCC[A/G]AATCAAAGGCTTTGACCTGTCGTTTTATTGTGTCA R 2 1 2 1 101000 f 74 goat Random2.2K-461 4 79681707 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384037 Affx-122972887 AX-123254395 4 79688873 CAAGAAAGGATACTTACTTGTAAATTGTAGTCTTG[C/T]AGAATTTTAACTAAGGAGTCTCTCAAATTAGGAAT Y 2 1 2 1 101000 r 74 goat snp38905-scaffold494-674536 4 38021975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402507 Affx-122958572 AX-123272860 4 79747692 AAGTAGATCTATCTAGTAGCCATACAAATATGTGC[A/G]TCTGAAGTTTCAGAGAGCTAGCTGCTGAAAGCATG R 2 1 2 1 101000 f 74 goat snp38904-scaffold494-615717 4 37963800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790815 Affx-122944295 AX-385277815 4 79806379 GCCATTTAAAAATGATGTCAAGTTCTGTGTTGCTC[A/G]TCTCCATGAGTATTTGGCAATTTGAATATAGGTGC R 2 1 2 1 101000 f 74 goat snp38903-scaffold494-557030 4 37904453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382621 Affx-122973699 AX-123252979 4 79859442 GACCACTTCCCCACCACCTAATTAAAACACAATAT[A/G]TTGACAAGTTCTTGAGAGAAATGTTCCCATGATTA R 2 1 2 1 201000 r 74 goat snp38902-scaffold494-503967 4 37849896 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771052 Affx-122927396 AX-385258212 4 79889134 TGTGTCCTCACGACTTCTACCTAAATAAAGTGGCC[A/G]TTACATAAATGTCTGGGCTTGAATCCAGTGTGCGA R 2 1 2 1 102000 r 74 goat snp38901-scaffold494-474275 4 37820179 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769647 Affx-122930246 AX-385256818 4 79943079 ATAGAGAAAAAAATTCTAACAGCAGAGAACTAATT[A/G]GCTCCACAGGGACACACTAGACAGGAAGACCAAGT R 2 1 2 1 102000 r 74 goat snp38900-scaffold494-420330 4 37765783 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272283 Affx-1111833439 AX-519546022 4 79955587 CATGATTTTTCCAACGTAAACAAACACCACACAAG[A/G]TGGAACAAATGATTCATTTTTCCTGTGGAATTTTA R 2 1 2 1 101000 f 74 goat 4_79955587_AF-PAKI 4 79955587 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784307 Affx-122925372 AX-385271358 4 79990179 GTGCATAATTGTTTCCACTTTACAGGTAAGTAAAG[C/T]GGGGCACAGAGAGGACAAAAAAAATCCCTAACATC Y 2 1 2 1 102000 r 74 goat snp38899-scaffold494-373230 4 37718609 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391946 Affx-122966922 AX-123262303 4 80047061 TTTACTTTTTGCTTTCTCTGACATTTGTTTGCACA[C/T]ATGCTCCACTGAGACAGCCTTCCAAGCTTTGTCTG Y 2 1 2 1 101000 r 74 goat snp38898-scaffold494-316348 4 37659232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798475 Affx-122920089 AX-385285408 4 80081906 AAACGTTGTTTACAATGGCTGCATAGTTTTCTATC[A/G]TTTGAACACAGTGTAAATCTTTCCCTGTTATTCAC R 2 1 2 1 101000 r 74 goat snp38897-scaffold494-281503 4 37628472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798166 Affx-122919831 AX-385285101 4 80110427 ACACAATAATAGAAAAATGTACCCATTATGCAGAT[A/G]ATGAAGAGTTGACCATTGTAGGGCACCATCTATCA R 2 1 2 1 101000 r 74 goat snp38896-scaffold494-252982 4 37599953 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776227 Affx-122947727 AX-385263355 4 80149813 ACTGTTTAAAAAGGGTTTTAACCAGAGGGAAAAGT[C/T]CAAACTGATTCCTTCTTATGGGCCCTCTGGGACCT Y 2 1 2 1 101000 r 74 goat snp38895-scaffold494-213596 4 37560549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429576 Affx-122937807 AX-123299918 4 80203709 ACTTGTTCATATCCAGGAAATTTATGGCTGATTCA[C/T]GTTGAGGTTTGACAGAAAACAACAAAATTCTGTAA Y 2 1 2 1 102000 f 74 goat snp38894-scaffold494-159700 4 37506581 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793758 Affx-122953459 AX-385280730 4 80237212 CTGTTTGGGTGCAAAAAACCCTGAAGCAAGGTATA[C/T]TCACACATGGATTGAGGTTTTATAGGGTGAGCTCA Y 2 1 2 1 101000 r 74 goat snp38893-scaffold494-126197 4 37472908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375444 Affx-122979173 AX-123245803 4 80266190 AAAGGTGCTAAACACGTTTTAAGTAAAGCAATAAA[C/T]GATTACCTTTATGCTCTAAACTGTTGGTATCTTTT Y 2 1 2 1 101000 r 74 goat snp38892-scaffold494-97219 4 37443844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791219 Affx-122956678 AX-385278213 4 80352083 TGAAGTGGCAGATCCATTGCAGGATTACAAATCTT[A/G]CATATTAGCAATGTAGGTTCTAATCAATCTTGCAA R 2 1 2 1 201000 r 74 goat snp38890-scaffold494-11326 4 37358060 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428518 Affx-122938755 AX-123298860 4 80364059 ATCTCATTTACAGAGATTAATTTGAAAAGGTGGGA[A/G]GGGGCTTTCCTGGTTGCTACAGAAAGAGAGTTGCA R 2 1 2 1 201000 f 74 goat snp13652-scaffold1527-551 4 37345719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405313 Affx-122956835 AX-123275665 4 80416424 TGCAAAAGTCAGAACTATTTTCACAGATGAACATC[C/T]AATCTGTTTTTAAAGTCCCCTGAGGGAAAGATATT Y 2 1 2 1 101000 f 74 goat snp13653-scaffold1527-52916 4 37292940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779794 Affx-122934454 AX-385266894 4 80447975 CAGTATGCCTGGGGTACTGAAATAAATTGGGAGGC[C/T]AAAGGTTAAGTGCCTTTAACAACTAGAGAATTTCA Y 2 1 2 1 102000 f 74 goat snp13654-scaffold1527-84467 4 37261610 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798419 Affx-122942182 AX-385285353 4 80484342 CAAAAAGTTTACTGTCTGGTCCTTGTAATAAAAGA[C/T]TGCTGGTTCCTCATCTAGCCTGTCTCAGGTCCATG Y 2 1 2 1 101000 r 74 goat snp13655-scaffold1527-120834 4 37224192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773286 Affx-122921985 AX-385260429 4 80550157 CCACTTCACTTCTAAAAAATCATTCTTATTCTTAT[C/T]AAGTGTCCCCAAAAGTGTCATGTTTGTTCATGTTT Y 2 1 2 1 201000 f 74 goat snp13656-scaffold1527-186649 4 37158285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381169 Affx-122975210 AX-123251527 4 80585378 CAATAGCATAGGTTATGAAATATAAGAGCAGACGT[A/G]TTTGTTCCATGCCTGATGTTGATCCTGTTGAATAT R 2 1 2 1 101000 f 74 goat snp13657-scaffold1527-221870 4 37123723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777970 Affx-122964199 AX-385265086 4 80614741 TCCATTGCTTACTGAAACTAGATTGTTAAAAAACA[C/T]TTGCTAAGTCATGACTCTAGTCATGCTTTCCATCC Y 2 1 2 1 101000 r 74 goat snp13658-scaffold1527-251233 4 37094993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388404 Affx-122969292 AX-123258762 4 80659977 TCATGGAAGGAAATATTGTTTAATAAAGCTCACTT[A/G]TATTTTTAATATTGTTTATTAGAAGTTCAATTTCC R 2 1 2 1 303000 r 74 goat snp13659-scaffold1527-296469 4 37048937 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417832 Affx-122946794 AX-123288180 4 80697113 CCATAGAGGATAATGAAATTCAGCTATATATTGAT[A/G]CACAAAATTTCCAAATAGACTTTGTCATATTGCAT R 2 1 2 1 101000 f 74 goat snp13660-scaffold1527-333605 4 37010736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425704 Affx-122940775 AX-123296050 4 80733391 CAAAAATGATTTTTCTTTCTGGATGTGCAACTAAA[C/T]GAAGATTCTATCATATAATATATATTTTTATAATA Y 2 1 2 1 103000 f 74 goat snp13661-scaffold1527-369883 4 36972549 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396364 Affx-122963042 AX-123266719 4 80769469 CTAATGACTATCAATTTACAAAGTAGAAACACTCA[C/T]AAACATGACCTACAACTGACAATTGCATAGTTAAG Y 2 1 2 1 101000 r 74 goat snp13662-scaffold1527-405961 4 36936334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413543 Affx-122950608 AX-123283892 4 80799668 ATGCAGCAGTAGAATGGCATTTTTAGGGAAATGCA[A/G]TTATAAAAAAATGAAAACTACATTAAAAAACACCA R 2 1 2 1 103000 f 74 goat snp13663-scaffold1527-436160 4 36905935 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413058 Affx-122950974 AX-123283407 4 80829555 AGTCATTAATATACCTGTTGTATTAATAATTAACT[G/T]GTCAAATCAAAGTAAACCTGATGAATTTAAAGTGG K 2 1 2 1 101000 r 74 goat snp13664-scaffold1527-466047 4 36876049 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433562 Affx-122934980 AX-123303903 4 80869588 TTTATTGGCAAATCTTTAAATCTTGTGTACTTGCC[A/G]TGATTTTATAACAATTCACAATAGATTGAAAATAT R 2 1 2 1 201000 r 74 goat snp13665-scaffold1527-506080 4 36835539 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788952 Affx-122977729 AX-385275965 4 80909294 ATCCCCCCAGAAATCAGTCTCTAAGTCAATAAGCC[A/G]TCATCTAGTATGGAAGATCTGCTTAGATGTTATAA R 2 1 2 1 101000 f 74 goat snp28359-scaffold3027-88649 4 36794937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398860 Affx-122961052 AX-123269215 4 80945915 GTCCAAAGGGTTGCAGAGTCAGACGTGACCAAGTG[C/T]ACATGCAATGCACACTAGGTAGCAACTATATAAGC Y 2 1 2 1 103000 r 74 goat snp28358-scaffold3027-52028 4 36757101 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419260 Affx-122946260 AX-123289608 4 80986528 TGCTAAGCTTGAAAGTGCTTTTGACTTTCCAACTG[C/T]ACACAATACTCTATTTTGAATTTTATTCTTCCAAA Y 2 1 2 1 201000 r 74 goat snp28357-scaffold3027-11415 4 36715757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411832 Affx-122951236 AX-123282182 4 81005063 CAACCCCTCTCATATTGTATGTATCACTTATTTTC[A/G]CTTAAAAATGAGAAACAGTGCTCATATTCATAGTG R 2 1 2 1 101000 r 74 goat snp23284-scaffold233-7021 4 36686178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387438 Affx-122970385 AX-123257796 4 81056965 TAGCTGTAAATTTGGTGCAGCCATGAGAGGAAGAG[A/C]GCTCAGGAGCCTCCTATGTCTCCATCTTAGTTAAC M 2 1 2 1 202000 r 74 goat snp23285-scaffold233-58923 4 36633984 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789616 Affx-122950016 AX-385276625 4 81102100 AATCATATCTCTTCTCCTAGCTAGTCTATACATGC[A/G]TCACTGGGTTTTTCAATTTCTGAATTAAAGAAACC R 2 1 2 1 101000 f 74 goat snp23286-scaffold233-104058 4 36587875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405654 Affx-122956575 AX-123276006 4 81132434 TTTCCTTTGCCTAGTTGTGTTCAACTCTTTATCAC[A/C]ACATAGACTGTAGCTCACCAGGCTCCTCTGTTCAT M 2 1 2 1 101000 f 74 goat snp23287-scaffold233-134392 4 36557203 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780538 Affx-122933673 AX-385267629 4 81187325 ACTACAAGCATGTAGATAATGTTGGTATTTACTTA[C/T]GTATATCTCTCAGGCATTATATTCAGAACACATCT Y 2 1 2 1 101000 f 74 goat snp23288-scaffold233-189283 4 36501286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764622 Affx-122952890 AX-385252263 4 81221600 AGTTAAGAAATTTTTACATTAATATAGTTAGTAAA[C/T]AAGACTATATTCGTAGGACCATAAATAATGGCCAT Y 2 1 2 1 202000 f 74 goat snp23289-scaffold233-223558 4 36465861 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441372 Affx-122928863 AX-123311709 4 81277890 AGGCTGCAATCATGGGGTAGTGGAGGTGATGGTGG[C/T]AACAATGGTGATGACAGGAGTGGTAACAGTGATGG Y 2 1 2 1 101000 r 74 goat snp23290-scaffold233-279848 4 36408658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769658 Affx-122933575 AX-385256828 4 81324706 GGCCTAAGATCTTCATTACACTTGAATATATATCC[A/G]TGAATATATATTAAGCATATATATTAAATGTATGA R 2 1 2 1 202000 r 74 goat snp23291-scaffold233-326664 4 36359863 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796792 Affx-122932855 AX-385283735 4 81427759 AAACAAACAGTCAAAACATAAAAATGCTTTGCACA[A/G]TTCCTGATAGGATTTCACTGAAGCTGTGGTAAGTT R 2 1 2 1 201000 f 74 goat snp23293-scaffold233-429717 4 36256991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430366 Affx-122937787 AX-123300707 4 81464780 CTTGGTCAAGTTTACTCTCAAAGATATAGGAGCCA[C/T]CTGTCATTTTTCTTCTGTAAAAATTAAGTTTTGAA Y 2 1 2 1 101000 f 74 goat snp23294-scaffold233-466738 4 36220103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379367 Affx-122976151 AX-123249726 4 81496825 TTTTCCACATCATATGGAAGTTCTAGGCAATGCAA[C/T]AAGAAAAGGAATTAAACTGTATTCAAATTAGAAGG Y 2 1 2 1 102000 f 74 goat snp23295-scaffold233-498783 4 36187567 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435412 Affx-122933552 AX-123305752 4 81526935 GCTCTCATCTGCTTTTCATTCTTCCTAGATCAATG[C/T]ATTTTTCCATTTACTTTTTGAGATCAATATTTTAA Y 2 1 2 1 101000 f 74 goat snp23296-scaffold233-528893 4 36156522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442866 Affx-122927671 AX-123313203 4 81558926 GAGCATAGAGCTAAGGTCTAAGTAACATCTCCTCT[A/G]CTGCTCAGAACAAATATGCCAGAAACAGAAATGGA R 2 1 2 1 101000 f 74 goat snp23297-scaffold233-560884 4 36124758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376013 Affx-122978407 AX-123246372 4 81591525 CAGGACTGTTCTGAAAGTAGCCTGAGGTGCCAAAG[C/T]GAAGAAAGACATGCTAGGCCTTTGCTATGTTTGGA Y 2 1 2 1 101000 r 74 goat snp23298-scaffold233-593483 4 36092017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773678 Affx-122977663 AX-385260818 4 81641639 AATTTGGGGATGAGATTGTGAATATTGCAACTACC[A/G]TGTAATAACCATTTGGAATGTTAGCCAAACCAACT R 2 1 2 1 101000 f 74 goat snp23299-scaffold233-643597 4 36041319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433691 Affx-122934543 AX-123304032 4 81672620 GTAAAGGAAGTATAGATGTTTTTCTTGGAGAATAG[C/T]GCAACGTTTGAAATACATTACATATGGAGATAAGC Y 2 1 2 1 101000 r 74 goat snp23300-scaffold233-674578 4 36008837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787700 Affx-122936596 AX-385274723 4 81710642 GTATAATACATATGACTGTGATGCCTTACACAGGG[C/T]AATAATCATAGATGGTATTAGAGTCATTCACTCAG Y 2 1 2 1 101000 f 74 goat snp23301-scaffold233-712600 4 35970419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442363 Affx-122928025 AX-123312700 4 81750111 CTTAATTATCTAGGGTTCAGTGTATACAAAGCGCC[A/G]AATACTGCCTATTGTTCTCCACCCTGAATTTCCCC R 2 1 2 1 101000 r 74 goat snp23302-scaffold233-752069 4 35931113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278115 Affx-1111836260 AX-519551605 4 81757831 CCCTTCCATTCTCATCATTTCTCCTTTACTGCTTA[A/T]GGCCCAGCCATGTCAACAAACCTGCAGTTCTTTCA W 4 1 2 1 102000 f 74 goat Random2.2K-463 4 81757831 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789334 Affx-122952367 AX-385276344 4 81806809 AGTTTGAGAGACAGAAGAAGGCAGTGCTTTCAGAA[C/T]GTGAAAGTCAAAAGCATAGAGTTAAGCTGTCCTGT Y 2 1 2 1 101000 f 74 goat snp23303-scaffold233-808767 4 35865105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802687 Affx-122956526 AX-385289586 4 81867271 TCTCCCCTGGGTTTGTTTCTTACAACAATTTCAGT[A/G]CATTAGTACCCTACATCCTGTCATAAGCAATGTAA R 2 1 2 1 101000 f 74 goat snp23304-scaffold233-869229 4 35804464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452751 Affx-122920269 AX-123323084 4 81908310 TGTTTCTGGGGGCTGTACAAGGGATATGATCATTT[A/G]CAAGAGTCACTGAATGTCATTGCACTTAGAGAATC R 2 1 2 1 101000 f 74 goat snp23305-scaffold233-910268 4 35763417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404538 Affx-122957395 AX-123274890 4 81945017 CTTTTTGTAGATTTCTGTAATATACTGTCCTTTAG[A/C]GGTCTTAGTGACTACAGAGGTAAATCACCAACAAA M 2 1 2 1 101000 r 74 goat snp23306-scaffold233-946975 4 35726521 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773702 Affx-122962791 AX-385260842 4 81989345 GAAATAAATTCACTCAGTCTACAACGTCTGTACTC[A/G]TCCAATTACTAAGATTCAATATGTGTATCTCTGAA R 2 1 2 1 101000 f 74 goat snp23307-scaffold233-991303 4 35681692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410071 Affx-122952853 AX-123280421 4 82031883 CTACTTGAATCAAACCTGTAGATAGTGCTTACAAA[G/T]CATAATATTTTTCGATCTTTTAAAAATGAAAGGGA K 2 1 2 1 101000 f 74 goat snp23308-scaffold233-1033841 4 35641191 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425566 Affx-122941431 AX-123295912 4 82106942 TTAAAAAACTCTCTACTTGTGAGAGGTCTACTCAT[A/G]TTTTCTGTTTTTATTCTTAGAATATTTGCTAGAAT R 2 1 2 1 101000 f 74 goat snp23310-scaffold233-1108900 4 35564934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393465 Affx-122965841 AX-123263821 4 82154804 GTATTTGGTCACTGTGACAACCAAAGCAATTAACT[C/T]TGACTCCAGTATAATTTGTCTTAATTGATATTGCC Y 2 1 2 1 101000 r 74 goat snp23311-scaffold233-1156762 4 35516888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770838 Affx-122925033 AX-385258002 4 82191042 AAACCTTCTGCTTAGGAAACAATCCATGAGTTGTA[G/T]ATCCCATTTGATTCCCAATTCGATACTTTTCTCTC K 2 1 2 1 101000 f 74 goat snp23312-scaffold233-1193000 4 35480505 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776646 Affx-122966730 AX-385263773 4 82221496 GGAGGTGGGAACTGTGACAACAGCATTTGCACTTC[G/T]GTCATGAAATATTAACAACCAGTGATCTGAAAGAA K 2 1 2 1 101000 f 74 goat snp23313-scaffold233-1223454 4 35450156 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798152 Affx-122966563 AX-385285087 4 82301280 ATCCTCCATAAAACTGATCAAAACATACTTGACAA[C/T]CTCATTGTAAGTAAAAGCAGTCTCCTAGATCCAGC Y 2 1 2 1 101000 f 74 goat snp23315-scaffold233-1303238 4 35369494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405733 Affx-122956518 AX-123276085 4 82336825 CTCTGAAAACTTGGGTTCAAATTCTAGCTCAGTTC[A/G]TACATCAGCTGTGTGATTTTAGACAGATCACTTAC R 2 1 2 1 101000 r 74 goat snp23316-scaffold233-1338783 4 35333893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803436 Affx-122933281 AX-385290267 4 82436747 AAACTAAATTGAAAACTTACTAACTTTTGATCCAT[C/T]ATTCATTTTATTGGTATAAATTCCTCAAATGCCAA Y 2 1 2 1 101000 r 74 goat snp23318-scaffold233-1438705 4 35234023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444841 Affx-122926303 AX-123315178 4 82466808 ATTTTGATTTCCCTTGTGTCAGGAGGTAAATATGA[C/T]TCCGCTCCACAAAGTCCTCAGGGACCCAGGCACCT Y 2 1 2 1 101000 f 74 goat snp23319-scaffold233-1468766 4 35203868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796225 Affx-122952644 AX-385283175 4 82511036 CTGTGTTACTCTAATACTCATAGTCTAGACAAGCA[C/T]GTTTGCTTCCTCTTCTCCATCCTTTCTACTCTCTT Y 2 1 2 1 101000 r 74 goat snp23320-scaffold233-1512994 4 35159810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442836 Affx-122927695 AX-123313173 4 82539892 TGGGGGGAACAGAAGGGCCTGACTATGTGGACACC[A/G]TTGCCACCTCGAAGGCTCTCCCTTCTTCAGAAAAG R 2 1 2 1 101000 r 74 goat snp23321-scaffold233-1541850 4 35130941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438398 Affx-122931293 AX-123308736 4 82579033 CCAATCAAAGCTTTCATCTGATTCTCAAAAGGATA[A/G]GTGGCCTCAAAGACATAACTTTTGTGAGATTTTCT R 2 1 2 1 101000 f 74 goat snp23322-scaffold233-1580991 4 35092246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422475 Affx-122943324 AX-123292821 4 82608924 AGGATCAAAATTAGACAAAGGTTATAAAGAGGCTA[C/T]AAATTAAATAGACATATTTTCCCACATGGCTAATA Y 2 1 2 1 102000 f 74 goat snp34081-scaffold400-21610 4 35064118 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775812 Affx-122920376 AX-385262943 4 82669077 GAGTACAAGTAATTTGTACAAGAAATTTGAAAGGA[C/T]TGTATTTTAAAAGATCAAACAGTTTTGACAGTTAT Y 2 1 2 1 101000 r 74 goat snp34082-scaffold400-81763 4 35004138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272284 Affx-1111833440 AX-519546023 4 82712352 ATCTTCAGCACCACCATGAGGGATTTGTCTGGTGT[A/G]CACACAAACGACGCTGTGACTTCCTTGTCCACCCT R 2 1 2 1 101000 f 74 goat 4_82712352_AF-PAKI 4 82712352 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392645 Affx-122966449 AX-123263002 4 82749536 TTATATGTAATCCCACTGCCAGCACCAAGCTCAAG[C/T]GAAAACTTATACAAAATAAAAATATGTATACAAAC Y 2 1 2 1 103000 f 74 goat snp34084-scaffold400-162222 4 34923277 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464315005 Affx-1110420485 AX-515789044 4 82796998 ATAAAATTGCACAGGTTACATGTATGAAAAGAATA[A/C]GAAGTGGTCAAATATTGATACTGCTTCAGTGTCTA M 2 1 2 1 101000 r 74 goat Random2.2K-464 4 82796998 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769270 Affx-122951877 AX-385256443 4 82800465 TAATACTTCCTAGAAAATAGACTGCATTCTGAATT[A/G]TAATGATTCCTTTGTATCACATGAGTAATTTTTCA R 2 1 2 1 101000 f 74 goat snp34085-scaffold400-213151 4 34871914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795297 Affx-122967088 AX-385282255 4 82863917 AGTGAAAAACTAGTAAACAGGAGTAACCGTTATTA[C/T]GTATTTTAGAGACACAGTGTTAGAGATCTTAATAC Y 2 1 2 1 101000 f 74 goat snp34087-scaffold400-276603 4 34808379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382600 Affx-122973715 AX-123252958 4 82981481 CCTTCTTACTGTCACACTGCTTAGCTACCTTTGTC[C/T]ATCTTTTCCTCCAGAGAAGTGACAGAAGCCTGAAT Y 2 1 2 1 201000 r 74 goat snp34090-scaffold400-394167 4 34689737 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770768 Affx-122978702 AX-385257932 4 83056964 TAAAGAGTGTCTATCAGAAACTCATGTCAAGAACT[A/C]AAGTAATAAAAGAACGCAGTTTATTATTTTTATTT M 2 1 2 1 101000 f 74 goat snp34092-scaffold400-469650 4 34613820 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787740 Affx-122949795 AX-385274763 4 83091656 ATCACAGACAGAATCAAATGGAGATTTTGAGAAAG[C/T]GATAGCATCGCCTTGCTTCATTTCCTTGAAAATGG Y 2 1 2 1 201000 f 74 goat snp34093-scaffold400-504342 4 34578989 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393278 Affx-122965448 AX-123263634 4 83184326 CTAGCAACCTATTTCTGGAACTTTTCTGTTTCTCT[A/G]CCATCTCTCTACCTCTCTTTGTCTTCCTCATTCTG R 2 1 2 1 201000 f 74 goat snp34096-scaffold400-597012 4 34486798 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389757 Affx-122968243 AX-123260114 4 83237640 TTGCTATTATTACGCTAATTATTGTGTTTGAGAAC[A/G]TGAGGCACAGAGAGGTTAGGTAACCGCCAATGTCA R 2 1 2 1 201000 f 74 goat snp34097-scaffold400-650326 4 34435790 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418972 Affx-122946075 AX-123289320 4 83283358 CAGATATCCAGTAAGTAAAGTAAAAGTAAGTAAAA[C/T]GTGTAGGAGAAGACAAATGAGAGAGGTGTGATCTT Y 2 1 2 1 102000 r 74 goat snp34098-scaffold400-696044 4 34389972 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275070 Affx-1111834580 AX-519548651 4 83309364 GTGA[A/G]CTTCCTAGAATCTCCTTTTACATTTGAATCTATGA R 2 1 2 1 101000 r 74 goat GoatD01.042191 4 83309364 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770373 Affx-122921467 AX-385257540 4 83331445 AATAGTCACTGGTGAATGAGGCAGATTAAAGAACA[C/T]AGTGGTGAAATTCCTTGTTGTAAAGGACTTTAAAG Y 2 1 2 1 101000 f 74 goat snp34099-scaffold400-744131 4 34343022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437857 Affx-122932078 AX-123308195 4 83370308 CTGTAAAATAGCTGTTTTTTAAATTTACAGAATCA[C/T]GGGAAGTATTTGAAATGCTAAAAGATACATGCTGA Y 2 1 2 1 101000 r 74 goat snp34100-scaffold400-782994 4 34304365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440251 Affx-122930661 AX-123310588 4 83412572 GACATTACTGAGCGATTGAGTACATACACACAAGG[C/T]AGATATTAACAGACAGGTAGATAGATAGACAGGTG Y 2 1 2 1 202000 r 74 goat snp34101-scaffold400-825258 4 34261730 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406099 Affx-122956222 AX-123276451 4 83497741 GCTTTTGACTTCTGAAAAGATTTTTTTCATATGGC[A/G]CTTATAAATTAATATTACCAAAACACATCCTATCA R 2 1 2 1 201000 r 74 goat snp34103-scaffold400-910427 4 34176064 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380082 Affx-122975547 AX-123250440 4 83607587 TCATTGATATGCTACCTTGCTGGTGTTTCAGTGAT[G/T]GCAGAAGAGAGCTAGTGTACCCTATAAATAAATAG K 2 1 2 1 101000 r 74 goat snp34105-scaffold400-1020273 4 34066129 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784292 Affx-122945878 AX-385271343 4 83643973 CAAGTGTTTGGAATACTGGAGAGAACCTGAAAAGT[A/G]TCTGGTCTTGCCATGGGCTCAGGAAAATCAAATCT R 2 1 2 1 101000 r 74 goat snp34106-scaffold400-1056659 4 34029442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447571 Affx-122924028 AX-123317907 4 83681809 GTTCTTAAGAGACTTTTTCCTTTCAGTGTATACTT[G/T]CCACCTCTTGGCCATTTACATGGGTTTAACTATTC K 2 1 2 1 101000 r 74 goat snp34107-scaffold400-1094495 4 33991684 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787921 Affx-122964368 AX-385274943 4 83774748 TAGGAACTTATTTTCTCATTTCATGAGATATTGTG[C/T]AGGCTGATATAGAAAGTATAAAGACTTTTGAAATT Y 2 1 2 1 101000 f 74 goat snp34109-scaffold400-1187434 4 33898389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783613 Affx-122926775 AX-385270672 4 83813604 TCATTGCTTGCATCCATTGTATGGTAATTGTTTAT[A/G]CATTTCTCATCCCATTCTAGTCTGTGACCTCTTGG R 2 1 2 1 101000 r 74 goat snp34110-scaffold400-1226290 4 33859544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383130 Affx-122973256 AX-123253488 4 83945407 CTCAGAATTCTGAAGAAGGAAATAAAATCACAGGT[A/G]TCATATCAGACGATCAGACTGATATGGAAAGAAGT R 2 1 2 1 103000 r 74 goat snp34113-scaffold400-1358093 4 33727902 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427417 Affx-122940062 AX-123297760 4 83987807 ATTTTAGATGGTTTAAATGTTTCACTTTAATTCTG[A/C]AACTGGTAAAACATATAGCATATATAAGAAGATTC M 2 1 2 1 101000 r 74 goat snp34114-scaffold400-1400493 4 33685237 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384515 Affx-122973046 AX-123254873 4 84060379 ATGAACATAAATATCAATATTGGTGTGCTACAATA[C/T]ACTACATAGCCGATAAAAGAGAAATAGAAATTTAA Y 2 1 2 1 201000 f 74 goat snp34116-scaffold400-1473065 4 33614682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447592 Affx-122924012 AX-123317928 4 84098316 CCTAGTCATAAAGTTATTAGCATGGAGCTATGACC[A/G]TGTAGATGGTAGAGAACGCTGGGGGAGGTACATGG R 2 1 2 1 201000 f 74 goat snp34117-scaffold400-1511002 4 33576800 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420460 Affx-122944882 AX-123290807 4 84251999 AACAAGCAGTGCCTGAACAAAGGAAGGAGGAAAGA[C/T]GCCTCTTGTCACTGAACTGACTGGCTGTACGCTTA Y 2 1 2 1 101000 f 74 goat snp34119-scaffold400-1664685 4 33421446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402272 Affx-122959116 AX-123272625 4 84299154 TTCAGGAGAAAAGCCAGGAGGACTGTAGCCTAAAA[C/T]AGCATTATGTAAAAAGAAAGCACACACACAAAAGC Y 2 1 2 1 101000 f 74 goat snp34120-scaffold400-1711840 4 33374024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418473 Affx-122946457 AX-123288821 4 84333684 GAATAGTTCTCAGGGAGGAACGCTCTGAAGGAGAC[A/G]TTACAGAAACGGTCTGTTTCCTCAGCAGGTGCTTA R 2 1 2 1 101000 r 74 goat snp34121-scaffold400-1746370 4 33339662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447021 Affx-122924544 AX-123317357 4 84402400 ACATTCTGGAACTTGCAAACAACTGTATTCCCAAA[C/T]AACAAGCTGCGCTCTGTGTGCTTAGGTGCTCAGTC Y 2 1 2 1 101000 f 74 goat snp34123-scaffold400-1815086 4 33271592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784486 Affx-122926639 AX-385271535 4 84432948 TCAGTTATTTGCAAAGGTATTTGAATGCCTCCTGA[C/T]ACATACCCCAACAGCCTTGTTCTACCTAAACTGTA Y 2 1 2 1 101000 r 74 goat snp34124-scaffold400-1845634 4 33240585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796119 Affx-122920783 AX-385283070 4 84463500 ATCAACTCAATTAGAGATGGGAAAGATGGATAACC[A/G]CACATCCATCAATACACAGGAAGCTTTTTCCTGAC R 2 1 2 1 201000 f 74 goat snp34125-scaffold400-1876186 4 33209992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771708 Affx-122948695 AX-385258865 4 84538778 GCTCAGGCATGCAAATTAGTAAATTCTGAGTGTCT[A/G]CTAGGTACTAGGATATAAGATTGATAGGACAAGAG R 2 1 2 1 101000 f 74 goat snp34127-scaffold400-1951464 4 33134522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793876 Affx-122919962 AX-385280845 4 84582639 CTGCTTGTCTATTAATTAATTCTGCTAATTTATTC[A/G]CTGGAAATGAGTCACAAATTAGTAATGCAAAGTAA R 2 1 2 1 101000 f 74 goat snp34128-scaffold400-1995325 4 33090116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413875 Affx-122949852 AX-123284224 4 84664479 AAGCACTTTTTAAATAAAGACTGTCCTCTGATGAT[A/C]GTCATAAACAGTTTTGCCACTAATTAGGCAATACG M 2 1 2 1 101000 r 74 goat snp34130-scaffold400-2077165 4 33009233 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776893 Affx-122958402 AX-385264017 4 84701023 ACTTACAGCTGAAGATATCTAAAGATAAATGTGTA[C/T]ATTCAACAAATGCCTTCAAAGGTTATTTGCATATG Y 2 1 2 1 101000 r 74 goat snp34131-scaffold400-2113709 4 32972873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773712 Affx-122970562 AX-385260852 4 84750083 CTATGCAAATCCATGAAAGGCAGTATTCTGTTCTA[C/T]GAGAAAATTTATCAGTGGTTATCTGCTGGCTTGGA Y 2 1 2 1 101000 r 74 goat snp34132-scaffold400-2162769 4 32924431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398051 Affx-122961753 AX-123268406 4 84783803 TTTCAATTCAAGGATACAACCTCTTGATAGCTTTG[C/T]GGGCCATTTTAGCCAAGCAGGAAAACAAAAATCAC Y 2 1 2 1 101000 r 74 goat snp34133-scaffold400-2196489 4 32890854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476192 Affx-1251763697 AX-586011618 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20000 f 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 539476447 Affx-1251763697 AX-586011848 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20000 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562165076 Affx-1251763697 AX-606940488 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 f 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562166408 Affx-1251763697 AX-606941816 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562166477 Affx-1251763697 AX-606941885 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 320780291 Affx-122953288 AX-385267386 4 84814495 ATGATCTGGAATTTTTTCAAAGTCCATAGCTCTCC[A/G]TTCAGTAGCAAAATTCCATTATTATTTGAAATGTG R 2 1 2 1 101000 f 74 goat snp34134-scaffold400-2227181 4 32859849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387558 Affx-122970286 AX-123257916 4 84849084 AAAGGATGGTTACTGTTTCTGCAAGACACAACAAA[C/T]GTCTTACTGAGCTATAACCATGGCTACCATTTGAG Y 2 1 2 1 101000 f 74 goat snp34135-scaffold400-2261770 4 32825885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779334 Affx-122950327 AX-385266438 4 84882926 GCCAGGGAATAAACTGGTCAAATTAAATTGCCAAT[A/G]TTTGAACAAATTCCAAGATGAACCTAGACTGGGTA R 2 1 2 1 201000 r 74 goat snp34136-scaffold400-2295612 4 32791355 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782839 Affx-122953723 AX-385269910 4 84917135 ATATCTACTTTTACATGGACTAATATAAAAATAGC[A/G]TGCATATCACAATAACTCGAGGTTATGATATTTAG R 2 1 2 1 101000 r 74 goat snp34137-scaffold400-2329821 4 32757094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802274 Affx-122939024 AX-385289178 4 84950268 AAGCGATGCCTGTGCTTCTAGAATAAATCTGTCAA[C/T]AGCATCTGCCATCCCAATCTCCATCTCCACATTTG Y 2 1 2 1 101000 r 74 goat snp34138-scaffold400-2362954 4 32723823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782178 Affx-122949106 AX-385269256 4 84996008 GCCCATTTAACACACTCTCTTGGTCTGATTGTTGC[G/T]ATCCAGATTGTTGAAATCTGGAATAGAATCTATAA K 2 1 2 1 101000 f 74 goat snp34139-scaffold400-2408694 4 32678491 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780888 Affx-122920248 AX-385267975 4 85028761 GGCAGAAAAGGCAAATGCTGCTATGACAAGGCAAT[A/G]TGGATAATGACTCCCCTCTGACTAAAGTTCTGAGT R 2 1 2 1 101000 f 74 goat snp34140-scaffold400-2441447 4 32645746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416553 Affx-122947675 AX-123286901 4 85066503 TATTCCTCCCATTGAAATGCCCTCCCTCATTCTCC[A/G]CTACCTTTTGGAATCAACATATATTTTTTTAAGAC R 2 1 2 1 201000 r 74 goat snp34141-scaffold400-2479189 4 32607929 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384687 Affx-122972122 AX-123255045 4 85143734 GCTCAGTGGTGTCTTCTAATCTCTTCTGTTCCTCC[A/G]CTTTATCCTTCTAATTCTTTCTTTTTATTATCTCT R 2 1 2 1 103000 f 74 goat snp34143-scaffold400-2556420 4 32533639 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272286 Affx-1111833442 AX-519546025 4 85226008 GAATGTCATCCCATATTAAGCCTTACTGAACCATA[A/C]TGCCAACAAGAGTCAATGAACCATTTGGCAAGAGT M 2 1 2 1 101000 f 74 goat 4_85226008_AF-PAKI 4 85226008 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426933 Affx-122940430 AX-123297278 4 85258048 AAGGGAAACATTATTCATGAGGTTTTCAGCACACA[C/T]GGTGGTGCTGGTGGTTTAGTCACTAAGTCGTGTCC Y 2 1 2 1 103000 f 74 goat snp34146-scaffold400-2670734 4 32417579 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395621 Affx-122963804 AX-123265976 4 85304044 AGATGTTTCAGTCCCAGAATTGGTGGATCCTGTGA[C/T]GAGAAGGGGCCTTAGGGTAACTAAAAAGATGACTG Y 2 1 2 1 101000 f 74 goat snp34147-scaffold400-2716730 4 32370744 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412253 Affx-122950900 AX-123282602 4 85339467 TCCTGTCTGCACACCTAGTTCATATTATAGTTATG[C/T]ATGGGGATAGCCTCCTTCAAAATTTCTTCTTGAGT Y 2 1 2 1 101000 f 74 goat snp34148-scaffold400-2752153 4 32334678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784456 Affx-122941071 AX-385271504 4 85359591 AAAATCCTAATAGTTTGGATATTATCCATCTCTAA[C/T]GCTTCCATCCATAACAATTTGGATTTCTTCCTGTC Y 2 1 2 1 101000 r 74 goat snp789-scaffold1021-9749 4 32312509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448712 Affx-122923850 AX-123319048 4 85389870 AATCCCAGAGCCGTGCGATCCTCCCCCCATCACCA[C/T]GTGACATTAGTGAGAAAGGCGACAGGCGATGTCAT Y 2 1 2 1 101000 r 74 goat snp790-scaffold1021-40028 4 32281906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774955 Affx-122920046 AX-385262088 4 85431376 ATTCACAACTACTGAATGTATAGACAAAATGTCAT[A/G]TATTTGTGTTGACACATATATAGTTCTCTATATAT R 2 1 2 1 201000 r 74 goat snp791-scaffold1021-81534 4 32240537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376215 Affx-122978804 AX-123246574 4 85465487 TTAACAGTTCACATCTCTCCCCTGAATCTGACTCA[C/T]AACCAAATGCCTACTCAACACCTACTTAACACCTA Y 2 1 2 1 201000 r 74 goat snp792-scaffold1021-115645 4 32206598 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403348 Affx-122957807 AX-123273701 4 85495641 TAATGGAATAAAAATGCAAACATTAAGAGTCAGTG[C/T]ATGTTAAATATTATCAACAAAAAAGATTATTGGAG Y 2 1 2 1 101000 f 74 goat snp793-scaffold1021-145799 4 32175964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445785 Affx-122926054 AX-123316122 4 85542051 ATACACATGTGTAATAATCTCCCAATGATTCCAAC[A/G]CATATGTAAACCTGAGAACCCTTCCTGCTCCATAA R 2 1 2 1 101000 f 74 goat snp794-scaffold1021-192209 4 32129620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396583 Affx-122962911 AX-123266938 4 85570697 CACTTATCAAACCCTTACCCTAAAATAACTTAAGA[C/T]GGGTTATCTACTCATCAGACCCCTACCTTAAAATA Y 2 1 2 1 101000 r 74 goat snp795-scaffold1021-220855 4 32101263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762314 Affx-986696845 AX-385250494 4 85653355 GACTAGAAACTATCTTACCAAAAACCATTTCACTA[A/G]CCCAAATAAAAATATCTACCACAATCACAAGCCAA R 2 1 2 1 600010 f 74 goat 4_85653355 4 85653355 Ancestral_priority_1043 ancestry 0.766 recommended IMAGE 10K 10K ancestral 38378041 Affx-122977569 AX-123248400 4 85672932 GAGTGAGAGCCTAGAGAGAACAGCAGGGCTGAGAG[C/T]AGAATTCATTTTCTGGGTGAAGGGGAAGCATTTGA Y 2 1 2 1 202000 f 74 goat snp797-scaffold1021-323090 4 31997698 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799771 Affx-122977744 AX-385286698 4 85716478 TCTCTTTTTGTAAATAAAGCCTTCTCTAAATCACA[A/G]TTTATCAAGATCAACTTACTGAATCTAATTTAAGT R 2 1 2 1 101000 f 74 goat snp798-scaffold1021-366636 4 31953951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408300 Affx-122953779 AX-123278651 4 85763552 AACTGGGATGTTGGGTCTGTTTGTTGCTCAGTCGT[A/G]TCTGACTCTTTGTGACCATATGGATGGACTTTGGC R 2 1 2 1 103000 f 74 goat snp799-scaffold1021-413710 4 31907771 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407372 Affx-122955268 AX-123277723 4 85792546 CACAGCTCAACCTTCAAGGATATGCTACAATTAAA[A/C]GGAAATTATGACCACGGCTACTTGGAAATCTTCAG M 2 1 2 1 201000 f 74 goat snp800-scaffold1021-442704 4 31878094 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772913 Affx-122937976 AX-385260057 4 85837976 TCAGACACAACTAAGCCATTAACACGTTCTCGTTC[A/G]CTTTTCAACCTTTAGGAATATGCACTCAGGTAGTT R 2 1 2 1 101000 f 74 goat snp801-scaffold1021-488134 4 31832045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797227 Affx-122964781 AX-385284166 4 85891617 TTTCTATGGCTACAATTTCCTTTTGTGTACTGTTA[C/T]AGTTTAAGAGTTCTATACAGAACATTTTATGGCTT Y 2 1 2 1 101000 f 74 goat snp802-scaffold1021-541775 4 31777797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429145 Affx-122937992 AX-123299487 4 85928511 CCAAAGGAAACGGAAAAATGTTTACAAGTGAGCCA[C/T]GGCAGCAATAGGCTGAAAACACATATCTGTATTCT Y 2 1 2 1 101000 f 74 goat snp803-scaffold1021-578669 4 31740807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405786 Affx-122955913 AX-123276138 4 85957357 TTAATATATGCACATGGTTAAAAAAATTAAAAAGT[A/G]CTGAAGGCTTTATCTCTCCACCCTCACCCCTAACA R 2 1 2 1 101000 r 74 goat snp804-scaffold1021-607515 4 31711681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776141 Affx-122921487 AX-385263271 4 86005165 TGAGATCTAATGATAGGATGCTTCTTCTACCTGCA[C/T]ACTTTACCTTCTCATTCCTAGAAACTTATTTATGG Y 2 1 2 1 101000 f 74 goat snp805-scaffold1021-655323 4 31663574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776917 Affx-122978523 AX-385264041 4 86034931 ACTGGATCTTTGCAATTTTATTGAGTGGATCAATT[A/G]CCAAGCTCTAGCCCTTCCCTCTAACCACTTTGCCT R 2 1 2 1 101000 r 74 goat snp806-scaffold1021-685089 4 31633981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428980 Affx-122938862 AX-123299322 4 86082059 TTCCTCTGTGTGTGTATTTGTTTTAATTTTCCCAT[A/G]CAATCACTTATCCAATTTCTTGATAAATTATCTCT R 2 1 2 1 201000 r 74 goat snp807-scaffold1021-732217 4 31588894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392923 Affx-122965709 AX-123263280 4 86117011 AATGGAATCTTTGTATTTCTCTTTCTAAAGAAAAC[A/G]ACAGCAACCAAAAAACCCAACTCTGACTCTTTTCT R 2 1 2 1 201000 f 74 goat snp808-scaffold1021-767169 4 31553758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438116 Affx-122931494 AX-123308454 4 86152818 AAGCTAAACCAGACTGTATGAGGCTCTGTTTTCTC[A/G]TTCATAAAATGGGAATAATAGCAGCACTTCCACTG R 2 1 2 1 101000 f 74 goat snp809-scaffold1021-802976 4 31517838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792308 Affx-122959095 AX-385279290 4 86191498 CAGACAGTAATAGGAAATCATAGAGAATGTAAAGC[A/G]TTGACAGAATGACAGAAGAGACATCAGACATCACT R 2 1 2 1 101000 r 74 goat snp810-scaffold1021-841656 4 31478750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789959 Affx-122936022 AX-385276965 4 86244084 TCACATAGCATTTACAAACACAAAATTTAACCAAT[A/G]CTATGAAATATAACCAATATTATTCAGCCTGGCAT R 2 1 2 1 101000 r 74 goat snp811-scaffold1021-894242 4 31425833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391264 Affx-122967365 AX-123261621 4 86272713 ATCCTATAACAAGCATGATGGACCCCATCAAAGTT[A/C]GATTCTATTCACATCCTTTATATGGCTTCTATGAA M 2 1 2 1 201000 r 74 goat snp812-scaffold1021-922871 4 31396840 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397525 Affx-122962046 AX-123267880 4 86320833 AATAATAGGCTACTTAAAATATATATCTAGACTTA[C/T]AGACAAGTCTGCCCAGAAAACGGTCTCAATTAAGG Y 2 1 2 1 101000 r 74 goat snp813-scaffold1021-970991 4 31348429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418422 Affx-122946533 AX-123288770 4 86352112 CCCTGCACACTGCTCAATTGTTCCCTGATGCGCCC[G/T]AAATGTGCTGACAACAGCTTTCCTTCATCCGTGCC K 2 1 2 1 101000 r 74 goat snp814-scaffold1021-1002270 4 31318196 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385002 Affx-122971879 AX-123255360 4 86406374 TCGTGCTAGATTTTCAGACAAAAGCAAATATCATA[C/T]ATTATCATTTATATGTGGAATCAAATATTTTAAAA Y 2 1 2 1 101000 f 74 goat snp815-scaffold1021-1056532 4 31263391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785918 Affx-122933065 AX-385272955 4 86439831 CGTTGCCTACATTCTTCAACTGCATTTTCCAAAAC[A/G]CTTTCCACCACCAATTCAAAGCCAACCCCAGTTCT R 2 1 2 1 101000 f 74 goat snp816-scaffold1021-1089989 4 31229873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770256 Affx-122969803 AX-385257422 4 86475937 ATACCTTAAAAATTGGACTGGTGAACTCTAAAAGT[G/T]ACCCTTTGGCCTTCTAGCCCAGTGTGTAACCACCA K 2 1 2 1 101000 r 74 goat snp817-scaffold1021-1126095 4 31193596 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796765 Affx-122964726 AX-385283709 4 86530627 ATATTTTCTTACATGGGAATGTGAAAATTATTATA[C/T]GGGATTAATAGGAAGTCATACAATATTTGTTAAGT Y 2 1 2 1 101000 r 74 goat snp818-scaffold1021-1180785 4 31139195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412169 Affx-122951071 AX-123282519 4 86568151 CCACCTCTGAAATCTTAACTTTAAAGTCCCACCCT[A/G]TGTACAGATTGTCACTCTTCCAGCGCTCTCACTGA R 2 1 2 1 101000 f 74 goat snp819-scaffold1021-1218309 4 31101217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447633 Affx-122923982 AX-123317969 4 86611229 TCCCTTAAAAAGATTACCATTCTTTCAAAACACAA[C/T]AGATTTAAACCATAACTGATTCACTTCCATGACTT Y 2 1 2 1 103000 f 74 goat snp820-scaffold1021-1261387 4 31058187 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784779 Affx-122931692 AX-385271826 4 86647557 TCTTGATATCAAACCAATTTCTACACTGACTTCTC[C/T]TAATCCTCCAAAAGGGATGTCAAAAGGCTGTCCTT Y 2 1 2 1 101000 r 74 goat snp821-scaffold1021-1297715 4 31021342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780742 Affx-122941495 AX-385267832 4 86750784 TTACCTTGCATGCACTTATTCACAATGAATATACC[A/G]CCTTGTGTGTTTTCACAATTTTGTCATCATTCTAC R 2 1 2 1 101000 f 74 goat snp823-scaffold1021-1400942 4 30916000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780383 Affx-122934798 AX-385267477 4 86785476 ACGTGACAGTAACTTTTGCTATGCTCATTTTACTC[A/G]TTTGGCACAGCCGTCTGATCTCTCTGCCTTTAGAC R 2 1 2 1 101000 r 74 goat snp824-scaffold1021-1435634 4 30881588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406386 Affx-122955402 AX-123276738 4 86865779 TAAAAATTTCATCCTCCTCACTCAGGAAGACTCTG[C/T]ATTTGCCTCCTTGACTTTTGTTGTTGGTTTAGATA Y 2 1 2 1 101000 r 74 goat snp826-scaffold1021-1515937 4 30801239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802395 Affx-122960932 AX-385289299 4 86884543 TCTCTCTACAGTATCTAACACTTCACTACTCTGTA[C/T]GCACATCCTGTGGTGACTTATTCAAACCTCAGTTA Y 2 1 2 1 201000 f 74 goat snp32055-scaffold360-310890 4 30781560 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393469 Affx-122965838 AX-123263825 4 86947057 CGAATAAGAGGGAGAACGGGACAGAAAGCTGGCTG[C/T]GAAGAGATCGTGCAGACTTTGGAAAGGCCACGGTA Y 2 1 2 1 101000 r 74 goat snp32054-scaffold360-248376 4 30719048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410013 Affx-122953260 AX-123280363 4 86978714 TTTGATTTTCCAGTTAAATTATCAAAATTTTCAAA[C/T]AACAGAATTGTTTTTGTTAATAAACTATGACTTAG Y 2 1 2 1 201000 f 74 goat snp32053-scaffold360-216719 4 30686843 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436394 Affx-122933035 AX-123306733 4 87025215 CCAAGCATCATTTTAAAGGAAGAATTCTGTTACTA[C/T]GAGGCGTCCATCATTGTCAGGGATCCTATCCTAAC Y 2 1 2 1 101000 r 74 goat snp32052-scaffold360-170218 4 30640914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771994 Affx-122964846 AX-385259150 4 87060757 AATATATAGCTTCATGATACCAAAGGGCAAAACAG[A/G]AAAGTGGTAAAGAGTTTCAGAATCAGACATACCTG R 2 1 2 1 102000 r 74 goat snp32051-scaffold360-134676 4 30604858 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382514 Affx-122973805 AX-123252872 4 87103187 ATGACAGACTTTAAGGAAGATTATTCCATCTTCTT[A/G]TTTAAAATCCTTATTCTTATCTTTAATATAATTTC R 2 1 2 1 102000 f 74 goat snp32050-scaffold360-92246 4 30561794 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451945 Affx-122920965 AX-123322278 4 87151482 ATTGATTATCCAGAACTCACAAGAGCTAAGGCTCA[G/T]ATTTACATCTACTCATTCCTTGAAATTTGATTAAG K 2 1 2 1 101000 f 74 goat snp32049-scaffold360-43951 4 30512291 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792876 Affx-122963508 AX-385279854 4 87191170 ATTAGTTCATTCCAAAAGAAATAGATCACATGAAG[A/G]TTGGTATATCAATTAATGACACTGAATTTATTGTT R 2 1 2 1 101000 f 74 goat snp32048-scaffold360-4263 4 30474799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766266 Affx-122972017 AX-385253660 4 87206795 TGGAAAGAAGAATAACGGAAGTATTTTCTGAGATC[A/G]TGGCATTTAATATCATAAAGTAGCTAGATGAAGAG R 2 1 2 1 101000 f 74 goat snp20009-scaffold1998-475680 4 30459135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408160 Affx-122954216 AX-123278511 4 87235444 CCACCCTCTCCATTCTGTAAGAACAGCCTCTCTCA[G/T]CTTCAAAGCAGGCTCCAGCTAAAGCTTTCAGAATC K 2 1 2 1 101000 r 74 goat snp20008-scaffold1998-447031 4 30430731 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780923 Affx-122963682 AX-385268010 4 87269800 CCAATAGCAAGACCTATTTCCCTTATTCTACTTCT[G/T]AATCACTATTTGTGCAATGGAACAATTAATTTCCT K 2 1 2 1 101000 f 74 goat snp20007-scaffold1998-412675 4 30396125 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383991 Affx-122972923 AX-123254349 4 87302323 AGCTATGTTCAGAGAAAGAAAATAACCATGTCCTG[C/T]AGAACAGAAATAACCAATGACCCAGTCTAAAACGT Y 2 1 2 1 201000 r 74 goat snp20006-scaffold1998-380152 4 30363499 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783863 Affx-122979177 AX-385270919 4 87357665 TAAGGATTATGTAAATAGAATCTCCTTCAAATAAT[A/G]TAACTCTATGAGTAAAGGTAGCCTAAAAGTATTAG R 2 1 2 1 201000 f 74 goat snp20005-scaffold1998-324810 4 30307042 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781996 Affx-122948405 AX-385269076 4 87393184 GGGGTTAATAGGTTAAATTAATTGTATAAGGCATC[A/G]CAGTAAGAGTCAGAATTAGAATTTTATTGCATCCA R 2 1 2 1 101000 r 74 goat snp20004-scaffold1998-289291 4 30271648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376196 Affx-122978817 AX-123246555 4 87435369 AGTCTAAAAAAGAACAAATATGAGAGTTATTTAAG[C/T]AGCACTGAGTGAAAACACAGCAAAAAGTGATACGC Y 2 1 2 1 201000 f 74 goat snp20003-scaffold1998-247106 4 30231360 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387395 Affx-122970418 AX-123257753 4 87495878 TGAGAGGCCTCAATGCCTTCCTGAGACACACAATG[C/T]AATCACTTCCTTCTTGATGCTTCCAGACCCTGTCA Y 2 1 2 1 201000 r 74 goat snp20002-scaffold1998-186597 4 30170210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438984 Affx-122930379 AX-123309321 4 87533347 CTTCTTTAGCTTCAGAAATGTGGCAAGAGCTGTTG[C/T]ACTCATTGCCTTCTGGGAGGAATTTGTTATGGGTC Y 2 1 2 1 101000 f 74 goat snp20001-scaffold1998-149128 4 30132784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278277 Affx-1111836261 AX-519551764 4 87566586 ACCTACTTTTTTAAAAAAGCTTCTCCCCCATAGTA[A/C]CAAAAAAAACTGACTATTCTACACTACTACCACTA M 2 1 2 1 202000 r 74 goat Random2.2K-466 4 87566586 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795966 Affx-122959410 AX-385282918 4 87593926 TCTAGAGTTTTAAATGCCTTGCCACAAATATTTAT[A/G]CTTTCACAATTAAGGCAAAGCAAGACAAAGTTTAT R 2 1 2 1 101000 f 74 goat snp20000-scaffold1998-88549 4 30071577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801271 Affx-122942519 AX-385288183 4 87629057 TAGCAGCAGCAGCTGACAAGCTCAATGAGGAAAAA[C/T]TCAATGAGAAATATACTTAAATGCCTCACCACAAA Y 2 1 2 1 201000 r 74 goat snp19999-scaffold1998-53418 4 30036298 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395646 Affx-122963783 AX-123266001 4 87705568 CTATAATGTATACACACCTGAAATGTTCAAAATAG[C/T]GCCTGAGTCCAGGCTTGATGTGTTGAAGATTGAAA Y 2 1 2 1 201000 f 74 goat snp912-scaffold1024-349093 4 29948853 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764471 Affx-986696847 AX-385252157 4 87720071 AATCACTTTAAACAATTTAGGTCCCTTATGCATAA[C/T]CTTAGTCACTGCTGAACCATTACACTCGATTTCTT Y 2 1 2 1 600010 r 74 goat 4_87720071 4 87720071 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 38407736 Affx-122954994 AX-123278087 4 87758165 GTGCCATCAAGAGATAAATATTTCTAGGTAAGTAG[C/T]AATAAAAAATATAAATCTGCCTTTTCCCCCTGATA Y 2 1 2 1 101000 r 74 goat snp911-scaffold1024-296496 4 29895433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792093 Affx-122922111 AX-385279081 4 87807301 ACTTCTTTTGCTTTTTCCCTACTGAGTTATGTTGG[C/T]AGAGCCTTGAAAGTTGAGCACTGTGTTAAATGAGT Y 2 1 2 1 101000 r 74 goat snp910-scaffold1024-247360 4 29850210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768720 Affx-122936480 AX-385255898 4 87879895 AGAGTTTATTATAGGTTCTATAAACTGTAGGGAAA[C/T]GTGTTTTGAGAGAAATAGGAAGAAGGGAAAGGCAC Y 2 1 2 1 101000 r 74 goat snp908-scaffold1024-174766 4 29777742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778177 Affx-122976650 AX-385265291 4 87931559 TATCTTGACTACTGAGCACCTAACTTTCAGCATTA[C/T]TTATTAATGGGTATTATAAATAGAGTTATTATAAA Y 2 1 2 1 201000 r 74 goat snp907-scaffold1024-123102 4 29725929 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385568 Affx-122971216 AX-123255926 4 87970411 CATCAATGGCACATTACCCATTTTGAAAACTGAGA[A/G]CTGAAATGCATGCATCAATGTCAGTGCTTATTCCT R 2 1 2 1 101000 f 74 goat snp906-scaffold1024-84250 4 29686924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385134 Affx-122971768 AX-123255492 4 88004210 TGGCTTTGTGTACAAACCATGATCTGGGCTTCCAG[C/T]GAGGTTGATTCCCTCACCTGCTTGATGGTTTTGAT Y 2 1 2 1 101000 f 74 goat snp905-scaffold1024-50451 4 29652495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423765 Affx-122942843 AX-123294111 4 88057352 CCATTGTAGGCTGGTGGGGGATAGGAGGTTTCTCC[A/G]TGGTGGATACTGACTGGTAGTTCTTGTCCTTCATG R 2 1 2 1 101000 r 74 goat snp7143-scaffold1264-1816508 4 29595888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777074 Affx-122945845 AX-385264197 4 88092897 ACTGAACAACTACAATGTTCCATCTTTCTTTTGAT[A/G]CCTTCACAGTTAAGAAAGCTCAGAGGTGCAATTTC R 2 1 2 1 102000 r 74 goat snp7142-scaffold1264-1780963 4 29561943 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452926 Affx-122920192 AX-123323259 4 88164213 ATGCAGGCCTTTTTCTTCATGGTTTATGATCTGCT[A/G]TATCTCATTTGGAAAATCTTCAAATACAATGAAAG R 2 1 2 1 201000 r 74 goat snp7140-scaffold1264-1709647 4 29493002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798851 Affx-122940502 AX-385285781 4 88231450 TCTTCATTGTGATGTAGATACAAATATACAGTTAT[A/G]TCATCTTTTCAGAGCCTTATTCTTTTTCAAGGCTT R 2 1 2 1 101000 r 74 goat snp7139-scaffold1264-1642410 4 29426199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403458 Affx-122957722 AX-123273811 4 88270866 GTAAACTGCAAAGTTCTGCATTTTGGGCAGTGTTC[A/C]GGATCTTGTTCACAGGGAGCAGTTTTAAATCAATC M 2 1 2 1 201000 r 74 goat snp7138-scaffold1264-1602994 4 29390697 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419013 Affx-122946046 AX-123289361 4 88301608 CCCATTTTCTTCATAATTACTGATTCTAACAGTTC[A/G]TAGGCTCTTGTCTTGCCTAGAATTATGACATTATT R 2 1 2 1 101000 f 74 goat snp7137-scaffold1264-1572252 4 29359703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799138 Affx-122921855 AX-385286068 4 88346728 TTTAAGGAGAACCATCTTTGCTGTCTATAATCAGG[C/T]CTATGAGTGAAGGGAGAGTCTGGAGTCATTGAAAT Y 2 1 2 1 101000 f 74 goat snp7136-scaffold1264-1527132 4 29313444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783813 Affx-122952518 AX-385270869 4 88383187 TGTTAAAAATTTCTGTCTAATAGTGATCAGAGAAT[A/G]TGAACTGAGAGTTCTAGTTTATGACAATTATTCAT R 2 1 2 1 101000 r 74 goat snp7135-scaffold1264-1490673 4 29276932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381576 Affx-122974810 AX-123251934 4 88413492 TTCAGCACAATTTATAAATTTCTATTAAATGATTC[C/T]TTCTCAGTTTCTTTTTCCTTTCAGTTTCCCAATCC Y 2 1 2 1 103000 r 74 goat snp7134-scaffold1264-1460368 4 29245539 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774052 Affx-122972613 AX-385261190 4 88487448 TGTTTTACAGAACTTAGTTGAAAGACTCTCATTTA[C/T]GGGATGTGTGGCTGGCGTATATTACTTAGTTTACT Y 2 1 2 1 101000 r 74 goat snp7132-scaffold1264-1386412 4 29175714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378974 Affx-122976404 AX-123249333 4 88533953 GCACATTATGGAAGATGAACTATGTTATAGCCCCA[C/T]GTAACAAATAATGGTATCCATTTACTCACTGTGTA Y 2 1 2 1 201000 r 74 goat snp7131-scaffold1264-1339907 4 29128448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397233 Affx-122962374 AX-123267588 4 88584786 TGTTTGAACATTAATTTGTACAGTTTTGCAAGTCT[A/G]TTATACTTATTGAAATGGCTTTGTTCCTTGCCAAG R 2 1 2 1 101000 r 74 goat snp7130-scaffold1264-1289074 4 29077371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272145 Affx-1111833443 AX-519545902 4 88613524 AACTCCTTGGACCACACAAAATAATTTTTCTCACT[A/G]AATTTAAAAAGCAGAATGATCCACAGCCATCTCTG R 2 1 2 1 101000 r 74 goat 4_88613524_AF-PAKI 4 88613524 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381880 Affx-122974172 AX-123252238 4 88684365 CTGAAGGTTCAAGATCTGACCTGTTGACAAACTCA[C/T]GTTTTAGGTCTAAATATCAGCTGTCTCTCCTCTCA Y 2 1 2 1 101000 r 74 goat snp7128-scaffold1264-1189495 4 28977725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446627 Affx-122924792 AX-123316963 4 88716341 TATACCATTATTAAAATCAATTTTAGAAAGTCACA[A/G]GCATGCTGTGGAGACCCATCCCTAAATACTTTTAT R 2 1 2 1 101000 r 74 goat snp7127-scaffold1264-1157519 4 28945291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789998 Affx-122951279 AX-385277004 4 88750968 ATTGATAATACAGAGTGTTATTTTTGTCACTGCCA[C/T]TGTGCTACAGGCCAAGCAAAAATCTTTCTAAACTG Y 2 1 2 1 101000 r 74 goat snp7126-scaffold1264-1122892 4 28910175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398810 Affx-122961405 AX-123269165 4 88803600 GGCTTGGGACCCCGAGCCTGATGCTGAGGATAGGG[C/T]TTTGTGGAAAACATTCCTGTCCATGGCACTACACA Y 2 1 2 1 101000 r 74 goat snp7125-scaffold1264-1070260 4 28858018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441858 Affx-122929037 AX-123312195 4 88881701 ATTTATTTCATGGTTTCAGTCAAGACTCAAGCCAA[C/T]AAGAAAATTGGCAGGGGTTCACAGTCTCAGAGTAA Y 2 1 2 1 103000 r 74 goat snp7123-scaffold1264-992159 4 28772683 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406603 Affx-122955845 AX-123276955 4 88971927 AGGAGGGTTCAAAGCTTGGAATGATGCCACTCACA[C/T]AGCTGACGCTGCCATGCAGGGGCTGTGAAAGGTGG Y 2 1 2 1 101000 f 74 goat snp7121-scaffold1264-901933 4 28684280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424607 Affx-122942198 AX-123294953 4 89010362 TTTCAGTATTGGCAATTTTAGAATGTGTGCTGGAG[A/C]GAACAATAGGAGAAAAATCACAGACTTTTAGAGCC M 2 1 2 1 201000 f 74 goat snp7120-scaffold1264-863498 4 28646034 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791237 Affx-122941347 AX-385278231 4 89046887 GAAACCCGTGGTGAATTCTTTTGTAATGCAAATAA[C/T]CACCTTTTAATTTATCTGTTTAGTAAGTTGAGCTT Y 2 1 2 1 101000 r 74 goat snp7119-scaffold1264-826973 4 28609327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464318428 Affx-1110422211 AX-515792438 4 89063503 CCTGCAGATAGTATGATCTGCTCCTTAGCACAGTG[C/T]GATCTGATATGAATTTCCTCCACCTTCTCTGCCTT Y 2 1 2 1 101000 r 74 goat GoatD01.011144 4 89063503 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38387961 Affx-122969607 AX-123258319 4 89079111 GATAATTCTTTCCTCTCTGTGTGTTTTAGGTGTCT[A/G]TCATGTGCCAGCCACTGTTCTGAGCATTAGTTTGA R 2 1 2 1 303000 r 74 goat snp7118-scaffold1264-794749 4 28576636 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771428 Affx-122942871 AX-385258586 4 89121883 TGATAGAACCCAGGGAGGTATGAGATATATATAGA[G/T]AGAGAGTTAGATGATAGGTAGCATTATCTATCTAT K 2 1 2 1 201000 r 74 goat snp7117-scaffold1264-751977 4 28533721 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409575 Affx-122953581 AX-123279926 4 89154109 GTATACACGTATATAAATTTTGGCTCATATAGATA[C/T]ACCCCCATATATATAAAATTTGGCTTATGTATTTA Y 2 1 2 1 201000 f 74 goat snp7116-scaffold1264-719751 4 28501449 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382764 Affx-122973979 AX-123253122 4 89200525 TTGAACATTTCCAAGTGATAGGGAATTTAACAGCT[C/T]CTGACACAATTCCTTCCAGTTAAGGACAGTTTGCT Y 2 1 2 1 101000 f 74 goat snp7115-scaffold1264-673335 4 28454545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452597 Affx-122920495 AX-123322930 4 89250066 CTAGGGTCATTCTGTATATGTTATCTGTTGTTAAG[C/T]AACAAACTGTCTCAAAACTCAGTGGCCTAAAACAC Y 2 1 2 1 101000 f 74 goat snp7114-scaffold1264-623794 4 28403663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445932 Affx-122925920 AX-123316269 4 89342676 CAATGACCCTCATGGTAAACCCTGTCCTTTGCCTT[C/T]AGCAAGGATACCATATCTGGTTCAGTGTAAATTTG Y 2 1 2 1 101000 r 74 goat snp7112-scaffold1264-531184 4 28310096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432830 Affx-122935383 AX-123303171 4 89378917 ACCCCAACAATGATCCGGGCACCCTGTGGTGTCCA[C/T]GGTGGGAACAGGAGTGTCATTCATAATTTAGAGTC Y 2 1 2 1 101000 r 74 goat snp7111-scaffold1264-494943 4 28273874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389593 Affx-122968774 AX-123259951 4 89409135 AGGACAGTTCTCCCCTATACTCTTGAGAAGAGGTG[A/C]TTCTCCCACACTTCACTTATCCCAGAGTCCAGTTT M 2 1 2 1 201000 r 74 goat snp7110-scaffold1264-464725 4 28242843 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393995 Affx-122965029 AX-123264350 4 89439642 AACTCATAAAGCTCTCCCAGAAGACCTAGTACATC[C/T]TGGAAAGCCCAGCTAGATGCTTGCCATGGCTGAGC Y 2 1 2 1 101000 f 74 goat snp7109-scaffold1264-434218 4 28212333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443827 Affx-122927542 AX-123314164 4 89514224 TTTTCTACACAGTAACTAGACATTGTAACACCCAT[A/C]TCACAGATTCAGAAACAGATTTAAAGTTAGTTATC M 2 1 2 1 101000 f 74 goat snp7107-scaffold1264-359636 4 28138056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418684 Affx-122946306 AX-123289032 4 89545485 ACTGGCGTAGCACAAAGACCCCAGTAGAGCGCTGG[A/G]AAAACAGAGGGATGGACTGCTGTGGGCTGAGCTAC R 2 1 2 1 103000 r 74 goat snp7106-scaffold1264-328375 4 28106806 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424526 Affx-122941726 AX-123294872 4 89581193 ACAAAGAGGGCAGACAAAACTGTAATATATACATG[A/C]TAAATTTCATATATATATATGTATATGAATGAAAT M 2 1 2 1 103000 f 74 goat snp7105-scaffold1264-292667 4 28071155 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446059 Affx-122925829 AX-123316396 4 89633807 ATTTCCTTTGTACATGATGAAAGGTCTAGAGGTGG[C/T]AAGTGGGAGGGGCTGGGGAGCAGAGGCCCCTGGAG Y 2 1 2 1 101000 f 74 goat snp7104-scaffold1264-240053 4 28018399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384201 Affx-122972396 AX-123254559 4 89671045 GAATAGTCACTGGATGAATTTCAGAGGTTTGCAGC[A/G]TGGCCAGCAGAGCCCCAAGCTCCCTCAGAGGACAG R 2 1 2 1 101000 f 74 goat snp7103-scaffold1264-202815 4 27981144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393800 Affx-122965182 AX-123264155 4 89700979 TCTAGCTTCCGATAGTATATTCATTTTTATTAACT[A/G]GTTAATTTAAAGCTGGCTTAGAACTGCAATACTTT R 2 1 2 1 101000 r 74 goat snp7102-scaffold1264-172881 4 27952097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405948 Affx-122955553 AX-123276300 4 89736460 TCTAGACAAGTAACGTGGCTACTGTTCCTTCTTAC[A/G]TTTGTCTCCTGGACAGGGAGGGGGCCTGCATGGAC R 2 1 2 1 101000 f 74 goat snp7101-scaffold1264-137400 4 27916586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793699 Affx-122924786 AX-385280671 4 89791815 TGAACACAGAATCCCAGAAGTTGCTTAAGCACATG[C/T]AAATAATCACCTCGTTTGATCTATACTGTTCTCTA Y 2 1 2 1 101000 f 74 goat snp7100-scaffold1264-82045 4 27861414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446012 Affx-122925865 AX-123316349 4 89831744 GGCAGATGTGGACACGCTGGCATTTGAGAATGGAC[A/G]TATCAGAAAAACCACATAATCAACAGCTGGACAGA R 2 1 2 1 101000 r 74 goat snp7099-scaffold1264-42116 4 27821465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426775 Affx-122940553 AX-123297121 4 89889600 CTGGGGTGAGCATTTCTGTTTACAGTCTTTTATGC[A/G]TATGCATAATGATCACCCTAGGGAATATGCCTGTG R 2 1 2 1 101000 f 74 goat snp24944-scaffold2551-446847 4 27765279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439075 Affx-122930307 AX-123309412 4 89918974 AGTCCTTGTTCTCTCTCATACGGTGCATCCTTTCC[A/G]CTCCCATGAGCACTGGCATCGCCCTCGGGTTCTGA R 2 1 2 1 101000 f 74 goat snp24943-scaffold2551-417473 4 27736075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436442 Affx-122932999 AX-123306780 4 90005102 GCTGGGGTTTTGTGAGCCTGGGAAGAGGCTGTAGC[A/G]TAGAAGGAGGAGAAAGAAGAGATCCTAAGTGAGCC R 2 1 2 1 201000 f 74 goat snp24941-scaffold2551-331345 4 27650106 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402207 Affx-122959163 AX-123272560 4 90039403 GCTCCACAGAAGGAAAGGGAGAGGAGAATCAGCCC[A/G]ATGCTGTTACCGGTCAGCAGTGCTTGCACTGCCGT R 2 1 2 1 101000 r 74 goat snp24940-scaffold2551-297044 4 27615790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409872 Affx-122952913 AX-123280223 4 90084163 CATCTGGATGGAATATGCTCAGGGCAGTAGGCTGC[G/T]CTGTGCTCTCTGCTTCTTCTCCTTTTAAACACTTT K 2 1 2 1 101000 f 74 goat snp24939-scaffold2551-252284 4 27571109 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416954 Affx-122948023 AX-123287302 4 90134661 TTTGGAGACAGATAGATTATAATTCAAAGGTGGTG[A/C]GGTGGTAAAGAATCCATCTGCAAATGTAGGAGACG M 2 1 2 1 201000 f 74 goat snp24938-scaffold2551-201786 4 27520531 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388294 Affx-122969390 AX-123258652 4 90172175 GGGTTGAAACTAAGACCATCTCCCAACAGCTGAAG[C/T]TGCAGCACAAGTCCTCATCTAAGAGAAGACAAAGC Y 2 1 2 1 101000 f 74 goat snp24937-scaffold2551-164272 4 27482448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438118 Affx-122931493 AX-123308456 4 90206419 ATTGCTGTTGATTATTTTTCTTGAGATTTACAGGG[C/T]ATTTGTGAAGCTTTCATCTCATTTCCATCACACAT Y 2 1 2 1 101000 r 74 goat snp24936-scaffold2551-130028 4 27448102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440689 Affx-122929914 AX-123311026 4 90363844 GAGCTGGGGACAGGGGCAAGAAGGAGACAAAGGCT[C/T]CTGAGCTCAGTAACGCAGGGCCCTGACATCTGAGC Y 2 1 2 1 102000 f 74 goat snp21932-scaffold2156-19824 4 27293141 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413437 Affx-122950689 AX-123283786 4 90441453 AAAAGCAGATTTGTTTTAAAGCCCAATTCAGCAAG[C/T]AACTCTCAATCAGTCTAGTTGAACAGGCTGCTCAA Y 2 1 2 1 101000 r 74 goat snp21934-scaffold2156-97433 4 27218232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393817 Affx-122965573 AX-123264172 4 90473835 AAAGCCAAGGAATGAGGAGGAAATAATGGTTGACT[A/C]GGATGAGATAATGAATTACGAAGCATGGCACACCT M 2 1 2 1 101000 r 74 goat snp21935-scaffold2156-129815 4 27185796 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796114 Affx-122937372 AX-385283065 4 90527034 AGCAGCTGTAAAGCAATTAGCATTTTACAAAACTG[C/T]GGAGTCAAACTGTCACTTATGGTCTTATTGAGACA Y 2 1 2 1 101000 f 74 goat snp21936-scaffold2156-183014 4 27132256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765851 Affx-122955960 AX-385253295 4 90578040 ATGTTGCCTAGGTCTCTGGAAAACATTAAATATCA[A/G]ACTTATTCTTGTGAAAAAATATCAATTTGTGTTTT R 2 1 2 1 101000 f 74 goat snp21937-scaffold2156-234020 4 27080720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388674 Affx-122969095 AX-123259032 4 90612924 TGGGTGAATCCTTAGCTGTTTTCTAACTTGTTCCC[A/G]TCCCAAAGACCAGATTTGTTAACAGGGCCAGGGGC R 2 1 2 1 201000 f 74 goat snp21938-scaffold2156-268904 4 27046153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412627 Affx-122951270 AX-123282976 4 90663048 TATATCCCTGAAACCGAGCAAGACTCTGTGGGACC[C/T]TCTTTGGGACAAAAGCTCTTCTGAGTCCTCTGTTT Y 2 1 2 1 201000 r 74 goat snp21939-scaffold2156-319028 4 26995550 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384363 Affx-122972237 AX-123254721 4 90711857 GTTCATCCACACTGTGTGAGTTCTGAGAATTTGTT[A/G]CCATGAACTTCTGTTGTAACCTTGGTTTAGAGTGT R 2 1 2 1 101000 r 74 goat snp21940-scaffold2156-367837 4 26946270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405594 Affx-122955931 AX-123275946 4 90742884 CATTCTCTTCAGTCCGCGTTCCTTTAGGCCTCAAA[C/T]GCCGCTTTCTCAGGAGTTGCTGTCGACCTTCCTTT Y 2 1 2 1 201000 f 74 goat snp21941-scaffold2156-398864 4 26915606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792992 Affx-122921995 AX-385279970 4 90801765 ATCTTTTCATGACTAATTGGGAGTCACTTTTGTGC[A/G]CGGTTTTGCTTTATATCTTCTGTGGATTATTTTTA R 2 1 2 1 101000 f 74 goat snp21942-scaffold2156-457745 4 26856396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377645 Affx-122977865 AX-123248004 4 90847455 GTCTTTGCTTATAGTTTCCTTGTTTCTGAGTGCCC[A/G]TTCCCCTAAGTTGAGCCAGCCAGTTATGTATTGGT R 2 1 2 1 101000 r 74 goat snp21943-scaffold2156-503435 4 26810586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410068 Affx-122953217 AX-123280418 4 90881322 AAGAACACAAGGGCCTTGGAGTCCAGCAGAGCATC[A/G]TTCTTTGTCTTACGGAATTCAGATACGTGTTGCAT R 2 1 2 1 101000 r 74 goat snp21944-scaffold2156-537302 4 26776840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401468 Affx-122958966 AX-123271821 4 90937440 GCCGTAAGAAGGTCTGGGTGGAGCCAGGAAAGCTG[C/T]GTTTTGTTGCTGAAGAGGTCTCTGGGTGGTGGAAC Y 2 1 2 1 101000 r 74 goat snp21945-scaffold2156-593420 4 26720329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419947 Affx-122945212 AX-123290295 4 90978559 GCAGATTATTTAATAATGTTTCATACTAGAACTTT[A/G]CTTGACTCCCAAAATATTTCATTCTGAAGTTTTAG R 2 1 2 1 201000 f 74 goat snp21946-scaffold2156-634539 4 26679046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443857 Affx-122927520 AX-123314194 4 91083773 CACGTGGTTCCAGTGCCTGTGCTGACCATCGCTGC[A/G]TTCAGAAAGGAAGCAGCCCACCAGTCCATCTGCCC R 2 1 2 1 202000 r 74 goat snp21948-scaffold2156-739753 4 26572959 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389514 Affx-122968295 AX-123259872 4 91125197 ACAAGTTTAGTCAGTGAGCTCCACAGGTTAGCGAC[G/T]TCTTCAGGCAGAGGGTAGGTGGCAAGGATGGCCAC K 2 1 2 1 101000 f 74 goat snp21949-scaffold2156-781177 4 26531465 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272288 Affx-1111833444 AX-519546027 4 91137679 ATTTATAAATTTTTACCTTGTTTCCATCTCACATG[A/G]TAAGAGTACTGAAAGGTGCTCATATTTCTTATTTT R 2 1 2 1 101000 f 74 goat 4_91137679_AF-PAKI 4 91137679 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449680 Affx-122922557 AX-123320015 4 91161577 CAATCAGAAATAATTTGATTTCAGTCAGTAAGGCC[A/G]TGAACCCAGGCAGGAAGTTATGAGATGAATGAAAC R 2 1 2 1 101000 f 74 goat snp21950-scaffold2156-817557 4 26495172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794680 Affx-122936578 AX-385281640 4 91194249 GTTCTGTATCTCTGCCTTCCTAGGTCTCATTTTTA[C/T]CATCTTTCAAATAAGGGAACTGGATGGTATAAAAC Y 2 1 2 1 101000 f 74 goat snp21951-scaffold2156-850229 4 26462500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773341 Affx-122921373 AX-385260483 4 91229964 AAGCAATTTACTGATTCCCATGACTACAAAATAAA[C/T]GGAATCCCAAACTGTACCTTAAATCCAATTCAGGA Y 2 1 2 1 101000 r 74 goat snp21952-scaffold2156-885944 4 26426619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405350 Affx-122956324 AX-123275702 4 91281449 AAATCTGGCCAGCACTGAGATAAATCACACTTCCA[C/T]AGGGGCTATTTTGCCTTTCCTGAAGTGGCCTGCTA Y 2 1 2 1 101000 f 74 goat snp21953-scaffold2156-937429 4 26375046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399847 Affx-122960248 AX-123270202 4 91329652 TGCTGCAAGTAAGTCTCCTCTTGTCAGACGCAGGC[A/G]GTGACACACATGTCTTTGCAAGGGCAGGGGCTCCT R 2 1 2 1 201000 f 74 goat snp21954-scaffold2156-985632 4 26326716 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399862 Affx-122960235 AX-123270217 4 91367725 GTTTATTTTTGTTATGCTAGCAGCCACTGGTTATC[A/G]TTGAGTAGGACTATTATGTCATAAGGGGTTACCAT R 2 1 2 1 101000 f 74 goat snp21955-scaffold2156-1023705 4 26288117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389883 Affx-122968135 AX-123260240 4 91399077 TCTGTTCAATTTGTTAGCTCTCTTTCTTTGGGTGT[A/G]AGTTCTTTTTGTAACATTAATACCTTTTTCATGTT R 2 1 2 1 201000 r 74 goat snp21956-scaffold2156-1055057 4 26256612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386722 Affx-122970155 AX-123257080 4 91474242 TCAGTGTTTAAGTATTTGCATTATTACTCACTGTC[A/G]TTTAACTGACCTAAAAGTTTTGGAAATATGTAGTG R 2 1 2 1 101000 r 74 goat snp30213-scaffold3325-331186 4 26192570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395998 Affx-122963497 AX-123266353 4 91512412 GAAAGGGACCATTTTGCCTTTTCTAAGACCAAAGA[A/C]GCTTTTCCCAGAATGTCCCCACTAGCAAGTGTCCC M 2 1 2 1 201000 r 74 goat snp30212-scaffold3325-293016 4 26154546 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400891 Affx-122959748 AX-123271244 4 91579650 TTGGGGGTGGGCAAGGGGTTCCACAAACAGAGGTT[A/G]CAGGCAAGTCACAGAGGCAAGCATGTTATATCTAC R 2 1 2 1 101000 r 74 goat snp30211-scaffold3325-225778 4 26086729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378500 Affx-122976654 AX-123248859 4 91614056 AACTCTCGAGGTGACTCCAGGACTCCGAGGTGGAA[C/T]AGGCATTACAGGGCACGACCAGGAAACCTGGGTTC Y 2 1 2 1 201000 r 74 goat snp30210-scaffold3325-191372 4 26052339 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406702 Affx-122955770 AX-123277054 4 91709869 AAACCTGGAGAAGCAGTGGCTGACTTGTGATACTT[C/T]GTCCTCAGCTCATGCCAAGGCAGGATGCAAGCAAA Y 2 1 2 1 201000 r 74 goat snp30208-scaffold3325-95559 4 25956685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796466 Affx-122921693 AX-385283417 4 91753949 TAAAACATTTTAAGTGCCTGAGAAAACATGTAACC[A/G]TACATAAATCCAAAGCTCTGGCTGGCTCTCAGTGC R 2 1 2 1 101000 r 74 goat snp30207-scaffold3325-51479 4 25912638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278279 Affx-1111836262 AX-519551766 4 91770963 GTAAGCCTCAGGCTCTCAGTGCTATGACAGATGCA[A/G]CTCCAAATTGGAATAAAAGCATAAAAAATCTGCTC R 2 1 2 1 201000 r 74 goat Random2.2K-467 4 91770963 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444728 Affx-122926410 AX-123315065 4 91794653 AGTCCTGTCCACATGCCCCAGCCTCCAAAGCTGCT[A/G]TCCTCCCAGCTTCCCCCAGTGTAACCTTCCATGTT R 2 1 2 1 103000 r 74 goat snp30206-scaffold3325-10775 4 25873739 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387976 Affx-122969595 AX-123258334 4 91807344 CTGGATGTGGGGAATAGAAGGCCGGCAGAATGGGA[C/T]GGAGAACCAGAAGAGTCTTAAAGCACAGCTGAGCG Y 2 1 2 1 303000 f 74 goat snp32082-scaffold362-1817 4 25870283 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443726 Affx-122927143 AX-123314063 4 91889219 TCAAATTTCTTATGAGGAGTGAAACTCAAATACCT[C/T]AGACCCAGCTCAAGTCCGAGCTGCACAAAGGATCT Y 2 1 2 1 201000 f 74 goat snp32083-scaffold362-83692 4 25776201 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381768 Affx-122974306 AX-123252126 4 91939722 AGTGCCCATGTGAGTGCAGAAAATGCATGAGATGC[G/T]ATGATCCTTGCCCTCATGAAGGGAGGCAAGAGGAA K 2 1 2 1 201000 f 74 goat snp32084-scaffold362-134195 4 25724749 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437948 Affx-122931623 AX-123308286 4 91973376 ATACTGTATCCCTCTTGCTCAAGTCTACCTCACCT[A/C]GTAGACTTCTCTCTGTCCCTCAGATATGCTGCATA M 2 1 2 1 201000 r 74 goat snp32085-scaffold362-167849 4 25690426 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777814 Affx-122966835 AX-385264931 4 92023324 TTAGTATTAGGGATGAACAAATTAAGGACAGTTTC[A/G]TTTCTAAAAATCTCACAAGGGTGGAAGACAGAAAG R 2 1 2 1 101000 f 74 goat snp32086-scaffold362-217797 4 25640617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382426 Affx-122974243 AX-123252784 4 92091834 ACCTTTCATTACCTTTCATTGCTTTATTCTTCATT[A/G]TTTTCTTCATTTTCTACTACCATTTAGGTATATAG R 2 1 2 1 101000 r 74 goat snp32087-scaffold362-286307 4 25569852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442720 Affx-122927859 AX-123313057 4 92135966 ATGCAGGCGGTGCCTTTTTCCATCAGCTGCTTGTA[C/T]GCTGGCCCAAGGGGCAGATGCTGTACATCAATCTG Y 2 1 2 1 101000 f 74 goat snp32088-scaffold362-330439 4 25525719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441262 Affx-122929486 AX-123311599 4 92171517 GTGGATAATAAAAAAAAGATGGGAGGCTCTTAAGG[C/T]AATTGAAAACAAAAACTTCTAAACGTGTCCTTGCC Y 2 1 2 1 101000 f 74 goat snp32089-scaffold362-365990 4 25490303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797139 Affx-122920804 AX-385284079 4 92210700 GAAACTAACATATAAGCCACGAAGCCTAAGGATTC[A/G]TTTCCAATTTAAAGTATGTCGCCAGACAAGCTGGA R 2 1 2 1 101000 r 74 goat snp32090-scaffold362-405173 4 25451180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798539 Affx-122944890 AX-385285472 4 92250838 TCTGACAAGGATTGCATCTGAGGATTAAAATGTCC[A/G]TGGACATACCTCTTAACTCCTCATCTTTTAATTGC R 2 1 2 1 101000 f 74 goat snp32091-scaffold362-445311 4 25410678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438631 Affx-122930915 AX-123308968 4 92298257 ACTAGACCCGCCACTGCGCCACTCGGTGTGCCCCT[G/T]TCAGAGACTCCTTCTCCTTGAGCACATACTCAGCC K 2 1 2 1 101000 r 74 goat snp32092-scaffold362-492730 4 25363317 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799558 Affx-122922782 AX-385286488 4 92348154 GATTTTGACCTGATACCTGTGTGACATTTTTCAAA[C/T]AGTGTTTCAAAAAGTACTTTGGTGCAGATCCCATG Y 2 1 2 1 101000 f 74 goat snp32093-scaffold362-542627 4 25313057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445811 Affx-122926033 AX-123316148 4 92403827 CACAGGGCATGTTTACATATTGTGTTTGTGTGTGC[A/G]TGTATGTGTCTAAAGAGTTAAGTTAACAAGCTGAA R 2 1 2 1 201000 r 74 goat snp32094-scaffold362-598300 4 25257225 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789986 Affx-122946179 AX-385276992 4 92441052 CCCTTTGTAAAATAGCTGACACTTTACCCAACTGG[A/C]TAGTGACTAGTTTTTAGTAAGTCAGATGATTTACT M 2 1 2 1 101000 f 74 goat snp32095-scaffold362-635525 4 25220228 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799310 Affx-122963639 AX-385286240 4 92471064 ATGAGTGGTCCAAAAAGAAGTACCAAAGGGAATAC[C/T]GAAGGTAGGCAAAAGAATTTCCAGTCAAAGTGACC Y 2 1 2 1 101000 r 74 goat snp32096-scaffold362-665537 4 25190221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379794 Affx-122975829 AX-123250152 4 92502525 GACTGGATATGTGAAGCATGGCTCAGAAGTTTGCC[A/G]CCTATATTTCAAAAGTTCTTCACTCTTTCTCAAAT R 2 1 2 1 101000 f 74 goat snp32097-scaffold362-696998 4 25158660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442372 Affx-122928019 AX-123312709 4 92538037 TTCAGTGTGGGAACTGTCTGCTGACTTAACTTCAA[A/G]CTTCCTGATTCTTTCCTTGATACATTACCCATCTA R 2 1 2 1 101000 r 74 goat snp32098-scaffold362-732510 4 25123081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430384 Affx-122937773 AX-123300725 4 92585577 CTTGTCAGAGGGAGGTGGGGAGGTGGGGGAAGAAC[A/G]TACCCCAATAGTGGTTTTCATGAGAGCATGTAGAG R 2 1 2 1 101000 r 74 goat snp32099-scaffold362-780050 4 25074834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426821 Affx-122940518 AX-123297166 4 92616687 CCTGCAGTCTAATTCTGTAATTGTTTTGCACCTTC[A/G]CTTTGTCACTCCACTAGTTTAGAGATTTTATGTTT R 2 1 2 1 201000 r 74 goat snp32100-scaffold362-811160 4 25043924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798647 Affx-122944742 AX-385285579 4 92645824 ACATCCTCACCTCTAAATGGTTACTAAATTATTAC[A/G]TTTCTCTCTGAAATTATGAGAGAAAAATTAAACAA R 2 1 2 1 201000 r 74 goat snp32101-scaffold362-840297 4 25014666 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778643 Affx-122937604 AX-385265754 4 92689890 CCATAGATATGTGTTGATTAAGTTATCAGATTACA[A/G]AGGATAAAAACATACTTAAGAGTATCTCACTGGAA R 2 1 2 1 101000 r 74 goat snp32102-scaffold362-884363 4 24970233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431582 Affx-122936181 AX-123301923 4 92723938 CTCATAAGAAGACACCAGGAAACTAGACTCCAGAA[C/T]CGAGACTGAAGGTCATGAATGACCTCTGTTAGTCC Y 2 1 2 1 201000 r 74 goat snp32103-scaffold362-918411 4 24936308 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433248 Affx-122935241 AX-123303589 4 92757567 GATGTTGGGACAGCACCCTGGGGAAGGGGCAGAGC[A/G]CCTTCAGATTCTCCTTAAGGTCTGTTTCAAGGACC R 2 1 2 1 101000 r 74 goat snp32104-scaffold362-952040 4 24904707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452885 Affx-122920223 AX-123323218 4 92760972 TGGGGTGTGGGTGTTCACACCTTCTGTCCTGGTGA[C/T]ATGGAGCCTCCTCGGCTACTTTTCTGTTCAGTTCA Y 2 1 2 1 101000 r 74 goat snp59342-scaffold976-368940 4 24901461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427909 Affx-122939677 AX-123298252 4 92792182 TGGAGAAAATGGCATCTGCTTTACAATGACTCATT[C/T]AACGGTTAGTTTCCAGGGACAGAGAATAGAGTAAA Y 2 1 2 1 201000 f 74 goat snp59341-scaffold976-337730 4 24875281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406443 Affx-122955193 AX-123276795 4 92840568 AAGGGACCCCAGGCTTTCAGAGGGGGCGCAGTGTA[C/T]GTGGAAGGCTGCAAGCAGGGGCCTAACAAACCAAA Y 2 1 2 1 101000 r 74 goat snp59340-scaffold976-289344 4 24826975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802141 Affx-122934556 AX-385289045 4 92894052 ACACGACTGAGAAACTCACTTTCACCTTTACTTAC[A/G]TTTACACTGTATGTACATACGCACTGGAATCCAAG R 2 1 2 1 101000 f 74 goat snp59339-scaffold976-235860 4 24772576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384310 Affx-122972278 AX-123254668 4 92922974 CCCCATCCAGAACTTCCCGTCCCACCTCCCTCCCC[A/G]TCCCATCCCCCTGATCATCTTTTTTAAAGCCCCTG R 2 1 2 1 103000 r 74 goat snp59338-scaffold976-206938 4 24743453 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421207 Affx-122944143 AX-123291554 4 92954103 GAGAAAATGAATGGTATAAATTCAAGCTACACATT[C/T]CCCAGCCAGATGAGTAGTTGCACTCTCTACCTGCT Y 2 1 2 1 201000 f 74 goat snp59337-scaffold976-175809 4 24711981 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412565 Affx-122951319 AX-123282914 4 92988105 CTCCACTTGAAATGGGACCCACTTTTTGGGTTCTC[G/T]ATGTTCTCGTGCTCATTAAGATAAAGGGGCTGGTA K 2 1 2 1 101000 f 74 goat snp59336-scaffold976-141807 4 24677992 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399907 Affx-122960200 AX-123270262 4 93016747 GTTTGCACAGCCATCGAGTCCATGGGCAGGCCCCC[A/G]TGGGCTTTGCACGTCATTTACCTCCTCCTCACGTC R 2 1 2 1 101000 r 74 goat snp59335-scaffold976-113165 4 24649707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382777 Affx-122973588 AX-123253135 4 93054676 AGATGGGAGCCTGTCCTATTTTTTTCAAAATACCC[A/G]CAAGAAATGCCACCATCTGCTTAGGTAGTCAAATG R 2 1 2 1 201000 r 74 goat snp59334-scaffold976-75236 4 24611761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444937 Affx-122926696 AX-123315274 4 93085133 TCCATCTGTTCCTACCTTGACAGCCAGCCACTGGG[C/T]GCTCTAATCGCAACTGTACAATAGCTCTGGGCACA Y 2 1 2 1 101000 r 74 goat snp59333-scaffold976-44779 4 24581336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408005 Affx-122954314 AX-123278356 4 93154433 TCCTATTGATGCTTTCAGAGCCTCAACAAGGCCTC[A/G]TTCCCACCCTACAAACAGGGAAGCTTCGTATGCCA R 2 1 2 1 101000 f 74 goat snp4529-scaffold1145-1614968 4 24390402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408601 Affx-122953646 AX-123278952 4 93188675 TCAGACGCAACTGGACAACTAAACAACAGCAACAA[C/T]GGGACACAGAGCATGTAGGCACAGAGAAGTCTCTG Y 2 1 2 1 201000 r 74 goat snp4528-scaffold1145-1580726 4 24355909 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448534 Affx-122923439 AX-123318870 4 93224543 CACGGCTGACACTGAACCCACACCCAAGAACTCAC[A/G]GAGAAGAACACACACATCACGGACTTCGTGGATGT R 2 1 2 1 101000 r 74 goat snp4527-scaffold1145-1544858 4 24320423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448259 Affx-122924194 AX-123318595 4 93275878 TTGACTTGAGTGAAGAAGCTGATAAAGACCAAGGT[A/C]GTGAACTGAACTCCTGTGTGGGCTCCTTTGCTCTG M 2 1 2 1 101000 f 74 goat snp4526-scaffold1145-1493523 4 24269256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427870 Affx-122939708 AX-123298213 4 93335425 AGCCTGGCTGGGCTGGAGGCCAAGGCCATCACCGC[G/T]CGGTCAGACTTGGGTGGTAATCCCAATTGGTTTTG K 2 1 2 1 101000 r 74 goat snp4525-scaffold1145-1433976 4 24210458 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439398 Affx-122930253 AX-123309735 4 93364968 CTGCTGAACGAGTGCACTTGTTGGTCTACCAGGCC[G/T]AGGACCCCAGCACAATTCCAGCCAGACAAGAGGAG K 2 1 2 1 201000 r 74 goat snp4524-scaffold1145-1404433 4 24180492 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278281 Affx-1111836263 AX-519551768 4 93441900 CAATTTCAGTTGAGATTGTCATTTTCCTGACATTT[A/C]GTGATTTTTTTTATACAAAGCAACAATATTTTCAA M 2 1 2 1 101000 r 74 goat Random2.2K-469 4 93441900 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416435 Affx-122947830 AX-123286784 4 93451003 GGGCTGGATGGTGTCCCTTACGTGCTCAGCTAGAT[A/G]CCGGACACTTGTGCTCATTGACAGATGTGTGACTT R 2 1 2 1 201000 f 74 goat snp4522-scaffold1145-1318398 4 24094709 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414052 Affx-122949775 AX-123284401 4 93480743 AACATGTCTCCAAACTGGGTGTAGTTTCTCTATAG[C/T]CTCCTTTACCGTATAGAACCAAAGGTCTTCACGAA Y 2 1 2 1 101000 r 74 goat snp4521-scaffold1145-1288658 4 24064961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411273 Affx-122952312 AX-123281623 4 93510691 AGAAACTCACTAGCGGTAAAGGATGGAACCCCAAA[C/T]TGGAATCCCCTTTCCCTACAGAGTGGTTCTCAGAC Y 2 1 2 1 102000 f 74 goat snp4520-scaffold1145-1258710 4 24035288 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397004 Affx-122963139 AX-123267359 4 93543974 TTAATGCCAGACAATTTCCATAACGAGAAAAGTGC[A/G]TCGCAGTTGTTGGCTCTTTGTTGTCATAGTTGTCA R 2 1 2 1 101000 r 74 goat snp4519-scaffold1145-1225427 4 24001812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395458 Affx-122963916 AX-123265813 4 93576541 GTGGACACAGCATAGTTACCATGACAGTGACCGAC[C/T]GTAGGAAGTGGACTTACTTCACACCCATGTATGCA Y 2 1 2 1 101000 r 74 goat snp4518-scaffold1145-1192860 4 23969428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454162 Affx-122919321 AX-123324495 4 93610090 ACAGCTGAGCTCTGCTTTTACACCTGTCGGTGGAA[C/T]GTGAAGTGCTGCCTTCTTGGGGGCTCTGCTTAGTG Y 2 1 2 1 101000 f 74 goat snp4517-scaffold1145-1159311 4 23936358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431129 Affx-122936587 AX-123301470 4 93655985 CCCCATTCACCTGAAAACCCCTAAGGAAGGGACTA[C/T]GTCTGAAACAGCTTTGATCCACAGTATAGTGACAT Y 2 1 2 1 101000 r 74 goat snp4516-scaffold1145-1113416 4 23890572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417380 Affx-122947701 AX-123287728 4 93689162 CGTGGCATATTAGGGAGCACGGTGCGTGGGGTGGG[C/T]GTGCTGGGTGTGTGGTGGTGATCAGTGTCAGGTAG Y 2 1 2 1 303000 f 74 goat snp4515-scaffold1145-1080239 4 23857694 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393984 Affx-122965037 AX-123264339 4 93723458 CTCGGGGAAGATGTGAAATGGTGGATGGTGTTGCC[A/G]TCAGGGGAGATGGAAGGAGCAGGAGTCGGCAGTTG R 2 1 2 1 101000 f 74 goat snp4514-scaffold1145-1045943 4 23823195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415145 Affx-122949413 AX-123285494 4 93782089 CCTGGTTAAAGCGTATTGAAGAGTCACTGAGAAGA[C/T]GGGGCTAATGACAATGTGATGTCCTCCTGTCACCT Y 2 1 2 1 101000 f 74 goat snp4512-scaffold1145-987312 4 23764734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430757 Affx-122937495 AX-123301098 4 93827917 AGTCCATTTTCCCTAGCTGTATATGATGGGGCTGT[A/C]GAACTTTCCTCAAAGGGTTCGTGTGAGGTTGAACC M 2 1 2 1 101000 f 74 goat snp4511-scaffold1145-941484 4 23718980 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802143 Affx-122923453 AX-385289047 4 93876626 ACCCCACTTTTAATATTCATTACTGTGGGCTTCAG[A/C]TTTAACCAAGAGGTCTGTTTTTCTCCTTAATCCTA M 2 1 2 1 101000 f 74 goat snp4510-scaffold1145-892775 4 23670187 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272149 Affx-1111833445 AX-519545906 4 93895476 CCATAGAAAGTATTTAGCAAAATTTGAATAAGTGA[A/G]TGGACATGCTCAATGACATCAAATGGGAGAAGACA R 2 1 2 1 101000 r 74 goat 4_93895476_AF-PAKI 4 93895476 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448567 Affx-122923415 AX-123318903 4 93911414 CACCACTTACAGTTAATCAATAGAGCTTGCTGTTT[A/G]CCAATCCTATTTCAGTGTTTTGCCCTTTTCCAAAC R 2 1 2 1 101000 f 74 goat snp4509-scaffold1145-857987 4 23635102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423049 Affx-122942963 AX-123293395 4 93954448 ATTTACATTTTGTCAAACTGACTTTTAAAATGCTT[A/G]TGCCAGTTTATATCCTGACGAACAGTGTCTTGAAG R 2 1 2 1 101000 r 74 goat snp4508-scaffold1145-814953 4 23592079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435188 Affx-122933645 AX-123305528 4 93985249 CAACCTCTGTGCTATCCACAGTCTTATCTACCCCC[A/G]TGATCAGCCATCAGCAATGAACCAGCGACCCTTGC R 2 1 2 1 201000 r 74 goat snp4507-scaffold1145-784152 4 23561298 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424691 Affx-122941701 AX-123295037 4 94031625 TAATGTAGTTGGGTTGGAGCAGTGTATCTTCAGCA[C/T]GTATTTTCCTTGTACCTTATAAATCCTCTCTGTTT Y 2 1 2 1 101000 f 74 goat snp4506-scaffold1145-737776 4 23515299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448843 Affx-122923293 AX-123319179 4 94067642 GCACCTTCAAAAACAGAAGAGTGAGTCCCCATGAC[A/G]CTGTTTCAACAATTTTTGTTTCATCTGTATCCTGT R 2 1 2 1 101000 f 74 goat snp4505-scaffold1145-701759 4 23478613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777981 Affx-122948444 AX-385265097 4 94129904 GGTGCCAGCTGTGCCTCTCATTAGCTGTGTGCAGC[A/G]TACTTGTAATACTTAACGTATTCAGACACTGCTTT R 2 1 2 1 202000 f 74 goat snp4504-scaffold1145-639497 4 23417597 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450975 Affx-122921738 AX-123321309 4 94161303 GCTTTGCCTATTTATTTTTGCCCGTGTGGCTAAAT[A/C]GGATGTCAAGTTAATAGAAAAATTATTTGGTGAAA M 2 1 2 1 101000 f 74 goat snp4503-scaffold1145-608098 4 23385860 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393019 Affx-122965646 AX-123263376 4 94193847 TCCCAAGGTAATTCTTTCATCTAACAAAGGCTGTA[C/T]AATGATTTCCAACAAAGAAGATGTTCAGAATAATA Y 2 1 2 1 101000 f 74 goat snp4502-scaffold1145-575554 4 23353535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398338 Affx-122962124 AX-123268693 4 94245769 GCAAGAAGAAATTTGCATTATAGTTTTCCATTTTA[C/T]GCCACACACATAAACAGATCTCCTTTAGAGTCAAG Y 2 1 2 1 202000 f 74 goat snp4501-scaffold1145-523632 4 23300985 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451522 Affx-122921103 AX-123321855 4 94309998 CCAGAAATAACTTACCGGGACGCTACAGCTCTGCA[C/T]AGCAAAACCCACAGTAAAATCAAACCTCTTCAGTG Y 2 1 2 1 201000 f 74 goat snp4500-scaffold1145-459403 4 23237013 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784332 Affx-122977555 AX-385271383 4 94366292 GAGGAAAAGCTGTCTCATTAAAAGTAATAGATGTC[A/G]CAGAATTAGCTTCCACTGAAATTTGCCATCACTGG R 2 1 2 1 101000 r 74 goat snp4499-scaffold1145-403109 4 23180925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444576 Affx-122926967 AX-123314913 4 94412598 GAAGAGAAACTATTTCTGCAAGAATAATCTCACAA[A/G]TTCTCCAGCCTAAAATACTTGGGGGCGGGAGGGGA R 2 1 2 1 201000 f 74 goat snp4498-scaffold1145-356803 4 23134506 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771815 Affx-122928645 AX-385258972 4 94444407 TTCATTTATTATCTATCAAATCCATTCTTAGCCCC[A/G]CTAATCATTAACTGATATATGACTTTCAAATCTCT R 2 1 2 1 101000 f 74 goat snp4497-scaffold1145-324994 4 23102677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792052 Affx-122967079 AX-385279040 4 94476223 CAATGAGTGTTTACTAAGTGAAGAAATTTCTCCTA[C/T]GTTCCTTTCTTTCTAACTATCCTTATTCTGTCCCT Y 2 1 2 1 201000 f 74 goat snp4496-scaffold1145-293178 4 23070814 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442927 Affx-122927622 AX-123313264 4 94515200 CACACCATGCCAGTCGTGCCTGGTAGGCTTTGTTT[C/T]CCAAAGCTCTGTTAATTCAGGGGAAGGACTGGCTT Y 2 1 2 1 102000 f 74 goat snp4495-scaffold1145-254201 4 23032011 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801712 Affx-122968330 AX-385288620 4 94559201 AGAGCAACAGAATGACCTTCCATGACTAATCGATG[C/T]AAACTAATAACTTGCGCTGCTTACATTTACAATGT Y 2 1 2 1 101000 f 74 goat snp4494-scaffold1145-210200 4 22987619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406928 Affx-122955082 AX-123277279 4 94588448 AGGGTAAACTGTGCTCCTTCCTTTGATAGCTCAAA[C/T]ATACTGTGTTCAAATATTTAATAAAAACGCTTGAA Y 2 1 2 1 101000 f 74 goat snp4493-scaffold1145-180953 4 22958335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404684 Affx-122957278 AX-123275036 4 94620783 AGATGATTGGGCAAGTGGGAAACCATAGCACCCTC[A/G]TTTCACTGAAGAGGAAAACAGGTCTACACAGATAA R 2 1 2 1 201000 r 74 goat snp4492-scaffold1145-148618 4 22926006 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382232 Affx-122973965 AX-123252590 4 94677059 GGGAGCATTTAGGACATAAGCAGAGAATCTTTTCT[A/G]GTCAGAATAATGAAATCAACAAAGAAACCCCCACC R 2 1 2 1 101000 f 74 goat snp4491-scaffold1145-92342 4 22870641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405599 Affx-122955927 AX-123275951 4 94718254 TACTACAGATATTCAGAAAATTTTAAGAATATAAA[C/T]ATTTTTCAATGGTATTACTAAGGATATAAAAGCTC Y 2 1 2 1 103000 r 74 goat snp4490-scaffold1145-51147 4 22829444 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431348 Affx-122937051 AX-123301689 4 94769005 TCTCACCAGAGCTCTAGTTCTACCTGACCCCTCAT[A/C]TTACTTTTCAGTGACTTTGGGTGTATATGTTTCAT M 2 1 2 1 201000 r 74 goat snp4489-scaffold1145-396 4 22778478 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384773 Affx-122972016 AX-123255131 4 94779475 GCGTGATGTTAATAGTCAAAGCCATGGCAGTGGTC[A/G]AAATGGGCTAGGGAGCTTGTTAAGTAAGAAGGTAA R 2 1 2 1 201000 r 74 goat snp14048-scaffold1559-9975 4 22768046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401363 Affx-122959242 AX-123271716 4 94813655 AGATATTCCCGTGCAATAAAAGCCTATGCATTCGC[A/G]TACCTGAAGCTTGTGGGAAAAATACATGCATCCCC R 2 1 2 1 101000 f 74 goat snp14049-scaffold1559-44155 4 22734084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789569 Affx-122961166 AX-385276578 4 94848340 ATAGTGTTAAGTGCTTTGAGTGTGATTGGAAATGT[A/G]CAAAGCACAGTTGCCGCTCTGAAGGAGCTCAATTC R 2 1 2 1 102000 r 74 goat snp14050-scaffold1559-78840 4 22699485 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415927 Affx-122948449 AX-123286276 4 94884129 CAGAATGTCCTTCTAGCTGTAAAGTCCCATGATGC[G/T]CTGAAGAAAAAGGGCCATAAAGTACCTGCCACATT K 2 1 2 1 101000 f 74 goat snp14051-scaffold1559-114629 4 22663389 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386198 Affx-122971360 AX-123256556 4 94915938 CGAGAGGTAAATTCTCCCCTAAGTACATCTTTCTC[A/G]TCTTCACTAAACATAGTTATTCTGTTTTTCTGTAT R 2 1 2 1 201000 r 74 goat snp14052-scaffold1559-146438 4 22631304 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382526 Affx-122973797 AX-123252884 4 94958364 ATGTGGCCTAATCTGTTGACGCTCTTGAATTTCAT[A/C]TGGCTGGCCTGGCACAGTGAAATATTTTCCCCTGT M 2 1 2 1 201000 f 74 goat snp14053-scaffold1559-188864 4 22588864 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443701 Affx-122927160 AX-123314038 4 94990429 CAGAAGATCCATTCAGGGATTCTTCTTGTGCTGAG[C/T]CTCTGGTACTTTGTGGTTCTGTGAAACAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp14054-scaffold1559-220929 4 22556379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769470 Affx-122942491 AX-385256640 4 95021003 AGCTCCCAGACTTGCCAATTCTTAGAACAGTGAGT[A/G]CTAAAGAAATTCTAGACACCATAGACAAGAAGTTG R 2 1 2 1 101000 f 74 goat snp14055-scaffold1559-251503 4 22525960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418707 Affx-122946289 AX-123289055 4 95064831 TAACCAGCTGATGTGAGATCATTTTCTTATAGGCT[A/G]TTGAGAAACAGAGCATCTCCTTTGCAATTCTTTCT R 2 1 2 1 101000 f 74 goat snp14056-scaffold1559-295331 4 22486992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416978 Affx-122948004 AX-123287326 4 95093499 TTAGCATCCTGGCTTTAGACACTTCGCCGTGAATA[C/T]ATTAGGCACAACGAAGAAGTAGGTTATCCCCATTC Y 2 1 2 1 101000 f 74 goat snp14057-scaffold1559-323999 4 22458294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387668 Affx-122969834 AX-123258026 4 95150841 AAATCAAATTCCTCCAAGATTATTTTTATTCAAAA[G/T]AATTTCATAAAAGCCACAAATCTCTTTCTGAATGA K 2 1 2 1 303000 f 74 goat snp14058-scaffold1559-381341 4 22400573 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436743 Affx-122932294 AX-123307081 4 95181615 TTGTATCCCCCAGGGTACCCTGAGTGACACTGTGA[C/T]GCAGCAGTCTGGAATTCTGTCTCCCAGAAAAATAG Y 2 1 2 1 103000 r 74 goat snp14059-scaffold1559-412115 4 22370617 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387397 Affx-122970417 AX-123257755 4 95210719 TTTTAATTAAGCCTCGTGGTATTGGGGTATGGCCT[A/C]ATGTTGCCATGTGGTGTGACACGCGGATCACAACG M 2 1 2 1 101000 r 74 goat snp14060-scaffold1559-441219 4 22340998 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779330 Affx-122930056 AX-385266434 4 95253139 ATATGCAATCAGTCTACTTTGCACATAGCAACTCT[A/G]TTTAGCAAGTCTAGAGTGAATAGCGATAGGATTTA R 2 1 2 1 101000 f 74 goat snp14061-scaffold1559-483639 4 22298665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438015 Affx-122931571 AX-123308353 4 95291483 GGAATGAAACCCATCACTGTGACGGTGTTGAAGAT[A/G]CTGGGAAATTGATACAGATGTGTGGCCTTCATGAA R 2 1 2 1 101000 f 74 goat snp14062-scaffold1559-521983 4 22259565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422788 Affx-122943214 AX-123293134 4 95329214 CAGCAACAGACCCACAGAGAAGAACGTCAGCTTTC[C/T]TCCTTCACTCTTCTGAGGGTGTAGCAGGGCAGGGG Y 2 1 2 1 101000 f 74 goat snp14063-scaffold1559-559714 4 22221598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420192 Affx-122945556 AX-123290540 4 95369849 GCTTGGTGCCTACTCATGGGCAGACTAGAGGTGGA[C/T]GAGAGGGTCCACTAACCAAGTTTCCCACTGCCATT Y 2 1 2 1 101000 r 74 goat snp14064-scaffold1559-600349 4 22180866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393457 Affx-122965847 AX-123263813 4 95431226 ACTTTTAGGGACTGCCGTACTCTTCTGCTCGAGGC[A/G]CTTCCGCACTCTGACTGGGGCTTCCGTCGTCATGT R 2 1 2 1 201000 f 74 goat snp14066-scaffold1559-661726 4 22119240 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794333 Affx-122972062 AX-385281297 4 95473833 AGCCTGGCATAAAATCAAGGGCAGCAATCCTAATC[A/G]TTTTTCATGCCAGGACCCCTTGGCATCCTGCAGAA R 2 1 2 1 101000 f 74 goat snp14067-scaffold1559-704333 4 22076193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789205 Affx-122969237 AX-385276217 4 95516074 ATTTGCACTATAAATCCCTTGACTGCAGCTTGTCT[A/G]TACATACATGCAACTTGTTTCATATTTATATGCAT R 2 1 2 1 102000 f 74 goat snp14068-scaffold1559-746574 4 22034983 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411233 Affx-122952343 AX-123281583 4 95551565 TCCAGCTGCCATGAGCTGCACAACGGGGCAAAGAA[C/T]GGTTAGTGCTCAGTCATGGTGCTGACCCCTGAAAG Y 2 1 2 1 101000 f 74 goat snp14069-scaffold1559-782065 4 22000016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375841 Affx-122978531 AX-123246200 4 95583571 TCCTTATTCCCGTCGAATCCTTAGTTATACAGCCC[A/G]CTCTACAACCTCCATCCAGCTCCCCTGAATGTCAT R 2 1 2 1 101000 f 74 goat snp14070-scaffold1559-814071 4 21967802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417607 Affx-122946874 AX-123287955 4 95627441 GGAAAGACGGGCAGCGGACCACAGAGGGCTTCCTA[C/T]GCCATATGATGGACTTTGGGTTTTGCCCTGAGATG Y 2 1 2 1 101000 r 74 goat snp14071-scaffold1559-857941 4 21923692 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424985 Affx-122941908 AX-123295331 4 95673433 GGAGTCTGGCACTCGCACGCCCACCCCTCAAGCTC[A/C]GACCCTCACTTATCCCCCAGGTCCCGCTCAGCTGT M 2 1 2 1 101000 r 74 goat snp14072-scaffold1559-903933 4 21877057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399619 Affx-122961084 AX-123269974 4 95706689 TGTCTTCTCACTCTGCCCACTGGATTGCTTTGAAA[C/T]GAATGCTGAATGTCAAATAGGATAGATTTTGAGAA Y 2 1 2 1 201000 r 74 goat snp14073-scaffold1559-937189 4 21843796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405527 Affx-122955986 AX-123275879 4 95738771 AATGTATATAGAATTCACCACCAGACACTATTGGA[C/T]AGTCTGAAAGAAGTAGGGAATGAAAAATTTTGTGC Y 2 1 2 1 201000 r 74 goat snp14074-scaffold1559-969271 4 21811618 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432326 Affx-122936294 AX-123302667 4 95797519 AGCAGTTGCCTTATTTGGGAAAGTCTACTTGGTTT[A/G]TTCTGATGGGTTCTCCTTAGGTTTGATTTCTTTAC R 2 1 2 1 201000 r 74 goat snp25705-scaffold2645-155523 4 21754720 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784492 Affx-122969626 AX-385271541 4 95827371 TCTTAAACACTGATAGCGGAATAAAATGTAAATGC[A/G]TTTGATTAAAAATGGTCACTTTTGGCTTCTTATCC R 2 1 2 1 101000 f 74 goat snp25704-scaffold2645-125671 4 21725087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384040 Affx-122972885 AX-123254398 4 95873892 GTGTTAGTCAGTGTCTTTCTTTAAAAAATTATAAC[A/G]TTAAATTTTGTCAAATTTCTTATGAAAATCACCAC R 2 1 2 1 103000 f 74 goat snp25703-scaffold2645-79150 4 21678567 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765795 Affx-122941386 AX-385253250 4 95915335 AAGGCCTTTGGAGACGCCTTGCCACTCTTCCATCA[C/T]AATTAGAAAACACTGACATTCAGAGCTGATTTAAA Y 2 1 2 1 101000 f 74 goat snp25702-scaffold2645-37707 4 21637181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399560 Affx-122961127 AX-123269915 4 95963819 AATTTCAGTGGGCCCAAGTTTCTTCATATGTGGGG[C/T]GGAGCAGGTGGGGGGAAAGAAAGGTATAGTATCTG Y 2 1 2 1 103000 f 74 goat snp46564-scaffold646-10678 4 21588903 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792379 Affx-122932924 AX-385279360 4 95999868 CCTAGTCATAAACCATCGAGAGCAGTGTTCCATGA[C/T]GTTTCAGGTCAGATCTCAAAATTGTAACCTCTAAC Y 2 1 2 1 101000 f 74 goat snp46565-scaffold646-46727 4 21552791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772208 Affx-122956019 AX-385259363 4 96092685 AACAGTTTGTGTCAGCAAGATAAGTTTTTAAAAGC[C/T]CCAAAGGGACTAAGAGATCATCAGGGATGCTAATG Y 2 1 2 1 101000 r 74 goat snp46567-scaffold646-139544 4 21459493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776198 Affx-122977899 AX-385263326 4 96126083 TGATTGGAAGAGGACACATAAAGAGCAAAAATATC[C/T]TATTTTATCGTGGGACATAAACATGTCAATTTTTA Y 2 1 2 1 101000 f 74 goat snp46568-scaffold646-172942 4 21425582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376475 Affx-122978039 AX-123246834 4 96162823 TTCATCATCGAAGATGAGAAGCTGAGAAAATTCAA[C/T]AGGGGAGATGATGAGACAAGCACTCTCAAACTTCT Y 2 1 2 1 202000 f 74 goat snp46569-scaffold646-209682 4 21388745 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379775 Affx-122975843 AX-123250133 4 96200158 CAATCTTGACATCCACGAGGTGCTCCTTTCAGAGC[A/G]CAGAGACTTCCCAGGGCTTCACCACAACGGCTGCG R 2 1 2 1 101000 f 74 goat snp46570-scaffold646-247017 4 21352048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788567 Affx-122965333 AX-385275584 4 96232359 GCTGTCGATGCTGGCGCAGAACGTTTCTGATTTTC[C/T]CGACATATATGCACAACCAGAGAACATTTATTTTT Y 2 1 2 1 101000 r 74 goat snp46571-scaffold646-279218 4 21319778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411940 Affx-122951152 AX-123282290 4 96268812 GAAAAACCTGGTATGGACAGTGTTTCTGATTTGAA[C/T]GTTCCCTATCCTATCACTGTAGCCCAGGCCCAGGC Y 2 1 2 1 101000 r 74 goat snp46572-scaffold646-315671 4 21282784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429024 Affx-122938324 AX-123299366 4 96316278 ATTTCTGTTACTACAGCCCAAGTAGACTAAGACCA[G/T]CCGGCATGTGTGGAATTCCCTTGTGATCTGATTTA K 2 1 2 1 101000 f 74 goat snp46573-scaffold646-363137 4 21235000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797940 Affx-122951554 AX-385284876 4 96354536 CAAAAATACCCTCGAAAGATGACTGAAAATTATCC[A/G]TGCTCTGAAATATGATTTTCCATGCTCTGAAATAT R 2 1 2 1 101000 r 74 goat snp46574-scaffold646-401395 4 21198187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789490 Affx-122973305 AX-385276499 4 96396661 CTAAAGGCCTTTACTACCACTATCTTGAATAATAA[C/T]GACAATGATTAGAAGTAGTAGTAGCTTATATTAAG Y 2 1 2 1 201000 r 74 goat snp46575-scaffold646-443520 4 21156079 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272290 Affx-1111833446 AX-519546029 4 96422352 CACTGTCACCTGCAGAAAAACTTAGGGTGTGCCTA[A/C]ATGTGGAGAAGCACGAAAGGTGGAGGATTAAGGAA M 2 1 2 1 201000 f 74 goat 4_96422352_AF-PAKI 4 96422352 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389109 Affx-122968568 AX-123259467 4 96433592 CATAAGACAGTAAAACTGCAGAACACTAAAGGAAA[C/T]AAGAATCTCAAAAGCAAACACTGAAAAAGAACCCT Y 2 1 2 1 101000 f 74 goat snp46576-scaffold646-480451 4 21119083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785479 Affx-122940457 AX-385272524 4 96474296 ACAGATCTAAGAAATAATATAGATCTATGAACATA[A/G]CAGATCTATGAACTAGATCTCCATCATTTACAAGG R 2 1 2 1 101000 r 74 goat snp46577-scaffold646-521155 4 21077666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403426 Affx-122957746 AX-123273779 4 96502919 AAATGCTACTTCCCTCTGAAATACCAGTTGTCTGT[A/C]TGTTAGATATTTTCTTCTCAGCATTGTTTATAATA M 2 1 2 1 101000 f 74 goat snp46578-scaffold646-549778 4 21048442 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427675 Affx-122939310 AX-123298018 4 96555332 GCTCGAATGATTCACATGAGTATGCAGATGGGGAA[C/T]GATCCCCCCATTTCGCTTAGAAGGGATCTGGAACA Y 2 1 2 1 101000 f 74 goat snp46579-scaffold646-602191 4 20995828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388001 Affx-122969575 AX-123258359 4 96592674 CTTGTTTTAGTTTCTGTTTCCTCCTGCTTAAGAAT[A/G]CCACGAATGTCGCAATAGGAGAAGCACTAAAATCT R 2 1 2 1 101000 f 74 goat snp46580-scaffold646-639533 4 20958056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382138 Affx-122974051 AX-123252496 4 96666888 GCTGGCGTGAGAGTAGACCGGATGAAAAAGACATC[A/G]TAAATCCTAGAAGGGCTGAAGCTGGGTGGCGAGAG R 2 1 2 1 101000 f 74 goat snp46582-scaffold646-713747 4 20883952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392586 Affx-122966063 AX-123262943 4 96730862 CATTTATTTCATTTTTGTTCCTGAAAGGAACTACC[A/G]CTGGATATACATTCTAAGTTGACATTCTAAGACTC R 2 1 2 1 101000 r 74 goat snp46583-scaffold646-777721 4 20820156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402855 Affx-122958245 AX-123273208 4 96761639 CACTTGGAACTGAAAGTGAGTCTCTCAACCTTCCC[A/G]TCCCTCAGTGACCAGTCTCTAGAGGGCAAGGCAAC R 2 1 2 1 101000 f 74 goat snp46584-scaffold646-808498 4 20789353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405782 Affx-122955915 AX-123276134 4 96806678 CTGAAATGTCATTAGTGCTAAGGATGAGAAATCCC[A/G]CCTTAAATTAGGAACAAATTTGGTTCATTTGAGGA R 2 1 2 1 101000 f 74 goat snp46585-scaffold646-853537 4 20744163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778855 Affx-122946161 AX-385265963 4 96868758 TTGCCTGATTACCCACGTGTTTGCCTCCATTAGTC[A/G]TCCGGTTTAAACCTGGCTGACCAGTACTGCTCGTC R 2 1 2 1 101000 f 74 goat snp46586-scaffold646-915617 4 20681473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404820 Affx-122956646 AX-123275172 4 96920869 TTATCTGAATTATGTCCACAGTCTTAAAAGGAAAG[C/T]AAACTGAACTCCAGTTTAAGCAACATATTCTAAGG Y 2 1 2 1 101000 f 74 goat snp46587-scaffold646-967728 4 20628470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383407 Affx-122973492 AX-123253765 4 96950142 CTTAAGCCACACACAGTTTTTCAAACTCAAATCCA[C/T]TGACTTGTTAGTCAAGCCAAAAGCCCATAAGTCTT Y 2 1 2 1 201000 r 74 goat snp46588-scaffold646-997001 4 20599458 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398091 Affx-122961720 AX-123268446 4 97012821 CTACTGTGCTTGAGTTGTCCTTTGACACTTTGAGG[C/T]GAGTGACATCCTGCTGTGCCACACTCCACCCCTTG Y 2 1 2 1 101000 f 74 goat snp46589-scaffold646-1059680 4 20536451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401074 Affx-122959638 AX-123271427 4 97045327 TCACTTTGTTCACAATTTGGCCTAGGCTTATTCCC[A/G]CCCATACTAAGTTAAATGAGCTCAGACATCTACCA R 2 1 2 1 101000 f 74 goat snp46590-scaffold646-1092186 4 20503743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400744 Affx-122959898 AX-123271099 4 97103754 TGATATGATGCCATCATAATTATGTATTTGTTTGC[A/G]TCTCACCACTAGGCTGCATATCTTTGAAGACAAGA R 2 1 2 1 101000 r 74 goat snp46591-scaffold646-1150613 4 20445788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396117 Affx-122963411 AX-123266472 4 97166331 TTCCTTTCAGTTTCCTGTCTCCCTCTCTCAGATGC[A/G]TCTCAGGACTTAAAGATTTACTGGGCATTATTCTT R 2 1 2 1 201000 r 74 goat snp46592-scaffold646-1213190 4 20382775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392459 Affx-122966159 AX-123262816 4 97210352 CTTTTATGATTCCAGCAATTAACTTTCTGCTTGCC[A/G]ATATCTTCATTCATTCTTTATTTTCATAAACTAAC R 2 1 2 1 101000 f 74 goat snp46593-scaffold646-1257211 4 20337886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407031 Affx-122954944 AX-123277382 4 97242285 TCTGATGTCCAAAGTCACACCAACATGGTTGTACC[A/G]CTCATTTGGCTAAATGTCCAGCAATCTGGAAGGAG R 2 1 2 1 201000 r 74 goat snp46594-scaffold646-1289144 4 20306017 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424410 Affx-122941812 AX-123294756 4 97310049 ACCTTTGAAGCTCTGGCTGTGAGGCTGAGGGAGCT[A/G]AGAAGGCATGGTGGAATCCAGGCCAGATGGAGGAC R 2 1 2 1 202000 f 74 goat snp46595-scaffold646-1356908 4 20237739 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418664 Affx-122946319 AX-123289012 4 97362793 CTTCTGTAGATTTTCTGAAAACTGCTTTTGCTCCT[A/G]TGAAGGGGGAAGGAATAGAGGAAATGGAGGAAGAT R 2 1 2 1 103000 f 74 goat snp46596-scaffold646-1409652 4 20185111 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450234 Affx-122922266 AX-123320569 4 97392417 TAGCATTCAAAAGCAGCTTAATGAACAGAAATATC[A/G]ATTAGGGACTGGATTCTGTGGCCAGAAATGAGAAC R 2 1 2 1 201000 f 74 goat snp46597-scaffold646-1439276 4 20155332 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421975 Affx-122943800 AX-123292322 4 97422548 CCCATTTATAGTCACTAGTGGAAAAATAAAACACT[C/T]ACTCCTCTGGCATAAAAATTTAAGTTTACTAAAGT Y 2 1 2 1 101000 r 74 goat snp46598-scaffold646-1469407 4 20125245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798164 Affx-122923935 AX-385285100 4 97478466 TGAGATTTGCATCAAGATATTTAATATTTACAACT[C/T]AAGAGGTTTGAGTAAATGTTATAAATGAAGCAAGG Y 2 1 2 1 201000 f 74 goat snp46599-scaffold646-1525325 4 20069618 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792494 Affx-122930078 AX-385279475 4 97551913 ATTAAGCACAGCACATATAGTGTAATGAGAAAATC[A/G]CAGTGCTAGTTATCAAAAAATCCAGGCTCCATCCA R 2 1 2 1 101000 r 74 goat snp46600-scaffold646-1598772 4 19993583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396205 Affx-122963361 AX-123266560 4 97599432 GAGAGGAGCTACCCCGGGCTGGAGAGAGACAGATA[A/G]AAATATAGAAACTGTGTTCTTTTCTTCTCTTTCAG R 2 1 2 1 101000 r 74 goat snp46601-scaffold646-1646291 4 19946199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401552 Affx-122958902 AX-123271905 4 97628159 CAACTGTAACATAATGAAGGAAATACTAAGTTTGG[C/T]TCTAAAACAAACTGAAAAATCTTCTGGGTCAATTC Y 2 1 2 1 103000 r 74 goat snp46602-scaffold646-1675018 4 19917402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439379 Affx-122930267 AX-123309716 4 97644567 TTATATATATCATGATAAAACAAAAAACAATAAAA[A/G]CAAAAAGAAGGTATTAAAAGCAGGCAAAGAGAAAT R 2 1 2 1 103000 r 74 goat snp10499-scaffold1375-13515 4 19884935 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451878 Affx-122921055 AX-123322211 4 97693363 TCCCTAGTGCTGCTGTGCTTTGTAAAACTGGCAGC[A/G]AAGATGCTATTTATATCTTTAATAAAACATTTAGA R 2 1 2 1 101000 f 74 goat snp10500-scaffold1375-62311 4 19835759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401600 Affx-122958867 AX-123271953 4 97731310 GTTCTGCATTCTTGTTTCCTTTTTAGGTATCATCT[A/G]TATATCCCTTCTCACCTGCCAGCATCTCTCTTTGG R 2 1 2 1 101000 r 74 goat snp10501-scaffold1375-100258 4 19797621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782720 Affx-122952222 AX-385269792 4 97783464 CAAAGGGCTGCTATGAGGATGAAATACAGAAGTAT[A/G]TGGATGTATTTCTTAAGGGAGTAAAGCACTGTTAA R 2 1 2 1 101000 f 74 goat snp10502-scaffold1375-152412 4 19745116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426635 Affx-122939950 AX-123296981 4 97830383 AAAATATTTATTGGAATATCAAGGAAATTTCAACT[A/G]TTTCAATTCAGAGGTCCCATCAGTCAGTTTATTGA R 2 1 2 1 101000 r 74 goat snp10503-scaffold1375-199331 4 19698124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278283 Affx-1111836264 AX-519551770 4 97859714 GAGAAGTTGTCTACTAATCACTTCCCAAGCTTTCT[A/G]TTGTAAAAATTATGCTACATGAAGATATTGGAGGG R 2 1 2 1 201000 r 74 goat Random2.2K-473 4 97859714 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446116 Affx-122925787 AX-123316453 4 97886090 CTAAAGATTTGAGAACTTTTCAGACTGTACTTTGC[A/G]GACCAGTCAATATCTCATCAATCCAGCAGATCCTT R 2 1 2 1 101000 r 74 goat snp10504-scaffold1375-255038 4 19642414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802552 Affx-122965195 AX-385289456 4 97920312 AGAAGGACATCTGACCTTAACTCTGAAGGACAGTA[C/T]GGTAACAACCAAAGTAGGTCTTGACACAGTTCTAT Y 2 1 2 1 101000 f 74 goat snp10505-scaffold1375-289260 4 19606878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404235 Affx-122957646 AX-123274587 4 97952854 TTTGGAGTTGGTGGAGACTCCTCCAAGTCATCCTC[A/G]CTTGGAGGCACAGGATGAGGAAGTCCTCACTCATC R 2 1 2 1 202000 r 74 goat snp10506-scaffold1375-321802 4 19574265 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425938 Affx-122941192 AX-123296284 4 97981683 ACAAGACTTCCTGACTAAACTCTGCCACCTTGTTT[A/G]CTTCTTTGAAAGTTAATCAGACATTTCCTTATTAT R 2 1 2 1 201000 r 74 goat snp10507-scaffold1375-350631 4 19545168 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782186 Affx-122977061 AX-385269264 4 98074997 TAATCTGTTCCTCATCACATTTTTATTGGGAGGGT[A/G]TTAAAATAGCATGTATGAGTGAAAAGCCAAGCAAA R 2 1 2 1 101000 f 74 goat snp10509-scaffold1375-443945 4 19451961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428298 Affx-122939382 AX-123298641 4 98133947 GGTAATTTGACATTCCTATGCTCTTCCCTTCCCCC[A/G]TCTTCCCTTGCAGTACACTAAGTTTGGTCTCATCC R 2 1 2 1 101000 r 74 goat snp10510-scaffold1375-502895 4 19393677 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434823 Affx-122934801 AX-123305164 4 98167616 GCTGGACTCCTGAGCTAGGGAGCCTCACATGGGGC[A/G]CAGAGCTCTCATTCCTGTGGGAAAACTTCTACAGT R 2 1 2 1 101000 r 74 goat snp10511-scaffold1375-536564 4 19359977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795827 Affx-122927715 AX-385282780 4 98283003 AAAATCTATGGCTAGCAGTGCCAATCCTTAAAGGG[C/T]AGAAATCAACTCTAGTCTAGTCTTTAAAAACACTT Y 2 1 2 1 101000 f 74 goat snp10513-scaffold1375-651951 4 19244774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424463 Affx-122941773 AX-123294809 4 98321156 ATTTGATCTACATCATCACCACTATGGAATCGCAC[A/G]TGTCTTCGATAAATTAGTAGGACACAATCCCACTT R 2 1 2 1 101000 r 74 goat snp10514-scaffold1375-690104 4 19205109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765660 Affx-122920978 AX-385253127 4 98407007 TCCAAACCTCTAATTTAAAAGTTCTGCTTTATCAC[A/G]TGCTTGCTATAAATTTAGGAATAACACTCTATCCT R 2 1 2 1 101000 f 74 goat snp10516-scaffold1375-775955 4 19118964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405403 Affx-122956290 AX-123275755 4 98457293 ACCACTGTAGAAACTGAGTAATTGTCTCTGTGAAT[A/C]TGATTTGAGATGTCAAGTATCCATCTATTTAGAGG M 2 1 2 1 101000 r 74 goat snp10517-scaffold1375-826241 4 19068575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795765 Affx-122941026 AX-385282718 4 98491488 TAACTAAAAATTGTTTCACTGTATATTGTCTACTG[C/T]ATCCAAGTTATTTATTCCTCTCCATTCTGACTTAT Y 2 1 2 1 101000 r 74 goat snp10518-scaffold1375-860436 4 19034400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408337 Affx-122953751 AX-123278688 4 98533465 CGAGATTTCTGGTCCAGTGGTTTTGAGGAAGGGTG[C/T]GGGGGTGGGGAGGCATAAATGTATATTTCCAATAA Y 2 1 2 1 201000 f 74 goat snp10519-scaffold1375-902413 4 18992274 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398278 Affx-122962170 AX-123268633 4 98567235 ACATATGTGAAAGTCAGCCTACCACAGGCACACTA[C/T]TCTATACATAAATATCAGAGGTAGTACTCATTCCA Y 2 1 2 1 101000 r 74 goat snp10520-scaffold1375-936183 4 18958145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391351 Affx-122967295 AX-123261708 4 98600410 TTTCTAGCCTAATAGGAAAATGAAGCAAACTCCAG[A/G]AAATAAATATTTTCAACAGTGATATAATCAGGCTT R 2 1 2 1 303000 r 74 goat snp10521-scaffold1375-969358 4 18926519 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387356 Affx-122970478 AX-123257714 4 98635562 TGATATTGTTGGAAAAAAAGGAAGCAATGGAGCAC[A/G]GACTTTGGACTTCTCTCTCTCCCTGGATGTGTAAG R 2 1 2 1 101000 r 74 goat snp10522-scaffold1375-1004510 4 18891214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778051 Affx-122971411 AX-385265167 4 98679445 AGTTCAAACACTTTGAAATTAGTCCATTTTTATAG[C/T]GATTTTGAACAAATTCAACTTCAAAGAAACATAAA Y 2 1 2 1 101000 f 74 goat snp10523-scaffold1375-1048393 4 18847338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425078 Affx-122941250 AX-123295424 4 98771364 AAACCACCCCAAAGAGAAGTGGCTTAAAATAGCCA[C/T]GATTTGTTGTTTCTCACTATGCTATGGGTTGGCTG Y 2 1 2 1 101000 r 74 goat snp10525-scaffold1375-1140312 4 18754454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449083 Affx-122923604 AX-123319418 4 98816325 ATAGGAAGGATTCGAGACCCTGGATGCAGGGAAAA[C/T]GTGAGAATGGCAAGAGAGGTCTCAGTCAGCCAGAG Y 2 1 2 1 201000 f 74 goat snp10526-scaffold1375-1185273 4 18709467 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421052 Affx-122944520 AX-123291399 4 98844414 CATTCACTGAAAGAACAAATAAATCTTTGAGTGAA[C/T]GCATAATCAGGCCACACTTTTTCCACTTAGAGGTC Y 2 1 2 1 101000 r 74 goat snp2022-scaffold106-12019 4 18681683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399785 Affx-122960295 AX-123270140 4 98878202 TTATATCTGCAAAAGTTTTATTTCCAAATAAGATC[A/G]CACAGTGAGGGCTTGGGTGAGCATGAGCTTTTGGG R 2 1 2 1 103000 r 74 goat snp2023-scaffold106-45807 4 18647831 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420950 Affx-122944981 AX-123291297 4 98922669 GAGCAGGAGCTAGAAACAAAGTAAGAAATTATTTG[C/T]GAATACTACAAAAGAATTTTAGTTATCTGGAGCTA Y 2 1 2 1 102000 f 74 goat snp2024-scaffold106-90274 4 18603009 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799549 Affx-122970397 AX-385286479 4 98952855 GATCAATATTCCTAAAAGATAGATCAGCAAATAGA[A/C]ACTATTTCCATGTGAGAGTCTCCTCCTTTGTTACC M 2 1 2 1 101000 r 74 goat snp2025-scaffold106-120460 4 18572955 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278285 Affx-1111836265 AX-519551772 4 98968111 ATAACTTATAGAATTTTTGATCCTGATCCACACTT[C/G]CCTTCCCCACAATATCATGCTTGGTTAAAAATATA S 4 1 2 1 101000 r 74 goat Random2.2K-477 4 98968111 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272291 Affx-1111833447 AX-519546030 4 98973553 TTGAGGTTGGTGAAAAGTCATTTAGTGTCAAGCCA[A/C]TGGGATGGACTCCTTGGCCTGGGTCAGTCACCTGT M 2 1 2 1 101000 f 74 goat 4_98973553_AF-PAKI 4 98973553 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320775935 Affx-122923926 AX-385263066 4 98989270 ATACTCAGCTTATTCTCAAGGAGACAAAAGAAAGC[A/G]TTGCTTTCCTTTATTACACCGGAATGGACTTTCAT R 2 1 2 1 303000 f 74 goat snp2026-scaffold106-156875 4 18534197 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765238 Affx-122961018 AX-385252775 4 99050114 ACTTGAGTTGTGTTCTGATTGTTTACAAAATGAAG[A/G]AGGCTTAATAGGCAAAAACTGCCAAGTTAGTATGT R 2 1 2 1 101000 f 74 goat snp2027-scaffold106-217719 4 18472671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797983 Affx-122970665 AX-385284919 4 99104793 TCACTTGCCCACATTCGCATAACTATAATAGTTAG[C/T]GGTGGAAGTGGTATTTGAATGACATATATCAGTCT Y 2 1 2 1 201000 r 74 goat snp2028-scaffold106-272398 4 18419865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452287 Affx-122920692 AX-123322620 4 99168427 TTATACAACCAAGGGACCATGGGGGAACAGATGCA[A/G]TATACATACAAAATACTCTCATTTGAAAAGGGAAT R 2 1 2 1 201000 r 74 goat snp2029-scaffold106-336032 4 18355680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380240 Affx-122975464 AX-123250598 4 99220213 CTCTTGATAATGATTGATACTTATGTGAAAGAAGG[A/G]AAATATTCTCAGGGGATGATGTATGATTGGACCTC R 2 1 2 1 201000 f 74 goat snp2030-scaffold106-387818 4 18303193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278287 Affx-1111836266 AX-519551774 4 99261900 GTAAAGAGTTGAGGATGACTTAGTGATCAAACAAC[A/G]ACATAGGGCTGAATACGTCGTACACTCTGTCCATT R 2 1 2 1 201000 r 74 goat Random2.2K-479 4 99261900 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416009 Affx-122948385 AX-123286358 4 99293666 GGACTGCTCATATTTGATGATGTCTTCAGTGTTTT[A/G]TAGAGGGATAGATACTTGTTGTTCTTGACACCTGA R 2 1 2 1 101000 r 74 goat snp2031-scaffold106-461271 4 18226138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784807 Affx-122952402 AX-385271854 4 99335818 ACTTGCATCTTTGGTTATATACATAGATTTATAAT[A/G]TAGCTTTAGGAGGGCTAGATGACTGCTGGCATCAC R 2 1 2 1 101000 r 74 goat snp2032-scaffold106-503423 4 18184231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429103 Affx-122938260 AX-123299445 4 99384670 AAAATAGGCCCCCTTAATATATATTATCTCATTTC[A/G]TCTTTACAAAATCCTATGAGAATGGTAGAATTATT R 2 1 2 1 201000 r 74 goat snp2033-scaffold106-552275 4 18135377 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382127 Affx-122974057 AX-123252485 4 99416680 AGGAGGTAAAAGTGAAATGGGTTGTTGTTCAGTCG[A/C]TCAGTCATGACTCTCTGTGACCCCATGGACTGCAG M 2 1 2 1 101000 f 74 goat snp2034-scaffold106-584285 4 18103371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406495 Affx-122955155 AX-123276847 4 99454734 GTTTCACAAGCGGGAATAATTAGGGGAAACACTCC[A/G]CAAAGCAAAGTGAGAACACCTTACCAAATGAAAAC R 2 1 2 1 101000 f 74 goat snp2035-scaffold106-622339 4 18065250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275321 Affx-1111834833 AX-519548896 4 99458637 TCACCCTTGTCCCAGCCCAGTGTTGTAGAATGCCT[A/C]CCCACTGCAGATGTGGCTGAGAGAAACAG M 2 1 2 1 101000 f 74 goat GoatD01.055812 4 99458637 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382896 Affx-122973411 AX-123253254 4 99484332 TTTAATGTGTTTGTTTTAACTGATTAGGTAGCTCC[A/G]TGGGTCATAAACACCCTACAAACTTCCCTTCTCTT R 2 1 2 1 101000 r 74 goat snp10825-scaffold1386-14123 4 18025129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396989 Affx-122963150 AX-123267344 4 99535200 CTTAAGACAGTTCTATGGTGACAGACCGGAGAAGG[C/T]GATGGCACCCCACTCCAATACTCTCGCCTGGAAAA Y 2 1 2 1 101000 f 74 goat snp10826-scaffold1386-64991 4 17974057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408381 Affx-122953722 AX-123278732 4 99583790 CCAAGTTCCACCTCCAGAACTAATCACACTTTTCA[G/T]ACTTGGGCAAGAATGGTGAAGGAACCAGGAATTCC K 2 1 2 1 201000 r 74 goat snp10827-scaffold1386-113581 4 17925525 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769288 Affx-122979111 AX-385256460 4 99612951 TTCTAAGCATGTTTAAGTTATGTTAGATATGCCCA[A/G]ATACAACCAGTGATCTGGTTTTCTGCTAGATTAAA R 2 1 2 1 101000 r 74 goat snp10828-scaffold1386-142742 4 17896446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436544 Affx-122932923 AX-123306882 4 99671642 GGCCAGGGCTGAGAAAACTCCAGGTTTGTGGAACC[A/G]GGAACAGAGGGCTGCAGTGACTGAGAACTGATTGC R 2 1 2 1 101000 r 74 goat snp10829-scaffold1386-201433 4 17837609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422616 Affx-122943719 AX-123292962 4 99703700 CTCATCTGAAAAATGGAGTTAATAGTTGTAGCTGA[C/T]AGAGTTGTTCCAGGACAAAATAATACTATTAATCC Y 2 1 2 1 101000 r 74 goat snp10830-scaffold1386-233491 4 17805523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438962 Affx-122930396 AX-123309299 4 99760571 GAATGTCTCACTAGACATTCGTGTATGACCTACAG[C/T]TCGCCTGCAAGAATATAGTACTTCCTTATTTTCTC Y 2 1 2 1 101000 f 74 goat snp10831-scaffold1386-290362 4 17748532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415578 Affx-122948630 AX-123285927 4 99811253 ATCTTTTCCCCTTCGATGGGGACTCCCTTAAGCCC[A/G]CAGAGTTGGTATAAAAGAAAAAAGTGAAAGTGAAA R 2 1 2 1 103000 f 74 goat snp10832-scaffold1386-341044 4 17697597 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451818 Affx-122921478 AX-123322151 4 99840878 AAAAACCAAGAAAGAAAAGCTCTACTCTTCAAAGC[A/G]TATTGGATCTTAGCAACTTTATCTTTAAAGACAGA R 2 1 2 1 101000 r 74 goat snp10833-scaffold1386-370669 4 17667587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452571 Affx-122920514 AX-123322904 4 99876300 CGATTTACTTTTAAATGAGCTCTCATTGATCTTGA[C/T]GCTCCAGCTTCTCCCTGCCATTTTTCTGTCTCCTG Y 2 1 2 1 201000 f 74 goat snp10834-scaffold1386-406091 4 17631720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426852 Affx-122940494 AX-123297197 4 99971478 AACGCGGCCACAGGCCGACCCTATCGCGACACCGC[A/G]GCCTATCGGTACCTCGTCAAAGCTTTCCGTGCACA R 2 1 2 1 101000 r 74 goat snp10836-scaffold1386-501269 4 17536895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445232 Affx-122925496 AX-123315569 4 100004169 AATGCATAAAGCTCACTTAATTTGTATTCTACATC[G/T]AGTGATGTTAGTTTATCTTAAAGTATTATTTTTAA K 2 1 2 1 101000 f 74 goat snp10837-scaffold1386-533960 4 17504192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432070 Affx-122935884 AX-123302411 4 100047859 GTTGTAGCTGCTTCCCATGAACCTTCCCCATCTGA[C/T]GGTCTAGAGACTAGAGACCAGGCTTTTCAAAATTT Y 2 1 2 1 201000 r 74 goat snp10838-scaffold1386-577650 4 17460449 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411321 Affx-122952279 AX-123281671 4 100129736 TGCTATCAACAGAGTTCACAAGGAAAAAGCAAGTG[C/T]ATTAAGAACCACCACCAGTTCCCTGGTCCCAGGTG Y 2 1 2 1 101000 f 74 goat snp10839-scaffold1386-659527 4 17378571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392553 Affx-122966087 AX-123262910 4 100166693 TCTCCTTGAAGTTTTCTTTCTCTAACATTTCTTAC[A/G]CACCTACCTTGCAGAGGACTGGTGTTGCTTATTCT R 2 1 2 1 101000 f 74 goat snp10840-scaffold1386-696484 4 17342069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404298 Affx-122957030 AX-123274650 4 100209478 CCGAGGGATGGAGGCCACCGGGGACAGCCAGGGAC[A/G]TCACCATGACAGACCTACAGCACACTGCAGATGAG R 2 1 2 1 101000 r 74 goat snp10841-scaffold1386-739269 4 17299547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381209 Affx-122974526 AX-123251567 4 100257942 GTCACTGTCCTTCACTTTTAGAGGACAAGTCCATG[A/C]ACTGCACATGGCACAGCACATGTAAAGACTCTGGG M 2 1 2 1 101000 f 74 goat snp10842-scaffold1386-787733 4 17251342 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432159 Affx-122936418 AX-123302500 4 100295814 CCACCTTCTTGATTTCGCAGGAAAGCCCACTCTAC[C/T]CTCAGAAAGTGTGTCATCTACTTGGAAGGGTGAAA Y 2 1 2 1 101000 r 74 goat snp10843-scaffold1386-825605 4 17213526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449306 Affx-122923005 AX-123319641 4 100338953 AACTTGGTGTAACTTATTTTGTACAGTCCTCCCCA[C/T]GGCCCCTGGGGTGGGATTAGATTAGAGATAAAATG Y 2 1 2 1 201000 f 74 goat snp10844-scaffold1386-868744 4 17170731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378337 Affx-122976841 AX-123248696 4 100388511 TCTCAGTGTGGCTTATCTTGCCTCGAAACCAGCCA[C/T]GTGCAAACCCAGGAGCAAGTGGTATGCTCCCTCCC Y 2 1 2 1 101000 f 74 goat snp10845-scaffold1386-918302 4 17121336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414423 Affx-122949966 AX-123284772 4 100455485 GAACATTAAAGAGATTTGTTTGTTATTCAGTCGCT[A/G]TCATGTCAGACTCTTTTTGTGACCCCACGGACTGG R 2 1 2 1 101000 f 74 goat snp10847-scaffold1386-985276 4 17054400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278128 Affx-1111836267 AX-519551618 4 100493515 AAAACCAAAGACTTTGATGGGGAAAGTGAAAATGA[A/C]AGTCGCTCAGCTGTGTCCGACTCTTTGCAAAGCCC M 2 1 2 1 201000 f 74 goat Random2.2K-480 4 100493515 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770484 Affx-122946998 AX-385257650 4 100539735 TATGTGAGATGGGTCTGTCTCATTCCTTTTAAAGC[A/G]GATATAAATAGATGCCACACACACCCTCCTAATTA R 2 1 2 1 101000 f 74 goat snp10849-scaffold1386-1069526 4 16970263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787544 Affx-122946598 AX-385274568 4 100589050 TGCACAAACAGACACAGATGATGTATTTCATACCC[A/G]TCTCTTGCAGGATTGCTATATGCCTCTTCAATAAG R 2 1 2 1 101000 f 74 goat snp10850-scaffold1386-1118841 4 16920473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476193 Affx-1251763698 AX-586011619 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 4 1 4 1 20000 f 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 539476448 Affx-1251763698 AX-586011849 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 4 1 4 1 20000 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165111 Affx-1251763698 AX-606940523 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165234 Affx-1251763698 AX-606940646 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 f 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165467 Affx-1251763698 AX-606940878 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 320782033 Affx-122956183 AX-385269111 4 100639988 GAGCATGCCAAAGCAAAATGTACAACAACATAGCT[A/G]TATCTCTGGACCACTTTAGGAGTCACAATTATGTT R 2 1 2 1 101000 f 74 goat snp10851-scaffold1386-1169779 4 16869425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405061 Affx-122957421 AX-123275413 4 100696026 CACACCATAGAAGACAAACACAAAGAGCTCTGGCC[A/G]CACATAGGAAGGACATCTAATCTGATGGAGTTAAT R 2 1 2 1 101000 f 74 goat snp10852-scaffold1386-1225817 4 16813517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440557 Affx-122929313 AX-123310894 4 100760486 CATGTATTTCTAGCCTTTTCTGCTAATTGTTTCAA[C/T]AGTTATTTTTATTTGTTTAAGCTACTTAGATGGGG Y 2 1 2 1 101000 f 74 goat snp10853-scaffold1386-1290277 4 16748566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401142 Affx-122959378 AX-123271495 4 100841421 GGGTATCAGATACAAGCTCAAGTGGTATCAATAAA[C/T]AAGCTGAGGGCCACTGTTCCTCTGGACATATATTC Y 2 1 2 1 201000 f 74 goat snp10855-scaffold1386-1371212 4 16667342 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432374 Affx-122935863 AX-123302715 4 100884224 GCAGAAAGCCTGAGGACTTACTGGGGGAGGCGGCC[A/G]GGGTCGGGGGAGAAGTAAGATTTCAGCTCACATGA R 2 1 2 1 101000 r 74 goat snp10856-scaffold1386-1414015 4 16623340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278130 Affx-1111836268 AX-519551620 4 100915908 AAATGGTACTTTATTAGGGGTAGCATATAAGACCC[A/C]AAATATATATCACACCACATTCACTTCTGTGTTGA M 2 1 2 1 101000 f 74 goat Random2.2K-481 4 100915908 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794192 Affx-122925807 AX-385281158 4 100924706 TTCCAAGCTGCTAAGTTTCAGGGTAATTTCTTTAA[C/T]ATCAACAGAAAACTAATACTCCTAGGTATTTTGTA Y 2 1 2 1 101000 r 74 goat snp10857-scaffold1386-1454497 4 16582984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423976 Affx-122942128 AX-123294322 4 100962187 TCTGCAGTGGAAGTGCCGAGTCCTAGCCATTGGCC[C/T]GCCAGGGAATCCTGAAAACAAGCCTAATGAGCAGC Y 2 1 2 1 101000 r 74 goat snp57592-scaffold9213-7093 4 16545078 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451063 Affx-122921427 AX-123321397 4 100975736 CCTCCTAAATGGGAGAATGCACGTACACATATGCA[C/T]ACATATGCACGCACAATGGAATATTACTCAGCCAT Y 2 1 2 1 201000 f 74 goat snp18319-scaffold1859-2117 4 16531551 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442086 Affx-122928367 AX-123312423 4 101007312 GTGGGCACAGTTGCCAATGCCCATCTCTAGCCTCC[A/G]CTCTTCTGATCTATTCCCTAAAGGAGCTCGCTGGC R 2 1 2 1 101000 r 74 goat snp18320-scaffold1859-33693 4 16500211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386091 Affx-122971443 AX-123256449 4 101038310 ATATAGGACTTTGGAGTTAAAGGGACCTGGGTTTG[A/G]ACCTTGGTTTCATTTTTTTCACCTTACAACGAGAA R 2 1 2 1 202000 r 74 goat snp18321-scaffold1859-64691 4 16469231 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392934 Affx-122965703 AX-123263291 4 101087061 GAAGGCACAAAGGAATGGGTGTTGGACCTGCTTCC[C/T]CTCGGCCATCTGATTGTCCTTTTTTTCTTTGCTGG Y 2 1 2 1 101000 r 74 goat snp18322-scaffold1859-113442 4 16420556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762303 Affx-986696834 AX-385250485 4 101103731 ATGGAGAGCAACTGGAACTCACATGTATTGTCGAT[C/T]AGATTGCGAAATGGTTGTTGGGCTGCACCCCACAG Y 2 1 2 1 600010 f 74 goat 4_101103731 4 101103731 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320762307 Affx-986696838 AX-385250489 4 101103803 CCTGCAAGCCCTGTACCTGCCCAGCTTCAAGATCA[A/G]AGAAAGAGCTTGGAGTTGGCGGTGACAAGCATCAT R 2 1 2 1 600010 f 74 goat 4_101103803 4 101103803 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320803573 Affx-986696120 AX-385290370 4 101103813 CTGTACCTGCCCAGCTTCAAGATCAGAGAAAGAGC[C/T]TGGAGTTGGCGGTGACAAGCATCATCGGTTTAATC Y 2 1 2 1 600010 r 74 goat 4_101103813 4 101103813 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320762311 Affx-986696842 AX-385250492 4 101103839 AGAAAGAGCTTGGAGTTGGCGGTGACAAGCATCAT[C/T]GGTTTAATCCAGGGATCCCCAATCTTTTTGACAAC Y 2 1 2 1 600010 f 74 goat 4_101103839 4 101103839 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38410837 Affx-122952625 AX-123281187 4 101116125 TTGGTCCAAACCAAAGAGCAATCATAACTAATAAA[C/T]AGAATTCAAAGGGACATATGTCAAACAGTTAATTT Y 2 1 2 1 101000 f 74 goat snp18323-scaffold1859-142506 4 16391453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422771 Affx-122943227 AX-123293117 4 101178484 TCCCCAATCTGTGGTCCAAAAAAACAGCAGAAAAA[C/T]AAACACACTTGAATTTTCTAGATTCGAACACTGCT Y 2 1 2 1 201000 r 74 goat snp18324-scaffold1859-204865 4 16328960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417678 Affx-122946823 AX-123288026 4 101245787 GACATTCATTTTTCTATCATAGCACCCAGCAACCA[G/T]CACAAGGGAGCTCAGTATTTTTAAACTTTAAACAA K 2 1 2 1 101000 f 74 goat snp18325-scaffold1859-272168 4 16261450 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384700 Affx-122972112 AX-123255058 4 101279854 CCCAATTACAGAATGGAATTCGTTAAATCTGGCTT[A/C]TTATTAAAAAATACATTTATGTGACAAGAAGGGGA M 2 1 2 1 103000 f 74 goat snp18326-scaffold1859-306235 4 16227401 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778345 Affx-122928350 AX-385265460 4 101326406 AAAAGAAAATTCCTTTGCTATCAAATAGCTACAGC[C/T]TTGGTGACTCAGCTGAAAAGCCCATTTTAACATGC Y 2 1 2 1 101000 r 74 goat snp18327-scaffold1859-352787 4 16180567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400011 Affx-122960800 AX-123270366 4 101375968 AGAGGGTGGTAGGGTATTTATTCCCTTGAGTCCCT[C/T]CAGCCTGGGTGGCTCTTTTCCCCAGAGCCCTTGGG Y 2 1 2 1 101000 f 74 goat snp18328-scaffold1859-402349 4 16131370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417361 Affx-122947717 AX-123287709 4 101407340 TATGCTTTCTGAAATCTGTTTCTTGCCCTGCTGAC[A/G]TGACTGTGCCCACAGGAAGACGTTTCTGATCACTG R 2 1 2 1 201000 r 74 goat snp18329-scaffold1859-433721 4 16100241 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452141 Affx-122921671 AX-123322474 4 101450733 AAGGGGCTGGGTGCTCTCCTCCTGCAGATGCAGCC[A/G]TCATGGATGTGGATCAGGGCAGGCCTCTGCCTTGC R 2 1 2 1 201000 f 74 goat snp18330-scaffold1859-477114 4 16056885 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447527 Affx-122924059 AX-123317863 4 101484475 AGGACCATCAACCAGAGGGGCCATCTCTTTTCGGA[C/T]AGAACCGGCCTTTTAACTGGGCAAGCAGATTTTGT Y 2 1 2 1 101000 r 74 goat snp18331-scaffold1859-510856 4 16023169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464326288 Affx-1110426179 AX-515800234 4 101494746 ATCTTTAAGTAAACAACAGAGAAAACACTTCTGCA[C/T]CTTGTGTCTTTCTGGTTTCCACTGTGTCTTTTTGT Y 2 1 2 1 101000 r 74 goat 4_101494746_AF-PAKI 4 101494746 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320788274 Affx-122974510 AX-385275292 4 101515320 TACCAGCTTAGCTCGATGGTACCCCTTTATCTTCC[A/G]CTGCTTTCCTTCAATGTGTCTGCCATCATTTCATT R 2 1 2 1 202000 f 74 goat snp18332-scaffold1859-541701 4 15992541 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436927 Affx-122933193 AX-123307265 4 101560316 CCCTCTGAGGATCATGCCGGGTTGATTGTCTATGT[A/C]TATTTTCGTCACTGTACTTCCTACAGGTCCATGCT M 2 1 2 1 101000 r 74 goat snp18333-scaffold1859-586697 4 15947709 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272435 Affx-1111834260 AX-519546161 4 101584647 A[A/G]TTCTGCCTGAAGTTCCTCCTTGGTTACAGCTTTCC R 2 1 2 1 101000 r 74 goat GoatD01.028071 4 101584647 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453942 Affx-122919482 AX-123324275 4 101604174 TGAGATGCACCAGAGGACTGTGAGCGTCCAAGCTG[A/C]AGTCTCCCTTTTCATAAAGATTTCCCGTCCTGTCT M 2 1 2 1 101000 r 74 goat snp18334-scaffold1859-630555 4 15903343 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376277 Affx-122978387 AX-123246636 4 101633193 CCAACAGGAAGTTCCCATCAGGCAGATGGTATTAG[C/T]GCACACGTGTGCCAGAATCCAGCCTTTCAGGGGCA Y 2 1 2 1 101000 f 74 goat snp18335-scaffold1859-659574 4 15874001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401088 Affx-122959626 AX-123271441 4 101699184 AACTTGTGATTTTCTTTTGAATGAAACCTCATACC[A/G]CAAACATTTTACACTGTTAAAAGGGCATCAAGAAT R 2 1 2 1 101000 f 74 goat snp18336-scaffold1859-725565 4 15807543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784302 Affx-122946918 AX-385271353 4 101728660 TTTATAGATTCTCAGATTCTAAGATACAGATAAAG[C/T]GAATTGCATAGCATGTATATCTATATGTATTCTTA Y 2 1 2 1 101000 r 74 goat snp18337-scaffold1859-755041 4 15778117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800209 Affx-122935369 AX-385287132 4 101764972 GAGAATCCTTTTCCATAGACTCTTGTTCTTATGTC[A/G]TGGAAGCAAGCTATGTTTCTTCTCTTTTCTCTTGG R 2 1 2 1 101000 r 74 goat snp18338-scaffold1859-791353 4 15741926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409866 Affx-122952918 AX-123280217 4 101815710 ACATAGAGTCTGACACAACCGAGTGACTAAGCGCA[C/T]GTGCACAGGCATTGTACAGGAAGACCTGCCTAGAT Y 2 1 2 1 201000 r 74 goat snp18339-scaffold1859-842091 4 15690977 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434278 Affx-122934777 AX-123304619 4 101858897 AAAAATGAGAACTTCTACCCATAAACCCTTTTGAT[A/G]TATTTCCCTTTCTAGATAATAGTAATACAATTACT R 2 1 2 1 101000 r 74 goat snp18340-scaffold1859-885278 4 15647883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416951 Affx-122948025 AX-123287299 4 101913007 TTTCTTGTGTGAAGTATTAATACCTTCACCTCTGC[C/T]CTGAATTCCCTCTCCTCCTCCTTTTTCATGGCCCT Y 2 1 2 1 102000 f 74 goat snp18341-scaffold1859-939388 4 15593630 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408720 Affx-122953422 AX-123279071 4 102006392 GATCAATCATTTCTTAGAAAAGGCAAGAACCTCTA[C/T]GGCAGGAGTTCTTAACGTTTTGGGGTCATGAGAAC Y 2 1 2 1 201000 f 74 goat snp18343-scaffold1859-1032773 4 15500675 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430599 Affx-122936985 AX-123300940 4 102088860 TGAAGAAGGGGTGAGTTGAAGAAGGAGGGATCTTA[C/T]AGATTGAATGGTTTAAAAAACAAACTAACTAAGAA Y 2 1 2 1 101000 f 74 goat snp18345-scaffold1859-1115241 4 15417155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390485 Affx-122967593 AX-123260842 4 102140202 AATGTCTTGTTTCAGGGTTTGTCCATGTTCATTCA[C/T]GTGAATGCAAATACAGAGAGATTTGTAACTTCTAA Y 2 1 2 1 101000 f 74 goat snp18346-scaffold1859-1166583 4 15365423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399312 Affx-122960526 AX-123269667 4 102176302 TTGGACACGACCAAGCAACTGAACAACAACAATGG[C/T]AACCCACTACATTTTATGGCAGACACCCTACATGA Y 2 1 2 1 101000 r 74 goat snp18347-scaffold1859-1202683 4 15328973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793206 Affx-122975301 AX-385280184 4 102222572 TTTCCTCAGTCCTTCACCCTCAAAGTGACAAGGTC[A/G]TAGGAGCACTTTGCGATGGAGTGAGATGATGTTGT R 2 1 2 1 101000 f 74 goat snp18348-scaffold1859-1248953 4 15281159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394329 Affx-122964674 AX-123264684 4 102319307 TCTTCATTTGTAAAATAATGTAGCAGGGTGTGTTC[A/G]TTATCTGTTGCTGTGGAAGAAATTATCTCCAAAAT R 2 1 2 1 201000 r 74 goat snp18350-scaffold1859-1345688 4 15183495 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800819 Affx-122967252 AX-385287735 4 102348289 CCATAATTTTTCAAATTTTCACTTCGTAATGCTGA[C/T]GGAAAATATTTATACACCCAGTACCACCTGCTTTC Y 2 1 2 1 101000 r 74 goat snp18351-scaffold1859-1374670 4 15154738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795524 Affx-122926567 AX-385282479 4 102384423 TGTGTGTGCATATATGTGTCTCTAGCAGAAGAAAT[C/T]TGGGAATTCCAAGGTGACTACCAAGAGGTTGGGAA Y 2 1 2 1 101000 f 74 goat snp18352-scaffold1859-1410804 4 15118604 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793887 Affx-122962560 AX-385280856 4 102422710 ATCTTGAGTTTTAAGAAGCTTCTGCATTATAAATA[G/T]ATGTAAATTGTATACATCATATTACTTGAGCATAA K 2 1 2 1 202000 r 74 goat snp18353-scaffold1859-1449091 4 15079594 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411604 Affx-122951603 AX-123281954 4 102458240 TTAGACACTGATGGCTAATTTTCCTGTTTATATGA[C/T]GACATGCCTAATCATAAAGTGAATCCCATGTTTAA Y 2 1 2 1 101000 f 74 goat snp43627-scaffold5842-23144 4 15037521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390097 Affx-122968022 AX-123260454 4 102466642 TTGAGAATTTTTTTAAAAGAAGGGCAACATGATAA[A/G]TTTGTTTCAAATTGCTACAGTTCCTTAAATGACTG R 2 1 2 1 103000 r 74 goat snp5893-scaffold1205-3128185 4 14596647 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398231 Affx-122962208 AX-123268586 4 102700456 CAGGCCCTTTCTAATCCTCAGCTTCCTCATCCTCT[A/G]CGCTATCTGAGTAGCAGACAGTCATTTTCCCTGGT R 2 1 2 1 101000 r 74 goat snp5888-scaffold1205-2894371 4 14369787 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388751 Affx-122968951 AX-123259109 4 102834412 CTTTTCCAACCTGATGAATATGATACAGTTGATGA[C/T]GGAGTAATGTTTGGCAAGGCACTTAATCTCTTACC Y 2 1 2 1 101000 r 74 goat snp5885-scaffold1205-2760415 4 14199311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382994 Affx-122973336 AX-123253352 4 102865342 TATAACACCTGCTGAATGTGACACACGTCAGTATG[C/T]GGCCCAGTAGGTGAGATCACAATCGGGGAAGTGGT Y 2 1 2 1 101000 f 74 goat snp5884-scaffold1205-2729485 4 14167918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404056 Affx-122957156 AX-123274408 4 102902339 CTGACACTTCTCTTAATGTCTGCCCTGATCCCAGC[A/G]CTTCTGTCTTAATGGTAGCTGCTGGAGACTTCTTC R 2 1 2 1 202000 f 74 goat snp5883-scaffold1205-2692488 4 14130929 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426154 Affx-122940603 AX-123296500 4 102937472 TCATTATTTTCTGAATTTATAAATTTGAGTATTCT[A/G]TCCATACCATCACTTCTTCATCCTTAAAGTGGACA R 2 1 2 1 101000 r 74 goat snp5882-scaffold1205-2657355 4 14095775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419554 Affx-122945414 AX-123289902 4 103025975 AGATCCTGAAAACTTCTAGAGAAAGAAAATAAATG[C/T]GAAAACTTACAAAGGACAAAGGCACATGTTGCCTG Y 2 1 2 1 103000 r 74 goat snp5880-scaffold1205-2568852 4 14006753 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390376 Affx-122967667 AX-123260733 4 103166818 AACTCTGCAACCCATCAGCCGTACCCCTGTTCCAA[C/T]AAGGAGCCACTGCTTTAGGGGCCACTGAAAGGTAT Y 2 1 2 1 103000 f 74 goat snp5877-scaffold1205-2428009 4 13865032 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385678 Affx-122971140 AX-123256036 4 103265072 ATGAATGCCTAAGACTGAAAAATCAAAAGTAGCAA[C/T]GCAAACATTTAGTTTAGAGACAAGGACAGAAACAC Y 2 1 2 1 201000 r 74 goat snp5875-scaffold1205-2329755 4 13766317 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422031 Affx-122943623 AX-123292378 4 103392114 CTGCACAGGCCCATGGCGAAGACAGCTGACAATAA[C/T]GAGGTTCCAAGAACCGGTTGAAAGCCTGCTGCAAA Y 2 1 2 1 201000 f 74 goat snp5872-scaffold1205-2202713 4 13637989 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429730 Affx-122937606 AX-123300071 4 103425001 TTCATCCCTAAAGGGTGTGCACAACCCCATCACTC[A/G]CAAAAATAGACCATGATGCCAAATTAAAATTGCTC R 2 1 2 1 201000 r 74 goat snp5871-scaffold1205-2169826 4 13604422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406800 Affx-122955696 AX-123277151 4 103453986 AAACAAAAACATGTTAAATTCAAGTCCAATTATGA[A/G]ATAATGATAACAAAAATTACTCATGGACTGTAAGA R 2 1 2 1 303000 f 74 goat snp5870-scaffold1205-2140841 4 13574787 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790976 Affx-122977577 AX-385277973 4 103498170 AAGTTAGCTTTGTAACCTAGCAAACTGTCAGTTTT[A/C]TTTGCTTGAAAATAATGTGTGGTCTCTAATTATCC M 2 1 2 1 202000 r 74 goat snp5869-scaffold1205-2096657 4 13530128 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771917 Affx-122945586 AX-385259073 4 103542561 TTTCAATTTACACTAGTTTCCAGGACAAGAGGGGA[C/T]GGTAGGTGACAATGAGAGGTAAGTTGATAAACAAT Y 2 1 2 1 101000 f 74 goat snp5868-scaffold1205-2052266 4 13485727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442130 Affx-122928335 AX-123312467 4 103601528 ATGGTCATTTTTTAAAAGGCTATGGATATACTGAA[C/T]ATGAAAATCAAGAAACATATCAAGGAGACTAAATG Y 2 1 2 1 101000 f 74 goat snp5866-scaffold1205-1993299 4 13426009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773378 Affx-122937710 AX-385260520 4 103652377 ATATGAATTTAAAAAACCCAGTGAGCTATGTTATA[C/T]GTTATGCCAGGGTGCAAACTATTCACTTTAATCCT Y 2 1 2 1 101000 r 74 goat snp5865-scaffold1205-1942450 4 13376616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774638 Affx-122956915 AX-385261772 4 103681710 AAAAAGAATCAAATATCTATTCTGAAACAGCAACA[C/T]GTATCATCTTAAATTAAGAAAACATTGGATAGATT Y 2 1 2 1 101000 r 74 goat snp5864-scaffold1205-1913117 4 13347102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386990 Affx-122969951 AX-123257348 4 103736131 CATTGCCCACTCCCTTCAAGTGATGGTTTTAAGAA[C/T]GGATGCTTCTCTACAATCCCCATAAAGGTATACAT Y 2 1 2 1 101000 r 74 goat snp5863-scaffold1205-1858696 4 13292595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412116 Affx-122951107 AX-123282466 4 103781854 CTAATATGGTTGTTGGGTGTATAACTATGTACATG[C/T]GCCCTTGCCAAACCCTCCTCAAACTGATGCAATCT Y 2 1 2 1 201000 f 74 goat snp5862-scaffold1205-1812973 4 13245997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381999 Affx-122974078 AX-123252357 4 103814501 ACGTCAAGATTCTGTCCACATAAAAAACTGTCTGT[A/G]TCTGTGAATATATTTTCCCATCATGAATTAAATGA R 2 1 2 1 101000 f 74 goat snp5861-scaffold1205-1780326 4 13213265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788536 Affx-122945064 AX-385275553 4 103859118 GTAGTACATATGTTTGTAAACTAAGCAGATATTGA[C/T]GGTAGGAATACTGGTGGTGTTCTAGTACCTAGAAT Y 2 1 2 1 101000 r 74 goat snp5860-scaffold1205-1735709 4 13168205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386713 Affx-122970160 AX-123257071 4 103978576 GAAGAGCATCCGCATTGTTTGTTATATTTTTTGCC[A/G]TGCCTGGTCTTACTGTGGCATGTGGAATCTGGTTC R 2 1 2 1 201000 f 74 goat snp5858-scaffold1205-1616251 4 13046480 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272243 Affx-1111833408 AX-519545986 4 103996662 GCCAAGAAGATCAACATATTAACTTTGGAAAGAAT[A/G]CTTGAACATACCTGAAGTTGCTTTTTATTTCTTTA R 2 1 2 1 101000 f 74 goat 4_103996662_AF-PAKI 4 103996662 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274147 Affx-1111834033 AX-519547749 4 104018753 AT[A/G]CTAAGCTCTCAAAAAGAGCACCCAGGGAGACTTGC R 2 1 2 1 101000 r 74 goat GoatD01.015228 4 104018753 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437936 Affx-122931632 AX-123308274 4 104027520 AAAGCTGGAGAGGGACAGGCCTGGAGGGGAGTGAA[G/T]CATAGATAAGGGACCGTGTGAGAGGAGGGAAGTGG K 2 1 2 1 201000 r 74 goat snp5857-scaffold1205-1567307 4 12997189 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389487 Affx-122968318 AX-123259845 4 104077433 CCTATTCATGAAAAAAATTTTCTAGGCCCCAATGG[C/T]CTACACATTCTGCTCTTTTATTTGCACTCCTTAAA Y 2 1 2 1 101000 r 74 goat snp5856-scaffold1205-1517394 4 12947445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386352 Affx-122970862 AX-123256710 4 104117708 TTGTTAGTCTCCAGTGACAAAAACCTTTGCTGATA[C/T]ATTGCCAGTGCCCACAAGACTGGTGACCCATTCAT Y 2 1 2 1 101000 f 74 goat snp5855-scaffold1205-1477119 4 12907167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788418 Affx-122946115 AX-385275436 4 104206249 TGCTTCTTGGATAAGTATTGTCTTTAGAAGTCATC[A/G]TTTAAAATGTCCATATCTTTTGGAGGAGCAAAGAG R 2 1 2 1 201000 r 74 goat snp5853-scaffold1205-1388578 4 12820444 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794930 Affx-122941493 AX-385281890 4 104238365 TGTTTTTGAGGACAGCATCTTCTAGAATTGGTTCT[A/G]TGATTCTAGTTTGTCTGAAATTGAAGATAATAGGA R 2 1 2 1 101000 f 74 goat snp5852-scaffold1205-1356462 4 12788489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443112 Affx-122928096 AX-123313449 4 104306059 CCCCCGTGAGTGCTTATTGTCAGGCCTTTTCTTTC[A/G]CTCATCCTCAGTAACTAGTTCACTCTGAACTTAAT R 2 1 2 1 201000 r 74 goat snp5851-scaffold1205-1288768 4 12720920 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382179 Affx-122974020 AX-123252537 4 104388806 GTTTTATAGTAAGATTACCAAACCTGGATGTACTC[A/G]TTCCTGCTACAGGGAGCTAATGCTCTTAGGAGGAA R 2 1 2 1 101000 f 74 goat snp5849-scaffold1205-1206021 4 12639311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278293 Affx-1111836269 AX-519551780 4 104432452 GTTCCCAGAGTGTGAGAGGAGAGAGTCTGGGAAAC[A/T]GAGGACATTGGTTAAAGTTTCTTTTTTCAAAATTG W 4 1 2 1 202000 r 74 goat Random2.2K-484 4 104432452 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407298 Affx-122955321 AX-123277649 4 104443953 GTAAGTGGCAGAGTCAAGGTTTAGACCTAGGCAGT[A/G]TGTCTGCAGAGCCTGAGGTGTAAGCATTCTGCAGT R 2 1 2 1 101000 f 74 goat snp5848-scaffold1205-1150874 4 12587079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405240 Affx-122956884 AX-123275592 4 104502295 ACATAAAAAGAATAAGTAGTTTCTTTCATTGTTAT[A/G]CATTACCCCCAAAATTGCTACTTTAAGTCACCATT R 2 1 2 1 101000 r 74 goat snp5847-scaffold1205-1092532 4 12534868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395875 Affx-122963999 AX-123266230 4 104544551 TTGATTCTTGAAAAAATAAGATTCAGAAATCACAG[C/T]GGATCACTATGATACTGCTTTTTAGCATACTCCTC Y 2 1 2 1 101000 r 74 goat snp5846-scaffold1205-1050276 4 12492229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450443 Affx-122922963 AX-123320777 4 104577513 TGACTCAGTTTGCAGTCTCTCTTTAGAATAAGAAT[A/G]TTAAGTATCGGATGCTAACAGTCTCCATACACAGA R 2 1 2 1 101000 r 74 goat snp5845-scaffold1205-1017314 4 12459247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434723 Affx-122933929 AX-123305064 4 104609667 CTAAACATTATCCACCCAGGTCTTCGCCTCAGCGT[A/C]TGCTTCTGAGAAAACCTAAATTAAGAAGAAACATT M 2 1 2 1 201000 r 74 goat snp5844-scaffold1205-985160 4 12426601 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391709 Affx-122967509 AX-123262066 4 104680484 GTCCCCATTTTTAAATGTGTAATCAGAATGGATAT[A/G]CTTAGAATCTGGCCAAACTCAGACCATACGGTAAA R 2 1 2 1 101000 r 74 goat snp5843-scaffold1205-914343 4 12355709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393666 Affx-122965276 AX-123264021 4 104718981 ATAATCTCTGAGCTCAGGTCATGGAAAATCTTTTA[G/T]CTTCTACTTTTCTTTTTTACAAGAAAAGTCTTGAG K 2 1 2 1 101000 f 74 goat snp5842-scaffold1205-875846 4 12317467 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432392 Affx-122935851 AX-123302733 4 104749225 CTAACCTCTTCTGTTCTAAATTTTTCTTCTATTAC[A/G]TTCCACACAGTCTTTGTTCCCTCTGTCAGGTCATT R 2 1 2 1 101000 r 74 goat snp5841-scaffold1205-845602 4 12287040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445457 Affx-122925221 AX-123315794 4 104862005 GTTTGGTATTCAATAAAAATTTACCAGGAACGCTA[A/G]AAAGCAAGCAAAAAAATTAATCAGAAACAACCCTG R 2 1 2 1 101000 f 74 goat snp5838-scaffold1205-732822 4 12169815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278134 Affx-1111836270 AX-519551624 4 104914172 TGGAGACCTACCAGGGGGTAGAGTTTGCACCAGTA[A/G]AACAACGGAGGCAAGAACAGAGATGAAATTTTTAT R 2 1 2 1 101000 f 74 goat Random2.2K-486 4 104914172 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439342 Affx-122930292 AX-123309679 4 104940302 CTTGCCCACTAAGTCCTCGTGACATACAATGACTT[A/G]CTTGGTGTTATTAACACACATCCTTACAGTGTTTC R 2 1 2 1 101000 r 74 goat snp5836-scaffold1205-654525 4 12090451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390197 Affx-122967797 AX-123260554 4 104971719 TCCATCAGAAGATGACTTGTGTCTTCATGCTCTTA[C/T]GTTCTTTCTTTAAATATTTTCAAAAATTGCTCTCA Y 2 1 2 1 101000 f 74 goat snp5835-scaffold1205-623108 4 12058855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394569 Affx-122964449 AX-123264924 4 105002508 AAAATTAATGTGACAGAGCTTAATATTGCCAGTTA[C/T]GGTCTTGGCAGAGTCGGCCCTAGAATTCTCATATG Y 2 1 2 1 201000 f 74 goat snp5834-scaffold1205-592319 4 12027779 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378125 Affx-122977134 AX-123248484 4 105039379 CAAAATGTATTTCTCACAGTTCTGAAAGCTGGAAA[G/T]CCAAGATCAAGGTTCAAGAATGACTGGGTTCTGGC K 2 1 2 1 103000 r 74 goat snp5833-scaffold1205-555448 4 11990909 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439132 Affx-122931088 AX-123309469 4 105070450 AATACAGAAGACCACAAAGAAAAGCTAAGGAAATA[C/T]GAGTATAAAGAGAGCTGTAGGAGGCAGCTGAAAGT Y 2 1 2 1 101000 r 74 goat snp5832-scaffold1205-524377 4 11959800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770937 Affx-122971782 AX-385258100 4 105191869 GCTCTTTGATCAAGTACTATTCAATGCTTTTGTTG[A/C]GCCTATGACCACTTTTTAACTTATGACATAAACTC M 2 1 2 1 101000 f 74 goat snp5829-scaffold1205-402958 4 11839760 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793365 Affx-122928113 AX-385280343 4 105224038 TAAGAAAACTCCGAAGGGAAGTTCAATGAGCTCAG[C/T]AACAAAATTGATGAAAAGAGAGAAATCTTTACCAA Y 2 1 2 1 201000 r 74 goat snp5828-scaffold1205-370789 4 11806821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770890 Affx-122951773 AX-385258053 4 105252895 GAAGTGCTTTTAAATCTTTAGAAATGGTAAGTAAC[A/G]TAACCAAGGTTAGTAAAGCTAGTGATAGGGGGAAC R 2 1 2 1 101000 r 74 goat snp5827-scaffold1205-341932 4 11777772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386917 Affx-122970009 AX-123257275 4 105289846 CACATCTGAACACAAGTAATGCAGAATGATACAGA[C/T]GACATTTTATTTTTAAATTCTTTTAAAAGAAACTG Y 2 1 2 1 101000 f 74 goat snp5826-scaffold1205-304981 4 11740460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391508 Affx-122966669 AX-123261865 4 105338786 TTGATACATAGGAAAAGTATATATTTAAGGTGTCC[A/G]TTTCAATTCAGTTCAGTTCAGTCGCTCAGTCCTGT R 2 1 2 1 201000 f 74 goat snp5825-scaffold1205-256041 4 11691150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376127 Affx-122978869 AX-123246486 4 105454372 GTTCTAAATTTTAATCCTAATGATATTGAAATAAA[C/T]GAAATGACTGCTTTCAGTGACTAAAGATGAATTAA Y 2 1 2 1 102000 r 74 goat snp5822-scaffold1205-140455 4 11580449 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438094 Affx-122931513 AX-123308432 4 105495302 AAGAGGCGATAACATTGATCCAAATCACCACCTGG[A/C]TCCTCCAGGGCTGAGGGACTGTGATTACCACAGAA M 2 1 2 1 102000 f 74 goat snp5821-scaffold1205-99525 4 11541870 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794876 Affx-122970370 AX-385281836 4 105535368 AGATGCAACAGATATCTAAACAAGTCATTTGATAC[C/T]GATACTGGTTAGCTGAGCTGTAGACAAGCAAGTTT Y 2 1 2 1 101000 r 74 goat snp5820-scaffold1205-59459 4 11501638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278297 Affx-1111836271 AX-519551783 4 105559823 TTGAGCCTACTCGCTTTTTGGGTCTTCATTTTCTT[A/G]TGGAGACTCTCCTATACATGTAAAACAAAATTTGT R 2 1 2 1 201000 r 74 goat Random2.2K-487 4 105559823 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781900 Affx-122960549 AX-385268981 4 105564423 AGTAAGCTGTGACATCTTCCAAACTATAAACTTTT[A/G]TGACATTTTCTATTTATCAGCATAGTTTGTATGTG R 2 1 2 1 101000 f 74 goat snp5819-scaffold1205-30404 4 11472430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778581 Affx-122957263 AX-385265692 4 105594136 TTTGAGTCTCAAAAAGTGGAATTAACTTTTCCACC[A/G]TCTCTGTGAGGAAGAAAACTTTAAACTTTTGATGG R 2 1 2 1 103000 r 74 goat snp5818-scaffold1205-691 4 11441976 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377733 Affx-122977384 AX-123248092 4 105603072 TTGCTGTTATTGCTTTATTCTGTTGTCTTAGTTTT[A/G]TTATTTCCCCTCATTCTTTGTCTATTATTTCGCTG R 2 1 2 1 101000 r 74 goat snp15287-scaffold1629-829571 4 11432005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429930 Affx-122938094 AX-123300271 4 105634830 TTAGAAGCCCCTTTTCTCCTCAAGATGCTTTTCAT[A/C]TTCCTCACTCACTCTCTTTGAGAGCTATTATCCTC M 2 1 2 1 101000 r 74 goat snp15286-scaffold1629-797813 4 11400072 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422116 Affx-122943561 AX-123292463 4 105670258 ATTTTAAAAAAGATATGCCCACTAAATCTATATGC[A/G]TAGTAGAGAGAAAGAATGACAAAGTCTCTTATTTC R 2 1 2 1 201000 f 74 goat snp15285-scaffold1629-762385 4 11364371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764667 Affx-122953323 AX-385252301 4 105722639 ATCATCTGTCAAAGAAGTCAATATCAAGCTTCTTC[A/G]TTCAAAAATTTTACCATTCTCAGAGATTCAACAAT R 2 1 2 1 101000 f 74 goat snp15284-scaffold1629-710004 4 11311936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769036 Affx-122931740 AX-385256211 4 105754797 ATTATAACCCAGTTTCCTTCCACCTCAACTTATCT[A/G]TCTTCCTGTTTGATGAGAGTAGGCAGAAGAAAAAG R 2 1 2 1 102000 f 74 goat snp15283-scaffold1629-677846 4 11279511 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409361 Affx-122954168 AX-123279712 4 105797490 CTGACGCGTCTGCCAGTCACTCTACAAGCCAGCCC[A/G]CAGGGAAGCCCTTGCTTACAATGAATACACTACAG R 2 1 2 1 201000 f 74 goat snp15282-scaffold1629-635153 4 11236924 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444691 Affx-122926437 AX-123315028 4 105847338 GCAGAAGATTTATCTAGATTCTTCTGTGAGTCAAC[A/G]TCAAGGGGAGTAATAGGTCCAGCTTTCTCATACTT R 2 1 2 1 101000 f 74 goat snp15281-scaffold1629-585305 4 11173393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448304 Affx-122924160 AX-123318640 4 105882800 AATCTTCCTTAATGAAGAATTCCAAATAATAAATG[C/T]AGAAAGAATGGAAGAAATCAAAAATTGCAAATAGC Y 2 1 2 1 103000 r 74 goat snp15280-scaffold1629-549843 4 11137652 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453874 Affx-122919519 AX-123324207 4 105915029 AGTTTGCGCTTTCTGGCAGGAGAGGAGGAAATTTC[A/G]TACCAGGTGAACAGAAAGAGTAAGACTGTCTTCTT R 2 1 2 1 101000 r 74 goat snp15279-scaffold1629-517614 4 11105767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417236 Affx-122947284 AX-123287584 4 105948315 CATCCATTCAACTATTCCCCTCATAAAAAATGACA[C/T]GAGAACCTTGCAATATTTCCAGAATCTTCAACAGT Y 2 1 2 1 101000 r 74 goat snp15278-scaffold1629-484328 4 11070578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476194 Affx-1251763699 AX-586011620 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20000 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 539476449 Affx-1251763699 AX-586011850 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20000 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562165265 Affx-1251763699 AX-606940677 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562165697 Affx-1251763699 AX-606941106 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166020 Affx-1251763699 AX-606941429 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166159 Affx-1251763699 AX-606941567 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166179 Affx-1251763699 AX-606941587 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166557 Affx-1251763699 AX-606941965 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 38398192 Affx-122962642 AX-123268547 4 105983513 TGAAGTTTCCTTTTTTCTTTTGCGAATCCTCTCTT[A/G]CTTTGTCTCCTCAAAAAGACTTATATATTGATAGT R 2 1 2 1 201000 r 74 goat snp15277-scaffold1629-449130 4 11034858 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440350 Affx-122929659 AX-123310687 4 106015385 AGACAGAATGAAGTCACTATACAATGAACTTCAAG[C/T]AGTAGTCTATCCACTCATTGTAATAGAAAAGTGAA Y 2 1 2 1 101000 f 74 goat snp15276-scaffold1629-417258 4 11002647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441824 Affx-122929062 AX-123312161 4 106051094 GAAAAGTCGCCCTAGAGATAAGAGACCCAAAGGAA[C/T]GGATATAAAATAAAATGAGAATGGAAAGTACATAT Y 2 1 2 1 101000 f 74 goat snp15275-scaffold1629-381549 4 10966745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438466 Affx-122931238 AX-123308804 4 106086408 TCAAAACTGGCAGAAAGGCCTTCTGAGGTTTTAAA[G/T]ATCACACCAAGAAGTGATCACATTTTATAAAATTA K 2 1 2 1 102000 f 74 goat snp15274-scaffold1629-346235 4 10931941 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423147 Affx-122942757 AX-123293493 4 106187564 TTTACATGAGCCTTCCACAGCAAGGAATAAATAAA[C/T]AAGGAATAAAAGAATTAGAAAGGTGTTCTTGATTT Y 2 1 2 1 102000 f 74 goat snp15272-scaffold1629-245079 4 10830973 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793212 Affx-122933056 AX-385280190 4 106224878 CTCAGGTCAATCACTGAAACCCATTTATAATCTAA[C/T]TATGAAGCTGTAGGAATGTACCAAGATGGCATTAA Y 2 1 2 1 101000 r 74 goat snp15271-scaffold1629-207765 4 10794232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781330 Affx-122934293 AX-385268415 4 106261548 TGACCAATAAAGCATTGTTCCATAGCTATGCTACA[A/G]AATTGCTTTCCTCAGCATAAGTTCAGTTCAGTTCA R 2 1 2 1 101000 r 74 goat snp15270-scaffold1629-171095 4 10757691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775670 Affx-122965098 AX-385262801 4 106294488 CAATATGAACAGTTTCAGAGGGTCAGATATATTGA[C/T]GCAAGTTATTGTTTTCAGTATATCTTATAACTTCT Y 2 1 2 1 101000 f 74 goat snp15269-scaffold1629-138155 4 10724737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388884 Affx-122968862 AX-123259242 4 106328024 TAATATTCAGCACTGTAATCATGATTTGCTTGTTA[C/T]GATCCCCTGGAGAAGGGAATGGCTACCCACTCCAG Y 2 1 2 1 202000 f 74 goat snp15268-scaffold1629-104619 4 10691369 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768332 Affx-122922529 AX-385255512 4 106370372 TAGAACTAGATTAAAGTTCCTTAGACCATTCATGC[A/G]TTACGGATAAGAAAAATTATTGTTGCTAGTTCTAC R 2 1 2 1 101000 f 74 goat snp15267-scaffold1629-62271 4 10648747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418740 Affx-122946218 AX-123289088 4 106405684 GCAGATGCAGTATGCATTATTTAATTTTCTTTCTC[A/G]TTGGATAAAAGCTGTGATTGTTTGTGCATACAACA R 2 1 2 1 101000 r 74 goat snp15266-scaffold1629-26959 4 10613316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435286 Affx-122934041 AX-123305626 4 106538367 GAATCACTTCCTATCATGTTTCAATGTAACTATCA[G/T]ACTACAAATGCCCCATGATGTCTGGGAATCTTACT K 2 1 2 1 201000 f 74 goat snp16356-scaffold1725-105625 4 10478364 A C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278140 Affx-1111836273 AX-519551630 4 106623206 ATTAGCTCATGGTCCTACCTACAACTATAATCTCC[A/G]TGGGGGGGAAAAAAAATCACAAGACTATCTCTAAT R 2 1 2 1 102000 f 74 goat Random2.2K-491 4 106623206 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381821 Affx-122974268 AX-123252179 4 106640422 GCTATTTGGATTTCCTTACAGGATAAGAGAAGCAA[C/T]AGGGCAAACACTGCTTCTCAAAACAGGAGTTGAAC Y 2 1 2 1 201000 f 74 goat snp16358-scaffold1725-207680 4 10375824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441378 Affx-122928857 AX-123311715 4 106670022 CCTTTTTTTTTTTTTCCTATTTCTTCATCATTAGC[A/G]TAAACCTCAGATACGATCTCTGGATTTTGTTAACA R 2 1 2 1 101000 r 74 goat snp16359-scaffold1725-237280 4 10346324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781400 Affx-122939351 AX-385268485 4 106699188 AGTGTACTAACACAGCAAAGCTTATTAATAAAAAT[A/G]CTTGAAGTCTTATGAAATATCTGAAAAGTAGAAAC R 2 1 2 1 101000 r 74 goat snp16360-scaffold1725-266446 4 10317241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426481 Affx-122940233 AX-123296827 4 106731950 TTCTTCAAGTATCGTATCAATTTCTCGAAGGTATG[A/G]ACCATTTATCAACAGCATTCCTGTCTTCAGCAACC R 2 1 2 1 101000 f 74 goat snp16361-scaffold1725-299208 4 10292998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272245 Affx-1111833409 AX-519545988 4 106747832 GGCTCCTTTGTCATAGATTAATTGATCATACATGT[A/G]TGGATTTATTTCTGGGTTCTCTATTCTGTTCCATT R 2 1 2 1 303000 f 74 goat 4_106747832_AF-PAKI 4 106747832 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438303 Affx-122931366 AX-123308641 4 106772042 CCTCTCTGAGTTATTGTTAGAAACTAAATCATGGA[C/T]GCACTCTGATTTTGCATTCCCTTTTTGACTAGCCA Y 2 1 2 1 101000 f 74 goat snp16362-scaffold1725-339300 4 10253048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417956 Affx-122946701 AX-123288304 4 106810114 AAGTCACAGTTTTCCATAAAAAGCTACTCATCTAT[A/G]TAACTTCATTCTTATCTGCAGATTGTAAATATACT R 2 1 2 1 101000 r 74 goat snp16363-scaffold1725-377372 4 10214409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795935 Affx-122977491 AX-385282887 4 106867607 TGCAATAATTTTAATCTTCACTCTAATTTTTCAGA[C/T]GAAGAAATCAAAGTTTCAAGTTATTATGGAACAGT Y 2 1 2 1 101000 r 74 goat snp16364-scaffold1725-434865 4 10156667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415804 Affx-122948899 AX-123286153 4 106904552 AAGGTTTTATTAAGGTGAGGACATTAATATGTTTC[C/T]AAGAGCTTCTACAAGGTATTAATTATAACTGAAAA Y 2 1 2 1 101000 f 74 goat snp53385-scaffold805-1222667 4 10120115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376370 Affx-122978113 AX-123246729 4 106934883 GTTTGCAAGGTTGAAATTCAGAGGCCTTCACTGAG[C/T]GCTGGGATCAAGCAAGCCAATTCTCTATGAGTCAT Y 2 1 2 1 101000 f 74 goat snp53384-scaffold805-1192336 4 10090238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384673 Affx-122972132 AX-123255031 4 106994037 TTCACATCATTACACAGTGTTTTATTATTTTCTAA[C/T]GCTGAATTTTCCTCTCTTCTAATTTTAGCCTCCAT Y 2 1 2 1 303000 f 74 goat snp53383-scaffold805-1133182 4 10031390 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787089 Affx-122969551 AX-385274116 4 107027902 AAGCCATGATAAAAATGGTGTCTAGGTTAAGTCTG[C/T]TGTCTAAAATGTACCATCTACTCTACTGAATGCAC Y 2 1 2 1 101000 f 74 goat snp53382-scaffold805-1099317 4 9997659 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386571 Affx-122970703 AX-123256929 4 107078257 TGATGGGTCAGAGCCACAGTGAAGTCAGACTTGAA[C/T]AGGCATGAAGTTCTGAATAATGTGAAGTTCATCTG Y 2 1 2 1 201000 r 74 goat snp53381-scaffold805-1048962 4 9947905 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378004 Affx-122977595 AX-123248363 4 107116204 TCCCCAGACTAAGACTATAAAGTTATTGAGAAAAC[A/G]TGCACAAATCCACTATATATTCTATCCCCTTTCTG R 2 1 2 1 101000 f 74 goat snp53380-scaffold805-1011015 4 9908657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782587 Affx-122963607 AX-385269661 4 107153473 CCTCAGGCTTTTTCAAGAACTTAACACACTGAGTC[A/G]CTACTTTCTCCACAATTATCAACTTTTCCCTCTCC R 2 1 2 1 101000 f 74 goat snp53379-scaffold805-973746 4 9869786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788681 Affx-122926868 AX-385275697 4 107196539 CACAGGCATTCTTCTTTGCTCATGCAAAGTTGAGG[A/C]AAACAGGTTATGTTTTCTCCAAAGACAACCAGCAC M 2 1 2 1 201000 r 74 goat snp53378-scaffold805-930680 4 9827024 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448601 Affx-122923391 AX-123318937 4 107241775 AACTCTATTAAGATTTCCCCTTTAAAAATGCTTTC[A/G]CAGCTCTTAAGTGTATACTATTATCTTCCATTTGT R 2 1 2 1 101000 r 74 goat snp53377-scaffold805-885444 4 9779867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389029 Affx-122968630 AX-123259387 4 107277134 TACTTATATTTCTACCTCATTCTCTCCCTTACTCC[A/G]TCTCTCTCCTTTTCTTTCATTCTACATATATATTG R 2 1 2 1 103000 f 74 goat snp53376-scaffold805-850085 4 9744677 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776643 Affx-122961470 AX-385263770 4 107306264 TAGTTGGATTTTGATATGAGTTTGAACTTGGACAC[G/T]AGGTAAATGTCATCTTGGGTCAATGACTGACCATT K 2 1 2 1 101000 r 74 goat snp53375-scaffold805-820955 4 9715553 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278142 Affx-1111836274 AX-519551632 4 107308408 ACACTCATTTAAGAATAACTGGTTGTACTGAAGTG[A/G]CATTTTTTATTTGGCTGCACAGTGACACTGTGTGG R 2 1 2 1 101000 f 74 goat Random2.2K-492 4 107308408 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797734 Affx-122976641 AX-385284673 4 107338606 CTATTAAAATTTTCCAGAACTCCTTTATTTTTTAA[C/T]GTAATAATTGCAGTAGCCTAAAGGAATAGGAGACA Y 2 1 2 1 201000 f 74 goat snp53374-scaffold805-788613 4 9683448 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772717 Affx-122974963 AX-385259863 4 107396998 TTTAACATGATCCCACACTTCAGGGTTATTAGCCT[A/G]CTTGGTGCTCCTCAGCACAAGAAGAAAGGAGATTG R 2 1 2 1 201000 f 74 goat snp53373-scaffold805-730221 4 9629051 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800880 Affx-122954204 AX-385287795 4 107427836 GTCTAGTAGTTGTTTTTGATCATAAAGATGACAAA[C/T]ACTCAAAGAAAATCCAAACATTAGAGAAAAATATA Y 2 1 2 1 202000 r 74 goat snp53372-scaffold805-699383 4 9597852 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435182 Affx-122933648 AX-123305522 4 107466910 TGTGTCAAGTGAAAGCATTTCTGATGTTCCAATTA[C/T]CTTCAAGTTTCTTTAAAATATCTATTCTCATCAAA Y 2 1 2 1 101000 f 74 goat snp53371-scaffold805-660309 4 9558792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419421 Affx-122945517 AX-123289769 4 107555942 ACAGTCAAGCAGCCACTAAACACTGGTGCGACACC[A/G]TCAGATCATTCTGTCAAATTAGACTTCTCTTCTCC R 2 1 2 1 201000 r 74 goat snp53369-scaffold805-571277 4 9469558 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431298 Affx-122937090 AX-123301639 4 107587228 TGAAAGATGGAATGTGGTATACACATACAAAGAAA[C/T]AGTATTCAGACTTAAAGAGAAAGGGGATCCTGATA Y 2 1 2 1 103000 r 74 goat snp53368-scaffold805-539991 4 9438548 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783543 Affx-122973415 AX-385270605 4 107632925 TCAAGCTAGTTAAAGTGAGTGCATATGAAAATAAA[C/T]GTTTTAATATTACCTGATAGAAGTAGCCTCCCCTT Y 2 1 2 1 201000 f 74 goat snp53367-scaffold805-494294 4 9392450 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440855 Affx-122929254 AX-123311192 4 107666795 CAAAAGAATAAAAGTTTTCATTTAGTTAAGATGAA[G/T]AAATGTGCAAAAGCCTTGTTGAGGTTAAAAAGAGT K 2 1 2 1 101000 r 74 goat snp53366-scaffold805-460424 4 9358864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793036 Affx-122976718 AX-385280014 4 107696816 CCATCAAGGGATCTTGTGCTTTGTGTCTAGGCATC[A/G]TTACCATGCATGATAGATGAATTGAGTTTAAGGAA R 2 1 2 1 101000 f 74 goat snp53365-scaffold805-430403 4 9328805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451371 Affx-122921222 AX-123321704 4 107735579 TCATAATGTCCAGATTAATAGAGGCATGTATTATT[A/G]TAACTATTTTACCCAGAACTCCTCTTGAGCTGATT R 2 1 2 1 101000 r 74 goat snp53364-scaffold805-391640 4 9290299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412598 Affx-122951291 AX-123282947 4 107793087 CCCTGTTCCTCCCAAAAGTTCCTTTGAACCTGAAT[A/G]GAGGTGCTATACAAAGATGGACATTTGGTATCTCT R 2 1 2 1 101000 r 74 goat snp53363-scaffold805-334132 4 9232000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774361 Affx-122976645 AX-385261497 4 107842250 TAGTCAATATGAAGAAAAATCTTTTGTCCTGAAAA[C/T]GGTCATGAAATATTATGCAAAGGATGCTAACGCCC Y 2 1 2 1 101000 r 74 goat snp53362-scaffold805-284969 4 9182562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792296 Affx-122968020 AX-385279278 4 107943372 TTGGGGAAAGATATGAGTAGCACAGAAGACTCTGC[G/T]ACAGGCTTCCAATTGACTTAAAGATTCTCCTGAAA K 2 1 2 1 101000 f 74 goat snp53359-scaffold805-183847 4 9082100 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418192 Affx-122947069 AX-123288540 4 108086796 TTAAGGTGATTCACGTTAACTCATTTTTCTTTCCC[A/G]TGTGTCCTGGGCTTGTATTTTATAAACCAGATAGG R 2 1 2 1 101000 r 74 goat snp53356-scaffold805-40423 4 8939735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393612 Affx-122965362 AX-123263968 4 108124660 CACGCCAGCATTTGGGATCTTACTAACAGCCACAG[A/G]TGCTGTAAGCAAGGGAACAAGGCCATCAAACTTCT R 2 1 2 1 101000 r 74 goat snp53355-scaffold805-2559 4 8902856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399218 Affx-122960599 AX-123269573 4 108136378 CTTGAGAGACCATGAACTTGAGCATGGGAAAGCAG[C/T]ATTTGTCATCTCTGCCCATCCACTCTCCTAGTTTA Y 2 1 2 1 101000 r 74 goat snp25283-scaffold2601-9060 4 8891513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419139 Affx-122945754 AX-123289487 4 108167714 ACTCTATCTCCACCCCTGGGTTCCCAGACCCGTTA[C/T]GCCCCCTCCTAGGGACAGTGCAAACATAATGGCTG Y 2 1 2 1 101000 r 74 goat snp25284-scaffold2601-40396 4 8860021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776923 Affx-122963737 AX-385264047 4 108196377 CATTAATAATAAATTTCCCATCAGACCTGTAAGTT[A/G]TAATTCTTTTACCTCTGCCCCGAGGAACTTGTTTA R 2 1 2 1 101000 r 74 goat snp25285-scaffold2601-69059 4 8831602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436485 Affx-122932966 AX-123306823 4 108314666 GCCTGGATGCAAAATATGTTTATTTCGGATTGTTC[A/G]TAGTTAGGTCATCTGTTTAATTTTAGGGTTCTGAC R 2 1 2 1 201000 r 74 goat snp25287-scaffold2601-187348 4 8713692 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382758 Affx-122973590 AX-123253116 4 108402661 GACGCCCTTCTTTAAAAGGCTCTTCATTCCCAAGG[A/C]TCTGCCGCATCAAGTCATTTGCCATCCACTCCCCG M 2 1 2 1 201000 r 74 goat snp25289-scaffold2601-275343 4 8625530 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396050 Affx-122963456 AX-123266405 4 108461114 TCAGAAGATGCCCAGAGATAAATATTAAGGAAATA[C/T]AGTCCAGAAAGCTTCCCTGTGAAGCCCGAAGCCTG Y 2 1 2 1 101000 r 74 goat snp25290-scaffold2601-333796 4 8566741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418213 Affx-122947054 AX-123288561 4 108492048 TTCGTGTCTAACAAACATACGCCACATCCTACCAG[C/T]AACTATTCTGGGGACTTCCCTGGAGGCCCAGTGGT Y 2 1 2 1 101000 f 74 goat snp25291-scaffold2601-364730 4 8535805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785811 Affx-122938746 AX-385272849 4 108522161 GCTGGCAGTTACTCTTGAATTTAACAAGATAACCT[A/G]CAGGTGTGGAAACAGCACTTTTTAAAATATTATTT R 2 1 2 1 201000 r 74 goat snp25292-scaffold2601-394843 4 8505674 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769906 Affx-122949782 AX-385257075 4 108557622 TGAAGGATTAGAACACCCATGGGATATTTTTTATA[C/T]GTATCTCCTAATCCGAGATGGATTAGCAGTCCATC Y 2 1 2 1 201000 f 74 goat snp25293-scaffold2601-430304 4 8470376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799275 Affx-122978847 AX-385286205 4 108589216 TTATAGACTAAAGGGATCAAGAGATACCAAGTTGA[C/T]GAAACATGATCTAGAAGTTTATCATTTAAATTATA Y 2 1 2 1 101000 f 74 goat snp25294-scaffold2601-461898 4 8438501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770766 Affx-122975830 AX-385257930 4 108637875 GAATTACTTGTTGATCAGTCAAACAGTTTCCTGGG[C/T]GTTCCTTAAATGATGCCTCTCTTCATTCAAGAATG Y 2 1 2 1 101000 f 74 goat snp25295-scaffold2601-510557 4 8390136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401241 Affx-122959305 AX-123271594 4 108667854 AAGGTGAAATAAAGGGACAGACTCGAGCTGTGGGC[A/G]CAGATGTTTCAAACTCATGTCTCCCATCCAAGTAC R 2 1 2 1 201000 f 74 goat snp31087-scaffold3433-338560 4 8359252 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436761 Affx-122932280 AX-123307099 4 108706272 CGACCCCATGGACTGCAGCAGCCCAGGGCACCTAA[C/T]AGGGAAGCCCTATTAGGCGCCAAAGTAATGACCAA Y 2 1 2 1 103000 r 74 goat snp31086-scaffold3433-300142 4 8320709 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402627 Affx-122958399 AX-123272980 4 108742729 GGTTTCAGGCGCTCAGCACAAAAACCTCTATTGGT[A/C]CTTCCAGCCTCAGGGCAATGCTCCCCAGCTTACGG M 2 1 2 1 101000 f 74 goat snp31085-scaffold3433-263685 4 8284264 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419325 Affx-122945658 AX-123289673 4 108852619 GGGTAGAAGTTTTAATTTTTGGCAGAGTCGTTAAC[A/G]CCAGTCTTTGCCTTTAAGATCTGTGCTTTTTCTGC R 2 1 2 1 101000 r 74 goat snp31083-scaffold3433-153795 4 8173751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428070 Affx-122939111 AX-123298413 4 108892240 AGTTAAGGATTCTTCCAAAATATCCAACCGTGGGA[C/T]GTGAACTTACTCCTAGATTTCCCCAAAGTGCCCTT Y 2 1 2 1 101000 r 74 goat snp31082-scaffold3433-114174 4 8134004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442655 Affx-122927907 AX-123312992 4 108922857 TCCTGGAAAAAAATCAAGAGGGTGTGGGCCCCCTG[C/T]ACTGGGTCCTACTCACTGATGGGGAGGGGGCTCCC Y 2 1 2 1 101000 f 74 goat snp31081-scaffold3433-83557 4 8103475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383401 Affx-122973496 AX-123253759 4 108966623 TCTGTGTACTGAAAGTTTCATTAAAATTACAATCC[A/G]AAGGTTCTGGGGCTGTGGAATGAATTGGGGATGGA R 2 1 2 1 201000 f 74 goat snp31080-scaffold3433-39791 4 8059287 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797695 Affx-122927696 AX-385284634 4 109051609 ACTTTGGACTCATGTTTCTTCAGACTTTGTGTAAT[A/G]TTTTTTAAATGCTGCACTGAGGGGGTAGAGCAAGC R 2 1 2 1 102000 r 74 goat snp16302-scaffold1718-45096 4 7978490 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453195 Affx-122920453 AX-123323528 4 109081891 GCCAGGTATTTCGGGGGAAATCCAAAGGGCGGAGA[A/G]CTAAGGGACCTTGGCAACTGGATGCTCCTGTGAGG R 2 1 2 1 101000 f 74 goat snp16303-scaffold1718-75378 4 7948436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400930 Affx-122959719 AX-123271283 4 109151936 GTGAACTGAACTCCGTCTTCCAGGCAGAGGAGATC[A/G]TTAGCTCATCCTGAGGTGTCTGTCGTTTGTGATGA R 2 1 2 1 201000 r 74 goat snp16304-scaffold1718-145423 4 7878599 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799156 Affx-122976607 AX-385286086 4 109189716 CTGAGGCCTGCCTGGCCGCGTTTTTATTACAGTGT[A/G]CAAATCAGGGACTATGCAGGCCGTTAGTAAATATT R 2 1 2 1 101000 f 74 goat snp16305-scaffold1718-183203 4 7840691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778725 Affx-122940616 AX-385265836 4 109270378 TTACACAGTAAATACTCTTTCAAATCTTTGCAAAA[C/T]GCTCAACAGAAAAACTTATTGCCCAACAGATGCCA Y 2 1 2 1 101000 r 74 goat snp16306-scaffold1718-263865 4 7758065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272247 Affx-1111833411 AX-519545990 4 109293711 ACGGACTGTAACCTGGCAGGCTCCTCCATCCATGG[A/G]ATTTTCCAGGCAGGAGTACTGGAGTGGCTTGCCAT R 2 1 2 1 303000 f 74 goat 4_109293711_AF-PAKI 4 109293711 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378227 Affx-122976915 AX-123248586 4 109304284 ACTATGCTTAGAAGGATTTTGCTCCACTGTTACCC[A/G]TTCAGAGAAAAGCAAGGATCAGGGGACCAACACCA R 2 1 2 1 102000 f 74 goat snp16307-scaffold1718-297771 4 7723311 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773912 Affx-122922731 AX-385261051 4 109323767 TCAATGTGGTAAAAATGATGAAGATAGTGGTGACA[A/G]TGTTGATGAACTTTAGCATCGTAATAATCCTCTGC R 2 1 2 1 101000 f 74 goat snp18280-scaffold1855-396008 4 6618097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783002 Affx-122976785 AX-385270070 4 109404365 TGCAAGTCATGTCACAGATGGTAATTTTTCAAACG[C/T]ACAAAGAACTCCTATAAAGACCAAAACAAAACAAT Y 2 1 2 1 201000 r 74 goat snp18278-scaffold1855-315410 4 6509798 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452129 Affx-122921680 AX-123322462 4 109492773 TGAAGTTGACTGATGGTGAGGACGATGGATGTCTA[C/T]ATTCCTGCCCTGGTGGGGGAAGAGAATGCGTTCCC Y 2 1 2 1 101000 f 74 goat snp18276-scaffold1855-227002 4 6418954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421146 Affx-122944187 AX-123291493 4 109564610 TTAGCCTGAGGCCACAACTCTCTCCTTGCCTGCCT[A/G]CCTCTAAGCACAGGACGAGGGCTACCTTGTGCCTG R 2 1 2 1 201000 f 74 goat snp18275-scaffold1855-155165 4 6347304 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278144 Affx-1111836275 AX-519551633 4 109691465 GAACTCAGTAAGGTAGAAGTGACCCTATGTAACTA[C/G]TGAGGCTATGTCAGAAAAAGAAAACAAAATAAAAA S 4 1 2 1 101000 f 74 goat Random2.2K-494 4 109691465 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390089 Affx-122968027 AX-123260446 4 109761528 AGTGGGAACAGTAGAAACAAACACAGCCCTGACCA[C/T]GCTCCAGACCTGTTCTAAGATGTGTTACCTTAGAG Y 2 1 2 1 201000 r 74 goat snp5817-scaffold1204-1492506 4 6115719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436523 Affx-122932940 AX-123306861 4 109860412 CTCGTCTTTGAGATTCTTCTCTATCCTCCTCTATC[C/T]GTACACAGAGGGTTTCCCTACTGTTTGATAGATTC Y 2 1 2 1 101000 r 74 goat snp5815-scaffold1204-1393622 4 6018143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414254 Affx-122949621 AX-123284603 4 109923025 AACAAAGCCACAATAATTAAAAACACACAAACAAC[C/T]CTATGGTTCTGGCTCAGGAACAAACCTACAGGTAC Y 2 1 2 1 101000 r 74 goat snp5814-scaffold1204-1331009 4 5955115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432868 Affx-122935354 AX-123303209 4 109959413 GGCGCTTGGAGGAGGAACAGAATGGAGCTTGTTCT[A/G]CAGAGGGAGTCGAGGGTGTTTTTCAACCTCTCCTT R 2 1 2 1 101000 r 74 goat snp5813-scaffold1204-1294621 4 5918247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278146 Affx-1111836276 AX-519551635 4 109976836 AGGGTACAGAGTGATGCAAAGTATTGGTTTGTATG[A/G]GATAGTCAGGAAAGGCTTCTCTGAGAAGGTGACCA R 2 1 2 1 201000 f 74 goat Random2.2K-495 4 109976836 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435784 Affx-122932862 AX-123306123 4 110020958 ACTGAATTTTAAGTTTAACCCAAATCTGGTCCTCT[A/G]CCGTGCTTTCTGATAGATGAGAAGAGAAGGCCTGT R 2 1 2 1 101000 f 74 goat snp5812-scaffold1204-1233076 4 5856240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394905 Affx-122964326 AX-123265260 4 110057477 CTTACCTGGGACGTGATTGTGCAAGATAAAGCATT[A/G]TGAAATCTTTAGTGCTCACAGTTGAGAGAACCTTT R 2 1 2 1 101000 f 74 goat snp5811-scaffold1204-1196557 4 5820055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802612 Affx-122952867 AX-385289514 4 110109751 AACATTGTCCACTTATAAAAGGCTTTCAAGTAGAA[A/C]GCAGGACATAAATGTAATTTATTTCACTGTATTAT M 2 1 2 1 202000 r 74 goat snp5810-scaffold1204-1144283 4 5768064 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420007 Affx-122945165 AX-123290355 4 110237504 CAGCCCGATCGCTTTTACATCTTATCAGAACCTTG[A/C]GAAAGCCTCATTCGCCTGCTCCTCATCAGGCGTTT M 2 1 2 1 101000 f 74 goat snp5807-scaffold1204-1016530 4 5640592 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386595 Affx-122970687 AX-123256953 4 110322594 TATATGGCAGACAAAGGGGTGAGTCACGTCCCGGT[C/T]GGGATGGAGCAGGATGGTGCAAGGTTTCATCAGCT Y 2 1 2 1 201000 f 74 goat snp5805-scaffold1204-931440 4 5556595 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392955 Affx-122965689 AX-123263312 4 110393376 ATCCATGCTCTTTCTCCTGCAGACTTTTCTTGATC[A/G]TGCTCCGAGTCCTTATGGGGTGGAGCAAAGACAGA R 2 1 2 1 101000 f 74 goat snp5803-scaffold1204-860658 4 5484351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411551 Affx-122951646 AX-123281901 4 110430057 TGTTCATCCTAAATGCTGAGGGGTGTGATATGACA[C/T]GTAAGAGAGGGTGTGAGCTGAGTGGCTGGGCTGCC Y 2 1 2 1 101000 f 74 goat snp5802-scaffold1204-823977 4 5447663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438692 Affx-122930866 AX-123309029 4 110459805 TTACTCACAAGAGCAAAATCTGGAAAATGTCCACA[C/T]GTTTAACAAGAAAAAGAGAAGGTAAATAATTTAAA Y 2 1 2 1 101000 f 74 goat snp5801-scaffold1204-794229 4 5417572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453285 Affx-122920381 AX-123323618 4 110490398 ACAAAATTTTAAAATTTTCACAGAGAAATTGTAGA[C/T]TTCTGAGGAACACTGATACAAACTAATCTAATTTA Y 2 1 2 1 201000 r 74 goat snp5800-scaffold1204-763636 4 5387546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397438 Affx-122962229 AX-123267793 4 110592386 TAAGGTTCCAAACGCCACTGCTGTGAGGGGGAGCC[A/G]TCACAGATGGCCATGGCAACAGAGCCTCTGCGACT R 2 1 2 1 201000 r 74 goat snp5798-scaffold1204-661648 4 5284383 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412198 Affx-122950941 AX-123282548 4 110628232 AGCAGAGCATGGTTCAGAAGCAGCTGGAGCAGGTA[A/G]CACACGGCTTGGCCAGACAGTCTGCTCTCGATTAG R 2 1 2 1 201000 f 74 goat snp5797-scaffold1204-625802 4 5248467 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379051 Affx-122976344 AX-123249410 4 110753993 TGTCCTTTAAGTGTCATTTATTTATTTGTATTTAC[G/T]CTTTGGAGAATGGTGAACTGTCCTGTAAACACTTA K 2 1 2 1 101000 r 74 goat snp5794-scaffold1204-500041 4 5122339 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443366 Affx-122927414 AX-123313703 4 110785072 CCATTCTCTGCTTTGTTTCCTTCTATTCATTTCCT[A/G]TCTTCTTTGGGTTAATTGAATATATTTTTAGGATT R 2 1 2 1 201000 r 74 goat snp5793-scaffold1204-468962 4 5091177 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382830 Affx-122973548 AX-123253188 4 110867895 GAGACTGCAGTCTCCCATCACCTCACTTCTGCCCC[G/T]ACATGCTGCTCTTTTCCCAGAGACAGAGAAACTCA K 2 1 2 1 201000 r 74 goat snp5791-scaffold1204-386139 4 5007847 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423218 Affx-122942704 AX-123293564 4 110897654 CTGGGAATCAAACCCAGGTCCTCTGCGTTGGGAGC[A/G]TGAAGTCTTAGCCATTACAGCACCAAGGGAATTCC R 2 1 2 1 103000 r 74 goat snp5790-scaffold1204-356380 4 4977824 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386672 Affx-122970190 AX-123257030 4 110930872 ATGGCCATCCTGTTTGTCTCTAAGCTCACTGTCTC[A/G]TTTTCAGAACTTGGTGGGCAGTTGTTTTGTTTATT R 2 1 2 1 101000 r 74 goat snp5789-scaffold1204-323162 4 4944453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415302 Affx-122948818 AX-123285651 4 111036349 CCTTGTCTAGGGACTGCTTTTGTTGTGAGTTGAGG[A/G]GGAACCAAACTGTCGGCAGGCAATAAGTCATCAGG R 2 1 2 1 201000 r 74 goat snp5787-scaffold1204-217685 4 4839020 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432805 Affx-122935404 AX-123303146 4 111093736 TATTGGGAGTTTGTTCTGGGTCACTGGGAATGTTC[A/G]TTATGGCTCTATAAAAATGTTGGTGATGTCCACCA R 2 1 2 1 101000 f 74 goat snp5786-scaffold1204-160298 4 4781134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396996 Affx-122963145 AX-123267351 4 111122236 TTCAGCACCCAAAACGAGCCCAGAAATAAGCAACC[A/G]CACAGACCAATGCAGTACGCAAGGAGAGCGGAATC R 2 1 2 1 101000 f 74 goat snp5785-scaffold1204-131798 4 4754092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441526 Affx-122928713 AX-123311863 4 111178252 ACTGCCCATCAAGAAGCATCACTAGTCAACACACC[A/G]CCAAGTGTGTCCTGTGAGAGAAGGAAAGCTTGACC R 2 1 2 1 201000 f 74 goat snp5784-scaffold1204-75782 4 4698186 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787372 Affx-122934231 AX-385274397 4 111263608 CAGCTGACTAACCAGAAGTCTAAGGAAACACTTGC[A/G]CATCTCAGGAGGTATGGGATGCGAACATTTGCTTG R 2 1 2 1 101000 f 74 goat snp27042-scaffold2876-9475 4 4610737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440780 Affx-122929848 AX-123311117 4 111334657 CCTGTGAATGCAGAAAAGAGAAGGGGCAGGAATCC[A/G]TCTGTCTCCAAGATGCACAGTGTTCAGGAAGCACA R 2 1 2 1 201000 r 74 goat snp27043-scaffold2876-80524 4 4538930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762313 Affx-986696844 AX-385250493 4 111338450 AGTATTAATACCTAGTCTTCCAGTTAAGAATTTTT[A/G]TAGCACTATTAAATATTTCTTCAAGGATTTTTTCC R 2 1 2 1 600010 f 74 goat 4_111338450 4 111338450 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320773294 Affx-122954386 AX-385260437 4 111367291 AAGTTTGGAACTGTTAACACCATACATCTTATATC[A/G]TTGACTTTCCATAGATCTTCTGAAAAGAAAGCCTC R 2 1 2 1 101000 f 74 goat snp27044-scaffold2876-113158 4 4506126 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278148 Affx-1111836277 AX-519551637 4 111391309 GCACAGGGGCAGACGTTAAAGCTAAGGAGCAGGAT[A/G]GGCCTTTCAACCTAGTCAGGCCAATCCAATTTACA R 2 1 2 1 101000 f 74 goat Random2.2K-496 4 111391309 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380778 Affx-122975107 AX-123251136 4 111398348 GTATTCTCTCTCCTGCATGGAGCACCATGCTGGGG[A/C]AACGATAGAGATGTCACACATACCTGGCGATCGGT M 2 1 2 1 201000 r 74 goat snp26966-scaffold2859-19792 4 4474769 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408386 Affx-122953718 AX-123278737 4 111514263 ATGTCTCCTATTTATAAGACGAGGTGCTATGAAAA[G/T]AGAGGATTGTTTCAAAACCCAAAATGATGTTTATA K 2 1 2 1 101000 f 74 goat snp26969-scaffold2859-135707 4 4356801 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422099 Affx-122943576 AX-123292446 4 111549514 TCTTTGTACCGTTACAATGTAGTTACCATGAAGAC[A/G]GGAACTGAAGCTCTCAGGGGTCGAGTGCCTTGCCT R 2 1 2 1 101000 f 74 goat snp26970-scaffold2859-170958 4 4321707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393957 Affx-122965058 AX-123264312 4 111563778 CCCTTGAGTAACCCTCCCCATCAAGCCTTCACTCC[A/G]CTCCTGTCAGCCACCACTGTACCCTCTGCTGCTGT R 2 1 2 1 101000 r 74 goat snp42422-scaffold5605-48780 4 4307391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395779 Affx-122963667 AX-123266134 4 111592956 GGTCTCGGGGGGAGAAACATCTCTCCACCAAGAAA[C/T]ATCAGATGTTTCCTTCCACAGGGCTGGAACTCTAC Y 2 1 2 1 201000 f 74 goat snp42421-scaffold5605-19602 4 4277728 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770543 Affx-122929383 AX-385257707 4 111627929 AAGGAGGTAAGAGTGTTCAGCCTTCCAATGATACA[A/G]AAGTTCTTTGCAGCAGAGGAGGTTTTTGCTTTGGG R 2 1 2 1 101000 f 74 goat snp1898-scaffold1053-15272 4 4243192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801096 Affx-122978866 AX-385288010 4 111665251 TTTCCGGAATGTCAGAAAACATATATTAGTGACAA[C/T]AATCATATACTTTACACGATCTGTGTTCTCTTTCC Y 2 1 2 1 101000 f 74 goat snp1899-scaffold1053-52594 4 4206251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802021 Affx-122921718 AX-385288925 4 111753628 CTATTCTCTTCCAATTCCTTGGAAAGGATTTAGAT[A/C]CTAATGGGGATAAAAGTTGCAAGTAGGTACACAAA M 2 1 2 1 102000 r 74 goat snp1901-scaffold1053-140971 4 4118764 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454040 Affx-122919408 AX-123324373 4 111810220 CTGTACACCCCCAAAGTAAGGGCTACAAGTCCTCC[A/G]AGCCACACAGAGAACATCCTGGGCACCTCAAGATG R 2 1 2 1 101000 r 74 goat snp1902-scaffold1053-197563 4 4062212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799274 Affx-122953573 AX-385286204 4 111839134 AAATAAAGAGCTTTTCAACAAGAGCTTAAGGATTA[C/T]AGAGATAAGCGTGTGAAGAAAAGTGTGAAACTGGT Y 2 1 2 1 101000 r 74 goat snp1903-scaffold1053-226477 4 4033243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401656 Affx-122959577 AX-123272009 4 111888692 ACCATTGCCTCCATCTCTAACAGGAAGACAGACAA[C/T]GGCTGGGTTGAGACCTGGAGGTCAGATTTTGCCCA Y 2 1 2 1 101000 f 74 goat snp1904-scaffold1053-276035 4 3983763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464325614 Affx-1110429532 AX-515799565 4 111949642 CACCATCACCAGGGCCCATTTTAAACCAAGGAAAG[C/T]AACCCACAGCCCCCAGGACAAATCCCTGCCCATCG Y 2 1 2 1 101000 f 74 goat 4_111949642_AF-PAKI 4 111949642 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421526 Affx-122943881 AX-123291873 4 112002258 AGGCCGTGTCACTCCCAGCGTGGCTCGAGGATTAC[A/G]TAGTGTTCCTTTCCCAAAGGCGACGATGCTCCCTG R 2 1 2 1 101000 r 74 goat snp1907-scaffold1053-389601 4 3874484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413476 Affx-122950659 AX-123283825 4 112038983 GCAGACTTTCAAAGGGAGGAGGACCAGGAACAGGA[G/T]CTCTACCCTCGATCTGTCCCCGTTCTGCCTGAGTC K 2 1 2 1 201000 f 74 goat snp1908-scaffold1053-426326 4 3837029 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767722 Affx-122962469 AX-385254956 4 112069519 GCCAAAGACATGCCGCAGGCAAATGGCATTAATTT[A/G]TCTAAGCCAAAACAGTCATTAGTATGGCTTTAAAC R 2 1 2 1 101000 f 74 goat snp1909-scaffold1053-456862 4 3806475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796776 Affx-122945784 AX-385283719 4 112099303 TGTCCCAGTGTTGCTTGGAGCTTTCAAATTCTCTA[G/T]CAGGTGATCTAAAGTGGATTCACTGATTCATTACA K 2 1 2 1 101000 f 74 goat snp1910-scaffold1053-486646 4 3776556 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428132 Affx-122939062 AX-123298475 4 112154732 GGTGCCCGGAGCGGAACCTGCTTGGTGACACCAGC[A/G]CATGTATTCTGATGACTCAGAAGGCAAGCTATTTA R 2 1 2 1 101000 r 74 goat snp1911-scaffold1053-542075 4 3721258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387151 Affx-122970639 AX-123257509 4 112203394 TCCTTAGTCTGCCTGTAGACTCTTGAGTGCCCTGT[A/G]CATGGGTGACAAGTTCAACCAAAGATAAAGTCCCT R 2 1 2 1 101000 r 74 goat snp1912-scaffold1053-590737 4 3673372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427984 Affx-122939179 AX-123298327 4 112242077 TCAGTTAACATTATAGATTATGTCACCAAGCAGTT[A/G]ATTTAGAGTGTCATTGCTTTGCAGCTTGTATCCTG R 2 1 2 1 101000 r 74 goat snp1913-scaffold1053-629420 4 3634608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790216 Affx-122922482 AX-385277220 4 112296876 CAACAGTCAATTTTAGGTGGATCATATGCCTAACC[A/G]TAAAATCTAGAATGATGATGGATATATTAATAGTC R 2 1 2 1 101000 f 74 goat snp1914-scaffold1053-684219 4 3579266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421931 Affx-122943833 AX-123292278 4 112355698 ACCGCATTTCACAAAAGTTTCACAAAATAATACCC[A/G]TCCCAGGAACTGTCTGCACTTGTATTTTCTGTTTG R 2 1 2 1 101000 r 74 goat snp1915-scaffold1053-743041 4 3520714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441020 Affx-122928947 AX-123311357 4 112418416 GTGTTGAGGGCAGTAAGCTTTAGTGATACTGCGTG[C/T]GTGCATGCGTGCTGAGTCGTTTCAGGCCTGTCCGA Y 2 1 2 1 101000 f 74 goat snp1917-scaffold1053-805759 4 3456926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430576 Affx-122937003 AX-123300917 4 112453311 AGCAGAAGAAATGACCACTAATGTGATTTCTGAAA[C/T]TAACGAGAGTCTTCTTTAGGGAGGGAGCTTAGAGA Y 2 1 2 1 101000 f 74 goat snp1918-scaffold1053-840654 4 3422573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404630 Affx-122957323 AX-123274982 4 112482275 ACATATCATATCGTATAAATGATGGTCAGAAGCCA[C/T]GCACTCTGAGTTGGGGACTCTCTGTTCAAATCAGT Y 2 1 2 1 201000 f 74 goat snp1919-scaffold1053-869618 4 3393563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273834 Affx-1111833847 AX-519547445 4 112491500 GACCTCTGCAGAGATCAAG[A/G]TTTATTACATTTCTGTGTCTCAGCTGTTATCTTCT R 2 1 2 1 101000 r 74 goat GoatD01.007134 4 112491500 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443213 Affx-122927578 AX-123313550 4 112522172 GAAATGAAAAGCTGCTCAATCAGTGAGATCTGATC[A/G]CTTCTTGTCATTGGCCAGTGATTTCCTCGCATAGA R 2 1 2 1 101000 f 74 goat snp1920-scaffold1053-909515 4 3354380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780191 Affx-122972085 AX-385267287 4 112557290 AATTCAGATTCAAACCTATAAACAGCTGCACTGGT[A/G]TCTATAAATAGCTACATTGTATTTAACCAAAGTCT R 2 1 2 1 101000 f 74 goat snp1921-scaffold1053-944633 4 3321554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441793 Affx-122929086 AX-123312130 4 112633603 TTAGCATATCTTTTTTACTACTAAACTCTTTTAAT[A/G]TTATTAAACTTATAGCTTAACTAACAGCCTTGAAC R 2 1 2 1 101000 r 74 goat snp1923-scaffold1053-1020946 4 3245681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405176 Affx-122956931 AX-123275528 4 112682397 CTCACCACGAGTACCAGAGAGCCATTCCCTTGAAA[C/T]GTAGGACTGTTCTTTGATCCAGAACTGGGTTCAGT Y 2 1 2 1 101000 r 74 goat snp1924-scaffold1053-1069740 4 3196377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436415 Affx-122933018 AX-123306753 4 112721100 TGACCCATGTTCATTCATCAGCTATTCATATAAGT[A/G]CCAACCTTGCTTCTAAATCACAGAAGAAAGCTCTC R 2 1 2 1 101000 f 74 goat snp1925-scaffold1053-1108443 4 3159243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780955 Affx-122972755 AX-385268042 4 112752034 GGACTGCGTGGCCTCTTTAATAAATTCGAAGCCTC[A/G]TGAACACCATTCTCACTTCGTGAAGAAGCAAAGAA R 2 1 2 1 101000 r 74 goat snp1926-scaffold1053-1139377 4 3128247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394948 Affx-122964289 AX-123265303 4 112812968 AATCTCGTTTAGTCCATTTGGTGATGCTGTTTCCG[C/T]AGGCTTGATTAGCTTCAAGGACAGTGAAAAATTAG Y 2 1 2 1 201000 r 74 goat snp1928-scaffold1053-1200311 4 3068376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446778 Affx-122925312 AX-123317114 4 112854118 GAGGCCTCTGCCCAGGATGCACACCCAGCGCTTGC[C/T]GAGTCACTCCTGCTTATATGCAGGGTACTGACCGT Y 2 1 2 1 201000 f 74 goat snp1929-scaffold1053-1241461 4 3027223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389695 Affx-122968694 AX-123260053 4 112932771 AAATTCAGCTTCTGAATTTCTGAGCTTCTTCATCC[C/T]GGCTTGTATCCCAACTGCAGTGGCTGCCCGGTTGT Y 2 1 2 1 101000 f 74 goat snp1930-scaffold1053-1320114 4 2949686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409157 Affx-122953208 AX-123279508 4 112976174 GGTTAAAATTGTTAAAAGTTAGTTTCAGATTTCTC[C/T]TTACTGATTTATGATCAAATATAAGTGTTTTGTTG Y 2 1 2 1 101000 f 74 goat snp1931-scaffold1053-1363517 4 2909497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798326 Affx-122960393 AX-385285261 4 113043453 CACTAGACCATTTACTGCTGAGGGCAGGAACTCGC[A/G]TACTCTCACTGTTGGTGAAGAGTTAGCTAACTGAC R 2 1 2 1 202000 f 74 goat snp1933-scaffold1053-1430796 4 2842530 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403268 Affx-122957867 AX-123273621 4 113111866 GACCTTCATTCATTCGCTCAAACGTTACCTATTGC[A/G]AAGGGAAGAAGTCCACTAGCAGATTAAATTGCTTT R 2 1 2 1 101000 f 74 goat snp1934-scaffold1053-1499209 4 2775189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397091 Affx-122962710 AX-123267446 4 113141053 TCAAAGGACGCGGTGAGCACAGTGCACTCACTCGA[C/T]GGCACAGCCCACGTTGGGCCCGGTATGCAAGTCCT Y 2 1 2 1 201000 r 74 goat snp1935-scaffold1053-1528396 4 2746300 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395882 Affx-122963625 AX-123266237 4 113243617 GTGATCAGTCATTTAAAAACCTTTCTTCATTCATC[A/G]TCTTATTTTCCCCATGTGGACTATCTCAGTGAACA R 2 1 2 1 101000 r 74 goat snp56264-scaffold8805-4754 4 2645141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441586 Affx-122928671 AX-123311923 4 113303617 GGGGCAGTGGCTGGTGTGGCCGCGGTGCTGGGAGA[C/T]GGCTTCCAGGGGGCGACATGGGTCCCCCCAAGAGG Y 2 1 2 1 103000 f 74 goat snp19460-scaffold1965-55147 4 2585014 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431339 Affx-122937059 AX-123301680 4 113334440 TTCAGAGGATTACTTTTGAACCTGGCACTTCTGGA[C/T]GGCAAGTAAACCCAGACTCATCCATGTGTGTGTCT Y 2 1 2 1 101000 f 74 goat snp19461-scaffold1965-85970 4 2554216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278150 Affx-1111836278 AX-519551639 4 113361909 GGTCGGATCTCGTCTGCTATGTGGTGCAGCCAAAA[A/C]CAAAGAAATAAATGAATACTTGCATAGAAGAATCA M 2 1 2 1 103000 f 74 goat Random2.2K-498 4 113361909 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425618 Affx-122940907 AX-123295964 4 113365196 TTCTTACGGATGCAGGAATGTTGTTCCTATTTGGC[C/T]GGGTGCTGAGCATCTTCACTAATTTAGCTGCACCA Y 2 1 2 1 101000 f 74 goat snp19462-scaffold1965-116726 4 2523203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774093 Affx-122964658 AX-385261231 4 113436637 GAATATGGACCTAAAATAAAAACAGATAAACGGTT[A/C]TTTCTTAAGATGTTAAAGTAAGATAAAAATTGTCT M 2 1 2 1 101000 f 74 goat snp19463-scaffold1965-188167 4 2453038 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398083 Affx-122961725 AX-123268438 4 113490813 GAAACCAAAGATCCCACTGAACACCCAAACCTTCA[C/T]ACAGTTCCCCAGTCTCCTCACTGCGGCCCAGAGCC Y 2 1 2 1 101000 f 74 goat snp19464-scaffold1965-242343 4 2401794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780731 Affx-122932691 AX-385267821 4 113514257 TTTGCTCATTCATTGTTTATGATACATTTTCATTG[C/T]GCTTGAATGATATTCAGTTAATCAAGGCACAGGAT Y 2 1 2 1 101000 r 74 goat snp38319-scaffold4847-17621 4 2382743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379074 Affx-122976325 AX-123249433 4 113551771 AGATGCAATATTTAAAAATCTAGTATATAATAAAA[C/T]GTGCATTTCACATTAGTGGGGAAAGAGTAAGTTAT Y 2 1 2 1 202000 f 74 goat snp38320-scaffold4847-55135 4 2345608 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278153 Affx-1111836279 AX-519551642 4 113562775 AACGTGCAAGCACATAGCTAGAGGGGCTAGCCCAG[A/G]TGTGCACACGATGGCAGGGCCAACGGCAGGGGTCT R 2 1 2 1 102000 f 74 goat Random2.2K-499 4 113562775 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430291 Affx-122937282 AX-123300632 4 113601120 TGTACCCAGCGACAGTCTGCCCGGGAAGGAGGCTC[A/G]TCTCATCTTAAAGAAGCAGGGGACCAAACAGACGA R 2 1 2 1 101000 r 74 goat snp38321-scaffold4847-104484 4 2297584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395246 Affx-122964470 AX-123265601 4 113654734 GCCGCCGTCAAAATCCTGCTTTTGAGCTGGTCGGA[A/C]GAACGCTGGTATTCCGAAGGCCACTCACAGTTGCA M 2 1 2 1 101000 r 74 goat snp38322-scaffold4847-158098 4 2250260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388993 Affx-122968655 AX-123259351 4 113770980 CTCAGTGGATCTGTTTTGTATGTTGGACTTCCCTG[C/T]GAGGTTTCCTCTGAAGCGTGTGGTGTCTTTGATGA Y 2 1 2 1 101000 r 74 goat snp20992-scaffold2056-470017 4 2134001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382067 Affx-122974920 AX-123252425 4 113806205 TTTCAGTCTTGCTCACCCCACGTGCACGCAGCCTG[C/T]ACTCCATGTCAGCTGTGCTTTCCAAGTATATGCGG Y 2 1 2 1 201000 r 74 goat snp20991-scaffold2056-434792 4 2098922 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447373 Affx-122924860 AX-123317709 4 113838709 ATTGTATAAATTGCTTTGGAAAGACACAGCTGCCC[A/G]TTTTATCTCCCCTCAAAGGATCTGTCTGTTGAAAT R 2 1 2 1 101000 r 74 goat snp20990-scaffold2056-402288 4 2066412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424488 Affx-122941754 AX-123294834 4 113878140 ATCTGGTTCTGAGGTTGATGGGGCCCAGTGATCAT[C/T]CTGGACCTTCTAGAACCTTGATGCTTCTCTGGACT Y 2 1 2 1 201000 f 74 goat snp20989-scaffold2056-362857 4 2027049 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441959 Affx-122928568 AX-123312296 4 113908043 AGTGACCGGTCCAGTCTGAGAGGACAGTGTGTCAG[C/T]GGGAGGAGTCCTTTCTTTCATATGTCTCGTGCAAA Y 2 1 2 1 101000 r 74 goat snp20988-scaffold2056-332954 4 1997388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450272 Affx-122922176 AX-123320607 4 113943774 ATCCTCAAGTGTGGCATATTGAGAAACCAGAGTTC[A/G]GTGTCTAAAGGGGAGTGTCCTTATAAGAGATTAAT R 2 1 2 1 201000 f 74 goat snp20987-scaffold2056-297223 4 1961864 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385168 Affx-122971742 AX-123255526 4 114020152 GCCAGAGCCTTGCTTTCTTGGAGGTTGGCGGCTGC[A/G]TTTGTGAAAATACCTGTAGCGAAAATCCATTGTTT R 2 1 2 1 101000 r 74 goat snp20985-scaffold2056-220845 4 1886015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422598 Affx-122943735 AX-123292944 4 114089311 GAGAGGATGGTGTCATATAAGAAGCATTTTAGAGA[C/T]GTGGATGTAGACACAGGGTGTGGTCCATGCCTGTA Y 2 1 2 1 101000 f 74 goat snp20983-scaffold2056-151686 4 1816351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382464 Affx-122974212 AX-123252822 4 114139903 AAGTGGTCGGATTCTCAGAGACGCAGAGGAAACTC[A/G]TGGTTGCCAAGGTGGGGAGAGGGGCGGGGAGTAAG R 2 1 2 1 101000 f 74 goat snp20982-scaffold2056-101094 4 1764953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408349 Affx-122953744 AX-123278700 4 114185583 GGTAGAGTGCCACAGGAACCCGTCTGCTGCCCAGC[A/G]TAATAGCTATGGTAGGGTGGGTCACGCCACCATGC R 2 1 2 1 202000 f 74 goat snp20981-scaffold2056-55414 4 1719317 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430759 Affx-122937493 AX-123301100 4 114228256 TCAGTGTTTATTAAACTACCTATTGTGTGCCTAGC[A/G]TTGTGCCATCAAAAAAAATAAAAAGTGTTACAGAA R 2 1 2 1 102000 f 74 goat snp20980-scaffold2056-12741 4 1676585 A G 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38427190 Affx-122939602 AX-123297533 4 114255764 TAAGTTTGTGTGACTCTCTGAATCGCTTGCTGTCA[C/T]CTCAGCAGTCTTCACAGTGTCTTTACCAGGAATGG Y 2 1 2 1 201000 f 74 goat snp20847-scaffold2044-855182 4 1648971 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453344 Affx-122919957 AX-123323677 4 114321536 TGGCTCTCTTATACTTCCAAAATCTAAAAGTTAAA[C/T]GAAATATTCCTTTGAAGTCATCTTTATTGGAAAAC Y 2 1 2 1 101000 r 74 goat snp20845-scaffold2044-789410 4 1583212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405843 Affx-122955867 AX-123276195 4 114350251 AATCATGATAGAATTATGGAAATGCCTCCATTTGT[A/G]CATATTTCACGATCACATACAAACTCGATGTGTGA R 2 1 2 1 101000 r 74 goat snp20844-scaffold2044-760695 4 1554221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476195 Affx-1251763700 AX-586011621 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 4 1 4 1 20000 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 539476450 Affx-1251763700 AX-586011851 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20000 r 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165269 Affx-1251763700 AX-606940681 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165819 Affx-1251763700 AX-606941228 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 r 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165905 Affx-1251763700 AX-606941314 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165988 Affx-1251763700 AX-606941397 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562166560 Affx-1251763700 AX-606941968 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 38423648 Affx-122942351 AX-123293994 4 114466374 ACACAGCAGATGACAATGCCACGTGTAGACGAGCC[A/G]CTGTCACGGGGGAGTTCTCGCTCATCTTTCTCGTG R 2 1 2 1 201000 f 74 goat snp20842-scaffold2044-644572 4 1438969 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797852 Affx-122951541 AX-385284791 4 114503388 ATGATTCTAAGGGTACTTGATGATAAACTCAAATC[A/G]TCCCAGGCATTTTCAACACATTCATTTCTGCTCAT R 2 1 2 1 101000 r 74 goat snp20841-scaffold2044-607558 4 1401747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464335124 Affx-1110430661 AX-515808991 4 114523140 CTGTGGTAGAGTTCCTTCATTTGCTCAGCCTTCAT[A/G]TCTAAGGAATATGACACAACCTGCCAAGTCATCTT R 2 1 2 1 201000 r 74 goat 4_114523140_AF-PAKI 4 114523140 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426028 Affx-122941121 AX-123296374 4 114556716 GCGTCATATTCTGCAAGTTCTAAGTGTAAGCAAAC[A/G]TTGTGTAACTGGGAAACGCCCAACCAAGGCACACC R 2 1 2 1 101000 f 74 goat snp20840-scaffold2044-554230 4 1348638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399245 Affx-122960577 AX-123269600 4 114657935 GAAACCCTCGCCACGCTCTACACCGCTCCACCCCA[C/T]GCACAACAAACCAACCCACAGTTTCGTGTGGTTCA Y 2 1 2 1 101000 r 74 goat snp20838-scaffold2044-453011 4 1257240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375929 Affx-122978465 AX-123246288 4 114700929 CCCTCAGACGTGATACAGAACCTTCTATGGGGACC[A/G]CAGTTCACAGACCCCCCTGGGCCCCCCAAGATAAC R 2 1 2 1 101000 f 74 goat snp20837-scaffold2044-410017 4 1224434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424198 Affx-122942508 AX-123294544 4 114735513 TGTCACTCACCATAAGCGAATTTATCAACATGTAC[A/G]GAATCGGAATACACATGAGAGTTTTAACTGTTTGC R 2 1 2 1 101000 f 74 goat snp20836-scaffold2044-375433 4 1191971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400285 Affx-122960085 AX-123270640 4 114799477 CACCTGACGACCTGGGATGAAGCTATCACGAGTGC[A/G]TGATCCCCAAAGGCACTCCTGCAAGACGGGAGGTG R 2 1 2 1 101000 f 74 goat snp20834-scaffold2044-311469 4 1133115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797398 Affx-122952673 AX-385284337 4 114920183 GACTTTTTATACTGCTTTTAAGTCATTTTGGTAGT[A/G]CAGGTAAATTAGGAACCCATTCTACTTAAAACTCA R 2 1 2 1 201000 f 74 goat snp20832-scaffold2044-190763 4 1020488 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445081 Affx-122926210 AX-123315418 4 114964055 GCTGGACAGTGTGACGACAGCATCGCCGTAATTGC[A/G]TCCTGTCCCCACGCCATCCTGCTGGGCCTGTGTCC R 2 1 2 1 101000 f 74 goat snp20831-scaffold2044-146891 4 977273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376674 Affx-122978999 AX-123247033 4 114999710 TTGTATACACATGTGGTGTGTTACATGTGTGCGTG[C/T]GTGTGTGCGTGTGTGCATGTGTACACGTGTGAGTG Y 2 1 2 1 103000 f 74 goat snp20830-scaffold2044-111236 4 942730 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377155 Affx-122978219 AX-123247514 4 115036030 CTGAAAAACTGTCTTCCAGAGTGGCTGTGCGTTCG[C/T]GCCAAGTCACTTCAGGCATGTCCGACTCTCTGCAA Y 2 1 2 1 103000 f 74 goat snp20829-scaffold2044-74916 4 909586 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409904 Affx-122952892 AX-123280255 4 115108601 TGGGTCCTTGGGGTCGGGGCACATTGTAGAAGCAC[A/G]TCAGCGACAAAAGAGAGAAAAGATGTAATCATTTT R 2 1 2 1 201000 f 74 goat snp20828-scaffold2044-2345 4 858890 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452889 Affx-122920221 AX-123323222 4 115114235 AAATGGGACCATTGGAATGGGAGCAGCAACCTCCC[A/G]TCCCACAGTATCTCAGGCCTTGAGTGTGACCGAAA R 2 1 2 1 101000 r 74 goat snp24717-scaffold2522-628716 4 851551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392601 Affx-122966052 AX-123262958 4 115182057 GACTTCCAGCCTCACTACCAAGTGAATCACGTGAG[A/C]AAGGCCGAAGCTGGTTTGATTTTTTGTGCTGTGAC M 2 1 2 1 102000 r 74 goat snp24716-scaffold2522-560894 4 783452 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769050 Affx-122920242 AX-385256225 4 115216900 CCTTAGTTGGATGAAGACGCACATGTTTAAGAAGG[C/T]GACTGAGATGATGAGGATGTGGGAATTTTGTCAGT Y 2 1 2 1 101000 r 74 goat snp24715-scaffold2522-526051 4 750270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410541 Affx-122952156 AX-123280891 4 115252040 TGTGTTCACATGTTAACACCCCTGAAACCAGCGTG[C/T]ATCCTACACCAATAGCGCGTCATCGTTTACCTTGC Y 2 1 2 1 101000 r 74 goat snp24714-scaffold2522-490911 4 715411 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446451 Affx-122925077 AX-123316787 4 115288986 CTGGACTTGTGTGCGTTAAGTGCAGATTGCTCACT[A/G]ATGGGCACGATCCTCACCTGCTTGGTCTGGGAGAG R 2 1 2 1 101000 f 74 goat snp24713-scaffold2522-453965 4 680392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389117 Affx-122968562 AX-123259475 4 115330846 GTGGGAGAACATTCTATGGAGGATGCCAAGAATCC[A/G]CTGGCAGCTGGAGGTTGCAAGACTGGACTGGAAGA R 2 1 2 1 201000 f 74 goat snp24712-scaffold2522-412105 4 642534 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444279 Affx-122926769 AX-123314616 4 115373814 TTGCCTTCTTCTAGAGCGTATTGTCAGCAGAACCC[A/G]TATCAGAGATGTCAGCGAGGCCGTGGAGACTGAAA R 2 1 2 1 201000 f 74 goat snp24711-scaffold2522-369137 4 600146 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378944 Affx-122976428 AX-123249303 4 115440920 GGTAATTTGTTTTATATAAGCCTAGGAAATAAACC[A/G]CTTTCCAGATCTACTTTCTCCTTAGAAGAAAGGCT R 2 1 2 1 101000 f 74 goat snp24710-scaffold2522-302031 4 534565 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384128 Affx-122972818 AX-123254486 4 115477722 GCTTCACGGAAGCCCACACATGCTGGAGTATGTAG[C/T]GTATCCCTTCTTCAGTGGATCTTCCTGGCCCAGGA Y 2 1 2 1 201000 f 74 goat snp24709-scaffold2522-265229 4 498220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441238 Affx-122929503 AX-123311575 4 115506942 AATTAATAGTAATTCAATGTATCTGGGTTAAGGTT[C/T]TTCAGAAACTGAGAAAGAAATTATTTCAAGTGACT Y 2 1 2 1 101000 f 74 goat snp24708-scaffold2522-236009 4 469314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380087 Affx-122975544 AX-123250445 4 115537623 CTGGGGATGTTTGTGTGGGTTTCCTACTCACGCCC[A/G]TTTGTCACAGGTGTGTCCGTGGCTCCCTTAGATAA R 2 1 2 1 101000 r 74 goat snp24707-scaffold2522-205328 4 442512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765121 Affx-122947895 AX-385252681 4 115609878 GTGTAAAATATAGATCTTGGTCCTGTGAAGAAACA[A/G]TTATGAACAACTGACTAGTCACGTAGTGTTCTCCT R 2 1 2 1 201000 f 74 goat snp24705-scaffold2522-133073 4 370795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794874 Affx-122956667 AX-385281834 4 115655238 TCATGTTCACTCAACTAACGACAAATGTCTTCTAG[A/G]TGCACTTAGGAACCACTTCTGCTCACTGCATCTAA R 2 1 2 1 101000 r 74 goat snp24704-scaffold2522-87713 4 325835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398006 Affx-122961788 AX-123268361 4 115727811 GAGGTCCATAGGCAGTGGGACCTTGTTCTCCCACC[A/G]CAGGAGCCAGTTTGGACCCAGGCTCGGACCACGCT R 2 1 2 1 201000 f 74 goat snp24703-scaffold2522-15140 4 255223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382115 Affx-122974884 AX-123252473 4 115771875 ATGCCCTGGCCACTGTAAACAGTGCAGTGATGAAC[A/G]CTGGGATGAACCTTTCTTTTCTAATCAGAATCTTC R 2 1 2 1 201000 r 74 goat snp18259-scaffold1851-28825 4 211277 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402674 Affx-122958362 AX-123273027 4 115815185 TGCCTTATTTTGGGATACCCTAGAAATTAAAGCAG[C/T]GTTAAGCGTAACAATTCCTGCAGCTCTTCCGCGCT Y 2 1 2 1 101000 f 74 goat snp18260-scaffold1851-72135 4 173068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392650 Affx-122966445 AX-123263007 4 115852329 TCCGTCTAGAACAGACATACTCTGATCACCAGTAC[A/G]TTTTCACTTGGATAAAAATAGAATTCATTTAGCTG R 2 1 2 1 101000 f 74 goat snp18261-scaffold1851-109279 4 135700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278158 Affx-1111836281 AX-519551646 4 115856329 CAGTGAACTGAACTCCTGGGTACACAGTTTCTTTG[A/G]TCAGTTAGGTTCTTACTGGAACTTGAGAGCCTTTG R 2 1 2 1 101000 f 74 goat Random2.2K-502 4 115856329 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378854 Affx-122976524 AX-123249213 4 115884268 AACGATTTATCTAAGTCTTGACCAAAACCTCAGCT[A/G]TACAGAACACGGCTGAGAGCCCAGTGGAAAAAGAC R 2 1 2 1 101000 f 74 goat snp18262-scaffold1851-141218 4 103204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385230 Affx-122972101 AX-123255588 4 115925391 GTTGGTCACTAGGACCTTCTGCAGTGTATATAAAA[C/T]GCCTTCCAAAATCATCCGCTAAAGAGGTGAAGGCA Y 2 1 2 1 101000 f 74 goat snp18263-scaffold1851-182341 4 62511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278160 Affx-1111836282 AX-519551649 4 116868085 CAGCTGCTATATAATCATGTATTATATAGCAAAAC[A/G]TGGGATGAAGGCAAGAGGCCATGGTGCACAAGAAC R 2 1 2 1 201000 f 74 goat Random2.2K-504 4 116868085 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272085 Affx-1111833412 AX-187122616 4 117691937 GGCTGTAGTCACCATCTGCAGTGATTTTGGAGCCC[A/C]CCAAAATAAAGTCTGTCACTGTTTCCATTGTTTTC M 2 1 2 1 303000 r 74 goat 4_117691937_AF-PAKI 4 117691937 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278321 Affx-1111836283 AX-519551807 4 118968983 TACGACTGAATTGAACTGAACTGAAACTAAAGAAA[A/T]TGGCTAAATGCTTCCATTTAAAGACCTAATATCCA W 4 1 2 1 201000 r 74 goat Random2.2K-509 4 118968983 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272088 Affx-1111833413 AX-519545849 4 120216251 ATTAGCATGGAGAGAACAAAAATCTGATTGGTGTA[A/G]ATATGGAAAGAATTGAAGTAGAAAAGTTGGAAATG R 2 1 2 1 101000 r 74 goat 4_120216251_AF-PAKI 4 120216251 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804311 Affx-986696775 AX-385290926 4 120290244 GCTGAATGAGGAAAGAAAATTATAATTACTGGAAA[G/T]TAGAAAGTAAAACTGTCTTTATTTGCCAGCTAGAT K 2 1 2 1 600010 f 74 goat 4_120290244 4 120290244 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320764489 Affx-986696857 AX-385252166 4 120290258 GAAAATTATAATTACTGGAAATTAGAAAGTAAAAC[G/T]GTCTTTATTTGCCAGCTAGATTCTGTATATAGAAA K 2 1 2 1 600010 r 74 goat 4_120290258 4 120290258 Ancestral_priority_1043 ancestry 0.692 neutral IMAGE 10K 10K ancestral 320764500 Affx-986696863 AX-385252177 4 120290297 TTTATTTGCCAGCTAGATTCTGTATATAGAAAATT[A/C]TAAGGAATCTGCAACCAAAATATGAAAAAATAATA M 2 1 2 1 600010 r 74 goat 4_120290297 4 120290297 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320762334 Affx-986696865 AX-385250508 4 120567632 CGGAGGCGGGCATGAGACAAAACACCTCTAACTCC[C/T]TGAAACAGCGAGGACTCAGGATCCCTACCCACACC Y 2 1 2 1 600010 f 74 goat 4_120567632 4 120567632 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 38396611 Affx-122962890 AX-123266966 5 22890 CATGTCTCCACTCGAGACGAGGACTGACTCCCCTG[G/T]GGAGACTCCAGAAGTACCCCATGATCCATGTCAGC K 2 1 2 1 103000 r 74 goat snp38525-scaffold487-1150834 5 28849 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375413 Affx-122979197 AX-123245772 5 102188 ACTTGCCTGACAGGTTTGTCTGGACTTTTTCTACT[A/G]CACTTGTGTTTGTTTACAACCTCCCACGCGAGAGG R 2 1 2 1 101000 r 74 goat snp38524-scaffold487-1071536 5 108900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431592 Affx-122936174 AX-123301933 5 234968 TTCATCTCAAGTTTCAGTGCTGGACCCAGGGTTAC[A/G]CTAGAGCCATGGTGGAGAATGTAGTGTGCCTATCG R 2 1 2 1 101000 f 74 goat snp38522-scaffold487-938756 5 242032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397865 Affx-122962449 AX-123268220 5 267098 GCTCAGCCCCAAATCCTTAGCACCCTGAATGCAGG[C/T]GCTGGAAGGGCCAGCCCCCTTGTGTAGTAGGGACA Y 2 1 2 1 201000 r 74 goat snp38521-scaffold487-906626 5 274017 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272178 Affx-1111833461 AX-519545930 5 276213 CACCGCAGCCTCAGAGCTGCCTCACCAGCACAGAC[A/G]CTCTCCAACCGTAACAACTGGAACTGCATCCATGT R 2 1 2 1 102000 r 74 goat 5_276213_AF-PAKI 5 276213 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770457 Affx-122952540 AX-385257623 5 319322 ATTGTTGATATATTTATTATCTTGATGGGGGACAC[A/G]TGTTTCCAACCATATCAAATTATACACTTTAAACA R 2 1 2 1 101000 f 74 goat snp38520-scaffold487-854402 5 327050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388179 Affx-122969438 AX-123258537 5 431566 GCCCAATATTTTGACTCCATGTCTAAAAGTTTTCA[C/T]TAGACCAGACAACTTATTTGAAACAAATGCTTACC Y 2 1 2 1 101000 f 74 goat snp38518-scaffold487-742158 5 439743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799301 Affx-122951475 AX-385286231 5 469026 GAAGCTGGATAGAAGAATGCAGTTATCCATAATTA[C/T]GGCAGAAACATACCAAAGAAGAAGTTGAAGATTTG Y 2 1 2 1 202000 f 74 goat snp38517-scaffold487-704698 5 478263 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454021 Affx-122919422 AX-123324354 5 540200 TCCCTGGATTTCCCAATCCTTATCAGGGAAATAAC[A/G]TCTCCAAGATTCCCTGAAGCTGTTTTGTTAGGTGT R 2 1 2 1 101000 f 74 goat snp38516-scaffold487-633524 5 550031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401989 Affx-122958771 AX-123272342 5 606053 AGTCCAAAATGGAATATTTTTTCATTCTTGTTTCT[A/G]CATTCAAGGAGGTAGGTGAGGTTACTCACATAATA R 2 1 2 1 101000 r 74 goat snp38515-scaffold487-567671 5 616218 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788540 Affx-122971798 AX-385275557 5 639191 TTGAAAAATGAGCTGAAGACTCACAATGCCAAATA[C/T]GCCCTCTAGTATAGAGTGATGGTGATAATGGGAGG Y 2 1 2 1 101000 r 74 goat snp38514-scaffold487-534533 5 649407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427339 Affx-122940120 AX-123297682 5 673882 AGGTTTCCCTCTGCCTACACAAAAAGTCCAGACTC[A/G]TTGGCAGAGCATGAAAGACTCTTGTGTGTCTCTTT R 2 1 2 1 201000 f 74 goat snp38513-scaffold487-499842 5 684201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449554 Affx-122923245 AX-123319889 5 739997 TGTTTCCTTGTCTAGAGAATAACCTGATTGGCTTA[G/T]ATGATTATAAATTGTATTCAGTGACCCTTCAGTAG K 2 1 2 1 101000 f 74 goat snp38512-scaffold487-433727 5 751276 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771201 Affx-122959174 AX-385258360 5 772860 ATCATCTCTTTAAGCATAATTACTCAAGTGAGATT[A/G]TTGCTGAGTTGTTGGCATCCAGGGGCATGTATCTG R 2 1 2 1 102000 r 74 goat snp38511-scaffold487-400864 5 785693 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779172 Affx-122959456 AX-385266276 5 801675 TACTTCCCTGCTTTAGTCTAGGGGACATAGCATTC[A/G]TGTTTACTGGGCATCTTTTGTGTGCCTGGTGACAC R 2 1 2 1 101000 r 74 goat snp38510-scaffold487-372049 5 814257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795695 Affx-122927920 AX-385282648 5 848039 CAACACATATGGATGCTACAAATGCCACTAAGTGA[C/T]GAAGATGACTAATATTCATAGTTAAAATTCAACCA Y 2 1 2 1 101000 f 74 goat snp38509-scaffold487-325685 5 861055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426553 Affx-122940179 AX-123296899 5 897556 CAATCATGATTAAATTTCAGTTTTGCCCTATGTAA[C/T]GTGACCTTAGGTATACAGCTTAGTAATTCTGGTAA Y 2 1 2 1 101000 r 74 goat snp38508-scaffold487-276168 5 911555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448766 Affx-122923315 AX-123319102 5 942776 ATCATCTGCATATCTGAGGTAAGATGCTGAAGGTA[C/T]TCAATGTTAATTCTGCTACAAAGCTTGCTCTGGAT Y 2 1 2 1 101000 r 74 goat snp38507-scaffold487-230948 5 953004 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771537 Affx-122968405 AX-385258695 5 980933 CTTTCTGGCTCAGAATCTTCCAGTGGATTCTCATT[A/G]CTTTCATAATAAAGTCTAAAATCCACGACATGTCC R 2 1 2 1 101000 f 74 goat snp38506-scaffold487-192791 5 990534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441755 Affx-122929120 AX-123312092 5 1017825 ACATGCTCTCCAGGTCTCCCTTTTCCAAGCGACAG[C/T]AGAGCCTGGTGTAGGCGACGGTCGTCACGAGGAAG Y 2 1 2 1 201000 r 74 goat snp38505-scaffold487-155899 5 1027487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431965 Affx-122935959 AX-123302306 5 1071689 TAAGTGAGGATTGGTATGATTTCTAAGAAAGTTTT[A/G]TTGGCTTGTGTCTTTTCTAACTTGTTTTGAAAAGC R 2 1 2 1 101000 f 74 goat snp38504-scaffold487-102035 5 1081890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417769 Affx-122947399 AX-123288117 5 1163092 CAGAAAACTCACCCTCATCCCTGCCATCTGTCTGT[C/T]GGCCTGATCTTGGTCTCTTCATCCCCGTATCTAGC Y 2 1 2 1 201000 r 74 goat snp38503-scaffold487-10632 5 1174059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801173 Affx-122943857 AX-385288086 5 1211298 CACGATCAAACCCTTCTAGAATGTAAGTTATATCA[C/T]CTGAAGTTAATATAAGATCAATGATCTAGACCCCG Y 2 1 2 1 101000 f 74 goat snp33879-scaffold399-2325009 5 1221605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779298 Affx-122969505 AX-385266402 5 1250915 AGACATTAAGCAATTTGACTGACATCACTAGTAAG[C/T]GTGAAGTTAGTTTTCGAAACTGGCTTGGCTCTCCA Y 2 1 2 1 101000 r 74 goat snp33878-scaffold399-2285392 5 1261542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440728 Affx-122929886 AX-123311065 5 1286691 ATTCATGATTCATTAGCTTCACGTTGCATTTTATA[C/T]AGTTTCTTATTCAATCAATGTTGGTAATTTTTAAA Y 2 1 2 1 101000 f 74 goat snp33877-scaffold399-2249616 5 1297127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438449 Affx-122931253 AX-123308787 5 1338422 GGATCAGTTTCCGGAAAGACTGATTCCCCCATGTC[A/G]CTTCTTTCTTGCTCCCGTTTTTCTGGCTGAATTCC R 2 1 2 1 303000 f 74 goat snp33876-scaffold399-2197885 22 21012306 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392811 Affx-122965964 AX-123263168 5 1378732 TCTTCTTTTTGTATTCTATGCCAGTATCCCACATG[C/T]GGGGTACAAGGGGACATTCTTTAATAGCTGTATAT Y 2 1 2 1 101000 f 74 goat snp33875-scaffold399-2157575 5 1388224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783281 Affx-122958920 AX-385270346 5 1435540 TGGTTAAACTTGGGGAAAAACTCAAGTGTGAAGTC[G/T]AGGTAGTTTGGGCCCTAGATCCTAAATAAAAACTT K 2 1 2 1 101000 f 74 goat snp33874-scaffold399-2100767 5 1444916 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464332608 Affx-1110433058 AX-515806509 5 1439425 ACTTTCAGAGCAAAAATAATGTAACTGCAGCTCCT[C/T]TCAAGAGCATGGTGAGTCATTTGGTTGTACAGAGA Y 2 1 2 1 101000 f 74 goat GoatD01.026425 5 1439425 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440544 Affx-122929323 AX-123310881 5 1470207 AAAGTATAGAAGCTGGCCACAGCTCCAGCTTCTAT[A/C]CTCTATTTCTTGATAAGCTGTAAAAGTAAACTATA M 2 1 2 1 101000 r 74 goat snp33873-scaffold399-2066100 5 1480291 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781489 Affx-122960466 AX-385268574 5 1501010 CTTACAACAAAAATTACTAGTATTCTTATGTCTCC[A/G]TACCGAAAGCAGACAAAAAGCTTTTATCTGCAATT R 2 1 2 1 101000 r 74 goat snp33872-scaffold399-2035297 5 1511491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412566 Affx-122951318 AX-123282915 5 1557865 GGTGGGAGGAGGTCAGAGCCACTCACATCAAAAGC[A/G]CTTTATTAATCAGAAGAGAGCTGGGGACTGGAAGC R 2 1 2 1 201000 f 74 goat snp33871-scaffold399-1978442 5 1568670 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418440 Affx-122946482 AX-123288788 5 1589020 AGCATGACAGTGTGACTCAGACACAGGACAACCTG[C/T]AGGCGAGATCTTGGAAGACATAAGCCATGTAATGC Y 2 1 2 1 101000 r 74 goat snp33870-scaffold399-1947287 5 1599869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376308 Affx-122978363 AX-123246667 5 1676686 TCTCTGTCCAGGGGATCTGTGGTTCCAACTAGAAC[G/T]ATTCTGGATTTCTCATGAAAAACCATAGCAATCAA K 2 1 2 1 101000 f 74 goat snp33868-scaffold399-1859621 5 1687465 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787234 Affx-122978330 AX-385274260 5 1723169 TCAAATATGCATACTTGATGCTCTGCTTCCATTCA[G/T]CTGTATATTAAGATGCTTTTCAAGTTACTCTCTCA K 2 1 2 1 101000 f 74 goat snp33867-scaffold399-1813138 5 1733976 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779125 Affx-122953213 AX-385266230 5 1836843 TGGAAAAAAATGATCTTATGGTTCCACCATTGTAG[C/T]AATGAGCTAAGGTTTAGGAGCTGTATAATTTTGAT Y 2 1 2 1 101000 f 74 goat snp33865-scaffold399-1699464 5 1847297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773324 Affx-122925028 AX-385260466 5 1899086 TTGGAAAATGGGCCATTTCCATTCTTATTTTCCAC[G/T]AATTTTCAAAGATATTCCCATAATAGTTCAGCAGA K 2 1 2 1 101000 f 74 goat snp33864-scaffold399-1637221 5 1909651 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796101 Affx-122978170 AX-385283053 5 1939114 TGCATGACAGGCCTAACTTTGTCTTTGAACAAAGA[C/T]GTTGCATCCTGATTTCTGAATGGAAAATACTGTTT Y 2 1 2 1 202000 f 74 goat snp33863-scaffold399-1597193 5 1949073 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392520 Affx-122966115 AX-123262877 5 1969077 TATTGCACTGAGGGATATGTGATGATGTATTAGAG[C/T]GGGCGTTACTGAAGGACTTTTGAATCTGAGAGAGA Y 2 1 2 1 101000 f 74 goat snp33862-scaffold399-1567230 5 1979075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446155 Affx-122925755 AX-123316491 5 2005940 TTCTGCATGATTATACATTCAATGCATACGTTTGC[A/G]TCAGTTGCTCAGTTGTATCCAAATCTTTGAGACCC R 2 1 2 1 201000 f 74 goat snp33861-scaffold399-1530367 5 2016169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802876 Affx-122971051 AX-385289774 5 2040781 GCACAGTGCGCTTTGGCATTGCATAATTAGCTCCC[A/G]TTCTCCTATCTCTTGTCCTGACTATCTCTGCTCAT R 2 1 2 1 101000 r 74 goat snp33860-scaffold399-1495526 5 2051367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772249 Affx-122958336 AX-385259404 5 2100804 GAAGCTCACCACTGTTGTGCATTTTGGATATAAAC[A/G]TATTTCACATCTCAAGTAACAGAACTATGGACATC R 2 1 2 1 101000 r 74 goat snp33859-scaffold399-1435503 5 2112670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432371 Affx-122935864 AX-123302712 5 2133523 AAGAATGTACACTGAATGCTTGCATTATCTGCTCA[C/T]CAACATAAAATAAGCAAGATTTGTTTATATAGAAA Y 2 1 2 1 101000 f 74 goat snp33858-scaffold399-1402784 5 2145620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430228 Affx-122937324 AX-123300569 5 2165226 AGTGCCGTGAAACCGAAATGAGAATTATCCTGAAG[C/T]ACCATAAATGTTTTGAAAAGAAGAATACATAAATA Y 2 1 2 1 101000 f 74 goat snp33857-scaffold399-1371081 5 2177381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440586 Affx-122929292 AX-123310923 5 2194693 AAATGAAGACTGGGCAAATTGCTGTAACTGAAATC[A/G]CCTTGAACTGATGAGAAACTGCATGCCCCTAATCA R 2 1 2 1 101000 f 74 goat snp33856-scaffold399-1341614 5 2207100 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417834 Affx-122946792 AX-123288182 5 2244014 CACTGTAGTGTAGGAAGCTTCCACACAGAGCTATG[C/T]CAAATTCTTTTAATATTCACCTCAGACTTTTCATG Y 2 1 2 1 101000 f 74 goat snp33855-scaffold399-1292293 5 2258598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397565 Affx-122962014 AX-123267920 5 2282826 ACTGAGTGAGTAAGCATGTCTAAGCACCTGAAGAC[A/G]TGAACAGAAAGGAGAATAACACATACAGAGACTGA R 2 1 2 1 202000 f 74 goat snp33854-scaffold399-1253481 5 2293959 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379423 Affx-122976110 AX-123249781 5 2314647 CAGACTGTTCCCTTTGCTTCTAACTCCCTTCCCCC[A/G]TGTCAGCTCATATCTCCTAGTTCTTGCCTAGGAAG R 2 1 2 1 101000 r 74 goat snp33853-scaffold399-1221660 5 2326548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797899 Affx-122937490 AX-385284837 5 2460736 CTTTCCTTAGAAGGTCCTTCTAATTCTATATAGCA[C/T]AGTGTCTATGTTGCTTTGTTCAGAGGTGACTACTT Y 2 1 2 1 101000 r 74 goat snp33851-scaffold399-1075571 5 2471520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432203 Affx-122936384 AX-123302544 5 2493778 AATAGATTCCATTGATATTTTGTTCTGATTGGCTC[A/G]AGCTACTGTCAGTTTTATTGAACAACTCTATATTT R 2 1 2 1 101000 r 74 goat snp33850-scaffold399-1042529 5 2504861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790267 Affx-122946394 AX-385277271 5 2526878 TCAGATCAGAAGGATGTCTATTTATCTTTCAGGTG[A/C]TTGTTTTAAACTGATTCCAAACGCATATATGTGTT M 2 1 2 1 101000 f 74 goat snp33849-scaffold399-1009429 5 2538157 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414474 Affx-122949557 AX-123284823 5 2588950 AAGATGAGATTGCAGAAGGACACAGATCATGTGAG[A/C]CGTTATAGGCCATGATAAGATGCTGAGATTTTATT M 2 1 2 1 201000 r 74 goat snp33848-scaffold399-947357 5 2601724 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780140 Affx-122949360 AX-385267237 5 2647243 AGAATTCATGGTCAAGGCTTGGCAGAACCAGTTCA[C/T]GCATGTTTAGAACAGGCAGCTTTCTTTGTGATGTG Y 2 1 2 1 101000 f 74 goat snp33847-scaffold399-889064 5 2661152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776602 Affx-122925038 AX-385263729 5 2736542 AAATCAATGCACTTAGAGAATAAGCCAAATCAGTC[A/G]TTAAATAAAAGATAGCATTTTCACCCATCTAAACT R 2 1 2 1 201000 r 74 goat snp33846-scaffold399-799765 5 2750802 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800506 Affx-122936040 AX-385287426 5 2785311 AATTATGATATTAGTGGAAATGGTATCACTCAGTG[C/T]GGACTTAGGATATCATTTTATATGCAAAATGTTAC Y 2 1 2 1 101000 f 74 goat snp33845-scaffold399-750996 5 2795956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773001 Affx-122926737 AX-385260145 5 2814502 GTATGGAGATCAATACGCTTAAAAGATTTATAAGG[A/C]AAAGTGAGATGTTTCTCAAAACAAGTAGGCCTAGA M 2 1 2 1 101000 r 74 goat snp33844-scaffold399-721805 5 2825337 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278165 Affx-1111836284 AX-519551654 5 2832184 CAAGTAATTGGTAGGGAATATCTGTTTCATGAAGA[A/G]AGAATATTCATTTTTTTCTTTATAATATAATTCAA R 2 1 2 1 101000 f 74 goat Random2.2K-511 5 2832184 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390564 Affx-122967208 AX-123260921 5 2845709 GCTTTGCTGTTCTTAGGGGGTGGCATTTGTCTGTG[C/T]GATCCAGATGGCTTTTTAGTTCTTCCACACTTTAA Y 2 1 2 1 103000 f 74 goat snp33843-scaffold399-690598 5 2857312 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383322 Affx-122972691 AX-123253680 5 2896095 CTGGCACAACACCTAAGTCCACCATTCAGAACCCA[A/G]GCACTCACTCCTTGAGCTGCCAGGTATATTGCCAG R 2 1 2 1 101000 f 74 goat snp33842-scaffold399-640212 5 2908117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272304 Affx-1111833462 AX-519546043 5 2946267 CAGACACGACTGAACAAATGAACTGAACTGAACTG[A/G]ACTGAACTGATGAGACCAGATGCCATGATCTTAGT R 2 1 2 1 103000 f 74 goat 5_2946267_AF-PAKI 5 2946267 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394312 Affx-122964685 AX-123264667 5 2952043 AGGATTTATGCTTTCTGTTGGTAATGGCCAGTTCT[A/G]TTTATTATGAAATAAGTCCTGATAAAAATTGATCA R 2 1 2 1 102000 f 74 goat snp33841-scaffold399-584264 5 2963602 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440012 Affx-122929780 AX-123310349 5 2994494 ATAACAGTGTACTTGGTCTTCTCTCTTGTACATCT[A/C]TTTTTGTAACCCCTATCCAAATGTTCAGAAAGAGC M 2 1 2 1 201000 r 74 goat snp33840-scaffold399-541813 5 3006775 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443969 Affx-122927001 AX-123314306 5 3066672 TGAAAATGGGTATGTCACTTAAGAGAATGGAGAGG[C/T]AATTAGGGGCCAGTTCAGGCAGTACCTGGTAGGAC Y 2 1 2 1 201000 f 74 goat snp33838-scaffold399-469635 5 3080386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430497 Affx-122937231 AX-123300838 5 3117946 AAATTTTAAGTTTATATAAAATTATACTCTAGCTG[C/T]GAGTGTTGTTGCATATGTTGGAATAGTTTCAGTAA Y 2 1 2 1 102000 r 74 goat snp33837-scaffold399-418361 5 3130943 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794639 Affx-122964265 AX-385281600 5 3163711 GCCAGATCTCTCAGATAGTACTTCTCAAACTATGT[A/G]TGGTAAAAGACTATTTTTCCCCTCTGCATCAGAGA R 2 1 2 1 202000 r 74 goat snp33836-scaffold399-372596 5 3177027 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431481 Affx-122936256 AX-123301822 5 3192218 TAAAGAGCTTTGACAACGTTATATTAAATATAAAG[C/T]ATGGAAGAACTATGTTTACACTGATATGAGGGTCC Y 2 1 2 1 101000 r 74 goat snp33835-scaffold399-344089 5 3205500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426784 Affx-122940548 AX-123297130 5 3233290 CTATAGAGGGATCTAAGAAAAGTGAAAAGAGAGAA[C/T]TAAAGAAATGTAATATGATGAATACTTCCAAGGAG Y 2 1 2 1 303000 r 74 goat snp33834-scaffold399-303017 5 3245241 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435918 Affx-122932761 AX-123306257 5 3276713 AGGCAATGAACAACACAGAAATGAAATTGTAAATA[A/C]AAAGCATTGTGAGGCACAGAAGAGTGGTGCTAGTA M 2 1 2 1 201000 f 74 goat snp33833-scaffold399-259594 5 3288723 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799816 Affx-122931978 AX-385286742 5 3312323 TTAAGGGTTCTCACCTGTGAACAATTACTTGTTCT[A/G]TCAACAGTATTAGAATAAATGGATGGTCTTAGCAA R 2 1 2 1 101000 f 74 goat snp33832-scaffold399-223984 5 3328188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437201 Affx-122932050 AX-123307539 5 3342461 ATCTGTATCAGAATTACCTGAATTGTTCATTGAAA[A/C]TGCTGACAGCTTAACCTCCCCCAGGACAATAATAT M 2 1 2 1 201000 f 74 goat snp33831-scaffold399-193846 5 3358775 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384250 Affx-122972357 AX-123254608 5 3372214 AATTACCAAGATAATCAATCATACAATCACCTTTT[A/C]TTTTTCTGGAAATATCTAATCCAGAAGAAGACTAT M 2 1 2 1 202000 f 74 goat snp33830-scaffold399-164093 5 3388252 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783961 Affx-122967004 AX-385271015 5 3402667 AATTACACATGTTTTGTTTTGATCTGAAGATTATC[A/G]TTCTTAAATTTAAATGTTATCTATTTGGCTACCAT R 2 1 2 1 303000 r 74 goat snp33829-scaffold399-133640 5 3419485 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408682 Affx-122953448 AX-123279033 5 3459064 ATTGGGTAGATTGCTTGTCTCTATTTAACTTAGTC[A/G]TTTTTCTTATATTTTGTCTTTTCCTTCATTTGAAA R 2 1 2 1 101000 f 74 goat snp33828-scaffold399-77243 5 3475878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404832 Affx-122956636 AX-123275184 5 3487621 ACATGACTACTGGAAAAACCATAGCCTTGACTAGA[C/T]GGACCTTAGTCGGCAAATAATATGCCATGCCCATA Y 2 1 2 1 303000 r 74 goat snp33827-scaffold399-48686 5 3504386 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768557 Affx-122946159 AX-385255737 5 3545385 AAAATTTTCAAAATTTGAGCAAACATCAGTTCTCA[C/T]GGGAACGCATCCAGCTGAAAGTGGTTAGGAGCTTT Y 2 1 2 1 101000 r 74 goat snp19014-scaffold1911-8979 5 3558208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440682 Affx-122929920 AX-123311019 5 3574084 CTTCACATCAATGTCAACCTTCCCTTGGCAGCTTA[C/T]GCACTGACTTCTGGCTACAGCTCCACCAAGCATAG Y 2 1 2 1 101000 f 74 goat snp19015-scaffold1911-37678 5 3587924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397276 Affx-122962341 AX-123267631 5 3608837 TACCACAAATCCTACTAGCTCCCAGAATCTTCCTC[G/T]CTGGAAGCCATCTTGACCAAGCAATGCATGTGCTA K 2 1 2 1 201000 r 74 goat snp19016-scaffold1911-72431 5 3623276 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786981 Affx-122941782 AX-385274009 5 3691732 CAAGCTGAAGAGACAAACACAGATACAAAGAGTCA[C/T]AAGGAACCCTTTCCTAAAATTCTACCTTACCAAAG Y 2 1 2 1 101000 f 74 goat snp19018-scaffold1911-155326 5 3707367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423903 Affx-122942283 AX-123294249 5 3842269 TTTGGACATAACTGATGGACAGGCCTTTATCGTTG[A/G]GCCGCAGTGGGACACCTCTGCTCTCTCAACCTTGG R 2 1 2 1 101000 f 74 goat snp19022-scaffold1911-305863 5 3857314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770951 Affx-122935945 AX-385258115 5 3896620 AACTTAGGACGCATGCATACTTAATTGCAGACTAA[C/T]ATTTTAAGAAAATATGAAGTGATAGACCTGCTCCA Y 2 1 2 1 201000 r 74 goat snp19023-scaffold1911-360214 5 3912927 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788569 Affx-122961735 AX-385275586 5 3926484 GACCACAGCCATTACAAAAATGCCCTGCAAATATA[C/T]AGCATTCTGTATTTACAACAACCTGCTTCCCTCCC Y 2 1 2 1 101000 r 74 goat snp19024-scaffold1911-390078 5 3943394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398132 Affx-122961694 AX-123268487 5 3964374 TCAGGTTTTCAATTCGTTTCACAGAAGCTAGTTCT[A/G]TCTAAAAAGGAAGGAAATAACTTTATCAAAAGGAT R 2 1 2 1 103000 f 74 goat snp19025-scaffold1911-427968 5 3981275 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278167 Affx-1111836285 AX-519551656 5 3978285 CATGATCCAGGGGAACCCTCAGGAGAAATGGCATT[A/G]GCAAATGAATGAATAAATGAGAGAGGAATAGAGGA R 2 1 2 1 303000 f 74 goat Random2.2K-513 5 3978285 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418223 Affx-122947047 AX-123288571 5 3998060 AAGACAGATCTTCAGGTCCTAAAGTATGTCTGTTC[A/G]TGTTCCACATGCATTCTAAAGGCTCTGTGAAGCAA R 2 1 2 1 101000 f 74 goat snp19026-scaffold1911-461654 5 4014996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448067 Affx-122924342 AX-123318403 5 4045145 CAAGTGATGCAGACACTACTCAGCCCCAGATCATT[A/G]TTGATTTGAGGAAACATGGGACAAGCATTGCAAAT R 2 1 2 1 201000 r 74 goat snp19027-scaffold1911-508739 5 4062602 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420747 Affx-122944726 AX-123291094 5 4075822 TTCTGCAAGAATTCACACAAAGCTTGCAAGTGAAA[C/T]GGACAGTTATCTTCAAAATCCAAGTGGTAGGGGTA Y 2 1 2 1 201000 f 74 goat snp19028-scaffold1911-539416 5 4093263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380456 Affx-122975737 AX-123250814 5 4109459 TCAGAATTTCACCTAAAACAAATAATTTTGATACG[C/T]AGGGTAATATATTTAGACACAAGATATGTGAGCTC Y 2 1 2 1 101000 r 74 goat snp19029-scaffold1911-573053 5 4127835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780072 Affx-122969128 AX-385267170 5 4146591 GTTATAGAGTTTATATGATACATAAAGATAAAGCA[C/T]AGAAAGCATTTGACCTGACATACAGCTAGCATATA Y 2 1 2 1 101000 r 74 goat snp19030-scaffold1911-610185 5 4165404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388310 Affx-122969377 AX-123258668 5 4188498 TCATTAGAGACACTTTACAGCAGCTTTTACATTAA[C/T]AGTAAAGTGAAGTGTTAGTTGCTCAGTCATGTCCA Y 2 1 2 1 303000 f 74 goat snp19031-scaffold1911-652092 5 4200640 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434118 Affx-122934930 AX-123304459 5 4227973 TGCTTAGAGTGATTTGCTTAAGGCCTCTGATTCTA[C/T]ATCCAGTCAATATTCCATTGGCTACTCATTAAAGA Y 2 1 2 1 101000 f 74 goat snp18733-scaffold1895-555496 5 4255662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389438 Affx-122968355 AX-123259796 5 4268370 CACTTAATCTTCTCAGTGCTTTCTCTGTCATGTCT[A/G]TTAGAAATCCATTCATTTCTTCTCCTTTCCTTTAT R 2 1 2 1 201000 r 74 goat snp18732-scaffold1895-515099 5 4296024 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385215 Affx-122971707 AX-123255573 5 4297190 AGATGAGTGACATAATTACATTTGTTCCCTTAAAG[C/T]GATGCTTATTCCTAGTAATCAAGGACAAGCTAATT Y 2 1 2 1 101000 r 74 goat snp18731-scaffold1895-486279 5 4325392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409286 Affx-122953112 AX-123279637 5 4329684 GTATAGAAATTTTCAGGAAACATTTCAAAGCTTTG[C/T]GCCTGGCAAACAGCAGGAGTGGGATTGTAGCTCTT Y 2 1 2 1 103000 r 74 goat snp18730-scaffold1895-453785 5 4357831 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441903 Affx-122928611 AX-123312240 5 4369651 GACTAAGTAGCCGAGGAGATGGTGTTCCTAAAGAA[C/T]GGACATGGATATTTCTGAACCTTTTAAAATTATGA Y 2 1 2 1 101000 f 74 goat snp18729-scaffold1895-413818 5 4398484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777038 Affx-122960094 AX-385264161 5 4412403 CCTGTGATTCATCCTTTATACTGTTACTTGGTGAT[A/G]TTCTCATCATGTAATTAACTGATTATGTTCCTTTT R 2 1 2 1 101000 f 74 goat snp18728-scaffold1895-371066 5 4441043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772970 Affx-122957779 AX-385260114 5 4523688 AATGAGCCAAATAAAATCGCTGAGCCCTTCTTTGT[A/C]TAACTGCTAAATCAGAACAGCTAATCCATGTTTTT M 2 1 2 1 101000 f 74 goat snp18726-scaffold1895-259781 5 4552766 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779707 Affx-122963450 AX-385266807 5 4576269 AATTATCCTCTTAATTAGTACTGTTATATGTTAAA[C/T]ATATAAAGCTTGTTTAGCTTTAGTATTGTCTCGGC Y 2 1 2 1 101000 r 74 goat snp18725-scaffold1895-207200 5 4605204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389234 Affx-122969045 AX-123259592 5 4662943 TTGAAACCCTGTGTATTGCTAGTAGGAATGGGAAA[C/T]ATGTAGCCACTATGAGAAAGAGAATATAAGTTCTT Y 2 1 2 1 101000 f 74 goat snp18723-scaffold1895-120526 5 4691919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422220 Affx-122944028 AX-123292566 5 4709049 CATGTTTTGAGGAAGAAACATTTACTGAAGGTTCA[C/T]GTCCTCTTGTGCTTCTTAATTTGAGAAATAGTCCA Y 2 1 2 1 101000 r 74 goat snp18722-scaffold1895-74420 5 4738366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429797 Affx-122938201 AX-123300138 5 4741965 GACCATATGGACGGAGTTCCTCCACTTGTGGGAGA[C/T]TGTGTTATAGTCTTTTTCACTAAGGTTCGTGGGAG Y 2 1 2 1 101000 r 74 goat snp18721-scaffold1895-41504 5 4776686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401250 Affx-122959299 AX-123271603 5 4795801 TACATAAATAGATTCATATGCCTGCTGTCTTATCA[C/T]GGATGTCTATTTTTTAAAGTCTTTTTGCCTACTTC Y 2 1 2 1 101000 f 74 goat snp27789-scaffold2973-83864 5 4831214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784412 Affx-122951566 AX-385271461 5 4848756 AAATAAAAGTTTGTGCAATAAATGTTGTGAAATTA[C/T]TTCCCACTAAAAAGTAAATAATTGGCAGCCACTTA Y 2 1 2 1 101000 r 74 goat snp27788-scaffold2973-30909 5 4883832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778423 Affx-122919288 AX-385265537 5 4891775 TATTTTAGCCAAAAGGATTAAGTCAACTAAGCACA[C/T]GCTAATTAGAATTTCTAACAATCAGACACAGGTTT Y 2 1 2 1 101000 f 74 goat snp15217-scaffold1622-12011 5 5105723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772597 Affx-122935779 AX-385259746 5 4924728 AAACATGAGACCATGAAGAGTAAACTACTCTGTAC[A/G]CTTTCGTCAAAGGTTGTCATCAACGTGGACTGAGT R 2 1 2 1 101000 f 74 goat snp15218-scaffold1622-44964 5 5138261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397646 Affx-122962612 AX-123268001 5 4972341 ACAATCTGTTGATTTGTTTCCATCTTGGTTCTTTC[A/G]TGCCTCTTCTTTCTCAGCTCACACCAGTGTGCAGT R 2 1 2 1 101000 r 74 goat snp15219-scaffold1622-92577 5 5186201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437647 Affx-122931799 AX-123307985 5 5030730 ACGCTTCCTTGTTGCTGGCTGCCACGATGAACTGT[C/T]TGTTGCTGTTGTCCAGTTGTTGAGTCCTGTCCGAC Y 2 1 2 1 201000 f 74 goat snp15220-scaffold1622-150966 5 5244140 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383240 Affx-122972754 AX-123253598 5 5065571 ATTTCCCACAGGAGAAAGGTTTTTAAACCAAAAAT[A/G]TTTTTCAAAACCAGAAGAAAAAAATAAGACAATCA R 2 1 2 1 103000 f 74 goat snp15221-scaffold1622-185807 5 5278802 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441260 Affx-122929487 AX-123311597 5 5102504 GAAACCAGCTTCATTAGAGAAAGGAGATTAGTCAC[C/T]ACCAGGTAGACAGGATTTCTTGGACCGCGCCCTGT Y 2 1 2 1 101000 f 74 goat snp15222-scaffold1622-222740 5 5315383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408282 Affx-122953794 AX-123278633 5 5145894 TAGGCAGTGATTTTCAGCCCTAAGACGATTTGCTA[G/T]CATCTATGGCTCTTTTTCAAACTGAAGTAGCATCT K 2 1 2 1 101000 f 74 goat snp15223-scaffold1622-266130 5 5358882 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383940 Affx-122972962 AX-123254298 5 5179055 ACATATTCTGGAAGTACCGAAGGCTTGCATATCCC[A/G]TAACTATAAACCCCACCGGGAAGTACATACACCAG R 2 1 2 1 101000 f 74 goat snp15224-scaffold1622-299291 5 5392011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403616 Affx-122957550 AX-123273968 5 5237155 GAGGATCCCTTCATTTGTCATTCCTTCAGATTCTG[C/T]GGCCAGGGAGCTTGCCGTCAACAGCAGAGAAAATC Y 2 1 2 1 101000 f 74 goat snp15225-scaffold1622-357391 5 5451052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767395 Affx-122948294 AX-385254668 5 5348475 AGATGGGAAAGTCAGAGGGAAAGAGCGTATAAGAG[C/T]GCTTTACTGCAGTTATCCTTAGAAGATGCCACACA Y 2 1 2 1 101000 f 74 goat snp15227-scaffold1622-468711 5 5562569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390873 Affx-122967809 AX-123261230 5 5410199 AACATACTCTTATTCTATTTTACAAAACTGACCAG[C/T]GTTTGAATTTATAAATGATCATTAAACAGGATATT Y 2 1 2 1 101000 f 74 goat snp15228-scaffold1622-530435 5 5625234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777519 Affx-122926912 AX-385264638 5 5424311 AAAGTAGCTAGTACTTCTTTTCCCAATTTTAGTTT[A/G]CCTGATATTTGATTAACACAGTCACTACTACCTAG R 2 1 2 1 101000 f 74 goat snp6035-scaffold1213-6500 5 5640982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774759 Affx-122941896 AX-385261893 5 5474583 AAATTGGTATAAATCAACATGTGTAAAAGAGACTC[A/C]GCCAGAAAACAATGCGAATCTTTGCCATTCTAAAG M 2 1 2 1 101000 r 74 goat snp6036-scaffold1213-56772 5 5688792 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272312 Affx-1111833470 AX-519546050 5 5501967 CCTGGGACCCCTTGCTACAACGCTTGCCCCTGGAC[A/G]AGTGTCTTCTCCAGCAACAAAATCCAAAGAAACTA R 2 1 2 1 303000 f 74 goat 5_5501967_AF-PAKI 5 5501967 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424267 Affx-122941997 AX-123294613 5 5508027 TTACAAAATATTTTAATACATATATTAAATGTAAA[C/T]GTGTTCTGAAGTATCCTGAGTATAAAGATTGAATT Y 2 1 2 1 101000 r 74 goat snp6037-scaffold1213-90216 5 5722309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776545 Affx-122930055 AX-385263672 5 5545906 ATGTGTATTGCTGATGTGACCAACAGAAGTTTGCA[C/T]GTACTGGAATACACGTTACATTTGCCTTTCCCCTA Y 2 1 2 1 101000 f 74 goat snp6038-scaffold1213-128095 5 5760707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453815 Affx-122919561 AX-123324148 5 5575663 AATGACTTTTGTGAATGGAAAATCTGCATATACTG[C/T]TGCTTCGGCTGGGCCGGTCTTGTGTGGATGGCTCA Y 2 1 2 1 101000 f 74 goat snp6039-scaffold1213-157852 5 5790791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408996 Affx-122953893 AX-123279347 5 5638113 TTAATACATAAAGTTCACCTAGGAGATCAAGATAA[C/T]GAAACTAATTTTGTTCAGTATGAAAAGAGGAAACT Y 2 1 2 1 101000 f 74 goat snp6041-scaffold1213-220302 5 5854049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395480 Affx-122963901 AX-123265835 5 5667778 CAGCGTTCAATATGTTAATTTCAGAGTACGTGTGT[A/G]TTGGGGGTAGGAAGGAGCCACACTTGAGTGACCTC R 2 1 2 1 101000 f 74 goat snp6042-scaffold1213-249967 5 5883267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792618 Affx-122929959 AX-385279599 5 5711854 GCTTATAAGGAACTCACATTTGCAGAAGAGGACAC[A/G]TAAATTGATAAGTACAATACAATAGAGTAGGTGTA R 2 1 2 1 101000 f 74 goat snp6043-scaffold1213-294043 5 5927775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383668 Affx-122972509 AX-123254026 5 5790406 AGTACATATCTTGATAATAACCTTCTTATAGTATT[A/G]CAAGGAGGCTTAGGTTTAACAGTAATAATTATAAG R 2 1 2 1 101000 r 74 goat snp6044-scaffold1213-372595 5 6008633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791663 Affx-122976238 AX-385278654 5 5820267 TCCTAGAAAACAGACTAGTACCTTGAATACTTTCT[A/G]CACATAGTAGGTATATTTGATAATTTCACCTCTGT R 2 1 2 1 101000 r 74 goat snp6045-scaffold1213-402456 5 6038517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393920 Affx-122965085 AX-123264275 5 5901989 GACTATTAGCAGGACCAGCTGCATTATTTGTAGAG[C/T]CCAGTGCTGAATGAAAATGTGGGTCTCTTTGTTCA Y 2 1 2 1 101000 f 74 goat snp6047-scaffold1213-484178 5 6120398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383146 Affx-122973242 AX-123253504 5 6040291 TTTTCTTCCCCCTTTGCTCTGTCTCTATGTAAAGG[C/T]ATACACACGGCTTCCCTGGTGGCTCAGATGGTAAA Y 2 1 2 1 303000 f 74 goat snp6050-scaffold1213-622480 5 6260315 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772624 Affx-122967662 AX-385259772 5 6101165 TCTGTAACAAAATAGAAACTGTTGTGGAAGAAAAT[G/T]TAATAAAAATATTAGCTAGATGTTGGTTCATGCTA K 2 1 2 1 202000 r 74 goat snp6051-scaffold1213-683354 5 6321852 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772947 Affx-122940298 AX-385260091 5 6137852 GTCTGGTCTAGACATATTAGTATATGTCTAATACA[C/T]ATCTTGTTTCTTAATTCTTGCTCCATTACTGCATT Y 2 1 2 1 101000 r 74 goat snp6052-scaffold1213-720041 5 6358276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791549 Affx-122960479 AX-385278539 5 6185804 CTATTTTTTGAAAATGAGGAGAACTGGACATGTGC[A/G]TTTAACAAGTAAATGGAACTGATTTCATTCATGGG R 2 1 2 1 102000 f 74 goat snp6053-scaffold1213-767993 5 6404546 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389689 Affx-122968699 AX-123260047 5 6283370 CCCATGCCTTCATATGCCTTCATTGTCTAGTGGGA[C/T]GATGGTGCAAATGAGTGTCAAGGATGGTCTGTTGG Y 2 1 2 1 101000 r 74 goat snp6055-scaffold1213-865559 5 6502219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796408 Affx-122972245 AX-385283358 5 6325527 TTGCTGAGGATTATTTATTACCGAGATATTTTAAC[A/G]TACACTTTTCTTTTTCCAAGTTGTAAGATGCAGCC R 2 1 2 1 101000 r 74 goat snp6056-scaffold1213-907716 5 6544791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376356 Affx-122978326 AX-123246715 5 6356750 ATACAAGCATGTAAAAGGAACCATATCTTCTTCAA[C/T]ACTATGCATTCAAACCTACCAAAAGCCAAGTAAGA Y 2 1 2 1 101000 r 74 goat snp20363-scaffold2019-183334 5 6575895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773332 Affx-122952897 AX-385260474 5 6403630 GTAGGTAGGAAGGATAAAGACGTGTAAAGTAGACT[A/G]CAAAAGTCAGTTATGTACACTGTAATTTTTTAAAA R 2 1 2 1 201000 r 74 goat snp20362-scaffold2019-136454 5 6622453 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795766 Affx-122968433 AX-385282719 5 6441582 AAGTGAAGACTCAAACTGCAACCTCCAGATTCAAC[A/G]TCTCATTATTTATTAATCAGGGATGCATATCTAGT R 2 1 2 1 101000 f 74 goat snp20361-scaffold2019-98502 5 6659685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453872 Affx-122919520 AX-123324205 5 6493852 AGAAGGCTTTGTGAAAGGTATATAAGGTAGGTCTT[A/G]TCAAATACTGAAGTTTCAGGACCTCTGAAAACCCT R 2 1 2 1 201000 f 74 goat snp20360-scaffold2019-46232 5 6712761 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434122 Affx-122934926 AX-123304463 5 6524178 TCTCTAGCTCACCAAGACCAATGCTTATAGCTGAA[G/T]AGATGAACAAATTAATATTCATAATCAAGTGTAAA K 2 1 2 1 101000 f 74 goat snp20359-scaffold2019-15906 5 6743295 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278169 Affx-1111836286 AX-519551658 5 6546009 AAATCTGTAACTCACTGACTTTAGCAAACTTGCCT[A/C]TAAGTCTTACCTCTCTCTGTCTCTCCACTTTCTAG M 2 1 2 1 201000 f 74 goat Random2.2K-516 5 6546009 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382018 Affx-122974062 AX-123252376 5 6563698 AATGTGAATTGACATCTCATACACAAAAGCACTGC[A/G]TGAGGGGAATAGCAACTTAGCTTAATGAAGATGTA R 2 1 2 1 201000 f 74 goat snp54018-scaffold822-23515 5 6779068 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425501 Affx-122941478 AX-123295847 5 6606867 GAGATGAACTATTATTGCCAACTAGCGCAGAGCAA[C/T]ATACCTTCTTTATTACAGAATCCGAGAGCACTCCT Y 2 1 2 1 101000 f 74 goat snp54019-scaffold822-66684 5 6821614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788501 Affx-122939637 AX-385275518 5 6656022 GTTACATGTGACCAGTGATAGGATAGGAACAACCC[A/G]CTAGAGGACTTAACTTGAGCATCTTTCACTGTCTT R 2 1 2 1 101000 f 74 goat snp54020-scaffold822-115839 5 6871387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430621 Affx-122936968 AX-123300962 5 6693380 GAATGTACACGGTAAGTAAACCTTAATTGCTCATA[C/T]AGTTGAAAATAATTTTATCATATTGAAAGAAGTTC Y 2 1 2 1 101000 f 74 goat snp54021-scaffold822-153197 5 6909014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786186 Affx-122971245 AX-190704346 5 6724928 ACTTATAACTGACATTTAAGCACTTAAATTTAACA[C/T]GTTTTAGTGGAAATTATCATTTCTATGGGAACCTT Y 2 1 2 1 201000 f 74 goat snp54022-scaffold822-184745 5 6940498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392570 Affx-122966076 AX-123262927 5 6753483 AAATACTCATTGTTTCTAGAAAGCACCATTCTAAA[C/T]GTACCCAGGCTCCCTCTAAAGTAAAATACATTGAA Y 2 1 2 1 101000 r 74 goat snp54023-scaffold822-213300 5 6970753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436838 Affx-122932219 AX-123307176 5 6792560 CAAAAAGAAAGACAACCCTGGGTAAGAGCTAAGAT[A/G]GGGTTTCACTGGGGGATCTCACCCTTGATTAGCTT R 2 1 2 1 101000 f 74 goat snp54024-scaffold822-252377 5 7008513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400555 Affx-122960425 AX-123270910 5 6841490 TAGAAACGAAACTGTTCCCAAAGCAGAAATGGAAC[A/G]TGGAGCTCAACTCCCATAGCTAATAAACTGAGGTA R 2 1 2 1 101000 r 74 goat snp54025-scaffold822-301307 5 7057035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404141 Affx-122957090 AX-123274493 5 6878482 TAGTTCCTGTCTCTATCCACCCCCTCACAATGGTG[A/G]CTTGTGTGAACACATTCAGCTGGAGCAGCTGCCCA R 2 1 2 1 101000 r 74 goat snp54026-scaffold822-338299 5 7093779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792705 Affx-122931159 AX-385279686 5 6909588 GCTATTTTCTTCTAGTATGTTTGCTAAGAGAGAGT[A/G]CAAGAGAGAGGATGCACTGATGAGCGTGTTTCATG R 2 1 2 1 102000 r 74 goat snp54027-scaffold822-369405 5 7124196 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789535 Affx-122946201 AX-385276545 5 7012191 CGATGCTTTAATCTTTCACATCACCCACCAACTAA[C/T]AGAGAAACTAGATGTTTAAACAGATGGTTCGGTGA Y 2 1 2 1 101000 f 74 goat snp54029-scaffold822-472008 5 7225957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410251 Affx-122952535 AX-123280601 5 7040791 GCACTCTTAAAGAGCATCCTGACTGGTCCTTTTTT[A/G]ACCCTCTCCTCTCATCTTCACCAAAAATCCCAGGT R 2 1 2 1 101000 f 74 goat snp54030-scaffold822-500608 5 7254631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768778 Affx-122971069 AX-385255955 5 7085429 ACTTAGGATTTTTTCTTCATGTAACTGCAAGGTAT[A/G]TCATGAAGTTAATGGAAATGGACTTTCCTTTTTTT R 2 1 2 1 201000 r 74 goat snp54031-scaffold822-545246 5 7299303 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385707 Affx-122971112 AX-123256065 5 7126020 ATATTCCTACGTCCGTGCTTCTTTGATTCCAGTAC[G/T]GCAAATAAATGTATAAGCTATGGAAAATTCAAAAG K 2 1 2 1 101000 f 74 goat snp54032-scaffold822-585837 5 7340355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449669 Affx-122922568 AX-123320004 5 7167583 GCCAACTTTTATCCTCAGAAACTCTCTCTGGTGTT[A/C]GTTTTTATTATCATATCATTTAAGAATTCATAGTG M 2 1 2 1 201000 r 74 goat snp54033-scaffold822-627400 5 7381998 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415812 Affx-122948894 AX-123286161 5 7200417 AGTAGCCTTCAGTATCAAACTGACGTTAGGAACTG[A/G]CTCCTACGTTCGAACTCTTCTCTCCTCTTGATTTG R 2 1 2 1 101000 f 74 goat snp54034-scaffold822-660234 5 7415185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418655 Affx-122946327 AX-123289003 5 7238973 AAAGAATTAGGACAATTCTACAATTGGGATCAGAA[A/G]ATCACAGCAGAGGCCCACTTCCAGGAAATAATGAC R 2 1 2 1 101000 f 74 goat snp54035-scaffold822-698790 5 7454139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392426 Affx-122966194 AX-123262783 5 7284652 CAAGTAAAAGGGATAGTGGAAATGCATGAAGTATC[A/G]CCCCTTTAAATAAGATAACTTTTTAAAGAGTAGGG R 2 1 2 1 103000 f 74 goat snp54036-scaffold822-744469 5 7499977 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278329 Affx-1111836287 AX-519551815 5 7327312 TCAAATTAACTTTTAAATGTTTTCTATCTTGCAAC[A/G]TGCTTTTGAAATAAATTTTCACCCACAAAAATGTT R 2 1 2 1 201000 r 74 goat Random2.2K-517 5 7327312 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406556 Affx-122955107 AX-123276908 5 7333911 TTCACCAGGGGCTGGGTGCTAACAGATGTGGGTAG[C/T]GATTTGCACTAGGAACACGTGATGGTGTAGAAATG Y 2 1 2 1 101000 r 74 goat snp54037-scaffold822-793728 5 7549368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427968 Affx-122939191 AX-123298311 5 7421904 TGAGAATGTCATTGTACAGGATGAGGATCCTTGTA[C/T]GTCTTAGGGTAAAGGCTAAGTTGCCCTATCAATAA Y 2 1 2 1 101000 r 74 goat snp54039-scaffold822-881721 5 7636070 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800660 Affx-122963690 AX-385287578 5 7456757 CAATATGTTACCAAAGAAATCATGAGCCAGACTTA[G/T]AGACTTCTTTTACTTTTCACCCCTTAAAACAAACT K 2 1 2 1 101000 r 74 goat snp54040-scaffold822-916574 5 7671183 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771408 Affx-122964599 AX-385258566 5 7531528 CCATATGTCTTATGGCTAAAGGCAGACTTTTAGAG[C/T]AAATTATGACATTTTATGTAGCTTTGAAAGAATAT Y 2 1 2 1 101000 f 74 goat snp54042-scaffold822-991345 5 7746988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396765 Affx-122962772 AX-123267120 5 7581676 TTCTTGCCACAAGCATACTGTATTATCAATTTGCT[A/G]TAAGGCTTGGGGAAACTGAAGTGGTCACTTCTTCG R 2 1 2 1 101000 f 74 goat snp54043-scaffold822-1041493 5 7797400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396110 Affx-122963416 AX-123266465 5 7624732 AACTCACTCTTTCTCACACTTAACTCCCCCTGAAA[C/T]GTTCCCTTGTCCAGAAAATTAACAACCTATTTCAA Y 2 1 2 1 201000 r 74 goat snp54044-scaffold822-1084549 5 7841370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798209 Affx-122923362 AX-385285143 5 7669179 CATTTTCCACTAAGCAACATGGAATTTCCTATGAA[C/T]GACTTCTGTTGATACACACAGGTCTAAAGTGTTTT Y 2 1 2 1 101000 r 74 goat snp54045-scaffold822-1128996 5 7886931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783938 Affx-122944747 AX-385270993 5 7700098 TGCAGTTTTCAGAAGTTATTGATGAGTGAAAAAGG[C/T]GCACAGAGAGGCGTGACAGTTACTCTGAATATACC Y 2 1 2 1 101000 r 74 goat snp54046-scaffold822-1159915 5 7919116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781154 Affx-122941913 AX-385268239 5 7744179 CTTCTACCTCTTCTGAAAATGGAAAGGAATTAATA[C/T]GATTATAAACATCCAATCTTCAATCCAGCCACCTT Y 2 1 2 1 201000 f 74 goat snp54047-scaffold822-1203996 5 7965213 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772448 Affx-122942313 AX-385259599 5 7809443 ATACCCGGAATGAGTGTGAAGCAGTTCTGCCAGGC[A/G]TTTGAGTATTATGGAGATGGGACGAAGTACAAGCA R 2 1 2 1 202000 f 74 goat snp54048-scaffold822-1269260 5 8029624 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430858 Affx-122937422 AX-123301199 5 7845430 GGAAGACTTGCAAGAAAGTTGGCAAAGTCTACAAT[A/G]CATTAATCTCTTTCAAAGAAGAAAAACTGCCTCAA R 2 1 2 1 103000 f 74 goat snp54049-scaffold822-1305247 5 8065766 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397396 Affx-122962262 AX-123267751 5 7895598 TGGAATGACCAGTATGAAAATATACCTGACAGTGC[A/G]TTTGAGACTGCTGAGATAAGAGGCATGGTGGACCA R 2 1 2 1 101000 r 74 goat snp54050-scaffold822-1355415 5 8116477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397575 Affx-122962007 AX-123267930 5 7990337 AATCAAAATTGTTTTGCTCACTGAACTCACAGAAA[C/T]AGACTAATTTACCAACTTTGAAGTTTTGTACTGGG Y 2 1 2 1 101000 r 74 goat snp54052-scaffold822-1450154 5 8209663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416244 Affx-122948208 AX-123286593 5 8049761 TGGCATTTTCATTTGAAAACTAAAATATATTATCA[C/T]AGAAACATTTTCATTTCTCTGTGATTGATTTATTT Y 2 1 2 1 103000 f 74 goat snp54053-scaffold822-1509578 5 8268460 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437833 Affx-122932099 AX-123308171 5 8081403 GTTAAAAAGCATAAGCGAGATATTGGGAGATAACA[A/G]TAATTGAGAATGAGATGTGGAAATAGGAGTTAACG R 2 1 2 1 101000 f 74 goat snp54054-scaffold822-1541220 5 8300616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383098 Affx-122973279 AX-123253456 5 8115301 AGTAGTTGTACCAAAAAGCACTATTGTCATTATTC[A/G]TTTACTGGCAATTCTGGAATATTCCTAGACTAGAG R 2 1 2 1 101000 r 74 goat snp54055-scaffold822-1575118 5 8334424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406607 Affx-122955843 AX-123276959 5 8171510 TAAAGCCAAAAGACCTTTAGGAATCATATAATATT[C/T]TTTCTGATTGCTAGTAGGCTGGTGGCAAAGCAAAG Y 2 1 2 1 202000 f 74 goat snp54056-scaffold822-1631327 5 8391671 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391043 Affx-122966862 AX-123261400 5 8201430 GATTTGCTCCAAATTGGAAAGTTACCTTGTGATAG[A/G]AGGACAGAGAGAATGCTATCACCTGCCCCCTAGAA R 2 1 2 1 101000 f 74 goat snp54057-scaffold822-1661247 5 8421801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397633 Affx-122962622 AX-123267988 5 8251572 TTTTACTCTATTCTAAGTATTTCTAATCATCTGTA[C/T]GTTGATACAGTAACGACCAGGAGAATGTACATGTT Y 2 1 2 1 101000 r 74 goat snp54058-scaffold822-1711389 5 8470845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797971 Affx-122941398 AX-385284907 5 8282239 GGAATGATTACATGTAGTAATGACTGATAAAATTC[A/G]TAAAAATATCAGTTGATCTAAATTTTAGTTCACTT R 2 1 2 1 202000 r 74 goat snp54059-scaffold822-1742056 5 8501612 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406179 Affx-122956154 AX-123276531 5 8321803 TTGTAACTCTATAGTTTATTTCTTTATACATTCAA[C/T]ATCACATCAACCCTTTGTTAGCATGGCTGACCTTT Y 2 1 2 1 101000 r 74 goat snp54060-scaffold822-1781620 5 8540781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438826 Affx-122930783 AX-123309163 5 8369325 GTCCTGCCTGCAGTGAGTGATGCTGTGCAGGGTGT[A/G]CCAGCTTTCAGTGAACCCACTAAACTGGGCAGCTA R 2 1 2 1 101000 r 74 goat snp54061-scaffold822-1829142 5 8588665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426004 Affx-122941138 AX-123296350 5 8398788 TCAGATACACATACAGTAAAGAATACGAGCAAGCA[A/G]CCTTAGCATAGCATAGCAGAAAATAAGCCTGTGGA R 2 1 2 1 102000 f 74 goat snp54062-scaffold822-1858605 5 8618487 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417998 Affx-122946667 AX-123288346 5 8453316 ACTAGTACAATTTTAAGAGAAACTTTGAAGGGGAT[A/C]TACAACATAAAAATTATTTAGAAAAAATAATTGAC M 2 1 2 1 103000 f 74 goat snp54063-scaffold822-1913133 5 8673872 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771179 Affx-122966845 AX-385258339 5 8489659 AGAAGCTAATGCCTCAGTCCTTGTAGAACAGATGG[C/T]AAGAGACATATGTTACTTGGAACTTTTTTAAAAAG Y 2 1 2 1 101000 f 74 goat snp54064-scaffold822-1949476 5 8710272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776725 Affx-122927219 AX-385263851 5 8551019 AACCAGCCCTGAAAAGCTGTATTACAGGGAAACTT[C/T]AGTTTACTATAATTAGAAATCTATTTTAACCTTAA Y 2 1 2 1 101000 f 74 goat snp54066-scaffold822-2010836 5 8772257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433981 Affx-122934255 AX-123304322 5 8585026 TGACATTTCTACACAATAGAGTTGTTTTGCTATTG[A/G]GTGTATTTAGTTATTAAATGGATTAGCCTGTCTAC R 2 1 2 1 101000 r 74 goat snp54067-scaffold822-2044843 5 8806800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401381 Affx-122959230 AX-123271734 5 8664523 TTTCTTCCACCTTTTTTAACATATGGCATGTATCT[A/G]TTTAGATGCTTTAGTATCCTTTTCTGCTAGTTCTA R 2 1 2 1 101000 r 74 goat snp54069-scaffold822-2124340 5 8886124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390985 Affx-122966910 AX-123261342 5 8717404 TAATTCTTTAACTACCTCATAATATAAGAAAACAA[C/T]GAACCCAAATAGACTTTAATTTTCTTTACTCATTG Y 2 1 2 1 201000 f 74 goat snp54070-scaffold822-2177221 5 8938912 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786318 Affx-122941729 AX-385273352 5 8748464 TGATCAGATTCCAGCCTGAAACAGCAAATACTACA[C/T]GGTACAGTAAAGAATGTATCAATGTGGAAAAACAA Y 2 1 2 1 101000 f 74 goat snp54071-scaffold822-2208281 5 8969998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445582 Affx-122925130 AX-123315919 5 8786012 CAAGGGGAGATCATATTATCTGAATTACCCCTTCA[C/T]ATAAAACCCAAAGGTTGAGCTAATACTTTAAACAT Y 2 1 2 1 201000 r 74 goat snp54072-scaffold822-2245829 5 9007613 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278174 Affx-1111836288 AX-519551663 5 8873575 AATTGTTTAAATCTAGTCTTTAGAGATGACAGGGG[A/G]AAATGTAGATAATTGCTGCTACAATAAATGGAAAA R 2 1 2 1 101000 f 74 goat Random2.2K-518 5 8873575 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395438 Affx-122963932 AX-123265793 5 8878419 CACAAGTTTAAAGTCATCAGCTGGTGACTCAGCTG[C/T]TAGAATGGAAATCAGAACTTTTCAGAGGAAGATGA Y 2 1 2 1 101000 r 74 goat snp54074-scaffold822-2338236 5 9095441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454078 Affx-122919378 AX-123324411 5 8913231 AGGTGCCCCTCTCACTCCTTAATGTGTTCTGCCTC[A/G]ATAATGGCTTGTTGCCAAACACGCTGAATGCTAGT R 2 1 2 1 101000 r 74 goat snp21401-scaffold2087-193717 5 9130582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402803 Affx-122958284 AX-123273156 5 8943319 ATTCTTTTAAAAAGGGAGAAAAATCTGTTTTGCTC[A/G]TAACTTCCTTTTATATTTTCAAACTTTCAATCTGT R 2 1 2 1 101000 r 74 goat snp21400-scaffold2087-163629 5 9160754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794765 Affx-122935428 AX-385281725 5 9054226 GAGTTTGTAGAATACTGTTTCACTGGAGAGACTCT[A/C]CTTTGGATGCTCATTTTACCTTATGTCTTGCTTTT M 2 1 2 1 101000 f 74 goat snp21398-scaffold2087-52722 5 9271737 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392345 Affx-122966260 AX-123262702 5 9104934 TAGTTGACAATGTTATCTTCATATACAAAGTGTAG[C/T]ATATTTCCATGAAGGTAGCCCAAAATCAAAGCACC Y 2 1 2 1 101000 r 74 goat snp21397-scaffold2087-2014 5 9314507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802559 Affx-122951183 AX-385289462 5 9153728 CATTTTCCTTTGGGAATTATGTTCCCAGAAGTGTA[C/T]GGACTCTCACGATGGAAACTGACATGTACCATGAA Y 2 1 2 1 101000 r 74 goat snp19067-scaffold1917-319225 5 9509945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440778 Affx-122929849 AX-123311115 5 9202798 TGCTCTCCAGCAACTGTCTGCTTGTTGCTGCTGTA[C/T]GTTAGCTCCTGAATCTTGCTTCAGAATAATGCTGG Y 2 1 2 1 101000 r 74 goat snp19068-scaffold1917-368295 5 9558939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396943 Affx-122963183 AX-123267298 5 9236189 ATCAGTTAACAATGGTATGTAAAGTGACAACTGCC[A/G]TCTCTTTTGAAAATATCATATTATGATCATATCAT R 2 1 2 1 101000 f 74 goat snp19069-scaffold1917-401686 5 9592472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441452 Affx-122928767 AX-123311789 5 9253935 CCAACTTGGGATGTTGAGGGTAGTTGTAAGGAGCA[C/T]AGCCTTTGGAGTCAGTTAGTACTCACTTAGAACCC Y 2 1 2 1 101000 f 74 goat snp17482-scaffold1809-4831 5 9621135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775631 Affx-122935147 AX-385262762 5 9336518 GCTGAATAACAAGATACAATATGTACCAAGGTAAT[A/C]GAATTTTAGCTCTTTAAAGAATCTTACATATCATA M 2 1 2 1 201000 r 74 goat snp17484-scaffold1809-87414 5 9702851 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416183 Affx-122948255 AX-123286532 5 9386435 AGTAATAGCAAAGACACATTTTTTCCCCCTAAAAT[C/T]TAGTCCTTTTCAAGACATGGTGACATGATTTGTTT Y 2 1 2 1 103000 r 74 goat snp17485-scaffold1809-137331 5 9752574 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789203 Affx-122977103 AX-385276215 5 9424858 TATAATAGCTTATTTATCTATTTGCAGAGCTGAGC[A/G]TGTAAGACATTATACTTGAATAAATTCAAGGATTA R 2 1 2 1 101000 f 74 goat snp17486-scaffold1809-175754 5 9791312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786612 Affx-122956351 AX-385273644 5 9455749 CTTCATTTACCTCATCTAGACAGCTATTCACCTGG[G/T]AAATCCTTCTAAGACTTTAAACTGATTGTATCCAG K 2 1 2 1 101000 f 74 goat snp17487-scaffold1809-206645 5 9822772 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278333 Affx-1111836289 AX-519551819 5 9467864 CCCAAGCATGGTAGTTGTCTGTAAACTGAAGGCCT[A/G]CTTAGAGTTTTCTCTTATCAACCACAAGGCTGTAG R 2 1 2 1 101000 r 74 goat Random2.2K-519 5 9467864 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802581 Affx-122973557 AX-385289483 5 9501959 CCTTTCAAAGAGTCTCAGACTTTGTCTAGGAAACC[A/G]TTCATGTTCACAGTTGGGAAAATAGGGAATTTTGT R 2 1 2 1 101000 f 74 goat snp17488-scaffold1809-252855 5 9865450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798690 Affx-122950820 AX-385285622 5 9556923 TTTAATATTTTTTGTCATATCTTACCGTATTTAAT[A/C]GAACATTAACCTCTAAAAAAGTGGCCTTACAAACA M 2 1 2 1 101000 r 74 goat snp34529-scaffold405-4073717 5 9919187 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448108 Affx-122924312 AX-123318444 5 9603941 TGACGCTATAACCTGCATAATGTAGCATATACACA[G/T]AAAGCATTTCTGTTTGTATCTGCAGAGGGTGATTT K 2 1 2 1 101000 f 74 goat snp34528-scaffold405-4026699 5 9966506 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476196 Affx-1251763701 AX-586011622 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 4 1 4 1 20000 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 539476451 Affx-1251763701 AX-586011852 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 4 1 4 1 20000 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165430 Affx-1251763701 AX-606940841 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165435 Affx-1251763701 AX-606940846 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165500 Affx-1251763701 AX-606940911 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165820 Affx-1251763701 AX-606941229 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165902 Affx-1251763701 AX-606941311 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 38391064 Affx-122966847 AX-123261421 5 9662168 GCCACATCTTCCTAAGAACATTAATGTTCCATGAC[A/G]TGGTGTTACATGTTTTGGGGTCAAAAGGGTTCAAG R 2 1 2 1 101000 f 74 goat snp34527-scaffold405-3968472 5 10025252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790988 Affx-122924883 AX-385277985 5 9694608 AGAGAAAAAAGGAAATGCCAACTTGGGAAATAACC[A/G]CTTTTTATTAGATTAGGTAATGGGAAAATACACAA R 2 1 2 1 101000 f 74 goat snp34526-scaffold405-3936032 5 10057900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454003 Affx-122919435 AX-123324336 5 9775143 CAAAAGAGAAAAGCATGACTAAAGGGAATGAATGG[C/T]GAATATGTGAGTAGAATTCAGTTTGAAAGAGGTAG Y 2 1 2 1 101000 f 74 goat snp34524-scaffold405-3855497 5 10137221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412039 Affx-122951725 AX-123282389 5 9846495 TGCTCAGGAGTTAATATAAATTTGGCAATGAATAC[A/G]CTAAAGTAGATCAGAAAATAATTATGTATACTGTT R 2 1 2 1 101000 f 74 goat snp34522-scaffold405-3784145 5 10208480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444716 Affx-122926418 AX-123315053 5 9886628 GCCCAAGTACTGTGCTTAGATCATAGGATAGATAA[C/T]GGAGGTATGAACCTGAGAGTTGGTAGATGAGAGGA Y 2 1 2 1 101000 f 74 goat snp34521-scaffold405-3744012 5 10248926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792710 Affx-122950153 AX-385279690 5 9928886 TTTTTTAATTTGGAGAGATTGTGGGGTGACTAATG[C/T]AATCTGTTGGCGCCAGAAGAAATGTTATGTGGTGC Y 2 1 2 1 101000 f 74 goat snp34520-scaffold405-3701754 5 10290789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417636 Affx-122946853 AX-123287984 5 9973946 TTGGTCATAAGTTCACTGTGGAAATTAATTATCCA[C/T]GTAAAAGACTCAACAGAATGCCTAGCACACAGTAA Y 2 1 2 1 101000 f 74 goat snp34519-scaffold405-3656694 5 10336989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780836 Affx-122955645 AX-385267924 5 10072571 TTATTTATAAATGACTAAGAGGTACTAATAGATCC[A/G]TTTCTGTCCCTGAGTAGCTCATAGTATAGTCAGGA R 2 1 2 1 101000 r 74 goat snp34517-scaffold405-3558069 5 10435170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431469 Affx-122936267 AX-123301810 5 10108099 AAACAGTGTTTTCCCGTGCATGTTATACCAAGTAA[C/T]GATGGCTATAAACTATTTAAGATGGTACAGAAGTG Y 2 1 2 1 101000 f 74 goat snp34516-scaffold405-3522541 5 10470304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787285 Affx-122963290 AX-385274310 5 10148306 GCTCTGCTTACTTAAAAAAATCCAACAACCAACAA[C/T]ATTCTTGCTCTTATGGTAGTTTTACAGATGATATC Y 2 1 2 1 101000 f 74 goat snp34515-scaffold405-3482334 5 10510974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781332 Affx-122959394 AX-385268417 5 10178016 TACGCATTTTTCATGATCTCCATTAAAAATGACAA[C/T]AGCAAGTCTCAAAATATATGAGAAGACAGAAAAAC Y 2 1 2 1 101000 r 74 goat snp34514-scaffold405-3452624 5 10540731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803004 Affx-986696122 AX-385289884 5 10203728 TATTGAGACTGATACTTATATCTACAGCTATCTAT[A/G]ATTTTTAAATGAATTTCTTTATTTTTCAGAATTGG R 2 1 2 1 600010 f 74 goat 5_10203728 5 10203728 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320764521 Affx-986696875 AX-385252189 5 10203748 TCTACAGCTATCTATGATTTTTAAATGAATTTCTT[G/T]ATTTTTCAGAATTGGAAACTCAGATAAGAGTTGAA K 2 1 2 1 600010 r 74 goat 5_10203748 5 10203748 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320764528 Affx-986696879 AX-385252197 5 10203836 ATGTGGACTCTGATTTTAAAATATTAAATACTTTC[A/G]TAACATTAAAAGTGAAGGTTGAGATCCCTCATGTT R 2 1 2 1 600010 r 74 goat 5_10203836 5 10203836 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 38431671 Affx-122936796 AX-123302012 5 10221140 ATAAGTAAATTCTCATATCACTTCCCTGTAGGAAG[C/T]ATCACCTATCAAAAATAACCACTCAGCGTATTTTC Y 2 1 2 1 102000 r 74 goat snp34513-scaffold405-3409500 5 10583762 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451228 Affx-122921956 AX-123321562 5 10281687 AGAGCAACTCATTGTGCAGTTTCTCTCCAGTGAAA[C/T]GAGCTACAGTTTCACAGAGCTAGCTGCTGTTTTGG Y 2 1 2 1 102000 r 74 goat snp34512-scaffold405-3348953 5 10644077 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790007 Affx-122939500 AX-385277013 5 10310410 ATTATCTCTCCATTCTCTCAATTTGGAAGAGAAGA[C/T]ATACACTTGAGTTTCTGTGCATTGGGCTATCATTT Y 2 1 2 1 202000 f 74 goat snp34511-scaffold405-3320230 5 10672828 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785362 Affx-122931042 AX-385272407 5 10434328 AATTATGTAGTTGGAACAACTTTCATCATGCTCAA[C/T]AAACAGCACTATATTGATCATGTGTATAAAATAAG Y 2 1 2 1 101000 f 74 goat snp34508-scaffold405-3196312 5 10797131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402738 Affx-122958335 AX-123273091 5 10469020 ACAGAACAGCACATTTTAATATATTTTATAACTCC[G/T]ATAACACCTCCTGCAGCATTTTAATTTGTGTGTGT K 2 1 2 1 101000 r 74 goat snp34507-scaffold405-3161620 5 10832744 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433436 Affx-122935075 AX-123303777 5 10516808 TAGAAATTTTTCATTTTTCAAAATCCTTCACATTA[C/T]AGAGTTAAGTTCTAGTTTCTTAGATAACACAGAGT Y 2 1 2 1 101000 r 74 goat snp34506-scaffold405-3113832 5 10880880 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797112 Affx-122926734 AX-385284052 5 10547799 TGGAAGATGGAATGTGAGATAGAATGGAAAACATG[C/T]GTGAGATAGATGTGAGATAGAATGGAAACATGCTT Y 2 1 2 1 201000 r 74 goat snp34505-scaffold405-3082841 5 10912285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272158 Affx-1111833450 AX-519545914 5 10564538 TTCATCCTCTGCCATCCCCTTCTCCTTTTGCCTTC[A/G]GTCTTTCCCAGCTTGCATTGCTGTGATTCGTTAAC R 2 1 2 1 201000 r 74 goat 5_10564538_AF-PAKI 5 10564538 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434106 Affx-122934939 AX-123304447 5 10584437 GTCCATGGGGTCATGAAGAGTTGGACACGACTGAG[C/T]GACTTCACTTTCACTAAGATAAAGTATTTAATTCA Y 2 1 2 1 103000 r 74 goat snp34504-scaffold405-3046203 5 10949157 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770162 Affx-122973425 AX-385257329 5 10615067 TTATGAGGTAAGTACTGCGATTACTACCATTTTAC[A/G]TGTGAAGAGCGTTGTTGGGCCATTGGAACTAGGTG R 2 1 2 1 101000 f 74 goat snp34503-scaffold405-3015573 5 10979832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781290 Affx-122969084 AX-385268375 5 10655390 TTCCATACCTCCAGTTAGTCAAGAGAGCCTTATTG[C/T]TAAAAATCCTTGCCTCTGAAGTTAGCCTGTCTAGA Y 2 1 2 1 101000 f 74 goat snp34502-scaffold405-2975250 5 11021445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393409 Affx-122965886 AX-123263765 5 10684878 TGAATGGTGCCTAAGCGTCAGGCACTGTCCCAACC[A/G]CTTTACTTGTGGCATTTTCATTTCATCTTCCCAAC R 2 1 2 1 101000 r 74 goat snp34501-scaffold405-2945762 5 11051719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800634 Affx-122976982 AX-385287553 5 10744591 ACTTTAGGGCCTAATCTGAGTCATGTTCTGTGTTT[A/G]CAGTATAGTGTGGCTGATATGTACTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp34500-scaffold405-2886049 5 11111610 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790526 Affx-122962414 AX-385277529 5 10799280 CATTTTAAGTTATATCTTCTATCAAAAAAAGTTAA[C/T]GTTTGGTCTTTGTCTTGCTGTCAAGAGCTGATTAG Y 2 1 2 1 101000 r 74 goat snp34499-scaffold405-2831360 5 11167116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447688 Affx-122924625 AX-123318024 5 10845868 TGTGATGAGGGACACCTCTATTGAAATGGGAAGGA[C/T]AAATAGGACAATGTGGACAGGTGGTTTGCAAGACT Y 2 1 2 1 101000 f 74 goat snp34498-scaffold405-2784772 5 11214796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454125 Affx-122919344 AX-123324458 5 10883744 GTTTTGCTTTTATGTCTTTGCATTTCCTAGATTAG[C/T]AAAAGAAAAAAAAAGTGTATTTTTTGCTTTTATAA Y 2 1 2 1 103000 f 74 goat snp34497-scaffold405-2746896 5 11252512 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453265 Affx-122920397 AX-123323598 5 10917098 CTTTCAATGTCCTAGTTTTTCTCCATAGCCATTAT[A/C]TTGTATACTATATATTTTGTTTATTTTGTTTCCTT M 2 1 2 1 101000 f 74 goat snp34496-scaffold405-2713542 5 11286611 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403863 Affx-122957926 AX-123274215 5 10945813 AAGCACTGTGTGAATGCTGTGTGTGCCATTGGTGC[A/G]TCAGTTAAAGCAGCCCTGGGCAACTTTTTACTTAC R 2 1 2 1 201000 r 74 goat snp34495-scaffold405-2684827 5 11315803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453281 Affx-122920385 AX-123323614 5 10981383 TAGAGCTACTTCTATAAAAGTAAAGCAGTATTTTC[A/G]TAGGAAAGTAATTCAAGGGCTTCTTTCTCTGGTTT R 2 1 2 1 101000 r 74 goat snp34494-scaffold405-2649257 5 11351418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791803 Affx-122950534 AX-385278793 5 11034120 AGCACACAATGTTCCCTAGATATTGCAAAAAGATT[A/G]TATTGTACTCTGGGAAAACTTTCTAGAATTGAATA R 2 1 2 1 201000 r 74 goat snp34493-scaffold405-2596520 5 11404252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783081 Affx-122943782 AX-385270148 5 11066517 CTCTTTCTTCCTATATTATGGGAATTTACATATTA[C/T]GCTTATTTTCTTGAGAGATTTATCCATAGGCACCC Y 2 1 2 1 101000 r 74 goat snp34492-scaffold405-2564123 5 11436571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431814 Affx-122936109 AX-123302155 5 11109812 TCAGCTAGCTAAAGCAATGTGCTCCCAGAATCTTT[A/C]TTTGTATTTACAGCAAGTCAGAAGAGTTAAAAGAG M 2 1 2 1 101000 f 74 goat snp34491-scaffold405-2520828 5 11480739 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396303 Affx-122963088 AX-123266658 5 11168253 CCAAATAGGCATATTATAAGCAAGATTTTGGAAAA[C/T]ATTAATACTTGTAGTCACAAATGGTAGGCTGCATG Y 2 1 2 1 101000 f 74 goat snp34490-scaffold405-2462387 5 11539863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440782 Affx-122929846 AX-123311119 5 11203545 TTTAATGTAACACATTTAATTCCATAGGGCAGATA[C/T]GCTCATGAGATTTCTATTTGCAGACAAGAAACCAG Y 2 1 2 1 101000 f 74 goat snp34489-scaffold405-2427095 5 11576006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380675 Affx-122975181 AX-123251033 5 11246408 AAATATATACATTCAACTAATTTTATTTTAATACC[G/T]CAATTCCTGTGCCTATATTCTATGGCTTGAAATCC K 2 1 2 1 101000 r 74 goat snp34488-scaffold405-2384232 5 11619476 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431452 Affx-122936497 AX-123301793 5 11286969 TGAACCATGACGCCACACTAGGTAGGAACAAAGTT[A/G]TAGGGAAGAGAAGATATTTTAGCTGTATATTTAGG R 2 1 2 1 101000 f 74 goat snp34487-scaffold405-2343671 5 11659619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792897 Affx-122953810 AX-385279875 5 11316777 TTATTTGGATGTCTTACTAGCAAGATTTAATGTCT[G/T]TCTTTCAACATCTCTCCCCCTGCCTTAAGTTGCAT K 2 1 2 1 101000 r 74 goat snp34486-scaffold405-2313863 5 11690185 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389177 Affx-122969087 AX-123259535 5 11396183 AGCTGAGAAGAAACTCTTAAAGCACTCCTTTCCCA[C/T]GCCTTTTAGAAAAATTATATAAAATGATATTCAGA Y 2 1 2 1 101000 f 74 goat snp34484-scaffold405-2234457 5 11770319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425633 Affx-122940896 AX-123295979 5 11458670 TTATTTCATTCTCATCTTGGTGTATAATCAGCTGC[A/G]TTTAACAGTTTGGGGCTTATTTATTGAGACAAAGG R 2 1 2 1 101000 f 74 goat snp34483-scaffold405-2171970 5 11832772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445920 Affx-122925930 AX-123316257 5 11488966 TTCCATGTTTCCTTTTGCCAAGACTCACAAATAAA[C/T]GAAAAAATGAGAAGTAAATTATACTATTTGACCAT Y 2 1 2 1 102000 f 74 goat snp34482-scaffold405-2141674 5 11863244 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379094 Affx-122976765 AX-123249453 5 11525503 GCCAATGCCTCAATTAGCCCTTGTGTTTTAAGTAG[A/G]GAACTGATTGTTAGACATTGTCCAGCATACCAACA R 2 1 2 1 101000 f 74 goat snp34481-scaffold405-2105137 5 11900470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448525 Affx-122923445 AX-123318861 5 11554629 CAATTTCCTTTACAGTGCTGTATCAACTGATACTG[A/C]AAAATGCAGGAGAGAAAGTAACATAATCAAAGAGT M 2 1 2 1 201000 r 74 goat snp34480-scaffold405-2076011 5 11927046 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438209 Affx-122931454 AX-123308547 5 11610348 CTAGCCCTGAATAAAGCATTTCTGACGAGATGCTT[A/C]TCTTGAAGAATCTTCTACATCGACTATAACACTGC M 2 1 2 1 101000 r 74 goat snp34479-scaffold405-2020292 5 11982438 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384122 Affx-122972822 AX-123254480 5 11662779 TGCAGTAACAAGGTGGGGTATGACAAAGTAAGTAC[G/T]CCTTTGAGTAAATTGTGCAATCTCACAGTTACTGT K 2 1 2 1 101000 f 74 goat snp34478-scaffold405-1967861 5 12033719 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447976 Affx-122923756 AX-123318312 5 11694287 AGGAAGGGAAAGGCAAATGCTAAGAAATATATGTA[C/T]GCTGGAAGAACAGTACGGATTTATCCACAGTCTCT Y 2 1 2 1 101000 r 74 goat snp34477-scaffold405-1936353 5 12065472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420133 Affx-122946006 AX-123290481 5 11731225 CTTAGGGTATTTCACTTTGATTCATTTGTTTCACC[A/G]CCTTATTACATCAACAGAAATGTTTCAAACAGAAA R 2 1 2 1 102000 f 74 goat snp34476-scaffold405-1899415 5 12102453 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794999 Affx-122921397 AX-385281958 5 11763843 CTCTTCCATTCAAAAGAATTAGTTAAGTCTGTTGA[C/T]GTTTTCCAGTAAATGGACAAGCTGTAATACATGCA Y 2 1 2 1 101000 r 74 goat snp34475-scaffold405-1866797 5 12135270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790041 Affx-122924858 AX-385277047 5 11794285 AGCACTCTGCTTTTAGCCAGCCACAGAGATAAGGC[A/G]TGCAGTCTCAGTAACAGAATCACCTCAATTTAATT R 2 1 2 1 101000 f 74 goat snp34474-scaffold405-1836355 5 12165569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378865 Affx-122976517 AX-123249224 5 11843290 CAACACCAAGGCTATTTAAAAATAGCTTGGTTATC[A/G]TCATATACAGAAAGTTGGCCTTGTCACCTCTATAT R 2 1 2 1 101000 r 74 goat snp34473-scaffold405-1787350 5 12214469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431804 Affx-122936116 AX-123302145 5 11898967 GCAGTTACTAACTTAAGAATAAGCAAGAGGAGTTC[A/C]AAAAATGAAAGTTTTAGCCTATCTCCTTCGGCCTG M 2 1 2 1 101000 f 74 goat snp34472-scaffold405-1731673 5 12270425 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772888 Affx-122957887 AX-385260033 5 11936101 TCTATACAACTTAGAAAAACTTCATGTAATCATTC[A/G]TTATATCTCAGTGATAATGATGACAATAGCATTCA R 2 1 2 1 201000 r 74 goat snp34471-scaffold405-1694539 5 12307733 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414105 Affx-122949738 AX-123284454 5 11974629 TTACCTTTTGCTTCTAAATAAACTATTTCCTACCA[C/T]GTAACTGTCCTTTAACTGTCTTCTTTTTTTTTGAA Y 2 1 2 1 101000 f 74 goat snp34470-scaffold405-1656011 5 12346052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384988 Affx-122971889 AX-123255346 5 12026106 GGTATCTCTAGAAAAACATGGCCCCATAAGACCAA[C/T]AGAGGATCAGAAATATAGATGTCTGAAAGGTTAAT Y 2 1 2 1 201000 r 74 goat snp34469-scaffold405-1604534 5 12397921 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783942 Affx-122973766 AX-385270996 5 12054956 AATGCCATTCAGAGCAATCATATTTCAGCATGACA[C/T]TAGAAGGCAGCAACTGTCCACCCACAGAATGAATA Y 2 1 2 1 101000 r 74 goat snp34468-scaffold405-1575684 5 12426494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425515 Affx-122941468 AX-123295861 5 12118152 TCACCTTTGTCTACCTAATTATTTACCTTTTAGGA[C/T]ACAATGCTTGACAGTGTCTATTTTACATGTATAGT Y 2 1 2 1 101000 f 74 goat snp34467-scaffold405-1512488 5 12491106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407220 Affx-122955383 AX-123277571 5 12184026 CTACAAGGAAAGGGAAGGTTTGTAGTCTATGTAGA[C/T]ATTCCCCATATAAAGGAGCCTAAGAGATAATATTT Y 2 1 2 1 101000 f 74 goat snp34466-scaffold405-1446614 5 12556850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800813 Affx-122932858 AX-385287729 5 12240004 TTATATCTCAGACTTAACTATGGTATATGTATGGT[A/G]TAAAGTATGAATATATCTTATCCATACTTTAAGTT R 2 1 2 1 201000 r 74 goat snp34465-scaffold405-1390636 5 12614285 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780472 Affx-122922216 AX-385267563 5 12281369 ATTAAATTCAAAACACAGCAAATTGTACCACTCTA[C/T]GAGAGTGGTTCCTTAACATCACTTCCTATATTGGT Y 2 1 2 1 101000 r 74 goat snp34464-scaffold405-1349271 5 12663231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448505 Affx-122923457 AX-123318841 5 12314446 CATATTACCTCTGGATGCTGGACAGAGAGACGAGA[C/T]GGACAGCTCCCAGTCAGCCACGTGACCACGAAAGT Y 2 1 2 1 101000 f 74 goat snp34463-scaffold405-1316194 5 12696718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786728 Affx-122960790 AX-385273759 5 12360528 TATTCAAGTAAGCAAGGATACCAGGCAATATTCAA[C/T]GGCATTATGTTAAGTAATAAAGAGTGATAGATAGT Y 2 1 2 1 201000 f 74 goat snp34462-scaffold405-1270112 5 12742809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449505 Affx-122922621 AX-123319840 5 12407672 TTGTTCTAAGTACTAAGAATGTACAACAGACAAAG[C/T]ACTAGAGATTCTGCCCATATGAAAAAGAAAGGACT Y 2 1 2 1 101000 r 74 goat snp34461-scaffold405-1222968 5 12790222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382962 Affx-122973362 AX-123253320 5 12462544 AACACATCTTCGTATATAAGGGATTTGAGCATTCA[C/T]GGATTCTGGTATTTAGGATGATCCTAGGACTAATC Y 2 1 2 1 201000 r 74 goat snp34460-scaffold405-1168096 5 12844157 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388577 Affx-122969167 AX-123258935 5 12508427 AAAAGCAATAATGTTTATTTGGAAGAAAATTTAAA[C/T]GAAAAGAACAATGGGTTGGGTGGAGAACAAAACAA Y 2 1 2 1 103000 r 74 goat snp34459-scaffold405-1122213 5 12889946 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789351 Affx-122976422 AX-385276362 5 12537723 TTTCTGAGGAGCAATGTAAGCAATCCTTCATACTG[C/T]AGGTAGTAAGCAAAAGGTAGACTTTGTAGAGATCT Y 2 1 2 1 101000 f 74 goat snp34458-scaffold405-1092917 5 12919585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801860 Affx-122956039 AX-385288767 5 12588217 AGTATGTTATTACAATGTTTTGAACTTTACTCAAG[C/T]ACCCACTGAATTTTGAATACATAGTCTAAATATGC Y 2 1 2 1 101000 r 74 goat snp34457-scaffold405-1042423 5 12969958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448773 Affx-122923309 AX-123319109 5 12617400 TTTGGTTGAGCCAACATTATGGTGAACCAATTATG[A/G]ATTCTGGAAAATAATAGGGACCATGGAAAGCTTTC R 2 1 2 1 101000 r 74 goat snp34456-scaffold405-1013240 5 12999817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476197 Affx-1251763702 AX-586011623 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 4 1 4 1 20000 f 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 539476452 Affx-1251763702 AX-586011853 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 4 1 4 1 20000 r 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 562165242 Affx-1251763702 AX-606940654 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 8 1 4 1 20100 r 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 562166420 Affx-1251763702 AX-606941828 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 8 1 4 1 20100 f 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 38394848 Affx-122964775 AX-123265203 5 12671367 AGATGATATTGTGAAGTTTTATCTGGTTTTTGTGA[C/T]ATTTTATTGTGAAGTTTATCTGCCCTCTTCAGTTC Y 2 1 2 1 101000 r 74 goat snp34455-scaffold405-959273 5 13054069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795233 Affx-122927255 AX-385282191 5 12700252 CTCAGTTATCTTCTGTTTTAACTCCTTCTTTGTTC[C/T]GTTTATATCATATACTAGAACTTTGAATGTTTATT Y 2 1 2 1 101000 f 74 goat snp34454-scaffold405-930388 5 13084173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796883 Affx-122925861 AX-385283825 5 12733275 AAGAGGCATGTGCTTTTGCTAAAGTATTCTTTGAA[G/T]AACAAGCTCACACCTCCCCTTTTATCCATTTTGTT K 2 1 2 1 202000 r 74 goat snp34453-scaffold405-897365 5 13117368 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771071 Affx-122933169 AX-385258231 5 12816267 TTAAAAGTAAGTTAAGCCCTTGCTTATTCAAACAT[C/T]AAACTGTCAGCATGGAAGTAAATTTAAAACTTATG Y 2 1 2 1 101000 f 74 goat snp34451-scaffold405-814373 5 13201598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445095 Affx-122926201 AX-123315432 5 12855027 GTATGGACACACAGTACCTCCAACTCCTATAGCTG[C/T]GTTCATTCCAGGAAAAATGATTCTAATTGTCCTTT Y 2 1 2 1 101000 f 74 goat snp34450-scaffold405-775613 5 13240231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768958 Affx-122950852 AX-385256133 5 12901288 TTACTGTGAGTTAATCAAGTCCATCCTGATATAAC[A/C]AGAAACTCTTCTTCTGGTACAATAACTTTCAGTTA M 2 1 2 1 201000 f 74 goat snp34449-scaffold405-729352 5 13287400 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768425 Affx-122965890 AX-385255605 5 12958055 AGCAAAGCATAAATCTGCTTAGGTGCTATGGATAT[A/G]CAGAATCAGATATTTAGCATTCTCCTTTCCTTTCT R 2 1 2 1 101000 r 74 goat snp34448-scaffold405-672585 5 13347337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394816 Affx-122964800 AX-123265171 5 12994692 AAGGAGCAAAATATCAACCATTCGGCTTTACCCAG[C/T]ATGGGGCTGCTAACCCTGTCTTGCTTTGACTTTCA Y 2 1 2 1 101000 f 74 goat snp34447-scaffold405-635948 5 13384774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438029 Affx-122931560 AX-123308367 5 13029227 CTTCTAAAATGTGTTCAGGATGGTCACAAACTAGA[C/T]GTAGATGCACAGGAGTTAATTTATTCTCCAACACC Y 2 1 2 1 101000 f 74 goat snp34446-scaffold405-601413 5 13419540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278178 Affx-1111836290 AX-519551667 5 13053984 CATTTTTTGTAACAGGCATCTTTGAATGGCAAAAT[A/C]GGAGTGTATGTTTATAGCAACAAATTTTTGGCTCA M 2 1 2 1 101000 f 74 goat Random2.2K-521 5 13053984 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392030 Affx-122966472 AX-123262387 5 13062243 TCAGTAAGCACTACACAGATCCATGATTGGTTGAA[C/T]GAGAGCATTCAGAACTGTGGCTTTGTAGGGTAGAT Y 2 1 2 1 201000 f 74 goat snp34445-scaffold405-568397 5 13452995 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768937 Affx-122943944 AX-385256112 5 13109948 TTTAACAACACCTATTTGCGACTTATCTTGACTAT[A/G]TTCATTTTCACACCAAGTGGCTGGATAATTTGACA R 2 1 2 1 101000 r 74 goat snp34444-scaffold405-520692 5 13500743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418803 Affx-122946171 AX-123289151 5 13157298 ACAACATGGAAAGCATGAGAAGACATCAATTCTGC[C/T]AACAAGCAGTGACTTTGGAGGTAGACTACAAGACT Y 2 1 2 1 201000 f 74 goat snp34443-scaffold405-473342 5 13549093 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429899 Affx-122938117 AX-123300240 5 13193135 AAATTCATATAAAATAAGGAAGGGAGTTGTGCTGT[A/G]TTAATTTATATTTTTCCTATTTCCTACTGCTGACC R 2 1 2 1 103000 f 74 goat snp34442-scaffold405-437505 5 13585671 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426397 Affx-122940847 AX-123296743 5 13237559 CAATTCCTTTTTAAAGACAGTTTCACCAAAGTATC[A/G]TTTATATACAGTAAAATGAATCCATTCTTAAGTGT R 2 1 2 1 303000 r 74 goat snp34441-scaffold405-393081 5 13630138 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272300 Affx-1111833457 AX-519546039 5 13254143 ACCTGGTGAGCTACACTTTTGGGGAAGCAAGAGTC[A/G]GACACAACTAAAGAGACTGAGCACCATTTCATACC R 2 1 2 1 201000 f 74 goat 5_13254143_AF-PAKI 5 13254143 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770180 Affx-122927022 AX-385257347 5 13322272 TTGTAAACTTCAAATTAGCAAGAATGAAATGTAAC[A/G]CAAAACAACAGCTTGGAATAGATCCATTGTTTATT R 2 1 2 1 101000 r 74 goat snp34439-scaffold405-308368 5 13719164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278180 Affx-1111836291 AX-519551669 5 13358822 TTTGGCAATGTTAAAAAATTTGCCCTACCTAAACT[A/G]CAAATGTTGATTTAATTAAGCAGTATCATCTACAA R 2 1 2 1 101000 f 74 goat Random2.2K-522 5 13358822 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424743 Affx-122941657 AX-123295089 5 13373151 GACTGAGCCTGGATTATATTAGTGGTTCTATAGTA[A/G]CAAAATTGCATCTGGAGACCATACGTACACTTTCT R 2 1 2 1 101000 f 74 goat snp34438-scaffold405-257489 5 13771877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776660 Affx-122932233 AX-385263787 5 13404837 CAGTGATACAAATTTCTGTTCAAATTTTATAAAAG[C/T]GTTTAATTTTAGAATGTAATTGCAGAATTCTGGAT Y 2 1 2 1 101000 f 74 goat snp34437-scaffold405-225803 5 13803158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794736 Affx-122936075 AX-385281696 5 13441236 TCTTTTAAACGTTTATGTTTCCACCCAAACACATC[A/G]TCAATAGAAAACAAACACTTCCTCTTAACAGAGAT R 2 1 2 1 101000 r 74 goat snp34436-scaffold405-189404 5 13840303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796340 Affx-122976767 AX-385283290 5 13491910 CTTTGCTGTTTTTATGTATTTCCTTTGTCAGTGAT[A/G]TTGAAAATCAATTTTTACAGTAATGCTGTTATTTA R 2 1 2 1 102000 f 74 goat snp34435-scaffold405-138730 5 13889797 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278339 Affx-1111836292 AX-519551825 5 13516520 GCCAGGAGTCTGCGAATCTCAGGCAAATTTTTAAT[A/C]TCTTTCCCCTCTGCCGTCAGAAGCCCCCGTTCTTT M 2 1 2 1 202000 r 74 goat Random2.2K-523 5 13516520 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381286 Affx-122974465 AX-123251644 5 13541555 CTAGAGAGAGAGGGAAAGATGGCGGAGGAATAGGA[C/T]GGGAAGACCACTTTCTCCCTCACAAATTCCTCAAA Y 2 1 2 1 303000 f 74 goat snp34434-scaffold405-89085 5 13940272 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431598 Affx-122936169 AX-123301939 5 13610697 AGAAGTTAGTATAGTAAGATTTCTCCCACTAATAC[A/G]TTTGAGAGCTTCTGGTGCAAATAAAGCAATTATGA R 2 1 2 1 101000 r 74 goat snp34433-scaffold405-19943 5 14008417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414631 Affx-122949335 AX-123284980 5 13637149 TGGAATACAGAGAGAAACTTGAGCTCTGTAACAGA[C/T]GTACATCTATTCACTTTGGAACACAAATATAATAT Y 2 1 2 1 201000 r 74 goat snp43287-scaffold577-6410 5 14036504 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448918 Affx-122923166 AX-123319253 5 13681883 GAGAGTGACTTCTGTCCCTTAAGAATCACTGGATC[A/G]TTAGTGGCTTATGTTCAGTTCAGTTCAGTCACTCA R 2 1 2 1 101000 f 74 goat snp43288-scaffold577-51144 5 14081951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398116 Affx-122961704 AX-123268471 5 13735826 AAACACTTAAGGATGAAAGGGTGCAGCATATTCAA[C/T]GGAAGGGAGAAATTATTTTGTAAATAAAGCATTAA Y 2 1 2 1 101000 f 74 goat snp43289-scaffold577-105087 5 14136024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429798 Affx-122938200 AX-123300139 5 13778481 AGTTAGGTGCCCTTATTACATCAATGTAGCATGCA[C/T]GAATTAACAATAGCAAAAAGTAATTTTAAATAGGT Y 2 1 2 1 101000 f 74 goat snp43290-scaffold577-147742 5 14179232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423354 Affx-122943153 AX-123293700 5 13808719 TTTATCCTTTCATCAAATTCCTTGCCCTTGAGTTA[C/T]ATCTTATTTTTGGCTGCTATATTGTCCATTGCACT Y 2 1 2 1 101000 f 74 goat snp43291-scaffold577-177980 5 14210211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780429 Affx-122976513 AX-385267521 5 13842599 ATCAGGTTTCTTGCAAATAGCCATACAGCTAGCAC[A/G]ACTGTGTGTTTGGGAAGACAGAATAAATAGTCTTT R 2 1 2 1 201000 r 74 goat snp43292-scaffold577-211860 5 14244421 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423917 Affx-122942272 AX-123294263 5 13877097 AGCTGCTCAAGCCCTGGCAGGGGGCTCTATGGGAA[G/T]AACAAGAGAGGACCTGTGCCTTCTCCTCTTGTTGA K 2 1 2 1 102000 f 74 goat snp43293-scaffold577-246358 5 14277388 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394010 Affx-122965018 AX-123264365 5 13908422 ATCTCAACAACTGAATCTCCAGACATCTGGCATCA[G/T]CCTGAACTCAATCAATCAGTAAACCTCAGTTTGTT K 2 1 2 1 101000 r 74 goat snp43294-scaffold577-277683 5 14309146 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476198 Affx-1251763703 AX-586011624 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 4 1 4 1 20000 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 539476453 Affx-1251763703 AX-586011854 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 4 1 4 1 20000 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165342 Affx-1251763703 AX-606940753 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165421 Affx-1251763703 AX-606940832 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165443 Affx-1251763703 AX-606940854 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165512 Affx-1251763703 AX-606940923 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562166219 Affx-1251763703 AX-606941627 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 320796319 Affx-122969964 AX-385283269 5 13938202 CCTGGGTGCTTTGGGGCAAGCAAACTAACTGGATG[C/T]AATCATAATGTATACTTTGCTAGATGAAAAGATCA Y 2 1 2 1 101000 f 74 goat snp43295-scaffold577-307463 5 14338672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437404 Affx-122932425 AX-123307742 5 13971861 AGTGGTTTGTCCCAACCTTTCATATTTGAGGGTTC[A/G]CAGGAATATCTTCTTTCCAGTGCCCATGGGTATTT R 2 1 2 1 101000 r 74 goat snp43296-scaffold577-341122 5 14372265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431948 Affx-122935971 AX-123302289 5 14001359 AAACAGAACTATCAGGAAGGACATGAAGTAGTGAG[C/T]GATAAAGTAGTGGTATCCTACAGGTCACATGAGCA Y 2 1 2 1 101000 r 74 goat snp43297-scaffold577-370620 5 14401603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380042 Affx-122975578 AX-123250400 5 14057165 TTATTTTGCTTAGTTATAATGTCTTCCAGGTTCAC[A/G]CATACTGTTACATATGGCAGGATTTTCCTATTTTC R 2 1 2 1 201000 r 74 goat snp43298-scaffold577-426426 5 14457816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408541 Affx-122953687 AX-123278892 5 14091055 AAGAGTGCTTCCTCATTTCTCCTCCAGTCTATAAT[A/G]TTTTGCAAACAGTCTTATTCCCCATGAGAAAAGGA R 2 1 2 1 201000 r 74 goat snp43299-scaffold577-460316 5 14492047 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422538 Affx-122943271 AX-123292884 5 14127562 TACTAAAAAGGTTGTCAGTGAAAATGATTTGCTTA[C/T]ACAAAGTTACACAAGTTAGTGCAGTTCCTATGTAA Y 2 1 2 1 101000 r 74 goat snp43300-scaffold577-496823 5 14528022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785879 Affx-122949771 AX-385272917 5 14165337 TCTCATGTCTTACTACTTAACCTCCCTTTTCTGCC[A/G]CCTGAAATTCAGCTTCTACTCACTTCTATACATTT R 2 1 2 1 101000 f 74 goat snp43301-scaffold577-534598 5 14566035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792226 Affx-122969033 AX-385279210 5 14194221 CACAAGTACATTCCCTGCTCTAAATGAGCTAATAG[A/G]AAATCCTGTTCTTGATTAGCTCTGAAAAACTTAAG R 2 1 2 1 101000 f 74 goat snp43302-scaffold577-563482 5 14595781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438300 Affx-122931387 AX-123308638 5 14236673 GTTGATTGATGGAATGCCAGATAATAGCCAATAGA[C/T]GTAGACTGGAAAAATGTTAGAATCTACTACTGGGC Y 2 1 2 1 101000 f 74 goat snp43303-scaffold577-605934 5 14642989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275362 Affx-1111834855 AX-515815391 5 14258585 ACATGGGTTCTTAGCTCTAATCTGCAGTGTCTATC[A/C]CTAGCCCATCTTCTGTTGTTTATCCCTA M 2 1 2 1 101000 f 74 goat GoatD01.056684 5 14258585 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782471 Affx-122973762 AX-385269547 5 14274494 AGAAATTCCGCTAAAATAAATAACAACTCCATAGA[G/T]CTTACCTGTTAAGTAGTAGCATCATTACTTTAGGA K 2 1 2 1 201000 f 74 goat snp43304-scaffold577-643755 5 14680113 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441443 Affx-122928773 AX-123311780 5 14306652 ATTTCCTATGGCTGGAAGGTCCATTGTTCTTTTTT[A/G]TCCCAGTAATTTAACATTTGAATAGGTTTAGAAGA R 2 1 2 1 201000 r 74 goat snp43305-scaffold577-675913 5 14712146 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402026 Affx-122958744 AX-123272379 5 14339212 TTCGCAAGCCAAATCTAGAGAGCAGTTTATGGGTT[A/G]CAGCTATAAAACTTTTTCAGCTTTTGATCTTTTCT R 2 1 2 1 201000 r 74 goat snp43306-scaffold577-708473 5 14744736 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391416 Affx-122966767 AX-123261773 5 14386598 TCCTTGAGTTTAAGAACCAAGCAAGTATCTATCAA[C/T]ATTAGATTCTAATGTGTTTCTAATTTATTAAAACC Y 2 1 2 1 101000 f 74 goat snp43307-scaffold577-755859 5 14791704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278341 Affx-1111836293 AX-519551827 5 14429047 CTTCTTGAATAGATGTTAGCTGGTCTTATTAGGGC[A/G]AATGAAGTCAGGAATGATTTATGTTACCATCTCAT R 2 1 2 1 201000 r 74 goat Random2.2K-525 5 14429047 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433459 Affx-122935057 AX-123303800 5 14473161 TGTGAATGTTACATTTTTGAGTTTGCTGCACTGGA[C/T]GATATCTTAAATTTCACTCCCTTCTCTGGGCAGCA Y 2 1 2 1 101000 f 74 goat snp43309-scaffold577-842422 5 14878228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378164 Affx-122976965 AX-123248523 5 14504023 CCTTAATATGGGAGAGTGCTTTAAAGATGAAATAC[A/G]TTAAGCACTAAGAAGTTGGGGCCTAGGTCTATCCA R 2 1 2 1 102000 r 74 goat snp43310-scaffold577-873284 5 14909181 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800533 Affx-122955044 AX-385287453 5 14548578 TGGTGTCCTACTAGCTTCCCAGGCTTCAGAAAAAA[C/T]GAAAAATCTGAGTTCTCCCATTATGAGATTTCACC Y 2 1 2 1 202000 f 74 goat snp43311-scaffold577-917839 5 14953370 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452409 Affx-122920597 AX-123322742 5 14616205 TACTGTAATGGAAGAATTCAGCCATCTTATTCACA[C/T]GTAAGATGGGGTTGTGGGCATGTTATGAGGATTTT Y 2 1 2 1 201000 f 74 goat snp43313-scaffold577-985466 5 15023010 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782088 Affx-122931831 AX-385269166 5 14674226 TAACCTCTTTATCACAGAAATGTTTGGGGTTTGGA[G/T]AATTTCACTTTTCATGTCTAGCTAGTATTTATCGT K 2 1 2 1 101000 f 74 goat snp43314-scaffold577-1043487 5 15082482 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787450 Affx-122972225 AX-385274475 5 14729185 ATTTGATGGGCTATAAACAGGGTGTATGTCACAGT[A/G]TTAACACCATGAATGGATGTATATGTACAGAACAA R 2 1 2 1 101000 f 74 goat snp43315-scaffold577-1098446 5 15137822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800300 Affx-122924031 AX-385287223 5 14782880 ACTAAGATACTCCCAATGCACACATGAGTGTAAAT[A/G]CGAGGGAATACTGTTAGCTCACTGGACACTATTGT R 2 1 2 1 101000 f 74 goat snp43316-scaffold577-1152141 5 15191827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402587 Affx-122958434 AX-123272940 5 14822710 TACTGTTCTCAGGTCTTTCTATGCGTTCTCATTTA[A/G]CCCTCACAACAATGTTATCAGGTAAATTTATTGTC R 2 1 2 1 101000 f 74 goat snp43317-scaffold577-1191971 5 15232284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412827 Affx-122950466 AX-123283176 5 14885298 ATATCATTAACCTGAGACATTTTCTTCTGCTGCTT[A/G]CTTCTACAACTAGTCCTTTATCAGCTTCATCATTT R 2 1 2 1 201000 r 74 goat snp43318-scaffold577-1254559 5 15295488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771585 Affx-122938137 AX-385258743 5 14921503 AAGTAAGGCCTTCAGCAGAATCTTAGTATGAAAAA[C/T]GGTAACATTAGATACTCCCCAAAACTGAAATATTA Y 2 1 2 1 201000 r 74 goat snp43319-scaffold577-1290764 5 15329809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446880 Affx-122925234 AX-123317216 5 14951037 ACACCACGTGGCTTATTTAGCTGCTTAGTTGGAAA[C/T]ACCCACAGTTTTACATCCCAAGTCACCTCTGTGGT Y 2 1 2 1 101000 r 74 goat snp43320-scaffold577-1320298 5 15359199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380861 Affx-122975436 AX-123251219 5 15010624 CCTTTGATATTCCCAAATGTAAATTGTCTGGTAAG[C/T]GGCTGAATAAAGGAGATAGCGTTTTAAGGAGAGGT Y 2 1 2 1 101000 r 74 goat snp43321-scaffold577-1379885 5 15417400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399279 Affx-122960550 AX-123269634 5 15069896 CTCCTTATAGCTAGGCAGGACTATTTCAACAACAA[C/T]AAAAAAATCCAGTTTTGCAAGAAGACAGTCTATGA Y 2 1 2 1 202000 r 74 goat snp43322-scaffold577-1439157 5 15477217 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404294 Affx-122957032 AX-123274646 5 15103922 TACAAAATATGTGGTAAGGACATGTAACCAAAAGC[C/T]AGTTTGCCTACTTCATAGTGGGTGGGATGGGGAGA Y 2 1 2 1 101000 f 74 goat snp43323-scaffold577-1473183 5 15511456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380291 Affx-122975407 AX-123250649 5 15177065 GGTCTCTGAATGTAAGACCTCTTTACATAATGTCC[G/T]CACTTATTTTCAATAGTCAAATTTTAATATCGGAA K 2 1 2 1 101000 f 74 goat snp43325-scaffold577-1546326 5 15586506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768712 Affx-122950069 AX-385255890 5 15224974 TGCACAGTGCTTAATAACAAGGAAATTACATTATG[C/T]GGTTAATACCTAATAAAAGGCATTGCTCATATTAT Y 2 1 2 1 101000 f 74 goat snp43326-scaffold577-1594235 5 15634884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402514 Affx-122958489 AX-123272867 5 15288767 ATGCAATTAGAGCAGTACAAGCAATTAACTTTGCT[A/G]TTTAGTATAAAGTTGAGAGCACTAAAGACTGAAGT R 2 1 2 1 202000 r 74 goat snp43327-scaffold577-1658028 5 15699060 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788433 Affx-122929933 AX-385275450 5 15321722 GTTACTCAATTCTGGCATTGATATTCATATCAATA[C/T]AAGATTTGAAGGAGACATAGAATTATGGTAATGCT Y 2 1 2 1 102000 r 74 goat snp43328-scaffold577-1690983 5 15732018 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452666 Affx-122920327 AX-123322999 5 15355511 CATGTGTTAATATCAGTTATGTTTTTTCTTATCAT[A/G]CTATTGTAAGAATAATATATCAAAATGTCTTTATA R 2 1 2 1 101000 r 74 goat snp43329-scaffold577-1724772 5 15765686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765319 Affx-122940426 AX-385252841 5 15470536 TCTGATTGAATGGTGTAATATGATACAAATACATC[A/G]TATAATGCCTAGCATCTGGTACAGGCACATTTTCC R 2 1 2 1 101000 f 74 goat snp43331-scaffold577-1839797 5 15882095 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787429 Affx-122972218 AX-385274454 5 15522930 TTGCTTCTATTTAGTTTGTGACTTTTGGGATAACT[A/G]TTTATAGGTACATACATCTCTTTTAGCTTAAAAAT R 2 1 2 1 101000 f 74 goat snp43332-scaffold577-1892191 5 15936205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393435 Affx-122965864 AX-123263791 5 15535777 GCAGTGTAGGGCAAAATGCCTAATGAATGATTCTT[A/G]TCACATCATGGTGAGCTCTACTGCTTCTCAGTATT R 2 1 2 1 101000 f 74 goat snp36630-scaffold443-1619 5 15950639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394094 Affx-122964950 AX-123264449 5 15619038 GAGCATATATTTTATGTTTCTTTTTGATTATTTTT[A/G]CAGTAACTTCCCAATGCAGGTAGGTTAAAAAAGGC R 2 1 2 1 101000 r 74 goat snp36632-scaffold443-84880 5 16034314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452342 Affx-122920649 AX-123322675 5 15665578 ACCATTGAATCTTTGGGTTGGAGAAGACCTTGACA[C/T]GTTCCAGTCTCAAGTCTAATAACTTTCCCTGTAAT Y 2 1 2 1 101000 r 74 goat snp36633-scaffold443-131420 5 16080623 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770265 Affx-122936769 AX-385257431 5 15712214 ATACTCAATCTACAGAATCCTGTGCTATCACTGTC[A/G]CTTGTCTATATGGCTTCATGAAGACCATCTCCATG R 2 1 2 1 202000 f 74 goat snp36634-scaffold443-178056 5 16127472 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794543 Affx-122939014 AX-385281506 5 15755281 GGTCTGATAAGACTACAGAAACTTTCACAATTCCT[A/G]TCTCTATAATATAGAACTTAGATAATCCCTTCCCT R 2 1 2 1 101000 f 74 goat snp36635-scaffold443-221123 5 16171178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429256 Affx-122937899 AX-123299598 5 15793252 CAGTAGTTACCCACAGTGTAGACAATGGACTTTTA[C/T]AATTTCTCATATAATGACTGATAGATGTGAACCAG Y 2 1 2 1 101000 r 74 goat snp36636-scaffold443-259094 5 16209854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278187 Affx-1111836294 AX-519551676 5 15846141 CTTACAAATAAGCATTGGTTATCTGTAAAGTAATG[A/G]GCTTCCTCTGGTAGCTCAGTTGGTAAAGAATCTGC R 2 1 2 1 201000 f 74 goat Random2.2K-527 5 15846141 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278189 Affx-1111836295 AX-519551678 5 15896894 CTGTGAGCATCAAATAGTCACTAGAGACTTCTTTG[A/G]TGATAGAAGGAAGAAAAGTTAAGGTTAAGTTTCAG R 2 1 2 1 101000 f 74 goat Random2.2K-528 5 15896894 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446209 Affx-122925714 AX-123316545 5 15907435 TGGAGAGGTGGCTGATCTGCAGGCTGGGAAAAGAG[C/T]ATGCATGAACTGCAAGTACAGAAGGAAGGGAGAGG Y 2 1 2 1 201000 r 74 goat snp36638-scaffold443-373277 5 16323879 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272301 Affx-1111833458 AX-519546040 5 15943891 GTGGCAACCCCTGGTAGTGGTCATTGTTCTGGAAT[A/G]CTGCTTTCTTAGCTGCCTGATCAGCGGCTTGGTTC R 2 1 2 1 101000 f 74 goat 5_15943891_AF-PAKI 5 15943891 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418300 Affx-122946987 AX-123288648 5 15946143 CATTATCTGGTTAAAAAAGAAATGCAATTATTGTA[C/T]GCCCAAGTAGCAAGCTATTATTTGGCATTGAAAAG Y 2 1 2 1 103000 r 74 goat snp36639-scaffold443-411985 5 16363364 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274810 Affx-1111834507 AX-519548395 5 15947334 AGAAAGCTTTACTGCAGGGCATCAAGCAAGCAAAA[A/G]GGGCATCTCACACTCA R 2 1 2 1 102000 f 74 goat GoatD01.038762 5 15947334 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783278 Affx-122934597 AX-385270343 5 16004059 AATTCTTTGCTTTAGTGAGCTTAAATGTAAAATCT[A/G]TTTTAGAAACTACATTTAATATTGCTAATGAACCA R 2 1 2 1 101000 r 74 goat snp36640-scaffold443-469901 5 16421629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417727 Affx-122947436 AX-123288075 5 16048126 CCGGTTCCACCCCATCCCGTGGGCAAACATCAGGC[A/G]TATTGATGTTTTTGCATAGTTGTCTGATAACATCT R 2 1 2 1 102000 r 74 goat snp36641-scaffold443-513968 5 16467185 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767634 Affx-122978578 AX-385254878 5 16090277 GTCCTGAACTTAGTTACTCATTCTCCCGATGTCCT[A/G]TTATAGAATTTCATCATGGCAATGATCTGTTAAGC R 2 1 2 1 102000 f 74 goat snp36642-scaffold443-556119 5 16510062 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790187 Affx-122950734 AX-385277191 5 16122206 ATGGTAGATTGCTTCACAGCTTCTCCACTGTTAGT[C/T]ACTGGTACAAGGTAGAACCCAATTGATTTTATGGA Y 2 1 2 1 102000 f 74 goat snp36643-scaffold443-588048 5 16542470 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393181 Affx-122965519 AX-123263538 5 16152507 AATATAGAAAAGAAATAAAATATTTGACATTAATG[C/T]AAATGCCGTTTCAACCAAGAGCTGGCTCTGTATTT Y 2 1 2 1 103000 r 74 goat snp36644-scaffold443-618349 5 16572585 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398965 Affx-122960971 AX-123269320 5 16214474 TTTTTCAGAGATCAAGGATCATTTTCACTCTCATT[A/G]TTCTGAATTTTTTCTAGGAAGTTGCCTATCTCCAT R 2 1 2 1 201000 r 74 goat snp36645-scaffold443-680316 5 16632368 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413379 Affx-122950134 AX-123283728 5 16248047 ATAAACTTAAGAATGTTTTGATAAGCCATCTGCAG[A/G]GCCAGAGCTCTACATAATCCAAACTCTGCAGTGTT R 2 1 2 1 101000 r 74 goat snp36646-scaffold443-713889 5 16665908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380312 Affx-122975391 AX-123250670 5 16303129 TGGTGAAAAATAGAATTATACCCAATGCTAGGAGG[A/G]AATTAGGGAGGCAGCAAAATCGCTGTAAATTCAAG R 2 1 2 1 101000 r 74 goat snp36647-scaffold443-768971 5 16721921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770918 Affx-122958804 AX-385258081 5 16332172 ATGCAATTTTATTATGTGTAGGTTTTTATATCCAC[A/C]ACTACTGTCAGGATTCTGAACACATTCCACACCAT M 2 1 2 1 102000 r 74 goat snp36648-scaffold443-798014 5 16751318 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792004 Affx-122964426 AX-385278992 5 16375327 CACAGCTCTGCTTCCTCAGAATTCACTTGCTTGAA[C/T]AGATATCCTAAATGAATATACTACATAAAGCAAAA Y 2 1 2 1 101000 f 74 goat snp36649-scaffold443-841169 5 16794442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403649 Affx-122957524 AX-123274001 5 16406791 TGGATGATTTGAGGAGCTGTAGAAAGGAGGAAAAG[C/T]AGTTCAAATCTAGAAAAACTAACAGAATTATTAAT Y 2 1 2 1 101000 f 74 goat snp36650-scaffold443-872633 5 16827066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452301 Affx-122920680 AX-123322634 5 16436391 TGTAGGATAGAGATATGAGTTGACAATTAATAAGC[A/G]AAGATTCTTTCAGGAAAAAAAAAAAGACGCATAAA R 2 1 2 1 101000 f 74 goat snp36651-scaffold443-902233 5 16856633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383600 Affx-122972564 AX-123253958 5 16486228 GTTAGACCCGTGGGGATGTATCCAGCTCCTGTTTT[C/T]AGAGGATTCTTTTAAAATGCTCATTTTAAAAAATG Y 2 1 2 1 101000 f 74 goat snp36652-scaffold443-952070 5 16907501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787780 Affx-122963724 AX-385274803 5 16524538 ACTAAATAATATGGTAGCAGAGAGAAATACAATGG[A/C]TTTCTCAACAAAGACTGGGAAGGTAGGAAAAGTGA M 2 1 2 1 101000 r 74 goat snp36653-scaffold443-990380 5 16949397 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775196 Affx-122962172 AX-385262327 5 16571266 ACCCACTAGTTTCCAGACATGTTTATTCAACATCA[C/T]GATGATCATATATGCTAATAATATAAATGAATTCA Y 2 1 2 1 101000 f 74 goat snp36654-scaffold443-1037108 5 16996437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406046 Affx-122955475 AX-123276398 5 16601310 TTGAAGAGTATATATTTATTTCATAAAATAATTTT[A/G]TAGCTTTTCCTCCCACTCAATATTATTTCATCATA R 2 1 2 1 103000 r 74 goat snp36655-scaffold443-1067152 5 17026638 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769782 Affx-122936210 AX-385256952 5 16638543 AAGAATTTAAGTGTAGGATGCAATTTATAATTGGG[C/T]AAGCCTTTTCCCAATTTTGTGGGATAGTATTGTCC Y 2 1 2 1 101000 r 74 goat snp36656-scaffold443-1104385 5 17064069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797198 Affx-122943409 AX-385284137 5 16668800 CGTCTTCTTTCCACAGATTCCTCAGAAGGAGAAAT[A/G]TGACCTAGTCTGTCATCTATGGACAACTTCAACTA R 2 1 2 1 101000 f 74 goat snp36657-scaffold443-1134642 5 17094695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770872 Affx-122977691 AX-385258036 5 16711276 GAAACAGGTCTTTTCAGTTCCCAGTTGACTGTTTT[A/G]CCTGAGAAAATATTCTGTCCATCATTTGGTTTGGC R 2 1 2 1 101000 f 74 goat snp36658-scaffold443-1177118 5 17138082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405438 Affx-122956054 AX-123275790 5 16740134 TCAGTTTCTTAAGTGCTAAGAAACTTATAGCAGCT[A/G]TACTGAGCTTGTGATCTTAGCACCCTCCATCGATT R 2 1 2 1 101000 r 74 goat snp36659-scaffold443-1205976 5 17167022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447548 Affx-122924042 AX-123317884 5 16773475 TTCTTTTCTACAGATTCTTTCAGTTCATGGTATAA[G/T]CAGTGATATCTACAGTTATATATGTGTGTACAAAA K 2 1 2 1 101000 f 74 goat snp36660-scaffold443-1239317 5 17200334 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766106 Affx-122964559 AX-385253518 5 16806052 TTTTGCACAGGTAGAAAAATTTCCCAGAAGTCATA[C/T]GATTTAGGAATTTTGAGATACTAATATTGGTATCC Y 2 1 2 1 101000 f 74 goat snp36661-scaffold443-1271894 5 17235589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450585 Affx-122922029 AX-123320919 5 16863668 TGATTAAACATGTACATCATCTCTGACTCCTGTTT[C/T]TGTTTTACTGATTTGTGATATTTATGGTAGTGCTG Y 2 1 2 1 101000 r 74 goat snp36662-scaffold443-1329510 5 17294147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411518 Affx-122951672 AX-123281868 5 16916022 TGGACATTCCTGAAGCAACTAAGCAGCATTCTATA[C/T]GGAAGAATGTCTCCCAAACCTATCAGTGATCACTC Y 2 1 2 1 103000 r 74 goat snp36663-scaffold443-1381864 5 17346674 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278191 Affx-1111836296 AX-519551680 5 16923227 TCAAGAAGCAAAAGGAAGATCGCTGTAAGTAACAG[A/C]CATACTAGGCGTAGGGATGGGATTGTTCCTTACTG M 2 1 2 1 101000 f 74 goat Random2.2K-529 5 16923227 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389809 Affx-122968198 AX-123260166 5 16966753 AGGACCCACCTTTATTTAACAAAGCTAACTATCTT[A/G]TTGTGCCAAATATAAATATCAGTGGAAAACATAGA R 2 1 2 1 201000 f 74 goat snp36664-scaffold443-1432595 5 17397867 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442294 Affx-122928254 AX-123312631 5 17021094 TTCTGTAAATTTTCCTAAAATCTTTCTTTTGGAGC[A/G]TCAACTTCACATTGGAAATGCAAACTGACCTGGCC R 2 1 2 1 101000 r 74 goat snp14305-scaffold157-2666725 5 17453016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796505 Affx-122935635 AX-385283454 5 17079707 TATCATAGGATTTTTTAGAGCCTTTAATATTCTAA[C/T]GTTCTTACAGAAAGAAATATTACTGTGTAGCTTTC Y 2 1 2 1 101000 r 74 goat snp14304-scaffold157-2608112 5 17513225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440037 Affx-122929760 AX-123310374 5 17128954 TGTCGTCTTGTATCCAGTGAGTATGTGTTAAGCTC[A/G]CTATACAGCAGACACCATGCTGTATGGCATGATTA R 2 1 2 1 101000 f 74 goat snp14303-scaffold157-2558865 5 17563212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381733 Affx-122974689 AX-123252091 5 17187161 CAGAATTGCTGCAATTTGATGAAGACATTATTGCG[C/T]ATCAGAATTGCTACAATTTGTAGAGTACTGCAGTG Y 2 1 2 1 101000 r 74 goat snp14302-scaffold157-2500658 5 17621760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792287 Affx-122929893 AX-385279269 5 17217530 TGTTCTTCTAATAAATTAAATCAGCCAGAATGAAA[C/T]ATTTGCTTACTTGATGAAATTTTGGTTCTAGGTGT Y 2 1 2 1 101000 r 74 goat snp14301-scaffold157-2470289 5 17651353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384936 Affx-122972325 AX-123255294 5 17256214 ACAGAATAGAAATGCAGAACTAGAGCTTGAACGTC[A/G]TAGAAGCCAGGCAGAACAGGTAGTGTAAAGGCAGA R 2 1 2 1 201000 f 74 goat snp14300-scaffold157-2431605 5 17689990 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385027 Affx-122971859 AX-123255385 5 17294104 AAATCATTTTGAAATAAAGTTTTTAAGGGTGTAGA[C/T]GGATGCAGGTCTTTATTATCCAGTATTGCTGAAAC Y 2 1 2 1 201000 r 74 goat snp14299-scaffold157-2393715 5 17728349 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379592 Affx-122976028 AX-123249950 5 17377809 TAATGATTCATTTCTTCAGTCCAGTTTCATAATTC[A/G]TCCAATACAATGCAGTGAAGGGCAGAGAATCTAGG R 2 1 2 1 201000 f 74 goat snp14297-scaffold157-2310010 5 17812744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417390 Affx-122947694 AX-123287738 5 17407794 AAGAAAACAAAGAGGACATTTCAAGAGATTGATTT[G/T]TCAATGCATGATCCAGTGTATGGTGAGAGGTTCTT K 2 1 2 1 201000 f 74 goat snp14296-scaffold157-2280025 5 17844091 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776304 Affx-122970347 AX-385263432 5 17448053 GGTATTATGACCCTTGATGTCAAACATCTTGAATA[C/T]GTATCCAAACTCTCAGATGCAAAATAAGCTAGCAC Y 2 1 2 1 101000 r 74 goat snp14295-scaffold157-2239766 5 17885832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771971 Affx-122947582 AX-385259127 5 17484048 TAGCAAACCAGCGAGGGTTGGGCTAAGTTTAGAAA[C/T]GCACACCCTTAAAATGATGCTGATTTTTTTCCCTC Y 2 1 2 1 201000 r 74 goat snp14294-scaffold157-2203771 5 17922160 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801992 Affx-122920179 AX-385288896 5 17513145 CACACTATTTCTTATCTTGAAATTCTAACAAAAGT[A/G]CATAGTATCTCAATGATTTTCCCAGATGGAGTTAC R 2 1 2 1 101000 r 74 goat snp14293-scaffold157-2174674 5 17950877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803151 Affx-122935845 AX-385290014 5 17571379 AGTTGCCATCAGGATTGCGCTGAATATTCTAACAC[A/G]TGTAGCAGTTTGAATAGTGATTACTCCTCCCAAGA R 2 1 2 1 101000 r 74 goat snp14292-scaffold157-2116440 5 18010213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414261 Affx-122949615 AX-123284610 5 17689586 CCCTCATCAAGGTCAGCTCCTCTAGGTCCTCTTCC[A/G]ACAACCAACTGGTTGACATCTTTTAGTGCTTGTTG R 2 1 2 1 201000 r 74 goat snp14289-scaffold157-1998233 5 18127556 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422256 Affx-122944000 AX-123292602 5 17744519 TACAACCTTCTATTTTTTAATAAATGAGGAAAATT[A/C]TCTGGAGAAGTAAAATACTGATGATTAAAAACAGC M 2 1 2 1 103000 r 74 goat snp14288-scaffold157-1943300 5 18183342 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769377 Affx-122956923 AX-385256548 5 17812167 ATACTTTCAAATAATGTGATTGAGTATACTTTATG[C/T]ATTTCCTGTTCTTTGCAAGATTTTTCACCTGTGAC Y 2 1 2 1 101000 r 74 goat snp14287-scaffold157-1875652 5 18251407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448117 Affx-122924305 AX-123318453 5 17882417 TATTCTTAAGGGTCCTGGAAAGATGATATTAAAAG[C/T]AGTGATAATTATTAAAAAAAAAAAAAAAAAAAAAA Y 2 1 2 1 101000 f 74 goat snp14285-scaffold157-1805402 5 18322515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794300 Affx-122979136 AX-385281264 5 17917339 ATACCAGAACAGTGCCTGCCTATGTGATGAAAACT[A/C]GCACTGCCTCTACTTGCTGCGATTTTACTTTGTGC M 2 1 2 1 101000 f 74 goat snp14284-scaffold157-1770480 5 18357488 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451089 Affx-122921407 AX-123321423 5 17950392 AGGGCATGCCCTCTTTTCCCCTGATATAAACCTTT[A/G]TCTAATTTTAAGTGTAACACCAATCAAATGAGTTT R 2 1 2 1 201000 r 74 goat snp14283-scaffold157-1737427 5 18389725 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428751 Affx-122938435 AX-123299093 5 18021302 AGTAAATACTAATCTCGTCCTTCTTGAATATTCCC[A/G]TTCTCAAGTTCTGTAAATCTTGCATTGTACAAATG R 2 1 2 1 101000 f 74 goat snp14282-scaffold157-1666517 5 18460920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424864 Affx-122941337 AX-123295210 5 18065454 TCAGGATTTTCCTAAAAGTAGAAATATCAAGTCAG[C/T]ATGCCAAGCAGTCATCTTCAGAGCCAAATGATAAC Y 2 1 2 1 101000 r 74 goat snp14281-scaffold157-1622365 5 18494563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275884 Affx-1111835058 AX-519549444 5 18111095 ATCATCAGTCACACGGTTCCGGCAGATCCCTTGAG[A/T]GTGGACGAGAGGATTAAATAGGAGCAGTTGAAGAT W 4 1 2 1 101000 r 74 goat ilmnseq_rs646080217 5 18111095 T A 1 recommended Goat_IGGC_65K_v2 Illumina 38388081 Affx-122969512 AX-123258439 5 18117905 AACAAATTCCTCTCAGTCTCCACTGACCTTGTGCT[A/G]TTTAATCCATCAAAGACTGCTGCTATCCTTTAGTA R 2 1 2 1 201000 r 74 goat snp14280-scaffold157-1569914 5 18554970 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432043 Affx-122935903 AX-123302384 5 18187525 TAGTGGACTCTTTCATATGTTGAAAAAGCAGTAGA[C/T]GTACAGGCTCATTGAGCTGTTAGTTTTTTCAGCAA Y 2 1 2 1 101000 r 74 goat snp14279-scaffold157-1500294 5 18625211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405480 Affx-122956021 AX-123275832 5 18275038 AAAATAAACTAGTTTTCCCAGTTGCTACAGGAATG[C/T]AGTATAGGGGGCATGGTGGGGAGATTTGGAGGTTT Y 2 1 2 1 201000 f 74 goat snp14277-scaffold157-1412781 5 18711563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435842 Affx-122932817 AX-123306181 5 18325018 AGTATTTAGTTTTCAATGTTAAATTTCATTGAAAT[A/G]CTCTAATAGATGGCAAGGCAGAGTATAGGCCAAGG R 2 1 2 1 201000 f 74 goat snp14276-scaffold157-1362801 5 18761482 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781887 Affx-122945233 AX-385268968 5 18369656 TTGTCTCTCATTTCATTCATGAGTCAAGAAAGGTA[C/T]GAGCAATGACTTTTGATATCGTCTTCTTTACTGGT Y 2 1 2 1 101000 f 74 goat snp14275-scaffold157-1318163 5 18805829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420023 Affx-122945154 AX-123290371 5 18409885 GGAACCACATTGAGGGGTCCACTAGTCCCTACTGC[C/T]ACTGACTTATTGACACTAAAGCAATCAAGTTTCTC Y 2 1 2 1 101000 r 74 goat snp14274-scaffold157-1277934 5 18846686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395856 Affx-122964011 AX-123266211 5 18450759 CAAAAGGTGTTGAATGCAGCGCTTGTAAAGCCATG[C/T]GGAGTGAAATGTCATGGCATAGCTTACAGGGCTCA Y 2 1 2 1 101000 f 74 goat snp14273-scaffold157-1237060 5 18887610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421836 Affx-122944304 AX-123292183 5 18479815 AGTAAGAAGCGGGACTGACTTGGTGTGCTGGGTCT[A/G]TACAGACAAAAGCATTCTGCTTCCAAAGGAGCCAA R 2 1 2 1 201000 r 74 goat snp14272-scaffold157-1208004 5 18916756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411177 Affx-122951860 AX-123281527 5 18510813 AGGAGGGCTTTATCTTTTTTGTTCACTGTGGTATT[C/T]CATTGCCTAGAACAGGATGTACTCATATTAGGGAC Y 2 1 2 1 201000 r 74 goat snp14271-scaffold157-1177006 5 18948122 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412464 Affx-122951398 AX-123282813 5 18546775 CATATTCCATTTGATTATTGTAAATATTTGATCTT[A/C]AGTCACTTGACAGTGTTTGTTTGAACTGTGTTTTT M 2 1 2 1 101000 r 74 goat snp14270-scaffold157-1141044 5 18983941 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380475 Affx-122975723 AX-123250833 5 18604264 TAGGACACTACTGAGCAAATAACACACATACATAC[A/G]CATCATGGAAGTGGGGTTGTGTTTCTCCCAGTGAG R 2 1 2 1 103000 r 74 goat snp14269-scaffold157-1083555 5 19041366 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404328 Affx-122957007 AX-123274680 5 18633519 CATCGTCTCCTCCCCTCAGAAGTCAAATAACAGTC[A/G]TCTTAATTGACGTGACTTTTAAAATCAAGAATCAG R 2 1 2 1 201000 r 74 goat snp14268-scaffold157-1054300 5 19070194 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464351742 Affx-1110439057 AX-515825414 5 18638450 CCAAAAGATTGTAGACTTTAAGCATTTAGCTAATA[C/T]CTCTAAGCCCCAGGCTTCTCCTATAAACTGGGGAT Y 2 1 2 1 101000 r 74 goat 5_18638450_AF-PAKI 5 18638450 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320796690 Affx-122932837 AX-385283635 5 18729598 GCTGAATTCAGAATTAAATCTTAACTAGTTCATTT[C/T]GCTGTAGACTTGTGAAAAATGCATGCTCCATAAAG Y 2 1 2 1 102000 r 74 goat snp14267-scaffold157-958221 5 19165860 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274033 Affx-1111833966 AX-519547637 5 18738730 TGTTTGTGATTGGGTGCCCTTAGCATTTTGATTTT[A/G]TAACCTTGAGGCATCTGCAGGCTTGGATTTGGTTT R 2 1 2 1 101000 r 74 goat GoatD01.011966 5 18738730 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407106 Affx-122954884 AX-123277457 5 18777206 AGGATTTTTTTCTGATAAAATCAGATTTATAGCAA[A/C]GATAGTTAGCTGACAGCTCCACATTACTTGGCTTT M 2 1 2 1 101000 r 74 goat snp14266-scaffold157-910613 5 19213942 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446747 Affx-122925334 AX-123317083 5 18827268 GTCGCTGTTGGACCCTCTTTGGTCAATTAGCAGGC[A/G]GTCTCCTGCCAGGCCAGGGAGTAGCAAAGTGCCCA R 2 1 2 1 101000 f 74 goat snp14265-scaffold157-860551 5 19263842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432472 Affx-122935603 AX-123302813 5 18907720 TTCAATTACTATGAGGATTTTGGAGATGAGTGAGA[A/G]ATGAGGTCTGAAATAGAGTCTTGTAGGTAAATGAA R 2 1 2 1 101000 f 74 goat snp14263-scaffold157-780099 5 19342177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390836 Affx-122967836 AX-123261193 5 18939903 TTTGGTTTTAAAAGGTCCCCAATGAAGAGATTTTC[A/G]TTCTCGAAATCCAAAACCTTGTTGGAAATCTCACA R 2 1 2 1 201000 r 74 goat snp14262-scaffold157-747916 5 19374317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375685 Affx-122978660 AX-123246044 5 18999826 TGCATTTCTCTGATCATTCCATGTGTCCTATCCCA[C/T]GATACAAAGCCCAATTTTTTAAGCTATAGTCTGTT Y 2 1 2 1 101000 f 74 goat snp14261-scaffold157-687993 5 19434932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769467 Affx-122962413 AX-385256638 5 19043264 ATCTATTTACCCTTTGAATCATTTTTAATTTAACT[C/T]TTAGCACAAATCCTATGAGTTCTTGCTATTCCCTT Y 2 1 2 1 201000 f 74 goat snp14260-scaffold157-644555 5 19478681 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791823 Affx-122920970 AX-385278813 5 19076785 TAAAAAGTGAATAGTTGATCTGATATCCCAAGAAG[C/T]AGTAAATTACCATGGCCTTATGTTTTTAAACGCTA Y 2 1 2 1 101000 r 74 goat snp14259-scaffold157-611034 5 19512408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434145 Affx-122934909 AX-123304486 5 19128084 TTCAGTATTTTCAAGGAATCAGCACCACTCGCTCT[A/G]CACAATATGCTCCTTTCTTTTGAGAAGAAAAGTGG R 2 1 2 1 101000 f 74 goat snp14258-scaffold157-559735 5 19563816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450462 Affx-122922947 AX-123320796 5 19198567 AAGATAATACAAATATGTGAATTATCCTTGTTTTT[A/G]CTGATACATTACAAAGAGGAAATGATTGACATAAA R 2 1 2 1 101000 r 74 goat snp14257-scaffold157-489252 5 19634110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436029 Affx-122932733 AX-123306368 5 19244402 TCAGGTCTCCCAGGCTCAGAGATGTTAAGTGGTTT[A/G]CTCAATCTGACAAAGCAAGTGGCAGATATAAAATT R 2 1 2 1 201000 r 74 goat snp14256-scaffold157-443417 5 19679840 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397660 Affx-122962600 AX-123268015 5 19297600 AACCCTCCATCTAATGAGCTTGCTCTCTTACCCAC[A/G]CCATCCATCATCTACTGATATCCATTGCTCCACCC R 2 1 2 1 201000 r 74 goat snp14255-scaffold157-390219 5 19733227 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384507 Affx-122973052 AX-123254865 5 19412365 AAAAGAGCATCTTGAGAACAGAGATATAGTACTCT[A/G]TTTTATCCCCATTTTTGTTCCAAGCAAAAGAGAGT R 2 1 2 1 201000 r 74 goat snp14253-scaffold157-275454 5 19848381 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435804 Affx-122932847 AX-123306143 5 19467409 GTGCAGACACAGAAAGAAAACCAGCAAAGAGTTTT[A/G]TAGTTTTGCTATATGCACAGTTTCCAGGGGAGATC R 2 1 2 1 101000 r 74 goat snp14252-scaffold157-220410 5 19902189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413510 Affx-122950633 AX-123283859 5 19499085 GGTGGGCGTTGCGGTTAGGAGGGCACATTAGCAGC[A/G]AGCATATTGAGTCTTCAGATTACCTGGAGCCAGCA R 2 1 2 1 101000 r 74 goat snp14251-scaffold157-188734 5 19934148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774798 Affx-122974303 AX-385261932 5 19541394 GGAGTGTATAACACATGCAAACATAGATATTGAGT[A/G]AACAGTTGATAAAAATTGCAAGCAGTCTGCGGTGG R 2 1 2 1 101000 r 74 goat snp14250-scaffold157-146425 5 19976541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441400 Affx-122928842 AX-123311737 5 19578480 GAAGAGGAAAAGTGCCTATGCTCTGTGCGTTTAAA[C/T]TACACTGCAAACATAATTGGAGACAGCGTTTGCAA Y 2 1 2 1 101000 r 74 goat snp14249-scaffold157-109339 5 20015454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799256 Affx-122925326 AX-385286186 5 19607848 TAATTACATGCTAGTTGCTTTATATACAGTACCTG[A/C]AACATGGTATTAGTCATTTTGGATGATGACAGATG M 2 1 2 1 101000 f 74 goat snp14248-scaffold157-79971 5 20045308 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431596 Affx-122936171 AX-123301937 5 19641065 ATCTCTCTAAATAATGGACATAGTGCATGAACGCT[A/G]TCATGTCTGACTCTTTGCAACCCCATGGGTTGTAG R 2 1 2 1 102000 f 74 goat snp14247-scaffold157-46754 5 20079492 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418090 Affx-122947144 AX-123288438 5 19685347 GTACAGGATTCAGTTGCAGTCAGCATATATTAACT[A/G]CAGATCAATGCAAGAGGCAGTAATTATACACAACA R 2 1 2 1 101000 f 74 goat snp14246-scaffold157-2472 5 20124247 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791892 Affx-122956112 AX-385278883 5 19689030 CATAAATGAATAAATACTGGCTATGTTTTAATAAC[A/G]TCTTATTTATAAAAGCCAGAGACACCTGGATTCTG R 2 1 2 1 102000 r 74 goat snp38501-scaffold486-5603502 5 20143470 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398439 Affx-122961613 AX-123268794 5 19749651 ATTTGAAGTCAATATCATTGTCATCATTTTGAGGA[C/T]AGCAAAGAATAGTTCTTACTTTTTCTTAGTTTTTG Y 2 1 2 1 101000 f 74 goat snp38500-scaffold486-5542881 5 20203977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393305 Affx-122965428 AX-123263661 5 19782498 AACAGTACTTTCTTGTAACTAAGAACTCTAAACAC[A/G]CATACTTAAAGTGTCAACTAATAAGAATTGCTATT R 2 1 2 1 101000 f 74 goat snp38499-scaffold486-5510034 5 20237382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379382 Affx-122976142 AX-123249741 5 19873546 GTGATTTAAATACGATGGTATTTTATGATAATTAC[C/T]GTCATTACTGAGCTACTTTTTCCACTGACCATGTG Y 2 1 2 1 101000 r 74 goat snp38497-scaffold486-5418986 5 20329430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416680 Affx-122947581 AX-123287028 5 19902330 AAAAGCAATTTTAACCTAAACATATGCAAAGTATC[A/G]TCAGAAAATAAACAAAAATCCTCAGATGAAACAGA R 2 1 2 1 101000 f 74 goat snp38496-scaffold486-5390202 5 20358348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398376 Affx-122961657 AX-123268731 5 19966342 GGTACCCTGCAGCTTAGGCTCTCTACTTAGACTGC[A/G]TCTTCCTGGATTGCTCTTTTCCCAGATAACTTGAA R 2 1 2 1 101000 r 74 goat snp38494-scaffold486-5326190 5 20422747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772876 Affx-122959256 AX-385260021 5 20037103 AAAACATGAAGAAACTAGCATAGTGTCTAGAAGAT[A/G]CCAATCACTCCTTAAATGTCACCATTATTTTCATT R 2 1 2 1 101000 r 74 goat snp38493-scaffold486-5255429 5 20495087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796023 Affx-122962881 AX-385282975 5 20066247 ACCCACTCCCTTCCCCAGACAGTGACAGAGCTTTT[A/G]TACTTCCAGTAAAAAGCCAGGCCTTGTCAATCTGA R 2 1 2 1 303000 f 74 goat snp38492-scaffold486-5226285 5 20524637 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772622 Affx-122949019 AX-385259770 5 20122772 AGTACTTGTGCTTTATTGTGTTAATTACCCAAAAA[G/T]ACCTCTTCTACATACATATTCCCAGATTCTGAGGG K 2 1 2 1 101000 r 74 goat snp38491-scaffold486-5169760 5 20582039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400316 Affx-122960060 AX-123270671 5 20163337 TCCTTGTGCTACATAAAATGAAAGTAATCAGTGTA[C/T]GCTACAAATGTAGAAACACATATAAAATGCATAGC Y 2 1 2 1 101000 f 74 goat snp38490-scaffold486-5129195 5 20622071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431847 Affx-122936083 AX-123302188 5 20205561 GACATTTGGTCACAATAGACCTGGTCGTATCTAAA[C/T]GTATATTCTGTCTTGTTAGGCTGCCCTCTTGCTAC Y 2 1 2 1 101000 f 74 goat snp38489-scaffold486-5086971 5 20663976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435272 Affx-122934051 AX-123305612 5 20237621 GGCTATATATTCACTTCAGAAGAACAGATGCACAA[C/T]AGAGAAAACACCTTTTGAGACTAAGCCTTCCTCAT Y 2 1 2 1 101000 r 74 goat snp38488-scaffold486-5054911 5 20695898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435007 Affx-122933813 AX-123305347 5 20273055 AGCAGATTATATTTGTCAGATTATACTGACACACC[A/G]CTGACTTCTTGTATTCTTTCATGCAACTACAACAT R 2 1 2 1 101000 f 74 goat snp38487-scaffold486-5019477 5 20731318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799663 Affx-122930680 AX-385286591 5 20301872 ACAGAGTTTGCTACTAGTTTCAGATAAACTTTGGA[G/T]AGCATAGCCTCAGGATGCTTCATATACAAAGGCTA K 2 1 2 1 102000 r 74 goat snp38486-scaffold486-4990660 5 20760425 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777398 Affx-122923639 AX-385264520 5 20403368 GAAGTCTAGTGTATATTTCTACAACTTAGAAAATA[A/C]TAGAAACTGTCACCAGAGAGGTGAAAACAAACACT M 2 1 2 1 101000 r 74 goat snp38483-scaffold486-4889164 5 20861799 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273984 Affx-1111833934 AX-519547589 5 20436497 ATTTGTAAATATTACAGACAATGTTCAAAATAATA[A/G]GTTTTAAACTCTTGTGAACACATTATCTATCAGCA R 2 1 2 1 201000 r 74 goat GoatD01.010929 5 20436497 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778043 Affx-122919401 AX-385265158 5 20461804 AGAAAAATATCTCCAAGTTAAATCTGGAAGAATCA[A/G]CATTGGTTGAGGTAAGAAGGAGAATGACATGGAGA R 2 1 2 1 101000 r 74 goat snp38482-scaffold486-4830728 5 20921004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423431 Affx-122942608 AX-123293777 5 20503921 GAATTAAAAAGAAGAATAAAGCTTATTTTAAACAA[C/T]GAGGGAAAACCGAATAATCTTAAAGTCTATGAATT Y 2 1 2 1 101000 r 74 goat snp38481-scaffold486-4788611 5 20963339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450371 Affx-122922094 AX-123320706 5 20535475 GACTATTGTAAATTTGCTGTTTTTCTTAGATTGAG[C/T]GTCTAATAAGTCCTATGCTTTACACTTGCTCAAAA Y 2 1 2 1 101000 r 74 goat snp38480-scaffold486-4757057 5 20995407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448172 Affx-122924259 AX-123318508 5 20569305 CCTTAATTTCCTCTTATTTAATTTTCTCAATTTTT[A/G]CAGTTTTGAAATCCTATACCTCTTTGGAATTATCT R 2 1 2 1 101000 r 74 goat snp38479-scaffold486-4723227 5 21029193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385664 Affx-122971151 AX-123256022 5 20629641 ATACAGTTCCACCCAGAAAAAGTAATTCTTGGAAC[G/T]CATCTCAGAGAGGAAGTCTTTCTTGGTCCAACACA K 2 1 2 1 201000 f 74 goat snp38478-scaffold486-4662891 5 21089836 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431433 Affx-122936513 AX-123301774 5 20662634 TGCCAGAAAAGCACTACCAAGTTTATGGAAGACAT[G/T]ACAATTTCTATATAGGATACTGTACACACACACAA K 2 1 2 1 101000 f 74 goat snp38477-scaffold486-4629898 5 21122756 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787998 Affx-122972224 AX-385275019 5 20694142 CTTTCAGTATCAGGTTCTGTGGCGGCAGCAAGTAT[C/T]CAAGGAACTGAGCTCACCATTTCCAAGTAATACCT Y 2 1 2 1 101000 r 74 goat snp38476-scaffold486-4598390 5 21154536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389602 Affx-122968767 AX-123259960 5 20763505 TTTGTCTGAAACTTCCTGCATCTATTCTGGTATGT[A/G]TAAAGAAAGCACCTCCAGTATATATCCCTTTCTTT R 2 1 2 1 101000 r 74 goat snp38474-scaffold486-4529027 5 21225152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431167 Affx-122937193 AX-123301508 5 20819541 AACAATATGCCCCTCCTCATTTTCCCTTCAGAGCT[A/C]AGTTCCCTGAAGGCTTGTCTATGTCTGCTTTGGCC M 2 1 2 1 101000 r 74 goat snp38473-scaffold486-4472991 5 21281835 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428900 Affx-122938925 AX-123299242 5 20873352 ATAACAAATATCTTTGTAATGAACATGATTTCTCT[C/T]AAATACAAGTCCACTGTTAGCTCCCTACTCCCACC Y 2 1 2 1 101000 r 74 goat snp38472-scaffold486-4419180 5 21336262 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445231 Affx-122925497 AX-123315568 5 20903202 AGTACAATTTCAACTTGCTGTAATTAGGGCTCTAG[C/T]GGGAACTTAGTACTTATAAGCTGTGTGTCTAAGTT Y 2 1 2 1 101000 f 74 goat snp38471-scaffold486-4389330 5 21366121 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401840 Affx-122959436 AX-123272193 5 20932359 GTGAAAGAGGGAAGATACAAGTAAGGGAAGGAACA[A/C]ATATTAATAGAGGAGGTGAGGTTAGAAGGCAAACA M 2 1 2 1 101000 f 74 goat snp38470-scaffold486-4360173 5 21395298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439566 Affx-122930087 AX-123309903 5 20979633 TTAGGAAGTTTGCTCCAAAGTAAACAAGCCACCAG[C/T]GCACTGGGAAGAATAGACCCTCTTTCCACTCAGCC Y 2 1 2 1 101000 f 74 goat snp38469-scaffold486-4312899 5 21442411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429245 Affx-122937908 AX-123299587 5 21016446 CAAAGAGTCAACAGCTGAACTGAACCCAAAATCCA[G/T]ACTCTTCCCTACTGTAGGCTTTTGTATCCTTTTCT K 2 1 2 1 201000 r 74 goat snp38468-scaffold486-4276086 5 21479200 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794594 Affx-122951308 AX-385281556 5 21053402 GCAAGATTGCTGTATGATATAGGATTGGACTACTG[C/T]ATTGCTAACCCAACTCTACTATATGTTTCTCCATC Y 2 1 2 1 101000 f 74 goat snp38467-scaffold486-4239130 5 21515678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779540 Affx-122944840 AX-385266643 5 21084333 CATTACTTACATCATGGATGGGCTTTTCAAAGCAC[A/G]GTTCTGTGGTTTACTATTCCTAGGAAACTTGTCCA R 2 1 2 1 101000 f 74 goat snp38466-scaffold486-4208199 5 21547169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421511 Affx-122943894 AX-123291858 5 21132398 GCCAAAGTAAAGAGTAACATGGATATAAATTTGGA[C/T]AAAAAGCCATGCTTCAGGTACACATATTATTTCTT Y 2 1 2 1 101000 f 74 goat snp38465-scaffold486-4160134 5 21595554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272302 Affx-1111833459 AX-519546041 5 21161885 TGGAGGCCTGAATGTTAAAGGAAAACTCCAAAGGA[A/G]CAGTGCAAATAGCAAGATTGCAATTATATTAGAAG R 2 1 2 1 101000 f 74 goat 5_21161885_AF-PAKI 5 21161885 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437095 Affx-122932185 AX-123307433 5 21181072 CTCAAACTAGTGGTCTACTGTGCTTCTTCCAGTAT[C/T]ACAAGGAAACAACTAGAACTTTCAGGTCACCAGGA Y 2 1 2 1 201000 r 74 goat snp38464-scaffold486-4111460 5 21644333 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438079 Affx-122931523 AX-123308417 5 21233085 AAGAAGATACCACATTGACAAATTTCTTTTCAGTA[C/T]GAAATCCACAGATAAAACAAATTTAAATCAGAACC Y 2 1 2 1 101000 f 74 goat snp38463-scaffold486-4059447 5 21696911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801957 Affx-122965506 AX-385288861 5 21278877 AAAGTGGGGCAAAACCTAGGGGTTCTGGAGATACA[G/T]CTTTATCTCACTGTCATGGTATCCATCTTATTTGT K 2 1 2 1 101000 f 74 goat snp38462-scaffold486-4013655 5 21742999 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452156 Affx-122921657 AX-123322489 5 21324444 TTGGTCATTTTCAGCCTTGAAATCATAATCTTTTT[A/G]CTCTCTATGCCCAGGAAGCATAAAATTGTCTTAAA R 2 1 2 1 101000 r 74 goat snp38461-scaffold486-3968088 5 21788691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770606 Affx-122937091 AX-385257770 5 21363244 ACACAAGAAATCATGACCAAAATAAGAAACCAACT[A/C]GACTAATCCCTTAGGGATTGCTTTGCTTTCTTAAG M 2 1 2 1 201000 f 74 goat snp38460-scaffold486-3929288 5 21827401 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792470 Affx-122922183 AX-385279451 5 21408146 CTTTTTTTTTCCTTAGCAAAATTTCTCTTTCTCAA[C/T]AGCAAAGTCACCATTCAACTACTATTGCAGAAGAA Y 2 1 2 1 101000 f 74 goat snp38459-scaffold486-3884386 5 21872228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380918 Affx-122975021 AX-123251276 5 21441188 CCACCTCTCTAAAATAACTACACACACACAAGGTT[A/G]ACTTAGGATCAGATTCTGGAGGTTTCCAGGCTGGC R 2 1 2 1 101000 f 74 goat snp38458-scaffold486-3851344 5 21905783 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429833 Affx-122938171 AX-123300174 5 21521519 CTGTTACTTGCTATCAAAAAGTTTCAACTAATGCA[A/G]GTAGCTATTACCATCTCGATGAGGCTGAGAAATTA R 2 1 2 1 101000 r 74 goat snp38456-scaffold486-3771013 5 21985656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393688 Affx-122965259 AX-123264043 5 21568760 AATGCAAATTACCACTCACAAATGAACAAAGGCCC[C/T]GCCACTCACCCCCAGATGGCTCAGCTGCCAGCCTG Y 2 1 2 1 101000 f 74 goat snp38455-scaffold486-3723772 5 22033072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414312 Affx-122949578 AX-123284661 5 21615386 CCCATTTTAAGCGGAATTCCCTCTCCCACAGTCTC[C/T]CTCTTGACTATTGACAGTCTGTGTTTCAGGAAGCT Y 2 1 2 1 201000 r 74 goat snp38454-scaffold486-3677146 5 22080295 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399072 Affx-122960890 AX-123269427 5 21653979 CTAAGTCCCCTTGGGGGGTGTTCATTATTTTCACT[A/G]CTGACCACTGCTTCTAATTGCCTGAGTTAGCATTT R 2 1 2 1 201000 r 74 goat snp38453-scaffold486-3638553 5 22119201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785999 Affx-122925564 AX-385273035 5 21689889 TTTGGGCTACTTGGAACACAGTTAATGTGCAGTGT[A/G]CTCTGTTACTAGCATGTATGTTGGGCACACAGTAA R 2 1 2 1 101000 f 74 goat snp38452-scaffold486-3602643 5 22155501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789772 Affx-122927533 AX-385276780 5 21752962 GTCTAGAAATTTCCATGTGAGCAAAAACTTGCTAC[A/G]CAGTGTCTGATGGTAAACTTTATGTGTCAACTTGA R 2 1 2 1 101000 f 74 goat snp38450-scaffold486-3539570 5 22218723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776968 Affx-122941417 AX-385264092 5 21813062 CTCACCATATCATTTTAAACAGAACTTTCTCTTGA[A/G]ATAACAGTAACAACTAAAGCATACGGAGTGCTATC R 2 1 2 1 101000 f 74 goat snp38449-scaffold486-3479470 5 22279486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774677 Affx-122974976 AX-385261811 5 21850068 TTTGCATTTTCTGACTTGTTCCTTTACAGAGTAGC[A/G]TTTCAGGAATCCTCATTTTACTTTGACATTTCAGG R 2 1 2 1 101000 f 74 goat snp38448-scaffold486-3442464 5 22316587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410287 Affx-122952506 AX-123280637 5 21905490 TGGGGACCTCCTACAGCAATTGGGACATGTGCCTT[G/T]TGTTGATGTCTGAAACCATAGTGACTGATGTTGTG K 2 1 2 1 201000 r 74 goat snp38447-scaffold486-3387042 5 22372298 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421733 Affx-122944381 AX-123292080 5 21949586 TGTCCCCTTTGTGTGGAAATAGAAGTTTTTAATCC[A/G]CTGGCATAACTTGAAAAACAGACTGAGGGAAGAAG R 2 1 2 1 101000 r 74 goat snp38446-scaffold486-3342946 5 22416667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451317 Affx-122921280 AX-123321650 5 22039701 AGTCTTTGGCTTATTTTAAATTATTGTGTATGGTC[C/T]GAATTGTGGTTGAGCTTCATTCCTTCCATGTGGAT Y 2 1 2 1 101000 r 74 goat snp38445-scaffold486-3252831 5 22506984 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390923 Affx-122967084 AX-123261280 5 22070448 TGATGTGTCAATAGATACCCAGAGGAAGAATGTGG[C/T]GTGAGGAGGAGAGCAAGAATACACAGAAAAACTAT Y 2 1 2 1 101000 f 74 goat snp38444-scaffold486-3222084 5 22537208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464353962 Affx-1110440192 AX-515827609 5 22087676 GGTTCTGATTTAATTACAGAGGGCTGCAGTCTGAG[C/T]ACTAGAATTTTCAATTACTCCCAGGTGATTCTAGT Y 2 1 2 1 201000 r 74 goat GoatD01.051531 5 22087676 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406499 Affx-122955152 AX-123276851 5 22102536 GCTCCTTACAAATAAAATTGGGCTAATTCTTATCT[A/G]CCAAGAGAGTCCTGTATTTTGCCTTTATTTTATTG R 2 1 2 1 101000 f 74 goat snp38443-scaffold486-3189996 5 22564964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376485 Affx-122978032 AX-123246844 5 22142163 TAAGAATGTAGGTGCTGTGATTTTGGGCTTCCTAC[A/G]TGGCTCAGTGGGTAAAGAATCTGCCTGCAATGCAG R 2 1 2 1 101000 f 74 goat snp38442-scaffold486-3150369 5 22604355 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428817 Affx-122938384 AX-123299159 5 22176114 TGCAAATGGAAAAAAAAAATTCACAGTCTGCTAGA[C/T]ATTTGGAATTTCATGAAGTTGATGAAAGCGATACA Y 2 1 2 1 101000 r 74 goat snp38441-scaffold486-3116418 5 22638443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424557 Affx-122942234 AX-123294903 5 22229205 GATCCTTCCCTGATTTTCCTTTTCTGAGATGCTAT[C/T]AAGACTTTGTCATAGAAATGTTTCCCTTACTCAAT Y 2 1 2 1 201000 r 74 goat snp38440-scaffold486-3063327 5 22691868 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401444 Affx-122958984 AX-123271797 5 22304894 GTCATAATAAAAATATAAACCCACAATGTTGACGA[C/T]GTGAAGGGTGTCCCCTTAAATGTGATACTCTCGTG Y 2 1 2 1 101000 r 74 goat snp38439-scaffold486-2987638 5 22768298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404768 Affx-122957213 AX-123275120 5 22343529 AAGTCTTTTCCCTAAATGAACATCTAGGTTGTATG[A/C]ATGGTGATCAGTACAATCATGAGACCAGTTAGCGC M 2 1 2 1 101000 r 74 goat snp38438-scaffold486-2949003 5 22808088 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800096 Affx-122937964 AX-385287019 5 22372709 TTCTGTAACTTGTTTTTTGCCAATAGTAAATTGTA[C/T]TGAGACATGCATTTGCATGTCATACCTTTTCTCAT Y 2 1 2 1 101000 r 74 goat snp38437-scaffold486-2919823 5 22837300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403226 Affx-122957897 AX-123273579 5 22427296 CATGAGATTTACTGCTGGGATGCTGTACATTTGTT[A/G]CCAAGAAACTGGGATCAGTCTTGTACTGAGTATAG R 2 1 2 1 101000 r 74 goat snp38436-scaffold486-2865236 5 22892046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776713 Affx-122966170 AX-385263839 5 22457228 CGTCAGACTCAAGCAGAATTACAATTCTAATATCT[A/G]CTCATGTCCCCCACATGCCCTCAGCCCTGCCCAGA R 2 1 2 1 303000 r 74 goat snp38435-scaffold486-2835304 5 22922091 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779553 Affx-122957319 AX-385266656 5 22522352 GTCATCCCTGTAATATTTGGTGCGGGAGCTCCTTT[C/T]ATTCTTTAATTTGATAATCTGCAATTATCTGCATT Y 2 1 2 1 101000 f 74 goat snp38434-scaffold486-2770180 5 22987123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393187 Affx-122965515 AX-123263544 5 22565432 GCGACTCTGTGGACTGCAGCACGCCAGGCTTCCCT[A/G]TCCATCACAGAGTAAAAGTCTGTTTTACTACTGTT R 2 1 2 1 103000 r 74 goat snp38433-scaffold486-2727100 5 23030421 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433157 Affx-122935671 AX-123303498 5 22620403 ATCTAGTATTCTTTATTCTGTTTCTGGTTATACCA[A/G]CATCTGACTCTCGCAGCAAGAAATTCTGTGGTTAT R 2 1 2 1 101000 r 74 goat snp38432-scaffold486-2672129 5 23085273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392808 Affx-122965966 AX-123263165 5 22669912 GGTAAAATGTCTCTATCTACACGGTTTTATTAACA[A/G]GGATTGAGTTGCACCTGTATAGCATGACATTCTTG R 2 1 2 1 101000 r 74 goat snp38431-scaffold486-2622620 5 23135294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781244 Affx-122949671 AX-385268329 5 22714358 TTGAAACTGTAGATGAATGCGGAGATGAGAGTTAT[A/G]TAAGTGGGATGAAGCTGGCCTCTAAAAATCCCATC R 2 1 2 1 101000 r 74 goat snp38430-scaffold486-2578174 5 23179267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765169 Affx-122958451 AX-385252720 5 22749602 CTCTTTGGAGAGCAGTTTGGTACATGTCACATCCC[A/G]TCATACAGAAACTCTCATATGTGCAAAAAACATGC R 2 1 2 1 101000 f 74 goat snp38429-scaffold486-2542930 5 23213882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445218 Affx-122925509 AX-123315555 5 22796142 AGCCATACACCGGATGATACAGATCACAGAATTAC[A/G]CCATTGGGAAAATCATGCATAGTTTCACTCAGTCA R 2 1 2 1 101000 f 74 goat snp38428-scaffold486-2496390 5 23261140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416087 Affx-122948325 AX-123286436 5 22827361 AGTTCCTGGAAGAAGGTGGGAAAGTCCTAAAGAGT[A/C]TTCATAAAACTCCCCAAGAGCCACTTTCTGTTCCA M 2 1 2 1 101000 r 74 goat snp38427-scaffold486-2465171 5 23292466 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768766 Affx-122932964 AX-385255943 5 22879856 TCAATAACACCTATCAGATTTTTTGTCCATTTATG[C/T]GTCTCAGAACATAGCTTAAGCTGAAAGACACAATC Y 2 1 2 1 101000 r 74 goat snp38426-scaffold486-2412676 5 23345368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777923 Affx-122978230 AX-385265039 5 22920767 TTCTGCGGGGAAAAAGGAGAGAGTAAACTAAAATC[A/G]TTTTCTTTTGGCTGGTGGTATATTCCTCCCAGTCT R 2 1 2 1 101000 f 74 goat snp38425-scaffold486-2371765 5 23504396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784580 Affx-122928574 AX-385271628 5 22963825 TTTTTTTCTTTGAAAGCACTGAAACCTGGATTTTA[C/T]GGTCTATGCTTTGAATTAATAACAGCTTTTATAGT Y 2 1 2 1 101000 f 74 goat snp38424-scaffold486-2328707 5 23429366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395853 Affx-122964013 AX-123266208 5 22996171 TGGTCAATGAAACCCCACAGTCCTATAGGAAGGCA[C/T]TGTCGCTTTAAATGAGGCTTGCTGTTATATAATTC Y 2 1 2 1 201000 r 74 goat snp38423-scaffold486-2296361 5 23462175 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777680 Affx-122921301 AX-385264799 5 23058006 TTTGAAGGTCTGCAAGCTCTTTGACGATGTCTTTC[C/T]GAATTTGTTTCTGGAGAGATCTTTAGCCCATGATA Y 2 1 2 1 101000 f 74 goat snp38422-scaffold486-2234526 5 23524219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404399 Affx-122956787 AX-123274751 5 23110876 AGATATCAAGACTGGGATTCTTTCCTGCATTCCTC[A/G]GTAATCAGTGGTTCTTTGGAACCGAGGTGACCAAA R 2 1 2 1 201000 r 74 goat snp38421-scaffold486-2181656 5 23578293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424084 Affx-122942042 AX-123294430 5 23154515 TGAGCTCCTGTAGGTAGGTTGTCATGTTTCAGCGT[A/C]CCTCCATGCAGATTGATGGGGCGGGGCGGGGTGAT M 2 1 2 1 101000 f 74 goat snp38420-scaffold486-2138017 5 23622867 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427767 Affx-122939236 AX-123298110 5 23201246 GCTTTGTGCTAAGAGCTAGTGATACACTTGGTACC[A/G]TCATCCATTTTTAGCAACGGGATATTCTTTCAACA R 2 1 2 1 101000 r 74 goat snp38419-scaffold486-2091286 5 23669928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442716 Affx-122927862 AX-123313053 5 23262939 GCCACTGTCAGCTGCCTGGGTGCCAAGAGCTGGGC[A/G]CCTTCATGGTTTCATCCCCTCTCCACCTTCTGCTC R 2 1 2 1 101000 r 74 goat snp38418-scaffold486-2029593 5 23731868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411009 Affx-122951984 AX-123281359 5 23320582 TATTTAAGGCACTGCTTTTTGGATCTAAACTTAAG[C/T]AGCACTGTTAAAACCTGTGGCATAGCAGTGTATCT Y 2 1 2 1 101000 r 74 goat snp38417-scaffold486-1971950 5 23789518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278350 Affx-1111836297 AX-519551836 5 23372374 TCCTGCCCCCAGTCCCTCCCAGCATCAGTTAAGGT[A/G]GGTGCAGATATAGTAGCTATTTCTTCTCTTGCTCA R 2 1 2 1 101000 r 74 goat Random2.2K-532 5 23372374 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793161 Affx-122963927 AX-385280139 5 23416676 CCAATAAACTGTACAGTTTTAAGGAAGTCATCCCA[C/T]GGAGTTATCCTTATTATGTAAATTAATAAGGTCAT Y 2 1 2 1 101000 f 74 goat snp38415-scaffold486-1875856 5 23884882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438438 Affx-122931261 AX-123308776 5 23453462 TATGAAACAACAAGTGCAACATATATGAATAGAAC[A/G]ATTCTGACGCACTCATTTGTTTATTCATGTCATTC R 2 1 2 1 101000 f 74 goat snp38414-scaffold486-1839070 5 23922667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427209 Affx-122939587 AX-123297552 5 23489466 GTCTGAAAGGGAGAGACTCCCTCCCCCCAACCCCC[A/G]CCACCACTCTAGTCTTCAAGTAGACTTGGAGGTTC R 2 1 2 1 103000 r 74 goat snp38413-scaffold486-1803066 5 23958700 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419786 Affx-122945854 AX-123290134 5 23521757 CTTCTTGTTGCATCACAGCAGAAAGCACATCAATA[G/T]CTGGCTGTTTTTCTTTTTCTGATGTAAAGGTTGAT K 2 1 2 1 201000 f 74 goat snp38412-scaffold486-1770775 5 23992266 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430227 Affx-122937325 AX-123300568 5 23611817 GAGAGTTACTATAGTAACAGAGAACCCTTGGCCCA[C/T]AGCGTATGTTCACAAAAAGGAAAGTAAATCAATGT Y 2 1 2 1 101000 f 74 goat snp38410-scaffold486-1680715 5 24083291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381618 Affx-122974776 AX-123251976 5 23643961 CCACTGCCCCTCTTTTAAAGCTCAAGTGAGTGTGC[A/G]CTACAGATGCAGCTCTGTATCTTTCTCCCTTAACA R 2 1 2 1 201000 r 74 goat snp38409-scaffold486-1648571 5 24115332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412789 Affx-122950496 AX-123283138 5 23684184 AATATAAAAATATTTTGTTTAAATATATAAACATA[C/T]ACAAATTGAGATAGAGGCCTGGCCAGCCCCAGGTA Y 2 1 2 1 102000 r 74 goat snp38408-scaffold486-1608348 5 24155506 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379834 Affx-122975817 AX-123250192 5 23727383 AATTATTGTAATATGAATGGAATGTATAAGACTCC[A/G]TCATGTCATATCTATCAAATATCTTCACGTTTAGA R 2 1 2 1 101000 r 74 goat snp38407-scaffold486-1565149 5 24198761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272573 Affx-1111833460 AX-519546288 5 23747150 TGACTGAGTGACTAACACTTTCTTAGGTTCCCTGC[A/C]AGAATAGTTAAAAAGCTGATGCCTTGGATTAAGGA M 2 1 2 1 201000 r 74 goat 5_23747150_AF-PAKI 5 23747150 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396384 Affx-122963026 AX-123266739 5 23766741 AATACTTGATCATTTTTAATAAGCTTTAATACTTA[C/T]GCAAATACACTTAAGGGGATGTCGCAAGAAATGGC Y 2 1 2 1 201000 f 74 goat snp38406-scaffold486-1525791 5 24237986 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795429 Affx-122923524 AX-385282385 5 23798215 TTCAACTGCTCACAGTTGTTAAGATTCCTTTCAGA[A/G]GCTGTTTTGAAGTCATCTGTCAGCAAGGAGTGGGG R 2 1 2 1 101000 r 74 goat snp38405-scaffold486-1494317 5 24269164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402553 Affx-122958460 AX-123272906 5 23836338 GATTGTTGATCGTTTTGTTGGTGGTGTTGAGGGCT[A/G]CTGCTATTTGTGACATTTCCACAGTAGTGTTGCAA R 2 1 2 1 201000 r 74 goat snp38404-scaffold486-1456194 5 24307745 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278195 Affx-1111836298 AX-519551684 5 23863229 AGCATCTTCCCTCACAAATGTCCCACCCAACTGAC[A/G]TGCCCCTGGGGATACCCTGGAACAAAATAATCAAA R 2 1 2 1 102000 f 74 goat Random2.2K-533 5 23863229 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383181 Affx-122973217 AX-123253539 5 23915701 TTTCAGGATCCCAGGAGGCAGAGACCAGTCAAAAG[A/G]GTTTTGCACTTCCTTTATTCCTATTATACCAGATG R 2 1 2 1 101000 r 74 goat snp38403-scaffold486-1376831 5 24388157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416479 Affx-122947801 AX-123286827 5 23970641 CTGCCCTGATTCCTGGATGTCTTCTTTGATTCTAC[G/T]ACTTCCTCCTTCCCCCAAATCCTCTTTTTGCTCAA K 2 1 2 1 101000 f 74 goat snp38402-scaffold486-1321891 5 24443150 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793763 Affx-122961594 AX-385280735 5 24039773 GGACCATTCTTTAGTTTGAGGAGAGCACAGAAACT[A/G]TTTTGCCTATGTATTCACTGAAATCAGTTTCACAT R 2 1 2 1 102000 f 74 goat snp38401-scaffold486-1252759 5 24513048 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791743 Affx-122940342 AX-385278734 5 24069726 ACATTCTGGGATTTTGGCAATCCAGTGAGTCAATC[A/G]TGCCATGGAACGGCAGGAGCTTAAACAGCTGCTTG R 2 1 2 1 101000 r 74 goat snp38400-scaffold486-1222806 5 24543119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780969 Affx-122944642 AX-385268056 5 24101378 ACTGATCTAAGTAAAAGTTACACATGTGTTTAATG[C/T]AGGTTTCATGCTGGGCTTGATTTTAATTGATGAAT Y 2 1 2 1 101000 r 74 goat snp38399-scaffold486-1191154 5 24574740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800885 Affx-122940994 AX-385287800 5 24154902 GGTTCCATGTAAGTGTGAATTGGAATAAGGTTGTA[C/T]GAGGTATTATTACCCTTTTATATGTAAAGAAACAA Y 2 1 2 1 101000 f 74 goat snp38398-scaffold486-1137630 5 24629064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412601 Affx-122951289 AX-123282950 5 24212634 AGGACTTCCTGTTGCAGGATAGTATGAAGTGAATC[A/G]AGTCGGAATCCAATATCCTTGCCATTGAAAGACCG R 2 1 2 1 101000 f 74 goat snp38397-scaffold486-1079898 5 24687668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797996 Affx-122963723 AX-385284932 5 24304129 GCATCCAAATTTACTAGTAGCAAAAGTCCACTTCT[G/T]GTTCAAAGGCACAACGTCATCCCAGGAATTTTTTT K 2 1 2 1 101000 r 74 goat snp38395-scaffold486-988403 5 24779337 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391134 Affx-122966793 AX-123261491 5 24380092 GTCAAAGATAGGGTGCACATAGGGGTGCAGGGACC[A/G]CATTTTGAGTTGCACTGTTCTGATGACCCTGCCAT R 2 1 2 1 101000 r 74 goat snp38393-scaffold486-912440 5 24855884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397313 Affx-122962314 AX-123267668 5 24414282 TACACAAGTAGAGACAGATGTACACATACATGAAC[A/G]TAGGAAAATATGGAAGGCTACCTGCTAGGTGGTTA R 2 1 2 1 101000 f 74 goat snp38392-scaffold486-878250 5 24890106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774285 Affx-122967369 AX-385261421 5 24494665 GCATTATCTCTATTTACAAATCATTGAGTTAGTAG[A/C]GATTTCACCTCTTACAGAGCAAAAACTTCAAGTAA M 2 1 2 1 101000 f 74 goat snp38391-scaffold486-797867 5 24970993 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780437 Affx-122970379 AX-385267528 5 24626253 CCGGTGTGACCAATACTATCTTGATTTGTCTCCAA[C/T]GATGTACATTTTCTCTAGCATATGATATCTGTCAT Y 2 1 2 1 101000 f 74 goat snp38389-scaffold486-666279 5 25098771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775131 Affx-122921627 AX-385262263 5 24657997 TTTCCAAATATCACTATCACTACTTACTATCCACC[C/T]GTTTCTCTAGTTGCCTCACTCCTGACTCCAGGAGT Y 2 1 2 1 101000 f 74 goat snp38388-scaffold486-634535 5 25130474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444354 Affx-122926713 AX-123314691 5 24689479 AACACCATAGCCTGGATAATGTAAATAAGAAATTA[C/T]GGAGCTATTCCATCATCTTGTGTTCTTAAGAACTA Y 2 1 2 1 101000 f 74 goat snp38387-scaffold486-603053 5 25162042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399764 Affx-122960312 AX-123270119 5 24748355 GCGGCCCACCTGGGCTGTGGGCATCCCCATTACTA[C/T]GGCTTCACGACTTCAGAGGCAGGAGGGAATAGGCT Y 2 1 2 1 101000 r 74 goat snp38386-scaffold486-544177 5 25220097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375665 Affx-122978676 AX-123246024 5 24836872 ATGGACAAGCTACACCTAAACTTGACGGAGTTGGC[A/G]CTGACAATGAATCATGTACAGAGCTTCTCTGTGTT R 2 1 2 1 101000 f 74 goat snp38385-scaffold486-455660 5 25308047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383311 Affx-122972700 AX-123253669 5 24880947 AGGTCATCTCCTCCCATCCCCCAGTTCCCCCCAAA[A/C]CAAACCACTAAGGACAGGAATCTAGTTTTTGTTTA M 2 1 2 1 101000 r 74 goat snp38384-scaffold486-411585 5 25352432 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385563 Affx-122971220 AX-123255921 5 24917540 TAATAATGAGAAATGCTTATGAGGGTTGTAGATCG[C/T]CATTCCACTCAGGACACACCCACTGCACACCCGGT Y 2 1 2 1 101000 f 74 goat snp38383-scaffold486-374992 5 25388949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376813 Affx-122977931 AX-123247172 5 24946802 GAGAGACTCTGATGGTGCTAGAGCCCAGCCAGAAT[A/G]CCACCTGCGCCGGACTCTGCCCCTGCCCCGCCCCC R 2 1 2 1 101000 f 74 goat snp38382-scaffold486-345730 5 25418267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449059 Affx-122923054 AX-123319394 5 25002667 CAGACCAATCTGCCTGTATATCATTTCCAGTCACC[A/G]TTAGCATTTGAGGTGAAGTTCTGTTATACACTCAG R 2 1 2 1 101000 r 74 goat snp38381-scaffold486-289865 5 25474077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762327 Affx-986696858 AX-385250501 5 25035333 TTCTTAAAAGTGATAACAGAGACAGGTCTGAGAGG[C/T]TGAGCAGGGGGCTATAGCTGAGGTGGTCTGCCTGC Y 2 1 2 1 600010 f 74 goat 5_25035333 5 25035333 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38396370 Affx-122963036 AX-123266725 5 25055831 ATGAAAGGAATCTACTCAGAGTAACCTAGGGAGGC[A/G]TGTTTTGGATTACCTGTTCTTCAAGTCAGTATTTC R 2 1 2 1 201000 r 74 goat snp38380-scaffold486-236701 5 25527980 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394211 Affx-122964901 AX-123264566 5 25148657 CATAGGAGGAGGAAATGTAAGTTCACACAACGTGT[A/C]TTTCTTTAGAAAGATGTTCCTGTTGGCGGATTATG M 2 1 2 1 101000 f 74 goat snp38378-scaffold486-143875 5 25620890 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423570 Affx-122942410 AX-123293916 5 25206461 ATGGACTTGGATCGCTATTTACCACCTGGTGTCTC[A/G]GTCTCCTCTGTGTTCCCCGCTGGCTTCAGGGGGAT R 2 1 2 1 101000 f 74 goat snp38377-scaffold486-86071 5 25678765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450822 Affx-122921796 AX-123321156 5 25238315 TGCTCCAGAGTGGCCCCTGGGCCAGCAGCAAATAG[A/G]ACAAGCTTTTATAGCCCCAGGGCAGATGTTGGCTT R 2 1 2 1 101000 r 74 goat snp38376-scaffold486-54217 5 25710260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411073 Affx-122951938 AX-123281423 5 25276368 CCTCATGACAACTCACGTGACATCATAAATGCTGC[A/G]TTCTTGTTCTTGAATTTTACAATTCTAAAAACTTC R 2 1 2 1 101000 f 74 goat snp38375-scaffold486-16164 5 25748363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436934 Affx-122933187 AX-123307272 5 25348305 GGAAATGAGGAAGGGATGGGGAGGGGTCCCAGGCG[G/T]GAACATCTGGGAGACCATCTCTCCACTCTTCACCT K 2 1 2 1 101000 r 74 goat snp17391-scaffold1802-55674 5 25820244 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779416 Affx-122950681 AX-385266519 5 25391371 AGATTATGGTTTTTGTAGAACAAAATGGCCAAATA[C/T]GTCAGCAATTGCATATGGTTCAAGCAATAAATGAC Y 2 1 2 1 101000 f 74 goat snp17392-scaffold1802-98740 5 25863055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444021 Affx-122926889 AX-123314358 5 25462384 TGGCAGATGTGGGCGAAGGAGAGAGGGGCGAGGAG[C/T]AGAGCTTCCATGAGCCCTCAGGGCAGTGACTGTGT Y 2 1 2 1 101000 r 74 goat snp17394-scaffold1802-169753 5 25934769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451211 Affx-122921970 AX-123321545 5 25569291 GCAAACTTGGGTACACACTTCTCCAGGCAGTTGTA[C/T]GTGAACTGTCACTGCTGACACATCTGTGTACCATT Y 2 1 2 1 101000 f 74 goat snp17396-scaffold1802-276660 5 26041321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431459 Affx-122936492 AX-123301800 5 25611388 TTTTGTATTTTTGAGGTTTTCTGTACTTTATCTCC[A/G]TCCCTCTCCACCACCATCCCCCAGGGTCCTCACAT R 2 1 2 1 101000 r 74 goat snp17397-scaffold1802-318757 5 26083849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443443 Affx-122927356 AX-123313780 5 25661697 CCAGGTCTTGCTACCAGCAACTCTTGCATTTGAGT[A/G]CCCCTCGCTCCCCCCATCTTTTCATGTCTGACTCC R 2 1 2 1 101000 f 74 goat snp17398-scaffold1802-369066 5 26134296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275344 Affx-1111834741 AX-519548919 5 25694161 CGGCTGCCTGGAGCCCAAACCTGGGCCCTCTGCGC[A/G]CTCCGCGCTCAGTGCTTCCACCGACTGCAGTTCTT R 2 1 2 1 202000 r 74 goat GoatD01.051001 5 25694161 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788525 Affx-122938975 AX-385275542 5 25734084 CTGTATCTCAGGGTGCTAACTGTTGCTCTGATCAC[A/G]GAAGGGTAAACAGGTAGCCATTTTATTGAATTTCC R 2 1 2 1 101000 f 74 goat snp17399-scaffold1802-441453 5 26206783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386981 Affx-122969958 AX-123257339 5 25798690 GAGGGATTATGGTCCTTAAACTAATTCATGGCAAA[A/G]TCAAGATTCTAGTTCTGATCTCTCCAAATCCAAAG R 2 1 2 1 101000 f 74 goat snp17401-scaffold1802-506059 5 26272082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780093 Affx-122950404 AX-385267190 5 25828193 CTCCAACAAACTACAGAAGCTGTTTAAGTCTTAAA[C/T]GCAGACTTCCTAAAATTACAATTTCCCAACATACT Y 2 1 2 1 101000 r 74 goat snp17402-scaffold1802-535562 5 26301500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405884 Affx-122955601 AX-123276236 5 25869765 GGTTCTCCCACATTGCAGACTCCTTACCTTCTGAG[C/T]GACCATTATAGGCTGACAAAAGGTCTCTCCAGGAG Y 2 1 2 1 101000 r 74 goat snp17403-scaffold1802-577134 5 26343253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396621 Affx-122962880 AX-123266976 5 25899136 GGTCCCCCTTAAAATGCATTAAGTGTAGGTAACTA[C/T]AGCACAATAGCAACTGGAGCTCCAAGAAGGCAAGA Y 2 1 2 1 101000 f 74 goat snp17404-scaffold1802-606505 5 26372618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434107 Affx-122934938 AX-123304448 5 26009025 CCACAGGGAATCCCAAAGAGGTCAGAACTATTCAG[C/T]AAGTGCTACTTGCCTGCCTGACAAGTGATGGCTCT Y 2 1 2 1 101000 f 74 goat snp17406-scaffold1802-716394 5 26482294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376205 Affx-122978811 AX-123246564 5 26092490 CTGGAAGCTTTACCTCTGGCCGCTGACTCTGAACA[C/T]TGGTTGGGAGAAAGGAGTTGACGCGGTAGGTTGCT Y 2 1 2 1 101000 f 74 goat snp17407-scaffold1802-799859 5 26564974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464356661 Affx-1110441558 AX-515830275 5 26097001 ACGACCCAAGGATGCCCTGCAGACTGCGTCAAGGT[C/T]GAGGCGGCCATATAGTGGCTATATAGTGGCATTCT Y 2 1 2 1 102000 r 74 goat GoatD01.005755 5 26097001 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38415429 Affx-122948720 AX-123285778 5 26168262 TGGATGGTGCATGTGTGGAACTGGACTCGGAATAC[A/G]AGGGTCCGGTCAGTCCCTCGGCTACCCTTGTGATA R 2 1 2 1 101000 f 74 goat snp17408-scaffold1802-875631 5 26640052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778239 Affx-122919391 AX-385265354 5 26255649 AGCAAGAAGCAAACTTTTGATAGTAGCAATTAACT[A/G]TTACAGTTATTTACAAGAAACCCACTCACACACAC R 2 1 2 1 101000 r 74 goat snp17410-scaffold1802-963018 5 26727278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441232 Affx-122929508 AX-123311569 5 26320406 ATGTGGACACACAGACAGACCTGTCCAGATCCTCA[C/T]GTACATGTAACACAGAGACATTTTCAGCACAATAG Y 2 1 2 1 101000 r 74 goat snp17411-scaffold1802-1027775 5 26792003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792765 Affx-122962602 AX-385279744 5 26357252 TTAATGCAGAATTAGGGTTCAGAAACATTGATTTA[A/G]TGTGATTTACCCAGGATACATGAGAAGAGGAGACC R 2 1 2 1 101000 r 74 goat snp17412-scaffold1802-1064621 5 26828519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382035 Affx-122974948 AX-123252393 5 26390605 AATAGTGGACACTGAGCACTTACCCTGTGCTAGGT[A/G]CTTTCTGGACATGACAATGACTATGAGAGAGGTAC R 2 1 2 1 101000 r 74 goat snp17413-scaffold1802-1097974 5 26861770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424865 Affx-122941336 AX-123295211 5 26432710 CAGCTGCTATATCATCATTCCTTGTGATTCAATGG[C/T]AGCCATCCCTCCTCCTGGCAAGACTTTGGCTACAA Y 2 1 2 1 101000 f 74 goat snp17414-scaffold1802-1140079 5 26903443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801704 Affx-122971297 AX-385288612 5 26445573 GACCATTATCTCCTTTACTCCTAGGCTCTTACATC[A/G]TGAGAGAAAGTTTCTTGGTTTCAATAACATGGAGA R 2 1 2 1 101000 f 74 goat snp26714-scaffold2809-1587 5 27157257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432035 Affx-122935908 AX-123302376 5 26486952 TAGCCTGGGAGAGAGAAATGCTCTTGTCCCTGGGA[A/G]CTGAAGTCCTCCAGCTTAACTCACAGACAGAGGGG R 2 1 2 1 101000 f 74 goat snp26715-scaffold2809-42966 5 27199533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429845 Affx-122938160 AX-123300186 5 26516061 AGCAGCAAAAGCCCCAGCCCAAAGTTTCCAGGGCT[A/G]CTCCTCCCCTCTCCCCACCTGCTACCCTTTGAAAA R 2 1 2 1 303000 f 74 goat snp26716-scaffold2809-72075 5 27227105 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803431 Affx-122969328 AX-385290262 5 26559848 TGAAAATTATAGTAACAGTTAGATGCCATTTACAC[A/G]TTATTAGAGCCACAAGAGTTCCAAAGTCTGGTAAC R 2 1 2 1 101000 r 74 goat snp26717-scaffold2809-115862 5 27270630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418843 Affx-122946141 AX-123289191 5 26624323 TGAATATGCATACCTCTGTATATGTGCTGAAGAGA[C/T]GACATTTGTGGGTCCATGAGGGTATGACTGCAGTG Y 2 1 2 1 101000 f 74 goat snp26718-scaffold2809-180337 5 27334001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442014 Affx-122928415 AX-123312351 5 26675612 TGGGGGACCATACTTATTCTTGAAGTCTTCCACGA[C/T]ATCCTGCATGTTCCGCAGCTCCACCTCTAGACGAC Y 2 1 2 1 101000 f 74 goat snp26719-scaffold2809-231626 5 27385593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402441 Affx-122958620 AX-123272794 5 26721834 GGTGGACAGACAGGGCTCACCTTCCTGTCCAGGCC[A/G]TTGGATCTGTTCAGCTTCCTGGGGTCAGAAGCGCC R 2 1 2 1 101000 r 74 goat snp26720-scaffold2809-277848 5 27431775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442082 Affx-122928370 AX-123312419 5 26755821 GGTGGGGGTGGAGGGAGAGGAACTCGCTGTATTGA[A/G]TCCAGAGCAGAGAGCAAGTTGGGCTCAATGCTGGC R 2 1 2 1 101000 r 74 goat snp26721-scaffold2809-311835 5 27465570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380470 Affx-122975726 AX-123250828 5 26785777 CAGAGTATGGGAGATGGGAGGCAGGACGTGGAGGC[A/G]GAGTTGAAAGTGGTTGTGATTTTGCAGTTAGTAGC R 2 1 2 1 101000 r 74 goat snp26722-scaffold2809-341791 5 27495628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464357083 Affx-1110441775 AX-515830692 5 26786194 GCTGCAGTCACCATCTGCAGTGGTTATAGGTTGTG[C/T]TTGGGCAAAAAGGAAGTTCATCAGGTGTCCACAGC Y 2 1 2 1 201000 r 74 goat 5_26786194_AF-PAKI 5 26786194 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399033 Affx-122961597 AX-123269388 5 26824028 ATCACGGAGTTCCTTGGGAAAAGCTGGCCCACGCC[G/T]CATTTGCACCCTCCTCAGTTCTCCTTCCATCCCCT K 2 1 2 1 201000 r 74 goat snp26723-scaffold2809-380042 5 27534006 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405145 Affx-122956954 AX-123275497 5 26856351 CCCCCAAATGCTGATCAGCAACTCCCTACCCCAGC[G/T]CGAGCTCCTCCCTGCTTTGCAGGCAGGCCTTTCCC K 2 1 2 1 202000 f 74 goat snp26724-scaffold2809-412365 5 27564742 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427667 Affx-122939315 AX-123298010 5 26901005 CACATCTGTTCCAGGGGCTCTTAACAAAACTAATC[C/T]GAGATTCTCTTTTTCTCTACAAGAGTTCACTTCTG Y 2 1 2 1 101000 f 74 goat snp26725-scaffold2809-457019 5 27607542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387870 Affx-122969636 AX-123258228 5 26937177 ACCTCGGGGGCCATGTACCGCTTGGTGCCCACTCG[A/C]GGGTTGTTGCCAATGTCCAGGTAATCGCTGCCCTG M 2 1 2 1 101000 r 74 goat snp26726-scaffold2809-493191 5 27643315 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380389 Affx-122975330 AX-123250747 5 26973098 ACTCGTCTTTGGGTTCGGGTGTCAATACATCACTG[C/T]ATTTATTTATCCTCCCTCTCTTCCTCATCCCCTAG Y 2 1 2 1 201000 f 74 goat snp26727-scaffold2809-529112 5 27679351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380896 Affx-122975038 AX-123251254 5 27007029 TATCAGACAGCTAACATTAAGCCCCAAATCTTTCA[C/T]GGCAAATTCAACTCATTTGAGGATGGTGGGAAGAG Y 2 1 2 1 201000 r 74 goat snp26728-scaffold2809-563043 5 27712909 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418676 Affx-122946311 AX-123289024 5 27096609 TGTAAAGAACCACCTAAATGTAAGGGGGAAAATAT[C/T]TTGCTTTTAAATAAAAGAGTAGGAAGAGAAAGACA Y 2 1 2 1 101000 f 74 goat snp26730-scaffold2809-652623 5 27802772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434829 Affx-122934795 AX-123305170 5 27144305 ACCCAGCTTAGAAACACTGAACCGAAAAGCAGGAC[A/G]TTAGGACACGGGCAGTTTTTTTTTTTCCTTTAGGC R 2 1 2 1 201000 f 74 goat snp26731-scaffold2809-700319 5 27850517 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452121 Affx-122920831 AX-123322454 5 27178880 TTACAGAGCATTTTCTTTCCTTTACCTCATCTCAG[A/C]CTCACTAGTGAGGTTAAAGGAGCAAATACTGCTAG M 2 1 2 1 102000 f 74 goat snp40702-scaffold521-32319 5 27884907 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781567 Affx-122967078 AX-385268652 5 27297239 GCTCCATCTCATCTTAAACACCATTTCCTTAGAGG[A/G]GCCTCCTCTGACCACACTAACAAAACACATCCCTT R 2 1 2 1 101000 r 74 goat snp40704-scaffold521-150678 5 28003309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431809 Affx-122936112 AX-123302150 5 27374275 ATGGCTCTGTTTCTCTGAAAAACAGGTTACCTCTT[A/G]CACTAGTTACTTAACCATTAGCTGTCTCCTAGCCG R 2 1 2 1 101000 r 74 goat snp40706-scaffold521-227714 5 28080799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417367 Affx-122947712 AX-123287715 5 27442653 TAGTCACTGTGTTTGATTCATCTTTGTATCAAAAA[C/T]ACAAAAGATACAAAGATGAATATAAACACAGTCTA Y 2 1 2 1 303000 f 74 goat snp40708-scaffold521-296092 5 28147484 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433760 Affx-122934494 AX-123304101 5 27490560 ACACTTTGCTGATGCCTGGGGCTACAGGCTTCTCT[A/C]CTCAGTCTAGATGCATTGTTGCCTACCTCCTCTGC M 2 1 2 1 101000 r 74 goat snp40709-scaffold521-343999 5 28195368 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440864 Affx-122929248 AX-123311201 5 27521185 GGATGTCAGTGATTATTACACCAATACCAGCAACT[A/G]TTACCCAGGGATGATGAAAGGATGACCAGTCATTT R 2 1 2 1 101000 f 74 goat snp40710-scaffold521-374624 5 28226107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407295 Affx-122955324 AX-123277646 5 27591715 TTATGATGGACAGTGTATTTAGATGAAATCCCTTT[A/C]TTTGTCACAAAATTTATCCACTACTTTTTAAAAAA M 2 1 2 1 101000 f 74 goat snp40712-scaffold521-445154 5 28296722 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445748 Affx-122926084 AX-123316085 5 27649486 GGAACTCAGATTCTGTTCGTACCTTTATTAGGGGG[A/G]ACATGGTTCCTGTTCTTTCATGTCCAGTTTATGTT R 2 1 2 1 101000 f 74 goat snp40713-scaffold521-502925 5 28354497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412376 Affx-122950811 AX-123282725 5 27684179 GTGGGGGTGGCATCTGGGAAGGAAAGCAATTCCTC[C/T]TACTCCACCCCTTTCCACCACTGGGACACACAGGC Y 2 1 2 1 101000 f 74 goat snp40714-scaffold521-537618 5 28389240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767285 Affx-122961797 AX-385254567 5 27745812 TTTTCCCCTAGAGTAGTAAATTCAAATGTTAAGGT[A/G]CTCATATTTTATGTATGTTCACTTGTATTTAGAAT R 2 1 2 1 101000 f 74 goat snp40715-scaffold521-599251 5 28451276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438206 Affx-122931457 AX-123308544 5 27774631 TGGGATGCTATATTTATGGATATATTTATACTTAA[C/T]ACCTCCTATATATCTGGCCTTTGTTAGTACCAGGT Y 2 1 2 1 101000 r 74 goat snp40716-scaffold521-628070 5 28480010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433195 Affx-122935640 AX-123303536 5 27827496 AGACATACTCCTTTGCCAGGAGAAACAGTCCTTCT[A/G]TCTCAGTCTTAAGAATGACTGAAACTTGGACCAAC R 2 1 2 1 102000 f 74 goat snp40717-scaffold521-680935 5 28534039 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448109 Affx-122924311 AX-123318445 5 27881240 TCCATCATGTGGCTTACAGGGAAATATGCCTTCTG[C/T]GAACTCACTGCTACATTTTCCCCTTCAGGTTTGCG Y 2 1 2 1 201000 f 74 goat snp40718-scaffold521-734679 5 28587718 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386550 Affx-122970717 AX-123256908 5 27910583 TGCACAGTGTGGCATGTATGCTTGGGTGCAAAATC[A/G]TCTCGGTTGTGTCTGACTCTTTACGACCTTATGGA R 2 1 2 1 101000 f 74 goat snp40719-scaffold521-764022 5 28616878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772784 Affx-122941035 AX-385259929 5 27967175 TCACATTTAAATCCTCAACAGCAATTTGGAAGTTA[C/T]GCTTGTGTGATCCTTATGGATCCATCTTTACTCTC Y 2 1 2 1 101000 r 74 goat snp40720-scaffold521-820614 5 28674375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418675 Affx-122946312 AX-123289023 5 28010183 TTATTGTGCATTTTTATTTCTAGGGCTCTGAAATC[A/G]TTGCTTTTGACAGTTTTTGAGTTTTTTTTTTCCAA R 2 1 2 1 101000 f 74 goat snp40721-scaffold521-863622 5 28717811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405988 Affx-122955519 AX-123276340 5 28053662 TAAACACTTGTAGAACAAAATATTTAGCTATCTTT[A/G]TTATAATTGGTTCTGACTGAAGCAAAACATATAAA R 2 1 2 1 201000 r 74 goat snp40722-scaffold521-907101 5 28761938 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436913 Affx-122933205 AX-123307251 5 28085843 TCAGGTTAAGGTAATAAAAGGAACATTCCATAGGT[A/G]TGGAGGAGGGAAGGGGTGAACAAAATGTTACTAGT R 2 1 2 1 101000 f 74 goat snp40723-scaffold521-939282 5 28794022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425502 Affx-122941477 AX-123295848 5 28127629 CAGCTCTCAGAAAAGAGAAGCGATATGTGTAACTG[C/T]AGACACAGTATACAATGGGCCAGGAAAAGAGGAAA Y 2 1 2 1 101000 f 74 goat snp40724-scaffold521-981068 5 28836460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415167 Affx-122949013 AX-123285516 5 28172375 CCCATCAAACGATGAATGACTACATGAAATGTAAT[A/G]TATCTATACAAAGGAATATTATATGGCAGTATAAA R 2 1 2 1 103000 f 74 goat snp40725-scaffold521-1025814 5 28881197 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396993 Affx-122963148 AX-123267348 5 28219803 ACAAAGACATCCAGACTAAAACAAAACAGAACATT[A/G]TCTTGACAACGGAACTGTCAACAGGTGATGGGAGA R 2 1 2 1 101000 r 74 goat snp40726-scaffold521-1073242 5 28929189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765588 Affx-122938734 AX-385253068 5 28292488 GAATGCATCTGAGATTTTGGATTTGTCTGTTAAAG[C/T]AGCAAGCATTCACCTTAATACAGATGATATTTAAA Y 2 1 2 1 101000 f 74 goat snp40728-scaffold521-1145927 5 29001781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404647 Affx-122957308 AX-123274999 5 28340797 CTGTAGCTGCCATGTGGAAACTAGATTAAAGAAAG[C/T]AGGGGACGCTAGGTGAGGCGCTATGGAAGCTAGAG Y 2 1 2 1 101000 f 74 goat snp40729-scaffold521-1194236 5 29050482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378169 Affx-122976960 AX-123248528 5 28380392 AATTTATCAAGTTACCTGCAGGGCCACAGCTACAG[C/T]CGCACTTATGTTACTATTACACGGTGAAGCAGTAT Y 2 1 2 1 201000 r 74 goat snp40730-scaffold521-1233831 5 29090156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403390 Affx-122957774 AX-123273743 5 28424572 AGCTTTAGTAAAGCAAAATAGGTAACAACTACAGA[C/T]GACTACATGCAAGAGTTGAGGCTCTAGAATCACAT Y 2 1 2 1 101000 r 74 goat snp40731-scaffold521-1278011 5 29134436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391981 Affx-122966511 AX-123262338 5 28459202 ATGAAGGAGCAGATGGGTTCCTTTGAGGAAGGACA[C/T]AGTCAGAAATTCATGCTATTAATTCTTCTCCAAGT Y 2 1 2 1 101000 r 74 goat snp40732-scaffold521-1312641 5 29168240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386774 Affx-122970113 AX-123257132 5 28517836 ATCTAGATTTTTCCAATTTTTAAATATCTCATTTC[C/T]GTCTCTTGACTGCCTGAATTGATTAAGACCTTAAA Y 2 1 2 1 101000 r 74 goat snp40733-scaffold521-1371275 5 29228511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448686 Affx-122923870 AX-123319022 5 28565959 AGTCAGACACAACTGAGCAACTGAAGTAAACTGAA[C/T]TGATGCTGCTGTTATTCCCAAAGAGCAGATTTATT Y 2 1 2 1 303000 r 74 goat snp40734-scaffold521-1419398 5 29277122 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762329 Affx-986696860 AX-385250503 5 28584923 CACTGGGTCCCTGAACGGGGCGCTTTCCTGAGTGC[A/G]CTGTTTCCCGTCCCCATTGCCAAACAACCAAACCA R 2 1 2 1 600010 f 74 goat 5_28584923 5 28584923 Ancestral_priority_1043 ancestry 0.41 neutral IMAGE 10K 10K ancestral 320764498 Affx-986696862 AX-385252175 5 28584933 CTGAACGGGGCGCTTTCCTGAGTGCGCTGTTTCCC[A/G]TCCCCATTGCCAAACAACCAAACCAAAACGTCCAG R 2 1 2 1 600010 r 74 goat 5_28584933 5 28584933 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 38434085 Affx-122934173 AX-123304426 5 28597312 AAATAAGCATCATGATAAGAGTTTCCTCATGAGCT[A/G]TTGTGAATATAAAATGAGATACTGTATATTGAATG R 2 1 2 1 303000 r 74 goat snp40735-scaffold521-1450751 5 29308652 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278198 Affx-1111836299 AX-519551687 5 28615547 TCACTCTCATATAGAAACTTGACTTATTTATCACA[A/G]ACATAAATGTCTAACATTAAATATTTGTGTATTCA R 2 1 2 1 101000 f 74 goat Random2.2K-536 5 28615547 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408516 Affx-122953707 AX-123278867 5 28636815 ATGGTTCCAGGTGAACAGCAAAGGGACTCAGCCAT[A/G]CACATGCATGGAGAAGAATGGCAAAAAGAATAGAA R 2 1 2 1 101000 r 74 goat snp40736-scaffold521-1490254 5 29347331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396626 Affx-122962875 AX-123266981 5 28669800 AGTAAATGATAATGGTGTTTAGAACTTCTTGGTAC[A/G]TTGACATTAATTTACACGTTAGGACTAAAGCTTAA R 2 1 2 1 101000 r 74 goat snp40737-scaffold521-1523239 5 29380339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444493 Affx-122926518 AX-123314830 5 28740939 CTAGGTGAGGTCCCCGGGGCTCTGACAGGGAAAGG[C/T]AAGATTCCCCCACCCAAATGCCCTGTTAGGACAGA Y 2 1 2 1 303000 f 74 goat snp40738-scaffold521-1594378 5 29451583 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764971 Affx-122938696 AX-385252550 5 28814447 TTAGCTGCATGAAAGAGGACCTGGACTAGAGCGTT[C/T]AAGGGATGATTAGGAGAACATAAGAAGAAGCCTTT Y 2 1 2 1 101000 f 74 goat "5_29524772_AF-PAKI;snp40739-scaffold521-1667886" 5 29524772 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412252 Affx-122950901 AX-123282601 5 28848760 AATTTCCCCCCTCCAGCAGAGTCAGGGCAAACTTC[A/C]TAGAGAAGATGGGCTTGGGAATAACTAGTGGCTGC M 2 1 2 1 101000 r 74 goat snp40740-scaffold521-1702199 5 29559231 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409187 Affx-122953184 AX-123279538 5 28881707 CCCATGCAGTAGGGCACAGGGATGAAGAAGACCTC[A/G]CCTATAGCCTCCTATAGCTCCCACCGCCCACAGGA R 2 1 2 1 101000 f 74 goat snp40741-scaffold521-1735146 5 29592330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797519 Affx-122975907 AX-385284458 5 28918028 ATGTTCTTACTGCAACAAAGCGTTTTTTAAAAAGC[A/G]CTCAAGAAGCATTAGTCCAGGTCACCTTGCCTTCA R 2 1 2 1 101000 r 74 goat snp40742-scaffold521-1771467 5 29628478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381178 Affx-122975202 AX-123251536 5 28948507 CACGTCACACACATACACCACATATACCACATACA[C/T]ACCTACACACATCACACACACCACTCACATACACA Y 2 1 2 1 103000 f 74 goat snp40743-scaffold521-1801946 5 29659223 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789796 Affx-122933388 AX-385276803 5 29011563 ACTATTTTCATCTGTTACCTGTTGGCAATATTTGT[C/T]TGTAGAGCATTTTCTTCTGCCACCATATTGGGTCT Y 2 1 2 1 101000 r 74 goat snp40744-scaffold521-1865002 5 29720002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376884 Affx-122977818 AX-123247243 5 29057198 TTTACCAAACAGTCCGGGTCCACTTGGTGAAGCTC[A/G]GCCGGAGAGCGGACTCTTGGAGCTTGCCTCTGCTG R 2 1 2 1 101000 f 74 goat snp40745-scaffold521-1910637 5 29765591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445900 Affx-122925946 AX-123316237 5 29090906 TTTAGCCAGATGCTTTGCACGTGATAAAAAATAAT[A/G]TCTTTTACATTTTGCTAAAAACCAAAGATTATGCT R 2 1 2 1 101000 f 74 goat snp40746-scaffold521-1944345 5 29799331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402419 Affx-122958639 AX-123272772 5 29125027 ATCATATGAATAATGGTACAATCAGTCCTTTAGAT[A/G]ACCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT R 2 1 2 1 101000 f 74 goat snp40747-scaffold521-1978466 5 29833399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278356 Affx-1111836300 AX-519551842 5 29150225 CAAGAGTACTGGAATGGGGTGCCATTGCCTTCTCC[A/G]GTGCTCCAACATACTTGGTTACAAAAATTCCGAGA R 2 1 2 1 101000 r 74 goat Random2.2K-537 5 29150225 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438184 Affx-122931830 AX-123308522 5 29187529 GTGCCCATCAGTCGCTGGAGGGACTCGGAGGATGC[A/G]TCTTTGGCGCCTCCCCCAAGCCGGGCGCAATCTGC R 2 1 2 1 101000 f 74 goat snp40748-scaffold521-2040968 5 29894418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406223 Affx-122956120 AX-123276575 5 29282027 AGTGAGAGTACATACAACCATCTCACTGTGATGAA[C/T]AATAGGGGAATGATGCCAGCAGATAAAAAATTAAA Y 2 1 2 1 101000 f 74 goat snp40750-scaffold521-2135466 5 29988432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389391 Affx-122968387 AX-123259749 5 29317810 TGGGGTGCAGAGAGCTTTCAGGTTAGTGAATGCAT[C/T]GGTATGCTGGAAGAGTAGTACACCTCAACTTCATG Y 2 1 2 1 101000 r 74 goat snp40751-scaffold521-2171249 5 30024444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772125 Affx-122964340 AX-385259280 5 29354577 ACAGATTATAAACATGGTTAAGCTCAATTTCTGTA[C/T]AGAAATTAAAACAGCTGAGCCAAGTACTAATTGGC Y 2 1 2 1 101000 r 74 goat snp40752-scaffold521-2208016 5 30062597 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794302 Affx-122971826 AX-385281266 5 29398586 CACTCTTTTCGGACCTTTATAAAATAGCCTAATGC[C/T]ACTATCTGAGGCCAAGCTGAGAAATATAAACGGAA Y 2 1 2 1 101000 r 74 goat snp40753-scaffold521-2252025 5 30107254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387744 Affx-122969736 AX-123258102 5 29448126 CCTATTAGTTTTCCTGTCTTTATTCCTGGTGATTT[A/G]TAAGATGCCACTGTGTATTCTGCATATTAATCCCA R 2 1 2 1 101000 r 74 goat snp40754-scaffold521-2301565 5 30156125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781660 Affx-122953098 AX-385268744 5 29482430 GCTCACCTTCCCAATGAGTTAAACTAATTTGTGAA[C/T]GTAGATAAAATTCTCATGTAATTAGGAATGCTTGA Y 2 1 2 1 101000 f 74 goat snp40755-scaffold521-2335869 5 30190829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786421 Affx-122970054 AX-385273455 5 29515888 TATAGCAGAGAGAAGTGAATTCAGATAAAACCAAA[C/T]CTTGGGTTTTTTAGTGTTGTCTCTACTAGGCTCAA Y 2 1 2 1 101000 r 74 goat snp24050-scaffold2447-16234 5 30229301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774903 Affx-122946636 AX-385262037 5 29562377 GGGGACATGAGCCTGCAGCAGATGATACTACAAGT[A/G]TGAGACATGTGTGGATCCATACCATAATAAAAGAT R 2 1 2 1 101000 f 74 goat snp24051-scaffold2447-62723 5 30276323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435112 Affx-122933700 AX-123305452 5 29614124 GGCTGAGGAGAGAAAGAGAGAGAGATTTTAAAAAG[C/T]ATTGGTTACAGAAACTGAGAAGTCTCACTCTGCCG Y 2 1 2 1 201000 r 74 goat snp24052-scaffold2447-114470 5 30325865 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414182 Affx-122949670 AX-123284531 5 29679998 TAAAGTGAACAGGATGGAGTATCTACAAGTGTTCC[A/G]CAGTATTCAGAGTCTGTCTTCAGTGGGGAGTCACC R 2 1 2 1 101000 f 74 goat snp24053-scaffold2447-180344 5 30391958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402680 Affx-122958358 AX-123273033 5 29788165 CAACATTTAAAGCAAAAAAAGGCCAGGAAAGAGAG[C/T]AGGAAGCAACCAAAAGGGTAAAAAGGAAATCAAGA Y 2 1 2 1 101000 f 74 goat snp26005-scaffold2691-365236 5 30500499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394239 Affx-122964878 AX-123264594 5 29818385 AAAACAAAAATCTGTTCCTGTTATTCCACTATGTA[A/C]ATCTCCTTAGTGGCTCCATAAATAATGGCTCCCTT M 2 1 2 1 101000 r 74 goat snp26004-scaffold2691-335016 5 30530766 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389371 Affx-122968453 AX-123259729 5 29864038 AAAATCTATTTCAGCGAGGTGCTAAATTCAGACAG[C/T]AAGTCTGAATCTGCCTCTATTCTACCATCTCCATC Y 2 1 2 1 101000 f 74 goat snp26003-scaffold2691-289363 5 30576461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396288 Affx-122963099 AX-123266643 5 29910593 GTAAGTGTATCTGGACAGTGCTATAAATACCCAGC[A/G]TTGAAAGCACCCTGGAACATAAGTAATGGAAGAGC R 2 1 2 1 101000 f 74 goat snp26002-scaffold2691-242808 5 30622975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450072 Affx-122922804 AX-123320407 5 29945471 AAGATTTCTTGAGAAGCAACAAATGCTAGCTGGCA[G/T]CAAAGGATAGCTCATCCAGACCCTGAAAGAGCCTG K 2 1 2 1 101000 f 74 goat snp26001-scaffold2691-207930 5 30658085 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410274 Affx-122952517 AX-123280624 5 29987011 AAATGTAGAGTTTAAGAAATAATTAGAAAGATTAA[G/T]CCAGTGGTAGATGGAACTAAAAGGAAGAAAGGATA K 2 1 2 1 201000 f 74 goat snp26000-scaffold2691-166390 5 30699834 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426602 Affx-122939975 AX-123296948 5 30073982 CTAAAGCAGGACCCAGGTCCTAACCCCTTCCAGAG[C/T]AGAAAGACTACTATTGACCTTAGGGACAATCCACC Y 2 1 2 1 101000 r 74 goat snp25998-scaffold2691-79419 5 30787445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434305 Affx-122934757 AX-123304646 5 30103706 TGAAAATATTTCTCTATAGGATGAAGGCCAGGGAT[A/C]TGGAACTAAATGAAACAGTCCCAACTTTAGTTAAA M 2 1 2 1 101000 r 74 goat snp25997-scaffold2691-49695 5 30818669 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765817 Affx-122931633 AX-385253264 5 30134204 AACGACTGGTTTGCACAATCAAGATCTATTTTAGT[A/G]TGTGTCATACCACAAGACAAATATTACTAACCTCG R 2 1 2 1 101000 f 74 goat snp25996-scaffold2691-19197 5 30849700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413569 Affx-122950589 AX-123283918 5 30183390 GCTGCTCACATGGAATATTCTAGTGTGTTTTCTCC[A/G]CAACAAGGACACTCTCCCAGGGAACCAGCATGCAA R 2 1 2 1 101000 f 74 goat snp10948-scaffold1393-29890 5 30900306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414418 Affx-122949970 AX-123284767 5 30222465 AGTATCCAAGGCCCTTGGTCACAGTGACTAGTCTA[A/G]GAGTGATTAGACTTAACCAGCCTAAGTGCTTCCTT R 2 1 2 1 201000 r 74 goat snp10949-scaffold1393-68965 5 30940176 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781503 Affx-122965461 AX-385268588 5 30292487 TACCTAGTTGTATATTCCTTCAAATATTTTTGTAC[A/G]TTTAAACTCAGAATCCAAAGATTTTTGAGTGTTTG R 2 1 2 1 101000 f 74 goat snp10950-scaffold1393-138987 5 31010202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419359 Affx-122945634 AX-123289707 5 30366725 ACAACAGTGCTGTGAGAAGCAGTGTACAAATCAGC[A/G]CAATCACCTTGTGGAAGGCATCCTTATCTCTGGGA R 2 1 2 1 101000 f 74 goat snp10952-scaffold1393-213225 5 31086141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378486 Affx-122976664 AX-123248845 5 30395275 AAGGCATACTTAAAACATTCAGCTCTCTATGTATC[A/G]CAGTTGTGTACCTTTCTGATCTTTATCCTTAAACA R 2 1 2 1 101000 f 74 goat snp10953-scaffold1393-241775 5 31114519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384209 Affx-122972390 AX-123254567 5 30437036 ATTTTCACTTTTCTAATTTTTCAATTTGTTTAACT[A/G]CGTTTCCATATTAAATTATATTGCTCTGTCCCATT R 2 1 2 1 101000 r 74 goat snp10954-scaffold1393-283536 5 31154833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386515 Affx-122970745 AX-123256873 5 30483158 ACTTCTCTCAGCAGCTTCCCTCAGCAGAAGCTGCC[A/G]GAGCCTGCAGGGACAACAAGAGCAGTTGTAGTGAC R 2 1 2 1 201000 r 74 goat snp10955-scaffold1393-329658 5 31201679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428315 Affx-122939369 AX-123298658 5 30552260 TAACGTCATGTAACCCGTAGCTGGTCCACATAAGT[G/T]AGCTGGACAGCATGCAGATGGCCAGTCACACAGCT K 2 1 2 1 101000 f 74 goat snp10956-scaffold1393-398760 5 31271557 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434071 Affx-122934182 AX-123304412 5 30585288 AATTAACCAGTTATGTCCCTTGGATAGGTCTTGAA[G/T]AGGAGGAAGAGTCTAAGTGACACAGCAGAGAAGAC K 2 1 2 1 201000 f 74 goat snp10957-scaffold1393-431788 5 31305571 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783973 Affx-122920263 AX-385271027 5 30614292 CACAAAACAGCTGTTTTCATTATGTTTGTGAATCC[A/G]TAATTTATTTGTAATGTGTTTGGTAGGTATAGAGG R 2 1 2 1 101000 f 74 goat snp10958-scaffold1393-460792 5 31334752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse470 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320799121 Affx-122945565 AX-385286051 5 30650224 TGCCAAAATTATTGTACCAAATATAATATTACGAA[C/T]AACGTATAAGGTCATATATGACTCACCAAATCTTG Y 2 1 2 1 101000 r 74 goat snp10959-scaffold1393-496724 5 31415706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse471 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402789 Affx-122958295 AX-123273142 5 30681285 CCTCCAATGTATATGTCCTTTCAATCCAAGAATTT[A/C]GTTCTTTCTCTATCCCCCTCAAATTAGATATTATT M 2 1 2 1 101000 f 74 goat snp10960-scaffold1393-527785 5 31446671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse472 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38386340 Affx-122970872 AX-123256698 5 30726256 TAAAAGGATGCAATTTGGACACAGAAACAGATGTA[C/T]AGAAAATAAAAATGACAAGACACACAGGGAGTAAA Y 2 1 2 1 103000 r 74 goat snp10961-scaffold1393-572756 5 31489870 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795554 Affx-122935703 AX-385282509 5 30771734 ATTAACATACCTTGTATTTCTCACCTGTGGAAATA[C/T]AAATGAAAAGAACCTCTGGATTTAGTTCCAGGAAC Y 2 1 2 1 201000 f 74 goat snp10962-scaffold1393-618234 5 31535900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse473 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410193 Affx-122952580 AX-123280543 5 30807534 AAGGACATTTGGAAATGTGTAGTCTAAACCCTTCT[A/G]CTTCAAGCTCCAGAGCAAGATCATTTTGTCCTTGG R 2 1 2 1 201000 f 74 goat snp10963-scaffold1393-654034 5 31571529 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse474 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 538942910 Affx-1251531480 AX-585490034 5 30812229 CCTTTGTGCCTTTTCTGATTGCTTCACTTGTATTA[C/T]CCCTGAGGCCCCCTTTGTTCCCGAAGTAGGTTGGG Y 2 1 2 1 400000 f 74 goat SNPs_027 5 30812229 T C SV-TF-chip candidate gene ou candidate region LALBA 538942861 Affx-1251531499 AX-585489985 5 30812424 GGGAGGAAAGGAAAAGTGGGGTGAAATTACTGAAG[A/G]AAGCTAGCAGGCTCAATGTTTCTTTGTTGGTTTGA R 2 1 2 1 400000 f 74 goat SNPs_028 5 30812424 G A SV-TF-chip candidate gene ou candidate region LALBA 538942872 Affx-1251531500 AX-585489996 5 30812436 AAAGTGGGGTGAAATTACTGAAGGAAGCTAGCAGG[C/T]TCAATGTTTCTTTGTTGGTTTGACTGGCCTCTCTC Y 2 1 2 1 400000 r 74 goat SNPs_029 5 30812436 C T SV-TF-chip candidate gene ou candidate region LALBA 538942865 Affx-1251531501 AX-585489989 5 30812466 GCAGGCTCAATGTTTCTTTGTTGGTTTGACTGGCC[G/T]CTCTCGTCCTCCTCTTCCTGGATGTAAGGCTTGAT K 2 1 2 1 400000 f 74 goat SNPs_030 5 30812466 T G SV-TF-chip candidate gene ou candidate region LALBA 538942867 Affx-1251531502 AX-585489991 5 30812545 CCCTGAGGCTTTTTCCACAAATAAAAGGAGGTGAG[C/T]AGTGTGGTGACCCCATTTCAGGATCTTGGGGGGTA Y 2 1 2 1 400000 f 74 goat SNPs_031 5 30812545 C T SV-TF-chip candidate gene ou candidate region LALBA 538942869 Affx-1251531503 AX-585489993 5 30812604 TCTTGGGGGGTAACCAAAATGATGTCCTTTGTCTC[A/T]CTGCTCCTGGTAGGCATCCTATTCCACGCCACCCA W 4 1 2 1 400000 f 74 goat SNPs_032 5 30812604 T A SV-TF-chip candidate gene ou candidate region LALBA 538942879 Affx-1251531504 AX-585490003 5 30812625 ATGTCCTTTGTCTCTCTGCTCCTGGTAGGCATCCT[A/G]TTCCACGCCACCCAGGCTGAACAATTAACAAAATG R 2 1 2 1 400000 r 74 goat SNPs_033 5 30812625 A G SV-TF-chip candidate gene ou candidate region LALBA 538942874 Affx-1251531505 AX-585489997 5 30812697 GAGGTGTTCCAGAAGCTGAAGGACTTGAAGGACTA[C/T]GGAGGTGTCAGTTTGCCTGAATGTGAGTTCCCTGC Y 2 1 2 1 400000 f 74 goat SNPs_034 5 30812697 C T SV-TF-chip candidate gene ou candidate region LALBA 538942883 Affx-1251531506 AX-585490007 5 30813685 TCATTTTTTTCCCACCTGTAACTCCTGCCAGAGTT[C/T]CTGGATGATGATCTTACTGATGACATTGTGTGTGC Y 2 1 2 1 400000 r 74 goat SNPs_035 5 30813685 C T SV-TF-chip candidate gene ou candidate region LALBA 538942885 Affx-1251531507 AX-585490009 5 30814450 GCTAACTCGTCTCTGAGCCCTGGGCCCTGTAGTGA[C/T]GATGGACATGTAAGGACTAATCTCCAGGGATGCGT Y 2 1 2 1 400000 r 74 goat SNPs_036 5 30814450 T C SV-TF-chip candidate gene ou candidate region LALBA 464352735 Affx-1110443188 AX-515826397 5 30814497 AAGGACTAATCTCCAGGGATGCGTGAATGGTGCTC[A/G]GGACATTTGACCCTTGCTCGGTGCCTCTGATAGCA R 2 1 2 1 400000 f 74 goat SNPs_037 5 30814497 G A SV-TF-chip candidate gene ou candidate region LALBA 464359845 Affx-1110443189 AX-515833426 5 30814523 ATGGTGCTCGGGACATTTGACCCTTGCTCGGTGCC[C/T]CTGATAGCACTTTTAATGCAACAGTGCATATTCCA Y 2 1 2 1 400000 r 74 goat SNPs_038 5 30814523 T C SV-TF-chip candidate gene ou candidate region LALBA 538942860 Affx-1251531494 AX-585489984 5 30814534 GACATTTGACCCTTGCTCGGTGCCTCTGATAGCAC[C/T]TTTAATGCAACAGTGCATATTCCACTTCTGTCCTG Y 2 1 2 1 400000 r 74 goat SNPs_039 5 30814534 T C SV-TF-chip candidate gene ou candidate region LALBA 320783939 Affx-122969665 AX-385270992 5 30848822 ATACTCCACAGAATAAATAAGCAATATATTGCTAT[A/G]TTATATTTTCTCTTCCTAGGTCATAGCATGCTAGG R 2 1 2 1 201000 f 74 goat snp10964-scaffold1393-695322 5 31613340 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426075 Affx-122941085 AX-123296421 5 30896769 CTCTCAATTCACCAGCACTGTTCTTTGAGAATTCA[A/G]CATATGTGTTTGTCAGCAGAATTCCTCACTCTCTC R 2 1 2 1 202000 r 74 goat snp10965-scaffold1393-743269 5 31661338 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse475 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771327 Affx-122967608 AX-385258485 5 30930789 TTTATCAAGTCTTTTATTGATTCTAGATTTTGAGT[C/T]ATATGAATGCTTTCCCCACTACCCCCATGGGTATA Y 2 1 2 1 101000 r 74 goat snp10966-scaffold1393-777289 5 31695495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse476 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425026 Affx-122941877 AX-123295372 5 30966107 CCTCCTGATCTGCCCCCACGGGGAGCCCCCCAGGT[C/T]TCCGGAGAAGAGGAAAGGGCTATTGCTTGTACACG Y 2 1 2 1 101000 r 74 goat snp10967-scaffold1393-812607 5 31731258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771934 Affx-122959816 AX-385259090 5 31007158 TAAAACATCATTTTAGTAAGCTATTTGTGGTTGCT[A/G]TAATACTTCACTAATCTAGTCTCAACCGAACATTT R 2 1 2 1 101000 f 74 goat snp10968-scaffold1393-853658 5 31772434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse477 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320799678 Affx-122938649 AX-385286606 5 31036451 AATCAAGAGCAGTCAAAAGTATCCACCAATTAAGT[A/G]TTTTTCTTTGAAGATATTAATGTGAGGTCTCTGGC R 2 1 2 1 101000 r 74 goat snp10969-scaffold1393-882951 5 31801705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse478 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418111 Affx-122947130 AX-123288459 5 31074313 GGCTTAGCAGAGAGGATGCAGATGGATCAAGATGG[C/T]CTCAGGGACTCTGGCCCCTTTCTCTGGGTGATGCT Y 2 1 2 1 101000 f 74 goat snp10970-scaffold1393-920813 5 31839621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426268 Affx-122940321 AX-123296614 5 31104511 GGCAGGCGAGGATAGGAGTCTCTTTAACCAGTCTC[A/G]ATTATTCAGGTAATCCGTCGACAGTCTCACCCATT R 2 1 2 1 101000 r 74 goat snp10971-scaffold1393-951011 5 31869701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse479 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424139 Affx-122942552 AX-123294485 5 31137250 TCTGGTGCATATGTTGTTCAGATAAAGAGAAATAA[C/T]AGGCCCTGCCCTCCAAGATTCCAGTTCCAGTTCTA Y 2 1 2 1 101000 f 74 goat snp10972-scaffold1393-983750 5 31902222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse480 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38396888 Affx-122963230 AX-123267243 5 31218670 ATTCCCATCTGGAGCCAGGGAGGGAGGAGAGAGAA[G/T]TGAGGAATGGCAGGGTGGGATTCAAAACCAGGAGA K 2 1 2 1 101000 r 74 goat snp10974-scaffold1393-1065170 5 31983701 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435699 Affx-122933316 AX-123306038 5 31354847 GTTGGGCGGGCTACAGTCCATGGGGTTGCAAAGCA[C/T]GATGGTGATAATAGTTCCTAACAGCTGTATGAAGT Y 2 1 2 1 101000 r 74 goat snp10977-scaffold1393-1201347 5 32119276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse481 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384889 Affx-122971927 AX-123255247 5 31366644 TGGGATGATGGGAGTCCTGAGAGCCTTGTGTCTTG[C/T]GGGGTCGGTCCATGGGGGAGAGGAATGTAACAGGG Y 2 1 2 1 201000 f 74 goat snp43251-scaffold576-10875 5 32131174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse482 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38378093 Affx-122977159 AX-123248452 5 31504569 TTTCTTTTTCACTCAAGAGTCTATCAGGGATCTTG[C/T]ATTGCATTTGATGATGAAAGCCCTGCCATATGGAG Y 2 1 2 1 101000 r 74 goat snp43254-scaffold576-148800 5 32270307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776189 Affx-122963970 AX-385263317 5 31550071 GACTCTTGGCAGGTCAAGTACATTAATCTATAGCT[A/G]CAGTTAACTTATTAAGAAGGAACTGAGGCAGGAGA R 2 1 2 1 101000 r 74 goat snp43255-scaffold576-194302 5 32317001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse483 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278358 Affx-1111836301 AX-519551844 5 31551302 CCCCTAGAGCTGTCTGGTGTTCCCCACTTTGTTGT[A/G]TCAGGAAAGAAGAGCTGAGAATGGAGGGTAGAGGA R 2 1 2 1 102000 r 74 goat Random2.2K-538 5 31551302 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768722 Affx-122927165 AX-385255900 5 31579900 TGATAAAGTCATAGTTCCTTCATTCAAGACATTGT[A/C]GTCAGTTGATTTCTGAGAGGAGATAAGCACATACT M 2 1 2 1 101000 r 74 goat snp43256-scaffold576-224131 5 32347688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse484 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399552 Affx-122961134 AX-123269907 5 31667114 TAAAAGATATGGAAACGGTTTATAAGTCACCAAGT[A/G]CTTCAACATGGAAGATACTATTGTCATTACTCTGA R 2 1 2 1 101000 f 74 goat snp43257-scaffold576-311345 5 32435566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772409 Affx-122920626 AX-385259561 5 31801769 GATGGTCCCAATAGCACTTTTAGATTAAATGGTCA[C/T]GGAAGACCTCTTAGGAGATGACTTGGAAGGTACAG Y 2 1 2 1 101000 r 74 goat snp43260-scaffold576-446000 5 32570974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse485 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38386208 Affx-122970992 AX-123256566 5 31844953 ATGTCTTTGGCCAGTGCTGTGCTGGGAATTCTGTA[C/T]AGTATCTGGATGATTCTGGGCCAGCCCTAAAAATG Y 2 1 2 1 201000 r 74 goat snp43261-scaffold576-489184 5 32614268 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse486 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410030 Affx-122953247 AX-123280380 5 31887772 TCGGACACGACTGAACAACTTTGACTTTCACTTTC[A/G]CTCAATATTTTCTCATCGGCCCTGAATTTGACCTT R 2 1 2 1 101000 r 74 goat snp43262-scaffold576-532003 5 32656339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378826 Affx-122976546 AX-123249185 5 32013219 TGGTGTGAAGTTAAGCAGCTTTATCAGGGAAAGAG[C/T]GAAGGTATCTGAGACATAACTAAGCAGGGGAACCT Y 2 1 2 1 101000 f 74 goat snp43265-scaffold576-657450 5 32782420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse487 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468272305 Affx-1111833463 AX-519546044 5 32043804 GTGCCCTCATTGGAGGGCCCTTCTGCAAGCTCTGC[A/G]ATGGGCCCAGGAGAGTGAAGGTGATCACTCACATC R 2 1 2 1 202000 f 74 goat 5_32043804_AF-PAKI 5 32043804 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449436 Affx-122922677 AX-123319771 5 32063215 TTTTTTGGCTAGGTACCAACTAGGAGAATACACAG[C/T]GGGTACCACCAATTCAATGGACGTGAATCTGAGCA Y 2 1 2 1 101000 f 74 goat snp43266-scaffold576-707446 5 32832954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse488 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38417522 Affx-122946940 AX-123287870 5 32092518 GCTTGAAGTTAAAAGGAGAAAACTTTTATTTCATT[A/G]CATAAAATATTATATCTCAGGGTCCGACAGAGTTA R 2 1 2 1 201000 r 74 goat snp43267-scaffold576-736749 5 32861661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383552 Affx-122972610 AX-123253910 5 32153443 AGTCTAAAGGTATATACATGGTATTTGTTATGTGT[C/T]TCTGTACTTTTTGAACAAGTGGAATATTTAATAAT Y 2 1 2 1 201000 r 74 goat snp43268-scaffold576-797674 5 32921038 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse489 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320789655 Affx-122926167 AX-385276664 5 32202795 AAAGCAAGTATCAGTCTTCCAATTGTTATTTATTA[C/T]ACTATACTAGATAATATAAAAATAGAATTAGAGAC Y 2 1 2 1 202000 r 74 goat snp43269-scaffold576-847026 5 32970509 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse490 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38394381 Affx-122964632 AX-123264736 5 32235854 TAAGTCCTCTTGCATGATCCAGACTATATCATCAC[A/G]TAGTGGCACTTGCTTCCCCACCTCCTACCCAGTCC R 2 1 2 1 101000 f 74 goat snp43270-scaffold576-880085 5 33003770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798134 Affx-122943145 AX-385285068 5 32265249 TTTAGTTTCCTCATATTTGTTGGAATAATTTCTGT[A/G]TAATGTAATTCCCAAGATCATTTAGCTTGTAATCA R 2 1 2 1 101000 r 74 goat snp43271-scaffold576-909480 5 33033334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse491 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433561 Affx-122934981 AX-123303902 5 32303550 ATGGGACTGTTCAATGGACTTTCCAAATCAGGGGT[A/G]TCTAAGGGTTCATCGTAAATTGCAGAGTTGTGATA R 2 1 2 1 101000 r 74 goat snp43272-scaffold576-947781 5 33072151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse492 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320797616 Affx-122923940 AX-385284555 5 32332647 TTCATGAAGAAAACAATACATGTGAGACAAGCAAA[C/T]ACATCTTCACCAAATGAAAGTGAATTAAGTGCTCA Y 2 1 2 1 101000 f 74 goat snp43273-scaffold576-976878 5 33101184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398322 Affx-122962136 AX-123268677 5 32370118 ACATCACCCACACTTCCTCTGCCCAAGCGTAAACA[C/T]GATGTTATCCCTACATCTGCCTGGAGGTGACACGT Y 2 1 2 1 201000 r 74 goat snp43274-scaffold576-1014349 5 33139887 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse493 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798118 Affx-122975600 AX-385285053 5 32439311 CTATGAAGTGATACAAAACGAATAGAAGCTCCATC[A/G]TTACCATAGAGAAGCTAAACAATTGTCTAAGAACT R 2 1 2 1 101000 r 74 goat snp43275-scaffold576-1083542 5 33210633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse494 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38446550 Affx-122924850 AX-123316886 5 32468931 TGAAATTCCCACCTATCCTCCTTAATCTCCCGCTT[A/G]CCACCTGTTTCAATGTGGAGAAGCAGGAAATGGTG R 2 1 2 1 101000 r 74 goat snp43276-scaffold576-1113162 5 33239455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419102 Affx-122945777 AX-123289450 5 32501198 ATTGTCAGCCAATGTTCTTATTCTTGTTTTCAACT[A/G]TAGGTCAGTCATTCCTTTCTGGGGATAGCTCTTGA R 2 1 2 1 101000 f 74 goat snp43277-scaffold576-1145429 5 33272152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse495 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320803013 Affx-986696127 AX-385289891 5 32504894 CCCTTGACCACCGAGGTACTGTACCTCCCAGCCAA[C/T]GCCTCTTGTGTCCTGGCCAATGACACTTCATTAAC Y 2 1 2 1 600010 f 74 goat 5_32504894 5 32504894 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 320764519 Affx-986696874 AX-385252188 5 32505118 TCCCTACCTGACCATTCTGACACCCCAGGCAATGG[A/C]GGACCAAACCCAGTCAACCCACCACCAGAGGGCAC M 2 1 2 1 600010 r 74 goat 5_32505118 5 32505118 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 320762345 Affx-986696876 AX-385250516 5 32505142 CCAGGCAATGGCGGACCAAACCCAGTCAACCCACC[A/G]CCAGAGGGCACTAGCTGCAGCTCCCCTGCTCCTCA R 2 1 2 1 600010 f 74 goat 5_32505142 5 32505142 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 468273709 Affx-1111833794 AX-519547321 5 32536056 GCAGACGTGTTCTGGCAGGTTTTTTTTCTGAGCAC[A/G]GAGTGCTTCATTTCTACTTTCCA R 2 1 2 1 102000 f 74 goat GoatD01.005381 5 32536056 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802498 Affx-122940089 AX-385289402 5 32550233 ATAGTCTCTCACTAAAAGAATTTATAGAACAAGAA[C/T]AATCTTGTGATTAAAGATTATTTTAATTTAGGAAT Y 2 1 2 1 202000 r 74 goat snp43278-scaffold576-1194464 5 33320813 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse496 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320780484 Affx-122924358 AX-385267575 5 32594485 CTGTCATCTTTCCCTCCCTTATATTTGGCTCAGGG[A/C]GAATAGTTCAGATCCCCACTTAAAGAGTCTGTACT M 2 1 2 1 101000 f 74 goat snp43279-scaffold576-1238716 5 33365253 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410020 Affx-122953256 AX-123280370 5 32640144 CAATAGGTCACCTGACTGTAAGGTTGTTCTCTTGA[A/G]CTTAACATTTTTAGTTTTAGGCAAGGGCCAGAAAT R 2 1 2 1 101000 r 74 goat snp43280-scaffold576-1284375 5 33411113 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse497 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38378794 Affx-122976992 AX-123249153 5 32722546 TTTCAGAGAATATATTTATGTATCTTTTGCCTAGA[C/T]GGGAGAGGAGCAGTCAGCTCAATTTACAGAGTAGA Y 2 1 2 1 101000 r 74 goat snp43282-scaffold576-1366777 5 33492408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412258 Affx-122950897 AX-123282607 5 32778784 TGACACAGAACAGCGCTTTTTGTAAGAAAGGGCCC[A/G]CACGAATGACAACAGGATTTCCAAGTGCCCCCAAC R 2 1 2 1 101000 r 74 goat snp43283-scaffold576-1423015 5 33547738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773617 Affx-122965264 AX-385260757 5 32822917 AATCACATGTGCTATGGGACAGCTGGTTCCTTCAG[C/T]GTCTGAGATCATTGTCAGATTACATCTTTTTGTGT Y 2 1 2 1 101000 f 74 goat snp47304-scaffold665-4902 5 33595238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406731 Affx-122955748 AX-123277082 5 32876057 AGTGAATTCCTTTAATGTCAGCATGCCCTCCAAAG[C/T]GTGTATATTGCCCCTCTTTTTAATTTATTTTCCTC Y 2 1 2 1 101000 f 74 goat snp47305-scaffold665-58042 5 33649076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440515 Affx-122929348 AX-123310852 5 32919606 GAACAGATGCTATCCTGCAGAGAACCAATTCTACA[A/G]CAAAGAACGACAGTGATGCAGAAAGAGACCATGCT R 2 1 2 1 101000 f 74 goat snp47306-scaffold665-101591 5 33693670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784676 Affx-122967255 AX-385271724 5 32984362 GTCATGGAAAGTTTTTAAGGGGCATATTTTTGTAT[A/G]CTTTTAGGTGGTAGTAATGGGTTTCATTGCTTATA R 2 1 2 1 101000 r 74 goat snp47308-scaffold665-166347 5 33755979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409233 Affx-122953151 AX-123279584 5 33021629 TCAGCTCTTTAATGTCTTGCTTCTCTATAAATTTC[A/G]CAGCCAGTTACTCTAACTATGCAAACATCTTTCCT R 2 1 2 1 101000 r 74 goat snp47309-scaffold665-203614 5 33793519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385158 Affx-122971750 AX-123255516 5 33128912 TCTCAATAAATGGCAACTGTTACTATTATTATTTA[C/T]GTTAATAGAGAAGTCCAAAGTGGAACCATATTCTA Y 2 1 2 1 102000 r 74 goat snp47311-scaffold665-310897 5 33901255 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275396 Affx-1111834874 AX-519548970 5 33142702 GGATTCTGATCCTTATTGAGTCTGAGAGATACAGG[A/C]CTGGTATCCCCAAACTCCTCCAGCTCCAACACTGC M 2 1 2 1 201000 f 74 goat GoatD01.057270 5 33142702 T G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402264 Affx-122959121 AX-123272617 5 33220511 TAAAACTGATCTTCCTGAAACTTAAAAATACCAAG[C/T]ACTTTTTCCAAAGTAGGAAAGTTACCTCCTTGGTA Y 2 1 2 1 101000 f 74 goat snp47313-scaffold665-402496 5 33993843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796887 Affx-122919830 AX-385283829 5 33272419 TATGAATCTAGCATTTGGGGGCAATAATTTATAAT[A/G]CAGCATCTACTCCTAGATATCACTAAGAGATTTCA R 2 1 2 1 101000 r 74 goat snp47314-scaffold665-454404 5 34046474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403581 Affx-122957574 AX-123273934 5 33344835 TCCTCAGGAATGGCTTCAGAATCCTAGATCTTTCC[A/G]TTACTCACCTGATGCCCTGAGTGCCTGTTGCTATT R 2 1 2 1 101000 r 74 goat snp47315-scaffold665-526820 5 34119539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414177 Affx-122949673 AX-123284526 5 33379404 ATGTAGTAGTGGCAGAAATAGCATTTGTTCTGGAG[C/T]CTTTAGACTCCAAATTCTTTTCTCATTTGATGGCA Y 2 1 2 1 102000 f 74 goat snp47316-scaffold665-561389 5 34154067 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412428 Affx-122951424 AX-123282777 5 33412564 GTCTCTGCTTTTTAATATGCTATCTAGGTTGGTCA[C/T]AGCTCATATCCATATCTATCTGCAAAACAAGAAAA Y 2 1 2 1 201000 r 74 goat snp47317-scaffold665-594549 5 34188399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766637 Affx-122965339 AX-385253988 5 33442929 CTGCAGGTTAAACATACTCTAATACACTGATTTTA[C/T]GAAAATCAGTATGATTACAAGAGATTAAATGCAGT Y 2 1 2 1 101000 f 74 goat snp47318-scaffold665-624914 5 34218177 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414538 Affx-122949507 AX-123284887 5 33563625 GTATCTTTAGCACAGAGAAACTAGAACTTGATAAA[C/T]ATTCAGTATAAACATATACACACACTGAAGTGAGT Y 2 1 2 1 201000 f 74 goat snp47320-scaffold665-745610 5 34341669 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419498 Affx-122945460 AX-123289846 5 33596723 TAGTGGTTCTCAAAGTGTGATTCCTGAGACCAGCA[A/G]CAAAGGGAATTCTCAAGTTCCACTACAGACTTACT R 2 1 2 1 201000 r 74 goat snp47321-scaffold665-778708 5 34374455 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766244 Affx-122929910 AX-385253640 5 33644202 ATTGTGAATTAATGTTTTCTGAAATTCAAGATGCA[C/T]GTGCAATTATAAGGGAAGACTTTCAGTGATAAACA Y 2 1 2 1 101000 f 74 goat snp47322-scaffold665-826187 5 34423847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411510 Affx-122951678 AX-123281860 5 33673456 GTCTGGGTCCTAGGGAGTTCTGTAGTTAAAAGAAA[C/T]GTTAAGATTTTAAAATTGCAAACAGCTTTGAGACT Y 2 1 2 1 101000 f 74 goat snp47323-scaffold665-855441 5 34453343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399046 Affx-122960913 AX-123269401 5 33743135 CTTCACCATGTGAGCCACTAAATAAGTAAACAAAA[C/T]GTTTCTGCAAATAAACCCTGCAAAACCCAAATTGG Y 2 1 2 1 201000 r 74 goat snp47324-scaffold665-925120 5 34523035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438324 Affx-122931348 AX-123308662 5 33780018 AATGATTCTAATGCTTCTGAAAAACTGAGTTCATC[A/G]CAGTGAACCAAAGCAGAAACAAGAAACAGATGAGG R 2 1 2 1 201000 f 74 goat snp47325-scaffold665-962003 5 34559800 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398624 Affx-122961471 AX-123268979 5 33842512 AAATGTTGGTAAACATTCTTAGCTGCTATCACTTT[A/G]TGTTTTCCTCTGTGTTTTCTCATCTTCTTCCAGTG R 2 1 2 1 103000 f 74 goat snp47326-scaffold665-1024497 5 34622136 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791000 Affx-122947617 AX-385277997 5 33877671 GCAATGGTTAGGTGTGAATTGAACCCTTGAGCAAT[A/G]TGAAAAACCATCATAACCAGAGGAAACAAGGTACT R 2 1 2 1 101000 f 74 goat snp47327-scaffold665-1059656 5 34657220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404855 Affx-122956620 AX-123275207 5 33910110 TAATAAACACTCAGTAAATGAAAGAAAGATGCCTC[A/G]CATTTTATAGGAATAACTAATGTGTCTTCCCATTC R 2 1 2 1 101000 r 74 goat snp47328-scaffold665-1092095 5 34684414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406945 Affx-122955069 AX-123277296 5 33957958 TTTCTACATATTTCAGTCCTAAAATGTCAGGTTCA[C/T]GCTATTCAAGAAATATACCTATACTGTACCAATCA Y 2 1 2 1 101000 f 74 goat snp47329-scaffold665-1139943 5 34732671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404149 Affx-122957084 AX-123274501 5 33998482 TTCCTTTCTTAAGGCTCTCACATACATTTTAGACT[A/G]CATAATTAAAATAAACTCCCACAGTTCATGAAAGA R 2 1 2 1 101000 f 74 goat snp47330-scaffold665-1180467 5 34773194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415939 Affx-122948440 AX-123286288 5 34030756 ATCAAGCAAAAAGTGTCTGGAATTGGTCCAGTAGG[A/C]TTTTAGAAAAGACAGATTAAAGAACAGTCTGAAGA M 2 1 2 1 103000 f 74 goat snp47331-scaffold665-1212741 5 34805399 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405678 Affx-122956558 AX-123276030 5 34088707 TAATTCTTCTGGGTAATTTGTGGCTTTTTCATATG[C/T]TTATGGTCATCTTTATTTGTCCAAAAGTTTCTCCT Y 2 1 2 1 101000 r 74 goat snp47332-scaffold665-1270692 5 34863272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423493 Affx-122942566 AX-123293839 5 34131356 GCAAGTACACTCACATTTCATTGGCCAAAGCAAGT[C/T]ACATGGTCACATGTAACTTCAAACAAGCCCATAAG Y 2 1 2 1 303000 r 74 goat snp47333-scaffold665-1313341 5 34904537 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796748 Affx-122978650 AX-385283692 5 34185139 ATCATAATTAAATGACTAATAGGCTGAAGGTGAAA[G/T]GGACCATTTTGGAAAATGGTGAATTCTCCTTCAGT K 2 1 2 1 102000 r 74 goat snp47334-scaffold665-1367124 5 34958839 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797116 Affx-122948739 AX-385284056 5 34239507 TATAAAATTAATGTTGTTATGAAGAATTTTGTGTG[C/T]AGTTACTGTTCTGCTAGGTATTAGGCATATAATAA Y 2 1 2 1 101000 r 74 goat snp47335-scaffold665-1421492 5 35013633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438394 Affx-122931296 AX-123308732 5 34295243 AACCTTGTGTCAACTGGTTTCATAATGACACAGTG[C/T]GCTTCAGAAAAATCAAGTCTATAACAATGCAGGTA Y 2 1 2 1 101000 f 74 goat snp47336-scaffold665-1477228 5 35068980 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38383629 Affx-122972543 AX-123253987 5 34333024 CTTCTGCTGGAGTTCAGACTAATAGAACTCAGACG[A/C]CCCTCCTCTTTAAAAATGTATTTAACCAATGTCAT M 2 1 2 1 101000 f 74 goat snp47337-scaffold665-1515009 5 35107087 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775755 Affx-122971439 AX-385262886 5 34367373 ATTGTGTAAGAAGCATATAGGAAAAGTATGACACT[A/G]TGAGAGGCAAATCTTGGGACTCAATTTATACAGAG R 2 1 2 1 101000 r 74 goat snp47338-scaffold665-1549358 5 35141359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435352 Affx-122933594 AX-123305692 5 34433186 TACATGGAGTGATTCTTCTCTCAATTTGCCAACCA[C/T]TGACATACAACAAACATTTGAGAAACTTCTCACCT Y 2 1 2 1 101000 f 74 goat snp47339-scaffold665-1615171 5 35207690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443557 Affx-122927351 AX-123313894 5 34466262 TTCTTTGGATAATAAAAATATAAATAATACCTATA[C/T]GCTTGAGAACTTTATAGTCTACCAGAGGAGATAGA Y 2 1 2 1 101000 r 74 goat snp47340-scaffold665-1648247 5 35241240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784099 Affx-122965533 AX-385271151 5 34510656 ATCAACATGCTGATATCTTGCAAAGTGCTCCAATG[A/G]AGATATATACATGATGTACCCTTTCTTTTTATGAG R 2 1 2 1 101000 f 74 goat snp47341-scaffold665-1692641 5 35285668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421186 Affx-122944158 AX-123291533 5 34553225 GTTCTAGCTTTTAAGAATCAATTTATATTTCCTTT[A/C]TTGGTGATTCTCTTTTAGGTATTACAGTAATGATA M 2 1 2 1 201000 r 74 goat snp47342-scaffold665-1735210 5 35328498 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380329 Affx-122975376 AX-123250687 5 34597585 AATCTCATCGGATAGCAAAAGGTAAGAGTTAGTCC[A/G]TTATGATGTTTCTGCTTAAATATTAATATTTCTCA R 2 1 2 1 101000 f 74 goat snp47343-scaffold665-1779570 5 35372408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272184 Affx-1111833464 AX-519545936 5 34638160 TTTGATAACATGAGCTGTATCTCTGTCCCTTTCTC[A/G]AGCTGTTTTACCAGTGGTACCTTAAATCTTGGCAA R 2 1 2 1 201000 r 74 goat 5_34638160_AF-PAKI 5 34638160 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454033 Affx-122919413 AX-123324366 5 34696711 GTTGGAAGGTTCTGAGCCTTTCTGTTTGTCTGTGT[A/G]TGGGGATACACTGATTGTTTGTTGAATGTACCTTT R 2 1 2 1 202000 r 74 goat snp47344-scaffold665-1878696 5 35473015 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415150 Affx-122949410 AX-123285499 5 34745541 ATAAGCAATTGAGTTATATGGTTAAGTGATGTTCC[A/G]TCTCTACCAGGGCCTAGTCCCACGTCAAGAGTTGT R 2 1 2 1 201000 f 74 goat snp47345-scaffold665-1927526 5 35522227 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783410 Affx-122971343 AX-385270473 5 34801240 ACTAAAGGCAAACCCCACTCCTGCAATGTTAAAAA[C/T]GTGATACTTTGGTTTTTATGTACAATCTTCTAAAA Y 2 1 2 1 102000 f 74 goat snp47346-scaffold665-1983225 5 35578214 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443634 Affx-122927289 AX-123313971 5 34868852 GTCTTCTTATAGCTAGAGGATTTGGCCTGTGAATA[C/T]GAGTTTTTATTTGCTCAAATGGATTTCTCTGAAAC Y 2 1 2 1 201000 r 74 goat snp16394-scaffold1728-163445 5 35649882 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774948 Affx-122966234 AX-385262081 5 34901536 TTTTCAATTTTATTATACAGCAGTAAATGGTTTTC[A/G]AAAGTGGTATAATAGTTTAAACAACATAATTCAGT R 2 1 2 1 101000 r 74 goat snp16393-scaffold1728-130761 5 35682290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777859 Affx-122953784 AX-385264976 5 34939479 ACAGTTGATGTCCTAAAAGCTGGCACTAACAACTA[C/T]AATAAAAATGCAGCATTTTACTAGGGGATGCTAGA Y 2 1 2 1 303000 r 74 goat snp16392-scaffold1728-92818 5 35721075 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445048 Affx-122926612 AX-123315385 5 34970113 TAATGTTAACACTTTAAAAGAGCATGAAGAAGTAT[A/G]TTTTAATGGATGATGAAAATGTTTCCTTACTCAAT R 2 1 2 1 103000 f 74 goat snp16391-scaffold1728-62184 5 35752730 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418452 Affx-122946474 AX-123288800 5 35025677 ACTTAGCACTGAGCCCCTAGATTGGAACAGCCTCT[G/T]GTTTTTCTCCCTTCCCAAATGAGAAGAATCCCAAG K 2 1 2 1 201000 r 74 goat snp16390-scaffold1728-6620 5 35806949 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407732 Affx-122954996 AX-123278083 5 35051581 AAAGGCATCATTCCATGCTCACTTAAGTATGAGGA[C/T]AGCAGAAACAATTCCTGAATTAGAGTAACCAGAAA Y 2 1 2 1 101000 f 74 goat snp9039-scaffold1329-19185 5 35833443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793431 Affx-122969252 AX-385280408 5 35093328 GGAAAACATATGAAGTTTGCTAAAAGAAGTAACTA[C/T]ATGGCAGGAAAAAGAAGATCTCAGAGAAAGTAATC Y 2 1 2 1 101000 r 74 goat snp9040-scaffold1329-60932 5 35875581 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786602 Affx-122922003 AX-385273634 5 35136750 GGTTAAAACCATGGCTCCAAGGTCTATCCCTTCAG[C/T]GGAACTTTAAACATGAAAGTTCACCTTCTCAGCAG Y 2 1 2 1 102000 f 74 goat snp9041-scaffold1329-104354 5 35918720 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387368 Affx-122970469 AX-123257726 5 35167421 AGGGAACCAAAGAAGCAGAAGTATAAAATCAGAAT[A/G]TCCTATGGTATCATTTTGGACACATGGGCATGCTT R 2 1 2 1 101000 r 74 goat snp9042-scaffold1329-135025 5 35949405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769360 Affx-122959670 AX-385256531 5 35215957 CTATTTCTATGTTGTAACAAAGTTGAGGAGGCTGT[A/G]TTAAATACATGATAACTGGGATAAAAGACAACAAA R 2 1 2 1 101000 f 74 goat snp9043-scaffold1329-183561 5 35998150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783178 Affx-122929524 AX-385270245 5 35244759 AATGAGAACTCTAGGAGCAGGCAACTTGACTCTTA[C/T]CAAGTAAGCTGTTGCTAAAACTATTGAAGTTCTGA Y 2 1 2 1 101000 f 74 goat snp9044-scaffold1329-212363 5 36028011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387142 Affx-122970645 AX-123257500 5 35276416 AAATGGTAATGGCAGTAGCAGAATAGGGAAAGATG[C/T]AGAAATGGACAGATGTCAGAGACAAATCTGGAATG Y 2 1 2 1 201000 f 74 goat snp9045-scaffold1329-244020 5 36059625 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386333 Affx-122970878 AX-123256691 5 35314475 AAGGAATTAAGATAGGACCTAGAAAGCTGATAAGG[C/T]GCCTTTTTCTATCAGAACAACACCTGAATGAATGG Y 2 1 2 1 101000 f 74 goat snp9046-scaffold1329-282079 5 36097872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796642 Affx-122941083 AX-385283588 5 35345962 CATTAGCCAGCTATCCCATCAAAACGGCCTTTTCA[C/T]GTCCTAAGTCGAAAAACAATCAACAATTAATTCTT Y 2 1 2 1 101000 f 74 goat snp9047-scaffold1329-313566 5 36127871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381984 Affx-122974092 AX-123252342 5 35380190 TATGTTTTCTTTCAAAACTTAAGTGTCAAATCATT[A/G]GTCGCTCAGTCGTGTCTGACTCTTTGCAACCCCAT R 2 1 2 1 201000 f 74 goat snp9048-scaffold1329-347794 5 36162380 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385311 Affx-122971675 AX-123255669 5 35450975 ATGCTACAGAGGCCTTTTTTATATATGTGAAAATC[A/G]TACTGTATATGTAATTTGTATTTTACTTAATAAAA R 2 1 2 1 102000 f 74 goat snp9050-scaffold1329-418579 5 36233085 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413412 Affx-122950707 AX-123283761 5 35486795 AAGAAACTTGTTTATATTTGAGCATTTATGGTCAC[A/G]TGGGATTGGGAAGGCCTTCTGGCGTTGTCTGGTTC R 2 1 2 1 201000 f 74 goat snp9051-scaffold1329-454399 5 36268945 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453293 Affx-122920373 AX-123323626 5 35542479 TGTAACATTGATTCCTGGAGCCTTTCAACCTAGTC[A/G]CATTTACCAGGAACACTTCCTAGTTTGTCAGTGTC R 2 1 2 1 101000 r 74 goat snp9052-scaffold1329-510083 5 36325761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278362 Affx-1111836303 AX-519551848 5 35585935 AGCATAATAAAAGGAGAGCAGTGGGAACAAATAAT[A/G]AAAGTCTGGCTTTCCAGCTAAGACCTAGATTGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-541 5 35585935 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404703 Affx-122957262 AX-123275055 5 35591977 TTGAGTCAGAAACAGGATATACAAAGAAAGATATA[C/T]GAGAAAAATCAAAGACAACTTTTAAAATAAGAAGT Y 2 1 2 1 101000 f 74 goat snp9053-scaffold1329-559581 5 36375399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 320779154 Affx-122961321 AX-385266258 5 35708039 TCTTGTGACTGTCTTACATGGTGATGTCTGTTAAA[C/T]GCTTTTCGTAGTAAATCTGTTTGCATGTAGACATG Y 2 1 2 1 101000 r 74 goat snp9056-scaffold1329-675643 5 36494319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382441 Affx-122974230 AX-123252799 5 35745646 GGCAAAACTGAAGGAGACAATCTAATGATGAGAAT[A/G]TGAAAAAGACATTTGCATGTGTGTTTGATTGAGTG R 2 1 2 1 101000 f 74 goat snp9057-scaffold1329-713250 5 36529393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783712 Affx-122970150 AX-385270768 5 35791915 GTTGTGCTCACTTGTCCTTGAAGGTAAAACATTTA[C/T]GAGCTGTAAAGAAATACAAGTGAAAAACAACATTA Y 2 1 2 1 101000 r 74 goat snp9058-scaffold1329-759519 5 36576488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772382 Affx-122947248 AX-385259534 5 35823004 TATAGCTCTAAATCTGTATGTATACTGAACATTGG[C/T]GTAGGCTTAATTAGCATTCATTAAACACTTCAGCT Y 2 1 2 1 10000 r 74 goat "snp9059-scaffold1329-790608;SV_224" 5 36606094 T C SV_224 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765519 Affx-122962055 AX-385253003 5 35869590 GGGTCTTGAACATTGTAAGTCACCCATGATTCTCA[A/G]TATGATTTATTGAGTTGACAAGAAAACAAAACAAA R 2 1 2 1 101000 f 74 goat snp9060-scaffold1329-837194 5 36651381 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387743 Affx-122969737 AX-123258101 5 35969164 TAGCCCATGGGGTAGCAAAGAGTTGAACTTCAGGG[C/T]ATGGCAGAAATGTTAGACTTTATGTGAAGAAGAGG Y 2 1 2 1 201000 r 74 goat snp9062-scaffold1329-936768 5 36750714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415236 Affx-122948957 AX-123285585 5 36008499 GTTACAATAATTTTAATTTGCATCTGTGTCCCATA[C/T]GCTCTATGATGTTACATACACCTTGCAATTTTTGA Y 2 1 2 1 101000 r 74 goat snp9063-scaffold1329-976103 5 36790974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782096 Affx-122944861 AX-385269174 5 36058910 ACTGAGGGAGAAGAACATGGACATAATACGTCTTT[A/G]TTAATAGTGGTTATTTTGGGTAGGAGTTAAAGGCA R 2 1 2 1 101000 f 74 goat snp9064-scaffold1329-1026514 5 36842333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391937 Affx-122966928 AX-123262294 5 36118073 GCATAAATGTGGTTCTTTTGATCCTTGTTTTTTGT[A/C]ATTTCTACTCTATTACAGAACAGTCATGAGATGAA M 2 1 2 1 201000 r 74 goat snp9065-scaffold1329-1085677 5 36896157 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376318 Affx-122978356 AX-123246677 5 36161080 CCTTGCACACAATTTTAATAACAAAGAAAAACTAT[A/G]TCCAGGGGTCAACTAAATCCTGTATCTATAAAATG R 2 1 2 1 101000 r 74 goat snp9066-scaffold1329-1128684 5 36939144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437955 Affx-122931616 AX-123308293 5 36202058 TGTGAAAGGAAAAAAGGGCCATGTCTTTCTGACCA[C/T]AGCAAAGTAGAAAAGGGAAGATTAAATAAGCCAAA Y 2 1 2 1 101000 f 74 goat snp9067-scaffold1329-1169662 5 36980714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392098 Affx-122966363 AX-123262455 5 36251305 AAGCTGTGAGCTTCTCACCTGTTACCAAGTTTAAA[C/T]CTCTCAGCTCACAGCATTAGTTGGAACAGAAGGAA Y 2 1 2 1 101000 r 74 goat snp26896-scaffold2844-2833 5 37031306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768368 Affx-122927875 AX-385255548 5 36289767 CCTCTTGGACTTCCTGAGATGATTTAGAAATGACT[A/G]CATATAAATGTTATTTGATGGCACAAGATGGGATG R 2 1 2 1 101000 f 74 goat snp12728-scaffold149-35530 5 37074793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385928 Affx-122971564 AX-123256286 5 36324830 TCCTTTGGTTTCACGGCTGCAGTCACTGTCTCCAG[C/T]GATTTTGAAGCCAGAGATCAAGTTGGGTTGTGTTA Y 2 1 2 1 103000 r 74 goat snp12729-scaffold149-70593 5 37109938 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394432 Affx-122965093 AX-123264787 5 36353590 ATTAGAATGTTTTTTAAAGCACAGATTTAGGGAGA[C/T]AAATAAAATTTGAAGCTTGTTGGGCCACGGTGGGC Y 2 1 2 1 101000 r 74 goat snp12730-scaffold149-99353 5 37138657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450950 Affx-122921758 AX-123321284 5 36393331 GTCAGAAGATAGGAAGTATTATTGTGGCAAATCCT[A/G]CAGAAGTATTACATAGTAACAATAGTTTGGTACAA R 2 1 2 1 101000 f 74 goat snp12731-scaffold149-139094 5 37179394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379324 Affx-122976185 AX-123249683 5 36431779 TCTGGAGGTGAGCCCTGCATTTATCTCCTCCCCGT[A/C]TAGAATATCAGGCACATGGTTGGAATTGGGAGCAA M 2 1 2 1 101000 r 74 goat snp12732-scaffold149-177542 5 37217919 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445402 Affx-122925387 AX-123315739 5 36469334 TCTTAAACTGATTTTACTTTTTAGAATTCCTCTTT[C/T]GTAGCTCTTAACTTGTCACACCTGTTGGGCATAAC Y 2 1 2 1 101000 r 74 goat snp12733-scaffold149-215097 5 37256426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432109 Affx-122936457 AX-123302450 5 36516250 ACTACTGTAGAGGCAACTGAAGTATGGCAGTTGAG[C/T]TCAGCCCAGCTGGGATTACTTGTGCTAAATTCCAG Y 2 1 2 1 101000 f 74 goat snp12734-scaffold149-262013 5 37304485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414455 Affx-122949572 AX-123284804 5 36548646 CAAAGAAGGTAATCATTGAGCTTAGCAAGGAAATA[C/T]GTCTCTGGGTAAGCAGGGGTGTTCTCCAGGTAAGG Y 2 1 2 1 101000 f 74 goat snp12735-scaffold149-294409 5 37340455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417253 Affx-122947269 AX-123287601 5 36601518 ATTCACCCAGAAGGCAAAAATAAGTGTAATGTTTT[A/G]TTATGGTAAGCAGTTTGGCCTAGTTTCAAAGGCTT R 2 1 2 1 201000 r 74 goat snp12736-scaffold149-347281 5 37394583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378916 Affx-122976449 AX-123249275 5 36653606 GCAGAAAGGACCCCACTAGGGAAAATGCTAACATT[C/T]ACTTTGTCTTTCTCCATCTACCTTCTATTCCAAGG Y 2 1 2 1 102000 f 74 goat snp12737-scaffold149-399369 5 37446624 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773428 Affx-122970134 AX-385260570 5 36689331 ATTGGTGAAGACTCTACTAATCATTTTACTCAGAT[A/C]TACAATTATGTGACATAAAAGAGAACACATTCTTC M 2 1 2 1 101000 f 74 goat snp12738-scaffold149-435094 5 37482167 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779725 Affx-122959017 AX-385266825 5 36767716 ATTCTGTTAACGAAGATAAAGTATTCCAACAATAC[A/G]TTGCATTCTTGGAAGTTTGGAAGCCGAGGGTAGAC R 2 1 2 1 202000 f 74 goat snp12740-scaffold149-513479 5 37559243 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799985 Affx-122950631 AX-385286909 5 36817705 TGCTGAGCTCTTAAGTCATTTGAAACTTGAAAATA[C/T]ATTGGAAATAATTATTTTTGCACATTCTTATTTAG Y 2 1 2 1 201000 r 74 goat snp12741-scaffold149-563468 5 37609251 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766827 Affx-122943936 AX-385254150 5 36858695 GACCTTGGAGTGTCTGGGTTTTGACCAGCTACTCA[A/G]TGAAAACTTGAAGTAGCTCCTCTGTCTCCTCGCAC R 2 1 2 1 101000 f 74 goat snp12742-scaffold149-604458 5 37650260 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397359 Affx-122962289 AX-123267714 5 36895038 CGATAACTACGAAAAATTTATCCAGAATAAGAGTG[C/T]CCGGGAGATCCAGGCCTACATCCAGAACGCTGACC Y 2 1 2 1 101000 f 74 goat snp12743-scaffold149-640801 5 37687125 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395778 Affx-122963668 AX-123266133 5 36966636 TATCTTAGAAGAAACTGTACCTATTCCAATGCCAT[C/T]TGAATTTCTGACACATGCATGCATAATCTACTTTT Y 2 1 2 1 101000 f 74 goat snp12744-scaffold149-712399 5 37759371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438380 Affx-122931308 AX-123308718 5 37058103 ATCAACCCCAATGTAAGCTGTAACCTAGCAGAAAT[G/T]ACAATCATGAAGGTGATATCACCCACCTAAGAGGG K 2 1 2 1 101000 r 74 goat snp12745-scaffold149-803866 5 37850809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795266 Affx-122921803 AX-385282224 5 37108589 TATACTTCATTCCTTCTTGTATCTGGGAACTTCTA[C/T]GTAGGACCATTCTCATTTTTTTGCCAAGAAATTCT Y 2 1 2 1 101000 r 74 goat snp12746-scaffold149-854352 5 37901045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388014 Affx-122969565 AX-123258372 5 37163826 TAAAATGCTCAATAAACAATGTTAAGAAAAGGCAG[A/G]AACTTTAATGTGGAGATAGTTATAATCTTAACTTC R 2 1 2 1 101000 r 74 goat snp12747-scaffold149-909589 5 37957640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783015 Affx-122965899 AX-385270083 5 37196676 AACCTTTCCTTCAAGATTATGTACGTTACTATATC[A/G]CTTTTAAATACTTGCACTTACTGTATATATATATG R 2 1 2 1 101000 f 74 goat snp12748-scaffold149-942439 5 37990539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401933 Affx-122958814 AX-123272286 5 37230630 GAGCATGGTGAAGGTGGGTCAGTTTATGATAGGCT[A/G]AAGAGATCGTCAGAAGCTGTGTTCCTCCTGCCTTC R 2 1 2 1 101000 f 74 goat snp12749-scaffold149-976393 5 38024708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381578 Affx-122974808 AX-123251936 5 37259615 CCCATTATTTAGCCAGGTGCTTGGCAACCAGTAAA[C/T]GACTAGTAATAATTTCCCCCAGCATTTCCAGACTT Y 2 1 2 1 101000 f 74 goat snp12750-scaffold149-1005378 5 38053692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797385 Affx-122924493 AX-385284324 5 37354018 TAATTACTGGGTGAATTTGTGATCCAACAGGTTTC[G/T]CCTCAATTACACCTAGAGAACACATCAATTCATTT K 2 1 2 1 101000 f 74 goat snp12752-scaffold149-1099781 5 38149524 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441671 Affx-122929184 AX-123312008 5 37385932 AGCACCAGACCTTCTCATCTGTCAGTTGTCTGTTA[C/T]GTCTGTTCCTTTTATTGCCTGAAAACTCCTTACTT Y 2 1 2 1 201000 r 74 goat snp12753-scaffold149-1131695 5 38181565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391874 Affx-122966976 AX-123262231 5 37440350 ACCACCAGGAGCTTGTTCATTAGTCCTCTTGAAAG[C/T]GTAGAAAATGTCCAACTATAGGTAGATGGGGCAGG Y 2 1 2 1 101000 r 74 goat snp12754-scaffold149-1186113 5 38237098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272307 Affx-1111833465 AX-519546046 5 37484341 TCCCATCTCTTTCAGATTTTCCCACAGTTTATTGT[A/G]ATACACACAGTCAAAGGCTTTGGTATAGTGAATAA R 2 1 2 1 103000 f 74 goat 5_37484341_AF-PAKI 5 37484341 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452080 Affx-122920863 AX-123322413 5 37486306 TTGACTATATCTGTCGCTTGGTCATTGCCATACAC[A/G]TTAGCGTAGTGAAGGCTCTGAGAAGTCTTTTAGTA R 2 1 2 1 101000 f 74 goat snp12755-scaffold149-1232069 5 38282736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425519 Affx-122941464 AX-123295865 5 37517925 GCAATCTTAACCTCAGTCATACTAGGTCAGGCATA[G/T]AGATTAAAGAAAAGAAATCTGGCCACCAGGTTTAT K 2 1 2 1 101000 f 74 goat snp12756-scaffold149-1263688 5 38314809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278364 Affx-1111836304 AX-519551850 5 37524393 CAAGAAAAAAAGATGTTATTTTCAAAGAACTTACA[C/G]TCTAGTAGGAATACAAGGGAGAAAATATCTGCCAT S 4 1 2 1 101000 r 74 goat Random2.2K-544 5 37524393 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278366 Affx-1111836305 AX-519551852 5 37575963 CGCAGAGCGGTGCCAGCCGTCCTTCCCCCACCCCC[A/C]CCTCCTTCTTCAGCCTCCTGAAGACAATCTGTGGA M 2 1 2 1 103000 r 74 goat Random2.2K-545 5 37575963 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399555 Affx-122961131 AX-123269910 5 37607391 CTATAGAGGCATCATCTGTATCTGGATGTTTAAGG[C/T]GAGTGGTTGTTATCTATGAATGGAGAGCCACGTTA Y 2 1 2 1 101000 f 74 goat snp12757-scaffold149-1353154 5 38405695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453097 Affx-122920035 AX-123323430 5 37674340 TGAGTTTTTAATATATTTTTAGAAAACCAATTGCA[A/G]AGGAAGTCAGTTTACAAGTTTTGTTCTTTTGTATT R 2 1 2 1 101000 r 74 goat snp12758-scaffold149-1420103 5 38473260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404377 Affx-122956803 AX-123274729 5 37708882 AGGAGGGACAGAATCATACAGGTTGAATAGGAATA[C/T]ATGGAAGAAGAGGGTCTTCTGTTTCTGTTCTAAGA Y 2 1 2 1 201000 f 74 goat snp12759-scaffold149-1454645 5 38507719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439301 Affx-122930963 AX-123309638 5 37756077 TTGTGTTTCTGGGGATGCCTGAGAAGCACTCTACT[C/T]GAAAATAAACAGCATGATTTTGGTTTCATACAGCT Y 2 1 2 1 101000 f 74 goat snp12760-scaffold149-1501840 5 38555394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442416 Affx-122927983 AX-123312753 5 37813816 CTCAAATCCATATTCTGAACTCTCTGAATCCAGGT[A/G]TGATCCAGACTAGTGGCCGCAGACAGGGTTTAACA R 2 1 2 1 101000 f 74 goat snp12761-scaffold149-1559579 5 38613802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399909 Affx-122960198 AX-123270264 5 37861027 TTATGTTGCCTAAGTGCCTGAAACAGTGGGTGTTC[A/G]TGAAATGTGCAAGGAGCATTGGAAGAATGAACTGA R 2 1 2 1 201000 r 74 goat snp12762-scaffold149-1606790 5 38661509 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784965 Affx-122920119 AX-385272012 5 37896242 ATATTTGAAATAATTTGGTTACTTCTCCAGGAAGT[A/G]CATACTATTTTTCCCAAAAACTGTTTAGAAAGCAG R 2 1 2 1 201000 f 74 goat snp12763-scaffold149-1642005 5 38697619 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786505 Affx-122929852 AX-385273539 5 37943297 ATTTAGTTTGTCTAACCTCTGGGTTCATGCACATA[C/T]ATATAATATGCATGATTTCACATACATATGTGTGT Y 2 1 2 1 101000 f 74 goat snp12764-scaffold149-1689060 5 38745515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781015 Affx-122919598 AX-385268102 5 37988022 CAGTCCCCAATATATGACAACTGGATGGTTTGGCC[A/G]CCACAATTAGGATTTTAATGTGATATAACTGATAT R 2 1 2 1 101000 f 74 goat snp12765-scaffold149-1733785 5 38790446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423939 Affx-122942254 AX-123294285 5 38023638 ACCACAAGATTAACAATAACTGGTAACAGTTACTA[C/T]GAAAATATGAAAATAATAGTTAACTATTTAGAGTT Y 2 1 2 1 103000 f 74 goat snp12766-scaffold149-1769401 5 38826483 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401402 Affx-122959212 AX-123271755 5 38056279 AAAAAGAGGCAGGGGTGAGGGGGCCAGTAAGAGAC[C/T]ATTCTTGGCTTCACGACTTGAACATTTCTCTCCTA Y 2 1 2 1 101000 r 74 goat snp12767-scaffold149-1802042 5 38859155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796496 Affx-122931224 AX-385283445 5 38085153 GCACAGATAGATTTAATCTGGTTTAATTCTATAAA[C/T]ACAAATTTGAGAATCCCTGAAATGAAATTTTCTGT Y 2 1 2 1 102000 r 74 goat snp12768-scaffold149-1830916 5 38887990 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382386 Affx-122973847 AX-123252744 5 38115858 CATGATGAATGCAGATGAAGCAGTCATTTTGATCA[C/T]GACATGACCTTGGGAATGAAAGCCAGGTGTGCCCA Y 2 1 2 1 101000 r 74 goat snp12769-scaffold149-1861621 5 38919029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394201 Affx-122964909 AX-123264556 5 38153866 GAGAAAGAGAGAAACTGTGAGACTCCTATTTATTA[G/T]ATCAGGATGTAAATTGTTTACTGTGAATATTAGAA K 2 1 2 1 101000 f 74 goat snp12770-scaffold149-1899629 5 38957214 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410510 Affx-122952181 AX-123280860 5 38183672 TAGAGAAGCAGAGTAGTAATTGCATTTCTCCAGTA[C/T]AGAAGTGAGTACAAATTTACAAATTCTTCCAGAAT Y 2 1 2 1 101000 f 74 goat snp12771-scaffold149-1929435 5 38986985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417316 Affx-122948157 AX-123287664 5 38227497 CTTTGCATATCAAGGACATTAACTTTATCTGTTAT[C/T]CGTGATACAAATACTTTCATTCAGTCGTATTTTTA Y 2 1 2 1 101000 f 74 goat snp12772-scaffold149-1973260 5 39031059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396974 Affx-122963163 AX-123267329 5 38259247 CTTTGGCTCAAAGGTGTTTGGGGTTTTAAATAAAA[C/T]ATGTTAATACCTGACATGGTGTCTTGCAGATAACT Y 2 1 2 1 101000 r 74 goat snp12773-scaffold149-2005010 5 39063099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782669 Affx-122926899 AX-385269742 5 38337458 TATGAAGATTAAAAGACAAAGTACAGAAACTCACT[A/G]CAATTATCTATGATAATTAGGTAAGGAATTCACCA R 2 1 2 1 101000 f 74 goat snp12775-scaffold149-2083221 5 39142559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418128 Affx-122947118 AX-123288476 5 38411732 TAGGGCCTCTGTCTTCCTCACTGTCCTGACACTGA[C/T]ACTGTTAATAAATTAGTCTTCAACATTTCAAAACT Y 2 1 2 1 201000 r 74 goat snp12777-scaffold149-2157495 5 39217021 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447946 Affx-122923780 AX-123318282 5 38457170 GAAAGAAAGACTAACAATTTGAAGTTTCCAAATAC[A/G]TGGAGTGATAATTCTCCACATATTCCATGAGATTC R 2 1 2 1 101000 f 74 goat snp12778-scaffold149-2202933 5 39262826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388756 Affx-122968948 AX-123259114 5 38501755 TTGGATAAATCAGAGATATATATTTGAGAGTTTTT[A/C]GCATTTATAGCCTTGACACAATAAGATTGCTTATG M 2 1 2 1 101000 r 74 goat snp12779-scaffold149-2247518 5 39307023 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407157 Affx-122954845 AX-123277508 5 38553726 CTGAGATTAAAAAATCTAAATTCTTATGATAATTC[C/T]GGCCAGATGATCAACCAAAGTATATTAAAGCAATA Y 2 1 2 1 101000 r 74 goat snp12780-scaffold149-2299489 5 39359513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376070 Affx-122978918 AX-123246429 5 38605217 AGTGTAGGGAGAATAAGGTAATTTGGATAATTTTG[C/T]GTGAACATAAAAATTTCATTAAGACTTCTCTGTTA Y 2 1 2 1 101000 f 74 goat snp12781-scaffold149-2350980 5 39410541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794309 Affx-122973251 AX-385281273 5 38647674 CTTGAACAGTCTCATGAACACTTCTTTGAATCTCT[A/G]TCAATTGCCCTGCTTTACTAACTGGAGAAATTTAG R 2 1 2 1 101000 f 74 goat snp12782-scaffold149-2393437 5 39453515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432575 Affx-122935524 AX-123302916 5 38685478 TGCTGAGAATGAAAGACTCCCAACCCACCTGGCAC[A/G]TATGTAATCACATAGATTTTGAACCTGATGTAAGT R 2 1 2 1 201000 r 74 goat snp12783-scaffold149-2431241 5 39492096 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775241 Affx-122944700 AX-385262372 5 38750391 ACTTTAATACACTGATTTAATTTGATCATCACAAA[A/G]CTCTTGTGAGACAAGTAGCATTTACCTCCACTTAA R 2 1 2 1 101000 r 74 goat snp12784-scaffold149-2496154 5 39556882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778263 Affx-122929753 AX-385265378 5 38818502 TTTTGAATTATAAAGAGCCATATTCCAACAGGAAA[C/T]ATAAATAGTAGTAACCTCTGGCAACTATAATCTAA Y 2 1 2 1 101000 r 74 goat snp12785-scaffold149-2564265 5 39626806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408463 Affx-122954433 AX-123278814 5 38850688 ATTGAGAATCTATTTCCAAATCTTTCCAGTACAAA[C/T]GAAAGGGTAAGGGAGTAGTTTTCAATCATGTTACT Y 2 1 2 1 101000 r 74 goat snp12786-scaffold149-2596451 5 39659011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775552 Affx-122935587 AX-385262683 5 38894423 TGAAATAATTATATTGGCTAGTGGCACAGAGGAAC[A/G]TTATGAAAACAGAATCACAATATGTCTGAGAGAGG R 2 1 2 1 101000 f 74 goat snp12787-scaffold149-2640186 5 39697234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801332 Affx-122955963 AX-385288244 5 38930703 TTTAGGGACATCAAGTTCCTATAAAAAAGTCAGAT[A/G]TAATCAAAATGATTCACAAAGTGTAAGAATTTATG R 2 1 2 1 101000 f 74 goat snp12788-scaffold149-2676466 5 39733551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781085 Affx-122955302 AX-385268171 5 38996654 AACATTGACAAAGAAATATCATAAGAACAAACAAC[A/G]AACAGGAAATTGCATCTTGCACAGCTGGCTTATTT R 2 1 2 1 101000 r 74 goat snp12789-scaffold149-2742417 5 39800510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394174 Affx-122964928 AX-123264529 5 39047682 ATGGAAGAAAGAAGTTAGGAGCCTCATATGCTACC[A/G]TCTTACTCAGTTCCATGTACAGCTCTTTATATACC R 2 1 2 1 101000 f 74 goat snp12790-scaffold149-2793445 5 39857559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420751 Affx-122944723 AX-123291098 5 39077421 GGCAAGGAAAGAGGGAGGAGGAAACAGGCAGATGA[C/T]GGGTTCATCTTTCTAAATTTTACTCATCAATTACT Y 2 1 2 1 201000 r 74 goat snp12791-scaffold149-2823184 5 39887271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393563 Affx-122965401 AX-123263919 5 39400443 GTCTGAAGTCCAAATCCTGCCTTTGTGCACCCTGA[G/T]ACAGAACTGTGTCTGCCTAGAAGGAGGTGCACATT K 2 1 2 1 202000 f 74 goat snp5577-scaffold1195-1813787 5 40229186 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415399 Affx-122948744 AX-123285748 5 39436115 GTGTAGTTTGAAAGCTCCTCTAGTAATTCTGAAAA[G/T]TCCTTTCGGTTCTCTTCCATCCCTCTCCCTCTACA K 2 1 2 1 201000 f 74 goat snp5576-scaffold1195-1778115 5 40265435 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428006 Affx-122939160 AX-123298349 5 39578139 CAAAATATATAAGTTCATGGGAACAACTTACATTA[C/T]AATCTATAAATATTATTTGTACTATGCCACTGAGA Y 2 1 2 1 101000 f 74 goat snp5572-scaffold1195-1636091 5 40409737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439601 Affx-122930060 AX-123309938 5 39610286 CATGTAGAAACAACTGAAAAATTTAAGGAGAAAAT[A/G]TTGTGATCCAAGTATATTCTGGCTAGTCTTCCAGG R 2 1 2 1 101000 r 74 goat snp5571-scaffold1195-1603944 5 40441025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278213 Affx-1111836306 AX-519551701 5 40041070 CAAGCATTTTCCAGAAGAGAAAACATATATTGCCA[A/G]TGAATATATAAAGAAATGCTCATCCTTATTAGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-546 5 40041070 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442143 Affx-122928325 AX-123312480 5 40041604 CTTTAATAATGCTCAACAAGGGATCTATTTAGTCA[C/T]ATGTGCTATAAATAAAGTGATATACTGGTGACATT Y 2 1 2 1 101000 f 74 goat snp5561-scaffold1195-1172626 5 40871415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448723 Affx-122923842 AX-123319059 5 40082511 AATTAACTTTGTACCTCGGTCAAAAATTAGTTGAT[A/C]ATGAAGTATGAGTTTGAATTGTTTATTACATCCCA M 2 1 2 1 101000 f 74 goat snp5560-scaffold1195-1131719 5 40913018 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439576 Affx-122930079 AX-123309913 5 40373042 TACTTAAGAATGGCAAGTCAATCTAATGAACAATT[A/G]CACTTACTCCTGGCTTTCCTATAGCAATAGCACTT R 2 1 2 1 101000 f 74 goat snp5555-scaffold1195-841188 5 41204780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425423 Affx-122941533 AX-123295769 5 40681465 AAGGAGACAGTTTTCCCAACTAGGGAGGAGACAGG[C/T]GCAAGAGGCCTCTGCTGGTGCCAGGGCTCCAGCTC Y 2 1 2 1 101000 f 74 goat snp5548-scaffold1195-532765 5 41513992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795741 Affx-122977348 AX-385282694 5 40717523 AAGAACAATGCTTCTGAGGCAGATATATCAATACC[A/G]TAAATTATATTTCTACACTTTTAAATTTTCTCATG R 2 1 2 1 201000 r 74 goat snp5547-scaffold1195-496707 5 41551386 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787750 Affx-122936612 AX-385274773 5 40785341 AAGCATACCATAATGGCAGTACTCTAAGCATAAAC[A/G]TGCCCTCTTTCACAGCTGCACAATTGTCTTAATTG R 2 1 2 1 101000 r 74 goat snp5546-scaffold1195-428889 5 41619228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415631 Affx-122948585 AX-123285980 5 40859372 CCCAAGAGATGCAGGGTTGGTAGAAAGAACTGAAA[G/T]AGACATTGAAGAAGCTTTCTCCAGATGAGTCTTTA K 2 1 2 1 101000 f 74 goat snp5544-scaffold1195-354858 5 41692570 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405600 Affx-122955926 AX-123275952 5 41044681 CAAACTTGCCTCTCAGCATTGCTTAAGCAGTGAAA[C/T]AATTTCAGAAAATGACTTACCCTCCCTTAATATAG Y 2 1 2 1 101000 f 74 goat snp5540-scaffold1195-169549 5 41881488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783407 Affx-122937891 AX-385270470 5 41074020 AGCATCCCAGGTATGGCCCAGGTATCTTGAACAAA[C/T]GTACCATTCTCCTTGTATCATGCTCAAATTCTTGA Y 2 1 2 1 101000 f 74 goat snp5539-scaffold1195-140210 5 41910947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776339 Affx-122932566 AX-385263467 5 41135357 GATCTGAACAGTATGAAAACTCCATTGAAATTTAT[A/G]CTTTCCCTGGCAAAGTTTGCAGAATGGGTCAAATA R 2 1 2 1 101000 r 74 goat snp5538-scaffold1195-78873 5 41973035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403051 Affx-122958532 AX-123273404 5 41176602 AAGATATAGTTCGGACCGAAGCAGAAAAGGAGAGA[C/T]GACCTCAATGGAGGTAGGTTAGCTTTATTCAGGTA Y 2 1 2 1 101000 f 74 goat snp5537-scaffold1195-37628 5 42019956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450973 Affx-122921740 AX-123321307 5 41206720 ACACTTCATAAACAGAAATGGAGAAGCAACGTAAT[A/G]CAACAATGCTTATGGCATATTTAATACTCCCAGGT R 2 1 2 1 600000 r 74 goat snp5536-scaffold1195-7510 5 41206720 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786752 Affx-122921740 AX-385273783 5 41206720 ACACTTCATAAACAGAAATGGAGAAGCAACGTAAT[A/G]CAACAATGCTTATGGCATATTTAATACTCCCAGGT R 2 1 2 1 101000 f 74 goat snp5536-scaffold1195-7510 5 42050664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441615 Affx-122928649 AX-123311952 5 41229011 ATCCTCGGTGCCCAGGACAGGGACTGGAACGAAAC[A/G]CATGCTTCATTAAGTGTGGGTTGCGGGTTGCGTGC R 2 1 2 1 101000 r 74 goat snp57564-scaffold920-14682 5 42073513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783539 Affx-122964821 AX-385270600 5 41264173 ATTTCACTGTGTTGCTTAGCAGATAGCCCAGACTT[A/G]TCCTCGGAGCTGCCTCCCTAACTAGTCTCACTGGC R 2 1 2 1 202000 r 74 goat snp57565-scaffold920-49844 5 42108726 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382624 Affx-122973696 AX-123252982 5 41339033 TTTCTTGATTCAAATCACTATTCATTAAGGAAACT[C/T]GAGGTTAAAGTTATTTAACCTCTCTGCGCCAGTCA Y 2 1 2 1 101000 f 74 goat snp57567-scaffold920-124704 5 42183861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794163 Affx-122953333 AX-385281129 5 41384602 CTAGACAGTTTATCATACTGCATCCTGGGGACCCT[A/G]CCTTTGTGTGCAGACTTCACGAAAAGACTAGTCAG R 2 1 2 1 101000 f 74 goat snp57568-scaffold920-170273 5 42229267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784919 Affx-122939444 AX-385271966 5 41417966 TTTAAAATGAAAATTATAAGCTGCAAAATAACTTT[A/G]TGGGATTATTTTAAGCTTCCTCTCATTGGTTTCTC R 2 1 2 1 101000 r 74 goat snp57569-scaffold920-203637 5 42262510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388211 Affx-122969415 AX-123258569 5 41447356 AACAGAGATAGCAATGGGTAAATATCTGCAAATGC[A/C]TTTCTTTTGGGAACTTATGGCAAGTGTGCTTTTCT M 2 1 2 1 101000 f 74 goat snp57570-scaffold920-233027 5 42292064 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278371 Affx-1111836307 AX-519551857 5 41465774 AGATCTGACCTTTGCATGGAGAGGTCTCCTGCTGG[A/G]TTAGAGTCAGATGAGGAAGTATGTGAAATGTGAGC R 2 1 2 1 101000 r 74 goat Random2.2K-548 5 41465774 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415067 Affx-122949472 AX-123285416 5 41480912 TTGGTTGGAAAATCATCAGAAAAGATGGGAATGAA[C/T]ATGAAAATCTGCTGTTTATGGTTTATTTTAGACTG Y 2 1 2 1 101000 f 74 goat snp57571-scaffold920-266583 5 42325547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799831 Affx-122927390 AX-385286757 5 41529120 CAGAAACAACATTTGACTTAGTTAACTGAATGTCA[C/T]AGTAAATATACTCCAAGCCTTAAAATTACACTGCT Y 2 1 2 1 101000 f 74 goat snp57572-scaffold920-314791 5 42374415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430927 Affx-122936846 AX-123301268 5 41560154 TATTGAGTCTCCACAACATGGGCATGGGGAGATAA[C/T]AAAGAGCCAAGACTTCTTCCTTCAAGAGTTTTCTA Y 2 1 2 1 101000 f 74 goat snp57573-scaffold920-345825 5 42405691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773550 Affx-122945231 AX-385260691 5 41601273 TGAGATTCCCTCCTCACTTATCCATCCCACAATAG[C/T]CATCATCTTGACTCTCATTTTTCTCTCTTGCCTTC Y 2 1 2 1 201000 r 74 goat snp57574-scaffold920-386944 5 42446770 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419478 Affx-122945474 AX-123289826 5 41648973 CCAACCTAGAAGAGTCTGATTAGGCTTCAGAGTAA[C/T]ACAAAATCTGTCACTTTCTCACACAAACATAATCA Y 2 1 2 1 101000 f 74 goat snp57575-scaffold920-434644 5 42494415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278372 Affx-1111836308 AX-519551858 5 41688044 GTTGTCTACTTTTGATGTCATCTTCTTGTCCTGGC[A/G]TTGGTCTTTCCCTGTTATCAGACACTGCTTTAAGG R 2 1 2 1 201000 r 74 goat Random2.2K-549 5 41688044 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427337 Affx-122940122 AX-123297680 5 41700744 CACCATGGGAAAGATGGGTTATTCAATAAATTGTA[C/T]TGGGACAATACTGATCATTTGGGGAAAAGGCATTG Y 2 1 2 1 201000 f 74 goat snp57576-scaffold920-486415 5 42546099 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441079 Affx-122928906 AX-123311416 5 41747270 AACACAGAACTACTAAATCAGAAACTAGGGTGGAA[C/T]CTCTGATTCAGTGGGTTTAGGATGGGTATTGAGAA Y 2 1 2 1 202000 f 74 goat snp33525-scaffold394-26343 5 42592363 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788641 Affx-122938608 AX-385275658 5 41775835 ACTTCTCACTTCACAATCCTCAAATCCTGAAAAGA[C/T]GTAACTGCCACCCCAAAACTGACAGTGCTTTTGCT Y 2 1 2 1 202000 r 74 goat snp33526-scaffold394-54908 5 42621112 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394589 Affx-122964433 AX-123264944 5 41869559 TGATTCTTTAGCTGTAAGTGTTCAGAACACTCTAG[A/G]CTACAGGAATTGAAAGCAATGGTTTAAGAGCATGT R 2 1 2 1 101000 r 74 goat snp33528-scaffold394-148632 5 42715795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423417 Affx-122942619 AX-123293763 5 41929344 TTGGGTAAATACCTAGAAGTAGAATTTCTGGATGG[C/T]ATGGTAGTTTTGTTTTTAATTCCATGCTGTTTTTA Y 2 1 2 1 303000 r 74 goat snp33529-scaffold394-208417 5 42776354 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454148 Affx-122919330 AX-123324481 5 41965035 GGCTCTGGAGGTCAAATCTTCATGAAGAAGAAAGA[C/T]GATGAAAGAAAAAATTTTAATTTTAATTTAGGTTA Y 2 1 2 1 101000 f 74 goat snp33530-scaffold394-244108 5 42812009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424782 Affx-122941399 AX-123295128 5 42006828 AAAAGAAACTAGAGGCTTCCTTTGTGTTTTATGTT[C/T]ACTTGCCGTAGACAAGTTAAACTGCTGTTAGGTCC Y 2 1 2 1 102000 f 74 goat snp33531-scaffold394-285901 5 42854111 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450920 Affx-122921781 AX-123321254 5 42035475 TGGCGCTATGCTTGAATCCTCTGACTGTAACGCCC[A/G]TATTCTTCATCACCACCTTCCTGTGACTGGAGGTT R 2 1 2 1 101000 r 74 goat snp33532-scaffold394-314548 5 42882788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419799 Affx-122945846 AX-123290147 5 42089316 TGCAGATGTTTATATATTGCTGAGTGGGAAAAAGT[A/G]TCCTCTGATTCTATTCACTTTGCTATACACCTAAG R 2 1 2 1 201000 f 74 goat snp33533-scaffold394-368389 5 42936199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442738 Affx-122927847 AX-123313075 5 42155846 CTCAAGTTCTTCAACTTCAAAATGGGGATAAGTAA[C/T]ACCAACCTTGTTTGATTTTGTGAGAATTCAATGAG Y 2 1 2 1 101000 f 74 goat snp33534-scaffold394-434919 5 42994733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798619 Affx-122933247 AX-385285552 5 42195986 CCACTCTTACAGAAGTAGTTCAAACACTCCCAACT[A/G]TCACTGCAAATTGCTCAAAATAAATTTCATGGGTG R 2 1 2 1 101000 f 74 goat snp33535-scaffold394-475059 5 43034788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433322 Affx-122935180 AX-123303663 5 42227363 GGAATGAAAGAGAGGGAAGGAGGAATGGAAGGGAA[C/T]GAGGAAGAAAGAATATTGATTGACACATGAATACT Y 2 1 2 1 201000 r 74 goat snp33536-scaffold394-506436 5 43065970 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386433 Affx-122970800 AX-123256791 5 42285901 GCTCAATTAGAAACAAAACTAAATTCAGAGGATAC[A/G]CTGTAAATTTCTATTATCTCTGCTTCTGTAAGTCC R 2 1 2 1 101000 r 74 goat snp33537-scaffold394-564974 5 43125566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387240 Affx-122970572 AX-123257598 5 42319954 AGGGATACCAAAATCAGTGTTATACTCCTGAGAAA[C/T]AAGTCTGTTGGGGGAGAAAATGGGAATATATATTT Y 2 1 2 1 101000 f 74 goat snp33538-scaffold394-599027 5 43159888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405120 Affx-122956972 AX-123275472 5 42362774 TGAACAAAAAGGAAGAAATAAATAAGACTAGCCTT[A/G]TATGAGTCACCTATGTTAATGCAGCAAGCACTAAC R 2 1 2 1 101000 r 74 goat snp33539-scaffold394-641847 5 43205265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786158 Affx-122941132 AX-385273194 5 42409573 TCCAGGGTTATTATTCAATAATTACTTAGTAAGCA[G/T]ATTCCAATAATAAACATAATTAAGACATTCTTTTT K 2 1 2 1 201000 r 74 goat snp33540-scaffold394-688646 5 43252162 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771882 Affx-122958057 AX-385259038 5 42446840 AGGTATTTCCTCACATCTTAATTCAAAGAAAGATG[C/T]AACTGACAAAGCTTATCCTTCTCTGTTGAATCTGA Y 2 1 2 1 101000 r 74 goat snp33541-scaffold394-725913 5 43289714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768339 Affx-122957621 AX-385255519 5 42491486 TTGAAAAGAAGGTAAAAAGATACTATTACTCATAA[C/T]AATGGTATTGACCATAACACAGGGTGATACATATG Y 2 1 2 1 101000 r 74 goat snp33542-scaffold394-770559 5 43334664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403022 Affx-122958556 AX-123273375 5 42523718 TCTCGTCCACTGCTTAACAGAATTTTGTCCTAAAA[C/T]GAACATATTTGCTTCAGGTTAAGACAGAAGTACAT Y 2 1 2 1 101000 f 74 goat snp33543-scaffold394-802791 5 43366931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383294 Affx-122972713 AX-123253652 5 42556574 GACCTTCCACCAACTCACAGTCATCAATTGTCCCA[C/T]AAAGCTTCTTAACTATTTTAATATCTCTAAGATCT Y 2 1 2 1 101000 f 74 goat snp33544-scaffold394-835647 5 43399844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440567 Affx-122929306 AX-123310904 5 42585867 AGTATTAATCATGAGGCCTCTCTCTCATCATTCAG[C/T]GATCATTCATCCCATCAGTGATCACTACTGAATTA Y 2 1 2 1 102000 f 74 goat snp33545-scaffold394-864940 5 43429583 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448750 Affx-122923320 AX-123319086 5 42617460 AAGATTACTTCAAAATATGAATGACACATGGTACT[A/G]TAACTGATTTATTCTCTGAATCTCCAATCAAAGTC R 2 1 2 1 101000 f 74 goat snp33546-scaffold394-896533 5 43460484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787601 Affx-122939242 AX-370700598 5 42652640 TTTCAGATACACATGGAGGTAGGAAAATACAGAGC[A/G]CATCCAGAGACCTTGAGCAGATCCTTTTAACTGAA R 2 1 2 1 101000 r 74 goat snp33547-scaffold394-931713 5 43496020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446675 Affx-122924757 AX-123317011 5 42687261 TTCCCGACTTCTCATTTTCCTTCTTCTTTTTCCAG[C/T]CCACAGTCTCTTCACAATTCTAACCCCCTCCACAT Y 2 1 2 1 101000 r 74 goat snp33548-scaffold394-966334 5 43530535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444405 Affx-122926584 AX-123314742 5 42741698 AGGCTTCACCTTGAATGACAAATGCAAATGACTGA[C/T]GCAGCTGCATGGAATGCTGTGTGGAGAGAGACACT Y 2 1 2 1 101000 f 74 goat snp33549-scaffold394-1020771 5 43586236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420268 Affx-122945052 AX-123290616 5 42803228 TGTTCATGGCAGAAGTATTCATTTCACTTCTAATT[A/G]TTACCAGGGTTATTGGGATTGTGTGAGGTAAAGGA R 2 1 2 1 201000 f 74 goat snp33550-scaffold394-1082301 5 43649575 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452341 Affx-122920650 AX-123322674 5 42860491 AGGACCCTAAGACATGAAGTAACAGTCAACATTTT[A/C]TTTGTCTAACTAACCACACTGGGTCTCAGGAAAGT M 2 1 2 1 101000 f 74 goat snp33551-scaffold394-1139564 5 43706924 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434996 Affx-122933822 AX-123305336 5 42894484 AGAATAAGAGAGAAGACAGAAACAGAAGTCTTGGA[A/G]CTTTCACTAGAAAAGGTAAGTGGTATAGGGCAGTC R 2 1 2 1 201000 r 74 goat snp33552-scaffold394-1173557 5 43741872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378898 Affx-122976492 AX-123249257 5 42927763 AAAGAAGGGAGGATGGACCCAGAGAGACATGAGCT[A/C]GGTTATGGTGGTGAGGAGGGGAGAGTTTTTATGAG M 2 1 2 1 201000 f 74 goat snp33553-scaffold394-1206836 5 43775455 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792118 Affx-122928430 AX-385279103 5 42988944 TTGTGTTCACAAAGTTTTCTAACCTGTTGATTCTG[A/C]TACTTTAACTGTAGTCTTCTCACCGTTCCCCATCT M 2 1 2 1 101000 f 74 goat snp33554-scaffold394-1268017 5 43837030 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272188 Affx-1111833466 AX-519545940 5 42992497 CGGAAGGGACAGAGGAGAAACTAACATCAAGAGAC[A/G]TAAACGCCATCTTCATGGTGAGTACCTCACTTCAT R 2 1 2 1 101000 r 74 goat 5_42992497_AF-PAKI 5 42992497 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789023 Affx-122962793 AX-385276036 5 43056289 TTAGCCTCGAAGGAAGAGTTACGTTTTCCTTTGTC[A/G]TCTGTCATAAGGATGAAAAACCATAAGATGAGAAT R 2 1 2 1 101000 f 74 goat snp33555-scaffold394-1335362 5 43904877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429678 Affx-122937648 AX-123300019 5 43112813 TCCCAGTGCCACTAGTTTTAGGGAGGTAGATCACA[C/T]GATACATTAAACAAGTATGAATCTTTGCCCAAGAA Y 2 1 2 1 101000 f 74 goat snp33556-scaffold394-1391886 5 43961680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441601 Affx-122928658 AX-123311938 5 43142247 TGAGGCAATGTACAAAGGTCTGCCCAGGTCGAAGA[C/T]GAAGGGATAAAGACCCCAGGAGGTGTTGATGGGGA Y 2 1 2 1 101000 f 74 goat snp33557-scaffold394-1421320 5 43991250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433737 Affx-122934512 AX-123304078 5 43198260 TTTTAAAATAAATGCCATGCTTAAAGAATGCCTAT[A/G]CTTACTAAGCTCAGAAAATATTTTCTTCTGTCTCC R 2 1 2 1 101000 f 74 goat snp33558-scaffold394-1477333 5 44047990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783964 Affx-122940964 AX-385271018 5 43256550 TGTCTACCCGATGTAGGTGAACTGTAAAAGGCTGG[C/T]TTACTTCGTCCCTTTTATGATCCATGGATATCAAA Y 2 1 2 1 101000 f 74 goat snp33559-scaffold394-1535623 5 44105972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774760 Affx-122971186 AX-385261894 5 43288354 TGTTTTTTGAGCATTGGCTCATGTAAATTTTTTGC[A/G]GTTTTGGTGCCAAATGTAAACAAACTAAAAAACTA R 2 1 2 1 101000 f 74 goat snp33560-scaffold394-1567427 5 44136084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400753 Affx-122959890 AX-123271108 5 43319468 TGGGAAGAGACTAAAGACATAGAGGCTACTGCTAG[C/T]GACACTGCAGGTCTGAATCACCATGGGTTCAGCCA Y 2 1 2 1 101000 f 74 goat snp33561-scaffold394-1598541 5 44167483 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780764 Affx-122931706 AX-385267853 5 43350076 TAATCCTAGAAACACTTATCAGAGCTGCAAAAACA[A/C]AGCTAAAGAACTAAGGATCTGGACCCAAAGCCAGA M 2 1 2 1 101000 r 74 goat snp33562-scaffold394-1629149 5 44198141 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803226 Affx-122931914 AX-385290081 5 43392555 AGACAAGTCTCAAAAGCCATAAAAAGACCATTTGT[A/G]TAAATGAACAAAGAATGTATTGGTATGTTTATCTG R 2 1 2 1 201000 r 74 goat snp33563-scaffold394-1671628 5 44240623 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395897 Affx-122963614 AX-123266252 5 43447786 TTGGACATGGCATCTGGCCCACTCTCTCTTGAGAA[G/T]AGTTTGCCAGTGAGCCACGTGCTATGTGAGCAAGC K 2 1 2 1 202000 r 74 goat snp33564-scaffold394-1726859 5 44296353 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443746 Affx-122927127 AX-123314083 5 43482236 GACATAATGTAAATCTCTCTTCAAAAAATGAATGC[C/T]ACTGAAATTCAATGAATAAATGCAGAATCAGGTTA Y 2 1 2 1 101000 f 74 goat snp33565-scaffold394-1761309 5 44330787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448748 Affx-122923322 AX-123319084 5 43514473 ACGACTAGATAAATATTTTCTCTGTTCAAAACTCC[A/G]TTTAAGAAAAAGGCCAAATTCCCTTGGCATTCAAG R 2 1 2 1 101000 r 74 goat snp33566-scaffold394-1793546 5 44363026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774441 Affx-122976893 AX-385261577 5 43564202 GGTTAAATAAATATGCAGGCTTCCTCATGTGGCAT[A/G]CCTAGTGTTCATGAGATTTTAGTTAAATAGAAAAA R 2 1 2 1 101000 f 74 goat snp33567-scaffold394-1843275 5 44413051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775434 Affx-122975684 AX-385262565 5 43601058 AACATTGGCAGACAAAGCTTTCTCAGTAAAACCAT[C/T]TGATGTATTCTTTCATGGTCTTCCTCAGCATCCTA Y 2 1 2 1 101000 f 74 goat snp33568-scaffold394-1880131 5 44450364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791620 Affx-122966937 AX-385278611 5 43639273 GTGTCTGAATTATATCCCACTAAAAAGTATTTATC[A/G]TATTTTATCCTTTATCCATCAATGGGATTTGGGTT R 2 1 2 1 101000 r 74 goat snp33569-scaffold394-1918346 5 44489252 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405682 Affx-122956555 AX-123276034 5 43675086 ATTGTCCCAAATGAAAGTTCTGAGATAGTTTAACA[A/G]ATTACCAACTGACCTTTGCTCATTTGATGACTCTC R 2 1 2 1 101000 r 74 goat snp33570-scaffold394-1954159 5 44525339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393461 Affx-122965844 AX-123263817 5 43711427 AAAGAGCCATGCATTCGATATTTAAGTGGCAAGGC[A/G]CTGATGGGAATGGTTGGGATGTCACAAGGTCAGAT R 2 1 2 1 101000 f 74 goat snp33571-scaffold394-1990500 5 44561414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802148 Affx-122966760 AX-385289052 5 43747465 GTCGATGGTGACTGAGACTGGTGTTTAAAGGGGCA[C/T]GGTTCTTTTGGCCAATATGACAGAGAGAGCTCAGG Y 2 1 2 1 101000 f 74 goat snp33572-scaffold394-2026538 5 44597424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793028 Affx-122934120 AX-385280006 5 43790550 GGCTAGATTAATACATAGTGATATTTTTGCACATT[A/G]CTAATTTTTTTCACAGAAAAGACCAAACTAATGTA R 2 1 2 1 303000 r 74 goat snp33573-scaffold394-2069623 5 44640779 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382511 Affx-122973808 AX-123252869 5 43826566 GTGTATCTATCTCACTGCCCATGAAATTTCTATCA[C/T]ATTGTATTACCGTCCAGATTTTAAAGGGTTTCCCA Y 2 1 2 1 101000 f 74 goat snp33574-scaffold394-2105639 5 44677090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375546 Affx-122979096 AX-123245905 5 43857283 CTTTGACCCTATCAGGTCAGAGACATAGAGGAGCT[G/T]AGGCCACTTAATCCTTTGTTGCCCTGTTTTGTAAT K 2 1 2 1 101000 f 74 goat snp33575-scaffold394-2136356 5 44707934 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393618 Affx-122965357 AX-123263973 5 43907176 TTTTGAGGAGTAAAGTGAAGGTGGTACAACTTGAG[C/T]ATAGTAAGAAGGGCATGGGTACAAGATGAGGTCAG Y 2 1 2 1 101000 f 74 goat snp33576-scaffold394-2186249 5 44757760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776536 Affx-122968705 AX-385263663 5 43952473 ACTTCCTCAGCTCCTCTCTATTTATGAAAGCTGTC[A/G]TTTCTATATGAAGTTCCTTATTCCTATACCACTTA R 2 1 2 1 101000 f 74 goat snp33577-scaffold394-2231546 5 44802395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394885 Affx-122964747 AX-123265240 5 43994232 CTGGTGGCTCAGGAATTCGGCCTAGCATTACATCC[A/G]TCATTTTCTTCAAATGTCTGTATATTCTCAAAAAA R 2 1 2 1 101000 f 74 goat snp33578-scaffold394-2273305 5 44844705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398982 Affx-122960959 AX-123269337 5 44032793 GGAACCTGTACTCATTTATATTATGACATATACCC[A/G]TGGGTATAGTGTTCCCTTTAAGATGAAGTAAAGTA R 2 1 2 1 101000 r 74 goat snp33579-scaffold394-2311866 5 44882353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453381 Affx-122919928 AX-123323714 5 44082655 AGAAATGTGTTGAAATCTGGACTTCCTAGGAGCAT[A/G]TCTCTGTGTGTGTGTGAGTGTGTGTACTTAGTTGC R 2 1 2 1 101000 f 74 goat snp33580-scaffold394-2361728 5 44932737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378578 Affx-122976593 AX-123248937 5 44114085 TGAGTGGGTCAGAGGTCCTGGAGAGAGAGGTCTCT[A/G]CTGAAGGTAGAGATTAAGAGGCCATCAGTATATAA R 2 1 2 1 101000 r 74 goat snp33581-scaffold394-2393158 5 44964614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413820 Affx-122949891 AX-123284169 5 44149409 GTGTTAGTCTCCATTTTATTTCTCAAATGGATTAC[C/T]AGTTTTACAGGGACAGAAACAATTTCTCATACATT Y 2 1 2 1 101000 r 74 goat snp33582-scaffold394-2428482 5 45000189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400515 Affx-122961269 AX-123270870 5 44194779 TTTTATATATATATATTTTTTGCTTGAGGTTTGTC[A/G]TGTTACTGATAAATGGTCACAGTAAGGTGTTGAGG R 2 1 2 1 101000 r 74 goat snp33583-scaffold394-2473852 5 45046609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441411 Affx-122928833 AX-123311748 5 44225520 CAGATCCCAAAACCCCGAAAGTGTCCACATCCTAG[C/T]GCCCAGAACCTCTGAATATGTGTTATAGGACAAAA Y 2 1 2 1 101000 r 74 goat snp33584-scaffold394-2504593 5 45077180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775738 Affx-122972103 AX-385262869 5 44255456 GGTCAGAAATGAGTAAGATTAAAGATAGAGAACAG[C/T]GACTTTGTAACAAGGATTGATAAAATATCACTTGT Y 2 1 2 1 101000 f 74 goat snp33585-scaffold394-2534529 5 45106620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783796 Affx-122938870 AX-385270852 5 44312350 ACTGAATGCTCCCAATATTATCATGAGAGCCACTT[A/G]TAGGTGATTTTATTATAGGAAGGAATCATGCATTG R 2 1 2 1 101000 f 74 goat snp33586-scaffold394-2591423 5 45163667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388346 Affx-122969349 AX-123258704 5 44369590 GTTTCTTTTCTTATAGGGTTCCTTTAATAGGACAA[C/T]GCATATTGTGAAACTTCAAGGGGAAAAGAAAGTAT Y 2 1 2 1 201000 f 74 goat snp33587-scaffold394-2648663 5 45221430 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444543 Affx-122926477 AX-123314880 5 44452956 GCTGTATTTTGCTCTATTTTCTTCCTGCTGAGTGT[A/G]CTGAGGAACAGTACAATTTCTGCCTCTTTTCCGCC R 2 1 2 1 101000 r 74 goat snp33589-scaffold394-2732029 5 45305306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395306 Affx-122964062 AX-123265661 5 44500603 TGATAAGATCTGGTTATACAAAATTAGTGGCTTTC[A/G]CTCTCAGTGAGGACTCATCCCTCCTCTATCCCTCT R 2 1 2 1 201000 f 74 goat snp33590-scaffold394-2779676 5 45351424 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422343 Affx-122943448 AX-123292689 5 44538187 TGGTGTGGGCAGAGACGGGAGATGAGAAGCCTTTA[A/G]AATGCACCCAGAATCCCTGCACACGCCCTCCTCTG R 2 1 2 1 101000 f 74 goat snp33591-scaffold394-2817260 5 45388775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784847 Affx-122973541 AX-385271894 5 44578989 CAGTTTCATTGTGCTGTAATATTAATATAAGAACT[A/G]CATATTTCAAAATAATGGTAAAATGGAAGTTGGCC R 2 1 2 1 101000 r 74 goat snp33592-scaffold394-2858062 5 45430324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407866 Affx-122954509 AX-123278217 5 44645507 ACTACAGTGGAAGCTGGGCAGGAGAGTTTCTACTC[A/G]GTGTAGATGGAAACACGGAGCCACTGGAGATTTCC R 2 1 2 1 101000 r 74 goat snp33594-scaffold394-2924580 5 45497028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449419 Affx-122922690 AX-123319754 5 44676409 TAAAGTTTTAAGTAAGCCTGAGCTTATTGCCATGC[C/T]AGATAAGCAAGAAGTTTCATTTCTTCCTCTCAAGC Y 2 1 2 1 201000 f 74 goat snp33595-scaffold394-2955482 5 45527801 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378955 Affx-122976419 AX-123249314 5 44762412 ATTCAAAGGGTTGAGAACCAGGCTCAACTTCTTGA[C/T]GCAATGAGCTGCAAAGTTAGATGCTACGGGCATGG Y 2 1 2 1 101000 f 74 goat snp33597-scaffold394-3041485 5 45614000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782683 Affx-122931568 AX-385269755 5 44825490 ACCTTTTCTTCCTCTGTCCCTATTCCTCTGTAAAT[A/G]ACTTAGTCATTCAGTACATAAAATAGAAGTGTGGC R 2 1 2 1 101000 f 74 goat snp33599-scaffold394-3104563 5 45677695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376057 Affx-122978927 AX-123246416 5 44877392 TAGTCCAGGTCTGGAAGCTGTCCTGTCAACCAGAT[A/G]CCCTTCCCTTTTACTTGGGGCTGAGAGGAGTAACA R 2 1 2 1 101000 f 74 goat snp33600-scaffold394-3156465 5 45728717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768894 Affx-122971310 AX-385256071 5 44970654 TCATTCGATATGGAATGTAGAGGTCCAAAGGAAAT[A/C]AAAGAAAAATCTGGCTACAAATTTCTAAGGGGAAA M 2 1 2 1 101000 r 74 goat snp33602-scaffold394-3249727 5 45822437 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446150 Affx-122925759 AX-123316486 5 45001392 GTTTAGAATGACCCCTCCGGGTGCAGTGCTGAAGC[G/T]CTATCTACTGTCCCTGATAGCACACAAGAAGGTCA K 2 1 2 1 202000 r 74 goat snp33603-scaffold394-3280465 5 45853538 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407411 Affx-122955240 AX-123277762 5 45075711 TGAAGGGAAAGACAGGGTCAGCTGAAATGAAATAC[A/G]TATGACAGCAGACATGGGGTCTGTGTAGGCACTTC R 2 1 2 1 101000 f 74 goat snp33605-scaffold394-3354784 5 45928224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415924 Affx-122948451 AX-123286273 5 45119866 CTGAACAGAGGAAAGCAAAATGCCTTAGAACAACA[C/T]ACAGCTGGGTTTGAATTCTAGCTCTAGCACTGACT Y 2 1 2 1 201000 f 74 goat snp33606-scaffold394-3398939 5 45972715 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391950 Affx-122966538 AX-123262307 5 45149442 GTCCGCTGACATTTGAGAAGCACTATAAATACTAG[G/T]GCAGACCAGGAGGATTAACTATGTATTATTTAAGC K 2 1 2 1 101000 f 74 goat snp33607-scaffold394-3428515 5 46001991 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441996 Affx-122928429 AX-123312333 5 45181614 GTATAAGGAAGAGGTGCAAAGGAACTATGTTTCTG[C/T]GGCCTACCTGACTGCTTTGGTTTGGCTGCACATAG Y 2 1 2 1 101000 f 74 goat snp33608-scaffold394-3460687 5 46033951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782407 Affx-122978800 AX-385269483 5 45210327 AATGTAACTTGTGAATAGTTCTCCTTGATACCCTT[A/C]TCTTGGCTAGGGTTTCTCTTGTTCCCAGTATTCAG M 2 1 2 1 101000 r 74 goat snp33609-scaffold394-3489400 5 46062745 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401475 Affx-122958960 AX-123271828 5 45240411 GAAAGCAGATAGTAAGGAATGGGCAACCCTCTTCT[A/C]GGGGCCCAGACTGTCCGGGAGCTTCTGTTGGGAGA M 2 1 2 1 101000 f 74 goat snp33610-scaffold394-3519484 5 46093126 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413181 Affx-122950334 AX-123283530 5 45280687 ATGGCTGCAAAGCACCTAGCGCAGTTCTTGGTGCG[C/T]GGAATAGTGTACAGCTGTTAGCGTCCTTTTCTTTC Y 2 1 2 1 101000 r 74 goat snp33611-scaffold394-3559760 5 46133409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770663 Affx-122925819 AX-385257827 5 45313955 TTTTGATACCAGAAGGTTTATCCCAATTTTGTTTA[C/T]AATATCAAAATGTATAGAAATAGTGCAAATATGGA Y 2 1 2 1 201000 r 74 goat snp33612-scaffold394-3593028 5 46166793 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406847 Affx-122955664 AX-123277198 5 45371352 CCATATCCCTGTACTTTCCTAGAACTCTTGCCTTA[C/T]GCATCCCTCAGGTCAACTGTTTCTTCTGGGTCAGC Y 2 1 2 1 101000 f 74 goat snp33613-scaffold394-3650425 5 46224170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390880 Affx-122967119 AX-123261237 5 45400683 CAGGCCAGGTCAGTGCTTTGTTCCTCCCTTAGAGC[A/G]TGCTTCGTGGTCTTCCTCGTTTCAGATTTATTTAG R 2 1 2 1 101000 r 74 goat snp33614-scaffold394-3679756 5 46253414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419650 Affx-122945958 AX-123289998 5 45417741 TGAACTCCAGTGGTTCCAAGAAAACCAGATTTTCT[C/T]TGAAATAAGGAAGCAGTTCTTTCTTCTCCCTGACC Y 2 1 2 1 102000 r 74 goat snp23603-scaffold2380-11002 5 46270016 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773185 Affx-122942325 AX-385260329 5 45463145 TATAGTACTTATTATCTGATGATAAATTTTTAAAA[C/T]GATGTCAAGTAAAAGTTCTTAGTGTATTTCACTCT Y 2 1 2 1 303000 f 74 goat snp23604-scaffold2380-56406 5 46315138 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795601 Affx-122925267 AX-385282556 5 45497851 CCAATTTGGTCAGCATTGATTGATCAAAACTGCCA[C/T]AAGTATATTATTCCATTGCCTTGATTATGGGTGAT Y 2 1 2 1 101000 f 74 goat snp23605-scaffold2380-91112 5 46349698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421261 Affx-122944752 AX-123291608 5 45542756 ATAAAACAAACTTTTGGAAAATGTGAGAACATAAT[A/G]CATGCTTAGCAGATAGCATTGTCGTGGGTGATCTG R 2 1 2 1 201000 f 74 goat snp23606-scaffold2380-136017 5 46394816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272309 Affx-1111833467 AX-519546047 5 45579589 TACTCTCTACTTGCAGCGTGAGCACTTCTCATTGC[A/G]GTGGCTTTCTTGCTTTGGAGCACGGGGTCCAGGCA R 2 1 2 1 101000 f 74 goat 5_45579589_AF-PAKI 5 45579589 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392770 Affx-122965992 AX-123263127 5 45592371 TTCTTCCCCAGGACACAGGGTAGCACCTTCTAGTC[A/G]TCTCCTATACTAGAGAACCATGGATTTGTTATTGT R 2 1 2 1 201000 r 74 goat snp23607-scaffold2380-185632 5 46443967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426645 Affx-122939942 AX-123296991 5 45629797 AAACTCTGCAGGGCTCTGTTACTCTCCATCTCTTG[A/C]TTCTCTTTTCCTCGGTCATGGCTGGCTTGGTTCAA M 2 1 2 1 201000 r 74 goat snp23608-scaffold2380-223058 5 46480641 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407648 Affx-122954612 AX-123277999 5 45691618 CAGACGTGTGAGCTCAAACAACTGCACAGGTCCTG[C/T]CACCAGCTGGTGGGGGCTCTGAGAAAACTGCGAAA Y 2 1 2 1 103000 f 74 goat snp19621-scaffold1980-874042 5 46542940 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788876 Affx-122944130 AX-385275891 5 45756176 GTGGGGGCTACCTTTAGTAGATGGTAAATATCCTG[C/T]CACTAAAATCATGAAGCAGGAGGAGTTAGATGTGA Y 2 1 2 1 101000 f 74 goat snp19619-scaffold1980-809484 5 46605890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397928 Affx-122961930 AX-123268283 5 45788547 CAATCTTGTGGGGGTCATATCTACAAACCAAGTAT[A/G]CATGCATGCTCAGTTGGTCCCACTCTTTGTGACCC R 2 1 2 1 101000 f 74 goat snp19618-scaffold1980-777113 5 46638441 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765140 Affx-122920537 AX-385252695 5 45835960 AGTTCACATCCTTCACTGACACCTTGAACAATTCC[C/T]GAATGTCTCATGAGCCCACCAGACACAACATACCC Y 2 1 2 1 101000 f 74 goat snp19617-scaffold1980-729700 5 46685638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432154 Affx-122936422 AX-123302495 5 45886340 TACACGGCCCAGGTGTCCTTACGCTTCTTTGCGTT[A/G]TTGCACCACCTTTGGTCCTTGGCAGTCCAGATATA R 2 1 2 1 201000 r 74 goat snp19616-scaffold1980-679320 5 46736169 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393990 Affx-122965033 AX-123264345 5 45931524 CAGGAAGCACATTGGAAATCAAATAATCACTACAG[C/T]GGGAGACAACGGTTCTACTTTGATAAGCCTTAGCC Y 2 1 2 1 101000 r 74 goat snp19615-scaffold1980-634136 5 46781804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441886 Affx-122928622 AX-123312223 5 45998955 CTATGATTTCAATATGCTCGGAAGAAAAAAAAGAC[C/T]CTGGAGCACTATTATCTATATTTATTCAGGACAAA Y 2 1 2 1 101000 r 74 goat snp19613-scaffold1980-566705 5 46849539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403223 Affx-122957900 AX-123273576 5 46048408 TTATACCCAGCTGTTGATTCCTTGTTAATCACAGG[A/G]AGCTGTGAAAGTCTTTGACATTAGGCTTTATAAAT R 2 1 2 1 101000 f 74 goat snp19612-scaffold1980-517252 5 46899680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444396 Affx-122926591 AX-123314733 5 46078027 GCTGATACAAGCTAAGGATTTTCTCCCCAGAAAAA[C/T]GTTCATATGCGTTTATACCAAAAAGTATCTGATTT Y 2 1 2 1 101000 r 74 goat snp19611-scaffold1980-487633 5 46928805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388288 Affx-122969395 AX-123258646 5 46111848 CATAGGAAGAGTCTGATTTTTCTTCTGACTGAAAG[C/T]AGAAGCCATTGTTGGCTTCTGAACAGAGGAGAGAC Y 2 1 2 1 101000 f 74 goat snp19610-scaffold1980-453812 5 46962628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796229 Affx-122953836 AX-385283179 5 46169954 GATGGGAAACAGATCTGTCTAGGTGCCATCAAGGC[A/G]TGGAACTGGCCATTAGTAACTCTGCTGAGGTCTCG R 2 1 2 1 101000 f 74 goat snp19609-scaffold1980-395706 5 47020770 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447525 Affx-122924061 AX-123317861 5 46206541 AAGCAACTTTTTTTTTCATAAAGATTGAACTGATC[A/G]TTGAAAGTAATTATTTTAAGCATCAAAGCAATGAA R 2 1 2 1 101000 r 74 goat snp19608-scaffold1980-359119 5 47057388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412946 Affx-122951463 AX-123283295 5 46270333 GGTTCCATGCAGGGTGGCTGAATAAGCTGACCTCC[C/T]CTTGCAGAAGGGGATACACCTCCCTTCTTCTTCAC Y 2 1 2 1 201000 r 74 goat snp19607-scaffold1980-295327 5 47121478 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453587 Affx-122920149 AX-123323920 5 46300801 CATTTTCCTCCTCTGCCCAGGGTTCTGCACCCAAC[A/G]CCCCTCTCCTGTGGTCTCCCCACCTCTCCCTCAAC R 2 1 2 1 101000 f 74 goat snp19606-scaffold1980-264859 5 47150792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421950 Affx-122943819 AX-123292297 5 46340397 CCAGGAGGGCTGCTACTGCTGCTGCCTTTGCTGTT[A/G]CTATTACTACTACACCACCCCCACCAGCCTAGTGC R 2 1 2 1 101000 r 74 goat snp19605-scaffold1980-225263 5 47190291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415138 Affx-122949419 AX-123285487 5 46387959 TTAGTGGGGAGTTCCAAAGACAGAAGTTTGATGCC[A/G]TCTCCTAAGGCCAGCTCTACGAAAGCAATGAAAAT R 2 1 2 1 101000 f 74 goat snp19604-scaffold1980-177701 5 47237701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432352 Affx-122936274 AX-123302693 5 46423464 TGCCAGAAGAGTGATTTTTGTAAGTATGAAAATGT[C/T]GGTCTGTCTGCTGCTTTATCTGCCCGTCGGTAACC Y 2 1 2 1 201000 f 74 goat snp19603-scaffold1980-142196 5 47273188 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787266 Affx-122931949 AX-385274291 5 46469180 TTTACAGAGCTTGAAACCAACTGGGTGAGATCATC[A/G]TGGTGCTATGATGAAACCATGAATATCTGCCTTTT R 2 1 2 1 101000 r 74 goat snp19602-scaffold1980-96480 5 47318992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443473 Affx-122927821 AX-123313810 5 46529205 TAAAATAAATCTTTACACTATACCAAAGGTAAGGA[C/T]AGACTTCCCTGTCTAGCCCTAGATGTCACCTGATC Y 2 1 2 1 201000 f 74 goat snp19601-scaffold1980-36455 5 47379202 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452881 Affx-122920698 AX-123323214 5 46570953 CAAACTTATATCACCAACTTAAGATGAACTCCTCA[C/T]CTTCTCATTTTACTTACTTCCTTACATTTTAACAT Y 2 1 2 1 101000 f 74 goat snp37629-scaffold463-5194 5 47420878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397318 Affx-122962310 AX-123267673 5 46630429 GCCTTAGAAAATATTGTTTTTATCCTACAGAGTAC[A/G]TGACTAAGAGGAAAACAGGAAATGTGACTTACTCT R 2 1 2 1 101000 r 74 goat snp37630-scaffold463-64670 5 47480416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796490 Affx-122938262 AX-385283440 5 46669554 TTCTCTTCTATGTGGGCAAGGCTGCCTTTTCCTTA[A/C]CTTGAAATATTCTTTCCCTGGATTCTGAAGGTCGG M 2 1 2 1 101000 r 74 goat snp37631-scaffold463-103795 5 47519427 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767017 Affx-122941766 AX-385254310 5 46748532 TCTACTGAGTCGTAAACTCCTAGAAAGAAGGGATG[C/T]GTCTCAGACCTCTTTGACACTTTCAAGGTATTTTG Y 2 1 2 1 101000 f 74 goat snp37632-scaffold463-182773 5 47598533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440158 Affx-122931139 AX-123310495 5 46778067 TTTGTATTCTCTAAGTGAACATCACTATACATCAG[A/G]TCTTTTATTTCTGACTACCTTGCTGAGCTACTTTT R 2 1 2 1 101000 f 74 goat snp37633-scaffold463-212308 5 47628433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783576 Affx-122928100 AX-385270637 5 46857252 GGGTCTCTAGCTTCCAAGATATCTTAATGTTATTA[C/T]TTTTTAGTGCTTTGTTGCTTGGCTCCTATTACTTT Y 2 1 2 1 102000 f 74 goat snp37635-scaffold463-291493 5 47708141 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802300 Affx-122955656 AX-385289204 5 46915432 GTCTCCACAGAGACACATTTCACTCCTTGATTATA[C/T]ACTTATATCTAAGTTCAAAGCTATTCAACCAGTTC Y 2 1 2 1 101000 r 74 goat snp37636-scaffold463-349673 5 47768456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777172 Affx-122928735 AX-385264295 5 46962938 AGGAGTAAATGTACCTCCCACAACATCTAAAGTCT[A/G]TTAAATGATTTCAAATTCTAGCCTTTAATAGTAAA R 2 1 2 1 202000 r 74 goat snp37637-scaffold463-397179 5 47814995 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783869 Affx-122923143 AX-385270925 5 46995229 TGTTGTTTTGCAAGGGAAGGTTAACACATTATATA[A/C]AACAGTCTGTATTTCCCTCAGGTAATAAGAGAGCT M 2 1 2 1 202000 f 74 goat snp37638-scaffold463-429470 5 47847658 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381210 Affx-122974525 AX-123251568 5 47043951 TCCACTTACACGTTTATGTAACCACTAAACCCGAA[C/T]TGATTTTCCCATATTCCAGCTGTAGCAAATGAATC Y 2 1 2 1 101000 f 74 goat snp37639-scaffold463-478192 5 47892665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801388 Affx-122951972 AX-385288298 5 47097551 AAATTACATATGGCTTAAAATTACATAATGACTTA[C/T]ACTACGATTTTATGAGACAGTTCTGGTCTAAAACC Y 2 1 2 1 101000 r 74 goat snp37640-scaffold463-531792 5 47946437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397552 Affx-122962023 AX-123267907 5 47142528 ATTGAAATTAAAGGAGGACAGGGAAGAAGACTAAC[A/G]TGGACTGAGAAGCTGCATGATCTGGGCATTGGGCT R 2 1 2 1 101000 f 74 goat snp37641-scaffold463-576769 5 47991270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784960 Affx-122944162 AX-385272007 5 47174471 TAAATTATTGAGAATTCTTCTCGGCACAGTTTCCA[G/T]AACCAACTCCTATTTACCCTTTTGGCTTCATCCAT K 2 1 2 1 201000 r 74 goat snp37642-scaffold463-608712 5 48023143 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406016 Affx-122955499 AX-123276368 5 47203683 GTTTCCATATGCTCTGCAAGGATGACGCTAATGAA[G/T]CATGAGTCTCCAGTCACTAAGAGCACAGAGCTAAT K 2 1 2 1 101000 f 74 goat snp37643-scaffold463-637924 5 48051210 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799042 Affx-122975519 AX-385285972 5 47242140 AAAGAAATCTATTTTGAGTTGAGCATAGGTTATAT[A/G]CAAGTCCCTGAAAATGAGGCTAACTAAAGTCAGAT R 2 1 2 1 101000 r 74 goat snp37644-scaffold463-676381 5 48087851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784996 Affx-122931662 AX-385272043 5 47312516 ATCCCATGTAGAGGTTTAAGCTTGTCTGCTATTGT[C/T]CTGGGAAACAAATTGGGAGCTCAGATTTGTACCAT Y 2 1 2 1 101000 r 74 goat snp37645-scaffold463-746757 5 48158561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390732 Affx-122967918 AX-123261089 5 47356861 TCTTCTTAAAACGGCAGCCCAGAAGTCATGCATAC[A/G]GCTACCACTTTTATTGTCAAGAAATGATCATGTGG R 2 1 2 1 101000 f 74 goat snp37646-scaffold463-791102 5 48203182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401970 Affx-122958783 AX-123272323 5 47401453 TTGTGATTTCCCATGGTGACAATCCTGCCCCCTAG[C/T]GAACATTTTGGGAATTTATAGGGGCTTTTCCCACT Y 2 1 2 1 202000 f 74 goat snp37647-scaffold463-835694 5 48247802 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449884 Affx-122922348 AX-123320219 5 47453883 CATATGATTTCATTAATAACATGGTCAGAGTACAC[G/T]CTCTTTGATGCCACAAAGGCTGCCAGCAGTTCAGT K 2 1 2 1 201000 f 74 goat snp37648-scaffold463-888124 5 48300116 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438478 Affx-122931231 AX-123308816 5 47491421 GCTCCTTCAACTCAACACCCAAGAAGGAGCCCACA[C/T]ACCTATGAGCCCATGGAGACGTCGTCATAACCATT Y 2 1 2 1 201000 r 74 goat snp37649-scaffold463-925662 5 48337663 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379322 Affx-122976186 AX-123249681 5 47505647 TGACACTCCATTGCTGAAATGTGGTTGCTGTTTGA[C/T]GCTCCATCCTCCTCTCTTCAAATTGTTCTTTCCCA Y 2 1 2 1 101000 f 74 goat snp40996-scaffold528-920051 5 48351949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274885 Affx-1111834554 AX-519548469 5 47539594 AGCAGCTGCAGGGTGACCAAGGCGCTGGGCTAGC[A/G]GGGGTGTGAATGCCAGAGGCAGCATCCAGTTCTCA R 2 1 2 1 303000 f 74 goat GoatD01.041397 5 47539594 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769933 Affx-122948476 AX-385257102 5 47549263 GAGAAAAAGCATTTACTCTCAGGGTTCTGAGATTA[C/T]AAGATGCCAGGATTTGCCCCTAATTATAGCTATGT Y 2 1 2 1 101000 r 74 goat snp40995-scaffold528-876435 5 48395365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423575 Affx-122942406 AX-123293921 5 47593428 GGCCTTTCATCAACCCGAGAGCCCCACCTACAGGA[G/T]GCCCTCAGAAAACACAACCTTCACCAACCCTTGGA K 2 1 2 1 201000 r 74 goat snp40994-scaffold528-832270 5 48439270 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791339 Affx-122920068 AX-385278332 5 47625500 AACAGATGTGGTTTGGGTATGCTGATATCCTCTGA[C/T]GAATACGCAATCTAGTCGCTAAGTGAATAATGGAT Y 2 1 2 1 101000 f 74 goat snp40993-scaffold528-800198 5 48471357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797310 Affx-122965704 AX-385284249 5 47688975 TAAAGTCCCTGTTTGGTTAACAAGGAAGTGAGTCA[C/T]GGATGTTGAGTATGTAACAAAGTCTATTTAGGGCA Y 2 1 2 1 101000 f 74 goat snp40992-scaffold528-736723 5 48535097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445573 Affx-122925137 AX-123315910 5 47812218 TAAAATTAGTGGGAATTGTAAGCAGTGAATAGATC[A/G]TTGTTAGAATGATTTCATCATTAAACATTGTTTAA R 2 1 2 1 101000 f 74 goat snp40990-scaffold528-613480 5 48658225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411630 Affx-122951582 AX-123281980 5 47860695 TCGACTTTGGTTTCTGGATGTATTAGACTTCGTGT[A/G]CTGGTTGAGATGTGTGTCTTGTAACACAAGATGAG R 2 1 2 1 101000 f 74 goat snp40989-scaffold528-565003 5 48707175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391689 Affx-122967584 AX-123262046 5 47910283 CTGAAATCAATCACAGAGCCCAACAAATAGAATAT[A/G]CCAGATTTAACAGGTAAGAGAGATGGATCTACATT R 2 1 2 1 101000 f 74 goat snp40988-scaffold528-515415 5 48757112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416773 Affx-122948173 AX-123287121 5 47948161 TGGAATCTCAACTAGAAATTTAGGCTGAAGTCCTC[A/G]CCACCCTGACTCCCTGATGCCCTTGCATTATGCTG R 2 1 2 1 101000 f 74 goat snp40987-scaffold528-477537 5 48795152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794717 Affx-122959341 AX-385281677 5 48003230 CAAGATAGAACTCTATGGCATCCTGGTATATTGAC[G/T]ATTTTAAGCTGAATGAATTTGAGAAATGACATGTG K 2 1 2 1 101000 f 74 goat snp40986-scaffold528-422468 5 48849266 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406721 Affx-122955754 AX-123277072 5 48074357 TTCCCATAGAGACTTGGAACTGTGGGGCAGCTTAG[A/C]AGTGAAGACTCTTCCCACAGAGCTCCCTAATGGAG M 2 1 2 1 101000 f 74 goat snp40985-scaffold528-351341 5 48920433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406693 Affx-122955777 AX-123277045 5 48114456 TATAAGCAAACTTTGCTAAAAAGTCATCATTTTCT[A/G]TAGAGAAAAATGGCATACTCATCCTATATGTCTTT R 2 1 2 1 101000 r 74 goat snp40984-scaffold528-311242 5 48960515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272310 Affx-1111833468 AX-519546048 5 48143879 TTTCTAGAATTCTTGTCTAAATGAAAACACACAAC[A/G]TGTACTTTTAGGGGTCTGACTTCTTTCCCTTGGCA R 2 1 2 1 201000 f 74 goat 5_48143879_AF-PAKI 5 48143879 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423999 Affx-122942108 AX-123294345 5 48164379 GATAATATAAAATTATTTTCTGTGGCTTACAGTGT[A/G]TCATAGTTGAGACATATAGTAGGTTAAGGCAACAA R 2 1 2 1 101000 r 74 goat snp40983-scaffold528-261319 5 49010512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408803 Affx-122954043 AX-123279154 5 48233650 GTAGCGCAGAGAAGTACTTGGCCAGGCTCTCTTCA[C/T]GCCTGTGCTTAAGCTTCCTTCAGCCTGGGATGCCC Y 2 1 2 1 101000 f 74 goat snp40981-scaffold528-192048 5 49080627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791709 Affx-122946650 AX-385278700 5 48287044 TGTTATTGCTAGAAAGAAGCATGCTTACTTGTAGA[C/T]AGTAGTTTTGCTTTTCTTGGGAGACCATATTCTGG Y 2 1 2 1 101000 r 74 goat snp40980-scaffold528-138654 5 49134334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377115 Affx-122978249 AX-123247474 5 48316861 CCCAACGCAGAGTAGGCTGTGCACCACACTTCCCT[A/G]TTCATTTGACTTTGAATAGGCCCTGGGGAATTTTC R 2 1 2 1 101000 f 74 goat snp40979-scaffold528-108837 5 49163933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453592 Affx-122920146 AX-123323925 5 48368776 AAGGGGTGGCAGTCTGGATTTTGTGCTATCTGCAG[C/T]GCTGACTGGCAGCATGTACTTCCAAGAATTGGTTT Y 2 1 2 1 101000 r 74 goat snp40978-scaffold528-56922 5 49216126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437610 Affx-122931853 AX-123307948 5 48399805 CATATGTCTTGTTTGGATAAATATCTATTCAAGTT[A/C]TTTACCTATTTTTTTGCTGTTGTTAGTTGACAGAG M 2 1 2 1 101000 r 74 goat snp40977-scaffold528-25893 5 49247024 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802780 Affx-122961741 AX-385289679 5 48450529 GGTAATAGGTATTGGATAGGAGAATGTATTTATTG[C/T]TATGTGATGATTGTAAGATTTAGCAAATAAATTTT Y 2 1 2 1 101000 f 74 goat snp21784-scaffold2136-24732 5 49298007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785833 Affx-122956074 AX-385272870 5 48478347 GTGTCTGGCAAGTAGAGTGATGTACTCTGAGTCCC[A/G]TTTGTATGGCTCTCCACCCTGGGTGGAATTTCTGT R 2 1 2 1 102000 f 74 goat snp52256-scaffold775-15664 5 49338783 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769008 Affx-122958904 AX-385256183 5 48513588 ATTTTTATCACTTCTAGTTGTACAGCCACTTTGGT[A/G]TTGCTCCTATCTCCTAAAGATGAACTTAATTGTAT R 2 1 2 1 101000 f 74 goat snp52257-scaffold775-50905 5 49374538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780895 Affx-122962032 AX-385267982 5 48563987 TGGAGAATAATAAGAAATTGTTAGGAAGAATTTTA[C/T]GAAGAATTGGGAGAAATATAAGCATGCTTAGAAAC Y 2 1 2 1 101000 r 74 goat snp52258-scaffold775-101304 5 49425424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397867 Affx-122962447 AX-123268222 5 48625533 AACAGTTACATAAGATGACAGATTTGAAAGTGTAT[A/G]CCCCTTCTGACTTCATAAATCATAGCAATTGTGTT R 2 1 2 1 201000 f 74 goat snp52259-scaffold775-162850 5 49487836 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380169 Affx-122975522 AX-123250527 5 48659907 GACTGCCATATCAGATATTTCCATGAAAAGGTTCA[C/T]CTAGGCTTTTGTATTTATTCTTTTGCATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp52260-scaffold775-197224 5 49522432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430130 Affx-122937400 AX-123300471 5 48691864 CTGCTTCTCGAGTAAACCAGATAAAAACACTGTCT[A/G]CTTTTCAGGGTTCTCAGGGTTAAATGAGGCATTGA R 2 1 2 1 101000 f 74 goat snp52261-scaffold775-229181 5 49555257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396623 Affx-122962878 AX-123266978 5 48722006 GCAGCATCAATTGATCTTTTTGTCTCCTTTCCCTT[G/T]TCTTTGCAGTTGCATTGGTTTTTTAAGCTCCCAAC K 2 1 2 1 201000 r 74 goat snp52262-scaffold775-259323 5 49585534 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378647 Affx-122977099 AX-123249006 5 48755696 CAGGTAATGAATTTACTCTCTATGGCAAGCAAAAA[C/T]GCACAGTTATACCATAATCAAAAAGAAAAATACTA Y 2 1 2 1 101000 f 74 goat snp52263-scaffold775-293013 5 49622046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433707 Affx-122934532 AX-123304048 5 48807829 CCGAGCGGGCAGTGGACTCTGGATTTCTAGGTGCC[A/G]TGTCTATTGAAGTCACATGCAGAGTTAAGGTGATT R 2 1 2 1 101000 r 74 goat snp52264-scaffold775-345146 5 49673636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440265 Affx-122930648 AX-123310602 5 48838489 CAAATATTGGGGATCAAAAAAGCATTCTGGAGGCC[A/G]TAAGTACTAAACTGGGTTTTGAAGGATAAGCTAGT R 2 1 2 1 101000 f 74 goat snp52265-scaffold775-375806 5 49704333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445283 Affx-122925459 AX-123315620 5 48913650 CAGCCGCACGACTCCTTCGCACAGCTAACTTTGTG[C/T]ACCCTGCAGCACTCAGAAAAGGAGTTCCATCCACA Y 2 1 2 1 101000 r 74 goat snp52267-scaffold775-450967 5 49781939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790106 Affx-122972845 AX-385277112 5 48958767 TTTATAAAGTAGCTCATAATTGGCCTGTGTTATTA[C/T]GCTTTTTGTGTCAAAGCATAGTGCAGTATGGAGAA Y 2 1 2 1 202000 r 74 goat snp52268-scaffold775-496084 5 49828239 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767499 Affx-122927773 AX-385254762 5 49012919 CCCTGGCTCTGAGTCCTCTGTGGACCAGGATACAA[C/T]ATAATTTCATGTACTGATCTCAAAATAAAGTTATT Y 2 1 2 1 102000 f 74 goat snp52269-scaffold775-550236 5 49882342 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423938 Affx-122942255 AX-123294284 5 49043332 GGTCTATCCTGACCAATCCATTAAAACTGAGACTA[C/T]AGGCCACCTCCCCTTACACACAGACACTCTTTCCC Y 2 1 2 1 101000 f 74 goat snp52270-scaffold775-580649 5 49912734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426969 Affx-122940400 AX-123297314 5 49072420 ACGTGCTGAAATAAAAAATATGCATAAATGGCGGT[A/G]TGTGACTAGAGGGTGAAAAATATTAAACAGGTAAG R 2 1 2 1 101000 f 74 goat snp52271-scaffold775-609737 5 49941846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404868 Affx-122956484 AX-123275220 5 49103471 GGGCTGTCACCCTCATGTTTGCCAGGTCTCTGTGC[A/G]TCATTGGAAACTTACATGTGCTTTATTACTACCCA R 2 1 2 1 201000 r 74 goat snp52272-scaffold775-640788 5 49970653 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785614 Affx-122925179 AX-385272657 5 49168219 TTTCAGTCTATATGTACTACATATCTAATACTTTT[A/C]TTAGTTTACTCATGAAGTCACACAGATCTGGTTGC M 2 1 2 1 101000 r 74 goat snp52273-scaffold775-705536 5 50033132 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376252 Affx-122978773 AX-123246611 5 49199090 TAGGATTGTAGTAGGCCTAAATGAGCTGATATTTG[C/T]AAAGCATTTGCAATATTGCCTGTTAAATGATGGGG Y 2 1 2 1 101000 f 74 goat snp52274-scaffold775-736407 5 50064330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380210 Affx-122975487 AX-123250568 5 49231307 GTACCATGGTCTATCAGGTAGGCTGACTGCAGAAA[C/T]AGTCAGGCCCCTGGAGAAGCAGCGGCTTGGTCTCT Y 2 1 2 1 102000 f 74 goat snp52275-scaffold775-768624 5 50097442 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380495 Affx-122975706 AX-123250853 5 49290230 AGGGGGTATATGACAGATGGTGCTGTTCACTGATT[A/G]CTGATGCCTTTGGTCCTTCGTTTTCATGGGTCGAC R 2 1 2 1 201000 r 74 goat snp52276-scaffold775-827547 5 50156516 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406733 Affx-122955747 AX-123277084 5 49336493 GTGGGCAGTTTCTGGAACCTCCTCTCTGGTCCCAC[A/G]TATACAGCATCTCACACATCTGCCTTCTCAGTTGG R 2 1 2 1 101000 r 74 goat snp52277-scaffold775-873810 5 50202487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775687 Affx-122939940 AX-385262818 5 49368774 ACAGCCTCATTTGGTCTCTGTCTACCTGGTCGCTA[C/T]AGAAACAAAACTTCATCTAAGACGCCAAGGCAAAA Y 2 1 2 1 101000 f 74 goat snp19147-scaffold1924-344913 5 50234529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799601 Affx-122926490 AX-385286531 5 49427276 ATAATTTGCCTTCTTAAGTGGCAGATATGCTTACC[A/G]TATGATTATGCAGTTAGCTTAATGCTTATTTTGAA R 2 1 2 1 101000 f 74 goat snp19146-scaffold1924-286411 5 50292984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782136 Affx-122931408 AX-385269214 5 49473167 TTTCCCTCCATTCTTTGGGATTATTTTTATGAGCT[A/G]TTAAAGAATATATGCAGATTTCTTCATTATGGAAT R 2 1 2 1 101000 f 74 goat snp19145-scaffold1924-240520 5 50340995 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405026 Affx-122956370 AX-123275378 5 49545588 GAGAGATCTAAATAAAAATTTCTTGGTTTATTTCC[A/G]TAGCACCAACTTTAGGAACACACTGGGACTAGACT R 2 1 2 1 101000 r 74 goat snp19143-scaffold1924-168099 5 50413523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441660 Affx-122929191 AX-123311997 5 49589380 TACACATGGTATGTATTCTATCTTGTTGATTTCTC[C/T]TCTTCTCCTTGGTATAGTTTTCCTCTGGTTACTCT Y 2 1 2 1 101000 r 74 goat snp19142-scaffold1924-124307 5 50456475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428307 Affx-122939376 AX-123298650 5 49650102 TCTTTTGATTAATCTTGCCTTTTGATTTGCATTCC[G/T]AACAAAACCTAACTGAACTACTTACAGTCTTTAAG K 2 1 2 1 201000 r 74 goat snp19141-scaffold1924-63585 5 50517258 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440372 Affx-122929641 AX-123310709 5 49697697 TTCAGATCACATTACAAATTGTCTGTCTTGATGCC[A/G]TTAGAATATGTAGCACCATACAGTTTAGGCCTTTT R 2 1 2 1 101000 r 74 goat snp19140-scaffold1924-15990 5 50565287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790160 Affx-122921394 AX-385277165 5 49729184 AATTGAATGGTCAGTCAGCCATACCCTTAGCATTC[A/G]CTTATGAATACACTTTGTTATTTGTGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp49857-scaffold712-15398 5 50596853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404982 Affx-122956402 AX-123275334 5 49776617 TCCCTTGCATTTGTTATTACTACTTGAGGGAACTT[A/G]ATTTCTATAGGTTTCCCATCAGTTGTCTAGCTAGA R 2 1 2 1 101000 f 74 goat snp49858-scaffold712-62831 5 50645481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791211 Affx-122974706 AX-385278205 5 49809705 CTCTTGAGTAAATACTACAAAAGTAATAAACAAGT[A/G]CATGACTCTGGTAGAGCAAATATGGAAATGGAAGA R 2 1 2 1 101000 r 74 goat snp49859-scaffold712-95919 5 50678387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449707 Affx-122922538 AX-123320042 5 49857130 TTAAACTCTTTATATATAATGCCTCAATATGTCTC[A/G]TTAAGCAACCCTTTGAAATGGTACCATTATCATTT R 2 1 2 1 101000 f 74 goat snp49860-scaffold712-143344 5 50725244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782232 Affx-122920618 AX-385269310 5 49895169 CCAGGGGATCTGGTTAATTCTTTGCTGTTAAGACA[C/T]GTAACAACTTTGAAGCCAAAATTGTATGTGAATTC Y 2 1 2 1 101000 f 74 goat snp49861-scaffold712-181383 5 50763472 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378529 Affx-122976628 AX-123248888 5 49928457 ATTCGCCGCCAACCCCAGGTTCCAGTCTCTCGCTC[G/T]CTCTCTCTTGATTACTTCTGCTCACTATTCAGCAT K 2 1 2 1 201000 r 74 goat snp49862-scaffold712-214671 5 50796539 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397815 Affx-122962487 AX-123268170 5 49964487 TTTTCAAAGGGCCCAAGAAACACAGATGGGGACGC[A/G]TTTGTGCCAAATGAGAGGAGAAGTGGAAATCAGCC R 2 1 2 1 101000 r 74 goat snp49863-scaffold712-250701 5 50832627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786993 Affx-122935495 AX-385274021 5 49999189 TGTGAACTGCAAATGCTCTGTAATAGGCTAAATTC[A/G]CATGGCAGCATCTGGAGATAATCTAAATGTTCCCC R 2 1 2 1 101000 r 74 goat snp49864-scaffold712-285403 5 50867311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425041 Affx-122941865 AX-123295387 5 50028383 ACAAATATGTGCCTTAACTTTTTTTTCTCCTGGTC[A/G]GAGGTATCTGAATCATGTAAGAAGCATTGGAGCAA R 2 1 2 1 201000 r 74 goat snp49865-scaffold712-314597 5 50896544 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402534 Affx-122958473 AX-123272887 5 50076785 ATTCCAGGAATGGAGACCTGGTTGGTGGGGGGAAC[A/G]TTTATTTGGGGTTTGTTAGGGCTGTAGCCCAGGAG R 2 1 2 1 303000 f 74 goat snp49866-scaffold712-362999 5 50944970 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785746 Affx-122952030 AX-385272786 5 50110615 GTTGGGATCATGATCTACTTGCTCCCTGTGGTTCA[C/T]ATCCTCCTAACTTCTATCCTAGGAAACTGAAGGAT Y 2 1 2 1 101000 f 74 goat snp49867-scaffold712-396829 5 50979552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395576 Affx-122963842 AX-123265931 5 50163484 TAACCACTGGACCACCAGGGAAGTTCCATAAATCT[A/G]TAAACTTTTGATAATTTAAAAATGGGAAATCCAGA R 2 1 2 1 303000 r 74 goat snp49868-scaffold712-449698 5 51033747 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800227 Affx-122923402 AX-385287150 5 50220605 TTCCTCAAAGAACCCTAATTACAAGCTCTTGTAGC[A/G]CTTTGCACTTCTTCATAACACTTATTAAAATTGTA R 2 1 2 1 101000 f 74 goat snp49869-scaffold712-506819 5 51091546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413336 Affx-122950167 AX-123283685 5 50261215 TCTGTACTCTTAAAGCTTCATGGATTTTACTGTTG[C/T]AGCAAATGACTTCCCAGCTCATTTCTCAGGCCAAT Y 2 1 2 1 101000 f 74 goat snp49870-scaffold712-547429 5 51132571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421912 Affx-122943845 AX-123292259 5 50290313 ACTAGGTAGTACGGAATATAATTTCTCAAAGAGCT[A/G]CTGGCATCTAAAAACTAAAACAAAGCCTTATCTAG R 2 1 2 1 101000 f 74 goat snp49871-scaffold712-576527 5 51161724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450129 Affx-122922760 AX-123320464 5 50320369 GAGGCCATGCCTTTCAGGTAAAGGGAAGAAAAAGC[A/G]CAAATACCTGCCATGGAAGCTCCTCTGGGAATATC R 2 1 2 1 101000 f 74 goat snp49872-scaffold712-606583 5 51192076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442550 Affx-122928524 AX-123312887 5 50360869 GGGCCACAGAGTGTTCAAGCAATTTCCCCAGTGTC[A/G]CATAATAGTAAGTGGCAGAGATAGGATTTTAACCT R 2 1 2 1 201000 r 74 goat snp49873-scaffold712-647083 5 51232688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778918 Affx-122952308 AX-385266025 5 50425282 TTTTCTGTACAAAATTCACATTCTAAGGTCTTGTA[C/T]GTTTCTTGGAGGAGGAATAAACATTTCTGTTCTGT Y 2 1 2 1 201000 f 74 goat snp49874-scaffold712-711496 5 51297438 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442246 Affx-122928289 AX-123312583 5 50464016 TTTAGCATTTGTCTCTATGCTCCCTTGAATTTTTG[A/C]TTTTGTTGCATCATTTCCCATTTTCTTATCTCTAC M 2 1 2 1 201000 r 74 goat snp49875-scaffold712-750230 5 51336065 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399591 Affx-122961105 AX-123269946 5 50507162 GTGCATAGGGTCGCAAAGAGTTGAACATGACTGAG[C/T]GGCTAACACTACCTAACCTATTATGGGCCCCTCCA Y 2 1 2 1 101000 r 74 goat snp49876-scaffold712-793376 5 51380235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443356 Affx-122927421 AX-123313693 5 50536419 TTCTTGCAGAAGAAAGAGCATATTGGTTGTTGTAT[A/C]GAACCAGCATAGTTCATTTCACAACAACACTGATA M 2 1 2 1 101000 f 74 goat snp49877-scaffold712-822633 5 51408009 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428483 Affx-122938784 AX-123298826 5 50568855 AACCTATCCCTATGACCCCTAGACCTTTGCTTCTG[C/T]CTTTCCAATACAAATATAGGACAAATTCCCTTAAA Y 2 1 2 1 201000 r 74 goat snp49878-scaffold712-855069 5 51434931 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406420 Affx-122955209 AX-123276772 5 50604117 GTTCATATAACCGAAGTTAAAACCTTTGGTATGCT[A/G]AGAATGTTTAACTAGTTATATCTCTTCTGTCAACA R 2 1 2 1 101000 r 74 goat snp49879-scaffold712-890331 5 51470824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435683 Affx-122933328 AX-123306022 5 50649383 CACCTGGTGAAATTTGCCCAAGGTAATGTAATTAG[C/T]AAGTGATGAAGATGGGAATCTTTCTGGTTTGATTC Y 2 1 2 1 101000 r 74 goat snp49880-scaffold712-935597 5 51516158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428263 Affx-122939409 AX-123298606 5 50685544 ATGTATATGAGAGAGATATCTCATTAAAAACAGTT[A/G]CAGAATAAGGTACTAAACTTCAGCTTGGATATTTC R 2 1 2 1 101000 f 74 goat snp49881-scaffold712-971758 5 51551473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796787 Affx-122961404 AX-385283730 5 50718989 GATGATTTTACTTCTAAATGATATCCATTTTACTA[C/T]ATGTTGTTAATGTGGTCATATAGGGTGCAGCATCT Y 2 1 2 1 101000 r 74 goat snp49882-scaffold712-1005203 5 51584761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423332 Affx-122943171 AX-123293678 5 50771276 GAGAACTGGAAACCTGTTTTTCTCTTGTCCACAGT[A/G]TTAAAACTGAAGCATCAAGAGAGTATTAGCAGCAA R 2 1 2 1 201000 r 74 goat snp49883-scaffold712-1057490 5 51636882 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796235 Affx-122919992 AX-385283185 5 50826724 CAAGTCTTTTTTGACTCTCATTGCCTCATATTGTG[C/T]ATTGAAAGAGTTGTTTCAGTCACCAAAGTTTCAAC Y 2 1 2 1 101000 f 74 goat snp49884-scaffold712-1112938 5 51692033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272193 Affx-1111833469 AX-519545945 5 50827811 TCAGCCAAACCTAAGTATGTATCCATTCTCCTTTA[A/G]CATTTCTCTGGGGGGATGCCAATGGAGGAAGTGGT R 2 1 2 1 202000 r 74 goat 5_50827811_AF-PAKI 5 50827811 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468273747 Affx-1111833786 AX-519547358 5 50831377 GCTGCAG[A/G]CCGTCTGTAATCTTTCTTGTCTTTTGTTGACTCTG R 2 1 2 1 101000 r 74 goat GoatD01.004867 5 50831377 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376822 Affx-122977924 AX-123247181 5 50868128 CTTCAACTTCATTATAATCATCATAATGTTGTTTT[A/C]TTCTTTTTCTCCCTTATTTGCTTTTATTGTCTTCT M 2 1 2 1 201000 r 74 goat snp49885-scaffold712-1154342 5 51733783 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771516 Affx-122920877 AX-385258674 5 50916964 TGATTAATGTATTCAATCAAGTCTAGTTTACCTAA[C/T]GACAAAATAGTACCTTGAGAAGGGAAATTCAATCA Y 2 1 2 1 101000 r 74 goat snp49886-scaffold712-1203178 5 51783067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377592 Affx-122978312 AX-123247951 5 50953646 CAGGCAAGAATCTTGGTTTATTTAGAGGTGTGACC[A/G]GGGTTAAGTCACATATTCAGTCCAGATGGTCTCAA R 2 1 2 1 101000 f 74 goat snp49887-scaffold712-1239860 5 51820024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381846 Affx-122974193 AX-123252204 5 50986943 ACAAAGGAAAAAACTTTTTTGCCTCTTTAGGTGCT[A/G]TCTTGTCAATGCAACTTAAATTGATGTTTCAAGTT R 2 1 2 1 201000 r 74 goat snp49888-scaffold712-1273157 5 51853604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410978 Affx-122952014 AX-123281328 5 51032082 TGGACAGAGGAGCCTGGAGCGCTGCTGTCCATAGG[A/G]TCATACAGAGTTGGACAGACTGAAGCTGCTGCTAC R 2 1 2 1 103000 r 74 goat snp48003-scaffold678-407628 5 -1 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438863 Affx-122930756 AX-123309200 5 51083875 TATAAAAAATGCTTAAAACCAGAGAAAAGGGAAAA[C/T]AAACAAAAGCAACAAATACAAACTGATTTGAGACG Y 2 1 2 1 103000 r 74 goat snp48002-scaffold678-355835 5 51949884 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428308 Affx-122939375 AX-123298651 5 51139189 CCTCCAGTCAAAACTCAACCAACCAGAAACAGCAG[C/T]GACACTCTTTCTTCTCAGATCCTCCAGGGAAAAAG Y 2 1 2 1 201000 f 74 goat snp48001-scaffold678-300521 5 52005547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381629 Affx-122974768 AX-123251987 5 51188657 AACCACTACAGCACAAACACTGAAAACTGCATTGC[A/G]TTTAAGACATTTGTATTATTTTTTTTAAAAAACTC R 2 1 2 1 103000 f 74 goat snp48000-scaffold678-251053 5 52055441 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771999 Affx-122939203 AX-385259155 5 51219795 ACGTGCGGAGCTTATTTAGTCTGATGCAGCCTGTG[C/T]AATATTGTCTTTAAAGTGCTAGAAGAATAAATGAC Y 2 1 2 1 101000 f 74 goat snp47999-scaffold678-219915 5 52086913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779127 Affx-122973726 AX-385266232 5 51263421 ACCGTTCTCATCACAGACTGCTCATGCTTTTCTAG[C/T]GTAGCCTCCTTGCTTACTTACTAGCTAAGTAATCA Y 2 1 2 1 101000 f 74 goat snp47998-scaffold678-176289 5 52131130 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765130 Affx-122932183 AX-385252687 5 51308185 TTTTGTGAGCAATTCAACTTGCCAATTAGTCCTAT[C/T]GCTCTGTTGAGGGAACAAAGATATTAAACAAAGCC Y 2 1 2 1 101000 f 74 goat snp47997-scaffold678-131525 5 52175504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768700 Affx-122919521 AX-385255878 5 51355684 GAACTGCATCATCCTGCTGTGGAAAAGGCTTCAGA[C/T]GGTATTGTTGATGGTACTATACATTTGCAAAGAAC Y 2 1 2 1 101000 f 74 goat snp47996-scaffold678-84026 5 52223469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401503 Affx-122958938 AX-123271856 5 51389370 AATCTCAGGCTTTAATTTCTTCCCCAAACAGACAG[C/T]TCACATAGTATTAGTTTGCATTGAATATTTTAGAA Y 2 1 2 1 201000 r 74 goat snp47995-scaffold678-50340 5 52257669 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790631 Affx-122947905 AX-385277633 5 51432080 TGGAAAATAAAAAATCAGGTCATCAATTATGTTGA[C/T]TGCTGCTGACCATGTAAGATGAAGACTGAGAATAG Y 2 1 2 1 101000 r 74 goat snp47994-scaffold678-7630 5 52301179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397257 Affx-122962356 AX-123267612 5 51455046 GCAAACAAGAGCAGCAACATGGTGTGTATGTGTGT[A/G]TCCATGTAAGACAGAAGAAGCGAGAGATGTATCTC R 2 1 2 1 303000 r 74 goat snp33477-scaffold392-5265732 5 52324968 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419291 Affx-122946240 AX-123289639 5 51556604 CCCTCGCATAGAAAAGCGTATCTTACCTTGATGTA[C/T]GCATGTTCATAAGAAATTAGATGAGGACCTCATGA Y 2 1 2 1 101000 f 74 goat snp33475-scaffold392-5164174 5 52428329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439326 Affx-122930305 AX-123309663 5 51592569 TCAAAAAAAGACATTTTTATTATAATAATATAAAC[A/G]CAATAATATATTTCAACAAAGAGAATGAGAGAATG R 2 1 2 1 103000 r 74 goat snp33474-scaffold392-5128209 5 52464317 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452087 Affx-122920859 AX-123322420 5 51649001 GTCCATGGGAGGAGGTGAGTTTAGGATATGTCATC[A/G]TCAACTCTCCTCTTCCACTGCTGTACTTTTTGAAT R 2 1 2 1 201000 r 74 goat snp33473-scaffold392-5071777 5 52520809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438554 Affx-122931177 AX-123308892 5 51720916 GGAAGGCTATTGTGACATTTCAGAGTAGTCATGCA[C/T]ATTTTCCTGGAGAGAAAATTAATTATAGAACAAAA Y 2 1 2 1 101000 f 74 goat snp33472-scaffold392-4999862 5 52594228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778996 Affx-122944229 AX-385266103 5 51763007 TGCTCTGAAGTGTTATACATTCAAACTTCAGTACC[A/G]TCATATTATAAATCATGAAAAAGCTTAATAGCTTT R 2 1 2 1 201000 r 74 goat snp33471-scaffold392-4957771 5 52636750 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783345 Affx-122922248 AX-385270409 5 51792002 ATTCTATGTCTTTGACTTAATCCATTTAATCCCTA[C/T]GACTATCCACAGAAATGGATACCTTGTTACATTTC Y 2 1 2 1 101000 r 74 goat snp33470-scaffold392-4928776 5 52665961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278221 Affx-1111836310 AX-519551709 5 51819972 GGGAACTTACCTACAAGGTTGTCTTGGGTGCTGCA[A/C]CTAGATCTCAGCACCTCAGGCAAGAATCTTGGTTT M 2 1 2 1 101000 f 74 goat Random2.2K-556 5 51819972 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439279 Affx-122930979 AX-123309616 5 51822229 TGCAAAGATAAGAATCTAGGCCATTAATTTCTAGA[C/T]AGTGTCAAGTCATGATCATGGTAATATCAAGATGA Y 2 1 2 1 101000 r 74 goat snp33469-scaffold392-4898549 5 52696385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788253 Affx-122950782 AX-385275272 5 51856479 GTGGGTGGATGGGTGAAAAAGATAATGAATATCAA[C/T]TATAACTTATACATTAGCAGCAAGTAGTAACTATA Y 2 1 2 1 101000 f 74 goat snp33468-scaffold392-4864299 5 52731092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385424 Affx-122971329 AX-123255782 5 51897844 AGAGAGTGGTGGGGCATACAAACCCAGCCAGCAGC[A/G]CACAACACTTGAAGCACAGAGGGTGAGTCCAGGTA R 2 1 2 1 101000 r 74 goat snp33467-scaffold392-4822934 5 52770249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399654 Affx-122960519 AX-123270009 5 51933002 GGTTTCAAAAGCCAAAGATAATTATTAGACAAATG[A/G]TCTCAGCAGAAAACCAAGAGGATTGATATCAGTCT R 2 1 2 1 101000 r 74 goat snp33466-scaffold392-4787776 5 52805588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377429 Affx-122977544 AX-123247788 5 52026715 TCCATCTCTTCTGGAAACAGCAGAATGCTTAAATG[C/T]GGTTGAGGACAAGGAGTTGTGGGGGAGTCATGAGT Y 2 1 2 1 101000 f 74 goat snp33464-scaffold392-4694063 5 52900929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410208 Affx-122952570 AX-123280558 5 52055996 ACTTCAGATTATAATTTACAATAGTGCAGGGAACA[G/T]AGTTTATGGATTGTTTATATTCCTTATTGTACTTG K 2 1 2 1 101000 f 74 goat snp33463-scaffold392-4664782 5 52930625 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451598 Affx-122921641 AX-123321931 5 52115250 TTCTGTAATTGCAAACAACTTTCTCCTAGTCCTGC[A/G]CTAGTGCTTTTTGTCATTTGACTTGACAGGATACC R 2 1 2 1 101000 f 74 goat snp33462-scaffold392-4605528 5 52989788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788231 Affx-122962737 AX-385275250 5 52147166 TTTGAAGTGATACTCAGTAGCCTTACATTGTTCTC[A/G]TTAGAATGTGCTCTCCATTCCCTAGGAATGTTTTA R 2 1 2 1 101000 r 74 goat snp33461-scaffold392-4573612 5 53022156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453456 Affx-122919857 AX-123323789 5 52192210 TATTAATTTTCTTTAAATTATTTTTATTGGAGTGT[A/G]CTTGATACTGTGTATGAAGAGTCCTTTGGAGAGAT R 2 1 2 1 103000 r 74 goat snp33460-scaffold392-4528568 5 53067116 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392141 Affx-122966327 AX-123262498 5 52231658 TAATACAGATTTTTCTCTCATCTTTGACTTCTCAA[C/T]TAGGAGGGCAGGTGATTTACATCTCCATAATAAAG Y 2 1 2 1 101000 r 74 goat snp33459-scaffold392-4489120 5 53107032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415061 Affx-122949478 AX-123285410 5 52262827 TATTCTAGGTTTTGCCTACATGAAGAACTCTGAGT[A/G]TTATTATAGATTCATAGTTGGGACCCTAGATGCAA R 2 1 2 1 101000 r 74 goat snp33458-scaffold392-4457951 5 53138546 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771755 Affx-122928712 AX-385258912 5 52306500 CTCCACTCACTCTAGTCTGAATTGCTATACCGCTT[A/G]ATCTGGGCTCCTATGCTAGCAGTTTCTTTCTACCT R 2 1 2 1 101000 f 74 goat snp33457-scaffold392-4414278 5 53181920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442215 Affx-122928782 AX-123312552 5 52353717 GCCTGGCACATGATAACAGTTCTGTTAACACTGCT[A/G]CTACATCAAATCTGTGGCAGTTGGACATCTTATCA R 2 1 2 1 201000 r 74 goat snp33456-scaffold392-4367061 5 53229370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385774 Affx-122971057 AX-123256132 5 52391129 CAGTTCAAGAAATACAGTACTCTCTTACATTTATG[C/T]GTTCAAATAACAGTTCATGACAAGCTCACAGATAT Y 2 1 2 1 101000 r 74 goat snp33455-scaffold392-4329649 5 53267677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438448 Affx-122931254 AX-123308786 5 52481858 ATCTGCTCTTACTTTTCTGTTTGTGAAACATAACA[A/G]ATTATAAAAATAGTTTATTTCTCTAGATGAAAAAA R 2 1 2 1 103000 f 74 goat snp33453-scaffold392-4238920 5 53359124 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438157 Affx-122931462 AX-123308495 5 52523994 GAGCAGATCCAGAATTTTCCTAGTCCCTATTCTCC[A/G]TGGCTGTCACTTTGCCTATAGGAAGATTGTTTCCC R 2 1 2 1 101000 r 74 goat snp33452-scaffold392-4196784 5 53401975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793815 Affx-122969614 AX-385280786 5 52564714 ACATTATGAGGGATTTAACACAGAGAGCTAAGTGA[C/T]GCAGGAAATAGCTCTGAGTAAGTCAAGATGTGGAT Y 2 1 2 1 101000 r 74 goat snp33451-scaffold392-4156064 5 53444475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395722 Affx-122963711 AX-123266077 5 52607761 AGAATATACCATGAACCTCATACGGTCTTATATGC[A/G]GATTTCTTTATTATCCTTCCTAAATGTTAATAAGA R 2 1 2 1 101000 f 74 goat snp33450-scaffold392-4113017 5 53487539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772384 Affx-122960656 AX-385259537 5 52638457 TGTTTGAGCTCTGTTGTTTATAAGAGAAAATGTAC[A/G]TGTTGAAATTATTAGCACTGAGGAGTTGGAGAGCA R 2 1 2 1 201000 f 74 goat snp33449-scaffold392-4082321 5 53518099 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431126 Affx-122936589 AX-123301467 5 52694832 AATTAAGATAGGGATAACAGAAAAATAGATTAGCC[A/G]TGACGGGAGTAGGGCCTTCCCTAAAATGTTGCCTG R 2 1 2 1 101000 r 74 goat snp33448-scaffold392-4025946 5 53574455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377247 Affx-122978150 AX-123247606 5 52729496 CAGAATGTGATTATATGCTTTCCTTAAAGAGGCAA[C/T]GTTAGAGTTCATCTCAAAACTCAAGAATCCTTAAG Y 2 1 2 1 101000 f 74 goat snp33447-scaffold392-3991282 5 53610425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390992 Affx-122966905 AX-123261349 5 52759491 AACTACTGGATTTCTCCTCCTTCATCTTGAGTGTA[C/T]GGCTCTCCCTCTTATAATCCAGCCTCATGGATTAT Y 2 1 2 1 201000 r 74 goat snp33446-scaffold392-3961287 5 53640419 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777393 Affx-122936053 AX-385264515 5 52801721 CAATTCTCTGATGCTGGAAGTTTATGGAGCCAGTT[A/G]CTCACACTTCCTATATTCCTGGGTTCTAACTGATA R 2 1 2 1 101000 f 74 goat snp33445-scaffold392-3919057 5 53683169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792436 Affx-122971722 AX-385279417 5 52839121 GAAGGTGACATAGTTAAAGTGCTTAACACAGTAGA[C/T]CTTATATGAAGGTTTTGGCATATTGCTATTAATCT Y 2 1 2 1 101000 f 74 goat snp33444-scaffold392-3881657 5 53720080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448536 Affx-122923437 AX-123318872 5 52885543 TTACTAACGATAGTAAAGGGCAAGGGCCTGAAAGC[G/T]ACAGTCCTTGCTCTTAAAGGGTATTCACTCACTGA K 2 1 2 1 101000 f 74 goat snp33443-scaffold392-3835235 5 53766954 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452153 Affx-122921660 AX-123322486 5 53020797 AAGGACAAGAGACATCACGAAGGTGAGAGATGCCA[C/T]AATGGACCATGTACCTGGGCAGCCGGAACTGGGCA Y 2 1 2 1 101000 f 74 goat snp33440-scaffold392-3699981 5 53902359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384019 Affx-122972900 AX-123254377 5 53123829 CCAACCTGAAATGGCTACTAGGAGAGGAAAAGAAA[C/T]GCCCACCTCTTACTACTTCCAAGTTTCCTTTTTAT Y 2 1 2 1 101000 f 74 goat snp33438-scaffold392-3596949 5 54006489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788659 Affx-122941712 AX-385275675 5 53176940 TTTATAGATCTACTAGCTGACTTTTCATGGATGTA[G/T]CGCTTTTTGTGTGTGTACCTTCTGTAGTATGGAAA K 2 1 2 1 101000 r 74 goat snp33437-scaffold392-3543838 5 54060917 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412568 Affx-122951317 AX-123282917 5 53207613 GCATCTTTAATACCACCCAGAAGGGGGCTTGGGGC[A/G]TTTCATTCCAGTCTTACTAGGATGAAAGTCTAGGT R 2 1 2 1 201000 r 74 goat snp33436-scaffold392-3513165 5 54092095 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797307 Affx-122949829 AX-385284246 5 53244372 CACCTTCTTTAAAATAGTACGTAAAATTCTCATAC[A/G]TTAATCCTCCACCCATTTTACACTGTGCCTTAGTG R 2 1 2 1 101000 r 74 goat snp33435-scaffold392-3476406 5 54128894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780203 Affx-122957440 AX-385267299 5 53284639 AACCATAAGTATTCTGATATGTCCCATTGGGATTT[C/T]TCCATGGCTGTACTGCTTTGTCAACTATCTCAGGA Y 2 1 2 1 101000 f 74 goat snp33434-scaffold392-3436139 5 54169099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381834 Affx-122974258 AX-123252192 5 53325910 GTCTGATTATAACACAAATATTTTCAGAAGGAACA[C/T]GGGAAATGTCAAAAATTGTCAGTTCAGTGAATATC Y 2 1 2 1 101000 r 74 goat snp33433-scaffold392-3394868 5 54209889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464366363 Affx-1110450022 AX-515839861 5 53350378 CATAAAAATCATTACTTACAATGTATTATAGACCT[A/C]AATATAAGAGCTAAAACTCCAAAATCTTGAATAAA M 2 1 2 1 101000 f 74 goat 5_53350378_AF-PAKI 5 53350378 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375361 Affx-122979235 AX-123245720 5 53357331 TTCCAGGGAAAAGAGGGCACAGAAGGGTCAGTAGC[C/T]AGCCTGATCCTACTTGGATCATAAAGTCAGATTTG Y 2 1 2 1 101000 r 74 goat snp33432-scaffold392-3363447 5 54241273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418246 Affx-122947031 AX-123288594 5 53412325 TCCTGATGAATTTTACACTTTCCAGGTAGGAAGTT[A/C]TAGACCCTATAAGAAAGCAGCATGGTGAATATTGG M 2 1 2 1 101000 f 74 goat snp33431-scaffold392-3308453 5 54296567 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443974 Affx-122926997 AX-123314311 5 53505262 GAGATCTTGAATATCATGTTAGGCTGCATTTTGAT[C/T]TGTATTCAGTGAAGAAATATGGAAGACTTTGAGCA Y 2 1 2 1 101000 f 74 goat snp33429-scaffold392-3215516 5 54392409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779234 Affx-122921347 AX-385266338 5 53535846 TAGTATCTAACTTGGACTTAATGGTTGTCATTTCA[C/T]GAGGTCTTTTATTATTTCAGAGACCTACTCACACC Y 2 1 2 1 101000 r 74 goat snp33428-scaffold392-3184932 5 54423278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778917 Affx-122978949 AX-385266024 5 53565750 TGCCACCCTTTGATCGGAGGTTTGCCTAGTTGGGT[A/G]TTAACTCTCCTGCCTGAGAATCTCCTGAGCCTCAC R 2 1 2 1 101000 r 74 goat snp33427-scaffold392-3155028 5 54454086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773019 Affx-122937041 AX-385260163 5 53605402 TTTAATTTAATTCAGTATACATTAGAATTGAGTAC[A/G]TATTTCATAGAGCACATCACATAAACGTGCAGGGC R 2 1 2 1 101000 r 74 goat snp33426-scaffold392-3115376 5 54495501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802218 Affx-122971962 AX-385289122 5 53661012 TATGCCATGAAGACTATGTAAAATCATAAAAGGAA[C/T]GCTTACCTTTCTTAGGCGAAGAAAATAAAGGTATT Y 2 1 2 1 201000 f 74 goat snp33425-scaffold392-3059766 5 54551973 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774568 Affx-122959092 AX-385261702 5 53738631 CATAATCTTTAGCTGCTGTGTGCTTTAGAATCACT[A/G]CTTATCCTTCTCCATATAGGTTTATAATTTATAAA R 2 1 2 1 101000 f 74 goat snp33423-scaffold392-2982147 5 54631025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389921 Affx-122968105 AX-123260278 5 53796113 AAGATATAGTATGCCAATATCTGGGATGCACTTAT[A/G]CTGAAAAATGATTTGTTATTTATCTGTGATCCAGA R 2 1 2 1 101000 f 74 goat snp33422-scaffold392-2924665 5 54690592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770036 Affx-122947314 AX-385257203 5 53855350 TATAGCAGATAGCATGTAGATATCTGCTATGAAAA[C/T]ATAGTAGATAGAAAACAAAGATATCATAGAAAGTA Y 2 1 2 1 201000 r 74 goat snp33421-scaffold392-2865428 5 54748929 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426823 Affx-122940516 AX-123297168 5 53897044 TGAGAATTGCATTGAAACAAAACACCTATAGCAGA[C/T]GACTTAAAAACTGCTTATTTTTCCCTCTTGTTTTG Y 2 1 2 1 201000 f 74 goat snp33420-scaffold392-2823734 5 54790547 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404794 Affx-122956668 AX-123275146 5 53929960 AAAGACATGAGAGCAGCAAAAATCATAGATCCAGG[A/C]CATATTTCAAAGTAGGTACTTTCTCTGGGGCAATT M 2 1 2 1 201000 f 74 goat snp33419-scaffold392-2790818 5 54823932 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792122 Affx-122923560 AX-385279107 5 54003436 GGTCCTTTAGGGAAAAGATCTGTGTTCCAAACAAG[C/T]TACTTTAGAAGATGTGAACTGATAGGCAATTATCA Y 2 1 2 1 101000 f 74 goat snp33418-scaffold392-2717342 5 54898557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450428 Affx-122922053 AX-123320762 5 54058400 GGTCTCTCCTTCCTGCCTCCTTCCCTCCACCATGC[A/G]CACAGCTGCCAAAGAATGGCCACACTGCTCCAGGT R 2 1 2 1 101000 r 74 goat snp33417-scaffold392-2662378 5 54952435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438334 Affx-122931341 AX-123308672 5 54124775 ATTAGAGAAATTCTTTCCTGACATTGGCACTGTCT[A/G]CTCTCTTCTGGGATCTTGCAATAGGCAGATGCCTT R 2 1 2 1 201000 r 74 goat snp33416-scaffold392-2596003 5 55017378 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389200 Affx-122969070 AX-123259558 5 54168470 GCACCTCTCACTCACTCACGCAAAACTCAGTTCTT[G/T]ATTGTCCAGCCACCTCTCTCACCTTGGCCTTTGGC K 2 1 2 1 101000 f 74 goat snp33415-scaffold392-2552308 5 55061052 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451236 Affx-122921951 AX-123321570 5 54219765 CAGTGTGCACAGAGTTTGGTAAAAGTGCATTTTCT[A/G]TGGAGTTTGGGAACAGTGGGTTAGCCATCTGGAAT R 2 1 2 1 101000 f 74 goat snp33414-scaffold392-2501013 5 55112544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770504 Affx-122969719 AX-385257669 5 54285459 GGATAAAAGATATATGGATTGGATAGGAGAAAAGC[G/T]ATAAGCAGGAAGTTATCTGAGAGCAACCAGAGGCG K 2 1 2 1 101000 r 74 goat snp33413-scaffold392-2435319 5 55175909 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441785 Affx-122929093 AX-123312122 5 54315214 ACTCATAGAAACGTTGAGACCTCCACGCTTCTTCT[A/C]GCCCTCTAGTCGACTGTGAGTCCTCCACCTCAGCG M 2 1 2 1 101000 f 74 goat snp33412-scaffold392-2405564 5 55204930 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380112 Affx-122975525 AX-123250470 5 54365665 GTGGTAGCCCCCGAGGGATTCCTAGGGAATTCCTC[A/G]CCTCCCCTCCTTTCCTAGGCTGGTTGGGACTGTCA R 2 1 2 1 202000 r 74 goat snp33411-scaffold392-2355113 5 55254685 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802329 Affx-122927274 AX-385289233 5 54396487 AGGTTTTTGATTCTTCCTTCAAGGAGATAAGGCAG[A/G]GTAGGTATGAATTAGTCGAAAAGGGAAGGGCAGCA R 2 1 2 1 101000 f 74 goat snp33410-scaffold392-2324291 5 55285642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794261 Affx-122940682 AX-385281226 5 54471648 ACCAGAAAAGACAATGAAGTGGAATGTTTTCTACA[A/G]AGGGTGAAAGGATACAGCAGGAGGAAAATACTAAA R 2 1 2 1 101000 r 74 goat snp33408-scaffold392-2249130 5 55360153 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278223 Affx-1111836311 AX-519551711 5 54489139 TCATCAATTTTCAATCTCTTCCAAGAAGCCCACCC[A/C]CCCCAACCCCGCCCCTGGATTCTAGGACTCAGAGG M 2 1 2 1 102000 f 74 goat Random2.2K-558 5 54489139 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776384 Affx-122974965 AX-385263511 5 54531739 CAGAACTGCAAGTATTGCATAAAAAAAGCTATACC[A/G]TAAGACACTCACAGAAAAGTGGCTACAAAAGAACT R 2 1 2 1 101000 r 74 goat snp33407-scaffold392-2189039 5 55419984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446710 Affx-122924729 AX-123317046 5 54622275 ATAGGTCTCTTAGATGATGTGGATGGAATAGAGGG[C/T]CAACATCTAGGAAAAGTACAAGGGGTCAGTCAGAA Y 2 1 2 1 101000 f 74 goat snp33406-scaffold392-2098503 5 55510831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384107 Affx-122972834 AX-123254465 5 54668482 TCCTTAAAATGCTCTTCCACGGTGAAAAATCCCAC[A/G]ATAAGAGATGAACACACTGGGATTGTGAACGACTT R 2 1 2 1 201000 f 74 goat snp33405-scaffold392-2052296 5 55557157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407013 Affx-122955022 AX-123277364 5 54699797 AGCACCACCCTGGTGATGCACATGAAGGTCTACGA[C/T]GAGAGCGTCCAGCTGGGTGAGGCGGGGCGAGGGCA Y 2 1 2 1 101000 f 74 goat snp33404-scaffold392-2020981 5 55588174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382369 Affx-122973861 AX-123252727 5 54732418 CAGACAAATTGAAGTGAAAGCCAGAAGTCACTAGA[A/G]GCCATGCAGGAGGTTTAGGATGGTGAACTGGGTGG R 2 1 2 1 101000 f 74 goat snp33403-scaffold392-1988360 5 55620836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278381 Affx-1111836312 AX-519551866 5 54751706 CTATCAGTCGTTTAAGGCTCCTTTCTCCTCCCAGC[A/G]TTTATTAGGTTGAACATATATAATTGCCAATATTT R 2 1 2 1 201000 r 74 goat Random2.2K-559 5 54751706 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392374 Affx-122966237 AX-123262731 5 54772939 AAGTACAATTTGGCATATACTAAGCTGTCAACTCA[C/T]GGTTGCTGGTGTTATTGCATTTGTCCCTGTGGGAT Y 2 1 2 1 101000 r 74 goat snp33402-scaffold392-1947839 5 55661765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379506 Affx-122976459 AX-123249864 5 54830114 ATCTACTTGATAATATAAGTTCTTAAAGTCAAAAC[A/G]TAGAAAATTTTTTAAAAACCTTTGAGTCGTGACCA R 2 1 2 1 201000 f 74 goat snp33401-scaffold392-1890664 5 55718968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278227 Affx-1111836313 AX-519551715 5 54839547 TCTAATTCTAGGAGAGTTGTTCCCTTTTTGCTATC[A/C]GTCTCTTGGGGGTAACACCACATATTTCACGGGGC M 2 1 2 1 101000 f 74 goat Random2.2K-560 5 54839547 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406563 Affx-122955102 AX-123276915 5 54906361 TAGAGTTCCTGGATCTCTGGGCTGGAACGATTCCA[C/T]GCTGTCCGAAGACTTTCATGAAATGCCTCATCTTG Y 2 1 2 1 102000 r 74 goat snp33400-scaffold392-1814417 5 55791623 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407047 Affx-122954933 AX-123277398 5 54951173 ATAGGAGGGCATACCAGACAGGTAATTTGCAAAGA[C/T]GCAGTCTTATCAGGGAAATCTCTCCCCAAAACTAC Y 2 1 2 1 101000 f 74 goat snp33399-scaffold392-1769605 5 55837438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415729 Affx-122948509 AX-123286078 5 54986503 TGAGAACAACCACAGGAAGGTCGGAAGAGAGAAGG[A/C]AGAGACAGGAGGCCGGGGTGACTCTCACTCACCTG M 2 1 2 1 103000 f 74 goat snp33398-scaffold392-1734275 5 55874001 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405179 Affx-122956929 AX-123275531 5 55020635 ACAGTGGGCCAGGACGGCCTGAGTAAAAAGTGACC[A/G]CAGCTTCCTATGGCATTACTGTGGATGTCAATAGC R 2 1 2 1 101000 r 74 goat snp33397-scaffold392-1700143 5 55906531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392353 Affx-122966254 AX-123262710 5 55063997 ATAAAATGTTGTTCACAGAATCAAAAATATTTACC[A/G]TGTTAGCATAACACCAACACTGAACATCAATCTAG R 2 1 2 1 202000 f 74 goat snp33396-scaffold392-1656781 5 55950625 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769110 Affx-122958095 AX-385256285 5 55101337 CCTTCAGCTGAGTGAGCATTCTGCAGACTAATAGC[A/G]GTAGGTGTTGGTTCTTTCTCCCTTTCTTGCACTCA R 2 1 2 1 201000 r 74 goat snp33395-scaffold392-1619441 5 55987675 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439270 Affx-122930987 AX-123309607 5 55144877 TTCTTATCTTCATGGAAGTCTGTGTCTGAGACACA[C/T]ACAGTATTAAGTCAAAAATACAGGGTCGCACGTAT Y 2 1 2 1 101000 r 74 goat snp33394-scaffold392-1575901 5 56031873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391159 Affx-122967446 AX-123261516 5 55177356 GTATTTGTTGAATACATGTAGGGATAGGAAGTAAC[A/G]TGAAAATGAGGAGGATCAGATTGCACTGAATCATC R 2 1 2 1 101000 f 74 goat snp33393-scaffold392-1543422 5 56064876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274326 Affx-1111834134 AX-519547922 5 55257378 CTGCAGCCCCTGGGCAGAACCATCTAGAAGCTGGC[A/G]GGATTGATTTTTCTCCACGTCACAGGGCCTCTGCT R 2 1 2 1 101000 r 74 goat GoatD01.020590 5 55257378 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777977 Affx-122959613 AX-385265093 5 55272918 CTTTTCCAATTGTTGCAAAGTGCATCTACAATTTT[A/C]TATTACAGATCCACTTTTAAAAGGTTTTCTCTGAC M 2 1 2 1 201000 f 74 goat snp33392-scaffold392-1447860 5 56160923 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377572 Affx-122977439 AX-123247931 5 55376044 CATACACGTAGGAGTTTTTCACCATCCCACTGCCT[A/G]CCTCCCTTCTAAAGGTAACTACTCGTATGGCAAAA R 2 1 2 1 201000 r 74 goat snp33390-scaffold392-1344734 5 56264175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394242 Affx-122964876 AX-123264597 5 55417202 ACTTCTCTGTACGCTTTCTGCCAAGGGAATGGGGT[A/G]TTTCAACTCTTTCACAAAAAGCACTGGCCTTAGTC R 2 1 2 1 101000 r 74 goat snp33389-scaffold392-1303576 5 56305839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774984 Affx-122944974 AX-385262116 5 55481324 TATAGAAGGGAAGGAATCAGAGTAGAGTTCTGCTG[A/G]ATTAAGTGGACTGGATTGAATTCTCTTTACTCAGA R 2 1 2 1 101000 f 74 goat snp33388-scaffold392-1239454 5 56370462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437240 Affx-122932022 AX-123307578 5 55543199 GGAAAGTTGTCCAGCATGGTGACCACGTGGGAAGG[C/T]AGAGCTGCCCTCTTTGCCCACTCCTGTGAGAGCCA Y 2 1 2 1 101000 r 74 goat snp33387-scaffold392-1177579 5 56432327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764579 Affx-122927968 AX-385252232 5 55593777 TTTACTCCACTTGAAATGATGCATGCAAGACAATA[C/T]AAGTTCTACATAAGTACAAAAATAGGCTAAATTAG Y 2 1 2 1 101000 f 74 goat snp33386-scaffold392-1127001 5 56483224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407097 Affx-122954892 AX-123277448 5 55645453 ACAGTGGTTAATTAGGACCTTGTAGAAACACCTTT[G/T]CCCAGCCCTTCCTTTGAGGGCAGCGTCCCCATCCT K 2 1 2 1 101000 f 74 goat snp33385-scaffold392-1075325 5 56534906 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440880 Affx-122929236 AX-123311217 5 55702705 AAATCAAGTAGCAGGTCCATGATTCAAAATCTTCC[A/G]ATGCATGTGCTCTTACTGTAAGGTATCAAGGAAAA R 2 1 2 1 101000 f 74 goat snp33384-scaffold392-1018073 5 56592282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420302 Affx-122945028 AX-123290649 5 55742738 CCAGGCTTTCTATTTGGAGCTCCTCCTGTTCTCGT[A/G]CTTCTCTGACACTCAGGTTGTTTCCTCTGCTCCAT R 2 1 2 1 201000 f 74 goat snp33383-scaffold392-978040 5 56632275 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401726 Affx-122959525 AX-123272079 5 55807399 TCCTTTCTAAATCTCTAGCCTCTCTCCACGTCCCT[C/T]ATCAAGTATTTTAGGATGTCTTTGGGAAGCCATTA Y 2 1 2 1 201000 r 74 goat snp33382-scaffold392-913379 5 56697273 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417363 Affx-122947716 AX-123287711 5 55836970 AGCACCAGCAAGATGCCCACAAACAGAGGAGCCTG[C/T]CTGAGGCCTGCTTCTTGCCCTATGGGTGGAATCCC Y 2 1 2 1 101000 r 74 goat snp33381-scaffold392-883808 5 56726936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402482 Affx-122958591 AX-123272835 5 55890460 ATGCTGCAACTTAGAATCTTCATGCCACAACTAAA[G/T]ATCGTACATGCCATGGTGAAGATCGAATGCCCTGT K 2 1 2 1 201000 r 74 goat snp33380-scaffold392-830318 5 56781111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769374 Affx-122922580 AX-385256545 5 55921928 GACTGACTTACAGAACTACAAAATTTCTTTAAGGT[A/C]TTTTTTTATCCCCCTCCCTTGGTCCAGCAGGAGGT M 2 1 2 1 201000 f 74 goat snp33379-scaffold392-798850 5 56812171 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402877 Affx-122958227 AX-123273230 5 55972924 GATCTGTTCAGTATGCCGCTACCTCTTCTAGCTGA[C/T]TGCAGTTCTGGCTCAACTCAACCCTCTCTTTAGAC Y 2 1 2 1 101000 r 74 goat snp33378-scaffold392-747854 5 56862768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38434799 Affx-122933872 AX-123305140 5 56004848 TCTTTCTGCATCTTGTCCAGGATTGATGCCGTCTC[A/G]TTGGCTTTTGGATAATTCTTCATCTGCTGCCGGAA R 2 1 2 1 101000 r 74 goat snp33377-scaffold392-715930 5 56894742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410872 Affx-122952602 AX-123281222 5 56048152 CTTCGCCCCCACGTTATTATGCCCCTATGTAATAA[A/C]ATTTGTTAAAGAGCCTGTGGGACTTTGGGATTGCT M 2 1 2 1 101000 r 74 goat snp33376-scaffold392-672626 5 56937794 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436342 Affx-122933074 AX-123306681 5 56100784 TATGCTCCCCAGCAGAAACAACATGCACACACAAA[C/T]GCACAAACGCTATCCCATGCAGAGCTCCCATTAGC Y 2 1 2 1 101000 r 74 goat snp33375-scaffold392-619994 5 56990814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405345 Affx-122956328 AX-123275697 5 56160164 AGGAGAGAAGCCTTTAATATATGATTATTTTAATA[C/T]AACTGGAAAAACATGGGGTAAAAGTTTAAATAACT Y 2 1 2 1 303000 f 74 goat snp33374-scaffold392-560614 5 57050669 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431919 Affx-122935995 AX-123302260 5 56209048 GATGGGTACAAAAATTTATTCTTCTGAAAAAAATT[A/G]AGTAATTATTCTGTAGGAATTCTCTTATGTGTGCA R 2 1 2 1 101000 r 74 goat snp33373-scaffold392-511730 5 57098635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272197 Affx-1111833471 AX-185192336 5 56282062 CCCGGAGTTCACTCAGACTCACGTCCATCGAGTCC[A/G]TGATGCCATCCAGCCATCTCATCCTCGGTCGTCCC R 2 1 2 1 303000 r 74 goat 5_56282062_AF-PAKI 5 56282062 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791303 Affx-122936534 AX-385278296 5 56284662 GGGAACTACCAGAAAGTAAGTATGAAATGTTTGTC[A/G]TTTATGTACCTAAAAGTTTGAAAATGGAAGCATGG R 2 1 2 1 101000 f 74 goat snp33372-scaffold392-436116 5 57175827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274431 Affx-1111834281 AX-519548022 5 56369656 AGCTGATGTACAGGTCCTGCAGCTTCAGCTGTACC[A/G]CCATGGGGGTGTAAATGCTACGCAGACCCTCATCA R 2 1 2 1 101000 f 74 goat GoatD01.028696 5 56369656 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428596 Affx-122938698 AX-123298938 5 56397107 TGGAGGAATAACAGATTAGGAAGACTGAAAAGAGT[A/G]TCCTTCCCTTTAATTAAAATTATTGATTGAATTTA R 2 1 2 1 101000 f 74 goat snp33371-scaffold392-323671 5 57196981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442400 Affx-122927998 AX-123312737 5 56443343 TAAACAAAAAGTCATGAGAGGGACAGGGGAAGAAG[C/T]GAATGAGAAAGTTATTTAGAGAATAAAATACTAGT Y 2 1 2 1 101000 f 74 goat snp33370-scaffold392-277435 5 57243762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793975 Affx-122952187 AX-385280944 5 56479955 CATTAGTAATGCTTAAGATAGGGCCACCAAGGACA[C/T]ATTTGTCTGCTTCACTTAATTAAAAATTAGGTCAG Y 2 1 2 1 101000 f 74 goat snp33369-scaffold392-240823 5 57279647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773952 Affx-122965249 AX-385261091 5 56526988 TTTTGCATTTGGCATTATTTGGGAAGCAATAATGA[A/G]AGGTAGGTTTCTAAGCAGCTAATGTTCTTTTCATC R 2 1 2 1 101000 r 74 goat snp33368-scaffold392-193790 5 57327477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765619 Affx-122971947 AX-385253095 5 56637105 TGAACTCATAGGAAATAGGAAACTCATAGGAACTC[A/G]TAGGAACTCATAGGAAAATAATGGAGTAATAGTAT R 2 1 2 1 201000 f 74 goat snp33366-scaffold392-83673 5 57439720 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432483 Affx-122935594 AX-123302824 5 56673532 GTCACCATCAGATGACATTAAACTGTTCAAGAGGG[C/T]ATCAGCCTTTCATCCAACTTTATCTACCCTGAGCC Y 2 1 2 1 201000 r 74 goat snp33365-scaffold392-47246 5 57476798 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430492 Affx-122937235 AX-123300833 5 56714066 GATTGCTGTCCAACTGTTTACTGACCCCATGGTCT[A/G]TAGCCTGCCAAGCTCCTCTGTCATATAAAGCTATG R 2 1 2 1 103000 f 74 goat snp33364-scaffold392-6712 5 57517992 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276125 Affx-1111835180 AX-519549675 5 56724702 GGAACTGGAGAGAAGCCACAGGAGGTGAGAGGAAT[A/G]GCAGCCTGCAGCACCACCTGTGCAGTGACTGGGCC R 2 1 2 1 202000 r 74 goat ilmnseq_rs660355352 5 56724702 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276155 Affx-1111835267 AX-519549705 5 56724720 TGCCTATCTGTGGTGCCTGGAACTGGAGAGAAGCC[A/G]CAGGAGGTGAGAGGAATGGCAGCCTGCAGCACCAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs669322912 5 56724720 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468275935 Affx-1111835159 AX-519549493 5 56725017 CCTGAAGTGTCAACTACAGAGCCCTCTGGAGCCAC[A/G]GTTACACGGGGAACAACTCCAGAGCTGGTGGAGAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs657580692 5 56725017 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275783 Affx-1111835082 AX-519549348 5 56725037 GCCCTCTGGAGCCACGGTTACACGGGGAACAACTC[A/C]AGAGCTGGTGGAGACCACAGCTGGAGAGGTGTCCA M 2 1 2 1 102000 f 74 goat ilmnseq_rs649139597 5 56725037 C A 1 neutral Goat_IGGC_65K_v2 Illumina 468275966 Affx-1111835096 AX-519549523 5 56725086 ACCACAGCTGGAGAGGTGTCCACTCCTGAGCCTGC[A/G]GGTTCAAATACCAGCCCCTTCATGCCTATAGAAGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs650402792 5 56725086 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275676 Affx-1111835029 AX-519549246 5 56726056 TTCTTGACTTTGCATCTTTAATCCTCTCCTGCCAG[A/G]CTCCCTGAGCCCCCTGCCGGATGATACCTTAGTCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs642561036 5 56726056 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276138 Affx-1111835259 AX-519549688 5 56726131 GGACAATGTCCAGGGTGAGGGAAAAGGAGCCATAG[A/C]GATACAGAACACAATCCGTGGGGGCTTGGCGCTTC M 2 1 2 1 201000 f 74 goat ilmnseq_rs668575715 5 56726131 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468276070 Affx-1111835151 AX-519549623 5 56726452 TTGAGAGTGCTGAGATCCTACAGGCTGTGTCATCC[A/G]GCGAAGGAGACGCATTTGAGCTGACTGTGTCTTGC R 2 1 2 1 201000 r 74 goat ilmnseq_rs657253964 5 56726452 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468276228 Affx-1111835232 AX-519549778 5 56726600 ATGAGATGTCCATGCAGGCTTCCTTGGGTAGCCTG[A/G]GAGAGATGTCAGCTTACGTCAGGGAATCTGGGAAG R 2 1 2 1 101000 r 74 goat ilmnseq_rs666666290 5 56726600 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275803 Affx-1111835093 AX-519549367 5 56726778 TGCCTCAATGTGTCTTTGGCTGATGCCAATAGCCT[A/G]GCGATGGTCAGCACCCAGCTTGTCATGCCTGGTAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs650000190 5 56726778 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276025 Affx-1111835207 AX-519549579 5 56726953 CAAGCAACAAAGCTGTCAGCACCAGCAAGATGCCC[A/C]CAAACAGAGGAGCCTGTCTGAGGCCTGCTTCTTGC M 2 1 2 1 102000 f 74 goat ilmnseq_rs663529192 5 56726953 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275630 Affx-1111835004 AX-519549200 5 56726980 GGGGATCTCACCTGTATATCAGAGATGCAAGCAAC[A/G]AAGCTGTCAGCACCAGCAAGATGCCCACAAACAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs639759960 5 56726980 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275658 Affx-1111835020 AX-519549228 5 56727673 AAGACCCAGGGCAGACGTAGCCACTGGGTTCTACC[A/G]TGTGGCAGCTGGGGAAGGGGGACTGCTGAGCCTTG R 2 1 2 1 202000 f 74 goat ilmnseq_rs641491076 5 56727673 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275824 Affx-1111835028 AX-519549387 5 56727711 TAGAACCCAGTGGCTACGTCTGCCCTGGGTCTTCC[A/G]CTCTTGCCCCATTGGTGAGAGCAAACCTCTCCTCA R 2 1 2 1 102000 r 74 goat ilmnseq_rs642542328 5 56727711 G A 1 neutral Goat_IGGC_65K_v2 Illumina 320801490 Affx-122941689 AX-385288399 5 56734400 AGCATTTTCTTGCTCACTGCTTGGATCTGAAAAGA[C/T]GTCTATAGTATTCCATTCACATTAAATTTTTGAGA Y 2 1 2 1 101000 f 74 goat snp12642-scaffold1482-13523 5 57548700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388847 Affx-122968880 AX-123259205 5 56763163 TGCAGTCATGATGAAGTTCTTACATGATCTTAGAT[A/G]TCAGCAAGCACAGTCAAGAGTGAAATGGATCATTC R 2 1 2 1 101000 r 74 goat snp12643-scaffold1482-42286 5 57578180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419945 Affx-122945214 AX-123290293 5 56804293 GCTCTATTATGGTTAAAAAGTCAATGCAAAAGTTG[A/G]TGAATATCCTCACTATGAAACTCTCTTTCCTCCAT R 2 1 2 1 101000 r 74 goat snp12644-scaffold1482-83416 5 57621275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406104 Affx-122956217 AX-123276456 5 56852820 TTTGAAGTCTGTTCCTGCACTAGAAATAAACTCTA[C/T]AATATCAAGAGGTTTTGTGTGCTTTGTTCCCTTCT Y 2 1 2 1 101000 r 74 goat snp12645-scaffold1482-131943 5 57670431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772087 Affx-122938358 AX-385259242 5 56900888 AATGATTTTGGAAATAAGTAAGGATACTAGTAGTT[G/T]ACAAAAAGTTAAAATTGAGACTTAAGTAAAGGTAC K 2 1 2 1 201000 r 74 goat snp56749-scaffold899-773366 5 57721308 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436235 Affx-122932567 AX-123306574 5 56930475 ACAGAGGGGGAAGAGTTGAGTAATTTCATCAGGGA[C/T]GCTATGGTCTGCAAATTCCAAATTATTGATATAGT Y 2 1 2 1 101000 f 74 goat snp56748-scaffold899-743779 5 57747630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784168 Affx-122947381 AX-385271220 5 56967132 AGGCTTGCCATCGTGCTAAATAAAATAGCTAGAAA[C/T]GACTTTCAGGACATCTCTGTCAATCTAAAGTAATT Y 2 1 2 1 101000 r 74 goat snp56747-scaffold899-707122 5 57784623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274753 Affx-1111834475 AX-519548339 5 56974041 AGGCTGAAGAGGGGGAGAGGGACCTGTCTGATGAC[A/G]GGGAACAAGGGAGCAGC R 2 1 2 1 102000 f 74 goat GoatD01.037422 5 56974041 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777241 Affx-122929211 AX-385264364 5 57027319 CAATAGTCTCATAAAAGATTAGTATTCAAAAGTAT[A/G]CAAGACTCCTACATCTCAACATGAAAGGAAACAAA R 2 1 2 1 101000 r 74 goat snp56746-scaffold899-646935 5 57978902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408341 Affx-122953749 AX-123278692 5 57114873 ATCCACTTCTCTTTTACATGGCAGTGTCTTCTGAT[A/G]CCTACATGACAAAAAATGATGTATGTTTTATAGGA R 2 1 2 1 201000 r 74 goat snp56744-scaffold899-559381 5 57922252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418013 Affx-122946656 AX-123288361 5 57163188 TTGAACCACTCCATTAAAAGTTAAAAAGGAAGGCT[C/T]GTCTCTGAAAACATCCTGCCACAGATATGACTGCA Y 2 1 2 1 103000 r 74 goat snp56743-scaffold899-511066 5 57973866 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762366 Affx-986696897 AX-385250528 5 57207476 TAGTCTATGACTATACCCCCTGAATGTGCCCATCT[C/T]GTCTGAAAAGTCTTCTAAAACTATTGCCCATAAAA Y 2 1 2 1 600010 f 74 goat 5_57207476 5 57207476 Ancestral_priority_1043 ancestry 0.44 neutral IMAGE 10K 10K ancestral 320764562 Affx-986696899 AX-385252218 5 57207477 AGTCTATGACTATACCCCCTGAATGTGCCCATCTT[A/G]TCTGAAAAGTCTTCTAAAACTATTGCCCATAAAAC R 2 1 2 1 600010 r 74 goat 5_57207477 5 57207477 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320764566 Affx-986696901 AX-385252221 5 57207514 CTGAAAAGTCTTCTAAAACTATTGCCCATAAAACT[A/G]TTAATTGGACCTTATTTGTGCTCCCATAACAAGTA R 2 1 2 1 600010 r 74 goat 5_57207514 5 57207514 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320803019 Affx-986696130 AX-385289896 5 57208370 TCTTTTTTGCTTTCGGGTTGAATCTGGTAGTGAGA[C/T]ACTTAAGCTGAAGGTCAAATTTGTATAGATTAATA Y 2 1 2 1 600010 f 74 goat 5_57208370 5 57208370 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 320803595 Affx-986696131 AX-385290388 5 57208386 GTTGAATCTGGTAGTGAGACACTTAAGCTGAAGGT[C/G]AAATTTGTATAGATTAATACACAATTTTCACAAGC S 4 1 2 1 600010 r 74 goat 5_57208386 5 57208386 Ancestral_priority_1043 ancestry 0.594 neutral IMAGE 10K 10K ancestral 320766984 Affx-122970545 AX-385254282 5 57235625 AGTTTTGAGAGAATATGAATAAAGAAATCATTGAC[C/T]GGAACTTTATTTCTTAATGCTACAGATATATGCAT Y 2 1 2 1 101000 f 74 goat snp56741-scaffold899-438629 5 58047688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421921 Affx-122943839 AX-123292268 5 57281230 TATTGCTATCGATAGTGAGGACTCAGTTAATCCCA[C/T]GTAACAGCAATTTTTAAAAACTGTGAGGGCATTAT Y 2 1 2 1 101000 f 74 goat snp56740-scaffold899-393024 5 58092636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782920 Affx-122961989 AX-385269990 5 57353194 GATGACTTTCTTTTCTTGTTCAATTAAAGAAATAT[A/G]CATACTAGAACCAAAATTTAATTGCTATGAAAAGT R 2 1 2 1 201000 f 74 goat snp56739-scaffold899-321060 5 58166544 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375791 Affx-122978575 AX-123246150 5 57405833 ACTTAAGTGAATGTCATTAAATTTTTAGAATTCCA[C/T]GCAATAAATAAAATAGTACATTCTCTGGAGCTACG Y 2 1 2 1 101000 r 74 goat snp56738-scaffold899-268421 5 58220829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397639 Affx-122962617 AX-123267994 5 57479206 CAGACAAGGAAGTGACACTTTCAGGGTGGGAGAAG[C/T]GCAAACCTGGGTCAGGAATCAAGAATGGGAAGTCA Y 2 1 2 1 201000 f 74 goat snp56737-scaffold899-195048 5 58295452 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762374 Affx-986696905 AX-385250536 5 57490972 GTTACAGAATTTTTTCTTCTGGCGGCTATGTCCTA[C/T]GACCGCTATGTTGCCATTTGCAAGCCTTTGCATTA Y 2 1 2 1 600010 f 74 goat 5_57490972 5 57490972 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38452686 Affx-122920312 AX-123323019 5 57516919 GGTCACCAGAGCCAAGGGGCATCCCTTGTGTGAAC[C/T]CTGTGAGATAACTATCTGTGGTGGGGGCACTACTT Y 2 1 2 1 201000 f 74 goat snp56736-scaffold899-157335 5 58333673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440468 Affx-122929384 AX-123310805 5 57578672 TCTAGAAAGTTTTTGATTTCTTCATCAAATCTAAA[C/T]GACAGGCTTCCTGGGTGGAGTGTACTTGGTTGTAG Y 2 1 2 1 103000 r 74 goat snp56735-scaffold899-95582 5 58396042 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793332 Affx-122929739 AX-385280310 5 57609620 CGTCTCTCAGACTATAGATTTCATTTTGCCCAAAG[C/T]ACAGTTCGACTCATGACTCTCAGTTGTGTAATTTT Y 2 1 2 1 101000 f 74 goat snp56734-scaffold899-64634 5 58427642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406762 Affx-122955726 AX-123277113 5 57696597 CAGAGTCTGCACTAATAGAAAAAAATTTTTGGTCT[A/G]TTTTTAAAAGTGCATATAGAGTTTGTAATCAGAAA R 2 1 2 1 303000 r 74 goat snp42457-scaffold562-22244 5 58516468 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403300 Affx-122957842 AX-123273653 5 57736927 CTGAGAGGCCAGACCTTTGTCCATCCAAGATGGTG[C/T]GTTGACCAACTCTGTCATCTCCTTGGGTTTCACAT Y 2 1 2 1 201000 f 74 goat snp42458-scaffold562-62574 5 58556893 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391961 Affx-122966530 AX-123262318 5 57781602 CCCATACCTGGGCCTACTGCAAAAAGCTTGAACAC[A/G]GATTTTGAGAAGATGAAGAGAGGGTGTAGATATTG R 2 1 2 1 101000 f 74 goat snp42459-scaffold562-107249 5 58601838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436049 Affx-122932717 AX-123306388 5 57833464 GTACATGACTACTGGAAAAACTGTAGCCTTAACTA[C/T]ACGGACCTTTGATGGCTTTTTCTGATGTTTAACAT Y 2 1 2 1 303000 r 74 goat snp42460-scaffold562-159111 5 58654251 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441739 Affx-122929131 AX-123312076 5 57862701 CAAGCTAGAAACAGCATTTTCCAGCTTTCTCTGAA[C/T]GTAGGCCATGTAACTAAGTTCTGGCCAATGGGATG Y 2 1 2 1 201000 f 74 goat snp42461-scaffold562-188348 5 58683901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771257 Affx-122936464 AX-385258415 5 57916918 TGAGATGAATTCTTGGAGTTAGCCTTTATTCTAAT[C/T]AAGTGGAACCCCAATCTTTCCTGCTTTTGTACCTT Y 2 1 2 1 101000 r 74 goat snp42462-scaffold562-242565 5 58738640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789612 Affx-122932094 AX-385276621 5 57951564 ACTATGTATGGGAAGAGACTTCTCACAATTTTACC[C/T]ACTGTATTTGCCTTTAAATCCTAGTAAAATTGAAG Y 2 1 2 1 101000 f 74 goat snp42463-scaffold562-277211 5 58773784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792569 Affx-122958226 AX-385279550 5 58016578 TGGTTTTATGAAACAAATACTATACTTAAAGTCTT[C/T]GTGATTTAGTCCAAGCTCTGTCACATAACTAACTG Y 2 1 2 1 101000 f 74 goat snp42464-scaffold562-342225 5 58839106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762376 Affx-986696907 AX-385250537 5 58038937 TATTATTCCTCTATATGTGTGTGAATATTCTGCTT[C/T]CTATCCTATGTTGTATTTTTATATTTTCCTTTTTT Y 2 1 2 1 600010 f 74 goat 5_58038937 5 58038937 Ancestral_priority_1043 ancestry 0.562 neutral IMAGE 10K 10K ancestral 320803597 Affx-986696132 AX-385290390 5 58041410 TGCTTTGGAAATGGTATTGATTAAAATTTATAAAA[C/T]GTTCATACAAGATTATGCTATTCTGACACTGAAAT Y 2 1 2 1 600010 r 74 goat 5_58041410 5 58041410 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38403688 Affx-122958051 AX-123274040 5 58073228 GCGAGCATCGTGCAGCGTTTCCCCACTCCCGCAGC[A/C]GTAGTCGCGATGGTAAGGAGAAAGAGAACGACCAG M 2 1 2 1 101000 r 74 goat snp42465-scaffold562-398875 5 58896316 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387045 Affx-122969911 AX-123257403 5 58107532 AATCACGCAGTGATGTGGGGTCTGATTATACAAGC[A/G]GGAAAATTAACTGCAAGGCATAGTTGGGAAGTTGG R 2 1 2 1 101000 r 74 goat snp42466-scaffold562-433179 5 58930515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399324 Affx-122961373 AX-123269679 5 58139145 TATCTCACCCAGCATGACAGGGAGGACACACCAGC[G/T]CAGGAGGTAGACCCAGAGCCCTAAAGTTTGTTTTC K 2 1 2 1 101000 r 74 goat snp42467-scaffold562-464792 5 58961828 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402090 Affx-122958698 AX-123272443 5 58188383 CATGTTACATGCCTGTCTGGGAGAGTCACCAGGAA[C/T]GCTGGCTTTCTGAAGGCTCTGCAGAGACCCAGAAT Y 2 1 2 1 201000 f 74 goat snp42468-scaffold562-514030 5 59011245 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792562 Affx-122953361 AX-385279543 5 58229385 CCAAATGGAGACAAGTTGTTTGTGATCAGATGGAA[C/T]ATGAAAAGGGTGGAGCTCAACCCACTTTGAAGCAG Y 2 1 2 1 101000 r 74 goat snp42469-scaffold562-555032 5 59052317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772518 Affx-122934442 AX-385259668 5 58268128 AAATAAGGATGGAAGTGTTGAATGGAGGTGGGACT[A/G]CTTTAGTCACTGTGTTCAGGATTAGCATTTTAAAA R 2 1 2 1 101000 f 74 goat snp42470-scaffold562-593775 5 59091840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415633 Affx-122948583 AX-123285982 5 58303806 TGACTGCATTCACCGAAGATGAGAAATTAGGTAGC[A/G]TATGATTGCTAGGGCAATTGCTGTAAGAAATGTTC R 2 1 2 1 101000 r 74 goat snp42471-scaffold562-629453 5 59126341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444457 Affx-122926545 AX-123314794 5 58336079 CCTGAACACCGGCAACTGAGACCCGCTTGTTACTG[C/T]AGCCACTGGGTGTTGGGGCTGTTTGCTACATGCTA Y 2 1 2 1 101000 f 74 goat snp42472-scaffold562-661726 5 59158656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801351 Affx-122974628 AX-385288263 5 58373095 ACCCAGATTCAGATCACTTCTATCATGAAAGCTGA[C/T]GCTAAATACATGTCAGAAAAAAGTTACTGCCTTTC Y 2 1 2 1 101000 f 74 goat snp42473-scaffold562-698742 5 59195464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396455 Affx-122962975 AX-123266810 5 58408362 TGCCTTAGAACCTCTTTTGAACTGAAATTCAGTGA[A/C]TATAATATCCAAGTAATGTTTTTATAAAAAACAAC M 2 1 2 1 101000 f 74 goat snp42474-scaffold562-734009 5 59231000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770860 Affx-122928732 AX-385258024 5 58503238 CTAACATAAAGATATTCTGTAAGGCTCAGCTAATC[A/G]TTCACTCTTCCAACCACCTCCTAACTTCAACAGAA R 2 1 2 1 101000 r 74 goat snp42475-scaffold562-828885 5 59326014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410656 Affx-122952768 AX-123281006 5 58549561 GGGTATCATTAGAGTTTGTAATGTAGCTAATTTCA[C/T]TCCCCTGACCCCTTTTCCCATCTACCTTTTATTGT Y 2 1 2 1 201000 f 74 goat snp42476-scaffold562-875208 5 59372294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390354 Affx-122967684 AX-123260711 5 58603628 TTGTTGCCTCTCGCAGTATTTTATGGGCCGCTGGA[C/T]GCAAAAAACCCACTCCTGGCCTCCTGTGAGAAGGA Y 2 1 2 1 201000 f 74 goat snp42477-scaffold562-929275 5 59425442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381111 Affx-122974583 AX-123251469 5 58643763 TATAGGTGAAATGAGAGAAAGAATATTCAAGGTAG[A/C]GGGAGCAGAAGTGTAAAGGCCCTGAAGTGAGAGTG M 2 1 2 1 101000 r 74 goat snp42478-scaffold562-969410 5 59465540 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431107 Affx-122936606 AX-123301448 5 58686698 TTTATAGCCTCATTTCTTTTTATTATTCCCTTTTA[A/C]GTTGGGAATGACTAGATAATGTGATATAAAATATA M 2 1 2 1 201000 r 74 goat snp42479-scaffold562-1012345 5 59509037 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424745 Affx-122941655 AX-123295091 5 58718449 TTGATTGTCAAGTAAGGAAAGAGACCAAAATAGGT[A/G]CCTGATTTAAAATCTGAAAATGCGGAACCTTTATG R 2 1 2 1 101000 f 74 goat snp42480-scaffold562-1044096 5 59540936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431252 Affx-122937126 AX-123301593 5 58811920 CAGGAACTTTCTAGAACATAGCTTCTGTGAATAAG[C/T]AAGTATGGGCATCAGCTGTGTGTACAGTAAAGGGT Y 2 1 2 1 101000 f 74 goat snp42482-scaffold562-1137567 5 59635759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775589 Affx-122930130 AX-385262720 5 58889429 TAGGATGCTTTAGATCACAAGCCAGCCTATTTGAG[A/G]TTCAGAATGAGACTGGAGTTATGTTTATAACTTGA R 2 1 2 1 101000 f 74 goat snp42483-scaffold562-1215076 5 59715152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777676 Affx-122969396 AX-385264795 5 58921345 AAGAAAAGGCTAAGCTGTTTATAGCATTTTCAAAA[C/T]GCTCATCTCTCAGAGATTTGCCAGCAACAGTGTCA Y 2 1 2 1 102000 r 74 goat snp42484-scaffold562-1246992 5 59745952 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272314 Affx-1111833472 AX-185174800 5 58953494 TGCTTTTGAACTGTGGTGTTGGAGAAGACTCTTGA[A/G]AGTCCCTTGGACTGCAAGGAGATCCAATCAGTCCA R 2 1 2 1 103000 f 74 goat 5_58953494_AF-PAKI 5 58953494 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776782 Affx-122932072 AX-385263906 5 58980449 TGTAGTATCTTCTTAGTCCTTTCTTTAATATATTC[C/T]ATAGAGAAGAGTAACAGTAAACATAGGAAGGAGCC Y 2 1 2 1 101000 r 74 goat snp42485-scaffold562-1306096 5 59805245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770755 Affx-122946421 AX-385257919 5 59035339 TTCACTAGCTTAGAACGTATATTAGTTTCTATTTA[C/T]GCATAAAAATTTGCCACAAATTAACAGCTTCAAGC Y 2 1 2 1 101000 r 74 goat snp42486-scaffold562-1360986 5 59860281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412996 Affx-122951019 AX-123283345 5 59104393 GAGTTAGGAGGTTTGGAATATATTGGAAAGAGTGA[C/T]GCTTCTCAGCTTTGCTAAAAGTCAGCAGTGTGTCT Y 2 1 2 1 101000 f 74 goat snp42488-scaffold562-1430040 5 59929528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778395 Affx-122926431 AX-385265510 5 59145344 GGACTACAACTGTAACAAACCTTAGCAAGGTGTCC[A/G]TATTTTCAGAGTCCTCAGAGATGTGTCTTAAAATG R 2 1 2 1 101000 f 74 goat snp42489-scaffold562-1470991 5 59970888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771374 Affx-122975043 AX-385258532 5 59244228 TGTGGTTTCAAAAGGTAACTTCAATACTATTGGTT[A/G]TCAATTTAATGATGGATTCTCAGTTTCTACTCACT R 2 1 2 1 101000 f 74 goat snp42491-scaffold562-1569875 5 60076394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380710 Affx-122975154 AX-123251068 5 59302690 TTGTCTGGCAATAACTTGGGTAGTGAACCTGTGCC[A/G]TTGTTAACTCATGTGGTGCTGACTCCAGCATCAGA R 2 1 2 1 101000 r 74 goat snp42492-scaffold562-1628337 5 60134798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771247 Affx-122954670 AX-385258405 5 59337754 TGAGAGTCACCACTGTGTATCCTATTCACATGATA[C/T]GTGTGCAAATGAGACAATTATTTACTTAGCAAACA Y 2 1 2 1 101000 f 74 goat snp42493-scaffold562-1663401 5 60169814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437536 Affx-122931908 AX-123307874 5 59385117 CTTCCTCACACATACCTATAATACTTTTCCCCCAA[C/T]ATTTTTTGCTTTTTATATGACCACAATTTTACAAA Y 2 1 2 1 303000 r 74 goat snp42494-scaffold562-1710764 5 60216850 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437982 Affx-122931593 AX-123308320 5 59427947 ATTTAGAGCCATTGGCTGATCTGGTTGACCACAAG[A/G]GCTGCTTTCCAAACATTTGAAAAAAAAAAAAGGAG R 2 1 2 1 101000 f 74 goat snp42495-scaffold562-1753594 5 60258551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452407 Affx-122920598 AX-123322740 5 59514321 ACACTCTAGAAATTGTTACCTCTCACTTCTGACAC[C/T]ACCCACACCAGCCTATCCATCTCCATGTGTTAACA Y 2 1 2 1 101000 f 74 goat snp42497-scaffold562-1839968 5 60345811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440835 Affx-122929268 AX-123311172 5 59564380 TGGCAAAATGGAAAAGGCATGGCCTGTCTGAAAAC[C/T]AAGACAATGCATTGTTATATAAAAATATGGCAATG Y 2 1 2 1 101000 f 74 goat snp42498-scaffold562-1890027 5 60395812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434893 Affx-122934337 AX-123305233 5 59599945 CAAACACCTTAACCTGATGCCTGTCATCAAGTTGA[C/T]AATAAATAATAAATATAATTACCATATACAGTAAA Y 2 1 2 1 103000 f 74 goat snp42499-scaffold562-1925592 5 60431276 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783193 Affx-122976576 AX-385270260 5 59632480 CTACTAGGGCAGGTGACATGAAGAATGAAGGTGAG[C/T]GGTGGAGCAGATATTTTAGAACGACTCAGCCATCC Y 2 1 2 1 101000 f 74 goat snp42500-scaffold562-1958127 5 60463806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397781 Affx-122962509 AX-123268136 5 59670181 ATCCCAGAAGGCAGCCTCCAGTTGGGCCTCTGCAG[C/T]GCACTCTACTGGCAGCGGTGAGAAACAAACTCTCG Y 2 1 2 1 101000 r 74 goat snp42501-scaffold562-1995828 5 60501440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449248 Affx-122923474 AX-123319583 5 59703102 ATGAAATGTTAGCCTGACTATAGCTGGTGGAAGCA[A/G]AAGAGGTTTCAGCATGGGTGTTAAAGTGCCATGTT R 2 1 2 1 101000 f 74 goat snp42502-scaffold562-2028749 5 60534377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774157 Affx-122974593 AX-385261295 5 59764637 GAGCTGCATGAATAAAGAGGGATCAAATTAAGAGA[C/T]GAGTCATAAAAAATGGATTAAGAGTGATATGAGAA Y 2 1 2 1 101000 f 74 goat snp42504-scaffold562-2090284 5 60595370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775733 Affx-122921181 AX-385262864 5 59794094 GGGCGCCACCTTCTCATTAGTATCCCAGTAGGAAA[G/T]ATACTTCACAGGGAAAGCTTGCTGAAGGTGTCCTC K 2 1 2 1 101000 r 74 goat snp42505-scaffold562-2119741 5 60624771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431118 Affx-122936597 AX-123301459 5 59837677 TCAGCCACAGGACTCTTTCCCCTCAGTTTGACTCC[A/G]TCTGAAACTTGACACCAAAGGCAAGTAATTTAAGC R 2 1 2 1 201000 r 74 goat snp42506-scaffold562-2163324 5 60668718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793108 Affx-122960741 AX-385280086 5 59889303 GGGGAGTTTTTCTCCCTCAAGTAAATAAGGAGCTG[A/G]CATGGTAACTCTGCTGTCTAAAAGTCCTCAGGACT R 2 1 2 1 101000 f 74 goat snp42507-scaffold562-2214950 5 60720741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419659 Affx-122945951 AX-123290007 5 59934753 TGCATAAAAACTTGCAAAAAATTCTACATTTATGA[C/T]ACACTATTTATTATATACTTAACCTTTGTATAGTT Y 2 1 2 1 101000 f 74 goat snp42508-scaffold562-2260400 5 60767260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453140 Affx-122919999 AX-123323473 5 59976863 ATACTCTATTAGAAGCATGTGAGTGTTTCAACTTA[C/T]AACAACCATACCAGCTCTGGATGTTTTATTAAACT Y 2 1 2 1 101000 f 74 goat snp42509-scaffold562-2302510 5 60808810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278229 Affx-1111836314 AX-519551717 5 60013870 TAGTTTCCTATACCATGCAGGCTAGTGTTCAGACT[C/G]CCTTGCAGCTCTGGTCCCATATATGACCTCAGTTC S 4 1 2 1 101000 f 74 goat Random2.2K-565 5 60013870 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786992 Affx-122944531 AX-385274020 5 60107837 CCTAGAGTGATGGTGATATGGTTTTTGACCTTCTA[A/G]ACCAGAGATTTGTACTCTTGTGACTGAAGATATCC R 2 1 2 1 101000 f 74 goat snp42512-scaffold562-2433484 5 60940927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419428 Affx-122945512 AX-123289776 5 60151110 CCATACTATATCCCACGAGTCCTACTCAAAACAAT[A/G]CCAGGAGCCTCTCCTCACCTCTTCCTCATCTCTCT R 2 1 2 1 101000 f 74 goat snp42513-scaffold562-2476757 5 60984476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770959 Affx-122929118 AX-385258122 5 60222400 TTAAAATATACATCCCTGTGATGTTCTGCTCTTAC[A/G]TTTATACTAAATGAGTATTTGGATATCATTAAACC R 2 1 2 1 101000 f 74 goat snp42514-scaffold562-2548047 5 61056344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399894 Affx-122960211 AX-123270249 5 60293250 TTCTCTTCCATTCTTTAGTCTCTCTCTGTCCCAGA[C/T]GAAAACTACCCACCTACACTTTTCAAAGCTCTTCC Y 2 1 2 1 201000 r 74 goat snp42515-scaffold562-2618897 5 61128408 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386544 Affx-122970722 AX-123256902 5 60363034 AAAATTGAAGCACAGAGGGTCCACACGACTTGCCC[A/C]AGATCACAATATAACCAGTGACAGGGTTGGATTTT M 2 1 2 1 101000 r 74 goat snp42517-scaffold562-2688681 5 61199200 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801518 Affx-122943326 AX-385288427 5 60397315 ATGAGTCACTGCTTGATTTGCAAGTTTCCCTACTT[C/T]AATGATAATATTGAAAGCCCACTAATATTAGTCAC Y 2 1 2 1 101000 f 74 goat snp42518-scaffold562-2722962 5 61232598 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444470 Affx-122926537 AX-123314807 5 60443406 AAAACCTTTTCCAAACACCGTTTTCCTCGCTTTCC[A/G]CATCACCATTAGGAAGCAAGAATTTGTAGCAAAAG R 2 1 2 1 201000 r 74 goat snp42519-scaffold562-2769053 5 61279940 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407762 Affx-122954974 AX-123278113 5 60474664 TCTCTGTGCTGTCCTTCCAATCTGACCCTGCTTCT[G/T]TTCACAGTACCCCATTGTTCTATGTTTCCAGCAGA K 2 1 2 1 201000 r 74 goat snp42520-scaffold562-2800311 5 61311162 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387317 Affx-122970508 AX-123257675 5 60509284 CCTTCTTAGTACCCTTTCAGGGTCACCTACATTAA[C/T]AGCCTTAGTTTTGTGTGTGTGGTCTTCTTGGACTC Y 2 1 2 1 101000 f 74 goat snp21680-scaffold212-1549745 5 61346574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770368 Affx-122934864 AX-385257534 5 60543850 AGTTTTTTTTTTCAAAGTGTATTTCCACTAAAATG[C/T]GACCAACCAAAAAAAAGCCACCAAAAATCAACCAA Y 2 1 2 1 101000 r 74 goat snp21679-scaffold212-1515179 5 61381147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788385 Affx-122976981 AX-385275403 5 60582364 AATCATAAAAGAGACACTTCTGAAACTGGAGGTGA[C/T]TGTATGAAGAATGTATAGAGCTTTGAACACAGATA Y 2 1 2 1 101000 f 74 goat snp21678-scaffold212-1476665 5 61419908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786358 Affx-122930326 AX-385273392 5 60624123 GAGGCAGCCAAATACAGTGATGTGCGCCACAGATA[A/G]GCATTCTCCTGAATGAAGAAACACAAGGAGGAACA R 2 1 2 1 101000 r 74 goat snp21677-scaffold212-1434906 5 61461511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389462 Affx-122968338 AX-123259820 5 60664641 TCATTCTCCTCCCCGATGGAAAGTGTCCTTCCTTT[A/G]CTCTAACTTTGTAGGTACATTATACTTCTTTCTAA R 2 1 2 1 201000 r 74 goat snp21676-scaffold212-1394388 5 61502027 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415762 Affx-122948929 AX-123286111 5 60700858 AATAGTCAGTAAATACATTTTAAGAGAAAAGACAG[A/C]TTATTCCCATGTTTCAAGCACAGGTGAGAAGAGAC M 2 1 2 1 101000 r 74 goat snp21675-scaffold212-1358171 5 61537864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416820 Affx-122948126 AX-123287168 5 60735787 TCACTGTGGATGACACTGCTAGCAGGTGGCAGAAG[C/T]GGAACAGATACCTGGTTTCCCAACCTTGTGCACCC Y 2 1 2 1 201000 r 74 goat snp21674-scaffold212-1323242 5 61572814 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802974 Affx-122969526 AX-385289860 5 60802668 CCCTGAAGCATTGTCGACAGGGAGCCATTCTGACT[C/T]GAAGTGAAGGATTTGTGATTTGTAGACACCTGGGA Y 2 1 2 1 101000 r 74 goat snp21673-scaffold212-1256361 5 61639499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379745 Affx-122975866 AX-123250103 5 60840166 ATTAATATTTCTGCTAATGGCCCTGAAAAATGTTT[A/G]TGTCAGGAGTAGCCAGACTTGGAGGTAGAACAAGT R 2 1 2 1 201000 f 74 goat snp21672-scaffold212-1218863 5 61676973 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439017 Affx-122930354 AX-123309354 5 60946302 CCCAGCCACAACGCATCCAGGATATGTGATGATGG[A/C]GGGGCTGTTAAGTAGGAAAGCAGCAAAGATGAGAC M 2 1 2 1 201000 f 74 goat snp21670-scaffold212-1112727 5 61783343 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429061 Affx-122938296 AX-123299403 5 60979691 CCAGGTCTTACTCTTCTGTCTCTTTCTCCTGGTCC[A/G]TTTGAAACCCTTGCTCAGGGAGTCACCCTGTTCCT R 2 1 2 1 201000 r 74 goat snp21669-scaffold212-1079338 5 61816698 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397325 Affx-122962305 AX-123267680 5 61028240 TTCAGGGAAAATGCAAAGCTCCAGGTGCGCTGTGT[A/G]TCCCAGGAGCCAAATGCTTAACATGGGCTGTGCCC R 2 1 2 1 201000 r 74 goat snp21668-scaffold212-1030789 5 61865159 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793497 Affx-122929476 AX-385280474 5 61078639 CACTGCAGAGTGACAGAAAGCCTAACATGTTTGAG[A/C]TTAAAATCTGAATCCCTGATGCTCAGACTAATCTT M 2 1 2 1 101000 f 74 goat snp21667-scaffold212-980390 5 61915179 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795773 Affx-122927600 AX-385282726 5 61113285 TAAATAGCTGTTCTACTTCAAATGGATCATTAAAT[A/G]CAAAGCACTGCTTTTTATTCTATCTGGTCATCTTA R 2 1 2 1 101000 r 74 goat snp21666-scaffold212-945744 5 61949834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394985 Affx-122964259 AX-123265340 5 61170113 CAGAGTTTCCTTCTGTAGACCCTTTAAAACAAATT[A/C]TTTAGTATTGCTCAACTATTTTTCAGCAGCCTCTC M 2 1 2 1 101000 r 74 goat snp21665-scaffold212-888916 5 62006461 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390501 Affx-122967254 AX-123260858 5 61212312 CATCCCCCAGCAGCACCACCAGATGAATGTATCCA[C/T]GCCAATGACCTGCAGCAAGCTCACCAGGAGAACTG Y 2 1 2 1 101000 f 74 goat snp21664-scaffold212-846717 5 62049815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405544 Affx-122955971 AX-123275896 5 61291360 TAGAGTAAATGGAGGTGGAAGTCGAGACTTGTATC[A/G]TTTTAGAGATTCCAGTCAGAATAAGAGAAAATAAG R 2 1 2 1 101000 f 74 goat snp21663-scaffold212-767669 5 62130041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414843 Affx-122949188 AX-123285192 5 61324687 CATCTTCCCAACTCAGGGGTTGAACCCAAGTCTTC[C/T]GCATTGCAGGGAAGCCCATGAAAATTCTATATTGG Y 2 1 2 1 101000 r 74 goat snp21662-scaffold212-734342 5 62171778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387926 Affx-122970440 AX-123258284 5 61390251 ATCACCTAACACAAAGCTGGACTGGATTTCAGGAG[C/T]ATGTTTCCTGGACAAACTGCAATGAGCTAGTGTGT Y 2 1 2 1 101000 f 74 goat snp21661-scaffold212-668778 5 62238369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278231 Affx-1111836315 AX-519551719 5 61413051 ACTCTGACAGATACAGTGACAATGAAGAAGGTAAA[A/C]TTCTGTGATGTTAATAAACTATATAATCAAAAAAT M 2 1 2 1 101000 f 74 goat Random2.2K-567 5 61413051 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414652 Affx-122949317 AX-123285001 5 61455319 ATAGAGCAAGTTGGGCTACTTCTCCTTTGCCCCAT[A/G]CATACCTTTATCTAGTCTACTGTCATAACTCTATC R 2 1 2 1 201000 r 74 goat snp21660-scaffold212-603710 5 62304120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384540 Affx-122973024 AX-123254898 5 61485215 GATGTATTTTCTCAGAAAACCAGTTAAGTATGGAT[A/G]TCAGTTTCCTTTCTGTGGTCACTTGTTAACAAATT R 2 1 2 1 101000 f 74 goat snp21659-scaffold212-573814 5 62333795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764853 Affx-122966572 AX-180660632 5 61563662 CTGCACACACAAATAAGTTTTCTTTAGAAACTAGA[C/T]GGATAAAGTACAAAAGCATGAGGAGGTAGAGGTAT Y 2 1 2 1 101000 f 74 goat snp21657-scaffold212-495367 5 62412915 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426718 Affx-122939885 AX-123297064 5 61626177 GTGGAACATTGGGGGATGAATCAACAGTAGCATCC[A/G]GTAAATCAGAAATTACTGACACCTTTGATTGTCCT R 2 1 2 1 101000 r 74 goat snp21656-scaffold212-432852 5 62477444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272575 Affx-1111833473 AX-519546290 5 61651502 TCACAGTCCCTGAGGAACCACGGCCAAATTAAATA[A/C]TACTTGTTAATTGTTCTGAAGACCAAGATCTGCAG M 2 1 2 1 101000 r 74 goat 5_61651502_AF-PAKI 5 61651502 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404236 Affx-122957645 AX-123274588 5 61678411 TTTCACTTCTCTTGTTTTCTGTGGCACACTGCTTC[A/G]CTTCCTTATCTCTCTTCTATCCAACTGCTTTGTTG R 2 1 2 1 201000 r 74 goat snp21655-scaffold212-380618 5 62532038 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791162 Affx-122959805 AX-385278157 5 61744989 ATATGTTTTCAAGGTCAAATATATATAGGTCAAAC[A/G]TTTGTTTTAACAGTTGCATAATCCATGGTATAGAT R 2 1 2 1 101000 r 74 goat snp21654-scaffold212-314040 5 62599364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448602 Affx-122923390 AX-123318938 5 61795202 GAATCTTTCTTGAAATAAGTAAAACCCAAAGTCAG[C/T]GAGACATATACCGGGAAGACATATTTTTCTAAACT Y 2 1 2 1 201000 f 74 goat snp21653-scaffold212-263827 5 62649026 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413701 Affx-122950087 AX-123284050 5 61831068 CTATTTTGGAATCCTCTAACTCACATTGACATCCC[A/G]TCACTGTTTCGGAACCTCATTATGGTTTTCTTGCT R 2 1 2 1 201000 f 74 goat snp21652-scaffold212-227961 5 62685497 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775410 Affx-122929365 AX-385262541 5 61917017 TAGTGAGAATTAAAGTGCTTCTTCCACCAAAGGAA[C/T]CCTTGTTCATGCTATTCTTTTGCTTGAAATACCTT Y 2 1 2 1 101000 r 74 goat snp21650-scaffold212-142012 5 62771709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377708 Affx-122977402 AX-123248067 5 61958551 TCAACATGTTTGAAGGAAGATTTAATAAATGTCTG[C/T]TGCTAGACTGTTAAAAATAATTTCTTTTTACAGTA Y 2 1 2 1 101000 f 74 goat snp21649-scaffold212-100478 5 62812822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779492 Affx-122939742 AX-385266595 5 61997517 TTTCTTTTTTTCTATTAAGTACACTTCATAGAAGC[A/G]TCTAAAATTGAGCAGGGTACCTGTTTCTTTCATGT R 2 1 2 1 201000 r 74 goat snp21648-scaffold212-61512 5 62851833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772240 Affx-122949827 AX-385259395 5 62026963 TTATCTTTCTGGAGAAATAGGGAGGTGGGCTTAGG[C/T]AAAAGCAATTAGGAATTCAAGTTACTAGTTGGGAA Y 2 1 2 1 101000 f 74 goat snp21647-scaffold212-32066 5 62881256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380248 Affx-122975457 AX-123250606 5 62057095 GGAGAAGAAACTTAAGAAAGGCATTGGCAGCAGAT[A/G]TGACATAAAAAAGCATAAGGTTGCAAAAAAAACTT R 2 1 2 1 101000 f 74 goat snp21646-scaffold212-1934 5 62911630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476203 Affx-1251763708 AX-586011627 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20000 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 539476458 Affx-1251763708 AX-586011858 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 4 1 4 1 20000 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165259 Affx-1251763708 AX-606940671 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165334 Affx-1251763708 AX-606940745 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165551 Affx-1251763708 AX-606940962 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165604 Affx-1251763708 AX-606941015 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165723 Affx-1251763708 AX-606941132 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562166044 Affx-1251763708 AX-606941453 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 320779911 Affx-122944297 AX-385267010 5 62160165 GACAGAAAATGAACCCGGGACAGCAGGAGGAATTT[A/G]TTATAGGCACTTAGTATGGAACCACTGACAAGCGT R 2 1 2 1 101000 r 74 goat snp28706-scaffold310-101037 5 63000047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776238 Affx-122949398 AX-385263366 5 62210127 TAATGAGTAATGATCTAGCTTTCTCTATAAAATAA[C/T]GCTTGGCCCTGTTCTGGTGATAATCTGATTCTCTT Y 2 1 2 1 101000 r 74 goat snp28707-scaffold310-150999 5 63050026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432118 Affx-122936450 AX-123302459 5 62247038 GGCTGTCAAGTTAGAAACATCTGAAAATGATTTCT[A/G]CAGAAGCGTTGTGGTTCATGCTTTCTTTCAGTGGT R 2 1 2 1 101000 r 74 goat snp28708-scaffold310-187910 5 63086660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386986 Affx-122969954 AX-123257344 5 62306573 GCCTGTCTTCTGGGTCGCCTGACTGAGTTGAGGAC[A/G]TTCAACCATCACCATGCAGACATGCTTATGTCATG R 2 1 2 1 101000 r 74 goat snp28710-scaffold310-247445 5 63145559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408499 Affx-122954406 AX-123278850 5 62339484 TTGATTGATGAGACCTCATAATTGATTTTCAGATA[C/T]GGGGTTGAGCCACCAGTATTAGTAAAACTTGAGAA Y 2 1 2 1 201000 f 74 goat snp28711-scaffold310-280356 5 63178478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766313 Affx-122948112 AX-385253700 5 62372487 CTCTAAAAATAGGCAAGACATAAATCTTAGCAAAA[C/T]GTGTTTTATGGTTAGGATTTTGATTAAATAAACCA Y 2 1 2 1 101000 f 74 goat snp28712-scaffold310-313359 5 63211463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779200 Affx-122942969 AX-385266304 5 62403305 GATGGTTGCTGGTGTTGGTTTCTCAGCTCAACCAC[A/G]TCAAGGATTATCTCCCCGAGATCCTTTTGGCCTTT R 2 1 2 1 101000 f 74 goat snp28713-scaffold310-344177 5 63241879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380236 Affx-122975468 AX-123250594 5 62453579 TGCATGGGATATATCAATCATCAATGACCTCCTAA[C/T]GGCCAAACCTAGTAAATATTTTCCCATCCTAATCC Y 2 1 2 1 101000 f 74 goat snp28714-scaffold310-394451 5 63292675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784536 Affx-122952139 AX-385271585 5 62484772 AATGTCTTGAGTGGGCCTCCCTTACTGATATGGAT[A/G]TTCTCCGTTCAGCCATCCCAAAGGGAGATTAGTTC R 2 1 2 1 101000 r 74 goat snp28715-scaffold310-425644 5 63324006 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38392091 Affx-122966368 AX-123262448 5 62525775 CAGCCATGAAATTAAAAGACTCTTGCTTCTTGGAA[G/T]AAAAACTATGGCAATATAAAGATGAGGATATTCAG K 2 1 2 1 303000 r 74 goat snp28716-scaffold310-466647 5 63365142 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384223 Affx-122972379 AX-123254581 5 62555140 TACCAATGCTATGGTGTCCATCCCCTGCCCAAAGC[A/C]AAGGACATAATATTCTTTCCTCATTTTCTGGCTCT M 2 1 2 1 101000 f 74 goat snp28717-scaffold310-496012 5 63394829 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391746 Affx-122967482 AX-123262103 5 62587149 CAAAGATTTATTTTAGTTTTAATTTTTCTTTTTTA[C/T]AGCATAGTCCCTGAAAGATGTTTGTCGTTCCATAT Y 2 1 2 1 101000 r 74 goat snp28718-scaffold310-528021 5 63427487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403626 Affx-122957543 AX-123273978 5 62620191 GAAAAGTCATAACTGAGAATGAGAAAGGAATGAGA[C/T]GGATTGAGAGGATGGTACGATGGTGTAGACAGTGG Y 2 1 2 1 101000 f 74 goat snp28719-scaffold310-561063 5 63460551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791254 Affx-122949325 AX-385278248 5 62658589 AGAGATAAAGGCCACATTAAAATCTGAGCCTGCTT[A/G]CTCTTTACCCTTGTATCCTGTTGATTCCTATTATC R 2 1 2 1 101000 f 74 goat snp28720-scaffold310-599461 5 63498948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442930 Affx-122927621 AX-123313267 5 62703503 AGTCCATGCTTTCTCTTCCTGCTTCTGCTCAGGCT[A/G]CCCGATGAAGGCTGGTTCACACCCTCAGGGGTTAT R 2 1 2 1 101000 r 74 goat snp28721-scaffold310-644375 5 63544140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447141 Affx-122924452 AX-123317477 5 62757548 CATATTTCTTTCTCATTGTGTTTTTGTCTTTGTTT[C/T]ATTCTCTTTTATGTTAATGGATTTCTTCAGATACC Y 2 1 2 1 101000 r 74 goat snp28722-scaffold310-698420 5 63579904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430518 Affx-122937213 AX-123300859 5 62877200 AGGATTTCTAACTGATTATAACACATTTGATAAAG[C/T]AATGGAGCTTTCTGCCCCTTGTTTGGCTGCTCTGG Y 2 1 2 1 201000 f 74 goat snp28725-scaffold310-818072 5 63699995 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783959 Affx-122950775 AX-385271013 5 62946693 CACTTTGTACATTAACTAGTGTAATTCTTACCATT[A/G]CCCTTCATATAGAAATCATCTCCACTTATCAAATG R 2 1 2 1 101000 r 74 goat snp28726-scaffold310-887565 5 63767217 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780184 Affx-122953050 AX-385267280 5 63019427 CTCATTAATCCTCAAGAATCTGATGAACAGAAGGC[A/G]ATATCTTTTGTAATATGGTTATTATGGACTGACAT R 2 1 2 1 101000 f 74 goat snp28727-scaffold310-960299 5 63840132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410338 Affx-122952467 AX-123280688 5 63053597 TAAAACTGTGTTGACTCCAAGTTTACTCATGATTA[A/C]TGATCTCTTCAGGTTTTGTTAGGTTCCTTTTGACT M 2 1 2 1 101000 r 74 goat snp28728-scaffold310-994469 5 63874244 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421617 Affx-122944475 AX-123291964 5 63087613 TGGCATCCTTTTTATTGTCATATTTCTAACACTCT[A/G]TAGAGTGTCTTGTGACATAAGCTCAATAAGAATGG R 2 1 2 1 101000 r 74 goat snp28729-scaffold310-1028485 5 63907786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787977 Affx-122959281 AX-385274998 5 63139411 TTCAAATTTCTCTTCTGCAGGCATGCATATGACTC[A/G]TTACAAGAAATAAGGATTAAATGATTTAATATAGG R 2 1 2 1 201000 r 74 goat snp28730-scaffold310-1080283 5 63959797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422689 Affx-122943662 AX-123293035 5 63180821 GATATTTTTAGAAGTAATTATATGTAGGGACCACA[C/T]GATATCACGATGATGTAAAAACATTTTTGTAGAGT Y 2 1 2 1 101000 f 74 goat snp28731-scaffold310-1121693 5 64001203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772538 Affx-122929074 AX-385259688 5 63238681 GTTAGAAACATGCAAGAATCTTATGCTATTAATAA[C/T]AGTTTTGCCTACAAATCATTTCTTAAGAATTTTCG Y 2 1 2 1 101000 r 74 goat snp28732-scaffold310-1179553 5 64059153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439343 Affx-122930291 AX-123309680 5 63275126 TGGGATCCCTCCTGGAGTAGGATAACTGGGAGGAT[A/G]AAGAATCCAGGAACCATAGTCCATTCACCTTGAAT R 2 1 2 1 101000 r 74 goat snp28733-scaffold310-1215998 5 64095273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436193 Affx-122932600 AX-123306532 5 63324587 ATTTGAAAAGAACAACACATTAATGAATGTTGCCC[A/G]CAGAGCTGTCTATCCCTGGGTAGTGCTGAAAGAAT R 2 1 2 1 201000 f 74 goat snp28734-scaffold310-1265459 5 64144693 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428953 Affx-122938883 AX-123299295 5 63397226 TGCTGCCTGCATAGGTGCCTGCAGCTCTGCTCAAA[C/T]GTAGCCCAAGGTCGCATCTTCTCCCCGACTCTGGT Y 2 1 2 1 101000 r 74 goat snp28736-scaffold310-1338098 5 64217662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379910 Affx-122975758 AX-123250268 5 63435746 GTGGAGAAGCACTGCTTGCCCACATACTCATGTGG[C/T]AGGCTTTCTCACCTCCTTCAAATTTTCATCAGAAA Y 2 1 2 1 101000 r 74 goat snp28737-scaffold310-1376618 5 64256286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781072 Affx-122940306 AX-385268159 5 63475565 TTCATATCTGACAGTATCTTCCACCATGTAGGGTA[A/C]AACTTGATCAATCATGTCTGAGAATCAGGCAAGTA M 2 1 2 1 101000 r 74 goat snp28738-scaffold310-1416437 5 64295887 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389882 Affx-122968136 AX-123260239 5 63560589 AATTACTCTTCTGGCAAAGTGCTGCCCAAGGGCAC[G/T]CATATGCTGTCTCCACTTCTCCCCATCACTGATTC K 2 1 2 1 201000 r 74 goat snp28739-scaffold310-1501461 5 64382412 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779654 Affx-122922569 AX-385266756 5 63609364 GAAGCTTTTTCAAAGAGCAGTGTATGAAAAAACAA[C/T]GGAGCTTCGAGGTGTGAATCCAGAGAGTCTTGACA Y 2 1 2 1 101000 r 74 goat snp28740-scaffold310-1550236 5 64431074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414023 Affx-122949799 AX-123284372 5 63638188 TCTACCAGTTAACAAGCTGTAGAAAGTTTCAGTCC[A/G]TTATTTGTACTTATACTTTGGCCACCTGACGTGAA R 2 1 2 1 101000 f 74 goat snp28741-scaffold310-1579060 5 64459954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793808 Affx-122964067 AX-385280779 5 63669283 AAGTGAGGCAGAATGTTCCACCCAGAAAGCAAAGG[C/T]AATGGAATTTTATGAGAAAGGGTATGGAGACAAGG Y 2 1 2 1 101000 f 74 goat snp28742-scaffold310-1610155 5 64491873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433211 Affx-122935628 AX-123303552 5 63705445 TTCCTCCTTACCAATCTGTAAAACTTATATGTGAG[A/G]GCCCTTACTTCTGTCATAGGTGGTCAGCAGGAAAA R 2 1 2 1 201000 f 74 goat snp28743-scaffold310-1646317 5 64528242 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391917 Affx-122966942 AX-123262274 5 63753825 TCCATTTTCCACAGTAAATAAGATTATTAGTCAAG[G/T]CAACTGAATATTTCTTTCTTCTTTATTACTGTTTA K 2 1 2 1 201000 f 74 goat snp28744-scaffold310-1694697 5 64576533 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407933 Affx-122954369 AX-123278284 5 63783672 TGCAAAAATCCAAATCCAGAGAAGCAACTTAGCAC[A/C]GAAGCAGAAAGCTATCTTAAGGACATCTGCCCATA M 2 1 2 1 101000 r 74 goat snp28745-scaffold310-1724544 5 64607093 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782106 Affx-122965341 AX-385269184 5 63840321 CTACCTCTGTTGCCAGTTTACTGCTAATATTAGGA[A/G]TTTTTCCTATACTTAGTAATCTTTTAATTACATGT R 2 1 2 1 201000 r 74 goat snp28746-scaffold310-1781193 5 64664389 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418279 Affx-122947004 AX-123288627 5 63872581 AGAGCTGTTTGGAGGTGAGAGTATGGGGGAGATAG[A/G]TGGCTGGAGTGGGTCACATTTAGATGGAGAGAAAG R 2 1 2 1 201000 f 74 goat snp28747-scaffold310-1813453 5 64696876 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794781 Affx-122955016 AX-385281741 5 63941497 TTAAGGGTGTACAGATAAACTAGCATGTGTTCATG[C/T]GACAGTGATAAGGCCAGTGATAATTTTTGAAACTC Y 2 1 2 1 101000 r 74 goat snp28748-scaffold310-1882369 5 64766268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394571 Affx-122964447 AX-123264926 5 63979229 CTGACCTTAACCGCTTTGGCATCCCCCTCCTACCC[A/C]CAAGGCACACAAAAGAGCTGTGCGAAAGTGCTGAT M 2 1 2 1 101000 r 74 goat snp28749-scaffold310-1920101 5 64804814 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781635 Affx-122926645 AX-385268719 5 64013364 TTTTCTTCTTCCTGTCTTATTTCCAGAAACCTGCC[C/T]CTCAACCTCTGATTTTTAAGTCTTACGTGATCTGT Y 2 1 2 1 101000 f 74 goat snp28750-scaffold310-1954236 5 64816648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278233 Affx-1111836316 AX-519551721 5 64043184 TAAGGCTCACGTTAGATACTTGACTGAACACTGAA[A/G]GATTCTAAATACAGAGCCAAGATAAAAACCCAACT R 2 1 2 1 101000 f 74 goat Random2.2K-569 5 64043184 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791840 Affx-122947764 AX-385278830 5 64068783 TAAAAGAATAACAATTCTACCAGTTGAACATGTGT[A/G]TGTGCTGGTCACTGTCTTATAAGTGCTAATTGTAG R 2 1 2 1 101000 r 74 goat snp28751-scaffold310-2009655 5 64873013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429446 Affx-122938498 AX-123299788 5 64120919 GATGTCTCTCTTAAAGTAACCCTGAAATAATGCCT[A/G]CAGTGGGAGGAGGTCACTGATCTTCTCAAAATCTA R 2 1 2 1 101000 f 74 goat snp28752-scaffold310-2061791 5 64925304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377724 Affx-122977391 AX-123248083 5 64161275 CTGGGCTGTGCCATGTCACAGAAATGTCTAATTAA[C/T]GTAGGTCTTTATTTTGAGGAACTGGTGCTTTTTCT Y 2 1 2 1 101000 f 74 goat snp28753-scaffold310-2102147 5 64965666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272202 Affx-1111833474 AX-519545952 5 64251298 GGGGAGTTCCCTAGTGGTCCAGTGGTTAGGACTCT[A/G]TGCTTTTACTGTTGAGGGTCCAGGTTCAATCCCTG R 2 1 2 1 102000 r 74 goat 5_64251298_AF-PAKI 5 64251298 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278393 Affx-1111836318 AX-519551878 5 64288473 TCTGTCCCCTGTGTTGGCAGGTGGATTATTAACCA[C/G]CAGACCAAGAGGGAGATCCCAGTCCCTGGCTTAAA S 4 1 2 1 103000 r 74 goat Random2.2K-571 5 64288473 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387149 Affx-122970640 AX-123257507 5 64289202 TGCATATTAGGGAAATCTTTCCACACACCTCCAAG[C/T]GTAAGCATTCCCTGTGTCCTCAGTTGCATCGTACT Y 2 1 2 1 101000 f 74 goat snp28756-scaffold310-2230074 5 65094787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404514 Affx-122956698 AX-123274866 5 64331912 TTAAATCTTAATGTTGGGCTGGGTCAGAGTTCCCA[G/T]ACCAGAGTCATTCAACCTTTAGCCTAGGGGATTAC K 2 1 2 1 101000 f 74 goat snp28757-scaffold310-2272784 5 65137480 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431485 Affx-122936253 AX-123301826 5 64411003 CAGCAAGCGAAGTCTGTCTCCACAGCTGCTCAGTA[C/T]ACCTTGATGCACAAGAAAACTAAAGGGCGCTTAGT Y 2 1 2 1 101000 r 74 goat snp28759-scaffold310-2351875 5 65217407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394377 Affx-122964635 AX-123264732 5 64445726 TATACCAATTCCATTTCAATAGCTACTTGTTTCAC[A/G]TGCAGATATCAAACTTTTCCATCATCACAGAAAGT R 2 1 2 1 101000 f 74 goat snp28760-scaffold310-2386598 5 65252327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404061 Affx-122957152 AX-123274413 5 64503270 CTGTGAAAAGAACACCAGGAAAGACCTGCCTACAG[A/C]GGCACCATTGTTTCAGGGTTAAGTGCTGACGAAGA M 2 1 2 1 101000 f 74 goat snp28761-scaffold310-2444142 5 65310529 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421809 Affx-122944322 AX-123292156 5 64535946 CCATGAATAGACATGCTTCTGACAGCTTGCAAGAG[A/G]GCAAGCCCTAGGCCAGCCTCCAGCTTCAGGGCTGC R 2 1 2 1 101000 f 74 goat snp28762-scaffold310-2476818 5 65343478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394768 Affx-122964838 AX-123265123 5 64565005 GGGTCTGACCTCAGAAAACTAAATAGATGACGTTG[G/T]GAATACTGGGCACTGTTGCTAAGGAGCAAAGGTGA K 2 1 2 1 101000 f 74 goat snp28763-scaffold310-2505877 5 65372239 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426763 Affx-122940562 AX-123297109 5 64617981 CTGCTCTGGCCTCCAGAGATTGGCTACATTCTAGA[C/T]GACTCAGCAGCTGACTGAACATGCATGATCATGTG Y 2 1 2 1 202000 f 74 goat snp28764-scaffold310-2558853 5 65425226 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416377 Affx-122947871 AX-123286726 5 64670902 CTTTAAATGAGTGACTATTTCTACTGTAAGAAAAT[C/T]AAAACACATTCTTGCCATTCTTCAGCTTTGAAAAA Y 2 1 2 1 101000 r 74 goat snp28765-scaffold310-2611774 5 65476286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434520 Affx-122934162 AX-123304861 5 64724351 CATGAACCTATTGCATGGAATGTGGAATCACTTCT[A/G]CTTTGGCATGTGAGGTATTTCTTTTTTTATCTGCA R 2 1 2 1 101000 f 74 goat snp28766-scaffold310-2665223 5 65531731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273793 Affx-1111833818 AX-519547404 5 64727873 AGAACTCAGACTAGAACTGCAGACTTAAACTCA[A/C]TGCACCTAGCTACCTATGGGATGGATATGATCGGG M 2 1 2 1 101000 r 74 goat GoatD01.005889 5 64727873 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792702 Affx-122974423 AX-385279682 5 64764874 CTGAATTAGAAAGGAAAAGAATGGATTAAAGAACA[C/T]GATTACAAAGCTCGAGAGACTAGCTTTGCTTCCGT Y 2 1 2 1 201000 f 74 goat snp28767-scaffold310-2705746 5 65573123 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787883 Affx-122965999 AX-385274905 5 64800911 CCTTTCATCTGTGTGTCTTGAGTGGAATCAATCTC[A/G]TGTTCAGCTTCAGGTAGATTGAGTTAGATTTTCTG R 2 1 2 1 101000 f 74 goat snp28768-scaffold310-2741783 5 65609309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788400 Affx-122932146 AX-385275418 5 64830339 TAGAGAGTCAGAGACTCAGGGTCTCATTGATTTTG[C/T]GGACATAGACAAACCCCTTAATCAGTGGGTCCTTT Y 2 1 2 1 101000 f 74 goat snp28769-scaffold310-2771211 5 65639337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278396 Affx-1111836319 AX-519551881 5 64858996 ACACCCCGGCTTATTCCTTCTTCCTGATCTCTATT[A/G]CTGTTAGTGCCTCCTTGTCAGCCAAACCTACCTGG R 2 1 2 1 201000 r 74 goat Random2.2K-572 5 64858996 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397185 Affx-122962411 AX-123267540 5 64874187 GAGAGGTCTGTTGATCAAGGCCAACTTTGATGCTC[A/G]TCTTAAACAACTCTCCTTCTCACTGGCCTTCGACA R 2 1 2 1 101000 f 74 goat snp28770-scaffold310-2815059 5 65682039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417933 Affx-122946716 AX-123288281 5 64940736 AGTGCAGACATAAAGTTCTGTCACTTCTTGTGTGC[A/G]TCCTCTCTCAAGGAACCCTCTCCCAGCACCTGCCC R 2 1 2 1 101000 f 74 goat snp28771-scaffold310-2881608 5 65748852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382738 Affx-122973606 AX-123253096 5 64989432 TCACTTATGCTCTCCCCAAGAGGGGATCACTAGCA[A/G]CTTGTGTGTACAAGGTAGGCTAGGGAGAACACTAC R 2 1 2 1 202000 r 74 goat snp28772-scaffold310-2930304 5 65798371 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802570 Affx-122968424 AX-385289472 5 65034724 ATGGTGAAATTTTATTTCATGTCTTTACACATATG[C/T]AAATATGCCATTTTGAACATATGCTTGGAGGGAAG Y 2 1 2 1 201000 f 74 goat snp28773-scaffold310-2975596 5 65844051 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392798 Affx-122965972 AX-123263155 5 65068067 CCAGCACCCAGATCAGGACCTGGCACAGAGCAGAT[G/T]CTCTAAAATAGTTGTTAAATGAATGATGTATTCTC K 2 1 2 1 101000 f 74 goat snp28774-scaffold310-3008939 5 65878001 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802286 Affx-122922508 AX-385289190 5 65101558 TTTTGTCCCCTTGATCTATCCATTACTGAGAAAGA[C/T]GTACTAAAATCTCCCTAGAGATTTGTCAGTTTTTC Y 2 1 2 1 202000 f 74 goat snp28775-scaffold310-3042430 5 65911846 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438882 Affx-122930739 AX-123309219 5 65130342 ACTTGGTAACTTTTCACAGCTTGGAGTAAGAAGTT[A/G]GGAAAAGTTTTATTTTAAATGGTTTGGGGGTCTTG R 2 1 2 1 201000 f 74 goat snp28776-scaffold310-3071214 5 65940461 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406405 Affx-122955222 AX-123276757 5 65188770 ACCCTCTGAACTTGCCCTTGCCCAGCTTTCTAGTC[A/G]AAACTTCACTGTCTCTTCTATCCCTGTCCTGTTTG R 2 1 2 1 101000 r 74 goat snp28777-scaffold310-3129642 5 65999922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429741 Affx-122937596 AX-123300082 5 65233719 TTACTCATAAGAGAAAGGATCTGACCAGGGTCTGG[A/G]CCAGAAAGGTTCCAGCGCAGCTGGGCCCAGATGTC R 2 1 2 1 101000 f 74 goat snp28778-scaffold310-3174591 5 66044597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781683 Affx-122934513 AX-385268766 5 65265493 TATTTGCCAGTTGGCACTTGCCCAGTTTTCCAAAA[C/T]AGTCTGTACAAGGAGCACAATCTGTACAAGGAGCT Y 2 1 2 1 101000 f 74 goat snp28779-scaffold310-3206365 5 66076883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384179 Affx-122972414 AX-123254537 5 65341137 AAAAAGTCAACATTCATCACAACAGAATTGAAACC[A/G]TTTCATTACCTTTCCCAGACACAACAGGCATTCAT R 2 1 2 1 101000 f 74 goat snp28781-scaffold310-3282009 5 66153133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400585 Affx-122960404 AX-123270940 5 65387676 TTTTTATGGAGACATTTTTGGAGTCGTCTTCATTA[C/T]GCAGGCATTTATGGAGTCTTTGTTACATGGGCAAT Y 2 1 2 1 101000 f 74 goat snp28782-scaffold310-3328548 5 66199394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410860 Affx-122952609 AX-123281210 5 65435546 GACTCTCCTCACCCTACCCCAGCCACCACCTGGAG[A/G]GCATCCAGCCATCTAGTGGTCAAGATGGAGCCAGG R 2 1 2 1 201000 r 74 goat snp28783-scaffold310-3376418 5 66247713 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799031 Affx-122976133 AX-385285961 5 65480171 GTTATTGTCACATCGAAACACAACAATGACACTCA[A/G]CACATCTGGGAGTCCGACTCCAATGAATTTTCTGT R 2 1 2 1 101000 f 74 goat snp28784-scaffold310-3421043 5 66292335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377979 Affx-122977615 AX-123248338 5 65523777 GTCCCTGGAGAAGCCATGATGCCAGGTAAGAGAGT[A/G]GAAAATCAATCTGATTGTTAAGGATCTCTCATCCC R 2 1 2 1 101000 r 74 goat snp28785-scaffold310-3464649 5 66336044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443271 Affx-122927485 AX-123313608 5 65561052 GATGACATGTGTTCTAAAGAAGGTTTCTTATTCTC[C/T]CCTATGCGTTTTACAAGAATTATAGATCTGCATAG Y 2 1 2 1 101000 r 74 goat snp28786-scaffold310-3501924 5 66373229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278240 Affx-1111836320 AX-519551728 5 65612579 GTGCGTGATCTTAATCTATCCTAGCATCACATCAT[A/T]GAGGGTGATGGAGTCAAGATTTTGTGACTGGCTGG W 4 1 2 1 101000 f 74 goat Random2.2K-573 5 65612579 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782754 Affx-122928271 AX-385269826 5 65617648 TGCTGGATTCTCAGGACCTGACACTGTGCCTAGGA[C/T]ATACATAGTTGAGAGATGTATGATTTGTAAATGGT Y 2 1 2 1 101000 f 74 goat snp28787-scaffold310-3558520 5 66430098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798360 Affx-122942319 AX-385285295 5 65711379 GAAGACTGTCTGGGTTGGATGACTCTTCAAGCAGA[C/T]ATCTATTTCTTATCCGGCTCTAGGGACACCAGAGT Y 2 1 2 1 101000 f 74 goat snp28789-scaffold310-3652251 5 66524332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415932 Affx-122948445 AX-123286281 5 65754015 TGGGGCGGAAGACTATTACTTGATGCTTCTAAAGA[C/T]GAATTCCCTAACACAGAACCAGATAATAGCTGCCA Y 2 1 2 1 101000 f 74 goat snp28790-scaffold310-3694887 5 66567994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391740 Affx-122967486 AX-123262097 5 65802767 AGTTTTAGTTTCTAATATTCAAAGCCCCGTCCACA[G/T]TATTCAAAGCTCTTTGTGGGAAATCCTAAATAATT K 2 1 2 1 101000 r 74 goat snp28791-scaffold310-3743639 5 66616878 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434691 Affx-122933954 AX-123305032 5 65837044 AGACTTTCTAGGGAAGGAGAGGAGCCAGTTATTGT[C/T]ATTCTTTTTCAAAAACAGTGTGTTGGATTCTTGGG Y 2 1 2 1 101000 f 74 goat snp28792-scaffold310-3777916 5 66651149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442110 Affx-122928351 AX-123312447 5 65873389 AAGACCCATGTCTGGCTCAGTGCTGGGTGCAAGCA[C/T]GCAACTCAGTAGCTGATACATTGTTGGTGCTCAAG Y 2 1 2 1 102000 r 74 goat snp28793-scaffold310-3814261 5 66687354 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768698 Affx-122953012 AX-385255876 5 65906689 ATGGTGACATTCTCTCTTAACTGCAATCAGTCCCA[C/T]GAACTTAGCTTTGCTTGATCTATGGGTTTTTCTGT Y 2 1 2 1 101000 f 74 goat snp28794-scaffold310-3847561 5 66721056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389411 Affx-122968373 AX-123259769 5 65936300 GATACAGCAGGGACCCAAGTGGACAAGACTTGAGG[C/T]GGGGAGACATAATATAAACAAATGCATGTTTGAAC Y 2 1 2 1 201000 f 74 goat snp28795-scaffold310-3877172 5 66750646 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439357 Affx-122930282 AX-123309694 5 65977957 CATGTTTGCATATGTGGTGATGCTGGCTGGCAGCT[A/G]CAGGGACCCAGTGCTCATTTTGCTTGGTTTACAGC R 2 1 2 1 101000 f 74 goat snp28796-scaffold310-3918829 5 66792530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422612 Affx-122943722 AX-123292958 5 66051414 TTTTTCCTCCTCCAAAGTGTTGCTATGTCATTGTG[C/T]GCTGAGGGCAACCTGCATGCATTTAACAGTTTACC Y 2 1 2 1 101000 f 74 goat snp28798-scaffold310-3992286 5 66865739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278400 Affx-1111836321 AX-519551885 5 66061080 TTTTTTTTTTTTAGTAATAATTTTTACCTTTCTAT[A/G]CTAATATCTTTTTCATGGAAGGGCACTTTAAATAG R 2 1 2 1 101000 r 74 goat Random2.2K-574 5 66061080 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390512 Affx-122967246 AX-123260869 5 66102999 GGGCAGCCTCCTGCAGCACCCTCTGCCTTGAATTC[C/T]GCCTTACCCAAGCATGATTTTATTAAGATGAGGCC Y 2 1 2 1 101000 r 74 goat snp28799-scaffold310-4043871 5 66917424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407583 Affx-122954663 AX-123277934 5 66135580 TTTTAGGCAAAACAAAGAGCAGCGCTCTGTGCCCA[C/T]GGAGCTTGCTCTTGGGTGATCTTAGTTTGGGTCAT Y 2 1 2 1 101000 r 74 goat snp28800-scaffold310-4076452 5 66950006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411197 Affx-122952369 AX-123281547 5 66225393 TGAATGACCCAAGGGAGAGCTAGAAAGACTGAGTG[C/T]CCAAGCTGGAAACCACAGTCTTCTATTTACATAAT Y 2 1 2 1 101000 f 74 goat snp28801-scaffold310-4166265 5 67036930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384307 Affx-122972280 AX-123254665 5 66305075 ATCCATCTTCCCAATGTTTACCTGTTAAAATGAAT[A/G]TTTTCATGTATCACTGAGTAAACTATATGCCCTCT R 2 1 2 1 101000 r 74 goat snp28803-scaffold310-4245947 5 67116313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779679 Affx-122968283 AX-385266779 5 66343962 CTTGCAACAATATTCATTCCCTCTCTATTGAGAAG[C/T]AGTTACATTCCTTTCTTTGTGTGCAGTTCTGGTAA Y 2 1 2 1 101000 f 74 goat snp28804-scaffold310-4284834 5 67155123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428390 Affx-122938954 AX-123298733 5 66397111 TAAATGGTCCCATGACTGATTTTCAGGCAACAATC[A/G]GCTCAAAAAATTACAAATAGCTAGCAATCAATTTT R 2 1 2 1 101000 f 74 goat snp28805-scaffold310-4337983 5 67208231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379959 Affx-122975638 AX-123250317 5 66426540 GTGTGCTTGATCAGTTTGAGGAACATCAAGGCAGC[C/T]AGGGTGGCTAAACAGAATGAGAGGGTAGATGATAG Y 2 1 2 1 101000 f 74 goat snp28806-scaffold310-4367412 5 67237819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425988 Affx-122941151 AX-123296334 5 66516888 GTCTTTATATAACTATTAAAACAAACAAATAAAAC[C/T]CAACACACCTCTTGCAAAGAAAGCTAAGACTAGCA Y 2 1 2 1 101000 r 74 goat snp28808-scaffold310-4457760 5 67328157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431446 Affx-122936502 AX-123301787 5 66598572 AGAACGGTCACCAAGCAGTCTTCCCACACTGTTCC[A/G]ACTGCCTCCCCACTTCTCAAAGCCTGCAGTCCTGC R 2 1 2 1 102000 f 74 goat snp28809-scaffold310-4539444 5 67409838 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421747 Affx-122944370 AX-123292094 5 66637415 AGAATGCTTCCTTTTAGTGAAATATTCTAGGTCAC[C/T]GATGACAGAAAAGCCAGGTGCTAGGTGGTTGGGCT Y 2 1 2 1 201000 f 74 goat snp28810-scaffold310-4578287 5 67448712 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770402 Affx-122922921 AX-385257568 5 66670319 TAAAGGGTGGGGAAGTACTCTACTTTTTCAGTATT[A/G]CTAGAAATGGTCCTAAGCATGACCCTCATTAGCCT R 2 1 2 1 101000 f 74 goat snp28811-scaffold310-4611191 5 67481464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417265 Affx-122947260 AX-123287613 5 66699787 TCCTGTATTCCTCTGCTAGCTTCCCTGCTATTTTG[C/T]AATTATGTTGCTTATAATCTAACTGCCTGGTTAAA Y 2 1 2 1 201000 r 74 goat snp28812-scaffold310-4640659 5 67511008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791794 Affx-122949323 AX-385278784 5 66735981 GTCTAGGAAAATTGTCAGTAAGTGAGTTACTAAGG[G/T]CAGTTGATAACAGGATCTTTCAAAATACACTCAGT K 2 1 2 1 101000 f 74 goat snp28813-scaffold310-4676853 5 67547272 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424161 Affx-122942534 AX-123294507 5 66794249 TTGCCTGATGGAGGGTGCCTGTGACGACGTGTTCC[A/G]CTGTGCAAGGGGGCTCGAGGGCATGCTCTGAATAG R 2 1 2 1 201000 f 74 goat snp28814-scaffold310-4735121 5 67605565 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278244 Affx-1111836322 AX-519551732 5 66816576 ACTAGACCTCGAAGGAATGCTCTACCAGTCAAAAA[A/G]GCAAAGGCAGGCACTCTTGGCAGAAGAAATTGCAA R 2 1 2 1 201000 f 74 goat Random2.2K-575 5 66816576 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781628 Affx-122935870 AX-385268712 5 66844021 GGGAAGGAATTGGCAGAAAAGAAGGGAGTTCAGAG[C/T]GAGAGGAGATGATTTCTAACTGAGAAGGGTACCCA Y 2 1 2 1 101000 r 74 goat snp28815-scaffold310-4784893 5 67656166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464373912 Affx-1110453853 AX-515847322 5 66875041 ATGCTACTGCCTGCTTACAACATAATATGATTTGT[A/G]TATGTTATTTGAAATTTTCTAGCAGTCACGTTTTG R 2 1 2 1 101000 f 74 goat 5_66875041_AF-PAKI 5 66875041 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378110 Affx-122977145 AX-123248469 5 66876251 ACAGGAAGCTAAATATTGAAGATGGAATTTGCCTA[C/T]GGCTCCATAGCTATCAAGTGGCAGGGTGGAGATCT Y 2 1 2 1 101000 f 74 goat snp28816-scaffold310-4817123 5 67691110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445252 Affx-122925481 AX-123315589 5 66920183 TCACCATTAGAATGAGAGTTCCCAGTGTGCAGAGA[C/T]GGGATTTGCACCTGGTGGCATCCCCAGTAGCTAAC Y 2 1 2 1 101000 f 74 goat snp28817-scaffold310-4861055 5 67735283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447668 Affx-122923956 AX-123318004 5 66971547 TTTGAACTTGAATATCCCTTCTCCTTCTGTGTGTT[A/C]GCAGTCCCTGGCCTCCCCTCAAGGAGTGTCCTGGT M 2 1 2 1 101000 f 74 goat snp28818-scaffold310-4912419 5 67786745 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772838 Affx-122921913 AX-385259983 5 67073281 AATTGCAAGGTTAAGTCTCAGTAGTAAATTTATAC[A/G]TTCAAGACCATTTCCAGCTATGCAAAGAATTTCTA R 2 1 2 1 101000 f 74 goat snp28821-scaffold310-5014153 5 67890089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780675 Affx-122968280 AX-385267765 5 67113079 GGTCAGCAAGAGTCAATTTATACTGTGGTAACAAA[C/T]AACCTCCAAATCACAGTGGCACAATTAACAAAACA Y 2 1 2 1 201000 r 74 goat snp28822-scaffold310-5053951 5 67926083 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394037 Affx-122964995 AX-123264392 5 67141675 CTGTTCAAATCTTATTGTCTCACATCTGGTTTATC[A/G]TGGTAATCTGCTCACAAATCACTCTTCTCTCAGTC R 2 1 2 1 101000 r 74 goat snp28823-scaffold310-5082547 5 67954671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800589 Affx-122929507 AX-385287508 5 67174079 AGATCATGACAGATATAAAAGCGTTATGTTCATTT[A/C]TAAAATGATGAGGAAGAAACAAGTTGGGCCTTTAA M 2 1 2 1 101000 r 74 goat snp28824-scaffold310-5114951 5 67987054 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381309 Affx-122974446 AX-123251667 5 67217856 TGGAAACAACTTAGCGACTAAGCCACTGCCACCCA[C/T]AGAATTTTTACAGTTCAAATTCCCTCAAGCCTTTT Y 2 1 2 1 101000 r 74 goat snp28825-scaffold310-5158728 5 68030912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443646 Affx-122927205 AX-123313983 5 67250823 CCTTGAACTCATATCCAGAGATTCTCCCCATCTTA[C/T]ATTCCATGTCCTGGTAAACTGCACCACATCCATTA Y 2 1 2 1 201000 r 74 goat snp28826-scaffold310-5191695 5 68063875 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393289 Affx-122965441 AX-123263645 5 67322821 TATTCAATACATGATATTGACACAATAGCTCAATT[A/G]CAAAGGGAAAAAATCAAATTAGATCCTACTCAATG R 2 1 2 1 101000 f 74 goat snp28828-scaffold310-5263693 5 68136147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443232 Affx-122927563 AX-123313569 5 67352820 CCCAGATGAAGAGAACCCTGGCAGGGGGCAGGCAG[A/G]GGAGGCTGACATGGGAAGCAAGTGTGGCTGAGTTA R 2 1 2 1 101000 r 74 goat snp28829-scaffold310-5293692 5 68166162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799905 Affx-122955954 AX-385286831 5 67386088 TGCTTTTGTGCCCTTGGATGAGAGGGGTTCGAGAA[C/T]AGAGGAGATGGTGAACTAACACTTAAAGGTATCAA Y 2 1 2 1 101000 r 74 goat snp28830-scaffold310-5326960 5 68199490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784774 Affx-122934877 AX-385271821 5 67424976 AAGCCTAGAATGAAGGAATCATCCAGATAAACCAA[C/T]ATTTGAGAACTGAGCTGGCTGAACTTTCTGATTGG Y 2 1 2 1 101000 f 74 goat snp28831-scaffold310-5365848 5 68238381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782174 Affx-122973261 AX-385269252 5 67466250 CTCTAGCACATTTTTCTCTAGCAGAGACAAAAGCT[A/G]TCAAATGTGTCATTCAGGCATTATCTGGAATGTGC R 2 1 2 1 101000 f 74 goat snp28832-scaffold310-5407122 5 68279634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775425 Affx-122922031 AX-385262556 5 67502193 CTTGTCAGGTGCCTCTTGCATTCACTGATATTTGG[C/T]AAAATGTTTGGCTATGGGCTCAACAAATGTCCACT Y 2 1 2 1 101000 f 74 goat snp28833-scaffold310-5443065 5 68315409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799952 Affx-122960591 AX-385286878 5 67536514 ACAGCCATGGCATCAGTTTCATCTGCATCCCCAAG[A/G]AAGTGACTGACAACTACTTCCATGTCCCCAAGAGA R 2 1 2 1 102000 f 74 goat snp28834-scaffold310-5477386 5 68349595 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413075 Affx-122950963 AX-123283424 5 67569878 GGGTTAGGTGATCCCCCCATGCCACCTTCCCCCTC[A/G]TGGACTGTGCTCTTCTGTCAAGATGGTCAATATGA R 2 1 2 1 101000 r 74 goat snp28835-scaffold310-5510750 5 68382932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453638 Affx-122919739 AX-123323971 5 67614291 TCTCTCACTATAGAGTTGTTTTAATGACCTTGCTT[A/G]TTAACCACTGTTAAGACCTTCCCATTTGGGAGGCA R 2 1 2 1 101000 f 74 goat snp28836-scaffold310-5555163 5 68427675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278246 Affx-1111836323 AX-519551734 5 67657632 GCAGTATAATTGAAGGAAACCCTCAAGGAGTAGGC[A/G]TATTTCTGAGGCATGCATCACCTGCCACAAAGTTG R 2 1 2 1 101000 f 74 goat Random2.2K-576 5 67657632 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791524 Affx-122949006 AX-385278515 5 67662170 TTCAGCTCCAAACTACTTGGACTTTTTTAAAGTTC[A/G]GTGTTAACGCAGCTTCTGTTTTGGTTTTTGTCTGA R 2 1 2 1 202000 r 74 goat snp28837-scaffold310-5603042 5 68475797 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388528 Affx-122969201 AX-123258886 5 67695115 AAATAGCTAAGGTCCATTTCAAAAGAAAAGTTGTC[A/G]TTGCTCAACTGATCATTTTACTCTTTGCTCCTCAT R 2 1 2 1 101000 r 74 goat snp28838-scaffold310-5635987 5 68508663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398233 Affx-122962206 AX-123268588 5 67762426 AGAATGGTTTGATAGTACTGTTGTGAGTATATGAT[A/G]TGAAAGGGGTACTAGGTAGCATATATTCAATACTT R 2 1 2 1 101000 f 74 goat snp28839-scaffold310-5703298 5 68575388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803599 Affx-986696133 AX-385290392 5 67825443 AGTGTGACCTACATTGTTTTACCAGCAGGGCTTCC[A/T]GAGGCTATTGATTTTGCTGAGAAGCAAGCTGAGGC W 4 1 2 1 600010 r 74 goat 5_67825443 5 67825443 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38409852 Affx-122952928 AX-123280203 5 67863451 GTTATTTCCAGGCCCAGGCCAGCTAATAGCCATCC[A/G]TTATCCCAATGACAATAAGAGCCTTGATAGGTGAG R 2 1 2 1 101000 r 74 goat snp28841-scaffold310-5804323 5 68676723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409513 Affx-122953629 AX-123279864 5 67893363 GGAGTTCAACCTGGGCAGTTTGATCCAGCCCCACG[C/T]GGTTACCCACCGTGCTCTATCTACGGCTCACAGGA Y 2 1 2 1 201000 r 74 goat snp28842-scaffold310-5834235 5 68706708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796190 Affx-122935608 AX-385283141 5 67926258 TGTGAAGACGACTTTCATGGTTCCTTCATAAGACT[A/G]TAATAATTTCCGACACTTTGATAGAAAAAATTCAA R 2 1 2 1 101000 f 74 goat snp28843-scaffold310-5867130 5 68739734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788883 Affx-122921674 AX-385275898 5 67973344 AGCTTTGCTTTTTGACTTTAGTTCATTCCTGAAAA[C/T]GTTACCTCTTAGTGAAAAGATTTTAAAGCAGAAGA Y 2 1 2 1 202000 r 74 goat snp28844-scaffold310-5914216 5 68786574 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431048 Affx-122936649 AX-123301389 5 68009418 TGCTAAATACTTCTTTATTCTTGCCTGATTATACT[A/G]CACTGTTCCTTGGCTCATCTCCACCGCTTTGCAGA R 2 1 2 1 101000 r 74 goat snp28845-scaffold310-5950290 5 68822646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786324 Affx-122953105 AX-385273358 5 68066504 ATAAAAGTTTGTAAAGTGAAACTGAGGAGAAAGGA[A/G]CTGAAGGGAAGGCAGGGGCACTTAAAAACTCATTA R 2 1 2 1 103000 r 74 goat snp28846-scaffold310-6007376 5 68880150 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382026 Affx-122974955 AX-123252384 5 68108449 GTTTCTACATATATTAAAATATGTAGAATAATGTA[A/G]CTAATTGATTTATAGTCTTTTTCGTATAGGGAAAT R 2 1 2 1 103000 r 74 goat snp28847-scaffold310-6049321 5 68923042 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383644 Affx-122972530 AX-123254002 5 68147151 TGTATGAGGAATGACAACACAACCCTGTACATTGT[A/C]ATCAACACTTGAAACTGACCAACTGAGCTATGCCA M 2 1 2 1 101000 f 74 goat snp28848-scaffold310-6088023 5 68962168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375995 Affx-122978420 AX-123246354 5 68190601 CTCTCTTCTCATGTAAGAAGAGAGGGACGTGGAGT[C/T]GGAGATGGAAGGTGACATGGAGAGAAGGGAAAATA Y 2 1 2 1 101000 f 74 goat snp28849-scaffold310-6131473 5 69005520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387454 Affx-122970371 AX-123257812 5 68303026 TGAATTCCTTAGGAGTGAGAAATGGACCTTTATTC[A/C]GAAATGGAGAGAGGAGGAAGGGGGATAGTTTCATC M 2 1 2 1 101000 f 74 goat snp28851-scaffold310-6243898 5 69119673 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384919 Affx-122972338 AX-123255277 5 68334219 CCTGTTGCGGCATGTGGTGTCAAGGGGAAGAACAG[C/T]GGTTTCTGGCCCCAACAAAACCCTGAAAATATGCC Y 2 1 2 1 101000 r 74 goat snp28852-scaffold310-6275091 5 69150811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446189 Affx-122925730 AX-123316525 5 68368902 CTAGTGAGTCCTTTCTTTATGGTCTTTTCCTGTTT[C/T]ACAAAGCATCCTCTGTTTCCAATGACACCAAAGCT Y 2 1 2 1 201000 r 74 goat snp28853-scaffold310-6309774 5 69185399 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398422 Affx-122961624 AX-123268777 5 68401727 AAAGAGTGGGACACGACTGAGCAACTGAACTGAAA[C/T]GAACTGAACTGAAGGAAGAATGCAAGTTTTCCAGA Y 2 1 2 1 103000 r 74 goat snp28854-scaffold310-6342599 5 69219008 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387269 Affx-122970549 AX-123257627 5 68440402 ATCTGGTGAGGAGATGGAGACTTACAGGTGGAAAA[C/T]AACAATAATGGTAGTATCATTTGAGGGGCAGATTC Y 2 1 2 1 201000 f 74 goat snp28855-scaffold310-6381274 5 69257345 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386873 Affx-122970060 AX-123257231 5 68489902 TGCTTAGAGTGCTGCAGGGTACGACATGTGCTGTG[C/T]ATTGCCCAACTCCTGGGGCACCTTTCACTTAGGTT Y 2 1 2 1 202000 r 74 goat snp28856-scaffold310-6430774 5 69306887 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420661 Affx-122944821 AX-123291008 5 68520308 TCTTGTGTATCCCCTTCACTAGGATGTTAGGTCTG[C/T]ATGGTTGGAGACTGTGGTTTGCGCAGGGCTGTCTC Y 2 1 2 1 201000 r 74 goat snp28857-scaffold310-6461180 5 69337616 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427007 Affx-122939848 AX-123297352 5 68551825 GCATGAGTATCCTAGGGCTGCTGTGACCTATTACC[A/G]CAATCTTTGTGTCTTAAAACAATAGAGATATATTC R 2 1 2 1 101000 f 74 goat snp28858-scaffold310-6492697 5 69369038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432496 Affx-122935584 AX-123302837 5 68593078 CTTTTAATCTGAGGGTGTGGGACTTTGAGATATGG[C/T]GCTCACGGCTCATCTAAATACAAACTGCTTCAAAA Y 2 1 2 1 101000 f 74 goat snp28859-scaffold310-6533950 5 69410361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446112 Affx-122925790 AX-123316449 5 68656668 TTGTGCCCGGAAGAGTATCTGAGACCTCGGGGAGT[A/G]CTGTCTCTTCAGTCGTGTCTAACTCTTTGAGACCG R 2 1 2 1 201000 f 74 goat snp28860-scaffold310-6597540 5 69473474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432137 Affx-122936435 AX-123302478 5 68701091 TCTCCACCCACTCCTTCCCCAATCTATGGAACCAC[A/G]TCTTTTCTGGGCTCAGAGGAGACTTAAGTGCTGCT R 2 1 2 1 201000 r 74 goat snp28861-scaffold310-6641963 5 69517705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402543 Affx-122958468 AX-123272896 5 68750664 CACATCGTGAATGCTCGGGAAGTACTAGAGTGCTC[A/G]CTGTACAACTGGTTACACAGCTTCCTTTTTCCTGG R 2 1 2 1 101000 r 74 goat snp28862-scaffold310-6691536 5 69567168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384214 Affx-122972385 AX-123254572 5 68864225 CCATAAAGTAAAATGAACCACCCTCCCATCCCCAA[G/T]CCAATTTAGGCAGCCGAAGACAAAAGTTTAGTATG K 2 1 2 1 201000 r 74 goat snp28864-scaffold310-6805097 5 69680939 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409380 Affx-122954153 AX-123279731 5 68895871 ATATTAAAGAGGTACACTTACTAAGCACACCCTGC[A/G]AAGTGTAAGGTGCACAGCTTTACACGAGATATGAC R 2 1 2 1 101000 r 74 goat snp28865-scaffold310-6836743 5 69713653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442670 Affx-122927897 AX-123313007 5 68925209 GAGATGTGAGGTACATTGAAACTGCCAAAATTTCA[C/T]GGGTATTCATCACAGGTAATAAGTAGTGAAGGGGG Y 2 1 2 1 101000 r 74 goat snp28866-scaffold310-6866081 5 69743011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436841 Affx-122932216 AX-123307179 5 68965839 TATTTTTAGGAAATTCAGTAAAATGAGGTTTTATT[A/G]TGAACGTCTCACTCTTTCATTTTTCAGTTTAGGAC R 2 1 2 1 201000 f 74 goat snp28867-scaffold310-6906711 5 69784150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398036 Affx-122961765 AX-123268391 5 69128759 CCAAAATCGAAGGCACAACATTTATGAGCATTAAA[C/T]GAAAAGTCAGCTGAGCTAAGTAAGGGCTGACAGAT Y 2 1 2 1 201000 f 74 goat snp28871-scaffold310-7069631 5 69947116 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453932 Affx-122919491 AX-123324265 5 69166557 GTTTTGAAACCTGGGAAGTCCCAGGCACATAGAAT[A/G]AGTAGGTCATCCTATACAACCCGTGACAGTCACGC R 2 1 2 1 201000 r 74 goat snp28872-scaffold310-7107429 5 69985342 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450360 Affx-122922102 AX-123320695 5 69258655 CAGTCATGTGCAGGGGAAAGTTGCAGGAGAAACTT[A/G]TAGTTTTCTGAGTTTTCACCATCTCCCCACTATGT R 2 1 2 1 101000 r 74 goat snp28874-scaffold310-7199527 5 70076623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431173 Affx-122937187 AX-123301514 5 69315153 GACTTGAGGTGAGTCCTGAGCACGAATCACCTGAA[A/G]TTTCCCTCTGAAAAGTTGGTGGAACCACAGTCCCA R 2 1 2 1 101000 f 74 goat snp28875-scaffold310-7256025 5 70133146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380641 Affx-122975226 AX-123250999 5 69353872 GTGCCTTACAAATATTATTTTATTCCTCATAACCT[C/T]CTTATAATAGAAGGATGATTATCATCCTAATTTTG Y 2 1 2 1 303000 r 74 goat snp28876-scaffold310-7294744 5 70171984 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464375651 Affx-1110454718 AX-515849041 5 69435586 TTCCAGTAAATAGCACTTGCATGCCTACTGTCTGC[C/T]CCCTTATCTTCCCCTCCAGGCTGAGGGTCTGTTGT Y 2 1 2 1 101000 f 74 goat 5_69435586_AF-PAKI 5 69435586 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38451731 Affx-122921540 AX-123322064 5 69466760 AATTTGTCTGACCTTGGGCAAGCCCATTCTCAGGG[A/G]GCCTTGGTTTCCTCATCTGAAAATAAGAACAGAAG R 2 1 2 1 201000 f 74 goat snp28878-scaffold310-7407632 5 70284420 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774305 Affx-122953139 AX-385261441 5 69607178 CCGATACTCACTGTCTCTGCAAAAGCCTAGCATAA[C/T]GGATGCTCAAAAAGCTATTTAGTGAATGAATAAAT Y 2 1 2 1 101000 f 74 goat snp28881-scaffold310-7548050 5 70424314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442314 Affx-122928239 AX-123312651 5 69649148 TTTTCTTTGTGACTTCTCAGTGAACACTTTCTTGA[C/T]GGAATAGTGCTAAAGCTGAGAATGAAAGGGTGATA Y 2 1 2 1 201000 f 74 goat snp28882-scaffold310-7590020 5 70466486 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413067 Affx-122950967 AX-123283416 5 69682626 TCATTCTGGACTTAAAAAAAATTCATATTGCAGTA[C/T]AGTTGAATTACAGTGTTGTTAGTTTCAGGTGTATG Y 2 1 2 1 201000 f 74 goat snp28883-scaffold310-7623498 5 70500098 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796468 Affx-122963808 AX-385283418 5 69715927 GGATGTTTTGTTTCATAATTTAACTAACATGACAG[C/T]GGATAATTATTTTACCATTGGACTTTGACCATTGG Y 2 1 2 1 101000 r 74 goat snp28884-scaffold310-7656799 5 70532925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416355 Affx-122947886 AX-123286704 5 69776381 CTGAACTTGGTCTCTGATGCTCTCTGGTTGTGTGA[C/T]GCTGGGACAGTCACTGAATGACTCTGTTCTCACCT Y 2 1 2 1 201000 r 74 goat snp32943-scaffold383-8054 5 70593210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451604 Affx-122921636 AX-123321937 5 69820383 GCTTCACTGCATGTTTATAACTCAACCAATGAGTA[C/T]GCAAACGCAGAAGGAAGAGGTGGGTTGTGCTGGTC Y 2 1 2 1 101000 f 74 goat snp32944-scaffold383-52056 5 70637445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378650 Affx-122977097 AX-123249009 5 69854979 CTGCTTTACATCAAGGCAGATAATACCATCTAGTA[C/T]GTAGATATTGACACATTTTCCCAAGGGAGACTATG Y 2 1 2 1 101000 f 74 goat snp32945-scaffold383-86652 5 70672319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444074 Affx-122926846 AX-123314411 5 69895669 ACTCTGCACAGTACAGATGGGTAAGGCCCTAGAGA[C/T]GGCTTGGTAGCTTTGAGTCTGTGGGTGAGCCTCTT Y 2 1 2 1 101000 f 74 goat snp32946-scaffold383-127342 5 70711845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399137 Affx-122960659 AX-123269492 5 69928227 GGTGGAGACCGAACACCAGCACGTTGGGTTAAGCC[A/G]TCTAATTAGACAGCTCCATCTCCCGGCTTTATTTT R 2 1 2 1 102000 f 74 goat snp32947-scaffold383-159900 5 70744300 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442635 Affx-122928456 AX-123312972 5 69972329 TTTGGGTCGGAACCCTGGCTGCATTAATGACTAAG[C/T]GAATGCAAGCATGTGACTTCATCTCTCTAGGCCTC Y 2 1 2 1 101000 f 74 goat snp32948-scaffold383-204002 5 70788311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390816 Affx-122967852 AX-123261173 5 70008210 CAATCTGAACTCAGGTTCACTGGCTCCAGATCAAT[G/T]TCTCTATTTGCCCCAACCATAATGTTTCCTATTTG K 2 1 2 1 101000 f 74 goat snp32949-scaffold383-239883 5 70824246 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797437 Affx-122936364 AX-385284376 5 70037956 GAAAAGAATGATTAGGCAAGGTACCACAAAGCCCA[C/T]AGCAACTAAATGGTGGAAATGGTATGTGAACCACC Y 2 1 2 1 101000 r 74 goat snp32950-scaffold383-269629 5 70854202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278248 Affx-1111836324 AX-519551736 5 70042223 GGAATATCGAGTGGAAAGGACCGAGATGGGAGCAT[A/C]CTTGGTGTGTCCAAGGAGTAGCCAGTGAGCAGTGG M 2 1 2 1 101000 f 74 goat Random2.2K-577 5 70042223 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401497 Affx-122958942 AX-123271850 5 70072332 GTCACTGAGCAAGGGACCCCTGTACTGACATCCTG[C/T]GGGTCCCAGCTGGCAGGAGGCTTTCTTTTCAGTGC Y 2 1 2 1 102000 f 74 goat snp32951-scaffold383-304005 5 70888541 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449407 Affx-122922698 AX-123319742 5 70172178 AGATTTGGGGGCTGTTAGTATAAATAGCATAACCC[A/G]ATCCATCCTGATAAATATAAATGGTATATTAAAAA R 2 1 2 1 101000 f 74 goat snp32953-scaffold383-403851 5 70988119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415858 Affx-122948859 AX-123286207 5 70223966 TCCGTGTATGTCATCCCTCACCCACAGCACTCAGT[A/G]CCCACCAGACATGGCCTTGTTTTGCTGTGTCCTTC R 2 1 2 1 201000 r 74 goat snp32954-scaffold383-455639 5 71035571 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391289 Affx-122967345 AX-123261646 5 70277682 CAATTTTCACTAAAGTGTAAAGTACTCTTGAAAAA[C/T]AAAGGTACACTAAGAGACGTGTGAAACCTTCAAGC Y 2 1 2 1 202000 f 74 goat snp32955-scaffold383-509355 5 71089122 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407141 Affx-122954859 AX-123277492 5 70328901 TCCATGCTATAGATGTAGTCTTTCAAACATGTTCT[A/G]CTAGTTACAGGATTGGGGGATGAGAGCTGGATGTA R 2 1 2 1 201000 f 74 goat snp32956-scaffold383-560574 5 71140318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424630 Affx-122942178 AX-123294976 5 70421860 GCAGTAAACCACAACTCCCTTGAGAATAACAGCTG[C/T]GGGGAAAACATTAACACCCAGGAGAATACTCATAG Y 2 1 2 1 201000 f 74 goat snp32958-scaffold383-653533 5 71232715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442521 Affx-122928545 AX-123312858 5 70471384 ACTGTCTCTCAGCTTTTCCACTGAGTAGATTTGGA[C/T]GCTAGGAATTCTCTTGATCTCTTCATCTGTAAATT Y 2 1 2 1 101000 f 74 goat snp32959-scaffold383-703057 5 71282015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792179 Affx-122972715 AX-385279163 5 70506233 TAATGATTTCTAAGAAATTAATGGCCATGTTTATC[A/G]TGATATCTCCACTGCAAATTGCAGGCACCCCATAA R 2 1 2 1 101000 r 74 goat snp32960-scaffold383-737906 5 71316861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775109 Affx-122964774 AX-385262241 5 70609547 ACGGCTTCTTTAGACACATTCTTCGTACAGTGATA[C/T]GGTTCAGAAGCACAAGAGGGAAAATCCAAATAGGA Y 2 1 2 1 101000 f 74 goat snp32962-scaffold383-841220 5 71421898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275182 Affx-1111834750 AX-519548761 5 70625092 GCTGGAATGGCCCAGCTTGTCACAGGAAGCACATG[A/G]AGACTGCAGCCTCGTTCAGAGGGGGCCTGCCCC R 2 1 2 1 101000 f 74 goat GoatD01.051345 5 70625092 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421312 Affx-122944090 AX-123291659 5 70649321 GGCAGGACTCCTCCCAGAGGCATTGCCACTATTCT[A/G]CCATTGCTACATACTAAGTTTCCATCTTGGATGTT R 2 1 2 1 101000 r 74 goat snp32963-scaffold383-880994 5 71462532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389320 Affx-122968494 AX-123259678 5 70684218 GAACTCACAGAAGGTTTTGAGTTTACGGAGTTTGG[C/T]TCCAGAGCCCACATTCTCAATCAGTGTGTCTCATA Y 2 1 2 1 201000 f 74 goat snp32964-scaffold383-915891 5 71496946 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783383 Affx-122948178 AX-385270447 5 70715073 TTGTTCAACCAGGAAGCCAGGAAAACAATGAAACC[A/G]CAGTTTAAGCCTCTAGTGAAGGAGGGAAGGGGTGA R 2 1 2 1 101000 f 74 goat snp32965-scaffold383-946746 5 71527955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414279 Affx-122949601 AX-123284628 5 70745989 TAGGATGAACCAGATAACCCTGGTTAATGGAATGG[C/T]AGAAAAAGCAATGAAGATCTCTCCAGGGTAATTTG Y 2 1 2 1 101000 f 74 goat snp32966-scaffold383-977662 5 71557457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444008 Affx-122926900 AX-123314345 5 70797438 GTTCTCAGTACTCTTAGATTAAGCTTGTCAATTAC[A/G]TTGCTCAAATTATTTTTCAATTGTGTTCTATTCTT R 2 1 2 1 101000 f 74 goat snp32967-scaffold383-1029111 5 71608949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278408 Affx-1111836325 AX-519551893 5 70833566 AAGAGGAGGACAATTCAGAGACCCTTACTGACCAT[C/G]CATGTTGGCTGAGTGAGTCTCAGACATTATCTTAT S 4 1 2 1 101000 r 74 goat Random2.2K-578 5 70833566 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416850 Affx-122948102 AX-123287198 5 70847211 CATTTCTTTCTTTCATCTCTTTTCTTTTCTTTTGC[A/G]TCTTTGTTCTCTGGAAGTTTTCCTCACATGTCTGG R 2 1 2 1 101000 r 74 goat snp32968-scaffold383-1078884 5 71659183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779135 Affx-122927641 AX-314363912 5 70889722 CAGGTACTTACTTAATCTGAGCAATCATAAAAATA[G/T]AAAACATGCATTTAGAAACTGCAAAATATGTACTT K 2 1 2 1 101000 r 74 goat snp32969-scaffold383-1121395 5 71702243 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386930 Affx-122969998 AX-123257288 5 70937806 CAGGAAACATGCAACTTCTGCCTTCCCCTAGGGCC[A/G]CATCTTCTTCAAAGCCACTTGCATGCTAAGTTGTT R 2 1 2 1 101000 r 74 goat snp32970-scaffold383-1169479 5 71750592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780313 Affx-122937717 AX-385267408 5 70975465 GTTTTATTTTGTTTTGGTGGACAAAAACAACAGAT[A/G]CCAACTCCTAATAGCTTGTAGTCATTGTCCTAAAG R 2 1 2 1 101000 r 74 goat snp32971-scaffold383-1207138 5 71788347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409447 Affx-122954087 AX-123279798 5 71006103 TCAGCCTCTGGACCATCATTCCTGGCCTCCTCTGA[A/G]CACACCCTTGTCGGTGAGTACCCATTTCCAGCACA R 2 1 2 1 201000 r 74 goat snp32972-scaffold383-1237776 5 71818614 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392915 Affx-122965716 AX-123263272 5 71079797 TCCTGATTCTTAAATCACTAAGCGGACCAACAGAC[A/G]GAGCCCACGAGACACATTCTTACAGGCCCTGTTCT R 2 1 2 1 101000 f 74 goat snp6384-scaffold1225-15706 5 71894800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405562 Affx-122955955 AX-123275914 5 71126119 GATAACTATCAGATTTTGATACCTTGGGAAGTCTT[A/G]CCAATTAAATCACATCTAATAAGGGTTCATATTTA R 2 1 2 1 101000 f 74 goat snp6385-scaffold1225-62028 5 71941070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440314 Affx-122930210 AX-123310651 5 71179951 TTCCCTCTAATACCCACTTGGCTCACCCACCCCTC[A/G]CTTCCTTCAGCTCATGGTCACCTACTCCACAAGTT R 2 1 2 1 101000 r 74 goat snp6386-scaffold1225-115860 5 72002876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449387 Affx-122922712 AX-123319722 5 71209845 GATGTTTTTGAATCCTTATCACCTTCATCGTCCCT[A/G]CTGATATAATTACAGACTTGTCCAAAGCGATATGA R 2 1 2 1 101000 r 74 goat snp6387-scaffold1225-145754 5 72032792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418151 Affx-122947099 AX-123288499 5 71372342 TGATGGCTAAGTTGGTTGCTGATTATATTACCCCA[C/T]AGCAGAATTTAAAAACAAAAACAAAAACCACTGAA Y 2 1 2 1 101000 f 74 goat snp34156-scaffold4005-143717 5 72193806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428730 Affx-122938450 AX-123299072 5 71440016 TCTCAGAAACCCTGCTGTTGTGTGATTGCCCCTGG[A/G]TCATCTGGTGAACTTGGACACATAACGTGGACACC R 2 1 2 1 101000 r 74 goat snp34158-scaffold4005-211391 5 72261468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441243 Affx-122929500 AX-123311580 5 71491573 CCCAGTTCCCACAGGGCCTCCAGATAGGAGGAGAG[C/T]GACAGAATTCTTCAACATCAGGGTTAGAAGGAATC Y 2 1 2 1 101000 r 74 goat snp16796-scaffold1759-626402 5 72310116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383875 Affx-122973133 AX-123254233 5 71527353 GATGGGGCACTTTTGGTGCTAACACCAAGAATGAC[A/G]TACATGTGTTACAGTCAAGGAAACTGAGACCCAGA R 2 1 2 1 201000 f 74 goat snp16795-scaffold1759-590622 5 72341102 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452909 Affx-122920205 AX-123323242 5 71579537 GATGGGGAAACGAGGCTCAGAGAGGCAAATGGCTC[A/G]CCCAAGTTCCCACTGCCAGGAAGTTGGAGAACTGG R 2 1 2 1 101000 r 74 goat snp16794-scaffold1759-538438 5 72393131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442357 Affx-122928029 AX-123312694 5 71608366 TGACAGCCAACTAGGCTGCTAGTCTAGCACCTCTC[A/C]TCTACAGAGAAGAGCCTTTAAACCCTCAACTCAAG M 2 1 2 1 101000 r 74 goat snp16793-scaffold1759-509609 5 72421963 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404992 Affx-122956394 AX-123275344 5 71652992 ATGTCCAAGAAGCACCTGGCATACAGTTGGTGCTC[A/G]CTAAGGGCTCTTTCCTTCCCTGCAGTAACCCTCTT R 2 1 2 1 101000 f 74 goat snp16792-scaffold1759-464983 5 72466642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437330 Affx-122931955 AX-123307668 5 71695539 AAATTCTGAAACCAGACTGCCCAGCTTTGAATTTC[A/G]TGCTTGGCCCGTTTCCTAGCCCTGTGACCTTGGGC R 2 1 2 1 101000 f 74 goat snp16791-scaffold1759-422436 5 72508643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447417 Affx-122924394 AX-123317753 5 71725002 GCTAAATGTTCTAAAGGAATCAAGCCAGAAGTCAT[A/C]GAATTGTAAGCAAGCAGATAAGTTATGGGGTCCCC M 2 1 2 1 101000 f 74 goat snp16790-scaffold1759-392973 5 72538406 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395558 Affx-122964244 AX-123265913 5 71763450 ACAAAACCTACCGGCACCATCCTCCTCCAGCAGCC[A/G]CAGTAGACTTGAGCCAATATTATCTTTCCTTGAAA R 2 1 2 1 101000 r 74 goat snp16789-scaffold1759-354525 5 72576756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801883 Affx-122936503 AX-385288790 5 71815928 ATGCTCATTTTCCTAACCTGTAAAACTGGTGATAC[G/T]AGTTCCTGACTCATAGAGTTGTTTTTAACAATAAA K 2 1 2 1 101000 f 74 goat snp16788-scaffold1759-302047 5 72629412 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476204 Affx-1251763709 AX-586011628 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20000 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 539476459 Affx-1251763709 AX-586011859 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 4 1 4 1 20000 r 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562165164 Affx-1251763709 AX-606940576 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166183 Affx-1251763709 AX-606941591 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166244 Affx-1251763709 AX-606941652 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166419 Affx-1251763709 AX-606941827 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166465 Affx-1251763709 AX-606941873 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 r 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 320778866 Affx-122964171 AX-385265974 5 71848626 GTTGGTCTGAGATTTATGAATCTTTAGAAATCCTG[C/T]AGTAAGTAGCCTTTAGGCTTTCAGCCATTGCTATT Y 2 1 2 1 101000 f 74 goat snp16787-scaffold1759-269349 5 72662228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454102 Affx-122919362 AX-123324435 5 71906246 AATCAGCCTGCTACATGCTTTCCATCTCATCTCTG[A/G]TACACAGCCTCTAAGATAGTCCCCATGATTCCTGC R 2 1 2 1 201000 r 74 goat snp16786-scaffold1759-211729 5 72720094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272316 Affx-1111833475 AX-519546052 5 71941838 GAACGGCACTGTTCAACGGAAGTTTCTGCAATGAT[A/G]ATGTTCTAAATCTGAGCTGTTCAGAATGGTAGCCT R 2 1 2 1 101000 f 74 goat 5_71941838_AF-PAKI 5 71941838 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399160 Affx-122960643 AX-123269515 5 72004015 AGGGAAGAGGCAGGAGGGGAAGGTGAGGGTCTCGG[A/G]AGACTCTGGGAGAAGGCTCTAGACCTTGTCCTGAA R 2 1 2 1 101000 r 74 goat snp16784-scaffold1759-113960 5 72818316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405442 Affx-122956050 AX-123275794 5 72045648 TGCAAGCAGGCAGCTTACATGGCTAAGGTTTCATT[A/G]TCTAATCCATCATAGATCGGCTTGAATAAACCCAT R 2 1 2 1 101000 r 74 goat snp16783-scaffold1759-72327 5 72859752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803034 Affx-122950222 AX-385289910 5 72104264 CTGTATAGAATCAACAAAGACTACTTTACCAGCTC[A/G]TGAATCTGCTCAAGGACTTGCTCAATCACTTCCTA R 2 1 2 1 101000 r 74 goat snp16782-scaffold1759-13711 5 72918907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445867 Affx-122925992 AX-123316204 5 72172517 CACAAGGGAAAACGAAGGTTCAGACTTGCCCCTCA[A/C]GTGGGGAAACTGTGCGGGTCTCCCTGCCTCTTGTT M 2 1 2 1 303000 r 74 goat snp294-scaffold1007-1177334 5 73383101 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396361 Affx-122963044 AX-123266716 5 72252668 TCTGTTTTCAGCTCCAGCAGATATCTGTGTAGTGC[A/G]TCTGCCTCTTCCCTGTAACAGTGAACATCAAGCGA R 2 1 2 1 101000 f 74 goat snp292-scaffold1007-1097183 5 73406369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409647 Affx-122953524 AX-123279998 5 72282485 CTGACTCCAAATTCCATTCCTAAGGGCTTCATGGA[C/T]GGAAAGCAGGCGTGTGTGCTCATGGTGAGTGGGCT Y 2 1 2 1 101000 f 74 goat snp291-scaffold1007-1067366 5 73436169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388165 Affx-122969448 AX-123258523 5 72312439 TCTGCCTTGGGTACCAGATGAGGCATGGCGGCACA[C/T]GGTATTCCAGATTAGGCTATGGCAGTAGGAGATGG Y 2 1 2 1 101000 r 74 goat snp290-scaffold1007-1037412 5 73464167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403471 Affx-122957712 AX-123273824 5 72343269 ATCACACAGTTCAGCTGGTGACGCAGATCTGAACC[A/G]GTTTAAGCATTTAAAAAAAAGCTGTTACAAGGCTG R 2 1 2 1 101000 f 74 goat snp289-scaffold1007-1006582 5 73494428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375900 Affx-122978486 AX-123246259 5 72373756 GAGAAGACAGTTACGAGCTCAGGGGAGAGGATTAA[C/T]AGCTTCTTATATTCTCCAGGAGAGGTGAGCTGGGC Y 2 1 2 1 101000 f 74 goat snp288-scaffold1007-976095 5 73525258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790107 Affx-122926951 AX-385277113 5 72450908 AAGAAATCATTTATAAATGAGTTTGTTAGATAATG[A/C]TGATGAATGTAGTTTCTGGTTCCCTGAGCTGTTCT M 2 1 2 1 101000 r 74 goat snp287-scaffold1007-898943 5 73602918 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788853 Affx-122947458 AX-385275868 5 72499036 GGAAACATGAGTGACGGTCTGCTTTTTGTCCACCT[C/T]CTCCATGAAACTCTGAACTTCTTTATTTTTTTTTT Y 2 1 2 1 101000 r 74 goat snp286-scaffold1007-850815 5 73650829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395448 Affx-122963924 AX-123265803 5 72536421 CTGGTGAAACAACACCTCCTCCAAGAAGTCCTCTA[C/T]GCCCCTGAAGGGGTTCCCAGAGCCTAGCATCTTTA Y 2 1 2 1 201000 r 74 goat snp285-scaffold1007-813430 5 73688816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425384 Affx-122941562 AX-123295730 5 72595640 TTGAAATTCATAGCCCAGGGCCTGCCTTTCTCCCA[A/G]TCCAGGTGAGACTGGTTTCCCTTTACCCTGTCCAC R 2 1 2 1 201000 r 74 goat snp284-scaffold1007-754211 5 73748022 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792209 Affx-122957472 AX-385279194 5 72628651 AGAGGGGGGAAAATCCTCTAAATAGACACAGGCCA[C/T]GCTTTCCTCTCTGTTCATCATCCAGGGTGTCTGTC Y 2 1 2 1 101000 f 74 goat snp283-scaffold1007-721200 5 73780967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446878 Affx-122925236 AX-123317214 5 72684411 TTCTAGGCTGGGCTCTGCCTAAGCCAGCTGGGCCA[C/T]TGCATGCCTGGGACCCCAGACCACTGTCTGTAAAA Y 2 1 2 1 101000 r 74 goat snp282-scaffold1007-665440 5 73833602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387211 Affx-122970594 AX-123257569 5 72719942 GGAAATTTACTGAGACCCTCCTCTGCCTTTGGTAC[A/C]TGGCTTGCCCATTCATTGCTGAAACCATCCATCAA M 2 1 2 1 201000 r 74 goat snp281-scaffold1007-629909 5 73869002 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416146 Affx-122948282 AX-123286495 5 72753659 GGCCAAATTATACAGTAGTGTTTGCAAACAAATGA[C/T]GATGGGACAGTGTGACTGAGCAATGGTAAAGAAGA Y 2 1 2 1 101000 f 74 goat snp280-scaffold1007-596192 5 73902741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772948 Affx-122957285 AX-385260092 5 72786485 CTGAGGCTCTATGGGATTAGGAGACTGAACCAAAG[C/T]GACTTAGTGGATGAGTGATGAAGTAAGATTTTGAC Y 2 1 2 1 101000 f 74 goat snp279-scaffold1007-563366 5 73935706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766862 Affx-122969732 AX-385254182 5 72816446 TCTCTTGCAAAATGTCTCTTTTGGCTCATGCTAAC[C/T]TGGATTTACGCAGTGGAGAAAATTCTAGGAAATAC Y 2 1 2 1 101000 f 74 goat snp278-scaffold1007-533405 5 73965943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411617 Affx-122951593 AX-123281967 5 72876171 AATCGTGGTGCACCTGTGAAATGGAGCAGGACCCC[C/T]TGGTCCTTGCCCACCCTCCACCCCACCACGTCCTC Y 2 1 2 1 303000 r 74 goat snp277-scaffold1007-473680 5 74025776 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767911 Affx-122945434 AX-385255129 5 73000764 CCCTTGGACACTTTCTCAAGATGATGGTTACCCTG[G/T]AGAACGGTCAGACTTCAAATGCCTGCTGGTTATAC K 2 1 2 1 101000 f 74 goat snp275-scaffold1007-349087 5 74150662 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408655 Affx-122953468 AX-123279006 5 73082246 TAGGGTATGGGTCTTGGGAGATGGGGTAAGGAGAG[A/G]GCAGCTGGCAGGGGCAGAAGAGATGAAGGAAAGAC R 2 1 2 1 101000 f 74 goat snp274-scaffold1007-267605 5 74222499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442206 Affx-122928789 AX-123312543 5 73145738 ACTGTGCCAGGATTCCCAGGATTCACCTGAGCCTG[C/T]GGCCACCCAGGCAGAGGGAGACACAAACCTTTGCT Y 2 1 2 1 201000 r 74 goat snp273-scaffold1007-204113 5 74286253 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404247 Affx-122957065 AX-123274599 5 73181734 GAGTTGGTCTAGATTTTCAACCTAGAATTCTAAGC[A/G]CAGCTGGGCCATCAACAAGGGTAGGAGGAGAATGA R 2 1 2 1 102000 f 74 goat snp272-scaffold1007-168117 5 74322729 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762360 Affx-986696891 AX-385250522 5 73196909 GTGTCCTTGACATGCAGGTGCCTGAAACTCACTCA[A/G]ACTTAGCTGAGACAAATTGTCACGCTGGTGCCAGA R 2 1 2 1 600010 f 74 goat 5_73196909 5 73196909 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 38431867 Affx-122936067 AX-123302208 5 73216593 CCACGGGCCTTTTTGCTGCGCCTGAGAACACTTCG[A/C]GCTCCTCCTCACCTTTGCCCTCGGCAGGTCCCTCC M 2 1 2 1 101000 f 74 goat snp271-scaffold1007-133258 5 74357529 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436550 Affx-122932919 AX-123306888 5 73270801 ACTGTGAATACTTAAGATTGAGACAGAAGTAGGTA[C/T]TGAGTCCCCTTCGTAGGTCCTGGGGCTAGGGGGCC Y 2 1 2 1 101000 f 74 goat snp270-scaffold1007-79050 5 74410627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278252 Affx-1111836326 AX-519551740 5 73275819 ACAGACTCACGTAAAGCATCAGGATCCCAGTTATG[A/G]TTTAATACAGGGAAGGGTGCAGTTTCCCATCAGCC R 2 1 2 1 101000 f 74 goat Random2.2K-579 5 73275819 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433184 Affx-122935649 AX-123303525 5 73312198 TAAGCACTATCAGACCCTGCATTCTGATTCTTGCT[A/G]TTAGATTTCTGGTTACTTCTGATATATCTATGCAA R 2 1 2 1 201000 r 74 goat snp269-scaffold1007-37653 5 74452011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392858 Affx-122965758 AX-123263215 5 73346815 GGGGATCCCAAGTGAGATGGGGACATGGCCTTGAC[C/T]TCACTGCACTTGGTTTCCCCATCTGTAAAGTGGAC Y 2 1 2 1 201000 f 74 goat snp268-scaffold1007-3036 5 74486262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398820 Affx-122961397 AX-123269175 5 73357479 AGACAGCAGTGCTTGCTGTATGCACACACGTGCAC[A/G]CACACATGGACACAGATGGGGGAGAACACAGGCTC R 2 1 2 1 202000 f 74 goat snp182-scaffold1003-7529 5 74496878 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412366 Affx-122950819 AX-123282715 5 73406401 GGGGTAACATGCAACCCGCTCTCTCTGTCACACAC[A/G]CTCACGTGCAGACACACAGTCGGAGACAAAACACC R 2 1 2 1 101000 r 74 goat snp183-scaffold1003-56451 5 74545499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430688 Affx-122936920 AX-123301029 5 73438665 GGAGGGGCAGACTCGAGTCCACCCTGTGGGATCTT[A/G]GGTGTGCAAACCAACGCACAGGACTGAGAACGCAG R 2 1 2 1 102000 r 74 goat snp184-scaffold1003-88715 5 74577831 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405308 Affx-122956838 AX-123275660 5 73492213 CCTCTGATGCAGGTCCTCTCTTTAACCCCATTTTA[C/T]AGAGCCCAAAACTGAAGCCAAGGAAGTTAATAACT Y 2 1 2 1 202000 f 74 goat snp185-scaffold1003-142263 5 74631596 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418763 Affx-122946199 AX-123289111 5 73547896 AGGAGTGAAGGAAATTATAGGTTGGGCAGGGCCCC[A/G]GTATTTCTCAGATGAATTGGGACTCCTGGTTCTGG R 2 1 2 1 101000 r 74 goat snp186-scaffold1003-197946 5 74688334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426341 Affx-122940267 AX-123296687 5 73606754 GGACAGTGGACCCACTGCAAGAGGAACACGCTCAG[C/T]GAAACAAAAGCAAGACCCAGCTGTTTATTTGAGAC Y 2 1 2 1 101000 r 74 goat snp187-scaffold1003-256804 5 74747006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772254 Affx-122953828 AX-385259409 5 73638841 CCAAATTCACTCCTTATTTGAAACCCAGATAACCA[C/T]GATCCAACACTGAAAACAGTTCACAGTTGAAAAAT Y 2 1 2 1 101000 r 74 goat snp188-scaffold1003-288891 5 74779556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419443 Affx-122945501 AX-123289791 5 73673587 CTCACAAGATGATAGCTGGTTTCCTTTTAGCTTGA[C/T]GCAGCAAAAAAGTACAGATCTTCCTCAACTTACAG Y 2 1 2 1 101000 f 74 goat snp189-scaffold1003-323637 5 74814370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768114 Affx-122954908 AX-385255316 5 73727678 CTTTCTCTCCTCGTTAGAACTTAAACTCATTGGGC[A/G]TTATTTAAGCTTTGACTGGCATTGTGTACTTTAGC R 2 1 2 1 101000 f 74 goat snp190-scaffold1003-377728 5 74868285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446092 Affx-122925806 AX-123316429 5 73778806 AGAATGCAAGTTCTCAGAAAGCATAGTCTTTATCC[A/G]TCTTCTATCAAGTTTCTTGAATAAATGAATCAATG R 2 1 2 1 101000 f 74 goat snp191-scaffold1003-428856 5 74919688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392036 Affx-122966467 AX-123262393 5 73814972 ACAAAAATGGAGCAAAACAAAATCTCAAACAATGA[C/T]GTGGGTATTTTTCTTCCTTTAAGTGAAAATATGTA Y 2 1 2 1 101000 f 74 goat snp192-scaffold1003-465022 5 74956848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376192 Affx-122978821 AX-123246551 5 73846948 AGCAAACCTATGACTTCCAATGTCAGTACCCTTCC[A/G]CAGAGCATGTCAAGTGCTCCCACTGAAGTCTTTGA R 2 1 2 1 101000 r 74 goat snp193-scaffold1003-496998 5 74988699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274545 Affx-1111834357 AX-519548135 5 73860416 GTAGCTTATCTGCAGGAGCCTAGAGATGCTCTTCT[A/G]GAA R 2 1 2 1 101000 f 74 goat GoatD01.031751 5 73860416 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440957 Affx-122928997 AX-123311294 5 73876003 GGGTTTTTATTTCATGGTCTCCATTGTGATTCTCT[A/C]TTAAGGAACAAACTAGATTATATTTCAAAGGAACA M 2 1 2 1 201000 r 74 goat snp194-scaffold1003-526053 5 75018424 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782453 Affx-122947934 AX-385269529 5 73882935 ATCCAGAAGAATACCTGGCAAATAGAAGAACTAAA[C/T]AGAAGTTATTGAACTGATAGATTAAGATCCTTAGT Y 2 1 2 1 101000 r 74 goat snp32385-scaffold368-1143239 5 75031756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392296 Affx-122967527 AX-123262653 5 73938048 CAGGCAGATCTTTACCAATTGAGCTACGAGGGAAC[C/T]AGTGAGCTACCAGGGAACCAGTACCTTTTGGCACC Y 2 1 2 1 103000 f 74 goat snp32384-scaffold368-1088126 5 75087691 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278414 Affx-1111836328 AX-519551899 5 73939655 ACACATCCACACTGAAAACTTGGCACAAAATTTAG[A/G]TATTCCCATATCTAGGCACTTTTCATGCATTTTTT R 2 1 2 1 101000 r 74 goat Random2.2K-581 5 73939655 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441356 Affx-122928874 AX-123311693 5 74002419 GTAACTATTAGCATTAAAGTGACATCCACTTTCTA[C/T]ATTCCCTGACAAAATGAAATATTGAGTGTAATCAC Y 2 1 2 1 101000 f 74 goat snp32383-scaffold368-1023755 5 75158434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787929 Affx-122966707 AX-385274951 5 74039859 ATTTGCAAAGAGTTGCCAAAAGATTTGCTTATTTG[C/T]ATTTTATCTTCAGGTTCTGCAGGTAAGCAAACAAA Y 2 1 2 1 101000 f 74 goat snp32382-scaffold368-986315 5 75196442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770786 Affx-122942000 AX-385257950 5 74105594 TTTTTTAGTTTCTAGACAAAGAAGCAATGAATTTG[C/T]GAAGACTGGACAGAACAAAGAAACTTAGTTTTGGA Y 2 1 2 1 102000 r 74 goat snp32381-scaffold368-920580 5 75263264 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787669 Affx-122938387 AX-385274692 5 74142156 ACTTCCTCTAGTAATAAAGCAATTACTAGAGTATT[A/G]CAAGAATGCAGTAATTAGTAAAACACCATTGCTGC R 2 1 2 1 101000 r 74 goat snp32380-scaffold368-884018 5 75300746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417447 Affx-122947201 AX-123287795 5 74189240 ACCACAAACCCTGTATGAAAGAGGTTAGGTGAACT[A/G]TAAGCATGGCTATACATGATAGAATGACCCTTAAA R 2 1 2 1 101000 f 74 goat snp32379-scaffold368-836934 5 75349132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433962 Affx-122934268 AX-123304303 5 74217770 GGTTGTTTGTCTTTCTGGTTTTGAGTTGTATGAGG[C/T]GCTTGCACATGCTGGAAATTAATCCTTTGTCTAAA Y 2 1 2 1 201000 r 74 goat snp32378-scaffold368-808404 5 75378752 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440263 Affx-122930650 AX-123310600 5 74260884 GTTGGAAGGTTCCTTTTCCTAAGGAAATAATTTTT[A/G]TTTCCTGGTGTAGCAATAGCCTGAAATGTCTCCTG R 2 1 2 1 101000 r 74 goat snp32377-scaffold368-765290 5 75422623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449902 Affx-122922334 AX-123320237 5 74320771 AATAGATCTAGAAATCTAAAAATATTTAATGGAAT[A/G]TTACTTTGGCTCAACATAAAAAGCACTTTTTAACT R 2 1 2 1 101000 r 74 goat snp32376-scaffold368-705403 5 75484660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446202 Affx-122925719 AX-123316538 5 74367681 GAAGGTAGAATTAATGGGGTTGCCTTGTGTAAACT[A/G]CTGCTGTGTCTTTTAATTTCACAGGCTTGTGTCTT R 2 1 2 1 101000 f 74 goat snp32375-scaffold368-658493 5 75532950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430148 Affx-122937386 AX-123300489 5 74401011 TACCCAGGCACCCAAGGGGGAACTGTTACAATAAG[C/T]AAAGTAGTAGTATTTTCAAAGTAAATGTAATAAAT Y 2 1 2 1 101000 f 74 goat snp32374-scaffold368-625163 5 75565957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429528 Affx-122937841 AX-123299870 5 74438340 AGTTACTGCTCCTCAGGCTCACAAAGGCCTGTGAA[C/T]GGTGCCTATTCTCACCAGCCAGCCAGATAGACAAG Y 2 1 2 1 201000 r 74 goat snp32373-scaffold368-587834 5 75604300 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274825 Affx-1111834441 AX-519548410 5 74468970 AACTGCAGGCGGCCCATGCCCCGCAGCATGCCCTC[A/C]GTCAGGTTGCTGAGCTTGTTGTAGCCCAGCTGCAG M 2 1 2 1 202000 r 74 goat GoatD01.036021 5 74468970 A C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272317 Affx-1111833476 AX-519546053 5 74484460 TGAGGCTTTGGAAAGAAGATGGGATACTGCACCCT[A/C]ACCTGTGCTCAGCGTGTCGGAGAGTCTCAGACTCT M 2 1 2 1 102000 f 74 goat 5_74484460_AF-PAKI 5 74484460 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38451337 Affx-122921268 AX-123321670 5 74525282 CTGAACCAGTGACTCTGGGCAAGCCAAAGGGAAAT[A/G]CCACATAATTGGGGCCTAGAAATTTTTAAAGGTTG R 2 1 2 1 201000 f 74 goat snp32371-scaffold368-500892 5 75691217 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795924 Affx-122932563 AX-385282876 5 74571360 TCTCACCTTCACTTTTCTGTCTTGCCATGGGCCTG[C/T]GAATTTTGAATCTTTGGCCCTTCGATCCAAGATAA Y 2 1 2 1 102000 f 74 goat snp32370-scaffold368-454814 5 75736491 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787041 Affx-122925265 AX-385274069 5 74618075 TGTGCCCCTGGGGGTTTCAAGCTATGACAAGTGAC[C/T]TTAACCACATTCTGTTCATAAGAAGAATTTTCGTA Y 2 1 2 1 101000 f 74 goat snp32369-scaffold368-408099 5 75783387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796462 Affx-122946928 AX-385283412 5 74648493 TAAGACTTTGTCGATCTTTATCCATCACATTTGAG[C/T]ATGTGTATCTGATAACTCAGAAATTTCATTCCTTA Y 2 1 2 1 101000 f 74 goat snp32368-scaffold368-377681 5 75813731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771437 Affx-122955396 AX-385258595 5 74684671 GGGAATCTCAGAAACTTCTTTATGTTGTGGTGACT[A/G]TTTAGTATGTTGGAAAGTTCTAAGAAAGAAATGAG R 2 1 2 1 101000 f 74 goat snp32367-scaffold368-341503 5 75850053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449315 Affx-122922999 AX-123319650 5 74720956 AGCATTGAAGTGATATTTTAAAGAAAATTTCAGAG[C/T]GAATATATCTGAAAAGTTTAACAATGAGATTGGAA Y 2 1 2 1 201000 r 74 goat snp32366-scaffold368-305218 5 75886454 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764558 Affx-986696896 AX-385252213 5 74738693 GTACTGGGCACTCAGGAATGTAGAGGAATTCATGA[A/G]TCACTTGGTGCCCGCATCTGACATTTTCTGGGCTG R 2 1 2 1 600010 r 74 goat 5_74738693 5 74738693 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38423664 Affx-122942338 AX-123294010 5 74861849 AGTATCGGAACTTAAAAATTTTTCTCTGTCCTTGC[C/T]TTGAAGCTGTAGTATTCACAGGGCAGAAAAACATG Y 2 1 2 1 101000 r 74 goat snp32364-scaffold368-164325 5 76025980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782263 Affx-122953326 AX-385269341 5 74909103 TGTCATATAACCATTAATTTCATAGTCACCTCTGA[A/G]CCAAAAAAGAAGTCATTGGTATACTCTCCATACCA R 2 1 2 1 101000 r 74 goat snp32363-scaffold368-117071 5 76073818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420028 Affx-122945150 AX-123290376 5 74942465 CATTTATTTAACTATTATTATTATTAACTGTTACT[A/G]TGGGTGATTAGCTCAAGGATTGTAATCTCACATGG R 2 1 2 1 103000 r 74 goat snp32362-scaffold368-83709 5 76107155 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422176 Affx-122943520 AX-123292522 5 74990610 TGGTGTAGATAGTTATCATTTATTTCTGTGTTTTA[C/T]GGCCTTGCTGTTTGCTGTTTTCTTCTCTTGACCCA Y 2 1 2 1 201000 f 74 goat snp32361-scaffold368-35564 5 76155531 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419432 Affx-122945509 AX-123289780 5 75021715 CGTGCGTGCACATGTGTGTGTGTGTGTATGTATCT[A/G]TAATTCCATGGCCAAATTCTTTTCTATATGTGGTA R 2 1 2 1 201000 r 74 goat snp32360-scaffold368-4459 5 76187227 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773392 Affx-122971361 AX-385260534 5 75034842 ATGGAATCATTCCATAGGCATTCTTTTGCAATTTG[C/T]TTTTTAAACTCAACTTTCAATTCCTAATATTCAAC Y 2 1 2 1 102000 f 74 goat snp2290-scaffold107-8569 5 76200730 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413862 Affx-122949860 AX-123284211 5 75087746 TTCTGGTTATGTATCCTCAGGCAAATTATTTACTA[C/T]GTTATAGCTCAGTTGGTAAAGAATCCGCCTGCAAT Y 2 1 2 1 201000 f 74 goat snp2291-scaffold107-61473 5 76254368 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795932 Affx-122943379 AX-385282884 5 75118309 TCATTTTCGGATTAATACACTCAGTAGAAACTTGG[C/T]ATATAACCGATGCTCTCTAAATAATAAATACATGA Y 2 1 2 1 101000 f 74 goat snp2292-scaffold107-92036 5 76285146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801444 Affx-122976277 AX-385288353 5 75155030 TAGCTTTTTGTCTTCTTTCTAAAGATTCTTAATAA[G/T]TACAAAGCACATGCTATAATAGCTCTCTCATCTGT K 2 1 2 1 201000 f 74 goat snp2293-scaffold107-128757 5 76321782 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383072 Affx-122973743 AX-123253430 5 75194884 TTCTGGAGCCAAGTTATTCAGATTCAACTCTCAGC[G/T]CTACCACTTAATAATTTTATGAAATTGGATCTAAG K 2 1 2 1 101000 f 74 goat snp2294-scaffold107-168611 5 76361961 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423843 Affx-122942781 AX-123294189 5 75224814 TTTCAAAGGAAAAAACAAAACAACGTCAGCAAAAC[A/G]CAATGAAACACAGTGCAATTAAATTGAATTCTTGT R 2 1 2 1 101000 r 74 goat snp2295-scaffold107-198541 5 76392253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380564 Affx-122975279 AX-123250922 5 75255749 TATATCCTTCCTTAATTGATCATTGTGTAAGGGAA[A/C]GCATTTAAGTTAATTTCTCTAGTGAACAAGAATAA M 2 1 2 1 101000 f 74 goat snp2296-scaffold107-229476 5 76423528 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430657 Affx-122936942 AX-123300998 5 75325365 CCTTTTGAGTGGATCAATATTTAACCATTTCTCTA[C/T]TGATGAATATTTGGTTTTCTTAGGTGTTTTTACTT Y 2 1 2 1 101000 f 74 goat snp2298-scaffold107-299092 5 76493705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800301 Affx-122949715 AX-385287224 5 75365922 TGCTGCGTTTTGTTTGTACCACCATTTTCCTTCTT[A/G]TAAAAATAATAGGACTTTCTGTGTCTGATCCCTGG R 2 1 2 1 101000 f 74 goat snp2299-scaffold107-339649 5 76534498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785259 Affx-122953280 AX-385272304 5 75406020 GCAGTACCCAGAACACATCAGGCTCCTAATAAATT[A/G]CATTGATTATCACTAAACATTTTCCTCTGGGAGAG R 2 1 2 1 201000 r 74 goat snp2300-scaffold107-379747 5 76575529 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426824 Affx-122940515 AX-123297169 5 75435047 TCCAAGAACCTTGAGTCATCACTCTTTAGGGTTTA[C/T]GTATGTTGGAGAAGCAGGAGTCCTTCTGCCTTATG Y 2 1 2 1 101000 f 74 goat snp2301-scaffold107-408774 5 76605256 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417537 Affx-122946930 AX-123287885 5 75477983 TTTCATTCACTCATTTCCAGTCTTTCATTATGGTT[C/T]TGTCCCCTCCACTTATAGTAGATTGGGGTGGTTAT Y 2 1 2 1 101000 r 74 goat snp2302-scaffold107-451710 5 76649018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787975 Affx-122927324 AX-385274996 5 75524454 TCTCCCTGACTGTCGCAGATGCAGACTGTTTTCTG[C/T]AAATGCAATTTTTCCATGTGATACATAGGTTGCTA Y 2 1 2 1 101000 f 74 goat snp2303-scaffold107-498181 5 76695775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410962 Affx-122952025 AX-123281312 5 75570305 AAGGAATCAGATAAGGAGAGAAAGAAAAATGTTTC[A/G]TTTTTGTTTATAGAAGTATACCAAATTGTAGGTTT R 2 1 2 1 303000 r 74 goat snp2304-scaffold107-544032 5 76741999 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451187 Affx-122921334 AX-123321521 5 75606859 CATTGACTTCATATTTTGATAGTTAAATAATTGCA[A/G]TATAATTTGGCACCCTCTCCTCAATTGTTTTAAGT R 2 1 2 1 101000 r 74 goat snp2305-scaffold107-580586 5 76779010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789617 Affx-122920743 AX-385276626 5 75641694 TTCAAATGAAATGTATTACTATCTATAATCACAAA[A/C]TTCTCTGAAATATACCATGCTTAAACTACCCCCAA M 2 1 2 1 101000 r 74 goat snp2306-scaffold107-615421 5 76814166 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397595 Affx-122961990 AX-123267950 5 75707106 GTAAAGTTTTCAAATTCCTGACACATATTAATCTT[C/T]GGGATTTAGGAACGAGATACCAGAATTCCCAAGAA Y 2 1 2 1 101000 r 74 goat snp2307-scaffold107-680833 5 76880666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400500 Affx-122961281 AX-123270855 5 75758911 TTTATTTCTGTGCCCCTGTGAACCAACCTTGTTGA[A/G]TAGATCAGGTGACAGCTTTTATCTGAAAGTCAGTC R 2 1 2 1 101000 r 74 goat snp2308-scaffold107-732638 5 76932574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401437 Affx-122958989 AX-123271790 5 75837303 GAAGGGGTTCAGTGTCTTTGTTGTCTTCCACTGTG[C/T]GCGGACTTTCTTTGGATTGATTGGCGGTGAGGTAA Y 2 1 2 1 101000 f 74 goat snp2309-scaffold107-811030 5 77011426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789869 Affx-122943824 AX-385276876 5 75893352 AATGCCTTCTGTACACATCTCTTAATTCTGCAAAC[A/G]CAAACACTGGCTGGGAAGCATTGATCTCACATACG R 2 1 2 1 101000 r 74 goat snp2310-scaffold107-867079 5 77067395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400658 Affx-122960353 AX-123271013 5 75925245 CTTCCTTCTTCTCAGTTCCACTTAATGACATCATA[A/C]CCCTCTTCTCAGTCAGGCAAGCCAGAAAGTCATCC M 2 1 2 1 201000 f 74 goat snp2311-scaffold107-898972 5 77099586 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401545 Affx-122958907 AX-123271898 5 75974556 ATCTAGACAAACCCAACAAGCACTAGCATAAAGAA[C/T]TGCAGGCATACAATTGCAGTCACAGTTATACATTC Y 2 1 2 1 101000 f 74 goat snp2312-scaffold107-948283 5 77148891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442853 Affx-122927680 AX-123313190 5 76030122 GATATTCTAAATTATTTATAAGGTGTATGTTTACT[A/G]CCAGCTGCCTTTTGTTGCAACCAGCCCTGGAGTTC R 2 1 2 1 201000 f 74 goat snp2313-scaffold107-1003849 5 77204473 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792712 Affx-122975085 AX-385279692 5 76077394 TTTGCTACTTCCCAGACAATATGAGAACTTTGACC[A/G]TTTGTACTCCATTTACCTTCCTTCAGCCTTTAAAC R 2 1 2 1 101000 f 74 goat snp2314-scaffold107-1051121 5 77253141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449385 Affx-122922714 AX-123319720 5 76107703 GGTCCTGTGAGATTTCTCATTAATTCTGGGCCTTA[C/T]GAAAACAGCAGTAGGGAGCCATTCAAAGATTTTAA Y 2 1 2 1 101000 r 74 goat snp2315-scaffold107-1081430 5 77283449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406487 Affx-122955162 AX-123276839 5 76147776 CAGTAAATGCTGATGTAAAGATCCAGATCATTCCT[C/T]ATTTCCTGAGTCATGTAGCCTGTGAAATGATACTG Y 2 1 2 1 101000 f 74 goat snp2316-scaffold107-1121503 5 77323953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799493 Affx-122942721 AX-385286423 5 76264815 TTGCCCTGCATTTACTATCTTCTAGTTATTTACAG[C/T]ATTGGTCTGTCTGGAACAGACTGGCCCTGAAAATA Y 2 1 2 1 101000 r 74 goat snp2319-scaffold107-1238542 5 77440566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273915 Affx-1111833929 AX-519547522 5 76278976 CCAAGCAGCCATTGCAAAACAGCACTGGTGCAGCT[A/G]TTGTCATCAGGATTTTAATTCTGCAGTATCAG R 2 1 2 1 101000 f 74 goat GoatD01.010794 5 76278976 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428437 Affx-122938819 AX-123298780 5 76329631 TGGAGTGATCTCCTAGAGGGGCAGGAATGAGTGGT[A/C]TCTTTCTCTACAGGCTTCTTATGGGGAGACTCTAA M 2 1 2 1 201000 f 74 goat snp2320-scaffold107-1303358 5 77506297 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766015 Affx-122929482 AX-385253434 5 76358748 GATGTTACCTTATCTTGTATACCTGGTATCACTAA[C/T]TTTAGCAACACACGATCCTATAAGATGTGCTTTAA Y 2 1 2 1 101000 f 74 goat snp2321-scaffold107-1332475 5 77536378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428878 Affx-122938337 AX-123299220 5 76393810 TGGGGAGGTTGATCCTTGTTTGAAAGTGATGATAA[C/T]AGGAGGTTGATAAGACCTGCCCAGGATGGCTGCCA Y 2 1 2 1 101000 f 74 goat snp2322-scaffold107-1367537 5 77571168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453171 Affx-122920469 AX-123323504 5 76457377 AAGCTGCAAGTCAATATTTTTAATGTTACATTTTT[A/G]TTGGTGAAGACACTTGCCAGCAGCTGCTCCTTGGC R 2 1 2 1 101000 r 74 goat snp2323-scaffold107-1431104 5 77634691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379095 Affx-122976764 AX-123249454 5 76503527 ATTATTGATTATCACCTAGAAGATGGTGCCTTTGC[G/T]CTGTAATATGAAATCAATAAGGAAAATAAACCTAA K 2 1 2 1 101000 f 74 goat snp2324-scaffold107-1477254 5 77681891 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409453 Affx-122954081 AX-123279804 5 76582877 TCTTGGGATGCTCCCTTAGTGGGTTGTGTGGACCA[G/T]CCATTTGTGGTGGAGCTGGCTACTACAATGGATAT K 2 1 2 1 201000 r 74 goat snp2326-scaffold107-1556604 5 77762147 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391474 Affx-122966720 AX-123261831 5 76645076 CTGACATTTAAAGCAAGGTAACATGCTGCCAATGA[C/T]ACTCTATGAGAAATTCTTGTTTATAGTAGAAGCAT Y 2 1 2 1 101000 f 74 goat snp2328-scaffold107-1618803 5 77821879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380051 Affx-122975571 AX-123250409 5 76744273 GACACTTGATTACATTGTGATAATTGCAGGATGAG[A/G]GCTGTAACAGGACACCTGACTGATAGGGGTTAATA R 2 1 2 1 201000 f 74 goat snp2330-scaffold107-1718000 5 77922470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797460 Affx-122973249 AX-385284399 5 76793933 CCTAAATCTCACAGTCTTGTACATGTGGTTTAGGG[C/T]TCCATTTCCCTGTAATCCTCATTCCTATATTCACT Y 2 1 2 1 101000 f 74 goat snp2331-scaffold107-1767660 5 77972547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766773 Affx-122945047 AX-385254107 5 76841966 GCCCCACATAAGCTATGAAATGATATACAAATACA[C/T]AATGGGTCTATTTAAATATTCTAGCAAATTAAATG Y 2 1 2 1 101000 f 74 goat snp2332-scaffold107-1815693 5 78021024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770621 Affx-122960844 AX-385257785 5 76877851 TTTTCTATGATGTCGTTTTCCATGGGGCATTTGCC[A/G]TGAGCTTGGTGTCTTCGTTTTCATGTTCACCATTG R 2 1 2 1 101000 f 74 goat snp2333-scaffold107-1851578 5 78056753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450425 Affx-122922054 AX-123320759 5 76935201 CAGAATACCCTGGCATAATCCTTTGTGTTGGAGAA[C/T]ATACAAAATTTCAGATCCCAGCCATTTTCAAATGA Y 2 1 2 1 101000 f 74 goat snp2334-scaffold107-1908928 5 78115600 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404817 Affx-122956648 AX-123275169 5 76983459 GATCTCAAGATAGAACACAAAATAAAGGGGACATA[C/T]GACACAAAAAGTGAATGCCATTATTATTTGATTGA Y 2 1 2 1 101000 f 74 goat snp2335-scaffold107-1957186 5 78164947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778584 Affx-122958357 AX-385265695 5 77049481 AAGCATCAGCAAATTAGTCCTTAGTCACACAAAGT[A/G]CTGTACTCCAAGACATGCTATTATAGTCTATGATT R 2 1 2 1 101000 f 74 goat snp2336-scaffold107-2023208 5 78231579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423746 Affx-122942855 AX-123294092 5 77078215 ACCTAAGAGAACACGAGGAACTGAGTTTCTCCTGT[A/G]CTTAGGTAGGGGCTGAGGCTAAGACAGTGATTCCA R 2 1 2 1 303000 r 74 goat snp2337-scaffold107-2051942 5 78260269 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793662 Affx-122961924 AX-385280635 5 77113642 AGCAGGTGAACTTCACTTAAGACTCAGCAATAGAA[C/T]TGATAGTTTTGAAACTCTTGGTGAAGAATTAAATA Y 2 1 2 1 101000 f 74 goat snp2338-scaffold107-2087369 5 78295741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393337 Affx-122965940 AX-123263693 5 77169156 TCCTGAAGACATGGAAGGCTCGTGCTTAGGACCCT[C/T]TCAGACTTGGCCCCATGGATCTTTTTTTTTCTATC Y 2 1 2 1 101000 r 74 goat snp2339-scaffold107-2142883 5 78352550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788178 Affx-122927102 AX-385275197 5 77218543 GACTCAGTTTAGTTCTGGGTTTTAATGAGAATATG[A/G]TGGATATTTTATTGGTTGCTTAACAATTAGATACT R 2 1 2 1 101000 f 74 goat snp2340-scaffold107-2192270 5 78402222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278258 Affx-1111836329 AX-519551746 5 77227212 AATTTAACTGCAGAAAACACTAAGGCTTGGCTTTC[A/G]GTTCTTCAAAAGGATTTAAGTTATCTTGTCAAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-584 5 77227212 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452726 Affx-122920286 AX-123323059 5 77250755 GTACTATCAGCAACACCGTCCCCTCAAGATCTTCC[A/G]TTCCTGTTAAGCTTCATTTTCCTTCACTTCTTCTC R 2 1 2 1 101000 f 74 goat snp2341-scaffold107-2224482 5 78434462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272318 Affx-1111833477 AX-519546054 5 77261845 TTACTAATCTACTGCTACATAACAAAGTACCCCAA[A/C]AAAAAATAAAAAATAAAATAAAAAAAACAAAGTAC M 2 1 2 1 102000 f 74 goat 5_77261845_AF-PAKI 5 77261845 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435739 Affx-122933286 AX-123306078 5 77288117 TATAAAAGCTGACAGTATCCCTGACCTTCCTCCTC[A/G]CCCGCTCTCTCTTGGGGGCTAAAGGAGACTAAAGT R 2 1 2 1 101000 f 74 goat snp2342-scaffold107-2261844 5 78473612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777013 Affx-122961698 AX-385264136 5 77323010 GAATATACGTATAAAATGGGTGGATTCTATTGTAT[A/G]TGAATTGTATCAATAAAGCTATGTTAAAAAAAATA R 2 1 2 1 101000 f 74 goat snp2343-scaffold107-2296737 5 78507446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780216 Affx-122921889 AX-385267313 5 77368015 ACAAACAACTTCGCTTTGTTGATCAAAGCCTTGTC[A/G]TGGCAAAGGGGCATGCGTAACTCAGCAAAGCTATG R 2 1 2 1 202000 r 74 goat snp2344-scaffold107-2341742 5 78552857 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768833 Affx-122978799 AX-385256010 5 77425871 GGAAGAGCACTGGTGCTTGACTCAGAGTCATAGTT[A/C]TATGAACATGATGAGTCGCTTAACTTTTCTGAATC M 2 1 2 1 101000 f 74 goat snp2345-scaffold107-2399598 5 78611222 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792192 Affx-122928228 AX-385279177 5 77478886 ACTGTCTTGGAATCTGGGTTCTTCTCTAGAATTAG[C/T]AGTTGGAGAAATTCAACAGTTGGTGGACACCCATG Y 2 1 2 1 101000 r 74 goat snp2346-scaffold107-2452613 5 78664753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427106 Affx-122939671 AX-123297449 5 77521009 CCAACATTGGTGTTAGTGTCTCTCTTAGTTCTTCC[A/G]CACTGTCAGTGTCTGTTTGCTAATAGGATTATATT R 2 1 2 1 202000 r 74 goat snp2347-scaffold107-2494736 5 78707358 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402325 Affx-122959075 AX-123272678 5 77570128 TAAACTGCAATCAACTGTGTACATTAATATAGTCT[A/G]TAAAAGTTATGTAGCCAAATTTTAAAAAATAGAGA R 2 1 2 1 101000 f 74 goat snp2348-scaffold107-2543855 5 78756383 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448946 Affx-122923142 AX-123319281 5 77598780 TAAACTAGGCATGCATTTATACTTCTGTAAATACC[A/G]TTGCTTATCTGTAGAACTGACGCTGTCCATTTTAT R 2 1 2 1 101000 r 74 goat snp2349-scaffold107-2572507 5 78785505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278419 Affx-1111836330 AX-519551904 5 77625832 GTATCTTTGAGATCTACATAACTGAAACCCCCACC[A/C]AATGGAAGATGTTCCAGCAAAAAGGTTACAGTTCA M 2 1 2 1 201000 r 74 goat Random2.2K-585 5 77625832 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408060 Affx-122954270 AX-123278411 5 77636759 AGTCCTGGTGAAAGAGTGAACTTCCCCACAGAAAA[C/T]ATGACTAGCATTTACATTTTTTGTTGGCAATTTTG Y 2 1 2 1 101000 f 74 goat snp2350-scaffold107-2610486 5 78823415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789724 Affx-122927567 AX-385276732 5 77684177 ACTGTTTCCCTCCAAAGTCTAAGCAAATAGAGGAA[G/T]ATTAGATTTCATATGGAGTATTTTCAACTTTTAGT K 2 1 2 1 201000 r 74 goat snp2351-scaffold107-2657904 5 78871158 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773560 Affx-122977562 AX-385260700 5 77740956 AATTAACTTTCTGGACAATCTTAATCAGCATTAAC[A/G]TTCAGCGAAAGATCTTAAGTGTACTTGTTAAAATA R 2 1 2 1 101000 f 74 goat snp2352-scaffold107-2714683 5 78928702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425195 Affx-122941036 AX-123295541 5 77801962 ATAGATATAGTAAAATAGGCAGGAGCCAAAATTGG[C/T]CCTCGAGTCACTGTTTGCAGACCCCTTGGCTAGAG Y 2 1 2 1 101000 f 74 goat snp2353-scaffold107-2775689 5 78989634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435580 Affx-122933366 AX-123305920 5 77836051 GGCTACAGTTTGCTAATTCAACTTTTAAAGTATTG[C/T]ATTAAAATATTATTTCTATTGATTATTGAGTATTT Y 2 1 2 1 101000 f 74 goat snp2354-scaffold107-2809778 5 79024630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777227 Affx-122976788 AX-385264350 5 77886180 GCTTGCTCCAAGCATGTATGTAAAGTCAGGATATG[C/T]GACTTCAGTCATTCGTTTCCAAGAGGTCTCCAATT Y 2 1 2 1 201000 r 74 goat snp2355-scaffold107-2859907 5 79076399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432353 Affx-122936273 AX-123302694 5 77946541 TGTTGTTCTAGCCTTCCAAATCCAGCTAAAGATAC[A/C]CATTTTTAGAAAGGCTTGTTTGAGCCCTCACCTTC M 2 1 2 1 101000 f 74 goat snp2356-scaffold107-2920268 5 79137217 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397104 Affx-122962698 AX-123267459 5 78048101 TCTAGCATATTAGCATTGTACCACAGGCCAGGTAT[A/G]CACAGATCAATTTATTCTGTGACTTCTGTAAACTT R 2 1 2 1 101000 f 74 goat snp2358-scaffold107-3021828 5 79240366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768526 Affx-122924140 AX-385255706 5 78081180 AAGTTTCATTTCGAAGGAAAGGAGCAGTTTTTGTA[C/T]GTACTGGTTGAATGTTATCCTGACTTACAATACAA Y 2 1 2 1 201000 r 74 goat snp2359-scaffold107-3054907 5 79273196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773844 Affx-122931130 AX-385260984 5 78118187 GTGAAGACGTGTACTCGTGCCCAGCAGATAGAGAA[C/T]TGGTGACTCTGCAATTAAATGAGAGAAATGATACA Y 2 1 2 1 101000 f 74 goat snp2360-scaffold107-3091914 5 79313143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785969 Affx-122938057 AX-385273005 5 78152318 TTCAGTGTTACTGTAGGGAATATTATTAACCTAGT[A/G]CAGGAATTAAAGCATGATTGTCACATAGTCATCTA R 2 1 2 1 101000 r 74 goat snp2361-scaffold107-3126045 5 79347750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418099 Affx-122947137 AX-123288447 5 78185504 CATGTGAGGATACAGCAAGAAGACAGCTCTCTACA[A/G]TCCAGGAAGAGACAGAAAGAGAGCTCTTACCAATG R 2 1 2 1 101000 f 74 goat snp2362-scaffold107-3159231 5 79381500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792996 Affx-122963177 AX-385279974 5 78250515 ATGCCTTATATATGCTATCAGCAAAATGGCAATTC[C/T]TCAGTTTTTGACCTCCCAAGGGCAAGAATTTAGTC Y 2 1 2 1 101000 r 74 goat snp2364-scaffold107-3224242 5 79445952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278262 Affx-1111836331 AX-519551750 5 78267410 AGATAGGTCAGAGAGACTGGGATGAAAAAAAGTCA[A/G]CATGCTGACTCTGAAGTGTAGGACCTCACGCAGGG R 2 1 2 1 101000 f 74 goat Random2.2K-588 5 78267410 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386160 Affx-122971390 AX-123256518 5 78338680 ATGTCCAGACTGCAGGACACAGAGCAAAAAAGCAA[C/T]TGCAAACAGGATCTCAGGAAGCAAAGTATCAAAGC Y 2 1 2 1 201000 r 74 goat snp2366-scaffold107-3312407 5 79535357 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379997 Affx-122975611 AX-123250355 5 78394649 TGAGCTCTCTGTGTCATGAAAAGAAAAATAATAAA[G/T]CTGATGTGACTTTCAATAAAAGTGTAGCTCAGTAG K 2 1 2 1 101000 r 74 goat snp2367-scaffold107-3368376 5 79592913 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801806 Affx-122974796 AX-385288714 5 78450639 CCAAATATTTATCTGAGTGAACCATTCTTGGAACA[C/T]GCCAGGTACATGTGCATATTTTGAGAATATCAAGA Y 2 1 2 1 101000 r 74 goat snp2368-scaffold107-3424366 5 79649158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776501 Affx-122944399 AX-385263628 5 78487795 TTACTAAAAAGAATAACCTGCTTCATATCAATATA[C/T]GATAGTTCCTACAACTGTGCTTTTCCAACATCCCA Y 2 1 2 1 101000 r 74 goat snp2369-scaffold107-3461522 5 79686555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771145 Affx-122947063 AX-385258305 5 78544457 CTTTCCAAAAAATTAGGTTTTGTATTCAAATGGTA[G/T]AGGAATAAAATATGGTGTTATAGCTTGGAGAGAAA K 2 1 2 1 101000 r 74 goat snp2370-scaffold107-3518184 5 79743593 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774725 Affx-122920340 AX-385261859 5 78585453 CTCCTAATTCAGACAATTTCCAGAACATCTGAAAA[A/G]AGCTACAGATTTAGGAAAATTTTACAACAAAAGTA R 2 1 2 1 202000 r 74 goat snp2371-scaffold107-3559180 5 79784623 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413028 Affx-122950996 AX-123283377 5 78621045 GCAACAAAGTTATTTCATATGCCAAATGTCCCCAT[A/G]GATGAGTAAAAAGCAGACATTAAAATTCTTATAAA R 2 1 2 1 103000 f 74 goat snp2372-scaffold107-3594772 5 79820490 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450648 Affx-122921978 AX-123320982 5 78688926 ATCAGTTTACAACTAGGCAAATCCAGAGTCACAAC[C/T]AAGATCATCTTACCAAGAGCAGAAGCTATTGGATA Y 2 1 2 1 101000 f 74 goat snp2373-scaffold107-3662653 5 79888527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441534 Affx-122928709 AX-123311871 5 78736279 GGCCTGACTACCCAGGCAGGCAGAAGTTAAGCAAC[A/G]TCTATAATCTTTAAGTTCAACCCTTGGGGAAAATG R 2 1 2 1 101000 r 74 goat snp2374-scaffold107-3710006 5 79936627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388934 Affx-122968825 AX-123259292 5 78765404 TGTCAAACCCAAAACCATCGTAAGAATGGGAAGAT[G/T]CAGGAAAATACCCTCACCTTAAATAAAGCTACAGA K 2 1 2 1 101000 f 74 goat snp2375-scaffold107-3739131 5 79966180 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420919 Affx-122944595 AX-123291266 5 78805627 GATAAAAAGGGGAAGGGTGCTTTTATAAAGTATTT[A/G]TAATTTTGTTATTATTTAAACTGTTTTATAAAATC R 2 1 2 1 103000 f 74 goat snp2376-scaffold107-3779354 5 80006568 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452071 Affx-122920870 AX-123322404 5 78869844 GCTGGTCCAACTCCCATTATTCCTTCTAAAGAGTC[A/G]GCTTGTGAAAGACAGTTTAGTTGCTTCCTATATAA R 2 1 2 1 101000 f 74 goat snp2377-scaffold107-3843571 5 80071332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432017 Affx-122935921 AX-123302358 5 78942284 TACACACCACCGGAGTGTCTATTATTTCTGTACTA[C/T]GGATGCTTCAAAATAAAACGATGATAAAGGTTGGA Y 2 1 2 1 101000 f 74 goat snp2378-scaffold107-3916011 5 80140224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438629 Affx-122930917 AX-123308966 5 78986373 AGGAGTCTTCCATATAAAATCTTCTCTCTTAACCT[A/G]CATTAAGATACATGGCCCCTTCATGGAACCACAGT R 2 1 2 1 101000 f 74 goat snp2379-scaffold107-3960100 5 80184561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450510 Affx-122922504 AX-123320844 5 79070645 AAAGTCTGTTTTTTCATGGGGTAGCTATTTAGAAG[A/G]GAGGGAGGGTTGAGCGTGAGATGACAGGACTTTGC R 2 1 2 1 101000 f 74 goat snp2381-scaffold107-4044372 5 80268366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390269 Affx-122967745 AX-123260626 5 79121352 TAGAGTCAACACAGCCCTCCTTGGGCGATGCAGCC[G/T]CCTCCGGCTCAAACATGCGTAACTTTTTCAGTGCA K 2 1 2 1 101000 r 74 goat snp2382-scaffold107-4095079 5 80319219 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777319 Affx-122976737 AX-385264441 5 79206910 AGCCCTGTAGAAAGATGAGACTCTTCATGATGAGC[A/G]CTTCTCTAGAGCACTAGTGATAATGATTAATTTCA R 2 1 2 1 101000 f 74 goat snp2384-scaffold107-4180637 5 80404683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774449 Affx-122966436 AX-385261585 5 79257026 ATGCATTGGTTTAATCACATTCAGTGTATTTTTAG[A/C]TATGATCCTAATTGTACATATTTATAACTAATTCA M 2 1 2 1 101000 r 74 goat snp2385-scaffold107-4230753 5 80455454 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384833 Affx-122971972 AX-123255191 5 79336570 AAATATTGATACAAGCACACCTTGCAAGTCGAATT[A/G]TTTCCAAACCTGGACAACAAGTTCAAATCTGCATA R 2 1 2 1 101000 f 74 goat snp2386-scaffold107-4310297 5 80535292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394793 Affx-122964819 AX-123265148 5 79378073 CCAGGAAGCCCAAGACTGGTACAATCAATGGCAAA[C/T]TGCAAATTGCTCCTCTCCTCAGCCTATGCTTTGCA Y 2 1 2 1 101000 f 74 goat snp2387-scaffold107-4351800 5 80576979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404681 Affx-122957279 AX-123275033 5 79420491 TTGCCTTCATCATAGGCAGAGTCTTCAGTACAACA[C/T]TGGCACTGGTGAGGGCATGAGGCTAAACTAGAATC Y 2 1 2 1 101000 f 74 goat snp2388-scaffold107-4394218 5 80619433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391991 Affx-122966503 AX-123262348 5 79524532 TCAAGCACTGCTGAGACCTGAGCATTAATTATGAG[C/T]AAAGCGTTTAAAAGAGTGCCTGGCACACGTAAGCG Y 2 1 2 1 101000 f 74 goat snp2390-scaffold107-4498259 5 80723549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447843 Affx-122923900 AX-123318179 5 79566166 TTCTCTCTATGCTCTTCAAGGCAAAACTCCAGATC[A/G]CGAATCTTCTCTCCCTGAGCCTCTACCTGGTCTGT R 2 1 2 1 101000 f 74 goat snp2391-scaffold107-4539893 5 80765343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449102 Affx-122923588 AX-123319437 5 79596033 CTCAAGTGATGGACATCAAATGCTTGCAGCACAAA[C/T]GCTCATGCCCAGGGGCCCCTCAAACATGCACACTG Y 2 1 2 1 101000 f 74 goat snp2392-scaffold107-4569760 5 80795244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418796 Affx-122946177 AX-123289144 5 79632075 AGGGGCAAATCACTTTTCCAAACTTCAAGAACATA[A/C]CATGAAAATGCTCAAAGGGAGCAAGGGGTCCAAGG M 2 1 2 1 201000 f 74 goat snp2393-scaffold107-4605802 5 80831322 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402757 Affx-122958322 AX-123273110 5 79664375 ACTAAGACACAGATTAAGCAAAGTACCTAATTTAG[C/T]AAACAGCCAAGTCAGGATTCTAGTCTTAATCCCTC Y 2 1 2 1 201000 f 74 goat snp2394-scaffold107-4638102 5 80863542 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393222 Affx-122965489 AX-123263579 5 79734410 TCATGATGCCCTACCCCTTATTTTAAACTTTGACC[A/G]TCTCGCCCTTGTTGTTGCTGTTGTTCAGTTACTCA R 2 1 2 1 101000 f 74 goat snp2395-scaffold107-4708137 5 80932600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272319 Affx-1111833478 AX-519546055 5 79768238 TTTATTGACTATGCCAAAGCCTTTTGACTCTGTGG[A/C]TCACAATAAACTGTGGAAAATTCTGTAAGAGATGG M 2 1 2 1 303000 f 74 goat 5_79768238_AF-PAKI 5 79768238 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406644 Affx-122955817 AX-123276996 5 79797072 TAACATCCACTTATGATGAGTCCACAAGTGGTTCA[A/G]TGAAAACTAGGCAACAGAAGAAACAGAGGTTGGGT R 2 1 2 1 101000 f 74 goat snp2397-scaffold107-4770799 5 80995815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788315 Affx-122930950 AX-385275333 5 79951065 AATAGCTTATTAAATCAGATATATATTCCATTCAG[C/T]AAAGGTTGATAAGAAATTTCCTATTCTCAGATAGC Y 2 1 2 1 101000 r 74 goat snp2400-scaffold107-4924792 5 81150661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798773 Affx-122930136 AX-385285704 5 79983932 GTTATACTGCAAATATATTCCTCTAATGGATTTCA[C/T]ACTGCTCTTTGTCTTTTATTTACTAAAGCCCTTTC Y 2 1 2 1 101000 r 74 goat snp2401-scaffold107-4957659 5 81183408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777544 Affx-122966307 AX-385264663 5 80033149 GGAAAATGTGGTCAACAAAAATGGATTGGCTGGTC[A/G]TGTTGCCTAACTAGTTAGTAACTCAGTGTTCTTTG R 2 1 2 1 101000 f 74 goat snp2402-scaffold107-5006876 5 81232813 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797260 Affx-122957258 AX-385284199 5 80088168 AGATTTTTAATTGCCTAAACTCACACACTGACAAG[A/G]TTGGAAGACATGTATACTTCATGCTTTTTCTATTG R 2 1 2 1 101000 f 74 goat snp2403-scaffold107-5061895 5 81286791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785120 Affx-122943726 AX-385272166 5 80152345 TGTACATAAAAGATAATTCACCATCCAGAAGAAGC[A/G]CTCAAGGAACGTCCTCTGTGGTCATCACTAGGACT R 2 1 2 1 101000 r 74 goat snp2404-scaffold107-5126072 5 81352549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445980 Affx-122925886 AX-123316317 5 80183239 TTTTTATGAGTAGTGATTGAATGCAGTTTCTGCCA[A/G]GCAGGGTTGTTAAAGTTGTCTTGACTTTCAGTGTG R 2 1 2 1 101000 r 74 goat snp2405-scaffold107-5156966 5 81383754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430884 Affx-122936878 AX-123301225 5 80224646 TGCCACTGTGTTTGTAGTTTTGGGGATTTGGTATC[A/G]CACCTTTGAACTTCAGAGTACAAAGTGGGGAGAAC R 2 1 2 1 201000 f 74 goat snp2406-scaffold107-5198373 5 81424743 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786370 Affx-122971852 AX-385273404 5 80264804 CTCTTCTTACATGTGCTTCATATTTATTAACTCCT[A/G]TGACTCTCACAACAGTCCTATGCGGTAATTACTGT R 2 1 2 1 101000 r 74 goat snp2407-scaffold107-5238531 5 81465117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794968 Affx-122962134 AX-385281928 5 80293541 TTTCTCTGGTCTTTGCCTATTGTGTCTTTCTGCCA[C/T]ACTGGGCTGGCTATGTATTCTTACTGTGCTGCTGT Y 2 1 2 1 101000 f 74 goat snp2408-scaffold107-5267268 5 81494484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376311 Affx-122978361 AX-123246670 5 80337774 TCCCACATGGAGTTTTTCAGCCAAAACTGTACTAC[A/G]TCACAACACAGCATAGAAAACAGCCTTCCAGGAAC R 2 1 2 1 201000 f 74 goat snp2409-scaffold107-5311501 5 81535871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381512 Affx-122974862 AX-123251870 5 80379363 TTGCACAGTTTGGCACACACCTCTTTGTCCGCCCC[G/T]GGTCCCTTCACCTTTCAGCAAACCTTGCTCTGGGG K 2 1 2 1 201000 r 74 goat snp2410-scaffold107-5353090 5 81577577 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786135 Affx-122924469 AX-385273171 5 80408985 AGAATAATTGTGTCACCTTATATGTACACAGTGTA[C/T]AAGAATTGGTTATTATGATGGAGATAGGTGTTAAG Y 2 1 2 1 101000 r 74 goat snp2411-scaffold107-5382712 5 81607166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436111 Affx-122932661 AX-123306450 5 80453004 GACCTGTAGAGGTCTTTGATTTAGTAAATGCACTG[C/T]GTGCTGAAGAATGGCACTTTATTCTTCCAGAGAGT Y 2 1 2 1 101000 f 74 goat snp2412-scaffold107-5426731 5 81651160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436736 Affx-122932299 AX-123307074 5 80512378 GGATGATTTCTTATGCATATACTCCTACTCTCCCT[A/G]TTTTACACAAACATAGCCCAGTTCTGCCCTTTCAT R 2 1 2 1 201000 r 74 goat snp2413-scaffold107-5486105 5 81710149 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387651 Affx-122969846 AX-123258009 5 80552285 CAACTGTCTGTGAGAGTTGAAATACAGGAAATAAA[C/T]GAAACTGCACAAAGGCACAAAGGCTGCCTAAATTT Y 2 1 2 1 201000 f 74 goat snp2414-scaffold107-5526012 5 81750251 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444359 Affx-122926710 AX-123314696 5 80618756 TCATTCCCTATATCTATTTAATTTTATATCCCTTA[C/T]GGTTGCCAACATAATTCCTGCCAGAAATGAAGCTG Y 2 1 2 1 101000 r 74 goat snp2415-scaffold107-5592483 5 81816863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793674 Affx-122931965 AX-385280646 5 80665362 GAGGAGTCATCCTGTCTTATACAGCACTACATACC[A/G]CTTGTATTTACCCTTGTGACCTTGTGAAAGCGCTT R 2 1 2 1 101000 r 74 goat snp2416-scaffold107-5639089 5 81861105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404816 Affx-122956649 AX-123275168 5 80712898 AAAGTTGCTTTACCTCTTTGGGTCTCTGTTTTCTC[A/G]TTAGCAAAATTAGCCTGTTAATAGAACCTAACATA R 2 1 2 1 201000 r 74 goat snp2417-scaffold107-5686625 5 81908610 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409297 Affx-122953104 AX-123279648 5 80748078 GTAGAGGAGTACAATGAGCTGCCCAGGGTGACACT[A/C]CAAGGAGGTGACTGGATAGAGGTTCCAAAACAGAT M 2 1 2 1 101000 r 74 goat snp2418-scaffold107-5721805 5 81943848 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794990 Affx-122927222 AX-385281949 5 80821300 ACACAAACCCATGAGAAAATGTAATTCGTAAACAC[A/G]TACGCCAATATAAAAACACTAATGTCCTGGCACAA R 2 1 2 1 101000 r 74 goat snp2420-scaffold107-5795027 5 82017600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408232 Affx-122953833 AX-123278583 5 80873311 AAATAATGCAGTGATTCTAGAACCAAAGAGATGGC[A/G]CTAAGTTTATGATAGCCGTGTTCTTTGGAAATCAT R 2 1 2 1 101000 r 74 goat snp2421-scaffold107-5847038 5 82070434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435785 Affx-122932861 AX-123306124 5 80907661 ATTAAGTACCCTTTCTTACTGATCATCTCTTCTCT[A/G]CTTGCCAAGGTCATGTTTCATAGGTCAGACGTTTA R 2 1 2 1 201000 f 74 goat snp2422-scaffold107-5881388 5 82104947 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411840 Affx-122951229 AX-123282190 5 80953245 ACACGACTGAGCAACTGAGCACGCACACAGATTAT[A/G]CAAGAGAATAGAATCTCCCCTTAGGAATCAACCAG R 2 1 2 1 201000 r 74 goat snp2423-scaffold107-5926972 5 82150517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386891 Affx-122970044 AX-123257249 5 80983014 TGATCCCTTTTACCCATGTCTCCCCTCTGGTAACC[A/G]CTATTCTGTTCTCTGTATCTACATGTTTGTTTTTA R 2 1 2 1 103000 f 74 goat snp2424-scaffold107-5956741 5 82180117 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397232 Affx-122962375 AX-123267587 5 81020582 CTTGGAGCCTCTCCTAACTCAAGGCTTCCTGCTAC[A/G]TGAGATAATAAATTTCCTTATTGCTTAAGCTGGCT R 2 1 2 1 101000 r 74 goat snp2425-scaffold107-5994309 5 82217573 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38437897 Affx-122931664 AX-123308235 5 81075141 CATCCTGGTCTATACCCCTGCCTTACATAGCAAAA[A/G]CTCCTTGGCAACACCCTGCAGCAGTTCTTCTCATT R 2 1 2 1 202000 r 74 goat snp2426-scaffold107-6048868 5 82272285 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411558 Affx-122951640 AX-123281908 5 81104193 TTCTAATAATGTGACCTAAATAGCTTGCAAAGACC[G/T]AAGAATTATAAAACCTCTTTCTCTATTTCTTTTCT K 2 1 2 1 101000 f 74 goat snp2427-scaffold107-6077920 5 82301308 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785003 Affx-122937985 AX-385272050 5 81159468 TATTCGAAGTTGGCTTTAATGTCATTGGAGGAAGA[C/T]GGTCTGATAATGGCTTAGAACAGTTCTTACTCAGA Y 2 1 2 1 101000 r 74 goat snp2428-scaffold107-6133195 5 82353482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394542 Affx-122964468 AX-123264897 5 81230239 CCCCTTCTCCTATTGCCCCCAACCAGACGATGGGC[A/G]TCAATTGCCCTAGTTGCACTGAACTACCACAAGCT R 2 1 2 1 101000 r 74 goat snp2429-scaffold107-6203966 5 82424230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375940 Affx-122978457 AX-123246299 5 81268431 CTAGGATGGGTTCACAATGGCAGAGCGTCCTATGA[C/T]GCTCGTGGAGCTGTAAATCAGCAATGCGTGGAGTC Y 2 1 2 1 201000 f 74 goat snp2430-scaffold107-6242158 5 82462498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402849 Affx-122958250 AX-123273202 5 81309041 AATGTGATGGATAACAATATATTCAGGAGAGAAGA[C/T]AGATTATTAAATTTTAGACTATGAAAAAATCATAC Y 2 1 2 1 101000 f 74 goat snp2431-scaffold107-6282768 5 82503210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389440 Affx-122968353 AX-123259798 5 81377693 ATTTCCGAGACAGGCCTAAAACTTATTGTCATTAA[C/T]ATAATGCCATCAAATTACATTCACTCAGCGCTGAT Y 2 1 2 1 101000 f 74 goat snp2432-scaffold107-6351420 5 82572037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409920 Affx-122952881 AX-123280271 5 81415772 TTTTACCTTGTTTAATATTTTCATAGTAGAAAAAA[C/T]GGAACCTGTTGATTTCTTACATTTTATTGTTCTAG Y 2 1 2 1 103000 r 74 goat snp2433-scaffold107-6389499 5 82610125 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777578 Affx-122922687 AX-385264697 5 81470174 GTTATAAATCTAGATTTTTCAGGTTTAAATGAAAA[C/T]ATGTGGTCCTTAATTATAGACAGCTACTGTTTCTC Y 2 1 2 1 303000 f 74 goat snp2434-scaffold107-6443901 5 82664845 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415880 Affx-122948485 AX-123286229 5 81507212 TTTGAGTCGGGTGCTAATTTTGTTTTTCTTATTGA[C/T]AGTGTCAAATATTTTAAAAGGAAATTTACGTAGAA Y 2 1 2 1 101000 r 74 goat snp2435-scaffold107-6480939 5 82701927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762367 Affx-986696898 AX-385250529 5 81517530 CATGCAAATTTTGTATTTACATTCATGCTAAGAGG[C/T]AAAAATGTCTCTGCAGGAGTGGAGAATGAATGATT Y 2 1 2 1 600010 f 74 goat 5_81517530 5 81517530 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 320762373 Affx-986696904 AX-385250535 5 81517599 TTCTTCTGAGAAACTTCAGGAGTCTCAGACACATG[A/T]CTATGGTCATGAAGATGCTTCTGTCCCAGCTGGCT W 4 1 2 1 600010 f 74 goat 5_81517599 5 81517599 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 38418331 Affx-122946962 AX-123288679 5 81537111 AGTCAGCTTGAAGGTCAGTAGGTTTGTGGTCCCTC[A/G]GTATTTTTCAGTATCGTTGTTGTTCAATCACTAAG R 2 1 2 1 201000 r 74 goat snp2436-scaffold107-6510838 5 82732716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403800 Affx-122957970 AX-123274152 5 81576804 ATTTTTAAAGCTCTGTAATTTGTTTCTGGGGTAGC[A/G]TTAGATTGTCTTACGTAAGTCTGCCTTGGTCTTTG R 2 1 2 1 201000 r 74 goat snp2437-scaffold107-6550531 5 82772128 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430627 Affx-122936964 AX-123300968 5 81617152 ATATATGCTTTTCCTAATTAAGCCCAATATGTCAC[A/G]TTGGTCCCACAGAAAGGATGGGAAAGATACCATAA R 2 1 2 1 201000 f 74 goat snp2438-scaffold107-6590879 5 82813213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376241 Affx-122978782 AX-123246600 5 81650947 AAGCTTGGCAAATCAAGGACCACACAGAGGGACAC[A/G]CCTGGAGAAAACTCCCCTCTCACCTCCTACTTCTT R 2 1 2 1 201000 f 74 goat snp2439-scaffold107-6624674 5 82848075 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796712 Affx-122964866 AX-385283657 5 81686493 AGGCCCTTCTACAAGAGGAAATTCAACATCAAAGC[A/G]TTAATTAGGAACAGTCTTAGAATTATCCTAGGGCT R 2 1 2 1 101000 f 74 goat snp2440-scaffold107-6660220 5 82884391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388185 Affx-122969434 AX-123258543 5 81744988 CTAAAATGTTTTAAAATAACTTCCAAAACCCTTGT[A/G]TAAGTAACAATCAGGCAGAGATGGACCAAGCAGTG R 2 1 2 1 101000 r 74 goat snp2441-scaffold107-6718715 5 82942831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414228 Affx-122949639 AX-123284577 5 81776387 GATAGCATGAGGATGTTTTCTGGGGGCAGGATTTG[G/T]GTTCTGTGGAATAGATCTTTTTTAAAAAATTGTAG K 2 1 2 1 101000 f 74 goat snp2442-scaffold107-6750114 5 82974290 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787718 Affx-122922981 AX-385274741 5 81813996 TGTATTTCAACCTACATGGATCAGATATAAAAAGG[C/T]TTTCTGTGCCTGTCCCCTGATCCAGTGCCAAGGAG Y 2 1 2 1 102000 r 74 goat snp2443-scaffold107-6787723 5 83011955 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409171 Affx-122953198 AX-123279522 5 81867534 AAAGGAAGGCAAATGAAATTACTATCCATGATATG[A/G]ACAACAGTATTTTTTCTTTCAGAAAAGCTAATCTA R 2 1 2 1 101000 f 74 goat snp2444-scaffold107-6841261 5 83066080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396045 Affx-122963459 AX-123266400 5 81906887 AATTATGAAAGGATAAATTGTTCTTATGATGAAGT[A/G]TTTTTGGTTAATTGCCAATGAGCCTTGTAGAGGAA R 2 1 2 1 101000 r 74 goat snp2445-scaffold107-6880614 5 83105952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789970 Affx-122939970 AX-385276976 5 81945593 TTCTTGAACAAGCAAGCACTAAGATAACCCATTAT[A/G]CAGTTTTATGTAGACACCAAGGACTAGTCAGGTCT R 2 1 2 1 101000 r 74 goat snp2446-scaffold107-6919320 5 83144702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427591 Affx-122939464 AX-123297934 5 81989085 GACATCTATTCTTGCCTATCTTGCCTCCTGTTGCT[A/G]CTGAGAACAACAGTATTTGCGCAGCGATCTAAAAA R 2 1 2 1 201000 r 74 goat snp2447-scaffold107-6962812 5 83188657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425205 Affx-122941028 AX-123295551 5 82051405 GCAGCAAATGATAAATAATCAAGTGAGTGATGAAC[A/G]TTAAGTACCTTGTAAAATGTTTGTTCATGGGTATT R 2 1 2 1 101000 f 74 goat snp2448-scaffold107-7025132 5 83251997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278263 Affx-1111836332 AX-519551751 5 82136972 TCTGAAGGCCTTTTGAGGCAATTGTGTAAAATACT[A/G]TAACAAGGATTGTTGGAAATATTGAATAATTTCAT R 2 1 2 1 101000 f 74 goat Random2.2K-589 5 82136972 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765045 Affx-122931743 AX-385252614 5 82190945 GGGTATGAAAATTCTCAGTATTGACCATTCTCTTA[C/T]GAATTCCCTTGACCATAGGTAAAATAATTGCATGA Y 2 1 2 1 101000 f 74 goat snp2451-scaffold107-7164672 5 83392142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428986 Affx-122938857 AX-123299328 5 82257850 AAACGAACAGCTTTGTATTAACTACCCAGGTTTAG[A/G]AAGAGAATTAGATGGTATTCTTTTACTAAGATAAG R 2 1 2 1 101000 r 74 goat snp2453-scaffold107-7231577 5 83459631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443146 Affx-122928068 AX-123313483 5 82310492 ATTCATGTAATGCTTAACTCATGAAAACAATTTCA[C/T]GATCATATGCCAATTTTTATAACTTCTGCATATAC Y 2 1 2 1 101000 r 74 goat snp2454-scaffold107-7284219 5 83513716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445535 Affx-122925165 AX-123315872 5 82342856 AAAATTTCTCTCAGAAATATTTCAGTCTGAGCCTC[G/T]AAAAGACAAGGACTGGAAATAATTTCTTTTTGTTC K 2 1 2 1 102000 f 74 goat snp2455-scaffold107-7316583 5 83546066 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764966 Affx-122969833 AX-385252545 5 82378012 CAATAGGAATTCAGTGAAAGGCATATAAAAAGAAG[C/T]AATTTAGACAAGGTTTAATATAGGCAATTTAGAAA Y 2 1 2 1 101000 f 74 goat snp2456-scaffold107-7351739 5 83577365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272320 Affx-1111833479 AX-519546056 5 82474999 ATCATCAGTGTTCTGCTCAAAATCCCTTAATAGTA[A/G]CCAGACTCACTCAGAAAATTTTAAAGTCTATGCAC R 2 1 2 1 201000 f 74 goat 5_82474999_AF-PAKI 5 82474999 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795861 Affx-122948548 AX-385282813 5 82489337 CAGTTAGCTTACTAAATCTCCTGGAGTTTAGTGAG[C/T]GAGGGGAAACATCATGAATACTCCTTTAAGCCATG Y 2 1 2 1 101000 f 74 goat snp2458-scaffold107-7463064 5 83688154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778270 Affx-122923226 AX-385265386 5 82528395 TATTGTTTGAGCTCAATATTATGTGAGATCTATCC[A/G]TCCAGGACCAATCCTAATGTCTGTGGGCTCTGGGA R 2 1 2 1 101000 r 74 goat snp2459-scaffold107-7502122 5 83727378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434042 Affx-122934204 AX-123304383 5 82564148 TTTTAGCCTCTTGTCTTACTTTTAGGGAATTTAGA[C/T]GTTGAACAATAGGTATTTCTTGATTATATTGAAAG Y 2 1 2 1 101000 f 74 goat snp2460-scaffold107-7537875 5 83763030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406631 Affx-122955825 AX-123276983 5 82600390 ACTTTTTCTTGAAACACCACTTACCTCCAAGCATT[A/G]AAGACGTCTCATCTAATTTTCTGTTCCGTCACTCA R 2 1 2 1 101000 f 74 goat snp2461-scaffold107-7574117 5 83799492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424828 Affx-122941365 AX-123295174 5 82629729 AATTGTCTCACAGGTGAATTCTTAACCACTGGACC[A/G]CCAGTGAAGTCCCCTTTGCCTTTTCTTCTAGATTA R 2 1 2 1 103000 r 74 goat snp2462-scaffold107-7603456 5 83829305 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426242 Affx-122940340 AX-123296588 5 82694221 GTGGTCACTGATTGTATAACACACAACATAAAATT[A/G]TGAAAAGATTTTCAGTGAATTTTTCTCCTTAACAC R 2 1 2 1 102000 f 74 goat snp2463-scaffold107-7667948 5 83894444 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402618 Affx-122958407 AX-123272971 5 82725017 GGGACTATCTATGTTGGGTTGGGTGTAACCACAGA[A/G]TTAGAAAGGACTGCTACAGGCACCGCTCAAAGGAA R 2 1 2 1 101000 r 74 goat snp2464-scaffold107-7698744 5 83925701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786742 Affx-122936011 AX-385273773 5 82781576 AAAGTGTTAAGAACGTTTTTCTATGCCTTGTTTGA[C/T]GTTTTACCTTACACACAGTGAGAGGAGAAAATATT Y 2 1 2 1 101000 r 74 goat snp2465-scaffold107-7755303 5 83982339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405369 Affx-122956312 AX-123275721 5 82816650 TTTTACAGGAAAATCGCCTATTGTATGAATGAGAG[C/T]AAAGGCCTCAAAATACCTATGTGTGATAGTGAATT Y 2 1 2 1 101000 r 74 goat snp2466-scaffold107-7790377 5 84017320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431738 Affx-122936742 AX-123302079 5 82847971 GGATAAATAGAACAGCAAAGGGATGCACTATTGGC[A/G]TTCCCTGGAAGCTCAGTGCCTTGTCCTTGCAGCAC R 2 1 2 1 102000 f 74 goat snp2467-scaffold107-7821698 5 84048953 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423698 Affx-122942892 AX-123294044 5 82882316 ATTAATTGTCAGTCCTCACCTTACTTGTCCTGTCT[A/G]CAACATTGGAAACTGTTATTTACACTTGTTGTCTG R 2 1 2 1 201000 r 74 goat snp2468-scaffold107-7856043 5 84083368 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452965 Affx-122920161 AX-123323298 5 82912871 AAGAGAGCCACTCCCAGCCCACGGACAAAACCTCA[C/T]AGTGTTAAGAAGGGTGTAATTTATTGAAAACTATA Y 2 1 2 1 201000 r 74 goat snp2469-scaffold107-7886598 5 84113790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411004 Affx-122951988 AX-123281354 5 82946143 TCTTTTGTAAATATATTGTCATTTGGTAGAAGGAG[C/T]GCAAATCTCAAGCCAAACACACACAGATACCTGAA Y 2 1 2 1 201000 f 74 goat snp2470-scaffold107-7919870 5 84146893 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787757 Affx-122956569 AX-385274780 5 82993462 AGAAATCTCAGAATAAATTCATAAAATATAGATAA[C/T]ATTTGCAAACAGTTCACAGTCCTGAAAATATCAAT Y 2 1 2 1 202000 f 74 goat snp2471-scaffold107-7967189 5 84192630 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441973 Affx-122928558 AX-123312310 5 83046258 AATGAGACAGGGAGCAATTGTAGTAGCATGTTTTA[C/T]GAAGACTCTGAGAGTCTTTTTAAGTGACCCCCAAT Y 2 1 2 1 201000 f 74 goat snp2472-scaffold107-8019985 5 84245431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425333 Affx-122941599 AX-123295679 5 83092007 GAATCACATGAAATGATTATGTTTAGATCTCTAGC[A/G]TGTCTGGCAACTATAAACACACATATTTGAACATT R 2 1 2 1 101000 f 74 goat snp2473-scaffold107-8065734 5 84291649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423913 Affx-122942275 AX-123294259 5 83129315 TATAAGATAGAGCCACTGAGACTGATGCTTTCAGT[A/G]AGTAATCCAGACACTTAGGGCATTTTGAGCAACTT R 2 1 2 1 101000 r 74 goat snp2474-scaffold107-8103042 5 84328917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394238 Affx-122964879 AX-123264593 5 83171692 CTCATTTCTTAATTAAGAACTCATTATGTGGTCTT[A/G]TATTTCCTGAATTGTATAAAATTTCTATATCTCCA R 2 1 2 1 201000 r 74 goat snp2475-scaffold107-8145419 5 84371248 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446523 Affx-122925024 AX-123316859 5 83204030 TTGCAAATTAGTAACAGAGGCACAGAGACCATAAA[C/T]GGAAAAGAAAAACATGAGGTCGTTTGGCTACTTCA Y 2 1 2 1 101000 f 74 goat snp2476-scaffold107-8177757 5 84403910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416256 Affx-122947965 AX-123286605 5 83258680 TAAAGTTTCGTTTGGGTCCAAGAATGACATGGTTC[A/G]TTTCCATGTTAAATGTCAATCTTTTTCTCCCATTG R 2 1 2 1 101000 f 74 goat snp2477-scaffold107-8232407 5 84458229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450753 Affx-122921851 AX-123321087 5 83410810 TGCTAGCATTGTGGAGTTTTCAACTAATTTCTCAG[A/C]AAAGTAAATATACTGTGCCCCGGTTGTATTTAGTG M 2 1 2 1 101000 f 74 goat snp2480-scaffold107-8384537 5 84611189 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801789 Affx-122970773 AX-385288697 5 83457829 ATCTGAATGTGGTGGGGTAGTTTGTTAAAGAGAGA[A/G]GTAAAGGTTTGAGGCAGCTACAAAAGGGAGTGAGA R 2 1 2 1 101000 f 74 goat snp2481-scaffold107-8431556 5 84658427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416033 Affx-122948366 AX-123286382 5 83497572 AGTCTCTGGCCTCTAGGTAATACACTATAGGACTT[A/C]TTCAATTAGTAAATCAATATTGCATATTGCAATAG M 2 1 2 1 101000 f 74 goat snp2482-scaffold107-8471299 5 84697956 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426934 Affx-122940429 AX-123297279 5 83543953 TTTATGCCTTTCTGTGGAGGGAGGGAAATTAAAGC[A/G]TCTACCTTTGTCTAGATTCCAGTAGTTAACAGCTC R 2 1 2 1 101000 r 74 goat snp2483-scaffold107-8517680 5 84744492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777620 Affx-122944936 AX-385264739 5 83623722 AAAGTTGAAAAATTAGATTAATGGCAGATTGTAAG[A/G]GGCCTTGAGTATTATCAGAAATTTGGAGTTTATAA R 2 1 2 1 101000 r 74 goat snp2485-scaffold107-8597449 5 84824038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440420 Affx-122929605 AX-123310757 5 83670177 TATGAACTTATTTCAATAAGAATAATTTAGCAGTC[A/G]TCTCTCAAGTAACATTCATAATATGCAAGGAGATT R 2 1 2 1 101000 r 74 goat snp2486-scaffold107-8643904 5 84870974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418527 Affx-122946416 AX-123288875 5 83735546 AGGGCTCTGTAAGGGCAGGGAGTTTGGAATTTATT[G/T]TATGTCCAGTATAAAGCTTTGAAATGGTTTTATTC K 2 1 2 1 101000 f 74 goat snp2488-scaffold107-8709273 5 84936163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432728 Affx-122935465 AX-123303069 5 83787187 AGAGTTTGAGACTGTACTTTCAGAGATGAAGAGTA[C/T]AATATCTGAGACAAAAATAGGCTGAATGCGATTAG Y 2 1 2 1 101000 r 74 goat snp2489-scaffold107-8760914 5 84987964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773568 Affx-122945482 AX-385260708 5 83816012 GAATCATGGATTTATCTTAATGTATGTGACCTTTT[A/G]TCTATATCTTAAGAACAGGAACACAAAGCAGCTGG R 2 1 2 1 201000 f 74 goat snp2490-scaffold107-8789739 5 85016718 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446539 Affx-122925012 AX-123316875 5 83847100 TAGCTTGCATGTGTATATGTATGTTTACACATTAA[C/T]ACATGTATAATATGGCATATGAATAACATTATAGT Y 2 1 2 1 303000 r 74 goat snp2491-scaffold107-8820827 5 85048163 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779995 Affx-122977194 AX-385267094 5 83908396 AGGAATGAGAATATGTTCCTTTGGAAAGAGACATA[A/C]TCCAAGCAATAGACTTGATGTTTCTCTTGAAACAA M 2 1 2 1 201000 f 74 goat snp2492-scaffold107-8882123 5 85110005 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775749 Affx-122961210 AX-385262880 5 84051222 AGTGGTAATATCACATGTCAGAATAAAAACTATTT[C/T]TTGTGGGCCTTAACAATGTTCCTAGTATGATTAAT Y 2 1 2 1 101000 r 74 goat snp2495-scaffold107-9024949 5 85254951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403119 Affx-122958121 AX-123273472 5 84088412 GCCCCAGGTTTGGTCAAAATGAACAACTGGGCAGA[C/T]GAAGATTTGAAAAAAATGTTTTTTTTGTTTTAGTG Y 2 1 2 1 101000 f 74 goat snp2496-scaffold107-9062139 5 85292830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388943 Affx-122968817 AX-123259301 5 84132393 TACCAGTTATTGAACTTGTGCTAGGTTCCAAGAAA[C/T]GGGTAGACAATGACATGCAAAATTGGTGTGGTGCT Y 2 1 2 1 101000 f 74 goat snp2497-scaffold107-9106120 5 85336862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435297 Affx-122934030 AX-123305637 5 84193840 TATAGTAATGTTTCCTCTAGACTCTGTTTCTTCCC[A/G]TATACCTGCACCCCTAGGAGTTCTTTCCTCATGTT R 2 1 2 1 201000 r 74 goat snp2498-scaffold107-9167567 5 85398316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378544 Affx-122976616 AX-123248903 5 84218731 AAGATGCCAGAAAATTTATCTTTCATATGTGAAAT[A/G]TATTTTATATGTAAAATATATTCTTAGATATTCAA R 2 1 2 1 303000 r 74 goat snp8884-scaffold1319-23999 5 85423412 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419137 Affx-122922134 AX-123289485 5 84264504 TGAATTTTTTACTTATATGTATATCCACTACCAAA[C/T]TCAGATATGGAATATATCTAGCCTCTTATCAGACA Y 2 1 2 1 101000 r 74 goat snp8885-scaffold1319-69772 5 85468310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272365 Affx-1111834099 AX-519546094 5 84281343 TGCAGCCAGCTTGTCTCACAGCTGGGCAAATGACT[A/G]CCTGGATCCACAGCATCCCCTAAATCTGGTTATTA R 2 1 2 1 202000 f 74 goat GoatD01.018281 5 84281343 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320789247 Affx-122963461 AX-385276258 5 84306687 GTGCTAACGCCTAGGGGACAGAGTACAGATGACTG[C/T]ATTTTCCAGGTTACCAGGTATAAGAAAAGGCAAAA Y 2 1 2 1 101000 f 74 goat snp8886-scaffold1319-111955 5 85510664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798708 Affx-122937251 AX-385285639 5 84342454 ACATGAGCCAACCATAACTGCACAGAACGGTGTCT[A/G]TGTTATCAATGTTTGCAATATTGAAAAAAATGAAA R 2 1 2 1 101000 f 74 goat snp8887-scaffold1319-147722 5 85546548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407115 Affx-122954877 AX-123277466 5 84371707 ACAGAACTTCAGTGGGTTAGAGATAGGTAAATAGC[G/T]ATCACACTTATTTTAGGCCCTCAGATAGCATTTTG K 2 1 2 1 101000 f 74 goat snp8888-scaffold1319-176975 5 85575758 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438261 Affx-122931415 AX-123308599 5 84408639 TTTAAGAAACTGATTTCCTGAAAATGTGTGACTTA[C/T]AGAACACTGATAGTGTCAGAATTTTCTCCAGTGAT Y 2 1 2 1 101000 r 74 goat snp8889-scaffold1319-213907 5 85613261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393434 Affx-122965865 AX-123263790 5 84445362 CCTACATACTATCATGCCTATCACTTTTTATTAAA[C/T]GAATGAAATAAACTCTATACCTGAATAAATGTGCA Y 2 1 2 1 101000 f 74 goat snp8890-scaffold1319-250630 5 85650067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413713 Affx-122950077 AX-123284062 5 84529090 TATATTATCCGAACAGTTATGAAAACATGGGAGGT[A/G]TGGAAAGCATTGACAACCCCCTTTTTCATATTCTT R 2 1 2 1 201000 r 74 goat snp8891-scaffold1319-334358 5 85733766 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415976 Affx-122948412 AX-123286325 5 84578067 AGGACACACAGGGAAATGACGCTGCTGGTGAGGAC[A/G]GAGACAAGTAATTGAATTTATACACACATACACAC R 2 1 2 1 201000 r 74 goat snp8892-scaffold1319-383335 5 85783108 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404837 Affx-122956633 AX-123275189 5 84627499 CTTCTGAGCTCTTAGCTAAGACTCCTGTAATAAAA[A/G]GCAGAATAGCAAGAGAAAAATTAACAAGTTCATTC R 2 1 2 1 202000 r 74 goat snp8893-scaffold1319-432767 5 85833492 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278425 Affx-1111836333 AX-519551910 5 84647755 CTTTGTATGCAGTTTAACAGCCATAGCTGAAGGTA[A/G]CAGCTCCTCTATAGTCAAGGCTTCACCAGTTCTAG R 2 1 2 1 101000 r 74 goat Random2.2K-590 5 84647755 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412963 Affx-122951042 AX-123283312 5 84717917 TTATGCTTCTTTTGGCTTTCCCTTAGTATTCTGTG[A/C]TTTCCTAGGGGCTCAAGAAAAAAGCATGTGGTGAA M 2 1 2 1 201000 f 74 goat snp8895-scaffold1319-523185 5 85924458 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435118 Affx-122933695 AX-123305458 5 84766372 TCTGAATGTTTGTGTGGGACCTCTTTCCCTGGTGG[C/T]TCAGCTGATAAAGCATCCGCTTGCAATGCGGGAGA Y 2 1 2 1 303000 r 74 goat snp8896-scaffold1319-571640 5 85973736 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389293 Affx-122968515 AX-123259651 5 84801604 TCCTGATGTTGTTGATAGCTGCAGGCAAGCATTCT[A/G]CAATTTTCTAAAGAACAAAATCAAGAATTCTCTCT R 2 1 2 1 101000 f 74 goat snp8897-scaffold1319-606872 5 86009352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796091 Affx-122932788 AX-385283043 5 84831542 TCATTTTTCCTACTTTAAGAAGGTATAAAAAGATG[C/T]GTGTCGTTGTAAAACATATGTGTGCTCATAAGTTT Y 2 1 2 1 101000 r 74 goat snp8898-scaffold1319-636810 5 86040318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783359 Affx-122957558 AX-385270423 5 84913933 GGCTAAACAGTTAAAATGGACACATGAACACAGAT[A/G]TAAGGCTGTTAAGAATAGTTTCTAAGCTGCTGATA R 2 1 2 1 101000 f 74 goat snp8900-scaffold1319-719201 5 86119339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410946 Affx-122952038 AX-123281296 5 84977694 TTATTTGTAGGCTGAACGTTGAACTAAAACTCTGC[C/T]TTGGTCCGAGCACATGCATCTTTCCCTTACCTCTC Y 2 1 2 1 101000 f 74 goat snp8901-scaffold1319-782962 5 86183316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272321 Affx-1111833480 AX-519546057 5 84988328 TGTACAGAAGAGTAAATTGTTGACAGGTTCTTCTT[A/C]TGCTATATATGATGTGGTATAACATTATATGAAAT M 2 1 2 1 101000 f 74 goat 5_84988328_AF-PAKI 5 84988328 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389953 Affx-122968082 AX-123260310 5 85011607 TAATCAATATGCTATTGAGGTACATTTTGGAGTGA[C/T]GTAGTCTGAACCCCAATACATGTAACACTTCAATT Y 2 1 2 1 101000 r 74 goat snp8902-scaffold1319-816875 5 86217175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802005 Affx-122975789 AX-385288910 5 85044011 AGGAAAGATGAGACAGTCTAGGAAGTAGTTTCTTA[C/T]CTGTTTTGCTCTTAAGCTTCCTGACCGCTTCTCAA Y 2 1 2 1 101000 r 74 goat snp8903-scaffold1319-849279 5 86249978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771626 Affx-122970051 AX-385258784 5 85086165 ATGAACAGCCTTTCTCATGCAGTTTGATTGTTTCC[A/G]TATTATGGCTTGGATGGACACATGAAATTATTAGT R 2 1 2 1 101000 f 74 goat snp8904-scaffold1319-891433 5 86292185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417168 Affx-122947335 AX-123287516 5 85172873 AGAGAAACCTAAAGTAAAGGGAGAGAAATATGAAG[C/T]AGTAATTTGTAAAATGAAGTTTTTTATGTGTGTAG Y 2 1 2 1 101000 f 74 goat snp8906-scaffold1319-978141 5 86381133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450162 Affx-122922321 AX-123320497 5 85235829 CATTGTTGCTTTGGTGTTTCAGGGTCAGAGACTGA[A/G]TCTTGTTTTAATTTGTTTTAGATCCCTCATCACAG R 2 1 2 1 101000 f 74 goat snp8907-scaffold1319-1041097 5 86445172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387309 Affx-122970514 AX-123257667 5 85267429 AGTTTAGACAAATCTGTATAGTTTGGAAGACTTAC[A/G]TGGTTTCTATCACATTTGTCTCCTTTTCTACTAAC R 2 1 2 1 101000 r 74 goat snp8908-scaffold1319-1072697 5 86476973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401268 Affx-122959285 AX-123271621 5 85309735 AAAGAAGAATGGATTCATCTGTTCTTCCTCATCCA[C/T]CTTCCTGGATTTGCCACAATCTGAAGATGTTTATA Y 2 1 2 1 102000 r 74 goat snp8909-scaffold1319-1115003 5 86519782 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396453 Affx-122962976 AX-123266808 5 85352445 AGACTGAGATGGTGATTTTGAGAAATGTTTTAACT[A/G]CAGCAGGAGAAAGCAAACTATTTCTTTCCTTTAAA R 2 1 2 1 101000 f 74 goat snp8910-scaffold1319-1157713 5 86562505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409965 Affx-122954107 AX-123280315 5 85355431 TTTGAGACTTCAACTTGGGAAGTTATTGTTTGCAG[C/T]GACAAAAAAGAGCAGCGATTTTCTGTGTGTGTGTT Y 2 1 2 1 101000 r 74 goat snp8929-scaffold1322-1600 5 86565319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434747 Affx-122933910 AX-123305088 5 85404815 CATAAGAAAATGGATACTACTGACTTTACTCCCAG[C/T]GTAGGCTGATCTGAATTTTTACCTGAAATAAATAC Y 2 1 2 1 101000 r 74 goat snp8930-scaffold1322-50984 5 86615106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800690 Affx-122943275 AX-385287608 5 85443274 GTATTCAGCAGGGAGCTAGGGAGATAAACATGAAT[A/G]CAACTTTATTTTGATGTGTGCTGCTTCCGAGAGAC R 2 1 2 1 101000 r 74 goat snp8931-scaffold1322-89443 5 86654136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447737 Affx-122924591 AX-123318073 5 85510216 CTACGTGGTTCTGAAGTTACTGAATAAGCCATTTA[G/T]AGGCATATTTTATGTATATGTCTTCCTCACATAAG K 2 1 2 1 101000 f 74 goat snp8932-scaffold1322-156385 5 86721819 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377033 Affx-122977709 AX-123247392 5 85539092 TCCTTTGCTACTTTTTTGCAACATTTTTGCAGGAA[C/T]AGTTTTAATTCTGTTTTTACATATATCTGCATTCC Y 2 1 2 1 101000 f 74 goat snp8933-scaffold1322-185261 5 86750725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435204 Affx-122933634 AX-123305544 5 85573865 CCTTCTCTGACTCCCTGCTTGCATGTGAAAGGAAC[A/G]TTTCCCAGTCCTCTTGCAGTCAGATGGGACCATGA R 2 1 2 1 101000 f 74 goat snp8934-scaffold1322-220034 5 86785489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784564 Affx-122924165 AX-385271613 5 85616577 CTTGTCACTTGAATTACATTTAATTGGTCTTTAAC[A/G]CTTGATTTTACTGTTGTTCAGAGAAAGGCTGCATG R 2 1 2 1 101000 r 74 goat snp8935-scaffold1322-262746 5 86828397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445157 Affx-122925554 AX-123315494 5 85648439 ATTAGGATGTCTAGCAGCGTCTCTGGCTTCCATTT[A/G]TTAAATGTCATTAGTACCATCAAAAATATCCCCAG R 2 1 2 1 201000 r 74 goat snp8936-scaffold1322-294608 5 86860215 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781517 Affx-122956590 AX-385268602 5 85679277 AAGCCACATTGTGAACTAGCATCAAGTTTGTAGCT[A/G]TTCATTATCATGACCGTGGTTTTCCAAGATAACTG R 2 1 2 1 201000 f 74 goat snp8937-scaffold1322-325446 5 86891601 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413868 Affx-122949856 AX-123284217 5 85771324 TTTATTTTTTTTTCTTTTTCTGTGGGCTGGAGCTC[A/G]TTTCCCGGAGTCATTTACACTACGGTCACCAATGC R 2 1 2 1 101000 r 74 goat snp8939-scaffold1322-417493 5 86985099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408172 Affx-122954207 AX-123278523 5 85822769 CACACAAGCCAGGATTAGACCATACAGCTGGAGGA[C/T]GCTAGAGCTTGAGATTTTGACTACATTCTCCATGT Y 2 1 2 1 101000 r 74 goat snp8940-scaffold1322-468938 5 87036947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278267 Affx-1111836334 AX-190769965 5 85844523 CCCCTCCAGTATTCTGGCCTGGAGAATTCCATGGG[A/C]ACAACTGAGTGACTTTCATGTGCCTCTTGTGGCCA M 2 1 2 1 303000 f 74 goat Random2.2K-591 5 85844523 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408683 Affx-122953447 AX-123279034 5 85872139 CCAGACACCAGTATTAACAAGGCTGGGGTTTGAGG[A/C]TTACAGTGATTGTTGATTCTATGTGACACCTTTAA M 2 1 2 1 101000 f 74 goat snp8941-scaffold1322-518308 5 87086697 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432240 Affx-122936357 AX-123302581 5 85908182 ATCGAATTCAGCCCTTTTTCTCTTTCTTTCCATAT[A/G]TAGTAAATTAATCTGCAAGACTCATATATTCTTGT R 2 1 2 1 201000 r 74 goat snp8942-scaffold1322-554351 5 87122811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395815 Affx-122963640 AX-123266170 5 85966322 TTTCAGCAAAGCAGAGATCAATAAAATGCAAAGTA[C/T]ATGTTTGAAGAGTCAGTCCAAATTCAATGACCCAC Y 2 1 2 1 101000 r 74 goat snp8943-scaffold1322-612491 5 87182649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398680 Affx-122961871 AX-123269035 5 86012095 TAGAGGTGGTCATGGCCCTGAATGATAATTCAGCT[A/C]TATTCATCCATTTATTCAACTAATTCAACTAAATA M 2 1 2 1 103000 f 74 goat snp8944-scaffold1322-658264 5 87227704 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774492 Affx-122951524 AX-385261627 5 86041847 AAGATATTAAGTTACATAACCCAAGTGGCTATTAT[A/C]CTATCAAAATGTAGGAATGATTTAACCCTTTATGT M 2 1 2 1 101000 r 74 goat snp8945-scaffold1322-688016 5 87255522 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784208 Affx-122920306 AX-385271259 5 86122302 CAGCACTTGAAGGAATTATTACTTAATTATTTTCT[A/G]TTTTAGCATGCAATGCAACATTTTGACATCAGCTA R 2 1 2 1 303000 f 74 goat snp8947-scaffold1322-768471 5 87336440 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409324 Affx-122953083 AX-123279675 5 86154919 GTTGTCTGTGGAGGTGTGTGAGTTTCTAAAGGGAG[A/C]GTTCAGTGACTCTAGCTTGAATCTCATGTAATTAT M 2 1 2 1 101000 f 74 goat snp8948-scaffold1322-801088 5 87369044 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798220 Affx-122944793 AX-385285155 5 86197224 ATTTCAGGCAAAAGTAGTTTTCTAACTCTATATCA[C/T]GATTCTCAACTTTCTTGTACATGTGTAGATTTTTC Y 2 1 2 1 101000 r 74 goat snp51087-scaffold740-2829307 5 87411492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793442 Affx-122966421 AX-385280419 5 86226951 AATATTCATTAGAAAATAACATACCCTTCATAAGA[C/T]GTGGTTATGCCAGCAACTGAAGAACTATCACAGAT Y 2 1 2 1 101000 r 74 goat snp51086-scaffold740-2799580 5 87441236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779687 Affx-122954768 AX-385266787 5 86262584 TGATTATCTCACAGTCACTTCATTTCCTTTAAAAT[A/C]TGTTCTCATTACACATGAGCTAAGCAGTCTTTGAG M 2 1 2 1 201000 f 74 goat snp51085-scaffold740-2763947 5 87477353 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781872 Affx-122959919 AX-385268954 5 86312770 AGAATTCTTTCAAATGTTACCACATTTATAGGAAC[A/G]TTGGCCTTTGCAGACAGAATTAACCACTGTCCTGT R 2 1 2 1 101000 r 74 goat snp51084-scaffold740-2713761 5 87528638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438244 Affx-122931428 AX-123308582 5 86353795 AGCCTAAGCCAAGAAGCATTGTCTTCTTAGGAGAA[C/T]GAGGTAAGAACAGAATTTATTTTGGATGTCCCATG Y 2 1 2 1 101000 f 74 goat snp51083-scaffold740-2672736 5 87569684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435694 Affx-122933320 AX-123306033 5 86412830 AACTCTCATTCAACATATGCTTTCTCCCTTTCTTC[A/G]TTTCTTTCCCACCCCTGGCTCTTTTCTCCTACAGC R 2 1 2 1 102000 r 74 goat snp51082-scaffold740-2613701 5 87628491 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278269 Affx-1111836335 AX-519551756 5 86426266 ACTGGAGTGGATTGCCATCTCCTTCTCCAGGAAGA[A/C]TGTAAGGATATCACTATCTTAAGACTAAGTAGATG M 2 1 2 1 103000 f 74 goat Random2.2K-592 5 86426266 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417586 Affx-122946892 AX-123287934 5 86455306 ACATAGAACAATCATTACATAAAGGCAAGGTAATA[G/T]ACACATAGAATCATTTAAAATTTCTACCACAGAAC K 2 1 2 1 101000 f 74 goat snp51081-scaffold740-2571225 5 87671047 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429993 Affx-122938043 AX-123300334 5 86505921 ATTTCCACAAAAATTTTGGTTGATGGCATATCTCA[C/T]AGCCATCGGCTTTGTTTGTTTGTTGTTACTATTTG Y 2 1 2 1 103000 f 74 goat snp51080-scaffold740-2520610 5 87722650 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274376 Affx-1111834219 AX-515859214 5 86544929 ACTATGGTACATTTGCTGCAGCTCAGCTTTCTGAT[A/G]ATCTTGCAGAGGT R 2 1 2 1 102000 f 74 goat GoatD01.025964 5 86544929 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38412689 Affx-122950761 AX-123283038 5 86545229 TATTTCATGAGCTGGGTCTTTTTCCTGGAGTCTCT[C/T]AAAATTATTCAAGAAAAATGAAGATAAATATGTTT Y 2 1 2 1 103000 f 74 goat snp51079-scaffold740-2481302 5 87762049 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799196 Affx-122932218 AX-385286126 5 86578450 AATATTCATCCTTATATCTCAATCCTATTACTTAA[C/T]GACTCCTTTCATATATGTAACAGATTATAGAAAGA Y 2 1 2 1 101000 r 74 goat snp51078-scaffold740-2448081 5 87795224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795521 Affx-122966088 AX-385282476 5 86625348 AAAGTGCCTGCATATTTGCGTATAAACAAATAAAG[C/T]AAAAGGCTTACAGATTTGGGTTGACTTCAAGCCCA Y 2 1 2 1 101000 r 74 goat snp51077-scaffold740-2401183 5 87845100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799600 Affx-122978484 AX-385286530 5 86668614 AAATAAGTTTTAAATACCCTTGCTAATGGTGTCAT[A/G]CATGCGAAGTGGTTTCAGTTGTACCCTACTCTTTT R 2 1 2 1 101000 r 74 goat snp51076-scaffold740-2357917 5 87888587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399760 Affx-122960314 AX-123270115 5 86722483 GCTATGACTCTATATGTTTTCCCCAAATCAATGAC[A/G]CTTTTATTTATAGTTTCCAGTCTTTGAGGGTAAGG R 2 1 2 1 101000 f 74 goat snp51075-scaffold740-2304048 5 87942690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796677 Affx-122978758 AX-191622040 5 86790013 GATTAATTTAGATCAGATAAGCTCAGTGTTAGGAC[A/G]TTGGGCCTGTCAGATAGTGACTGGTCAGAGAAAAA R 2 1 2 1 101000 r 74 goat snp51074-scaffold740-2236518 5 88010006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445591 Affx-122925124 AX-123315928 5 86866910 GTTACCGATTAGATATATGTACACAGAGGCCAAGT[A/G]TGTTGTGGAGAATAAGTGAACCCATACTGCGGGGT R 2 1 2 1 101000 r 74 goat snp51072-scaffold740-2159621 5 88087732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439365 Affx-122930277 AX-123309702 5 86914366 ATCATTAATTGACAGCTTGGTTGGAAATGTAAAAG[C/T]AGACTCTCAATAATTTTTTCATTACAGTTTTGAAG Y 2 1 2 1 101000 f 74 goat snp51071-scaffold740-2112165 5 88135074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435295 Affx-122934032 AX-123305635 5 86947566 TCAAAGCTAAAGAGATCTGAAGGTCATCTAGTGAG[C/T]GACCGTGATGGGGAGACCATTTTCTGGCTATGTTT Y 2 1 2 1 201000 f 74 goat snp51070-scaffold740-2078965 5 88169415 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775329 Affx-122919361 AX-385262460 5 86981634 AATATGATGCTGGTGTGGACTTCTTTGTAGTTCCA[A/G]TTGAACTTGACTGGGTTCATTCTAATACACTAAAG R 2 1 2 1 101000 f 74 goat snp51069-scaffold740-2044897 5 88203831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385121 Affx-122971777 AX-123255479 5 87017848 GAGATGGCCCCATATTCTTAGGTTAAGCTTCTGGA[C/T]ATTTAGGGGTCTATTTGTACCCTTTTGATTCTGAA Y 2 1 2 1 201000 r 74 goat snp51068-scaffold740-2008683 5 88240726 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778708 Affx-122952754 AX-385265819 5 87050443 TAAGAGTTGGGCCAGTTACTCAAGTTCTTCAACTA[C/T]CTATTGCCTACAAAATGTTTAACATGGAATTTGTA Y 2 1 2 1 101000 f 74 goat snp51067-scaffold740-1976088 5 88273642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405960 Affx-122955542 AX-123276312 5 87105223 ATTGTTGAAGGAGAAAAATCATCAGGGAATTAGAA[A/C]TATACTACTTTGAAATGATGAAGGAAAGAAAGTAG M 2 1 2 1 101000 f 74 goat snp51066-scaffold740-1921308 5 88328603 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394575 Affx-122964443 AX-123264930 5 87134540 ACAAACTTCAACCATGAAGGAGGGGGAGGAATGTA[C/T]GTCAGGGACAATTTCCAATCTCAGTCACAAAATTA Y 2 1 2 1 201000 r 74 goat snp51065-scaffold740-1891991 5 88357886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791926 Affx-122930438 AX-385278916 5 87193988 CAATTCAGAAGCTCATTATCATTAAATAAGGGGTC[A/G]TTATCCCAGGAGATACTATAGAGAAATGTTAGTTT R 2 1 2 1 101000 f 74 goat snp51064-scaffold740-1832543 5 88418021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378827 Affx-122976545 AX-123249186 5 87236004 ATTCTGCATAATGTGAATGAGTCAGAGAAAAACAC[G/T]CTGGTTCCGTCAACAGCAGCTCTTTCTCTTCATGT K 2 1 2 1 201000 f 74 goat snp51063-scaffold740-1790527 5 88460205 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423953 Affx-122942145 AX-123294299 5 87290882 TCCCATTTTCCACAGCTAAAAGATCCCACATGTCA[C/T]GACTAAAGATCTGTGTGTGGCAACTAAGACCCAGT Y 2 1 2 1 303000 r 74 goat snp51062-scaffold740-1735649 5 88514076 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451205 Affx-122921322 AX-123321539 5 87334480 GTTTCTGAAGCAAATTCATGCCTTTTTATCTTCTC[C/T]GTCCTTCCACTGCCAATATTCACTTTTGTGGTACC Y 2 1 2 1 101000 r 74 goat snp51061-scaffold740-1692051 5 88557676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387265 Affx-122970552 AX-123257623 5 87388172 CCCGGCTGCCCCTCTCCATTGAATTCTGGAATTCA[A/G]CCTTGGTGGGAGACAGGGGCTTCTTTCAGACTTTC R 2 1 2 1 103000 r 74 goat snp51060-scaffold740-1638359 5 88611714 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398221 Affx-122962214 AX-123268576 5 87434707 CTATCTGTGGATATGAAATGCCAACTGTGTGTCTC[A/G]TAACTGTTCATTCATATTTATTGCTCCTTCTAAGA R 2 1 2 1 101000 f 74 goat snp51059-scaffold740-1591824 5 88658836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783422 Affx-122946525 AX-385270485 5 87485243 TGCACTCACCTCATTTATTCCTTCATGAGTAAATA[C/T]GTGAGCACTTTCTGTCTGTGATATCCCACGTCATT Y 2 1 2 1 101000 r 74 goat snp51058-scaffold740-1541288 5 88703853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402703 Affx-122959608 AX-123273056 5 87517064 ACCTCAGGCATCTCTCTGGATAGCAGTCTTTTGAG[C/T]AGAGGGAGGCAACAAATTATAACAGAGAACATGGC Y 2 1 2 1 101000 f 74 goat snp51057-scaffold740-1509467 5 88735700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422323 Affx-122943462 AX-123292669 5 87545603 CATAGCCTGTCATGACAACTTTAGAGTTAAGTATA[C/T]AGACAAAAAGCTGCATTGTAAACGGAGGCCTTTGG Y 2 1 2 1 101000 f 74 goat snp51056-scaffold740-1480928 5 88765443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802666 Affx-122932994 AX-385289565 5 87582361 ACTGGAGGTAAAATCCCGGGACTGTTAACAGAACA[A/G]TCCCAGTTGGCTAGACTGAGGCCAATACTTAATGA R 2 1 2 1 101000 r 74 goat snp51055-scaffold740-1444170 5 88802263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403517 Affx-122957626 AX-123273870 5 87611230 ATGTGGTTAATGGGGTCAAGTGCATGATATTCATT[A/G]TGGCGCAGGACAGCTTGATGAGCCTTGCAAACACA R 2 1 2 1 201000 f 74 goat snp51054-scaffold740-1415301 5 88831202 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768788 Affx-122939139 AX-385255965 5 87655635 AACTGTTTGGTTGAAATAAAACATACGTACTGAGA[C/T]GGACACAGACCATAAGGTGTAACTCAATCAATTTC Y 2 1 2 1 101000 r 74 goat snp51053-scaffold740-1370896 5 88876582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425275 Affx-122940972 AX-123295621 5 87694257 TAGTGGTATAACACAATCTGTTTATTTCTCACTTG[C/T]ATAGAGTCTGATATGGGCCAGGCCATTTTTTCTTC Y 2 1 2 1 101000 r 74 goat snp51052-scaffold740-1332274 5 88915511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781261 Affx-122949899 AX-385268346 5 87725899 ATGAATGGATTAGTCTGAAATTTGAGCTTGTAAGA[A/G]AGTGAGGTGAGGAAGAAAGCTATAAATAGAGGACT R 2 1 2 1 101000 r 74 goat snp51051-scaffold740-1300632 5 88947226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428126 Affx-122939066 AX-123298469 5 87768747 CCAGTGACTGAAAAAGCAATAATTTAAGGTCTGCA[C/T]AAAAACGAAGAAAACCGAATGGGAGTTAACTGTGT Y 2 1 2 1 101000 f 74 goat snp51050-scaffold740-1257784 5 88990079 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320774039 Affx-122967173 AX-385261177 5 87799929 CTTGTTAGTATTGTATCAAACAAATGTTGCATAGA[A/G]TTAATAGAACATTGCTTGTAAATATTTCAGATTTG R 2 1 2 1 101000 f 74 goat snp51049-scaffold740-1226602 5 89021255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278431 Affx-1111836336 AX-519551916 5 87840555 CAAAAGGTTAGAATGAAATTTGCTTGGAATTTCAC[A/G]GAACTACAACCTTTAGTGTCGTCCTGCAGAATTCG R 2 1 2 1 101000 r 74 goat Random2.2K-594 5 87840555 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778952 Affx-122956238 AX-385266059 5 87843544 TTTGAAAAGCACGGCTTTAAGTTACTGAAACTTAT[A/C]TGAATAGACTGAGTGCTTTTTCTGGCTCAGATTTT M 2 1 2 1 101000 r 74 goat snp51048-scaffold740-1182987 5 89064850 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410343 Affx-122952462 AX-123280693 5 87930720 CACCGTCTTTTCCTTGTCTCTTATCACTTTCAAGG[C/T]AATATGCATGGGCATTCTCATTTTTTCCAAAAGAT Y 2 1 2 1 101000 f 74 goat snp51047-scaffold740-1095811 5 89151882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278273 Affx-1111836337 AX-519551760 5 87969152 TCTGGGTATGTATCCAGAGGAGATAAGGTTAAGAT[A/C]TTGAAGAGATACCTGCATCGCCATGTTTTTGCAGT M 2 1 2 1 101000 f 74 goat Random2.2K-595 5 87969152 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438738 Affx-122930833 AX-123309075 5 87974373 CTTGACCATCTTTCAAATCCCCAGGCCCTCTACCC[A/G]CTTCCTCCCAACCCCCAACCCCCTCACCTAATCTA R 2 1 2 1 303000 r 74 goat snp51046-scaffold740-1052158 5 89195957 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383289 Affx-122972717 AX-123253647 5 88004443 AGTAGCACCCAGCTCTTTAAGATTATGCCCTCCCT[A/C]ATTTAGGGGTATCTTTTTATCTTTTAAGTATATTA M 2 1 2 1 202000 r 74 goat snp51045-scaffold740-1022088 5 89226046 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272322 Affx-1111833481 AX-519546058 5 88022737 AAACATTTCAGGATTAACATCTCAAGAAAGAAGTC[A/C]GTTGAGGAGGATATGAGTCTATGAGTGTGTACATT M 2 1 2 1 101000 f 74 goat 5_88022737_AF-PAKI 5 88022737 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766410 Affx-122962837 AX-385253786 5 88046073 ACTGGAGTATATACCCTGTGCTCATTTTTACTCTT[A/G]TGTGGTTTTACATAGATCATTCAACAGTAAACTTT R 2 1 2 1 101000 f 74 goat snp51044-scaffold740-980458 5 89267755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451357 Affx-122921251 AX-123321690 5 88102089 TTCACTGTGCTCGTCACCTGCTTCTGGAATGATGT[A/G]TCGACATGTGCCAGACACCTGCCAGGATGGGGCAC R 2 1 2 1 101000 f 74 goat snp51043-scaffold740-924442 5 89323362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417027 Affx-122947966 AX-123287375 5 88137659 TGAATGTAGACCCGAAATATAATGAGATAACAGAC[A/G]CACTGGTTGTTTTCCTCACACGACAGTCCAGGGTA R 2 1 2 1 101000 f 74 goat snp51042-scaffold740-888872 5 89358394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796973 Affx-122923243 AX-385283914 5 88177818 TTGTTAAATAGTGATGAATAGTGATAACTGCCCTG[A/C]TGGTAGGTGATTAGAAAAAATGCTAGGATAATGAG M 2 1 2 1 101000 f 74 goat snp51041-scaffold740-848713 5 89398740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426140 Affx-122940613 AX-123296486 5 88232809 GTGTACGGGCAGAACATTTTGACCTGAATGGTTTG[C/T]GGAGGCACCTATTAGCCAAGCTGACTGAACAGATG Y 2 1 2 1 101000 f 74 goat snp51040-scaffold740-793722 5 89453989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414758 Affx-122949250 AX-123285107 5 88265986 AGAGACAAAGTATTTTGAATCACCTAAACAATTCT[G/T]CAAATCAACAACAATAATAATAAAATCTGGGACTT K 2 1 2 1 101000 f 74 goat snp51039-scaffold740-760545 5 89487339 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402442 Affx-122958619 AX-123272795 5 88310318 TATAGAAATAGGCTTCTTTGCTGTGTTAGCTATGA[C/T]ATACAGGACTAAAATTTAAGTTCAACTGCAGTGAG Y 2 1 2 1 101000 f 74 goat snp51038-scaffold740-716213 5 89531205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395678 Affx-122963748 AX-123266033 5 88345132 CATTCACTCAGCAATTAATATCCCACATCTGCTCC[A/G]TGCAATGTAATATGTCAGGTCAGTGGTAGATAGGA R 2 1 2 1 201000 r 74 goat snp51037-scaffold740-681399 5 89566019 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449494 Affx-122922630 AX-123319829 5 88377818 TTGAATGAATATACCAATAACACACATTGTTAGTA[C/T]AGTAAGGATCCCAAATGCTAAAATTTTACTGGTCA Y 2 1 2 1 101000 f 74 goat snp51036-scaffold740-648713 5 89601025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777574 Affx-122958370 AX-385264693 5 88411672 GCATAACTACAAAACACTCAGAAAGGTAATATTTC[A/G]TCTATTATTCTGATTTGGAAAACTACATGCAAAAA R 2 1 2 1 201000 r 74 goat snp51035-scaffold740-614859 5 89635206 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801787 Affx-122967514 AX-385288695 5 88443267 GCCAGTCTTCATTCTTTTGAGGACTCTGTAGACAG[C/T]ATTTTTTTAGTTTCTGTCTTAGAAGTTTTGGGCTG Y 2 1 2 1 101000 f 74 goat snp51034-scaffold740-583264 5 89667497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768486 Affx-122932109 AX-385255666 5 88499139 CTTGTGCTTTTCAGAGCAATGCTGTAACACACACA[C/T]GTACTAAAAATTATACTGGAATGCCCAATGAAGCC Y 2 1 2 1 101000 f 74 goat snp51033-scaffold740-527392 5 89721779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407540 Affx-122954692 AX-123277891 5 88554088 ATGGGTGTTCCGAGAAAATGCGACAGCAGTAGATG[C/T]AATCACTCTCTTATTCTGAAAAGTTATAAAAACAA Y 2 1 2 1 101000 f 74 goat snp51032-scaffold740-472443 5 89776741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415643 Affx-122948575 AX-123285992 5 88595271 GAGATAACTTGCAAAAGGTTCATGCCCTACTCTAT[A/G]TCACAAGTGATTCTGCACATTTGCTTCTTCATAGT R 2 1 2 1 101000 f 74 goat snp51031-scaffold740-431260 5 89818435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406569 Affx-122955096 AX-123276921 5 88628358 TTCAAGGAATATTTACCAGTAACTCAAGGAAAGGG[C/T]GATGGTAATGTGTTTCATGGTAGTGACAATCATAA Y 2 1 2 1 101000 r 74 goat snp51030-scaffold740-398173 5 89849204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789586 Affx-122953844 AX-385276595 5 88673570 ATTACCAAATTATTCCATTTGACCCAGATGTGATT[A/C]TAGTAGAATCCACATTCTCCAATATTTATGGTCGA M 2 1 2 1 101000 f 74 goat snp51029-scaffold740-352961 5 89892651 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381728 Affx-122974692 AX-123252086 5 88702519 CTTATTTACTATCTGCATATCTTCTTTGGTGAAAT[A/G]TGTCGGTGTTTTTGTTCATTTTCTAATTAGAGAGT R 2 1 2 1 103000 r 74 goat snp51028-scaffold740-324012 5 89921559 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788572 Affx-122943273 AX-385275589 5 88739695 TATTATTGATATGAAAATATCTCCAAGACGGTTGT[A/G]CAGAATAGTAAAGATGCTATTCTTTTTGAGGAAAA R 2 1 2 1 201000 f 74 goat snp51027-scaffold740-286836 5 89955646 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445883 Affx-122925962 AX-123316220 5 88795533 CTTAAATATAAATAATCATAATAATAAAGCAGAGA[C/T]GATCCAAAACTAAACCAGAAAAAATAAATACAAGT Y 2 1 2 1 101000 r 74 goat snp51026-scaffold740-230998 5 90012167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795675 Affx-122955393 AX-385282630 5 88828758 TTGAGACAGTGTAGGTCAACTTTGTAAAATAACTT[A/G]TCCTTCCTTCTCTGTTACAGCTCAGATACATTATT R 2 1 2 1 101000 r 74 goat snp51025-scaffold740-197773 5 90046486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773621 Affx-122931477 AX-385260761 5 88863753 ATATTACAAGATGAATTTTCACCAGATGGTCATAA[G/T]CTGGTATTAAAATGCCAATATAAACTACATAATAA K 2 1 2 1 101000 f 74 goat snp51024-scaffold740-162778 5 90081778 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786716 Affx-122963751 AX-385273747 5 88904394 AATCAACATTCTAGAAATGAGCTAGTCATAGGAAA[C/T]GGTTATGTTTGCAAGACAATAAAATGTATCAGCTA Y 2 1 2 1 101000 r 74 goat snp51023-scaffold740-122137 5 90121504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431702 Affx-122936771 AX-123302043 5 88940487 TATGTACACTACTAATATAGCTCATTCTTCAGTGC[C/T]ACTATCATTGGCCTCATTTCTGTGTGAGCCTGTTC Y 2 1 2 1 201000 f 74 goat snp51022-scaffold740-86044 5 90157928 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437304 Affx-122931974 AX-123307642 5 88977054 TGAGCTCCTGCTTCTTCATATTCAGCATATTTACC[A/G]CTGAACTCAATGCCTTACCCTGCTCACTCAGGTCT R 2 1 2 1 101000 f 74 goat snp51021-scaffold740-49477 5 90194352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774158 Affx-122957946 AX-385261296 5 89024240 GTAGAGTCTATAGGTTTGTAGAATTTCCAGGTCTG[C/T]GGTAAAGGAAGTGAGGGACAAAGTTTAGCAACATG Y 2 1 2 1 101000 f 74 goat snp51020-scaffold740-2291 5 90241292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405689 Affx-122956549 AX-123276041 5 89032770 ATAGAAAGACTTTAAGTCTGCATATTTTCAGGTCG[C/T]GTGTATCTTGGAAAAATAAAGACAGAAATGCTCAT Y 2 1 2 1 101000 f 74 goat snp49212-scaffold702-6140 5 90249608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399291 Affx-122960541 AX-123269646 5 89066877 AGGAGCACCAGTCTAATACTTTAGAGATTAAGCAT[A/G]TTTGTAATGTATTTTGAACACTGGAGAAGATTGCT R 2 1 2 1 101000 f 74 goat snp49213-scaffold702-40247 5 90283660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792604 Affx-122963158 AX-385279585 5 89114085 GTGCCAGCTATCAGTTTATTGACCCTGAGCTCCAC[A/G]TTCACTTTTGTTGTCTGATCTGTAAATGTGGATCT R 2 1 2 1 101000 f 74 goat snp47384-scaffold666-1627339 5 95447425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790032 Affx-122946495 AX-385277038 5 89162496 AATTACAAAGCACTCAGAACGGTGCCTGGCACATT[A/G]TAAGGAAGATCTATGTAGATCTGTGTCTTATATTG R 2 1 2 1 101000 f 74 goat snp47383-scaffold666-1578928 5 95495641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411003 Affx-122951989 AX-123281353 5 89248174 AGGGCACTTATCACTTACAACTACATTTCTTTCTC[A/G]TTTTACTTGTTTTTGGCCCACTATTCTGAAAGTTT R 2 1 2 1 201000 r 74 goat snp47381-scaffold666-1493250 5 95581822 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378904 Affx-122976488 AX-123249263 5 89286456 ATACTCAGTTATGCCTCTCAGAATGTATAGAAATA[C/T]AGCAAGGGTACCAAATCCTAATCACAGAAAACAAG Y 2 1 2 1 201000 f 74 goat snp47380-scaffold666-1454968 5 95619570 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409243 Affx-122953144 AX-123279594 5 89332463 GCATTTAGTTATATTTCCACCAATATGGGAATGGT[A/G]CAGAGAGCATTTCTCTGCTATTATGGATATGCTTT R 2 1 2 1 101000 f 74 goat snp47379-scaffold666-1408961 5 95666162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785526 Affx-122949994 AX-385272570 5 89363461 TTTTTATTTTCAGAATCTAGCATGGTGTCTGATAC[A/G]CCCAGATATTTGATACATGTTTGTGGAGCTGAAAT R 2 1 2 1 101000 r 74 goat snp47378-scaffold666-1377963 5 95697011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451138 Affx-122921371 AX-123321472 5 89397302 TGGAACTAATCTAAGTAACAGCCCCAATCACAGTC[A/G]TTTCTGCTTCAGTCTTTGGTGTTAGGCTTCCATAT R 2 1 2 1 201000 r 74 goat snp47377-scaffold666-1344122 5 95730613 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418851 Affx-122946133 AX-123289199 5 89441075 TCTGAACTCTGCATGGCCATTTGGGCCAACGGCAA[A/C]TTTTCTACAGCGTACACAGACATACAGAGCAGCTG M 2 1 2 1 303000 f 74 goat snp47376-scaffold666-1300349 5 95774388 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395394 Affx-122963963 AX-123265749 5 89529649 TTTTCCCACTGGAGAGCCCTGGGGCTGTAGAGTTA[A/C]GCAGAGAAATGAATTATTTGTTTTCATCAAGGCTG M 2 1 2 1 101000 f 74 goat snp47374-scaffold666-1211775 5 95863069 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432710 Affx-122936021 AX-123303051 5 89574111 CATGCTGCAACCAAAAGAAAGCAGAAAGGGAACAA[C/T]AGATTTCAAAAGATGAACAACACACCCCGTTTAAA Y 2 1 2 1 201000 r 74 goat snp47373-scaffold666-1167313 5 95907779 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785417 Affx-122932785 AX-385272462 5 89605006 TCAGAAGCGCTGATGAGGCAGAGAACAGAGAAAGT[A/G]GCTTGACCAGAGACGCAAGAGCTCTGTAAGCTCGA R 2 1 2 1 101000 f 74 goat snp47372-scaffold666-1136418 5 95938450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779458 Affx-122969310 AX-385266561 5 89683259 ATCTTTACATTTTAGTTCAAAAGCTTGACTGAGAT[G/T]CCAGCAATTACCACTTACATTTAATTGTCTAAGAG K 2 1 2 1 101000 r 74 goat snp47370-scaffold666-1058165 5 96016833 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391154 Affx-122967449 AX-123261511 5 89732570 TGTAATAGCGCTTCAGTTAACTTTTTAAACATGGC[C/T]GTTAACCAGTGAAGTGTGAGTCTTATTCAGAAGAG Y 2 1 2 1 101000 f 74 goat snp47369-scaffold666-1008854 5 96065880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416544 Affx-122947752 AX-123286892 5 89768794 AGCTAGATGATCAAGTCAAGAACTACAACTCGGGG[A/C]TTCCCTGGTGGTCCAGTGATAGAGAATTCGCCTGC M 2 1 2 1 103000 f 74 goat snp47368-scaffold666-972630 5 96102019 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446853 Affx-122925257 AX-123317189 5 89825762 AATTGTTAACTGAAACCAAAGCTTCAAGTCATTCC[A/G]TCAATTGGTACTTAAATTCCTCTGCTGGTAAATGC R 2 1 2 1 101000 r 74 goat snp47367-scaffold666-915662 5 96159353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437344 Affx-122931945 AX-123307682 5 89923134 TCTGCAAACCCCAGATTAGCTTCAGCAAATAATCA[C/T]CTTAGCTGGCTTTCTGCTCTACCGTTACTTCATCT Y 2 1 2 1 201000 r 74 goat snp47366-scaffold666-818290 5 96254213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453954 Affx-122919471 AX-123324287 5 89956313 CCTAGACATTTATATGAAGTTTTATTAACAGTATC[A/G]TATCTAACCTATGGTAAACAGCAGCCACTGATTTT R 2 1 2 1 101000 r 74 goat snp47365-scaffold666-785111 5 96287196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783883 Affx-122976730 AX-385270939 5 90000487 CCTGTACCCAAAATAGTCTCTATACTGTGATTATT[G/T]ATGTTGTGTCACATAAATATACACAGTTCATTAAT K 2 1 2 1 202000 r 74 goat snp47364-scaffold666-740937 5 96331556 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383243 Affx-122972752 AX-123253601 5 90045426 GGGCCACACACACACCTCAAGGGCAGCAAAGTGAT[A/G]CTGTCACGGAGGGAAGGAATTACACCAAGTTTTTA R 2 1 2 1 101000 r 74 goat snp47363-scaffold666-695998 5 96377077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779524 Affx-122949336 AX-385266627 5 90104066 TTACAAAGCATATTCTCTTATGCTGCTATATTTTA[C/T]ACTAAACAACCCTAATAATCAAGATTAAAGTCATA Y 2 1 2 1 101000 r 74 goat snp47362-scaffold666-637358 5 96436168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412766 Affx-122950510 AX-123283115 5 90137307 GAATCAGCGTTAAGCACTCTTAAATTCACATGTTC[A/G]TTTGAGCCTCTCGGGTCTGCCAACCAGTTGGAAAC R 2 1 2 1 101000 f 74 goat snp47361-scaffold666-604117 5 96470238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405831 Affx-122955877 AX-123276183 5 90169271 TGCAGATCCTCCTCCTAATCCATCCCCACAGAGGC[A/G]TTTTAACTTCTTTCTTGACTTGTTTTGAAAAGTCA R 2 1 2 1 101000 r 74 goat snp47360-scaffold666-572153 5 96502605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435623 Affx-122933778 AX-123305963 5 90208669 GCAAACAGAAATGGAAACATTACTTTAAAAAAATG[C/T]ATTCCTTTCCAGGAAGATCTGAACAGTGCAGGTAG Y 2 1 2 1 101000 r 74 goat snp47359-scaffold666-532755 5 96542039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384731 Affx-122972048 AX-123255089 5 90261736 GCCTTTCATTGAGCTCCTTGGAGTTTCCCCTGCAC[A/G]TTGCTGTTTAGGAGCACATGTTAAGGATTTGGGAG R 2 1 2 1 101000 r 74 goat snp47358-scaffold666-479688 5 96595092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453389 Affx-122919923 AX-123323722 5 90361913 TGAGGCAGGTTCCGAGACAGATCAGATGAGGAGGG[C/T]AAGGGAAAGAAGCTGAAAAGATGACTCTTTGGGGA Y 2 1 2 1 101000 r 74 goat snp47356-scaffold666-379511 5 96695139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439682 Affx-122930581 AX-123310019 5 90393111 GGGTTGTCCTTACCTGGTGCTGTGGGTTGTTTACC[A/G]TGAGAGAGAGACAGAGATACCTGGCTCCATTCTAC R 2 1 2 1 201000 f 74 goat snp47355-scaffold666-348313 5 96726329 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376917 Affx-122977794 AX-123247276 5 90442136 GACCAGCTTTTGTAGTATTTCCTGCACTGAGAGTA[C/T]GTCACTCACCAGGAAAGCAAGAAAGGAGTCAATGC Y 2 1 2 1 101000 f 74 goat snp47354-scaffold666-299288 5 96775413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406921 Affx-122955610 AX-123277272 5 90500671 ACTTTTACTGAAATCACCATACTGTTTGACATTTC[A/G]TTACTGCCTATTTGTAAGATTTTTTGGTACAAGAG R 2 1 2 1 101000 r 74 goat snp47353-scaffold666-240753 5 96834110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432192 Affx-122936393 AX-123302533 5 90538561 GGTTTTGCCATATGGCATGTGGTAAGTTGTTGCAG[C/T]AGGATGAAAGGACACGTGGAAAACTCTGGCCCTTC Y 2 1 2 1 201000 r 74 goat snp47352-scaffold666-202863 5 96872236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379467 Affx-122976082 AX-123249825 5 90570742 TGTCCTCATGGGCACGATGAATGATAAGCAGACTA[A/G]TAAAAACAAAGGAGAGCTAGAAAAATTCCCTAGTG R 2 1 2 1 101000 f 74 goat snp47351-scaffold666-170682 5 96904583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272323 Affx-1111833482 AX-519546059 5 90586894 AGTGAAAATAAAACTAACAAGTATGTTGAGAGGAA[A/C]GGAAAGAAAGCAAAGAAAAAAATCATAGATATGCA M 2 1 2 1 103000 f 74 goat 5_90586894_AF-PAKI 5 90586894 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379771 Affx-122975846 AX-123250129 5 90613401 TGAGGTGTGACCACTAGATGGAACCCCTGAGCCCA[G/T]GTCCATGCTGATGCTTTATAAGGAGAGGTGGTGAG K 2 1 2 1 201000 r 74 goat snp47350-scaffold666-128023 5 96948283 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789261 Affx-122964428 AX-385276272 5 90643018 AGAACTGTGGTTTTTAAAAGCCCATAATGTAGAAT[G/T]TACCATCTTAGGCTAATTTACCATCCAGTGGCTAA K 2 1 2 1 101000 r 74 goat snp47349-scaffold666-98406 5 96978712 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387937 Affx-122970024 AX-123258295 5 90688525 ACTGTGAATCCAGGTCTTTGTGAGAACTCAGTCTT[A/G]TGCAAGTTACTTGAACCTTCAAAATGCAGGGGACA R 2 1 2 1 101000 f 74 goat snp47348-scaffold666-52899 5 97020952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792596 Affx-122927053 AX-385279577 5 90727371 CAACTGAAAAGAAGAATGCATGTACCTAAAAAAAG[C/T]ATGGAAACAATACCTTATTGTGAAATTATTAAAAT Y 2 1 2 1 101000 f 74 goat snp47347-scaffold666-14053 5 97060163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774252 Affx-122963536 AX-385261388 5 90748500 CGGCACAGCCACGAGCACTAAATATTCACTGGCTC[A/G]TAGATCTTCAATAATAGTCCCTGAATTTCTTTGCA R 2 1 2 1 102000 f 74 goat snp56978-scaffold903-6977 5 97131125 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445011 Affx-122926637 AX-123315348 5 90817334 CTTTCCCTTTCTCCTAGGACCTGCTTGTCAACTAC[A/C]AATTTCCCTCTTACCCTTAGCTTCATTTTGCAGGG M 2 1 2 1 201000 r 74 goat snp56979-scaffold903-75811 5 97201888 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386525 Affx-122970736 AX-123256883 5 90849114 TGAACTGAGACAAGTAAAATGATTAACAGTGAAGA[C/T]ACTGATTAGACAGAGCAAGAGCCCAGTAGATGTCA Y 2 1 2 1 101000 r 74 goat snp56980-scaffold903-107591 5 97227891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439718 Affx-122930554 AX-123310055 5 90935916 AGCTGTTTCTTTTAAATGATTTTTAAATGAGAAAT[A/G]TATCTGGGAGCCAGTTACAGTTTGGCTGATTGTCA R 2 1 2 1 101000 r 74 goat snp56982-scaffold903-194393 5 97315438 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798182 Affx-122951032 AX-385285117 5 90987594 GAACCTGACTTGCTTCATGGAATTCTTCCTTTTGC[A/G]TATATACTGCGTCATGAGTATCACTGCAGTTCTCC R 2 1 2 1 102000 f 74 goat snp56983-scaffold903-246071 5 97365311 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435716 Affx-122933304 AX-123306055 5 91028831 ATCTGTGTCTCTACACTGATCTGTGTCCCACTTCC[A/G]CGACTGAAGCCTTTATGCTTTGACCCAGGTGTATG R 2 1 2 1 101000 r 74 goat snp56984-scaffold903-287308 5 97405907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411636 Affx-122951578 AX-123281986 5 91063138 TTGTAAATGAATTCAAAGCTATTTATTTTATGCCT[A/G]TTGATTTAGGTACATTCCACAGCATTGACAAATGG R 2 1 2 1 101000 r 74 goat snp56985-scaffold903-321615 5 97440697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784072 Affx-122942678 AX-385271125 5 91094813 GTGACAGAGTGTTTTGGTGGTATTGGGCATACATC[A/G]TACATTTAATACTCTTTTAAGTTATAGGTTTACTT R 2 1 2 1 201000 r 74 goat snp56986-scaffold903-353290 5 97472519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411467 Affx-122951803 AX-123281817 5 91151715 GTTGAACTCAATAAGGCTAAGCTTTGTGCAGGGAA[C/T]GATGCTCATCTTTGCTCGTGCCCACGTCTGTGTTG Y 2 1 2 1 101000 f 74 goat snp56987-scaffold903-410192 5 97529808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769612 Affx-122941513 AX-385256782 5 91189871 CAGGCCTCAGCACACAACGACTAATGTTAGTTTTC[G/T]TGCTGTGTCGAATCCCCTTAGTCTCCACGTCTTCA K 2 1 2 1 201000 r 74 goat snp56988-scaffold903-448348 5 97567890 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385916 Affx-122971571 AX-123256274 5 91219419 GTGGCCCAGGAGACACAGTGCTGGTTTCTTCAATT[A/G]CAGTGTGGGAAGAGAATGATTTTTTGACACTGAGA R 2 1 2 1 101000 f 74 goat snp56989-scaffold903-477896 5 97597665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278275 Affx-1111836338 AX-519551762 5 91262824 AGGCTGTATAACCAATGAGTACCACATTAAAGATC[A/G]CCAAATCTTTAAAAGATACACCTAGTACTTCACAG R 2 1 2 1 101000 f 74 goat Random2.2K-599 5 91262824 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802023 Affx-122937416 AX-385288927 5 91271808 AAGATAACCTCTTTCATTTTAGAGGATCTGGATCA[C/T]GTTACAGCTGTACCTAGGCAACTGACCAGCCATGA Y 2 1 2 1 101000 r 74 goat snp56990-scaffold903-530285 5 97650337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423665 Affx-122942337 AX-123294011 5 91302985 AACACACACCTTTGGGCCTATTTGTGTTCAGACCT[A/G]TCCTTTGCTCTTCCCTCCTCAGCTTCTTATTGTGG R 2 1 2 1 101000 f 74 goat snp56991-scaffold903-561462 5 97681489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431911 Affx-122936000 AX-123302252 5 91422708 AGGGGACACAGGTGTAGCAAAGACTTGGAAGAATT[A/C]TTTGTTAAACCAAGAGAAATAGCTTTCCTGTGCAT M 2 1 2 1 101000 r 74 goat snp56994-scaffold903-681185 5 97801997 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454084 Affx-122919373 AX-123324417 5 91462928 AGTACCTCTGAGAATTGTTTTCACTTTCTGAAAGA[C/T]AATGGGGGACAAAGGACGTGATCACCATGTTGTTA Y 2 1 2 1 202000 f 74 goat snp56995-scaffold903-721405 5 97840405 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416142 Affx-122948286 AX-123286491 5 91488692 TATGACATTTTACAATAGAGAAGTAGAGTCAACAG[A/C]TGTAGTAAATAAATTTATGGTTACCACCTAGACAG M 2 1 2 1 101000 f 74 goat snp22602-scaffold2239-298641 5 97886752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765570 Affx-122966523 AX-385253050 5 91564436 AAATAAATTTCCAGTAATAAGATTTTCTCCAACTG[A/G]TATATCAATACAGCTGATTTTTGTTAATAAAATCT R 2 1 2 1 101000 f 74 goat snp22600-scaffold2239-222897 5 97963504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408929 Affx-122953946 AX-123279280 5 91613126 CCCAATAGAGCCTTGAGAACAAAACTTGCCAGCTT[A/G]CATAATATTAAGGAACTCAGTCCTGTCTCTTTGTG R 2 1 2 1 102000 f 74 goat snp22599-scaffold2239-174207 5 98012304 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404978 Affx-122956404 AX-123275330 5 91661845 GTAATATCTGAAATTAAAAACTCAGGGGATATACA[C/T]GATGGAGTATTACTCAGCCATTAAAAAGAATACAT Y 2 1 2 1 103000 f 74 goat snp22598-scaffold2239-125488 5 98061390 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780417 Affx-122921791 AX-385267509 5 91695356 GAAAGATAACTTTGCAAAAAGGATTTTGTTAGTAA[C/T]AGTGGTAAAGTAATGGAGGTTTAAAGTCTCTAGAG Y 2 1 2 1 101000 r 74 goat snp22597-scaffold2239-91977 5 98095595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429306 Affx-122938604 AX-123299648 5 91742116 AAGCTAATGTTGCTAACTGTGATGATGCATGTCCA[A/G]TGAATAACAGTACTAATGTGACAAAGCGACAGTTA R 2 1 2 1 101000 r 74 goat snp22596-scaffold2239-45217 5 98142806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791496 Affx-122932853 AX-385278487 5 91783769 GAGCAGAAGCAACATTATAATGACAGAATTAGATA[C/T]AATTGTCCCCTGATATTTACAGGAGATTGCTTCCA Y 2 1 2 1 101000 r 74 goat snp22595-scaffold2239-3564 5 98183523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385766 Affx-122971063 AX-123256124 5 91800737 AAGGATCGGGGGGTGGGCAAGTTGGGGCCAGAGAC[C/T]GTGGACCACAGTAACTTCCTGCTCTCCTTTGCTTT Y 2 1 2 1 101000 r 74 goat snp12674-scaffold1486-607537 5 98208521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785734 Affx-122958741 AX-385272775 5 91832593 TGGGATGAAGTAAAGGTGATGTAATGTATGTGATC[A/G]TGTATATGTGGTTACATAAGGTATTGTACCTATCT R 2 1 2 1 101000 f 74 goat snp12673-scaffold1486-575681 5 98241569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764881 Affx-122928075 AX-385252476 5 91861811 TCAAAGTCCCTGAGATTTTCTTATGGTCCATGTAC[A/G]TCAAATGCCTAATACTCTTACTTAAAATTCTGAGT R 2 1 2 1 101000 f 74 goat snp12672-scaffold1486-546463 5 98270898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408746 Affx-122953403 AX-123279097 5 91911206 TATAGAATAGACACCCAGAATGAGTTTACTGAAAA[G/T]ATGGGGTCACCAGCCTCTTTCTTCTCAGCCCTTCA K 2 1 2 1 201000 f 74 goat snp12671-scaffold1486-497068 5 98319196 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406170 Affx-122956161 AX-123276522 5 91953286 GAACATAACCTCAATAAGAGCACAACTCTCATATG[C/T]GTCTTTTACCACTTAATCCCCCAGAAAATAGAACA Y 2 1 2 1 201000 f 74 goat snp12670-scaffold1486-454988 5 98361317 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425573 Affx-122941427 AX-123295919 5 92024157 CCCTTGATGCTCCCTGCTCCAGTTTCAGCTTCACC[A/G]CCCAGCTCCAAGTCAGGAGTTTCATGGCTATCTTT R 2 1 2 1 101000 r 74 goat snp12669-scaffold1486-384117 5 98431410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406300 Affx-122956067 AX-123276652 5 92079890 AACTTATTTAGGGCAATAGGTAGAAATACAGAGAT[A/G]CAAGTAGACAAAGAGAAATAATGGATATAAATAAG R 2 1 2 1 101000 f 74 goat snp12668-scaffold1486-328384 5 98487960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438179 Affx-122931833 AX-123308517 5 92116974 CTACAGTCCATGAGGTTGGAAAGAATCTGACATGA[C/T]TGAGCACCTAACACTTTCACATAATTTCAGTATTG Y 2 1 2 1 103000 f 74 goat snp12667-scaffold1486-291300 5 98526514 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410405 Affx-122952423 AX-123280755 5 92158267 CAGAGAACTAATATTCAAAAAACAAACACAGTAAG[C/T]AGAGAAAATAATTGTAACCTTAGAGCACATTACCT Y 2 1 2 1 101000 r 74 goat snp12666-scaffold1486-250007 5 98568346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797486 Affx-122924092 AX-385284425 5 92196647 TTTCCAACATAATATCTTCTCCATGACCACAAGCA[G/T]CACATCTTTTGGAATCAATCCTTGAGTAATACCTT K 2 1 2 1 101000 f 74 goat snp12665-scaffold1486-211627 5 98605966 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427118 Affx-122939661 AX-123297461 5 92295801 TGTAGTAGAGAGTTTAAGGAAATGGGTGGGGAGCA[A/G]CAAAATCTGATAAAAGGAAACAAAACAAGGATAGT R 2 1 2 1 101000 f 74 goat snp12663-scaffold1486-112473 5 98705724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434914 Affx-122934319 AX-123305254 5 92356456 TCACTAAAACTCTGACTGTGATAATAGTCATACCT[A/G]TCTCAAAGAACTGTTATTGTTTTGTTAATAAGTAA R 2 1 2 1 101000 f 74 goat snp12662-scaffold1486-51818 5 98767194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448680 Affx-122923875 AX-123319016 5 92393428 GTACTTCCCCAAGAGAAATGGAAGAGTATGTCAAT[A/G]CAGAGATAGGTACCTAAATTTTTATAGAAGCTTAA R 2 1 2 1 201000 r 74 goat snp12661-scaffold1486-14846 5 98805158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797499 Affx-122958456 AX-385284438 5 92440648 AAAACAGATGGATAATAAAAAGGCCAAGTGAATGC[A/G]TATGACTTGACAGGGCATTTCTTTAATCCTTTGAT R 2 1 2 1 101000 f 74 goat snp43893-scaffold593-1071376 5 100698068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431400 Affx-122936541 AX-123301741 5 92469468 AATCTGCCAAAGATCAACTAGCTCACCTAATACAT[A/C]GGAGAGGGGAGAGGATTCCAGTCAGGAGTCCTAAT M 2 1 2 1 201000 f 74 goat snp43892-scaffold593-1042556 5 100670978 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392398 Affx-122966216 AX-123262755 5 92550937 CTGGAAAAATGGATAGACTAGAAAAAAAAGCTTTC[A/G]TTTAGTGATAGAGTTAGTAGAAATTTAATAACAGA R 2 1 2 1 201000 r 74 goat snp43890-scaffold593-961087 5 100581649 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401829 Affx-122959446 AX-123272182 5 92635892 CTAGAGGCAGAAAGGAGGCTCTGCAGCTACTCCAT[A/G]TTGTTCTAAGTGGAAAGGGTTATGACTTGAGATCT R 2 1 2 1 101000 r 74 goat snp43889-scaffold593-876132 5 100496745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415102 Affx-122949446 AX-123285451 5 92679764 CACTGCTTTCGACTTCCTCATTAGAACAGTAAACC[G/T]CAAAATTTTTCACATTGCAGCACACATGGAAAATA K 2 1 2 1 101000 f 74 goat snp43888-scaffold593-832260 5 100451811 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396834 Affx-122963269 AX-123267189 5 92734904 TACCATATGTTCATGTTTTTGCTTTTGTCACATAG[A/C]GTTATTATATTCCTTTTTCCACATGTTAAATGATT M 2 1 2 1 201000 r 74 goat snp43887-scaffold593-777120 5 100394370 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404055 Affx-122957157 AX-123274407 5 92798538 TTTGGATACCATATGTTTATGTTTTGCTTTTCTAA[C/T]GTAGCATAATTTCAGTCCTTTTTCCACACGTTAAA Y 2 1 2 1 103000 r 74 goat snp43886-scaffold593-713486 5 100328328 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781329 Affx-122922471 AX-385268414 5 92866491 GTAATTTAAGCCTCCAAAACCGGACTGCACTTAGT[A/C]GGTGCTCTAGAAATGTGTTGAATGTTCAAAGGCTG M 2 1 2 1 101000 f 74 goat snp43885-scaffold593-645533 5 100261940 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278278 Affx-1111836340 AX-519551765 5 92950138 AACTTCATGCAAATGATGAGGCTAAAGACTTCAGA[A/C]TTCCTTGGCTTTGACTCCCATGTATTTTTTTTTTT M 2 1 2 1 101000 f 74 goat Random2.2K-601 5 92950138 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451425 Affx-122921177 AX-123321758 5 92956576 AGAGTCTCATTCCACAAATATTTACGGGATCTACT[A/G]CGTGCCGCACACTCTTTTAGATGTTTGGGTTAAAT R 2 1 2 1 101000 r 74 goat snp43883-scaffold593-555448 5 100170789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406737 Affx-122955744 AX-123277088 5 92986513 ACTTAAAGGACACCAAAAAGATACTTTGCTTCCCC[G/T]CTCCCCTTGTCTATACTAGTCTGTTGCTGGAAAAC K 2 1 2 1 102000 f 74 goat snp43882-scaffold593-525511 5 100140908 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801534 Affx-122977688 AX-385288443 5 93020975 GGTGTCTCCAAAGAGGATGCGAATGATAATACCTT[C/T]CTAGATCTGGAGCTACTTCCAAAAATAACCCAAAG Y 2 1 2 1 101000 r 74 goat snp43881-scaffold593-491049 5 100106444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443074 Affx-122928123 AX-123313411 5 93052542 GAATTAGATTGCAACTAGGCTTCAAGAAATATGAA[A/C]AATGCATTTAAATCTCATCATTGAATGAAAAGAAA M 2 1 2 1 101000 f 74 goat snp43880-scaffold593-459482 5 100075452 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440539 Affx-122929328 AX-123310876 5 93096471 GTTAACGAGGCAACTTTTGGAATGCCCTTATGTTG[C/T]CTAAGGAAAAGGGCTGGTTGCCAAGGGAGATAGAC Y 2 1 2 1 101000 f 74 goat snp43879-scaffold593-415553 5 100031323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788192 Affx-122940807 AX-385275211 5 93146761 GATAAAGATGTGATTCTTTTTCCCATCTAAGATTA[C/T]AGACCTTCTAAATCCTATTCAGGATCCCTTGGGGA Y 2 1 2 1 101000 r 74 goat snp43878-scaffold593-365263 5 99979645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447153 Affx-122924442 AX-123317489 5 93187287 GAAATATTTTTTTAAATGAAGAAAATATAAATAAA[C/T]AAATAAATACAATTCCAACCATGTGAAATGAGTTA Y 2 1 2 1 103000 r 74 goat snp43877-scaffold593-324737 5 99938841 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272224 Affx-1111833483 AX-519545971 5 93192235 CTGTGGAGTCACACAGAGTGGGACACGACTGAAGC[A/G]GCTTAACAGCCATGCAAGTGTGGGGAATGGAGTAG R 2 1 2 1 102000 r 74 goat 5_93192235_AF-PAKI 5 93192235 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320765464 Affx-122957026 AX-385252962 5 93243172 AAGGCTACGGCCCTCACCAAACCACCATCTATATT[A/G]CTTGGATTATTCCAGTAGCCTCTCAACTCATCTTT R 2 1 2 1 101000 f 74 goat snp43876-scaffold593-268852 5 99882273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438237 Affx-122931433 AX-123308575 5 93276141 GGTATGTGACAACTTGGCCAGCTCTCGCTCCCTTA[A/G]GTTCTAAAATTGCCTCAAGGCATTTTTGGGAATGG R 2 1 2 1 202000 f 74 goat snp43875-scaffold593-235883 5 99849530 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437953 Affx-122931618 AX-123308291 5 93306307 AGTGGAAATTGGTAACTTAATAGTGCCAAGTCTCC[A/G]CTGGCTATTAAAAGGGCACACGGTGGGTGAGAGGA R 2 1 2 1 201000 f 74 goat snp43874-scaffold593-205717 5 99819492 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447615 Affx-122923994 AX-123317951 5 93340470 CATGGGAGTATATGTGACCATCATATCTACTACTG[C/T]GGGCAGGAATCCCTTAGAAGAAATGGAGTAGCCAT Y 2 1 2 1 103000 f 74 goat snp43873-scaffold593-171554 5 99785222 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772715 Affx-122946222 AX-385259862 5 93368997 AAGATAAGTCTACTCCCTGAATCTACCCGGGAGAA[G/T]CTACCTACCTGTGAAAAGTTACCAGTGAAAATGCT K 2 1 2 1 101000 f 74 goat snp43872-scaffold593-143027 5 99756163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442344 Affx-122928039 AX-123312681 5 93401605 TTAAGATACTAAAAGTGTGGGAACTCCCTGGTGGT[A/C]CAGTGGATAAGATTTTGCCCTCCCAATGCAGGGGG M 2 1 2 1 303000 r 74 goat snp43871-scaffold593-110419 5 99723618 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786655 Affx-122957102 AX-385273687 5 93438419 CTATTTAAAAACTAAATGTAAGGACTCCCTTCAGC[A/C]AGTAATATCCAAACAGGTACTAAGGGAAGAGGTGA M 2 1 2 1 101000 r 74 goat snp43870-scaffold593-73605 5 99686788 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398892 Affx-122961027 AX-123269247 5 93482469 CAGATGAATGTGGAGTTAATTTAATTAATATCCAT[A/C]TGTTTTGTTCAATTCAGAGTATTCTGAAGACAAAG M 2 1 2 1 101000 r 74 goat snp43869-scaffold593-29555 5 99642510 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775649 Affx-122938045 AX-385262780 5 93513447 TCTTCAATCTTCATAACTGCAACTATCATCAATTC[A/G]TATTTTAAAATCTTAGTCATAATTAAATATGCTTC R 2 1 2 1 202000 r 74 goat snp28633-scaffold308-274286 5 99610616 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418608 Affx-122946353 AX-123288956 5 93548875 AGCATAACAATATACAATTGTTATTTATTGTTATT[A/G]TTGTCATATAGATGTTTATCTCAGTGATGAAACAG R 2 1 2 1 101000 r 74 goat snp28632-scaffold308-238858 5 99573680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441415 Affx-122928830 AX-123311752 5 93611281 GATGAAACTTATGAAATATTTTATAAATTAAAATT[A/G]CCATGTAAATGAAATGAATAGCATTGCACAGTGGA R 2 1 2 1 101000 r 74 goat snp28631-scaffold308-176452 5 99509933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395079 Affx-122964178 AX-123265434 5 93643684 GGCATTCTCAAAAGGAACACAACTGCTTTGAACAA[C/T]GATGAATAAATTCTTCTTACCTCACCAGGTTACAA Y 2 1 2 1 101000 f 74 goat snp28630-scaffold308-144049 5 99476638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379063 Affx-122976333 AX-123249422 5 93685434 AGTGTGAGTTCTATGGAAAGTGAAGTGAAAGTGTT[A/G]GTCATTTAATCATGTCCAACTCTTTGCAACCCCAT R 2 1 2 1 103000 f 74 goat snp28629-scaffold308-102299 5 99434832 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448132 Affx-122924293 AX-123318468 5 93809820 CCATTATGCCAAAGAATACAGAACAATTACCATGA[C/T]GAGACTATGTCACAGAGGTCAAACACAGCAGCTGT Y 2 1 2 1 101000 f 74 goat snp53179-scaffold80-449962 5 101130227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781067 Affx-122976401 AX-385268154 5 93933284 GACTTTGAATTTTTTATTTACCCTGTTTTTCTGCT[A/G]TTAGGACAGTTACCTACATATTGTATGCACTCATT R 2 1 2 1 201000 f 74 goat snp53177-scaffold80-326498 5 101257555 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414924 Affx-122949103 AX-123285273 5 94043055 AAAAAAAAGGGAACCACAACTTTCCTTCACACCCT[A/C]TTCACCTTTCACCTTCAATCTTTCCCATTGGTCTT M 2 1 2 1 201000 f 74 goat snp53175-scaffold80-216727 5 101366646 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417600 Affx-122946880 AX-123287948 5 94078007 TACTAGGTACATTCGAGCATGGGGATTACACAAGG[A/C]TGTGAACACAGGTAACAGAAACATCCGGGACACTG M 2 1 2 1 201000 r 74 goat snp53174-scaffold80-181775 5 101401688 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775389 Affx-122941199 AX-385262520 5 94135526 GTCACTTGATTGGTCCTGAGGAAATGTCACTTGTG[C/T]AAGGATGTTTAATTATTACCTTCCTCAGAAAACAG Y 2 1 2 1 101000 f 74 goat snp53173-scaffold80-124256 5 101459541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446816 Affx-122925285 AX-123317152 5 94292519 CTTTAAGTGACTAGATTTTAAAGTAATTTTGTTTC[A/G]TGGGAACAGTAACTAGAAAACACTCTCAGCATCAA R 2 1 2 1 101000 r 74 goat snp14503-scaffold1584-32638 5 102084477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423068 Affx-122942947 AX-123293414 5 94307142 TTTCTGCTCTGGATTTCTCCTAAACATAGTACTTC[A/G]CCTCCAAAAATCCAGTAAAGGGGATGAAACTCTCC R 2 1 2 1 101000 f 74 goat snp20971-scaffold2055-13810 5 102108018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410755 Affx-122952693 AX-123281105 5 94353657 CCCTCCCCCTGTGGAGGTGGTACGGGGGAAGAAGG[A/C]AGGCAGAGGCTCAAGGTAAAGCTGAACCCTCTCTT M 2 1 2 1 101000 r 74 goat snp20972-scaffold2055-60325 5 102154877 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390638 Affx-122967150 AX-123260995 5 94382834 CTACTCCAGGGCCTTAACCTTTCCTATCCCACCAC[C/T]GGCACCACACACAACACTTCCTGCCCGTAGAAGCA Y 2 1 2 1 202000 r 74 goat snp20973-scaffold2055-89502 5 102184157 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401744 Affx-122959512 AX-123272097 5 94418667 CCTGCCCTAGGACCTCTTCCCCTGAAAGCAAGTTA[C/T]ACCCACCCAGCTTTCCCATGAGCCTGGCTCCAGCC Y 2 1 2 1 101000 f 74 goat snp20974-scaffold2055-125335 5 102219590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448433 Affx-122923656 AX-123318769 5 94478063 TATTAGTTTTATTTATCTTTATTTTTATGTCTAGA[C/T]ACACATCTAGATATATATTTTCTGCCTTGGCAGGG Y 2 1 2 1 103000 r 74 goat snp20975-scaffold2055-184731 5 102278436 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791970 Affx-122935719 AX-385278958 5 94542950 CTCTCTAGACCTGGGATCACTCACCACATTTCTGG[C/T]AATTTGTTCATCCCTGGTGAGCAGCTCATCTCTTG Y 2 1 2 1 101000 f 74 goat snp20977-scaffold2055-249618 5 102343637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445681 Affx-122926132 AX-123316018 5 94584186 GTTGTACTTTCTCTTCTGGACTGAAATCCCTTTCC[A/G]AGTGAGTACGCATGCTAACATGTGATTATATATGT R 2 1 2 1 201000 r 74 goat snp20978-scaffold2055-290854 5 102385231 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453721 Affx-122919630 AX-123324054 5 94613150 GGAAGACGGGGCTCCCCAGCTGTGCCTCTGCCGCC[A/G]GCCACATCTCCATTTGGGGCCAAAGGGGAAACTCT R 2 1 2 1 103000 r 74 goat snp20979-scaffold2055-319818 5 102414044 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392312 Affx-122967517 AX-123262669 5 94663190 TCCTGGAGCTCCTGGGATGGGCCAGCACTGTCTGG[G/T]CAGCACCCCCTGCAAGCTGCAGAGGCCTGAGGACA K 2 1 2 1 303000 r 74 goat snp2707-scaffold10780-9376 5 102464695 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278441 Affx-1111836341 AX-519551926 5 94669432 CATACCACATTTTTTTTTAGTTTTATGCCCAGTGA[A/G]TAAAGATATTATCTCTGCCTTATGTACCATGAAAC R 2 1 2 1 201000 r 74 goat Random2.2K-602 5 94669432 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774506 Affx-122976760 AX-385261641 5 94682371 GGAGGGGGGATGTTATCAATCCTGTAGAATCTGAT[A/G]TAGATACGGCAAGGTCACAAGGTAAGATACCATGT R 2 1 2 1 101000 f 74 goat snp51115-scaffold748-9706 5 102482386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413730 Affx-122950062 AX-123284079 5 94729498 CACTTGTAATACTTCTTTACTTAAGTGGGACCTGT[A/G]TCTTTCCAGAAGAGGAGAGGATGGGAGACAAACAT R 2 1 2 1 101000 f 74 goat snp51116-scaffold748-56833 5 102526672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411162 Affx-122951872 AX-123281512 5 94762021 AGCACCACTCTGCTAGCCTCTCAGAGCGCATTCTC[A/G]TTCAGTTATAATGGAGGAAGCACAGCTTCTGAGGT R 2 1 2 1 101000 r 74 goat snp51117-scaffold748-89356 5 102559185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439484 Affx-122930157 AX-123309821 5 94887862 GTTCTGAGGAAAATCTGAGTATCCAGATGTTTTTT[A/G]TCATCTTAGGAGAAAAAAGTCGTTAATTCAAAGCT R 2 1 2 1 101000 r 74 goat snp51119-scaffold748-215197 5 102684909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422798 Affx-122943208 AX-123293144 5 94931312 CGCCCCAGTGCAGAACCCACTGTGGCTGAGTGAGC[A/G]CTGAGAACAGAGCTCATTCATGGTTCCAATGGTGT R 2 1 2 1 101000 r 74 goat snp51120-scaffold748-258647 5 102728816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781797 Affx-122972421 AX-385268879 5 95025634 TTCGTTGATGACCTGCACAACCTGAACAAACGCAT[C/T]AGCTTTCTCTACAAACGCTTTAATCGACATGGGAA Y 2 1 2 1 101000 f 74 goat snp51122-scaffold748-352969 5 102823118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407459 Affx-122954780 AX-123277810 5 95068430 AGTCTCTGTGCTCATTAAAAATGACCTTTTGGAAA[C/T]GAAACAGCTCAAGACTGGGAGGTCCATGTTCCTCT Y 2 1 2 1 201000 f 74 goat snp51123-scaffold748-395765 5 102865142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382131 Affx-122974055 AX-123252489 5 95103609 TGGGCTGGAAATGGGAATGGGAGGCAGTAAAGGGA[A/G]GGTGGGCTTGGGGTTGTGAGCAGACATGGCTGCGG R 2 1 2 1 101000 f 74 goat snp51124-scaffold748-430944 5 102900900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272345 Affx-1111833766 AX-519546076 5 95110783 GGGGCAGGGGACAACCTGCAGACAGGCAGGGCACA[A/G]CAGGGAGGCTCAGGGGAGGCGAGCGGAGGCCCCCT R 2 1 2 1 202000 f 74 goat GoatD01.003970 5 95110783 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393364 Affx-122965920 AX-123263720 5 95153072 GATAAATATATTCCTACTGCCCAGCACTGACTCCC[A/G]TCTTCCCACTTTGGTTATCACTGGCTTTTACTGGA R 2 1 2 1 101000 r 74 goat snp51125-scaffold748-480407 5 102947848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433947 Affx-122934282 AX-123304288 5 95192209 AAAAAAAAAAAAAAAGTGTTAGAGCAAGATTGAGG[A/C]GACCTGGGTACTTCTTCACCAGAGACAAACAGGCT M 2 1 2 1 101000 r 74 goat snp51126-scaffold748-519544 5 102987044 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379764 Affx-122975850 AX-123250122 5 95224466 CGAAGGCTGGACGTCCAGCTCCAGGGAGTTCTGAT[A/G]CCCAGGCTCTGGAGTCCTCTGCGATCCTGAGATGT R 2 1 2 1 201000 f 74 goat snp51127-scaffold748-551801 5 103019030 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799263 Affx-122924519 AX-385286193 5 95300374 TTATTGACACCTTATGTTAATGTGATATACACGTT[A/G]CTATTGATGAAGCCATATAAGTACATTGTCAGCTC R 2 1 2 1 101000 r 74 goat snp51128-scaffold748-627709 5 103095868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441408 Affx-122928835 AX-123311745 5 95336900 TTTTTTCTGTCTTATTTTATGGTATCTGTCCTGCT[A/G]TTTCAGTCTAGTTGTCTTTATTTCTAGTTCCCCTC R 2 1 2 1 101000 r 74 goat snp51129-scaffold748-664235 5 103132789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419677 Affx-122945938 AX-123290025 5 95398265 GACGGTTGGGGGCCGGGCAGAGGAGGACATGTGAG[C/T]AAAGCCCCCTTTAAAGTTCTTGTGATTAAGCTAAT Y 2 1 2 1 101000 r 74 goat snp51130-scaffold748-725600 5 103193840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400416 Affx-122959983 AX-123270771 5 95445123 CGACACTGTGGCTTTGCTGTCATTTTTCATTCATT[A/G]TTGTTGAAGGACCTAAAACTGTAGGGTATTTATTA R 2 1 2 1 201000 r 74 goat snp51131-scaffold748-772458 5 103240788 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392945 Affx-122965697 AX-123263302 5 95487487 ATCTCCCGGGGGAGGTACCCCAAGCAGCCTGGGGG[C/T]GGGGATTCAGAGAGAAGCAAAGAGAGCAAGTCAAG Y 2 1 2 1 101000 r 74 goat snp51132-scaffold748-814822 5 103283373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376301 Affx-122978368 AX-123246660 5 95533650 TGTGAGCATCAGGAGACACTCAGGCTGATGATACA[C/T]GCATGCTGATGCAATAGACCTCTAGGGGTGGGAGT Y 2 1 2 1 101000 f 74 goat snp51133-scaffold748-860985 5 103329403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444991 Affx-122926654 AX-123315328 5 95564117 TTCAGAATTACTGGGTCGGAAAGAGTGTAGAGTGT[A/G]TGTATGAGTGTGTGTGAGTGTGTGTAAGTGTGTGT R 2 1 2 1 201000 f 74 goat snp51134-scaffold748-891452 5 103359924 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399899 Affx-122960207 AX-123270254 5 95594534 GCAAAGAGTCGGACACGTCTGAGGTGACTGAGCAC[A/G]CACACGCCTCCTGTTACAGGGCAGAGGCCCTGATC R 2 1 2 1 201000 r 74 goat snp51135-scaffold748-921869 5 103388917 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404117 Affx-122957108 AX-123274469 5 95650657 TGTCCTTAAAGCTCCAGGTATTCAGCTTGCCTTTG[A/C]GCAGGTGGGCATTCGATGACCATGGATTGAGTTCA M 2 1 2 1 101000 f 74 goat snp51136-scaffold748-977992 5 103445136 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443331 Affx-122927441 AX-123313668 5 95701540 TTATCGTGTTGAGTGTCTGGCCCAAGGCAGGCAGG[C/T]GCTCGATGCATATTTGCGAGCTGGTGCTCTTATCC Y 2 1 2 1 201000 r 74 goat snp51137-scaffold748-1028875 5 103495707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453165 Affx-122920473 AX-123323498 5 95755008 ACACTGCTATTTGCAAAAGCTGGATCTGCCCTGGG[A/G]GAGAAGTGGGAAGCGTGCGGCACCTTTGCTTTCTG R 2 1 2 1 101000 f 74 goat snp51138-scaffold748-1082343 5 103548872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272226 Affx-1111833484 AX-519545973 5 95784797 CAAGCATACGCTTATGGTATAGCAGGGCAGTGCTT[A/G]TCCAAAGTGTCAAAATATGTCCCAATCAAAGGGTG R 2 1 2 1 101000 r 74 goat 5_95784797_AF-PAKI 5 95784797 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417365 Affx-122947714 AX-123287713 5 95788107 CTGTGAATTTGATGAATGGATTGGCAAGAGAGACC[G/T]CAATTACCAAACACACCAGGGGCTTCCCTGGTGGC K 2 1 2 1 101000 f 74 goat snp51139-scaffold748-1115442 5 103581920 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415339 Affx-122948791 AX-123285688 5 95844482 ATGCACTATCTCTCTCTCTCTGCCCTCAAAATCCC[A/G]CGAGACAGGCATCATTCTATCGCCATCAGACTCTG R 2 1 2 1 201000 r 74 goat snp51140-scaffold748-1171817 5 103638244 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384891 Affx-122971926 AX-123255249 5 95881684 CACCAACACTTTGGACCCAAAGCTGTCTTTCATCA[C/T]GGACACAGTCCTCATAATTGCTCATAAACCGCTAG Y 2 1 2 1 101000 f 74 goat snp51141-scaffold748-1209019 5 103675737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378610 Affx-122976570 AX-123248969 5 95917848 CCCAGCAAAGGAGACCTTCTGGATAGATGGCCCTG[A/G]TCTGTGGTCAGCCAAGTGAAGATCCCACGCAAATA R 2 1 2 1 201000 f 74 goat snp51142-scaffold748-1245183 5 103711870 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778011 Affx-122954223 AX-385265127 5 95994148 AGAGAAAAAGAGAAGGGCTTACCAACTCCCATGGA[C/T]TGACACATTTTTCACTCACTAGATGTGGTACTATG Y 2 1 2 1 101000 f 74 goat snp51144-scaffold748-1321483 5 103787873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407598 Affx-122954651 AX-123277949 5 96035591 GCCTGTGCTGAGAGGCCCAAGGCTAGTGCATCTGC[A/G]CAAGGGCCCCTCTGTCCAAGTTTGGGGCTGCAACC R 2 1 2 1 201000 f 74 goat snp51145-scaffold748-1362926 5 103829943 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398096 Affx-122961718 AX-123268451 5 96081258 CCATCTTCTGAGCCAGGGCAGACAGCAGAAGACAG[C/T]GGAGAAGGCCTTGCACAGAGCTGCAATTGCCTGTC Y 2 1 2 1 201000 r 74 goat snp51146-scaffold748-1408593 5 103875563 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421656 Affx-122944448 AX-123292003 5 96129109 GTGTCTCCTGCTTGGTGGAGCCCAGCAAATCCGAA[C/T]CAGAGCAGACGCTACCCTGAGGGTCACCCCGGGAA Y 2 1 2 1 101000 f 74 goat snp51147-scaffold748-1456444 5 103923118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381664 Affx-122974743 AX-123252022 5 96163845 ACCAGAAAGGGGGAGGGAGAGGACCAGAAGACAAT[A/C]GGGAGAAGGAAGTTCAGTAAAAAAAATCCCACCTC M 2 1 2 1 101000 r 74 goat snp51148-scaffold748-1491180 5 103957785 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428780 Affx-122938414 AX-123299122 5 96231144 AGTGATGCTGGGAGAAGGAGCAGGCAGTGTGATGT[A/G]GAAATCACAATGGGGTGGGAGAAATGGCCAAGGGC R 2 1 2 1 201000 f 74 goat snp51149-scaffold748-1558479 5 104026265 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451730 Affx-122921541 AX-123322063 5 96271751 GAACTATCCCTTCTAAGTCTGGGAAGAAAACATGT[A/G]TTCACTACACGATTCATGCAGGCCAGACAGTCCCC R 2 1 2 1 101000 r 74 goat snp51150-scaffold748-1599086 5 104066983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379316 Affx-122976192 AX-123249675 5 96318398 TCCCAAATAAACCATGTGCTCCTTGAAGGTGGAAA[C/T]GCTGCCTTATATGTTTATGCAACCCCAAGATGCAT Y 2 1 2 1 101000 r 74 goat snp51151-scaffold748-1645733 5 104112465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408230 Affx-122953835 AX-123278581 5 96346978 GAGGGCAGTGTAGCCACATTCCCCTTCACTGTCCT[C/T]GCCCTGAGCATTGCAAGGTGCTTTCCCAAAGATCA Y 2 1 2 1 101000 r 74 goat snp51152-scaffold748-1674313 5 104140979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419903 Affx-122945340 AX-123290251 5 96381478 AAAAACCCGATCAGATAAACCTAAGGAGAGAAGCC[A/G]AAAAGATAGTCACTCCATAATAGGCAGTTTCGTGA R 2 1 2 1 101000 r 74 goat snp51153-scaffold748-1708813 5 104175628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770123 Affx-122956379 AX-385257290 5 96398899 CCCAGAAGACACTGCTATAGCCATGTCTCCTATTC[A/G]TCTTCTAGGAGTCATCTGATTTGTTACCTTGCCAT R 2 1 2 1 101000 f 74 goat snp51699-scaffold76-1286632 5 104193232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383059 Affx-122973753 AX-123253417 5 96440683 TGGGGATTGTCGCACTCATAGGGAACAGTCACCGC[A/C]GTGGATGCTAGCACAGCTAAATCCCCAAGGAAACT M 2 1 2 1 201000 r 74 goat snp51698-scaffold76-1244848 5 104236500 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399742 Affx-122960329 AX-123270097 5 96478316 AGAGCTGTCTCTCTCATATCCTGAAAGCAGAGTTC[A/G]TAAATCCCAGTGGTGTGAAGTGCAGGGGACGACTC R 2 1 2 1 101000 f 74 goat snp51697-scaffold76-1207215 5 104274127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426278 Affx-122940314 AX-123296624 5 96527448 AGGCCCCAGGTGTCATCCATAGCAGCCGTGAGCAT[C/T]CCAGTGGTCTTTAGGACAAGCATCTTCCTCATCTG Y 2 1 2 1 201000 r 74 goat snp51696-scaffold76-1158083 5 104317848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278443 Affx-1111836342 AX-519551928 5 96531456 ATTTCTTTCCAAGTCAGACAAAGTACAAATATTTT[A/G]TCTCCAGCACTGTCCAATCCACAAGTCTTTTTAAA R 2 1 2 1 101000 r 74 goat Random2.2K-604 5 96531456 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380819 Affx-122975080 AX-123251177 5 96564176 TGAAACTCTACCTCCTGTGAATTCTTGTATCTTGG[C/T]GTCTGCTTCCAGTAAGGGCAGGAGTCATGGGCTTC Y 2 1 2 1 101000 r 74 goat snp51695-scaffold76-1121355 5 104354519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274083 Affx-1111834028 AX-519547686 5 96571007 TTATCTGGAAGCCCCAGCTTCATGAGATTAGTTTG[A/C]AAGTGCTGCAGAG M 2 1 2 1 102000 f 74 goat GoatD01.015073 5 96571007 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785406 Affx-122973569 AX-385272451 5 96593466 CATTATACCTTTAATGCTACAAATCTAATTACCCT[A/G]TGACCTTATTCTAAGTTCCTACACCAGAATCTAAA R 2 1 2 1 101000 r 74 goat snp51694-scaffold76-1092065 5 104384845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379021 Affx-122976366 AX-123249380 5 96720600 TCTTCTTTGGGGAGCTGAATTCCCCTCCTCTCCAA[C/T]ACACAAACTGACAAACTTTATTTCCAGTCATACTG Y 2 1 2 1 202000 r 74 goat snp51691-scaffold76-964931 5 104513366 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442410 Affx-122927988 AX-123312747 5 96753647 AGGAGTGCGGCTTGATATACCACTGTGAATTAAAA[C/T]GGGACTCTGGATGCAGACTTAATGTCCTGCAGCTG Y 2 1 2 1 101000 f 74 goat snp51690-scaffold76-931884 5 104546760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387383 Affx-122970428 AX-123257741 5 96787501 TCTGAGCCTCATCTGCAAGATGAGACCATTACCAC[G/T]CAGGGTTCTTATATATTAGTGACAATATATGCAAA K 2 1 2 1 201000 r 74 goat snp51689-scaffold76-898030 5 104580521 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450237 Affx-122922264 AX-123320572 5 96817435 AGATAGTGACTATGTAAAAGTGAATTGATCTGAGC[A/G]CTGCCTTCAGGAAATGGTCCTCTGCTTCTCCTAGT R 2 1 2 1 201000 f 74 goat snp51688-scaffold76-868096 5 104610351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397603 Affx-122961982 AX-123267958 5 96888865 AAGAATAGCTTTAAAAGGGAAATCAGTGCTGAGAC[A/G]GTGAAGTCCCTTACCCAGCACGCGCCCTGTAGCTT R 2 1 2 1 101000 f 74 goat snp51686-scaffold76-796666 5 104681817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376471 Affx-122978043 AX-123246830 5 96934010 TTCACTCAACAGAGCCCCTCAATCTCCTTCTTCCT[A/G]TACTCCTGTAACACTGAGGGGATCCTTATCTCCCT R 2 1 2 1 101000 r 74 goat snp51685-scaffold76-751521 5 104727166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788702 Affx-122966533 AX-385275718 5 96985650 GTGATAGTAAAGCCACGAGGAAAAGTTGAGAACCC[G/T]AAGGGAGACTATGTAGGGTGAGAACAGTAAAGAGT K 2 1 2 1 201000 f 74 goat snp51684-scaffold76-699881 5 104778868 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415533 Affx-122948666 AX-123285882 5 97015668 TACATTCTAATGTTCATCAATATTGCTCTGTATGC[A/G]TGCGCGCATGCTCAGTCGCTTCAGTCGTGTCTGAC R 2 1 2 1 101000 f 74 goat snp51683-scaffold76-669863 5 104808889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426124 Affx-122940625 AX-123296470 5 97087706 TCTTCAGTCTTTTGGACAGTGCTAAGCATCACCCC[C/T]TGATTTCCCTCTCACCTATCCCTACTTCACCTCCC Y 2 1 2 1 101000 r 74 goat snp51681-scaffold76-597825 5 104881092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789624 Affx-122956272 AX-385276633 5 97116768 CACTCTGGTATACTGTAAGAATGTGGTACAAAAAT[G/T]AACTGATCCCTGTTCTTTCTAGTGAAGGAGATATT K 2 1 2 1 201000 r 74 goat snp51680-scaffold76-568763 5 104910704 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417847 Affx-122946783 AX-123288195 5 97155727 ACTTATCACGGTGATCATTTCACAGTGCGAGCAAA[C/T]GGCCAATCAACAGAGCACAGCTGAAACTAGCATCG Y 2 1 2 1 201000 r 74 goat snp51679-scaffold76-529804 5 104949685 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394264 Affx-122964722 AX-123264619 5 97207120 CCAATAGTCAACCATTTAGAAAAATTAATGGATGA[C/T]ATGTGCCAGCAGCAAAAAAGAATGACCATCACTCT Y 2 1 2 1 101000 r 74 goat snp51678-scaffold76-478411 5 105001387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436477 Affx-122932973 AX-123306815 5 97239766 GCAAGACATGTACTTAGATGAGTGAAGATGTGTTA[C/T]GGAGAAACCAGAAAGAGGACAGCCAATAAAAACTT Y 2 1 2 1 101000 f 74 goat snp51677-scaffold76-445765 5 105034060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425542 Affx-122941449 AX-123295888 5 97269325 ACTTTTTTACAGACAACATTATTTTTCAAAAGAAC[A/G]ATGCAGAAAGAGACCTATAACCCAAAATAATAATG R 2 1 2 1 101000 r 74 goat snp51676-scaffold76-416206 5 105063980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445780 Affx-122926059 AX-123316117 5 97313846 CCCTTATCATCAGCATCTGAGGATTGGAAGGGCTC[C/T]TGCAGATCACATGATGTGAAATCTACCCACCCCCA Y 2 1 2 1 101000 r 74 goat snp51675-scaffold76-371685 5 105108527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793170 Affx-122963350 AX-385280148 5 97346724 TATGGAATTGACATATGATCATTTAAATGAACACA[C/T]GCCCAGCCTGGTACTTTGCATATGACAGGTGTTCA Y 2 1 2 1 101000 r 74 goat snp51674-scaffold76-338807 5 105141398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431980 Affx-122935949 AX-123302321 5 97410065 GCACCTTGGGGCACAGCCCATGGTTTAAAGCAGGA[A/G]CCTGTGAACCAAGGTGAGGCCTCAGGGAGAGCCCT R 2 1 2 1 202000 r 74 goat snp51673-scaffold76-275466 5 105204794 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395025 Affx-122964216 AX-123265380 5 97441708 TGCTACGAGGGAGTAGAGACTTTTAAGAGATCAAG[A/C]GCCTCTCTGAAGACATGACTTGAAATGGAAACTCG M 2 1 2 1 101000 f 74 goat snp51672-scaffold76-243823 5 105236092 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434411 Affx-122934677 AX-123304752 5 97473625 TGTGTGGAGAAACAGGCAGATGCTGCAAGTCAGGG[C/T]ATCCTTCCTTCCTGGAGAACCCCCTGTTAAGTGTC Y 2 1 2 1 101000 f 74 goat snp51671-scaffold76-211906 5 105267854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447656 Affx-122923965 AX-123317992 5 97511787 AGCTGAAATGGTCCCCAAAACCATGGTCTGCACGC[A/G]TTTCTTCTCCCTCAGCAAACACGGATTTCCGTCCT R 2 1 2 1 101000 r 74 goat snp51670-scaffold76-173744 5 105306033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394938 Affx-122964297 AX-123265293 5 97554355 ACCAAACTTCTTCTGGTGCACACTCTCTATGTCCT[A/G]TGGCCCTTCCATTTGGACCACCTCCCTGACCTTTC R 2 1 2 1 101000 f 74 goat snp51669-scaffold76-131176 5 105348638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401007 Affx-122959687 AX-123271360 5 97590599 GTCTGGAAGGAACAGACTGGAAATGTGGATGAGCC[A/G]CTGGCAGAGGGACAGGCAGTGCAGAGCTTCTTAGC R 2 1 2 1 201000 f 74 goat snp51668-scaffold76-94932 5 105384757 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273920 Affx-1111833893 AX-515873128 5 97607451 CAACA[A/G]AACAGATCTCCTTGCTTATGGGGGGAAACTGCCAA R 2 1 2 1 102000 r 74 goat GoatD01.009628 5 97607451 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375427 Affx-122979187 AX-123245786 5 97621714 GCAGTACTAGCTATATCGCCGCTGGCTTTACAGTT[A/G]CTTCCAGACATCCTGGGCTTGAAATAAAGACACTG R 2 1 2 1 101000 f 74 goat snp51667-scaffold76-63817 5 105415820 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420756 Affx-122944719 AX-123291103 5 97671154 CCAGGGACTGGTTCCGGGGCCAGCATGGGTCTTCC[A/G]TGGATGCTCAAGTCCCTTATATAAGATGGTGCAGT R 2 1 2 1 201000 f 74 goat snp51666-scaffold76-14377 5 105464946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404493 Affx-122956714 AX-123274845 5 97751449 CATACTTCCATGGCGGACCCCTTTCATGGTACACC[A/C]GCCGAACCAACAGAAGGTACAACCAGGGTGAACTC M 2 1 2 1 101000 f 74 goat snp23103-scaffold2301-60270 5 105539243 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385106 Affx-122971787 AX-123255464 5 97810898 GCTGCTCTCACCATACCCATACTTCCCCCTCAGAC[A/G]GTGGGCTGCTCTAAGGGACCCCTGAGGTCCCTAGA R 2 1 2 1 201000 r 74 goat snp23104-scaffold2301-119719 5 105595613 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449545 Affx-122923250 AX-123319880 5 97842602 TTTAAATTGGGCTTTCAGAGCCCATTTGGAAGGCC[A/G]GAGCAGAAAATTCTTCTATCTGACAAAGACCATCT R 2 1 2 1 101000 r 74 goat snp23105-scaffold2301-151423 5 105626278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778782 Affx-122929370 AX-385265891 5 97879869 CAGTATTCACGACAAACACCACCTGGTACATGATG[C/T]GTTCCTCTAGAATCACGGTGATCAACTCCAACCCC Y 2 1 2 1 101000 f 74 goat snp23106-scaffold2301-188690 5 105663212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411974 Affx-122951779 AX-123282324 5 97930804 GGACATACAAAGACCCTGAGGTGGGAAGGCCTGGC[A/G]CGTCCAGCAAAAGCTCAGAGCCTCAAAGGTTGGTG R 2 1 2 1 201000 r 74 goat snp10771-scaffold1383-755892 5 105714166 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383380 Affx-122973512 AX-123253738 5 97972119 GCAGAGCAACTTGTACCGTGCAGGAACAGCCAGTG[C/T]TTCCTAACCCTATTTCACCACAGAGCCTCTTTATC Y 2 1 2 1 201000 r 74 goat snp10770-scaffold1383-714577 5 105755480 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434078 Affx-122934177 AX-123304419 5 98028379 TGAACAGCTCAATTTTCACTTATGCACACATCCAC[A/G]TAAATTTTCCCCTTTAAAAATTATTGATGGGACTT R 2 1 2 1 103000 f 74 goat snp10769-scaffold1383-658317 5 105812631 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404512 Affx-122956700 AX-123274864 5 98071956 CCCGAGCCCCTCTCTATTCTCTTGCAGCTCACTTG[C/T]GTTGGGGTTGGAGACGTATGTAATAAAGGAAAGGT Y 2 1 2 1 101000 r 74 goat snp10768-scaffold1383-614740 5 105854568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425624 Affx-122940903 AX-123295970 5 98131213 TGACATGAGCTGTGTGCAAGGGTTAAGTTATCCCA[C/T]AGACCCTCAGGCCTCTGAGCTGCTCAAGGACAGAA Y 2 1 2 1 101000 f 74 goat snp10767-scaffold1383-555483 5 105913611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435124 Affx-122933690 AX-123305464 5 98214573 CTGCTGTGTAGCATTGCGCCAGTAGCTACAATGTA[C/T]AGCCAGGAATCTGTTAAGCAAGTGGATCTTGCATT Y 2 1 2 1 101000 f 74 goat snp10766-scaffold1383-472123 5 105996073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423788 Affx-122942824 AX-123294134 5 98261007 GGACTATTAATAAAAGGAAGAAACTAGTTCCCAGC[A/G]TAATGGGTGAAGAAAGAGCCAAAGAAGGCACACGA R 2 1 2 1 101000 f 74 goat snp10765-scaffold1383-425689 5 106041744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272326 Affx-1111833485 AX-185175994 5 98293519 TTTATGGGGTCGCAAAGAGTCGGACACGACTGAGC[A/G]ACTGAACTGAACTGATACTTATTAAATAAAGTAGC R 2 1 2 1 103000 f 74 goat 5_98293519_AF-PAKI 5 98293519 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413521 Affx-122950625 AX-123283870 5 98308076 GACACTGAGTCCCAGGCTTCATGGGTCCTCAGACC[A/G]TGCTCACACATACAACAGGTCTAGGACCCACACGT R 2 1 2 1 101000 r 74 goat snp10764-scaffold1383-378620 5 106096905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409068 Affx-122953346 AX-123279419 5 98348373 ACATATATGTCTAATGAAATAGATGTATGTATATA[C/T]ACATCTCTTCATTTAATCCTCATGGCTAAGTGTAT Y 2 1 2 1 103000 r 74 goat snp10763-scaffold1383-338323 5 106137302 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442745 Affx-122927843 AX-123313082 5 98383623 CCTTTGCCTGCAGCCTCCCTCCGCCAGCAGAGGGC[A/G]TTAGAGAACATTAAAAGGCCGCGTAGTGAGGAGGG R 2 1 2 1 101000 r 74 goat snp10762-scaffold1383-303073 5 106172998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774205 Affx-122969686 AX-385261342 5 98426855 TTTTAAAATTATTGCTGTGACTGCATAAATTTGTC[A/G]TTGTGCTTAATAGCATGCTATGATTGTTTGAACCA R 2 1 2 1 201000 f 74 goat snp10761-scaffold1383-259841 5 106216238 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381856 Affx-122974187 AX-123252214 5 98459448 CTCACAGGGAGGAAGCCTGCAGGGCACAAGGGGAC[C/T]GGCGACAGGAAACCCAGCTTGGTGACAGCAATGAT Y 2 1 2 1 101000 r 74 goat snp10760-scaffold1383-227248 5 106246036 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278445 Affx-1111836343 AX-519551930 5 98520551 GGTCTTGTGTCTCCCTTTGACCAATAGAATGTGGT[A/G]GAAGTGACACTCTGGGACTTCAGAACATAGACCTT R 2 1 2 1 201000 r 74 goat Random2.2K-605 5 98520551 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796092 Affx-122957884 AX-385283044 5 98559003 ACAGACTATGATGTAGTTACAATCTTTCAAAATAA[C/T]TGGTTCATTAAGAAAAATGATCCAAACTGGCCTCA Y 2 1 2 1 101000 r 74 goat snp10758-scaffold1383-127693 5 106345047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435430 Affx-122933485 AX-123305770 5 98597471 TTAGACAGTCCACTAGCCTCTCCCTCTAGGAAGCC[A/G]TTTCCCAAAGCAGGGCTCTGTGACCCCCAGACAAA R 2 1 2 1 101000 f 74 goat snp10757-scaffold1383-89225 5 106384137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386679 Affx-122970184 AX-123257037 5 98631265 TGGGGGATCACAGGAAGACAGGCTAACCAGGAAGT[A/G]TCCTGTGGGCTAGAATCAGGGAGATGCCAGGACAC R 2 1 2 1 101000 f 74 goat snp10756-scaffold1383-55431 5 106417843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403901 Affx-122957487 AX-123274253 5 98676557 AAAAAAGAAAGGAAAAAAAAAACAAAAAACAGAGA[C/T]AGTGTTCTTTCTTTAGAATAGAATAGAGCTTGGGG Y 2 1 2 1 101000 r 74 goat snp10755-scaffold1383-10139 5 106463206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424792 Affx-122941392 AX-123295138 5 98693050 AAATAAGATGTACAGGTTTAAAATTCAAGCAGTAC[A/C]GAAGAGTAAGCAACGCTAAGCAATGATATGGACAT M 2 1 2 1 201000 f 74 goat snp19986-scaffold1996-6255 5 106479948 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776649 Affx-122967159 AX-385263776 5 98738675 CATATTGTATGGTCCTACAGTTTGCTAGTTTCATT[A/G]CATAGCAGAAACGTTTTCCTTAAACATTTGAGGTT R 2 1 2 1 101000 r 74 goat snp19987-scaffold1996-51880 5 106525552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430793 Affx-122937469 AX-123301134 5 98770160 TAGTAGACTATATATTGGAAATATAAAAATTAAAT[A/G]CTACTTAATGGTAGGTAGAATATTATAATTCATTT R 2 1 2 1 103000 r 74 goat snp19988-scaffold1996-83365 5 106556927 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405820 Affx-122955887 AX-123276172 5 98811604 CTTATCTAATGCAAAGATCCCCACAGAATAGTTTT[A/G]TTGACCCTGGATGTATTTAATGGGTTTTTACTATG R 2 1 2 1 201000 r 74 goat snp19989-scaffold1996-124809 5 106598433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425661 Affx-122940877 AX-123296007 5 98859585 CGCCTTAAACACAGGCCGGGGGCACAGTTCCTCAA[C/T]GCCTGGCTGTCTCCGAATAGGCCTCTGAACCCCTC Y 2 1 2 1 101000 f 74 goat snp19990-scaffold1996-172790 5 106646304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387004 Affx-122969941 AX-123257362 5 98946961 TCCTGAATTTCTTTGGGCGTTTTTGGTGATAGGTG[A/C]TTGTTTTCAAGAATAGCACGTTGGTTCTCAGTTGT M 2 1 2 1 101000 f 74 goat snp19991-scaffold1996-260166 5 106734515 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779089 Affx-122961116 AX-385266194 5 98986299 GTGCAGTTACGATAGCGGTTTTCTTAGATGATTTC[C/T]TCTTAAAACTGTTTATATTGTATACATCTGTATTC Y 2 1 2 1 101000 f 74 goat snp19992-scaffold1996-299504 5 106773914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430025 Affx-122937582 AX-123300366 5 99063256 CGAGCCAAGCAGTAGTTTCTACAGTTTCTTCTTTG[C/T]GACTTTTGCTAAGGTTTGGGTTCCTCATAGTGTCA Y 2 1 2 1 201000 r 74 goat snp19994-scaffold1996-376461 5 106850758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790060 Affx-122928477 AX-385277066 5 99119707 TCTTAGCATTGGAATAGATTAGGCTCTGCCTGCAC[A/G]TCTTTGACAGTGATCCATCCAGAGCCAGCAATCTC R 2 1 2 1 101000 f 74 goat snp19995-scaffold1996-432912 5 106907220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380006 Affx-122975605 AX-123250364 5 99152261 AGGATGTCAGCTGGGTCTGTAGTTTAAAGCTTGAT[A/G]TAGCCAGAGCCCACGTGGGTGCATATTCACTCACG R 2 1 2 1 101000 f 74 goat snp19996-scaffold1996-465466 5 106939743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784642 Affx-122958347 AX-385271690 5 99180953 AAATCATTCCATCCACTCAGACTAACCACTCTTCA[G/T]ACTTATGTCTGTCTTTGTCCATACATTTTTCTGTA K 2 1 2 1 101000 f 74 goat snp19997-scaffold1996-494158 5 106968539 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408555 Affx-122953678 AX-123278906 5 99250675 GCAACAGCTCGACAACCAGGATCTGGCTCCTCGCT[G/T]ATGGGGAACACCTGGGGCCATCACCTGGGCACAGT K 2 1 2 1 101000 f 74 goat snp19998-scaffold1996-563880 5 107030224 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422460 Affx-122943338 AX-123292806 5 99289382 GAAATGATCTGGACGTTTAGAGAGACTGTGCCGAG[C/T]GTCTGTGCCCCAGCGCTGCTGGGTGGGAGGCAGTG Y 2 1 2 1 101000 f 74 goat snp12155-scaffold1450-110289 5 107069761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399856 Affx-122960241 AX-123270211 5 99320626 TTTTTATTTCACTTTCTGTTTTCTAATTTTCTTAT[G/T]AAGACTAAGTACATTTACAGAAATCAGCAATGGTC K 2 1 2 1 103000 r 74 goat snp12156-scaffold1450-141533 5 107101395 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441395 Affx-122928845 AX-123311732 5 99393386 TGTGTCAGGTACACTGAGCCAGCGGACAAGGAGAC[A/G]TGGGGTCAGCTGTGAAGCTGGGCAGCTGAGAGGGT R 2 1 2 1 101000 f 74 goat snp12157-scaffold1450-214293 5 107173759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377349 Affx-122977659 AX-123247708 5 99428561 GTCTCATTGGACACCGGGGTCCAAGGGAGGTTGCC[A/G]GGTTAAGCTGCAGTGTCTGAACTACTGGTCAGTCC R 2 1 2 1 101000 r 74 goat snp12158-scaffold1450-249468 5 107208739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796554 Affx-122963740 AX-385283500 5 99503928 TGTACTCATTAAATATTAGCTTTCTATAAGAGCCC[A/G]TGATGTTCAGAACACGGAGATCTAAGTTGGCGTGA R 2 1 2 1 101000 r 74 goat snp12159-scaffold1450-324835 5 107283855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422277 Affx-122943494 AX-123292623 5 99580241 CCAATAAGGCAGATCCCGTCTCTTAGATGTGACCT[A/G]CTGGCGCCCAAGGCAGATGGGTAGCTCAGAGTCTT R 2 1 2 1 101000 f 74 goat snp12161-scaffold1450-401148 5 107360471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795515 Affx-122932049 AX-385282470 5 99637994 AAAATGTGTTTGGAAAAGGAAGGCCTTTTCTAGCA[C/T]GATGCGTTACCGTAAAATGACACAGCCTCACTCTT Y 2 1 2 1 101000 f 74 goat snp12162-scaffold1450-458901 5 107417156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398492 Affx-122961568 AX-123268847 5 99667103 TTCAGAGGCAATGAGAGGTTCGTAAATCTGCTTCT[A/G]CAGCAAGGCTTCACACCTAGACATTTGGTCTGCTG R 2 1 2 1 101000 f 74 goat snp12163-scaffold1450-488010 5 107446297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774173 Affx-122976848 AX-385261310 5 99721587 TTTTTTAATTTCATGATGACACTGAAACGTAGGAT[G/T]AAAGTTCTAAAGATGAAGCTGGTAACTTCACAGCG K 2 1 2 1 101000 r 74 goat snp12164-scaffold1450-542494 5 107498021 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378573 Affx-122976596 AX-123248932 5 99773142 GGCAGCTTTCCTTGGTGTCCACCTGGCCTCCACTC[A/G]TCTGATTTCACTCCTGGGCAGCCCTCACACTAGTA R 2 1 2 1 201000 f 74 goat snp12165-scaffold1450-594049 5 107550298 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404386 Affx-122956797 AX-123274738 5 99803558 AGGAGGAAAGGCCTTGAAGGGTAGGTAAGGAGGGG[C/T]ATCTGGAGCCTCAGGACAAAGAGGTAGGATAACTG Y 2 1 2 1 101000 r 74 goat snp12166-scaffold1450-624465 5 107579312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406087 Affx-122956231 AX-123276439 5 99838150 AGGCCCTCGTCCTCATTCTCAGGGTCGATGTCCTC[A/G]GCCTGCGTGATCCAGTCCAGGTAGCCCTTCAGGTC R 2 1 2 1 101000 f 74 goat snp27784-scaffold297-471761 5 107615021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274551 Affx-1111834361 AX-519548141 5 99858320 AAGTTCTTCTTCAGAATAAGCACAGGCTGCAATAG[A/G]CTATTTTTCCTGTCTCTCTTCTCTAAA R 2 1 2 1 102000 f 74 goat GoatD01.031902 5 99858320 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392111 Affx-122966353 AX-123262468 5 99890587 CGGCTGCCCAGGCAGGACCAGAGGAAGAGTGGCCA[C/T]AGGAGAAAGGGCAAGTGGACACTGGAAAAATGGGG Y 2 1 2 1 101000 r 74 goat snp27783-scaffold297-419324 5 107667228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413459 Affx-122950672 AX-123283808 5 99972276 GGCCACACGTGGGTTCAGGCCCTGCTGAGGCCATC[C/T]GGGCTCATTCACTTCTATCCAGTTTTTCTCTGGAA Y 2 1 2 1 101000 r 74 goat snp27782-scaffold297-337635 5 107748993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395511 Affx-122963879 AX-123265866 5 100016630 ACGTACATTGACCAAGGTCGTGAGTGACAGATGTA[C/T]ACACAAGAAAGTCAGAATACAGTCTTCAGAGAAAA Y 2 1 2 1 201000 f 74 goat snp27781-scaffold297-293281 5 107793101 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384631 Affx-122972162 AX-123254989 5 100052198 TGGGTGTCCGCCCACACCTGACACACGCAGGGCTT[C/T]GCTGCCTTTGTCCTCAAGCCTTCAGCAGCATCACA Y 2 1 2 1 101000 r 74 goat snp27780-scaffold297-257713 5 107828724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439839 Affx-122930461 AX-123310176 5 100082278 CATGCCTTTCTCAATACAGTCATATCTTCAGGGAA[C/T]TGATTGACTCCAGGACCCCCAGGATAACAAAAGTC Y 2 1 2 1 101000 f 74 goat snp27779-scaffold297-227633 5 107858467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441318 Affx-122929441 AX-123311655 5 100127628 CTGAATAATACTCAATATCCTGTAGTAAACCACAA[C/T]GGAAAAGAATATGAGAAAGAAGGCATGTTTAACGG Y 2 1 2 1 303000 f 74 goat snp27778-scaffold297-182283 5 107903798 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385805 Affx-122971035 AX-123256163 5 100176401 TACAGTTACTATAAAACACTGGCACATCCCCGCGC[C/T]GTACAGGGCGGCCCACCAGCCTTTTGTGAGACGTA Y 2 1 2 1 201000 r 74 goat snp27777-scaffold297-133510 5 107952878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441458 Affx-122928762 AX-123311795 5 100295301 TTGAAGAGCCTGTTGATGACGCCGCTCTTGACTCC[A/C]CTGTCAGAGATGGCTGCACCGTCGGCATTAGGGGT M 2 1 2 1 101000 f 74 goat snp27775-scaffold297-14610 5 108071900 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410322 Affx-122952480 AX-123280672 5 100330212 CTGCCTCCCCTTCGATCTCTGCTGGTTCCGAGTCC[A/C]CGTCTCCCTCCAGGTCATCCTCATCGAACTGGACT M 2 1 2 1 101000 r 74 goat snp20265-scaffold2006-20202 5 108106683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385956 Affx-122971541 AX-123256314 5 100359180 GATTCTCTGGGCCCCAGTGAGAAGGGGCTGAGAAC[G/T]CAGTGAGCGGTAACTGCTTCATTTCCTGCAGGTTT K 2 1 2 1 101000 r 74 goat snp20266-scaffold2006-49170 5 108135407 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421919 Affx-122943840 AX-123292266 5 100388942 GGCTAACTGAATCAGACCATCTGGGAATGAAGGTC[C/T]TTGTCACCCCAACTGCTTCCCAGCTCTGGTCCCAA Y 2 1 2 1 101000 f 74 goat snp20267-scaffold2006-78932 5 108165237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766504 Affx-122950317 AX-385253868 5 100423783 TATTTGGGAGGCTTTATGTTTTGGTCTCCTGCTTC[A/C]AAGAAAGTACCACTCTAAACCAAGTATTAATACTG M 2 1 2 1 101000 f 74 goat snp20268-scaffold2006-113773 5 108199920 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405871 Affx-122955609 AX-123276223 5 100470876 CTGGTAGAAGCAGTGTCTTGGTCAGGCTCTCAGCC[A/G]TGGCTCTGAACTCACATGATACTGCTCCGGGGGAG R 2 1 2 1 201000 r 74 goat snp20269-scaffold2006-160866 5 108247156 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378929 Affx-122976439 AX-123249288 5 100568344 TCTCCAGTTCATCTGCTCCCTTTGTGAGACCAACT[C/T]TCTCCCAAGCTCACCTGTGGACACTCTTACCCCAA Y 2 1 2 1 101000 r 74 goat snp20271-scaffold2006-258334 5 108343873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450843 Affx-122922241 AX-123321177 5 100644429 TATTGGTCAAAAAGGTCAATCCCTCTCCCGGCAGG[A/C]GGCGAGTCGGAGCTGAAGCTCTGCGGCTACTGGTC M 2 1 2 1 101000 f 74 goat snp20272-scaffold2006-334419 5 108420020 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476208 Affx-1251763713 AX-586011632 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20000 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 560378494 Affx-1251763713 AX-605230909 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20000 r 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562165782 Affx-1251763713 AX-606941191 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562166001 Affx-1251763713 AX-606941410 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562166007 Affx-1251763713 AX-606941416 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 r 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 468278286 Affx-1111836344 AX-519551773 5 100688052 GTGACACTTGATACTAAGTTCCTACCTATCAACGA[A/T]GTGGTGAGTTCAGTCATTTCAAAGGCATAATGAAA W 4 1 2 1 101000 f 74 goat Random2.2K-606 5 100688052 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405914 Affx-122955577 AX-123276266 5 100736156 TTCTAACACGACCTTGGGGACTTCCTAAGGCACTC[A/G]GGAGAGGCCACCCTGCAGGCCAGGCATGGGGAGAA R 2 1 2 1 101000 f 74 goat snp20274-scaffold2006-426146 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272521 Affx-1111833448 AX-519546239 5 100795869 GTACTAAGTAAAATGGTGAAGATCAGACATAGTAA[A/G]CAAGGACTAGGAGTTGGTGAGAGATATAGCCAACA R 2 1 2 1 201000 f 74 goat 5_100795869_AF-PAKI 5 100795869 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408840 Affx-122954016 AX-123279191 5 100798026 CTCCTCAATGACACTACCTCTATATTAGAGGGTAA[C/T]AGAAAGCAATACTTTTATCATCAGAGAAATGGACA Y 2 1 2 1 101000 f 74 goat snp28480-scaffold3035-31924 5 108574327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437429 Affx-122932408 AX-123307767 5 100840521 TAAATTATATGAAGTACTTAGCACAGCACCTGGCC[A/G]TCATGTGCAATGAAAGAATGAAGTCCATTGTTATT R 2 1 2 1 201000 r 74 goat snp28481-scaffold3035-74419 5 108617444 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443264 Affx-122927491 AX-123313601 5 100870851 TTTATTTTTAAGAATTATCGTATAGCAGCATTGAC[C/T]TTTTTTCTTTTTGTATACAGTTCTCTGAATTTGTG Y 2 1 2 1 102000 f 74 goat snp28482-scaffold3035-104749 5 108647769 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435853 Affx-122932809 AX-123306192 5 100931130 AGTTCCTCAGGGGCTTTGTGTCCGACTATCCCTGA[C/T]AGTCTATCCCTGATAGATCTTTCCCTGATAGATAG Y 2 1 2 1 102000 r 74 goat snp47462-scaffold6689-76365 5 108708180 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440679 Affx-122929922 AX-123311016 5 100989577 TTCTTGTCACCTTCTCAGCTACATAAATCACAGGC[G/T]ACCACCTCCAGGAAGCCTTCTGCTGTTAACCTATG K 2 1 2 1 101000 f 74 goat snp47461-scaffold6689-17918 5 108764764 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429779 Affx-122938241 AX-123300120 5 101043075 CGTGGGCCACCACACGGCCAGTGGAGAGCACCCTG[A/C]GTGATGAATTTAAGACTTGGGTCTTGATTCCAATC M 2 1 2 1 101000 r 74 goat snp48873-scaffold698-35481 5 108818624 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417325 Affx-122947744 AX-123287673 5 101107987 GTGTCTGGCTCAAAGGAGGCATCTCATAAGCATAA[C/T]AGACATAGTAGAGTCAGAAGTAATAAGCAGTGGGA Y 2 1 2 1 101000 f 74 goat snp48874-scaffold698-100393 5 108883859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441504 Affx-122928728 AX-123311841 5 101188789 ACACAGGAAAGAGAAACCAGACACCAGTGATGATC[A/G]TGGGTAGGAACACAGTGGAGGGGGCAGGGATGGTA R 2 1 2 1 101000 f 74 goat snp48875-scaffold698-181195 5 108964332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764627 Affx-986696935 AX-385252269 5 101208804 TCCCTAAAGCTTTCCTCCTTCAAATCTTGGATGAG[A/G]TTAGACACTGAGATTTCCTTATGTGTCAGAGAAGA R 2 1 2 1 600010 r 74 goat 5_101208804 5 101208804 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 38432458 Affx-122935801 AX-123302799 5 101225206 TACACAACCACTCATTAGCCAGGCCACGGGAATTA[C/T]GATGATTGCCATGGCTAATAATCCCAATTCCCACA Y 2 1 2 1 101000 r 74 goat snp48876-scaffold698-217612 5 109001429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780743 Affx-122921545 AX-385267833 5 101272889 GGGATTACACCCACTTCACGGGCATGTTGCAAAGA[C/T]GATAAGTGACCTTGGAGGGTAAAGCATTATCAGCT Y 2 1 2 1 201000 r 74 goat snp48877-scaffold698-265295 5 109048924 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419968 Affx-122945195 AX-123290316 5 101317253 ACAAAAATGCTCTCAATATTCAAAAAACCAGAGCA[G/T]AGCTAGGCAAACTCTGGTCTACGGATCAAATGTGG K 2 1 2 1 101000 r 74 goat snp48878-scaffold698-309659 5 109093134 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787239 Affx-122974658 AX-385274265 5 101356476 TATGTACAGGAATGTTCTTCTTCTTAGAAGAGATA[C/T]GCTGAAATTTAAGAAGTGAGGTGTCATGATGTCTG Y 2 1 2 1 201000 f 74 goat snp48879-scaffold698-348882 5 109131458 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785187 Affx-122975313 AX-385272233 5 101397892 GTTGATTAAGATACTGAGCTTAGAGTTGAAGGTGC[A/G]CACATGAGATCTTGAAGCCAGTGGGCTATTGAACT R 2 1 2 1 101000 r 74 goat snp48880-scaffold698-390298 5 109172218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388639 Affx-122969120 AX-123258997 5 101432824 AGATTCTGGTAGCGTCTGGATGATGCCAGAAGGGG[C/T]AAAGTCTGGCCCAGGTAGAGGTGCTGGCAGGTTAG Y 2 1 2 1 201000 r 74 goat snp48881-scaffold698-425230 5 109207190 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790714 Affx-122933948 AX-385277715 5 101474220 CAGTGCTCCAGCTTCATCATCTTATTTAGTACAAA[C/T]ACGTAGTAAAAATGAGAAACGTATGTAAGAAATCT Y 2 1 2 1 101000 f 74 goat snp48882-scaffold698-466626 5 109258593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432463 Affx-122935611 AX-123302804 5 101517114 GAGGCAGCCCTGACTAAATTATGTTGACTCTATGG[C/T]GAACCATGGGTGCCAAAGATATTAGGTTCTAATCC Y 2 1 2 1 101000 f 74 goat snp48883-scaffold698-509520 5 109301287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439247 Affx-122931004 AX-123309584 5 101549885 CGGGGATGAAGGACTTGCTCTGCTCTCCTGTAGAT[G/T]CCCCCAGAGCAGCATCCAGTGTCTGGCACATGGGA K 2 1 2 1 101000 f 74 goat snp48884-scaffold698-542291 5 109334129 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410949 Affx-122952035 AX-123281299 5 101605679 CACTTCTCTGAAGCCCCTCACCTGGCTTAAGTTGG[G/T]GAGTGATGTCAACTGTCTCTAAAGACACCTCCCTT K 2 1 2 1 101000 r 74 goat snp48885-scaffold698-598085 5 109378932 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430831 Affx-122937441 AX-123301172 5 101649720 TGCTGAGACACTCCTGGAGAGAAGAAACTGGGACT[A/G]TTTCTTCTGAGTGTCATTTACAAAGTTTTATGGTC R 2 1 2 1 101000 r 74 goat snp48886-scaffold698-642126 5 109423413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786932 Affx-122936327 AX-385273961 5 101720341 GAGACGGTCTCTTTAGCAGTTGCTCTCCAAACCCA[C/T]CTAAAGTTTTACTGATTAACACGAGGGATGTTAGG Y 2 1 2 1 101000 f 74 goat snp48887-scaffold698-712747 5 109494091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396696 Affx-122962826 AX-123267051 5 101758021 TTCCGAAGCCAAAATGCTGGGTCTTCACCACTGAA[C/T]GCCAGGAGAGGCCAGAAGCAGGGGAGCAGAGGCTC Y 2 1 2 1 101000 f 74 goat snp48888-scaffold698-750427 5 109531976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405629 Affx-122956596 AX-123275981 5 101843862 TGTGTGGTGCCTGGGAGTTGTCCTCATTGAGAATC[A/G]GGCGTTGCACTGTCAGCTCACCTCTCTGGAGCCCC R 2 1 2 1 101000 f 74 goat snp48889-scaffold698-836268 5 109617413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431176 Affx-122937186 AX-123301517 5 101875068 CCCACACCCCCTGCATACACCCCAGTACAACACAC[C/T]CCCCCAAAAAACACCTGGAATCTTGGACCTCGGTC Y 2 1 2 1 101000 r 74 goat snp48890-scaffold698-867474 5 109648306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448041 Affx-122923706 AX-123318377 5 101904593 CCACCCCGTTCTGTTCTTTGATTCTGGGCCTGGCC[A/G]TTGCTCACACCGTTATTAAGAAAACGTTCTCAACT R 2 1 2 1 101000 r 74 goat snp48891-scaffold698-896999 5 109677702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443047 Affx-122928145 AX-123313384 5 101935487 TTTGCTTTGCAAAGGCAGCGCCTTCAAAATTAGAC[G/T]CCCTGTCTCTATTCCCAACCATTTGCCCTCCCTGT K 2 1 2 1 101000 f 74 goat snp48892-scaffold698-927893 5 109708866 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425390 Affx-122941558 AX-123295736 5 101975510 AAAAAGAACCTAGAAGGGCAAAGGGAAATTCTTCC[C/T]ATCCTAGAGGATCAAGAAAAATGCCAACGGCTCTC Y 2 1 2 1 201000 r 74 goat snp48893-scaffold698-967916 5 109749033 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454267 Affx-122919642 AX-123324600 5 102017717 CCCTACACAAACCCCTCCTGTGCAGAAATGTGGTC[C/T]GACAGTCCCACCGGGGCGGGCTGAGCACCCTGTTT Y 2 1 2 1 101000 f 74 goat snp48894-scaffold698-1010123 5 109789751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782721 Affx-122945243 AX-385269793 5 102056504 ATAAACTGCAAACAAGTAGAGAATGGTCATAATCA[C/T]GATCCCTCATAGAGAATGATTCATTCCAAATGAGT Y 2 1 2 1 101000 r 74 goat snp48895-scaffold698-1048910 5 109828561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278288 Affx-1111836345 AX-519551775 5 102073885 TTCCATTTGTCTCTATGTGTAACAAAAGGTTACCC[A/C]AAAATAAAGAAATCGGATCAGTTTCTGGAAAAACT M 2 1 2 1 303000 f 74 goat Random2.2K-608 5 102073885 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394659 Affx-122964378 AX-123265014 5 102093627 TGGGACCGCTGTGTAGTAGGGGGCTACCTTTCTCC[A/G]AAGACGGTGGCAGACACGTTTGAGAAGGTAGTAGC R 2 1 2 1 101000 r 74 goat snp48896-scaffold698-1086033 5 109865705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278290 Affx-1111836346 AX-519551777 5 102108628 CTTTACCACTAGCGCCACCTGGGAAGCCCATCAAG[A/G]CATCATTTTTCTTAAAATAATAATATTAGAGGCTT R 2 1 2 1 103000 f 74 goat Random2.2K-609 5 102108628 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419456 Affx-122945489 AX-123289804 5 102166218 AGGCTGGCAGGGCTCAGGTGAGAGATGCTGAAGAT[G/T]AGCTGAGGCCTCAGAGGAGGGCAAGGAAAGACACA K 2 1 2 1 201000 f 74 goat snp48898-scaffold698-1158624 5 109938580 T G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377462 Affx-122977516 AX-123247821 5 102213044 TAGACATTCTTTTTTCCATTCAATACCATGTCTTG[C/T]ATAAGTTTACTTTTGTATATGGTGTGAGGTAGGGA Y 2 1 2 1 103000 f 74 goat snp48899-scaffold698-1205450 5 109985903 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381958 Affx-122974110 AX-123252316 5 102256926 CTAATGGATGATTCACGCTGAGTGTCCTGGGAGCC[A/G]TGGGGAAAAAGGAAACAGGTTGGCACACACAGCTC R 2 1 2 1 101000 f 74 goat snp48900-scaffold698-1249332 5 110030041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803031 Affx-986696136 AX-385289907 5 102268262 CAGACACCTTTTCCCTTTTGGCAGGTGGCTCTTAT[A/G]CCTCCTGCTGCTGGTCCTGTTCTACGGGGTTGGAG R 2 1 2 1 600010 f 74 goat 5_102268262 5 102268262 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 38405534 Affx-122955980 AX-123275886 5 102364494 TTCACTGTTCATTAACACAAACTGGGCAACTGAAG[A/G]TTCAATAATCAATAGACTAGAAAAGTCTCCAAAGC R 2 1 2 1 201000 r 74 goat snp48903-scaffold698-1356900 5 110137907 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426642 Affx-122939944 AX-123296988 5 102434263 GTCCACACCCTGCAAAGAGGAATGAGGCATGGTTC[A/G]TATCCTCTGGGGCTTACAAGTTAGCTAAGGGCAAG R 2 1 2 1 201000 f 74 goat snp48904-scaffold698-1426669 5 110207716 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388064 Affx-122969527 AX-123258422 5 102476878 TTCCAGCAGCGTGGTGATGGCTATCTGTCACATCC[A/G]TTTCTAGGAACGCCGTGGAACCAGCCTGGACATAA R 2 1 2 1 101000 r 74 goat snp48905-scaffold698-1469284 5 110250631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444251 Affx-122927217 AX-123314588 5 102528118 AGATCTCCCCCGATATGGCTTCTGAAGGGCTGCTG[A/G]GAAACCCCCAGGGTAGGCAGTGGGGATTTGTCAAG R 2 1 2 1 103000 f 74 goat snp48906-scaffold698-1520524 5 110301636 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417967 Affx-122946692 AX-123288315 5 102566658 GTTTAACATTTATGATGTTTTAATTTTGCAGTGTG[A/G]CTCTATACCCGTAAACCAAAGAGCACACTAATTAT R 2 1 2 1 101000 r 74 goat snp48907-scaffold698-1559064 5 110340686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410484 Affx-122952201 AX-123280834 5 102631469 CTTTTAAGGAGGACAGTTTTGGAATGGCATTGGTA[A/G]AGAAGGTGCTAAGAATAGCTAATAAGTGAATAAAA R 2 1 2 1 101000 f 74 goat snp48908-scaffold698-1623875 5 110405663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415885 Affx-122948481 AX-123286234 5 102753822 GCCTTCATCAGCTTCTTGTTTATTCTCATAGTAAG[A/G]AGAGAGGAGATTGGGAATGCCGTGTGCTGTGGAAT R 2 1 2 1 101000 f 74 goat snp48910-scaffold698-1746228 5 110520580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375479 Affx-122979146 AX-123245838 5 102808594 TTAGGACTGAGGCTGTTAGTTACGAACCGGAACCC[C/T]TCCTCACTCTCAAATACAAGAAAGGTCCCCTGACT Y 2 1 2 1 101000 f 74 goat snp48911-scaffold698-1801000 5 110575334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801693 Affx-122965204 AX-385288601 5 102856660 TATTTACCATAGACTTGGCATAGTTCTAAGAATTT[C/T]ATATATATTAACTCAGTCTTCACAACTATCCTGTA Y 2 1 2 1 201000 r 74 goat snp48912-scaffold698-1849066 5 110622299 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444238 Affx-122927227 AX-123314575 5 102905491 GACCAAACGTTGTGACTGAGGCAGCCCAACCAAAA[A/G]GACGTACATCTACTCGGTGCCGTGTCCTTCCTCGG R 2 1 2 1 101000 f 74 goat snp48913-scaffold698-1897897 5 110670757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429896 Affx-122938119 AX-123300237 5 102989548 CTTCATAAGAGATGCTTTTTCATTTCCTATCATAG[A/G]TATGCCTGTCATTTACTATTACAATCCCATATAAT R 2 1 2 1 101000 r 74 goat snp48915-scaffold698-1981954 5 110755697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453034 Affx-122920085 AX-123323367 5 103067723 TGGTGACACTGAGCAACACTATTCCATCAACAAAT[A/G]GAATGAGACAGCACACGCGAAAGCACCAAACAGCG R 2 1 2 1 101000 f 74 goat snp48916-scaffold698-2060129 5 110834285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424051 Affx-122942068 AX-123294397 5 103113897 ATGAAAAAGAGTGGGAGCACCATGGCTCCTAAAGC[G/T]TTTATGAAGTCAAGAAGCTCGGAAAGCAAGGGAGG K 2 1 2 1 101000 r 74 goat snp48917-scaffold698-2106303 5 110879447 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381224 Affx-122974511 AX-123251582 5 103164543 TTTTTAAATATGAGTTACATGAGACAGATGTGCCC[A/G]TGCAGTTGTTGTCCAGGTGGGGAGACATTCCTAGT R 2 1 2 1 101000 f 74 goat snp48918-scaffold698-2156949 5 110931023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438976 Affx-122930384 AX-123309313 5 103197356 TTTCAATGAAGCAAGCATGAGAATTTTCATTTTTA[C/T]AGAGAATCACGGGGAAAATTCTACCTCAAAAGAAA Y 2 1 2 1 303000 f 74 goat snp48919-scaffold698-2189762 5 110964320 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419296 Affx-122946236 AX-123289644 5 103249133 TGGACAAACCCCTGAAGCATAAATATCATTAATGC[A/G]CACTTCAAAGTCAAACTCGACTATATCACCCAAGA R 2 1 2 1 101000 r 74 goat snp48920-scaffold698-2241539 5 111017040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438136 Affx-122931479 AX-123308474 5 103292477 AGCTCTAGTTTCATCTTTTGTCTTTACAAAAAAAC[A/G]CTGAGGTTTGAGGGTGGAAAAAGCCGTATATCCAG R 2 1 2 1 101000 r 74 goat snp48921-scaffold698-2284883 5 111060434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415758 Affx-122948932 AX-123286107 5 103343314 AACCACCATCGTCAGCCCGCTGCCTCTCAGCCCTT[A/G]CTGCTTCATCAGTCTTGCCTGCTCAGAGCTTCCTC R 2 1 2 1 101000 r 74 goat snp48922-scaffold698-2335720 5 111111883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272292 Affx-1111833449 AX-519546031 5 103352994 TTAAGACTCAAGATAGGAATTTTGTGGGAACAGAA[A/C]CATTCCAACCACAGCAACCACTGTTTCGTGTTTTT M 2 1 2 1 101000 f 74 goat 5_103352994_AF-PAKI 5 103352994 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446476 Affx-122925060 AX-123316812 5 103392015 AGAAATTTCATGTCCCCTTAGGACTGTTAGAACAA[C/T]GCCTGGCGACCAGGAAGTACTCACTAAATGGGTGT Y 2 1 2 1 202000 r 74 goat snp48923-scaffold698-2384421 5 111161053 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418892 Affx-122946104 AX-123289240 5 103423965 ACTATAGAATGTTTTTATTGGCTTAAGACTAGCTC[A/G]CATGCTTCATCCTTGGTAAGGGGCTGGAAGAAGCT R 2 1 2 1 201000 f 74 goat snp48924-scaffold698-2416371 5 111193182 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772744 Affx-122964934 AX-385259889 5 103478018 CCCAGATTTATGTGTAAATAGACCTGTCATAGTGT[A/G]TTGGCCCTATTGCAGTCATCACTGTTAGCTCTACT R 2 1 2 1 101000 r 74 goat snp48925-scaffold698-2470424 5 111247679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415465 Affx-122949163 AX-123285814 5 103541688 AAACCCCCATTTTGAAGTTCATTCCGGGGTCGATC[A/G]GGCCGTAGAAAATTACTCCCCTACTGTGCCGTACT R 2 1 2 1 201000 f 74 goat snp48927-scaffold698-2534094 5 111311080 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438643 Affx-122930904 AX-123308980 5 103598142 ATGGGTGCCTTTTACCCATGATCTTGGGTTTCTTA[C/T]AGGTGACCCAGCAGTGCTTGTCAGAAATATTAAAT Y 2 1 2 1 101000 r 74 goat snp48928-scaffold698-2590548 5 111367368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410766 Affx-122952684 AX-123281116 5 103726978 TCAGTAAGATGCCACATTATAAGAAACCACAAATT[A/G]GTCCTTTGGCAGCAGTGCCCACAGATATTGTCCCT R 2 1 2 1 101000 f 74 goat snp48930-scaffold698-2719384 5 111496180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430683 Affx-122936923 AX-123301024 5 103792186 CTCCAGCCTCATTTTATTCTCTCCCGGCATTCCAG[C/T]CTCATCCATCTTCCTATGGTAGCTAACGTGGGCTT Y 2 1 2 1 101000 r 74 goat snp48931-scaffold698-2784592 5 111561549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403837 Affx-122957943 AX-123274189 5 103840495 AAAGCGTGGCTGTTGCTGCTTGGACTCTACAGGAG[C/T]CACGGAGAAGTTGAGATGTGTGGGGAGCAGGGTAA Y 2 1 2 1 101000 f 74 goat snp48932-scaffold698-2832901 5 111610456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425757 Affx-122940734 AX-123296103 5 103953753 TATTATGGTTCCTTGGAAGACTGTTTGGTTTATGT[A/G]TAGAGATGTTGGGCGGCAGAGAGACAGGGTGTGTT R 2 1 2 1 101000 f 74 goat snp48934-scaffold698-2946159 5 111724595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435315 Affx-122934017 AX-123305655 5 103984768 CATCCATCCCAGCCTTGGAGGGAATGGCCTGCGGG[G/T]GAGCAAGATGCGGGAGAAGGCAGACGATGACTAGC K 2 1 2 1 101000 r 74 goat snp48935-scaffold698-2977174 5 111755696 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386400 Affx-122970827 AX-123256758 5 104046005 ACTTCTGCCCTTGAGGTTTTTGATGGTCAAACTGT[A/G]TAAGGAAATCCAATAAGTCAGTTCTCCGTCATGTG R 2 1 2 1 101000 f 74 goat snp48936-scaffold698-3038411 5 111817018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464397450 Affx-1110465657 AX-515870566 5 104114369 AGGGAGGTGCTCCAGCCTGCAGACCGCAGCCCTAC[A/G]CCTCCCCAAGCCTCAAGGGCAGCCTGGGAAGAGCC R 2 1 2 1 202000 f 74 goat GoatD01.004835 5 104114369 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38403700 Affx-122958043 AX-123274052 5 104117349 GATCCCAGAGAGGCCAGGGCATAAGATGAGGGTGA[C/T]GGGAGACAGACCTGGAGGAACACTTTGTCCTTTTG Y 2 1 2 1 101000 r 74 goat snp48937-scaffold698-3109755 5 111886538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449344 Affx-122922977 AX-123319679 5 104169840 AATCACCGCTGGTGACTGGCCCAGAGTGCAGCCAC[A/G]CACCCTCCCTACCCCATATAGCAGCCATTTAGGAA R 2 1 2 1 201000 r 74 goat snp48938-scaffold698-3162246 5 111938644 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382872 Affx-122973516 AX-123253230 5 104217974 TCCCCAGGCAACCAGTATACACTGACAGGACAAAC[A/G]ATTATTGCTAACTCAACACTGTTGTGTACTTAATG R 2 1 2 1 101000 f 74 goat snp48939-scaffold698-3210380 5 111987474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452475 Affx-122920998 AX-123322808 5 104259714 TTTTGTCCCCTTTTATATTTGTTTATTGTGGGAGG[A/G]TAAATCCAACATGAGCCACTCCCTCATGGTTAAAA R 2 1 2 1 101000 r 74 goat snp48940-scaffold698-3252120 5 112029471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390293 Affx-122967727 AX-123260650 5 104272207 TCATTATAGGGCCAGTGCTTGTTGCTAAGTTTTCA[C/T]ATCTCCAATCCACTGTGCACCTGGGAGTGCATTAG Y 2 1 2 1 303000 r 74 goat snp12654-scaffold1483-402121 NW_017189770.1 21117 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403432 Affx-122957741 AX-123273785 5 104336470 AAACAAACATCAGTGTTTCACCCCTTCTCAAACCT[A/G]TCCTCTGCCAGTTTCCTCTGTTTCTGAGCAAAATA R 2 1 2 1 101000 f 74 goat snp12653-scaffold1483-337858 5 112121302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431760 Affx-122936724 AX-123302101 5 104365279 ACATTTACAGTTATGTATTGAGTCATGTCTCCGTG[C/T]TTTAGTCTGAAGGTCATATTCCAAACACAGAAACA Y 2 1 2 1 101000 r 74 goat snp12652-scaffold1483-309049 5 112150129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278457 Affx-1111836348 AX-272527278 5 104397928 GGGGTGATTCGGGCCCCCAGGAGTCTCGGGCAAAC[A/G]CCTGGAGAGTTTTAATCGGCACAGTTTGCGGGGGA R 2 1 2 1 102000 r 74 goat Random2.2K-610 5 104397928 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380183 Affx-122975510 AX-123250541 5 104426123 CTGCCCAGCAAGGCAGCTGTTCCTGTCCCGTCTTC[A/G]CTGAGATGGAAACTGAAGCCCCGAGAGATTAAGGA R 2 1 2 1 101000 r 74 goat snp12651-scaffold1483-248205 5 112211269 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416057 Affx-122948345 AX-123286406 5 104457257 ATCCGCATGCACTCTAGCCCCGTGTAACCTGAGAT[A/G]TGTTGGAATAGACCGTCCTCCAACTTGAGCGCGTT R 2 1 2 1 201000 r 74 goat snp12650-scaffold1483-217071 5 112241620 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434702 Affx-122933946 AX-123305043 5 104528563 GCACCCGTCACACTTGGCTGGGTCTGACCTCCCCT[C/T]CTAACCTGGCAGCTGGCTTTTCTTCCTTAGCACGG Y 2 1 2 1 101000 r 74 goat snp12649-scaffold1483-145765 5 112306448 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397686 Affx-122962580 AX-123268041 5 104559445 TCCAGTCTTTGTTTCAGCCGCTGAACCGCACTCTG[C/T]CACTGTGTTGCGTTTACGTGATCATAGGTTTCTGC Y 2 1 2 1 101000 r 74 goat snp12648-scaffold1483-114883 5 112334517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446275 Affx-122925668 AX-123316611 5 104665534 AGTGGGGAATTATTTTATGATACTTCATCCAGGCT[A/G]TGGTGAGGTGCTGTTCTTCCCCCAACACAGCATGT R 2 1 2 1 201000 f 74 goat snp12646-scaffold1483-8794 5 112441733 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780426 Affx-122978027 AX-385267518 5 104698413 GTGAAATTTGGAGGTGACTAAGTTGGCTTTCTCCT[C/T]TTAATCATCCTCTCACAAGCCGTGAAGAATTCCCA Y 2 1 2 1 101000 f 74 goat snp49599-scaffold709-23986 5 112475388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382518 Affx-122973803 AX-123252876 5 104731514 CCCTGGGGCTCCTCTAACCTAGGAGGCATATGCCC[A/G]GGTGGTGGGTTCCTCATCTGGCTCAGTTCAGGCCA R 2 1 2 1 102000 r 74 goat snp49600-scaffold709-57087 5 112508458 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379843 Affx-122975809 AX-123250201 5 104777954 CTCACAACTCCTTGTCAAGTGGACCTCCAACCACC[A/G]TCCCCCTGAGTTTCTTCTGAGGTGTCAACCTCTCT R 2 1 2 1 201000 f 74 goat snp49601-scaffold709-103527 5 112555181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420039 Affx-122945141 AX-123290387 5 104901383 TGTTTTGCGAGAGACAGAAGGGAGGTAAAACCTGC[A/G]TCGTATAATGGGTTTCCCTGGTGGCTCAGTCGGTA R 2 1 2 1 101000 f 74 goat snp49603-scaffold709-226956 5 112678786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424821 Affx-122941370 AX-123295167 5 104939177 AGCAAAAAATAAAATAGTGCACAGACCTTTAGTAC[A/G]CACAAATGTTAAAGGCAAGGATTATATATTTTCTT R 2 1 2 1 101000 f 74 goat snp49604-scaffold709-264750 5 112716566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441297 Affx-122929458 AX-123311634 5 104973056 CACTCTTCTGATTAAAAAACTTCATTGATTCCCAA[C/T]GCCTATAAAGTCCCTAAATTTCTAATGAATTTTAC Y 2 1 2 1 101000 f 74 goat snp49605-scaffold709-298629 5 112750370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791476 Affx-122940741 AX-385278467 5 105002881 GTGTCATTGAACTCTGAGATCAGAAAAAGCATCTA[C/T]GAGAAATTTGGATAAACATGTGAGGAGTTATATGA Y 2 1 2 1 101000 f 74 goat snp49606-scaffold709-328454 5 112780093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388509 Affx-122969214 AX-123258867 5 105034110 AACATGTTGTCCAGCTCACTGGTGCTCGGGGTGTA[C/T]TTCACTGTGCAGAAGCGGCAAAATCCAAGTTTATA Y 2 1 2 1 101000 r 74 goat snp49607-scaffold709-359683 5 112809172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429701 Affx-122937628 AX-123300042 5 105071160 TGGAGCTGAGATTGCCATGATCAGCAGTTGTGAGA[C/T]GAGGAAACCCCAGGACCTGGAATGAGAAGCCGGGT Y 2 1 2 1 101000 f 74 goat snp49608-scaffold709-396733 5 112846109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443301 Affx-122927463 AX-123313638 5 105106479 ACGCGGTCCTGTCTCAGCTCCGTCACTCACTAGCT[C/T]GGTGGCCCCAGGCAAATCTTTGAACTTCTTTTATT Y 2 1 2 1 101000 r 74 goat snp49609-scaffold709-432052 5 112881482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408254 Affx-122953815 AX-123278605 5 105154744 ACAACCTCAAGACCAGGAAATCTTTGTCTCTAAGC[C/T]ACCCGTCAACCACGCCTTTGCGTTCACGCACTCAT Y 2 1 2 1 101000 f 74 goat snp49610-scaffold709-480317 5 112929984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428147 Affx-122939051 AX-123298490 5 105225577 GATGGGCCAGAGGGATGAATGAACGAGGAGATAGA[C/T]GGCTCTTTTGGTCTGCAGACTGAGCTCAGCTGAAG Y 2 1 2 1 201000 f 74 goat snp49611-scaffold709-551150 5 112997433 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392588 Affx-122966061 AX-123262945 5 105265037 TTGGACTTGAATGTCCAACAGGCAGGACAAACCTA[A/C]CAAGCCTAACATGGCCCACAGTGAGCTATCTCCAC M 2 1 2 1 101000 f 74 goat snp49612-scaffold709-590610 5 113036945 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440404 Affx-122929615 AX-123310741 5 105302253 AGTTTAGGTTATGAGGGTTCCTGGCACTCCCTACC[A/G]CCTTCCCTCCATATACACTATCAGTCTGGAATCGC R 2 1 2 1 201000 r 74 goat snp49613-scaffold709-627826 5 113073386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375987 Affx-122978425 AX-123246346 5 105356206 GGATTGGCAGAGGGGGCGCGAAGGCTCAGAGAATG[C/T]GGAGGGTCTCCCCAGAGGTGATCCTGGAACCGGGG Y 2 1 2 1 201000 r 74 goat snp49614-scaffold709-681779 5 113125430 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430686 Affx-122936921 AX-123301027 5 105450730 ACTTCTATCATCAATATTACCATCAACACTATCAA[C/T]ACCACAACCACCACCACCATCATTATCTCCATCAC Y 2 1 2 1 201000 f 74 goat snp26711-scaffold2806-593794 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377287 Affx-122978120 AX-123247646 5 105528453 GACCTTGGACCAGTGGCTCACCTTCTCTGAGCTTC[A/G]GTCAGCTATCCCATGGATGGCATGGCCATGTGACC R 2 1 2 1 101000 r 74 goat snp26709-scaffold2806-516071 5 113296647 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320771067 Affx-122927703 AX-385258227 5 105577265 TGGGGGACATAAAATGACTAAACACCCAAGGACAC[A/G]TAAGTCAAGATTAGTCTAATTGAGTAGTTAGACTA R 2 1 2 1 101000 f 74 goat snp26708-scaffold2806-467259 5 113344488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272460 Affx-1111834411 AX-191821404 5 105578461 TGCAGTTGGGTGAACTATC[A/G]CATCCAGGTGTGGCCTGCCTGCAGAAAACAATTCA R 2 1 2 1 102000 r 74 goat GoatD01.034327 5 105578461 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797439 Affx-122938969 AX-385284378 5 105617170 GTGAATCTACATGTGTGATAAATTCATGTAAATGT[A/G]TACACACAAACCCATTTTTACTGCACTTGAAATTG R 2 1 2 1 201000 r 74 goat snp26707-scaffold2806-427354 5 113384823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424437 Affx-122941794 AX-123294783 5 105667875 ATTATAATAAATATTCCATTTAAATGTAAAGTCCA[C/T]GAAAAGAAAAACCTAAACATAAGTTTATAGGAAGG Y 2 1 2 1 101000 r 74 goat snp26706-scaffold2806-376649 5 113435720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451477 Affx-122921136 AX-123321810 5 105712845 TGTGAGTTCGAGTTATGGGAAGAGAAGTGGTGCTC[A/G]TGGTGCTGGCATAAAATATCTCTACGTGAGAAACC R 2 1 2 1 101000 f 74 goat snp26705-scaffold2806-331679 5 113480884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385960 Affx-122971538 AX-123256318 5 105750695 GACGAGGAACCAGGACCTCAGAGTTCTCAGCACAA[C/T]GCTGGCAGCTGGAAGATGGGAACAGTGCATTCAGG Y 2 1 2 1 101000 f 74 goat snp26704-scaffold2806-293829 5 113518085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436353 Affx-122933067 AX-123306692 5 105792332 TTGGGTGCAGACCTGGCAAGTACTCCTGGTGCCCA[C/T]GGTGCCCTGCAGCCTGGCAGCCCCTTTCCACTTCC Y 2 1 2 1 101000 f 74 goat snp26703-scaffold2806-252192 5 113555452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448402 Affx-122923679 AX-123318738 5 105828300 GTTCAAGCAAAACGCAAAACAAAGGAGCTGCCTTC[A/G]GCTGGCAGACAGGGACACTGCAGAGGGAAAGGAGC R 2 1 2 1 101000 f 74 goat snp26702-scaffold2806-216224 5 113591475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401349 Affx-122959254 AX-123271702 5 105965222 AAGGAGGAAAGAGAATCAAGAACTAAAACCTCAGA[C/T]GTCTCACAAAGGGCCTGCCATTTATACCCCAGGCT Y 2 1 2 1 101000 f 74 goat snp26700-scaffold2806-79302 5 113726590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800607 Affx-122977502 AX-385287526 5 105998365 TTCCCTGTCTCATTCCAGAAAAGATTTCCAGCAGC[A/G]TAAAGAAGTTTTAATTCATATGCTACAGGTATTGA R 2 1 2 1 102000 f 74 goat snp26699-scaffold2806-46159 5 113759860 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404281 Affx-122957041 AX-123274633 5 106034109 TGCAGAAAAGGGGGCAGAGCACGTGGGGAGCGTGC[A/G]AGCAGGAACGTGGGGCTCCTCACGAAAGGTCACGG R 2 1 2 1 101000 r 74 goat snp26698-scaffold2806-10415 5 113794220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272159 Affx-1111833451 AX-519545915 5 106038681 GGCCCCAGTCGTTCTCCAGGTTGGTCCTGTCACTC[A/G]CTCATTCATCCACCCCAGGAATGTTTATTGAGTTC R 2 1 2 1 101000 r 74 goat 5_106038681_AF-PAKI 5 106038681 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437642 Affx-122931803 AX-123307980 5 106064745 AACGTGAAATCAGTGGAGTCAGCAGGCTGGCTGCA[C/T]GTGGGGGCCTTGGAAGGTGGGACATTTGTCCCCAG Y 2 1 2 1 101000 f 74 goat snp30016-scaffold3274-189409 5 113816926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392343 Affx-122966681 AX-123262700 5 106104359 AAACGACTCTCAGTGTCTAGGAGACAAAGATGGCA[C/T]GTGTTCAGAGAAAAACCTGGCTTCTCCTGTCACTG Y 2 1 2 1 101000 f 74 goat snp30015-scaffold3274-149795 5 113856721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450089 Affx-122922790 AX-123320424 5 106147545 CAGGTTTCTGTGATCTGCACATTCACACAGGATGC[A/G]CGTGGAATTCTCCACCACGTCAGCACGATGGGTCC R 2 1 2 1 101000 f 74 goat snp30014-scaffold3274-106609 5 113896622 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385599 Affx-122971202 AX-123255957 5 106282493 CAGACACCCCAGCCTCCAACACTGAGAACAAACAC[A/G]AAGAAGACATGTGCCCAGCATCTGCTCTGGAGCCC R 2 1 2 1 101000 r 74 goat snp29274-scaffold3154-28240 5 114016665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403457 Affx-122957723 AX-123273810 5 106314645 TTCCATGACCAGATTAGCAAATATTTAACCAGATG[C/T]GAACACTCAGTGCTGGCAAGATGGGCACATTTATC Y 2 1 2 1 101000 r 74 goat snp29275-scaffold3154-60392 5 114048663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451971 Affx-122920945 AX-123322304 5 106399967 TCTTGACGTTGGGAAGCTGGTTTCAGCGCCCTGCC[C/T]GGCTCTCTGCTGGGTGGCAGGTGACAGGCGATCTG Y 2 1 2 1 101000 r 74 goat snp52043-scaffold7677-9635 5 114134337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464399268 Affx-1110466570 AX-515872370 5 106430751 CTCCTGTGGAGGATGGAAAAGGCAGCAACAGGGCT[C/T]CCCCTGCCCTGTCTATATCCCTCGGCCTCTCTTTC Y 2 1 2 1 202000 f 74 goat GoatD01.042622 5 106430751 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379759 Affx-122975854 AX-123250117 5 106435784 CTTTCTTTTTTTCTAACATTCCCAGCAAATTCTTG[C/T]TAAGACTGTACTGTTAAAGTGGAAATTACAGGGGG Y 2 1 2 1 101000 f 74 goat snp10800-scaffold1384-1417254 5 114530148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797325 Affx-122970883 AX-385284264 5 106487092 CTCCCCCACAAAAAATCCTAACGTTCTAGATTAAA[C/T]GTAAACAATGTCCTCTTAAATGCATGACCGGGCTT Y 2 1 2 1 101000 r 74 goat snp10799-scaffold1384-1365946 5 114477636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449370 Affx-122922724 AX-123319705 5 106535849 CTCTCAACCCTAGATTGTGATGATGGCGAATGTCA[C/T]GTGCCTTGAGATGAGAGAGGGGTCTGAGCGGACAG Y 2 1 2 1 101000 f 74 goat snp10798-scaffold1384-1317189 5 114430058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424040 Affx-122942077 AX-123294386 5 106663901 CAGAATGGGACTCTAGTCTGGGCTTCAGCACACAT[G/T]AACTGTGTGACCTTGGGCAGGTCACTGAACCTCTC K 2 1 2 1 101000 f 74 goat snp10796-scaffold1384-1189137 5 114305112 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387285 Affx-122970536 AX-123257643 5 106762138 CTGTCCTTGTGCTGGCCCCAGGTAGCACCTCGCTC[A/G]GTCTGGACCCTTCTGTGTGTGCAGGGCATCGAGCT R 2 1 2 1 101000 r 74 goat snp10794-scaffold1384-1090900 5 114219895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391428 Affx-122966756 AX-123261785 5 106809983 AACTAATACATTACTACCCAAAAGCCTTGAAGAGA[C/T]GGCCAGGAACCAAGGACAGTGGTGTCTTGTTCACA Y 2 1 2 1 101000 f 74 goat snp10793-scaffold1384-1043055 5 114172320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406521 Affx-122955135 AX-123276873 5 106857731 GAAGAACCTGGGCTCGTCTTCCGCCCTGGGTTTGA[A/G]GCACAGGCAGCAAAAAGCAGATCTTACCCGGTGAC R 2 1 2 1 202000 f 74 goat snp10792-scaffold1384-995307 5 115510321 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783119 Affx-122973662 AX-385270186 5 106910186 TTTCTCCATTTCTTCCAGTAAAATTAAGCTCCAAA[A/G]ATGAGCAATTTTGCTTTTAGTGCTGAACGAAATGC R 2 1 2 1 101000 r 74 goat snp10791-scaffold1384-942852 5 115467854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392291 Affx-122967530 AX-123262648 5 106941335 TAGCAGAGGGTGGAGGAGGTATGTTCTGAATGTTG[A/G]GAAAATATTTATCCCCAAGGCCAACGACAGACAAT R 2 1 2 1 101000 r 74 goat snp10790-scaffold1384-911703 5 115436762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406524 Affx-122955133 AX-123276876 5 106973484 AAATAGCTCCATTGAGATGTCGTTTACATACCATA[A/C]ACTAGTATGTAACTGGTATGTTTAAACAATGGTTT M 2 1 2 1 101000 f 74 goat snp10789-scaffold1384-879554 5 115404053 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784916 Affx-122949101 AX-385271963 5 107003959 CACTAGTGAAATTTTTCTGCACAAAGTAGCTGGGC[A/G]TTGTTAAATCTGAACATGCACGATGTAAAATCTTT R 2 1 2 1 101000 f 74 goat snp10788-scaffold1384-849079 5 115374655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390135 Affx-122967995 AX-123260492 5 107094012 GCTGCTGTGTCCCCGTGAGCTGTTTAGTGTTTAAG[A/G]GGGGGCAGGTTTCTTAGAGAACCCAGCCCCAGCCC R 2 1 2 1 101000 f 74 goat snp10787-scaffold1384-759026 5 115299207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378829 Affx-122976544 AX-123249188 5 107124639 TGTGGCATTGTGGAGATTTTTCTTTTTGTTCATTT[A/C]TTTATCTTGCTTGATGTTCACTGAGCATTTTCAAT M 2 1 2 1 103000 r 74 goat snp10786-scaffold1384-728399 5 115268419 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434844 Affx-122934378 AX-123305185 5 107230349 CCAGCTCTCCGACAGCTCCAAATGCTGGCAAGGAC[A/G]TGGACCAACCAGAACACTCGTGCCTTGCAGGCAGG R 2 1 2 1 201000 r 74 goat snp10784-scaffold1384-622689 5 115164585 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383478 Affx-122973439 AX-123253836 5 107320833 GTTTGTTCAGCCACTGAAGTGTGACCTTGTAGACC[A/G]TGTGTTTTGGGTGGGAATTATACCCCAAGTACCAA R 2 1 2 1 101000 f 74 goat snp10782-scaffold1384-532205 5 115082295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440884 Affx-122929233 AX-123311221 5 107402299 ACCATTCCTCTAGTCAGAAGTACAAGAGAGATTCC[A/G]GTCAACCTCAACTAAAGCTGATGTTGCCAAGCCTG R 2 1 2 1 101000 f 74 goat snp10781-scaffold1384-450739 5 115003901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453431 Affx-122919875 AX-123323764 5 107434224 GTTCCATTTCAGTTTTTCTGTTGGCATCTTATCTA[C/T]AATTCTTCGCATTTTTAAAGTAGTTGCCACCAGGA Y 2 1 2 1 101000 f 74 goat snp10780-scaffold1384-418814 5 114971832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393381 Affx-122965907 AX-123263737 5 107490463 ATGGCAAGAGAAGACCAGTTCTTGCCCGGATTTTA[G/T]GAAATTTTGACATTTGGTACTTTTTTTTTTTTGCC K 2 1 2 1 103000 f 74 goat snp10779-scaffold1384-362575 5 114916795 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410201 Affx-122952575 AX-123280551 5 107523634 TCTTATCATCTCACAGAAGGTTAGAACCTGTCCCC[A/G]TCCTGTCACAGGAAGTTAGAATCTATCTTTATTCT R 2 1 2 1 303000 r 74 goat snp10778-scaffold1384-329404 NW_017212681.1 7951 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274959 Affx-1111834514 AX-519548541 5 107538028 GGGCCTCCTGCTGCCCAGGCTGTCACACTCTGCAT[A/G]GTGTAAAAATTAGGGGGGCCACTCCCCAGCTGGTG R 2 1 2 1 202000 r 74 goat GoatD01.039109 5 107538028 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278296 Affx-1111836349 AX-519551782 5 107562959 GGGATGAGTGAGGGGATGAGTGGCTGCATGAATGA[A/G]TGAGTGAGGGGATGAGTGGCTGAGTGAATGAATGA R 2 1 2 1 103000 f 74 goat Random2.2K-614 5 107562959 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450965 Affx-122921747 AX-123321299 5 107636146 TATTTTTAAAACTTTTGGCGAATCTTCTTGCCTCT[A/G]CTGAGTGTTTTTCTCTTGCTTTTGTCTGTTTTCCA R 2 1 2 1 101000 f 74 goat snp10776-scaffold1384-216892 5 114771051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787867 Affx-122945396 AX-385274889 5 107708062 TCACTGCTTTTTACATGTAACTATATCCACAACTC[C/T]ACCTTCCCTTCTTCTGATAAAAGATTGGGCAACTA Y 2 1 2 1 101000 r 74 goat snp10775-scaffold1384-144976 5 114698103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432268 Affx-122936336 AX-123302609 5 107748386 ACCATGAAGGGGCTAAAAAGACAGCCCTTCAACTG[C/T]GGGCTCAGCTCTGTCGGATGGGCCACCTGCTGGCG Y 2 1 2 1 101000 f 74 goat snp10774-scaffold1384-104652 5 114658003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387995 Affx-122969579 AX-123258353 5 107787195 CCAGACTTGTCCACTCTGCCTGGTCATTGTGTGCT[A/G]TGGTCTGTCTCCCATAGAATCTCAGCTCTTTGGGG R 2 1 2 1 101000 r 74 goat snp10773-scaffold1384-65843 5 114619211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390121 Affx-122968006 AX-123260478 5 107880268 CCAGCCCGTGAACCAAACGCTGGATGCTGCCAACG[A/G]GGGTGTCAGTGCCCACTTCACGGATGAGGAAACTA R 2 1 2 1 201000 r 74 goat snp14413-scaffold1573-144238 5 115530453 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448903 Affx-122923179 AX-123319238 5 107955211 GACCTCCATCTCCTACTTCTTTGGATGGAGCTGCT[A/G]CTGCTGCTAAGTCGCTTCAGTCGTGTCCGATTCTG R 2 1 2 1 103000 f 74 goat snp14412-scaffold1573-69295 5 115601050 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442816 Affx-122927710 AX-123313153 5 107995138 CCCATGTGACTTCACTCTCTAGAATGTCTGGCTCT[A/G]GGTGATGTTATTAGGCCATGTTATTAGGTGCGTAC R 2 1 2 1 101000 r 74 goat snp14411-scaffold1573-29368 5 115644711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381559 Affx-122974824 AX-123251917 5 108077456 CCCCATCGAGCTACGATACCACTGCGTTAAGAGAA[G/T]AGTTCAAAACACAAAAGAAGTGTGCAAGATGTAAA K 2 1 2 1 101000 f 74 goat snp23854-scaffold2401-52851 5 115724526 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434121 Affx-122934927 AX-123304462 5 108108946 AAAAGAAGGCAGAAGCCGTGGGTTTCTAGTGTTGT[A/G]CATGTTCTAAACAGCAGCCCCAAATGCTTTTTGCC R 2 1 2 1 201000 r 74 goat snp23855-scaffold2401-84341 5 115796351 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385985 Affx-122971521 AX-123256343 5 108226821 GTAGGCATATACGCTCCCAGCAGCAGAGAGAAAAC[A/C]GCACAGGAAGGGTTTCTAGAGAGGAAAGGACAAAA M 2 1 2 1 101000 r 74 goat snp15139-scaffold1618-38721 5 115839398 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793327 Affx-122932062 AX-385280305 5 108280848 GAATAAGAATGACCGCCGTTCCTTTGAACTGATAC[A/G]TAGAGCTGAGCTGAGCACAAAATCAAGCTAAGACA R 2 1 2 1 101000 r 74 goat snp15140-scaffold1618-92748 5 115893270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784364 Affx-122972328 AX-385271415 5 108334644 AGACTCACAGTACAGATGAGTTTGGAGTTGTGATG[C/T]TGGCATTGTTTTCATAAAGACAGTTCTGAATTTTA Y 2 1 2 1 101000 f 74 goat snp15141-scaffold1618-146544 5 115942653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762412 Affx-986696943 AX-385250563 5 108340022 TCAACAAGAGGCTGGCAGGGGCTCAAGCTGCCCAC[C/T]GAGGTGGAGTCAGGGTCCTAGAGGGGACGGCCCAC Y 2 1 2 1 600010 f 74 goat 5_108340022 5 108340022 Ancestral_priority_1043 ancestry 0.424 neutral IMAGE 10K 10K ancestral 320779151 Affx-122976595 AX-385266255 5 108372729 TGTTCCATATAAAATTCTGTTTCACGCCTTTTCCC[A/G]TTTAACCTTAGAACGTTAGCTTGTTCCTGTATTAT R 2 1 2 1 101000 f 74 goat snp15142-scaffold1618-184629 5 115980821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448631 Affx-122923368 AX-123318967 5 108421288 GGCAACGAAAGACTGAGGCCCTTGGGTTTAATGCA[C/T]GTAAATCAGCTACGACAATTCTCTTGAAGAAAACC Y 2 1 2 1 101000 r 74 goat snp15143-scaffold1618-233188 5 116025461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762416 Affx-986696947 AX-385250565 5 108502201 AGGTGTGCTGAGTGTGAGGGCTGAAGCTCAGGGAT[C/T]CTGAGTGTGGGTCTTTGGGGAGAAGCATCAAAATA Y 2 1 2 1 600010 f 74 goat 5_108502201 5 108502201 Ancestral_priority_1043 ancestry 0.548 neutral IMAGE 10K 10K ancestral 320764647 Affx-986696949 AX-385252286 5 108502377 ATGGTTCAGAAAGAACCTTGTAAGTGGTTTCAACC[C/T]GGTTTCCTATCAAGATCACCTGACCAGTGTTAAGC Y 2 1 2 1 600010 r 74 goat 5_108502377 5 108502377 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 38396130 Affx-122963402 AX-123266485 5 108544853 TTCTTTTAGTGAACGCAGTCTGATTGTCTGTCTCC[A/G]TTTTGGGGGGATCCTGGCTGAGAATTGTGTGATGC R 2 1 2 1 201000 f 74 goat snp15145-scaffold1618-356753 5 116152661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397187 Affx-122962409 AX-123267542 5 108613329 GTTTGGTATTGGAACCACCTGAAGTCAATTAAGGA[C/T]CCACAGAATCAATTATTCTCTCTGGGCTGAAATCA Y 2 1 2 1 101000 f 74 goat snp15146-scaffold1618-425229 5 116220567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413906 Affx-122949831 AX-123284255 5 108642407 GTTCACGGTGCTTTGGTTTCATTGCCATAGGGGAG[C/T]GGGCAGAAACTCAACTGGAGGCAAGATTTCATTTA Y 2 1 2 1 201000 r 74 goat snp15147-scaffold1618-454307 5 116249705 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421291 Affx-122944730 AX-123291638 5 108700461 GCCAGTGTAGTCAGAGGGTGCTTGTGGGAGACAGA[C/T]GGGAGCAGGAGGGCAGAGCGTGACCTGAGAGGGAG Y 2 1 2 1 101000 f 74 goat snp15148-scaffold1618-512361 5 116308114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410667 Affx-122952759 AX-123281017 5 108728068 ACAGAGATATCACCAATGCTGTTGGAAGGATTATC[A/G]TCTTGATTTTACAGATGAGGAGACTGACCCTCAGC R 2 1 2 1 101000 f 74 goat snp15812-scaffold1657-664435 5 116336065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450372 Affx-122922093 AX-123320707 5 108767113 AGCTCAAAGGATAAATGGAAAACAAAGAGAACAGA[C/T]GAGCCGGGCATTCTCCCGACTCTACAGAAACACAA Y 2 1 2 1 101000 f 74 goat snp15811-scaffold1657-625390 5 116375129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272295 Affx-1111833452 AX-519546034 5 108781988 TATGTGACTCCGTAACTCCATCTTGTGGCAGCTGG[A/G]AGAGCTGGGGCTGAGGGTTGAGGGATGGCACCTAC R 2 1 2 1 102000 f 74 goat 5_108781988_AF-PAKI 5 108781988 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392382 Affx-122966230 AX-123262739 5 108864631 TGCCCAAGAACGCATCACCCCTACCTCGCCCCAGA[C/T]GGTGGGCTCTGGGTCTATGCCACAGGCACCTCCCA Y 2 1 2 1 303000 r 74 goat snp15810-scaffold1657-527872 5 116473495 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382497 Affx-122973818 AX-123252855 5 108896470 GTGTTCATTTAGCTGTCAGTTTGCTTGGCCACGGC[A/G]CAGAGGACTCAAGGGCAGGAGAAAGGGAGGACTCC R 2 1 2 1 101000 f 74 goat snp15809-scaffold1657-496033 5 116505565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391934 Affx-122966930 AX-123262291 5 108943148 ATTTCTGCAAGACTGCTCTTGCTCTAAGAGGAGCC[C/T]GGATCCTGCTGAAAGCAAACAGCCCGGTGAGCAGA Y 2 1 2 1 101000 f 74 goat snp15808-scaffold1657-449355 5 116552451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777250 Affx-122961736 AX-385264373 5 108979481 TGTAATTTTCAAGGCAATACAAAAGCAATCGCATA[C/T]ACTAATAACAACAATGTAGCAGCAGAAGCCTCAGT Y 2 1 2 1 101000 r 74 goat snp15807-scaffold1657-413022 5 116589281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408143 Affx-122954230 AX-123278494 5 109018726 ATGATAAACTCAAATGTAGTGGATTCAACTGCCTA[G/T]TTCTTCAGGAGCCACTGTCACCGAGAGTCCAGAGC K 2 1 2 1 201000 f 74 goat snp15806-scaffold1657-373777 5 116629121 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384334 Affx-122972258 AX-123254692 5 109055588 CGGATGAATTAATCTCCTGCGGCATAAAGACCTCA[C/T]GATGACCCCACCTGCAGTAGCTGCCCCATAAAGGG Y 2 1 2 1 101000 f 74 goat snp15805-scaffold1657-336915 5 116662402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446216 Affx-122925710 AX-123316552 5 109089389 CCTACTGCGCATCTGGTTCCATTCCGTGGAGGTAC[A/G]CAGCCTCCACTTTTCCGTGTCACGTTCATGCACGT R 2 1 2 1 201000 r 74 goat snp15804-scaffold1657-303114 5 116696476 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415768 Affx-122948925 AX-123286117 5 109126422 GGTGCCCTGGAATTAGACTGTAAGGATCTGCACAC[A/G]CTCGTGAAGATACTAAAAACCACTGAACTGTACAT R 2 1 2 1 101000 f 74 goat snp15803-scaffold1657-266081 5 116734104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441692 Affx-122929168 AX-123312029 5 109168208 TGCAAAGATATCAGGAGCTCTTCATGGAGGAAAGC[A/G]CTGTCCCAGGCAGTGAATCCCACATCCTGCGCAGC R 2 1 2 1 101000 f 74 goat snp15802-scaffold1657-224295 5 116776787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386833 Affx-122970090 AX-123257191 5 109198873 TTACATTCATTACTAAAGGGAGACGCTGGAACGAG[C/T]GCAAAACTGAAGTCTGTCTATACGTTATCTAACAA Y 2 1 2 1 101000 f 74 goat snp15801-scaffold1657-193630 5 116807516 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393178 Affx-122965522 AX-123263535 5 109237211 ATAACTTCCTTGTGACTGTCAGATATAAATGCCTC[C/T]GTCCTTGGGGTTTGCAGAGCAGATATTTCTAGTAA Y 2 1 2 1 101000 f 74 goat snp15800-scaffold1657-155292 5 116845863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390389 Affx-122968178 AX-123260746 5 109291877 GGTCGCAAGGAGTCGGACACGACTGAGCAACGAGC[A/G]CTTCACTTCACTGAAGGATAACATTCCTACAGGAG R 2 1 2 1 101000 r 74 goat snp15799-scaffold1657-100626 5 116899637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415405 Affx-122948738 AX-123285754 5 109321445 CTGTGTGCCATCTCAGGTGGTAAAATAAATGCACC[A/G]CATTGCAGGGACACAGACACAGCTTCATCATGGAG R 2 1 2 1 101000 f 74 goat snp15798-scaffold1657-71058 5 116929596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781213 Affx-122939683 AX-385268298 5 109369751 ATGTCCTTCATCATTACCAGAAGCCAGAAGTCATA[G/T]AATCTGCTCTAGTATGAGTCACCTTACAGCGTTGA K 2 1 2 1 101000 f 74 goat snp15797-scaffold1657-22752 5 116979586 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393076 Affx-122965606 AX-123263433 5 109409502 AAGGTGTCATGTGACCCGCGTGTTGGGCCGGGTGT[A/C]GGGGTGACTTCACACTGGATCCCACACTGCCTAAC M 2 1 2 1 101000 r 74 goat snp3419-scaffold1104-321302 5 117019919 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410746 Affx-122952698 AX-123281096 5 109449917 GAAGGAAGAGGAGTTCCTTAAGAACAATAACAACC[A/G]CCACAGTAATAACTGTGTATAACTTTGTATTTTTA R 2 1 2 1 101000 f 74 goat snp3418-scaffold1104-280887 5 117060343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422085 Affx-122943588 AX-123292432 5 109480591 CTCACCCCAGGTGGCAAGAATCTCAAAGACCATCC[A/G]CAGTATCTCAGCAAAGAAGGAAAAAAGCCGGAACT R 2 1 2 1 101000 r 74 goat snp3417-scaffold1104-250213 5 117088450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418911 Affx-122946092 AX-123289259 5 109517281 AAAATATTAGAGTGTTCTTTTTTATCCCCAATTAA[C/T]GTAGGAATAATCATATCACATTCTCATAATGATCT Y 2 1 2 1 101000 r 74 goat snp3416-scaffold1104-213523 5 117125837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414963 Affx-122949071 AX-123285312 5 109549187 GAGAGGTGATAAGAACTTTCTCTTGGGGCAAGAAC[A/G]TATGACAAGAAGCAAGGAGACGTGTAGAGACACTC R 2 1 2 1 101000 f 74 goat snp3415-scaffold1104-181617 5 117157387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784090 Affx-122953190 AX-385271142 5 109594632 TTCCTCCTTACACTAAAAGGAATTTACTAATGCTC[A/G]TTAATTTTTTGTGGTGTGAATAAATTGCAGGGAAT R 2 1 2 1 101000 f 74 goat snp3414-scaffold1104-136172 5 117202064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792086 Affx-122977265 AX-385279073 5 109642153 TACCTTCTGACATCATGTATCAGCACGCTAAGCAT[C/T]GGCTGAGAAGCAAATAACCTTTCAAGCAGAATGAA Y 2 1 2 1 101000 r 74 goat snp3413-scaffold1104-88651 5 117248547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779222 Affx-122954358 AX-385266326 5 109743089 CTTATTATGCACACAGAGCAAGCAAACAGAAAAGC[A/C]AAAATTAAATTAGACGGCAGCCTGGAGATGCCCAC M 2 1 2 1 101000 f 74 goat snp12979-scaffold15-526697 5 117337522 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387627 Affx-122969862 AX-123257985 5 109796958 GCGGGCTACATTCCATGGAGTCACAAGAGTCAGAC[A/G]TGACTGAGTGACTAGCTCATTCCACCTACTGACTT R 2 1 2 1 101000 r 74 goat snp12978-scaffold15-472828 5 117390384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799287 Affx-122977642 AX-385286217 5 109825874 CAACATTCACAAAATGCACATTTATTTCAAGTGAG[C/T]ACAGTCACCACGATAGATCATGCAGAAGGCCCGCA Y 2 1 2 1 101000 f 74 goat snp12977-scaffold15-443912 5 117417259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422204 Affx-122943497 AX-123292550 5 109869117 CTGAAGCACGTGGAAGCCCGAGATGCACCTTATGC[A/G]TTCGCTATTATTCTTTGTGTTAGAAGGTTTACAAA R 2 1 2 1 201000 r 74 goat snp12976-scaffold15-400669 5 117457386 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407116 Affx-122954876 AX-123277467 5 109897638 CAGACACTGCAGAAATAGCACGTGTGCAAGCATTA[A/G]CAACGGAGCAGACTCCAGAAGAACCGCCCAGAAGC R 2 1 2 1 103000 f 74 goat snp12975-scaffold15-372148 5 117486496 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445307 Affx-122925439 AX-123315644 5 109932167 TTCTTTGTCTCTCCTCTTCACATGAATATTTATCG[C/T]GAGGAAGGCCCAGCCAGCACGCCAGCGGCCCCATT Y 2 1 2 1 101000 f 74 goat snp12974-scaffold15-337619 5 117521641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399294 Affx-122960538 AX-123269649 5 110053631 AAGGAAAGAGAGTCCTTGGTCAGCTTGCTGGGAAA[G/T]TGTCCCCTTGGCTGAAGAGTGGGTGGATACTCAGT K 2 1 2 1 101000 f 74 goat snp12972-scaffold15-216155 5 117632862 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795951 Affx-122966128 AX-385282903 5 110086932 AGATAACAGATAGATGATGATGGCACACAGATAGA[C/T]AACAGACTGATGCTAGATACAGATGCATAACAGAT Y 2 1 2 1 101000 f 74 goat snp12971-scaffold15-182854 5 117666597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418931 Affx-122946509 AX-123289279 5 110141988 GGGGTAATCATCTACACCCTGTCTATCCCTCTAAA[C/T]ACTACTCTGAAACCCCGACACAGTGCCTGGAGCAC Y 2 1 2 1 101000 f 74 goat snp12970-scaffold15-127798 5 117721039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445884 Affx-122925961 AX-123316221 5 110174076 CGAGCACAAAAGTTTCCGAGCTTTGGCTTCCAGAG[C/T]ATCATGTCAGACAAGACCTGGATTCACTCCCGAAA Y 2 1 2 1 101000 f 74 goat snp12969-scaffold15-95710 5 117754742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430443 Affx-122937732 AX-123300784 5 110235979 TGCCCGAAACGGAGGCAAAATCACTCTCTGCTCTG[C/T]GATGAGAGTCGAGGCTAATTTTATCCCCACTGTGC Y 2 1 2 1 101000 r 74 goat snp12968-scaffold15-33807 5 117814863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430512 Affx-122937218 AX-123300853 5 110292410 GCGTGCACGCCTCAGCTGATCCGCCTGGAATCAGC[G/T]TCCACGCCTTGAAACCTCTCGTGTTTTTCCCCGGG K 2 1 2 1 101000 r 74 goat snp22113-scaffold2180-22525 5 117872641 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442697 Affx-122927877 AX-123313034 5 110353295 GTTGATGGGCTTTCCTTCCCCATCAAGTGAAATAG[C/T]AGCCTGTTATCGGTCAACAAAAAGACGTTTGTGCC Y 2 1 2 1 101000 r 74 goat snp22114-scaffold2180-83410 5 117932089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375690 Affx-122978656 AX-123246049 5 110408532 AAGCAGAAAGAAATGACAAATGTGAGATGAACTGC[A/G]AATAAACTGTGAACAATTAACTATGAAGAACTGTA R 2 1 2 1 201000 r 74 goat snp22115-scaffold2180-138647 5 117980961 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445674 Affx-122926138 AX-123316011 5 110463870 TAAGCTCCAAGAGGAAAAAATAAAATATGAAGAAC[A/G]CTACAGCCATTTAAATACTTTATTACACAATTGCG R 2 1 2 1 101000 f 74 goat snp22116-scaffold2180-193985 5 118032865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802763 Affx-122956956 AX-385289662 5 110506902 TCTGGAATACACCCTATTGAGTTCCTCCAGTGAAA[G/T]CAAATTCCTGGTCTTGGCCTCAGACTGTCAGTCTT K 2 1 2 1 101000 r 74 goat snp22117-scaffold2180-237017 5 118074684 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419169 Affx-122945730 AX-123289517 5 110533033 TAAAAATGATAGCTTGGCTCACAGGAGAAACAGTA[C/T]GTGCATGGCCCGTGGACGTCAGGCCTCCTTTAATC Y 2 1 2 1 101000 f 74 goat snp7077-scaffold1262-10037 5 118110963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440741 Affx-122929875 AX-123311078 5 110620954 TCAGGCACAGAAAATCCTGTGCGTTAAAGTCCCTT[A/G]CTGACCATTCTTTGTTTGCAGTATGGTCGCTTATC R 2 1 2 1 101000 f 74 goat snp7078-scaffold1262-97958 5 118246438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376490 Affx-122978029 AX-123246849 5 110691148 TTTCCAAGCCTTATCCATTCTTGGGCAAGGCTCCC[A/G]CCTTGGCGGTGACAGCCTCCTATCTTCCTGGCGGG R 2 1 2 1 102000 f 74 goat snp7079-scaffold1262-168152 5 118301420 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428875 Affx-122938340 AX-123299217 5 110743657 GGGTTTCGGCTCTCTGGCCTCTGAGATGGGACTGC[A/G]TTCTGTCTACGGGGTGTGCCTCTCCCAGAATAAAC R 2 1 2 1 101000 r 74 goat snp7080-scaffold1262-220661 5 118353537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792496 Affx-122932235 AX-385279477 5 110797980 AAAACTCATAGCAACATCATACTTCATGGTGAAAC[A/G]CTGAGCACTTTCCTCTGGAGTTCAGAAACAAACAA R 2 1 2 1 101000 r 74 goat snp7081-scaffold1262-274984 5 118407105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454111 Affx-122919355 AX-123324444 5 110861971 CCATTCTGGCTTCATGTGTTCCTTCTGCCCTGCTC[A/G]CCAGGCTCCTGGGACGGGCACATGCGGCCACATGA R 2 1 2 1 103000 f 74 goat snp7082-scaffold1262-338975 5 118466679 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403760 Affx-122958001 AX-123274112 5 110903832 TTTTTTTAGCAATAAAGTGTTCTTAAGGTATGTAC[A/G]TTGCTCTCTAGACATGCACATAGTATGCAGATACA R 2 1 2 1 101000 r 74 goat snp7083-scaffold1262-380836 5 118507888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449440 Affx-122922674 AX-123319775 5 110954957 TAACAGCACTCAAACAACTAGGAAAAGAATGGAAG[C/T]GGCTCAACGGGATAAAGACTGTGTGTGAAAACTCC Y 2 1 2 1 101000 r 74 goat snp7084-scaffold1262-431961 5 118558584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377607 Affx-122977894 AX-123247966 5 110992449 TGATCAGGCCTGAACCCCATTCGGAGTCTGAGACC[C/T]CTTGGAAAACGGGGGAGGGGACAGGGCTCACGGAG Y 2 1 2 1 101000 f 74 goat snp7085-scaffold1262-469453 5 118593702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272296 Affx-1111833453 AX-519546035 5 111337928 GGGGCTCAGTAATCATCTCAGCAAGAACGAGTCAC[A/G]CCCCAACAACGAACAAGTGAGCAGCCTGGGACCTG R 2 1 2 1 101000 f 74 goat 5_111337928_AF-PAKI 5 111337928 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278461 Affx-1111836350 AX-519551944 5 111503812 ATTGGGAAATACATCATTCTGGTTCCCTATTCACT[A/G]TAGTACCTTCTCAGGTGAGCAGTAGTTAGTTGTTG R 2 1 2 1 101000 r 74 goat Random2.2K-617 5 111503812 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 464402868 Affx-1110468381 AX-515875929 5 112142244 AGGGACTTGACGACGGTGACAAACTGCAGCAGCCA[C/T]GTGACAGTCACCGCTCCGTGTCCCCTACAGGTAAA Y 2 1 2 1 202000 f 74 goat GoatD01.015571 5 112142244 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320764651 Affx-986696951 AX-385252288 5 112828562 ACTTAGATACTTGGGTGAAGCTAAGGAAACAGCTA[A/G]AAACTTATTATAGTTTACATGGGCCTGTAAATGCT R 2 1 2 1 600010 r 74 goat 5_112828562 5 112828562 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 320764654 Affx-986696953 AX-385252290 5 112829169 AAAAGGATTCTAAAAATAAAAAGTTTCTCTTGTGG[C/T]CAAATGAGGCATTTTGTCGGCAGTGTCCTGCTAAA Y 2 1 2 1 600010 r 74 goat 5_112829169 5 112829169 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 468273635 Affx-1111833711 AX-519547248 5 113205026 AGCCTCTCACAGTGCCCGCTCCCGCAGGACAGGTG[A/G]GCTTCCGCTTCCGCCTCTCCTTCTGCAGGAGGAAG R 2 1 2 1 202000 r 74 goat GoatD01.002213 5 113205026 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278302 Affx-1111836352 AX-519551788 5 113489131 GGGACACGGAAGACAAAGGGGACAGCAGATTTAAC[A/G]TCTCCGGTAAGCGATTCTTGACAAATATCTACAAG R 2 1 2 1 101000 f 74 goat Random2.2K-620 5 113489131 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272297 Affx-1111833454 AX-519546036 5 113851836 CTCGGCCATGGCCGGTTCCCCAGACTTCTCCATCT[A/G]CAGCGGGAACTGTTCCCAGAGGGGTGCTGGGTAAA R 2 1 2 1 303000 f 74 goat 5_113851836_AF-PAKI 5 113851836 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 464404651 Affx-1110469283 AX-515877687 5 114105129 CAGGGTCTGCAGTGGGAGGCCATCCTGGCAGGAAG[A/G]CACAAGGGACGCTGGGCAGGAGTCCCCAGACAAGG R 2 1 2 1 202000 f 74 goat GoatD01.055655 5 114105129 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278304 Affx-1111836353 AX-519551790 5 115004333 GTGTGAAAGCAGCCCTACGCTGTGCGTGAAGAGAC[A/G]CGCGTGCTGTGTCCAGTGAAGCCTCATTCGTGAGC R 2 1 2 1 202000 f 74 goat Random2.2K-622 5 115004333 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273845 Affx-1111833852 AX-519547454 5 116281982 CTGCAGAGCAACGGCTGCTC[A/G]GGCCTCCAATCCGTGGTCTTTGTCTAAAGCAGCCT R 2 1 2 1 102000 r 74 goat GoatD01.007349 5 116281982 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272298 Affx-1111833455 AX-519546037 5 116371807 GAGCTGCAACCATTGGACTCCTGAAGTAAGCACAC[A/G]CGGTGCTCTCTTAGACATCAGTCTCAGCAATCCTT R 2 1 2 1 101000 f 74 goat 5_116371807_AF-PAKI 5 116371807 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278306 Affx-1111836354 AX-519551792 5 117627326 TGGGGTTTAAGAAGCTCAGGCAGGAGAGCTGGCCT[A/T]GCCACCCCATTTCCTGTTCCTGAGACCCCTCGCCA W 4 1 2 1 103000 f 74 goat Random2.2K-625 5 117627326 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273858 Affx-1111833889 AX-519547468 5 117907093 GAGCAGGGCTGCAGAGGGAGTGGACGGAGATGCGG[A/G]GGGAGTGGGGACTGTGTTGTGACTGCGGGGCCGTC R 2 1 2 1 303000 f 74 goat GoatD01.009515 5 117907093 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468274471 Affx-1111834312 AX-519548062 5 118555833 GTGCCATCTGGAGAAGGCAGAGTGGAGGGCTAGGG[A/G]TTGAGGGGTGGGTTCAGTGGAGAGGAGTTCCTGCA R 2 1 2 1 303000 f 74 goat GoatD01.029799 5 118555833 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272299 Affx-1111833456 AX-519546038 5 118976440 AAAAAGCAAAGACATTACTTTGCTGACAAAGGTCC[A/G]TCTAGTCAAAGCTCTGGTTTTTCCAGTAGTCATGT R 2 1 2 1 303000 f 74 goat 5_118976440_AF-PAKI 5 118976440 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392776 Affx-122965988 AX-123263133 6 25231 ACATCATCAATTGTTGCAGTACTCCTGGTGAGAGA[C/T]GACAGTGGCTTGGGCCAGGGTGGTGGCAGTGGCAA Y 2 1 2 1 101000 f 74 goat snp31735-scaffold354-25231 6 484197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414442 Affx-122949952 AX-123284791 6 54326 CATCTGTGGCTTGGTTAGTCTTCTGGATGATGACT[A/G]TCACCTGGAAGCCTGTTAGAAATGCAGAAATGCCC R 2 1 2 1 103000 f 74 goat snp31736-scaffold354-54326 6 513324 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437220 Affx-122932036 AX-123307558 6 90072 ACACCATACCTATACTTCCAATGCCTTGTATTCAG[A/G]TTGTTATTTGATGTGTATTATCAGTCTTTGGATTC R 2 1 2 1 101000 f 74 goat snp31737-scaffold354-90072 6 549401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272337 Affx-1111833496 AX-519546069 6 164375 GTGCAGCTCGGCCATGTTTTCACCAAACCTGAATC[A/G]GACTGTTGCCCACTGAGCTGCTCTGATATAGGTTC R 2 1 2 1 201000 f 74 goat 6_164375_AF-PAKI 6 164375 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38420220 Affx-122945536 AX-123290568 6 184232 CGTGTGTGGTGATTAAGGCCCTGTTTAATTAGATA[A/C]TTTTACCATCTCTGCAGAGGTGAAAAATAGACACA M 2 1 2 1 101000 f 74 goat snp31738-scaffold354-184232 6 645298 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796582 Affx-122933047 AX-385283528 6 231230 TCTCCTTGCAGCTTCAGGAGGATGTCTCATTTATC[G/T]CAATTACTGCCTGGTAAACACTGCTGACCAAAGGG K 2 1 2 1 101000 f 74 goat snp31739-scaffold354-231230 6 692622 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432615 Affx-122935494 AX-123302956 6 290051 GACAGTTCCTCAAATATTAGCAGCCTGTATCTGTT[A/G]CTGTTTGTGATATGGTTGAGAAATTGTCCCCAGGC R 2 1 2 1 101000 r 74 goat snp31740-scaffold354-290051 6 752376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801550 Affx-122925352 AX-385288459 6 353088 ACTCACACAGGGATAGTTTAACCCAAATTTCAACC[G/T]ATTTAACTTGACTGTTTAAAGGGCCAACATTTTTT K 2 1 2 1 101000 f 74 goat snp31741-scaffold354-353088 6 816392 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393811 Affx-122965172 AX-123264166 6 420831 AACTAGGGTTTATTTCCTTAATATGGAGATGGGTA[A/G]CCAAGAGTTGTGGCCTGAATTATATCCCATCAAAA R 2 1 2 1 101000 r 74 goat snp31742-scaffold354-420831 6 884237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382563 Affx-122973768 AX-123252921 6 463461 AGTGGGAAACAGATGGACGGAGGGGTTGGGATTAG[C/T]GAATGCAAACTATTATACAAAGGATGAGTAAACAA Y 2 1 2 1 201000 f 74 goat snp31743-scaffold354-463461 6 927062 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415512 Affx-122948683 AX-123285861 6 545755 TGGCCACCACCCCTGACCTCTACCTTATCTGATTA[C/T]GGTTTCAGTGTCTCCAAAAATGCAGTTTTTACCAG Y 2 1 2 1 101000 r 74 goat snp31745-scaffold354-545755 6 1009718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439327 Affx-122930304 AX-123309664 6 602324 GTCTTTTTTTTTTTTCTGTTAACTTATGACTATGA[G/T]ATGCAGAGTAGATTGAATTGCACAGCTTTGCTATT K 2 1 2 1 101000 r 74 goat snp31746-scaffold354-602324 6 1066471 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800764 Affx-122947451 AX-385287681 6 655359 TAATTAAGGGGCTAGAGCAGCTCTGAAGAGAGAGA[A/G]TAAAAGATTGAATAGTATTACAAGATTATATAAGG R 2 1 2 1 101000 f 74 goat snp31747-scaffold354-655359 6 1118891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437061 Affx-122933090 AX-123307399 6 688912 AGTAGTGTAACACAGAAGGCATCTACTTGGATGCA[C/T]GGTAGCATGGTGCCTGGCCAAGTTTAATTACCCAG Y 2 1 2 1 102000 f 74 goat snp31748-scaffold354-688912 6 1152513 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384340 Affx-122972253 AX-123254698 6 730671 TGTGTTCTTCATTTATTCATTCAACAAATATGAAG[C/T]ATTTAGGATTGGCCAGACACAGTTCAAGGAGCATG Y 2 1 2 1 101000 r 74 goat snp31749-scaffold354-730671 6 1194797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773168 Affx-122948545 AX-385260311 6 785947 GACAGACAAAAGGCTAGGCTTTAGGATTTATAGGT[A/G]TCTCAAAAGCTCATTATGGTCAGCAAGAAACTCCC R 2 1 2 1 101000 f 74 goat snp31750-scaffold354-785947 6 1250595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429394 Affx-122938536 AX-123299736 6 832609 TTGCTGCTCATGGTTCTGCTAACTCTCATTACTTT[A/C]TGTTAGTGTTACTGAATCTAAGCTGTTCTCCTTGC M 2 1 2 1 101000 r 74 goat snp31751-scaffold354-832609 6 1297065 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387910 Affx-122970454 AX-123258268 6 865635 TACATTTTCTATCCTCTCACTTTCAGTCTATATGT[A/G]TCTTTAGGTCTGAAGTGGCTTCCCTATAGACAGCA R 2 1 2 1 303000 f 74 goat snp31752-scaffold354-865635 6 1328827 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278308 Affx-1111836355 AX-519551794 6 880718 GTGACCCTGGAGGTGGGTGTGATGTCATAGTAAAT[A/G]TCATGTGTTCATACTGACATTACTTTATTTGAATA R 2 1 2 1 101000 f 74 goat Random2.2K-630 6 880718 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773813 Affx-122926870 AX-385260953 6 885962 AATTTATGGTTTCAAGTGTGCATCACTGTGGTCTT[A/G]TAAAAAAATAATGGTTCAGTAACTCTTTAATTTGG R 2 1 2 1 101000 f 74 goat snp18258-scaffold1850-423514 6 1480210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448561 Affx-122923420 AX-123318897 6 938062 TGCTCTCAGCATGGAAATCTTCAATATTAATACAA[C/T]AGGTTTATTGTACTTTTACTTTTTTAATTACTACA Y 2 1 2 1 101000 f 74 goat snp18257-scaffold1850-371414 6 1532051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785910 Affx-122927549 AX-385272947 6 971396 AATAGCAGTCAATTCAACATGGAACCTCAACATCA[C/T]GATGAACACTCCATCAATAATTAATTCCTAAATGT Y 2 1 2 1 101000 f 74 goat snp18256-scaffold1850-338080 6 1566215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405965 Affx-122955538 AX-123276317 6 1013672 GAAAGCATTAATAATGTTATACACAATATATCAAC[A/G]TCAGTGTTATAGTCTGTTACATCGGTATCTCACAA R 2 1 2 1 101000 r 74 goat snp18255-scaffold1850-295804 6 1608499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767817 Affx-122974119 AX-385255041 6 1063089 CATTGGAGGACAACTACATTTTGAAAAGAAATGAA[C/T]TATTATACAAGACAATACCTGTTACTATTTATTTA Y 2 1 2 1 103000 f 74 goat snp18254-scaffold1850-246387 6 1658648 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445982 Affx-122925884 AX-123316319 6 1116256 TTAGAAAAAGCTGGGATCACACAACATTAAAAAGG[C/T]AAAATTTAGTCTTTGTCAGGAAGAGTGGGGCTTTC Y 2 1 2 1 201000 f 74 goat snp18253-scaffold1850-193220 6 1711791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788319 Affx-122950309 AX-385275337 6 1160929 TTTGTGCAAAGAGTTGTACTCAATATGTGGAGTAT[A/G]TGGAAAGGTTTTGACAACACCTCCACAGACTATCA R 2 1 2 1 101000 r 74 goat snp18252-scaffold1850-148547 6 1756523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406931 Affx-122955081 AX-123277282 6 1201806 AGCTAGGTGTGAGAAGAAACGTGGCTTCCAGGCTG[A/G]ATTGGCTTGGCAGTTTTCCTCTATTTTATTAAAGC R 2 1 2 1 101000 r 74 goat snp18251-scaffold1850-107670 6 1797675 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395262 Affx-122964092 AX-123265617 6 1257189 CCCAGCAGAAAGAGAGCCATGCCGATTTCTCTAGG[C/T]GATACGTATTACATGTATCTTAAAATGCCCTACGT Y 2 1 2 1 101000 f 74 goat snp18250-scaffold1850-52287 6 1854104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442146 Affx-122928323 AX-123312483 6 1345539 TTTCCATAATTGTGTTATTTATCTCTGTTTGCTTA[G/T]ACTTTATTTTTTCCATGTCTTTGGTGATTGCATTA K 2 1 2 1 101000 r 74 goat snp59983-scaffold999-35964 6 1951800 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780033 Affx-122953336 AX-385267132 6 1395105 GATTTTATGGGGGTTAATGAGATGATATGTAAAAA[C/T]GTACAAAATTTGAAAATCCCATACTGATAGAAATA Y 2 1 2 1 101000 r 74 goat snp59984-scaffold999-85530 6 2003532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795151 Affx-122923512 AX-385282109 6 1438392 TACAGTGTTAAGAAACATTCCAAAGTCTGTTTCTG[A/G]TGTCGCTTCCTTCCAGACTCAAGGCTGCCCTCCAT R 2 1 2 1 202000 r 74 goat snp59985-scaffold999-128817 6 2047262 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433538 Affx-122934999 AX-123303879 6 1484900 GCAGTATTTCCATTAGGAGAGACTAAACTGTTATA[C/T]AAAGAAACCCAAAAATGTGGTGACCCCAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp59986-scaffold999-175325 6 2094606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768502 Affx-122933916 AX-385255682 6 1518467 TCACCCATTTGGTAATGCAAGGAATGATAATATTG[C/T]AAAATAGAATATGAGTAATGGAAAGCACAAGTAAT Y 2 1 2 1 101000 f 74 goat snp59987-scaffold999-208892 6 2128119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412486 Affx-122951381 AX-123282835 6 1552910 CAAAGATAGAAATAAGATAGAGACTAGCAGTGCTG[A/C]AGACAGGATGATCTGAGATTATTCCTAATATTAAA M 2 1 2 1 101000 f 74 goat snp59988-scaffold999-243335 6 2162545 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778721 Affx-122952333 AX-385265832 6 1584320 CTGGCCTTGCCTCTGTGTAAACATTTGCCTGATTT[A/G]CTAGCAATTGTTTGCCACCTTTTTATTCAGATACA R 2 1 2 1 101000 f 74 goat snp59989-scaffold999-274745 6 2194700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433060 Affx-122935749 AX-123303401 6 1621541 CTCATGCTGGCCTGTCTTCAGGTCTCTGAAAGAGC[C/T]ATACTCTCACCTTTCAGGAATGCCTTCATATTATC Y 2 1 2 1 201000 r 74 goat snp59990-scaffold999-311966 6 2231932 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778381 Affx-122944180 AX-385265496 6 1657055 ACCAAAATTATAAGGTAGGATCTGCAAAGGTAAAC[A/G]CATTGGGAAAAATCCATTCCTTTACTGAGAAATGG R 2 1 2 1 101000 r 74 goat snp59991-scaffold999-347480 6 2267878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379078 Affx-122976323 AX-123249437 6 1694216 TGTTTAAAGCTGTAGAACTACCCTCTTTTTTAATG[C/T]AATTCTATTCATAATTCAATGGAGAAGGAAATGGC Y 2 1 2 1 101000 f 74 goat snp59992-scaffold999-384641 6 2305576 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38411250 Affx-122952331 AX-123281600 6 1736025 TGTATGACTGCTTATAACCTAGGGCCACAGAGAAG[C/T]AATATGTAGGAACCTGAACCGAAATGTTTTTGAAA Y 2 1 2 1 201000 r 74 goat snp59993-scaffold999-426450 6 2347436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422720 Affx-122943262 AX-123293066 6 1741481 TATTCACGATAACTAGTGCCTGACCAAGCCACAAC[G/T]AGACTGTGGGGGGCCTTCCAATCATTAGCCAAAGT K 2 1 2 1 101000 f 74 goat snp4846-scaffold1161-283736 6 2352757 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388620 Affx-122969135 AX-123258978 6 1807664 AAAATTGTTTAAGTCTGTGAAGACAGGTATAAAGT[A/G]TGCTTCACTCTGTTATTACTGCAAAAGCATATTTT R 2 1 2 1 101000 f 74 goat snp4845-scaffold1161-217553 6 2418255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443584 Affx-122927328 AX-123313921 6 1851675 GAGTGTAGGTGTTCACCAGACAAAAACCAAAGAAA[G/T]AGCAGAATCAGATTTTGGCTTACCTGTTGCAAGGG K 2 1 2 1 101000 r 74 goat snp4844-scaffold1161-173542 NW_017202586.1 12842 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431134 Affx-122936583 AX-123301475 6 1894738 AATTTTCTCATAAAATGGATTTATCTGTTCTTTTC[A/G]CTTGTTTGCTTTTATTGAGACATAACTGAGGAATT R 2 1 2 1 201000 r 74 goat snp4843-scaffold1161-130479 6 2506358 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445349 Affx-122926385 AX-123315686 6 1974800 ACTTGTTGAACATTTGGGAAAGACTCTGGATGTTG[C/T]AAGGGAGCAAGAGTGAAAGTGAAGCAAAGCTATTA Y 2 1 2 1 101000 f 74 goat snp4842-scaffold1161-50417 6 2586355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384635 Affx-122972159 AX-123254993 6 2013767 ATACCAGACCACCTGACCTGCCTCCTGAGAAATCC[A/G]TATGCAGGTTGAGAAGCATCAGTCAGGACTAGACT R 2 1 2 1 103000 r 74 goat snp4841-scaffold1161-11450 6 2626228 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395720 Affx-122963712 AX-123266075 6 2060276 TATGTTTCTGTTTAAATGGTAGAACAAGACTGTTG[A/C]GTGAGAGAACATGAGAATAAATCACTAATTTAATT M 2 1 2 1 101000 f 74 goat snp37610-scaffold461-34960 6 2685229 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441133 Affx-122929583 AX-123311470 6 2100509 ATGGGTTGTGGTCCTAACAAACTAAACAGAAAATG[A/G]TCACTTTTCTGAAATGAGAGTAGTTTTTAGCTCTT R 2 1 2 1 201000 r 74 goat snp37611-scaffold461-75193 6 2725719 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464409166 Affx-1110471556 AX-515882151 6 2121068 GAAAATCTGAACCCAGAGTTCTTGCACAGTGAGTG[A/G]CAGCTCTTTAATGCCAGGAGCAGTGTGGGCATGGA R 2 1 2 1 202000 f 74 goat GoatD01.006192 6 2121068 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770680 Affx-122952773 AX-385257844 6 2135328 CTAGATTACAACAACTTGGAAGTAAAAATAGAATC[A/G]CAGTTATTATAAACCCATTTTCCTCTTTTCTCTAA R 2 1 2 1 101000 r 74 goat snp37612-scaffold461-110012 6 2760631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393154 Affx-122965541 AX-123263511 6 2180449 TGCCAATGTTCCTTTGGTATTCTCTTAATGCCAAA[C/T]AGATATTGTTTTGAATTTCTGTCAGTCTTCTCCCT Y 2 1 2 1 101000 f 74 goat snp37613-scaffold461-155133 6 2805884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278310 Affx-1111836356 AX-519551796 6 2208063 AAAGCTGTCCAAAAGACTTCTTTTGGTGGTGAAAT[A/G]ATACTTAAAGGTTAAACATAAATTTAGAGAATTGT R 2 1 2 1 101000 f 74 goat Random2.2K-631 6 2208063 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384242 Affx-122972363 AX-123254600 6 2215019 TTTACCGGGAAGGAACGGAGACAAAACTGTGGACA[C/T]GGCAGGGGAAGGATAGGGTAGGACAATTGAGAAGG Y 2 1 2 1 101000 f 74 goat snp37614-scaffold461-189703 6 2840854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776433 Affx-122955862 AX-385263560 6 2245869 TTAAGGAGAAACTAAAGTACTTTAAACTTGTAAAT[A/G]CAATTTGAAATGTTGAAGACAGTTAACTGCCTAAG R 2 1 2 1 101000 r 74 goat snp37615-scaffold461-220553 6 2873688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791979 Affx-122925851 AX-385278967 6 2304485 ACTAATAAGACAGGTTCCTGGCCCAGAATTCTCTT[C/T]GGTCAGTGACTTGTCACATGCTTCAGACTGGTGTA Y 2 1 2 1 201000 r 74 goat snp37616-scaffold461-279169 6 2926846 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450328 Affx-122922128 AX-123320663 6 2364398 CATTACTTTGCCATGCACCGCTGCTATCTGGGGTC[C/T]GAGTCCTGTGCTTTCTCATCTTGAGTGTGCACAGG Y 2 1 2 1 202000 f 74 goat snp37618-scaffold461-339082 6 2986906 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795415 Affx-122944879 AX-385282371 6 2425075 AACTCAGGAAGATGGGATTTATTATGGTGTGTTCC[C/T]ACCAGAAACACGGTGGAGCAGATCTTGTGGGAAGA Y 2 1 2 1 101000 f 74 goat snp37619-scaffold461-399759 6 3047826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801557 Affx-122924695 AX-385288466 6 2454886 TATTAACCCATCTGCCTTGTTATATTCTATGTTAT[A/C]TTCATAACAAGTGCCTTGAAAATCTCATTGAGAAA M 2 1 2 1 201000 r 74 goat snp37620-scaffold461-429570 6 3077912 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388397 Affx-122969298 AX-123258755 6 2506796 AGTAATAGGCTCAACTTCTCTTTGTCATCTGCCAG[A/G]TGTACAGAGCAACATCCTAGAACTTAAGAATACCT R 2 1 2 1 201000 r 74 goat snp20348-scaffold2016-29488 6 3294463 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802514 Affx-122946038 AX-385289418 6 2536003 AACTGTGGCAACAGATTCATGGGGTGGCTTACTGA[C/T]GGTGGAAGTTCTTTCTGGAGACTCATTCTAAAGGT Y 2 1 2 1 101000 r 74 goat snp20349-scaffold2016-58695 6 3321029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803400 Affx-122962221 AX-385290231 6 2571274 CATGCTATTAATTTCAGTTGCTAGCAGGATGACAT[A/G]CAATGAAAGATGAAGAAAGGCACTGTGGAAGAGAG R 2 1 2 1 101000 r 74 goat snp20350-scaffold2016-93966 6 3359749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376723 Affx-122978963 AX-123247082 6 2684490 CAGTCTTCCACTGCAAGGGGCCTGGCTTCCATCCA[C/T]GGTGGAGGAATAATCCTACATACCTTACAGATTGC Y 2 1 2 1 103000 r 74 goat snp4245-scaffold1131-661201 6 3578055 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272528 Affx-1111833501 AX-519546246 6 2697706 TCACACAACCGCACACGTACTTAAGTACTTGATAT[A/G]CTACTTGATTAGGCTAAGTGCTTGAAACCCTCACT R 2 1 2 1 101000 f 74 goat 6_2697706_AF-PAKI 6 2697706 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434279 Affx-122934776 AX-123304620 6 2722066 ATGAGTTTAAGTATCTGATAGCATGGAATGACAGA[G/T]AATCTGAAAATTAGGTTTTAAGAACAGAAGAAGCA K 2 1 2 1 101000 f 74 goat snp4244-scaffold1131-623625 6 3615807 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407688 Affx-122954583 AX-123278039 6 2759590 TTACATGTACAACAGTTATTGAATTGTTAACCTGT[A/G]CTACCACGAGAAGCAAATTTCTCAGTTTGAGTACA R 2 1 2 1 101000 r 74 goat snp4243-scaffold1131-586101 6 3654783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441182 Affx-122929545 AX-123311519 6 2799996 TTCCCACAGCCCTTCTGTAAGCTCTTCTGATTTAC[A/G]CGCCAGGTAATGGAGTCACCTTCCTGGTGCCAGAC R 2 1 2 1 101000 f 74 goat snp4242-scaffold1131-545695 6 3701959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767164 Affx-122971163 AX-385254449 6 2828708 ACATCTCAGACCTATCACTTTTAAATTACAGTCTG[C/T]GAATATGATAATGTAATAATCACTTCCTTGACTAG Y 2 1 2 1 101000 f 74 goat snp4241-scaffold1131-516983 6 3728885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444950 Affx-122926685 AX-123315287 6 2901557 AAAGGAATGGCCAAACAGGTGAATCAGATGAATTA[G/T]AAATCACTATGGTTGTGATAGCTGGACTGTAAAGA K 2 1 2 1 101000 f 74 goat snp4239-scaffold1131-444134 6 3801285 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411327 Affx-122952273 AX-123281677 6 2939447 AACATTGTGGTGAATACCAAGACTTGGGGTGAAAA[C/T]GCAGTAAGGAAGACAGTGGGGCAGTCGTTTAGGAT Y 2 1 2 1 101000 f 74 goat snp4238-scaffold1131-406244 6 3839505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408734 Affx-122953409 AX-123279085 6 2972121 ACAGATAGATAGCAGTGGTCTCCGTGTGAACCAGC[A/G]TAACCTGAGGGGTGGGAGCATCGGCCACAGACACC R 2 1 2 1 101000 f 74 goat snp4237-scaffold1131-373570 6 3872769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772809 Affx-122924269 AX-385259954 6 3054604 GCAATGAATAATTTTTGTGAAGCTGTCATTTGTTA[C/T]CTTAATTTCTTCTTTAGAGAACTGCATATGTTAAT Y 2 1 2 1 201000 r 74 goat snp4235-scaffold1131-291087 6 3961495 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770476 Affx-122940283 AX-385257642 6 3083435 AGTAAAAATTAAGAATAAAGAGAGACTACTAAAGG[C/T]AACAACACAAAAGCAACTAGTTAGTACCAGAGAAT Y 2 1 2 1 101000 r 74 goat snp4234-scaffold1131-262256 6 3990308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768965 Affx-122973757 AX-385256140 6 3116474 CCAAGTAATATTGTCCTATTTCATGAATAATACAC[A/G]TCTATTTCTCTCTTCCTAGGTTTTTGCTTTGTTGC R 2 1 2 1 101000 r 74 goat snp4233-scaffold1131-229217 6 4023430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427605 Affx-122939364 AX-123297948 6 3163924 GCCATCTCCCCATATCATCCACCATCTCCCTGGGA[C/T]AACTGCTTTCCATCACTCCCAGAGAGTTTCCATAT Y 2 1 2 1 101000 r 74 goat snp4232-scaffold1131-181767 6 4079987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445170 Affx-122925544 AX-123315507 6 3197710 GAGGTGTCAAGAGAGCACCAGGATGGAAGGAGCCT[A/G]TGTCCCAAATGACAGTGTGGAATGAAGTCAGGGCT R 2 1 2 1 101000 r 74 goat snp4231-scaffold1131-147981 6 4114292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767680 Affx-122949406 AX-385254920 6 3261961 GTAGGGGTGTACACAATGCTATACAGCAGATCTTT[A/C]GAGCTTATTCATCTTGATTAACTAGAATTTCATGC M 2 1 2 1 103000 f 74 goat snp4230-scaffold1131-83730 6 4194777 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433439 Affx-122935072 AX-123303780 6 3298931 ATACTCTACATGGCAAAAGAGATTTTGTAGACACC[A/G]TTAAGTTAAGGACATTTAGATGAGAGATGATCCTG R 2 1 2 1 201000 r 74 goat snp4229-scaffold1131-46760 6 4231437 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385581 Affx-122971836 AX-123255939 6 3336946 ATCTCCAGTATTTTCTGACTTAAAGTGGATAATCT[A/G]CTTCTGGAGGTGAGCCCTAACTGACACTTTGAGTT R 2 1 2 1 101000 f 74 goat snp4228-scaffold1131-8745 6 4267111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408602 Affx-122953645 AX-123278953 6 3366130 AAAATGGTTGAAGAACTCAAACAGGCTTGTGCATC[A/G]TATGGGCCTAAAGCCCAGTACACTAGGCAATTGGT R 2 1 2 1 303000 r 74 goat snp27465-scaffold2927-304597 6 4310648 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431697 Affx-122936775 AX-123302038 6 3420556 AAATAAGAATCTCTAGGGGAAAAGCATCAGGCATC[A/G]TTTTCAAAACTTCCCAGGTGATTCATGTGTTTTTC R 2 1 2 1 103000 f 74 goat snp27464-scaffold2927-250171 6 4365278 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436163 Affx-122932621 AX-123306502 6 3452025 CACCTGGGAGAACCTTCCCCACCTGTACTAGGATG[C/T]AAACACTCTGAGAGTAAGGGTTTTTGTCTCTTTTT Y 2 1 2 1 101000 r 74 goat snp27463-scaffold2927-218702 6 4396329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449686 Affx-122922553 AX-123320021 6 3482450 GTATCTCACAAAGATACCTTTCTATGGGATTTTGT[A/G]GGGGATATGATCCAGGTGACCACATTTCTCATACT R 2 1 2 1 201000 f 74 goat snp27462-scaffold2927-188277 6 4428208 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390082 Affx-122968032 AX-123260439 6 3523198 TAATTTTCCCCCTAAGCACTCCTCCCTTAGCCTCC[A/G]TCCACTGCCTTGAATAGGGAGTCAGGCGAACAAAG R 2 1 2 1 201000 r 74 goat snp27461-scaffold2927-147529 6 4468954 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426914 Affx-122940446 AX-123297259 6 3558936 ATGTTGGTATTTTCCTCTTAGTTTGAATTTTGTAC[G/T]AATTTTCTTTTTAAAATAACCTTTCTATTTTGTGG K 2 1 2 1 101000 f 74 goat snp27460-scaffold2927-111791 6 4504717 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399037 Affx-122960921 AX-123269392 6 3592526 TTGGCAAATTAAACTCTCTGAGCCCCAGTATCCTC[A/G]TCTGTGAAGTGACAGTAATACTTCCTATCTTCAAA R 2 1 2 1 201000 r 74 goat snp27459-scaffold2927-78201 6 4538212 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408200 Affx-122954187 AX-123278551 6 3624918 GACCCGTCCTCCTCTTGCCAAGCTGGGCACCCCTG[C/T]GTGGGGCTGCACACATCCAGAAGAACGAGCCCCTG Y 2 1 2 1 101000 r 74 goat snp27458-scaffold2927-45809 6 4570669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762396 Affx-986696927 AX-385250549 6 3644698 GGATAGAATAACTAGGTGATATGTTCTTAATTTTT[G/T]GAACAATCTCCATACTGTTTTCCATAGTGACATCA K 2 1 2 1 600010 f 74 goat 6_3644698 6 3644698 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320764618 Affx-986696930 AX-385252260 6 3644719 TGTTCTTAATTTTTGGAACAATCTCCATACTGTTT[C/T]CCATAGTGACATCATCAGCTTTTAGTAGCAACTGG Y 2 1 2 1 600010 r 74 goat 6_3644719 6 3644719 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320762403 Affx-986696934 AX-385250555 6 3646718 CTTCTCATATTCTGTAAAATACCTTTTGTTTTGAG[A/G]TGTTTTCCTTCACTATTCAGAATTTTTTACCTTGA R 2 1 2 1 600010 f 74 goat 6_3646718 6 3646718 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38414852 Affx-122949156 AX-123285201 6 3667906 ATTTGCGCAAGCATTGAGAGACTGAGTGAGAGATG[C/T]GTAGGTGAGTAAGAAAGAAGCATTTGCTCTCAGTA Y 2 1 2 1 101000 f 74 goat snp27457-scaffold2927-2821 6 4613501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476209 Affx-1251763714 AX-586011633 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 4 1 4 1 20000 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 539476463 Affx-1251763714 AX-586011863 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 4 1 4 1 20000 r 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165150 Affx-1251763714 AX-606940562 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165185 Affx-1251763714 AX-606940597 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165210 Affx-1251763714 AX-606940622 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165357 Affx-1251763714 AX-606940768 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165576 Affx-1251763714 AX-606940987 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165713 Affx-1251763714 AX-606941122 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 r 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 320769025 Affx-122973521 AX-385256200 6 3705960 AGGCAGCTCAACATATCTCACGCTTCTTTCTCTCC[A/G]CACTAATTTTGATTGAGTCCACATCTGAGGGGAGG R 2 1 2 1 101000 f 74 goat snp27337-scaffold2900-35134 6 4651684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802736 Affx-122932361 AX-385289635 6 3758186 CTATTTATTAATATTATCATAGCCCTTGACTGTTT[A/G]TAAGATATTTCCACATCTATCATTTTCCTTAATCT R 2 1 2 1 201000 f 74 goat snp27338-scaffold2900-87360 6 4703353 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384192 Affx-122972404 AX-123254550 6 3788964 AGTATCAATTGCATGAAACATGTAGAAGAAAACCT[A/G]CTAGAAATCAAACTATTAATACACAACTGTCTCTG R 2 1 2 1 101000 f 74 goat snp27339-scaffold2900-118138 6 4734499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401137 Affx-122959383 AX-123271490 6 3825336 AATACATACATAGAATCCTTCCACACCCATTTTTT[A/G]TTAGTAACTATTTCTACTTCCTTTATGAGGAGTAA R 2 1 2 1 202000 r 74 goat snp27340-scaffold2900-154510 6 4770790 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433080 Affx-122935734 AX-123303421 6 3858412 GACTCTAGGCTGCCTTTACGCAAACATTTGCCGCT[A/G]TCCTCAAGCTGTACCCTTGGTTCTATTCTGCCTAC R 2 1 2 1 101000 f 74 goat snp27341-scaffold2900-187586 6 4803684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378255 Affx-122976892 AX-123248614 6 3909488 CAGGCAGGCTTTAGCCTGCTAATGAAGAAGGAATT[A/G]GAAAGGAGAAAAAAATTTAAAGTCTACATTAGAAC R 2 1 2 1 101000 f 74 goat snp18704-scaffold189-977811 6 4854791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798522 Affx-122926988 AX-385285455 6 3967403 CTCAATTTGGTATAATCCATCAAATCCATCATATA[C/T]GATTCACAAAACTTTAAATGTAGTTAACATTTTAT Y 2 1 2 1 201000 r 74 goat snp18703-scaffold189-919896 6 4912682 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779230 Affx-122950546 AX-385266334 6 4000730 AAAACTTTGCTTTAAAAGACATACCTTCTCTGTAT[A/G]TACAAATGTATTTTCATGTGGTTTCACTCAGGTGC R 2 1 2 1 101000 r 74 goat snp18702-scaffold189-886569 6 4945869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415902 Affx-122948467 AX-123286251 6 4043062 CTAGAAGAAAACAGTGAATATTTAAATAATTTTTG[C/T]GTAAGGAAAGACTTTCTAAGGATGGCAGAAATCCA Y 2 1 2 1 101000 r 74 goat snp18701-scaffold189-844237 6 4986566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476210 Affx-1251763715 AX-586011634 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 4 1 4 1 20000 f 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 539476464 Affx-1251763715 AX-586011864 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20000 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165173 Affx-1251763715 AX-606940585 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165214 Affx-1251763715 AX-606940626 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165694 Affx-1251763715 AX-606941103 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 f 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165744 Affx-1251763715 AX-606941153 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562166062 Affx-1251763715 AX-606941471 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 38451296 Affx-122921295 AX-123321629 6 4073579 TGTGGTACTTTGTTACAGCAGTACCAGCAAACTCA[C/T]AGAATCGCCTTGTTCATAATGGAGGGAATTATTAT Y 2 1 2 1 201000 r 74 goat snp18700-scaffold189-813720 6 5018034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379236 Affx-122976269 AX-123249595 6 4122008 ATTTCTGAGCGTGCACAGCCAGCTGCACACGATCA[A/G]CACGGTCCCAGGTTCCCACTAACGAGCAGCCTTGC R 2 1 2 1 101000 r 74 goat snp18699-scaffold189-765291 6 5065967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476211 Affx-1251763716 AX-586011635 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 4 1 4 1 20000 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 539476465 Affx-1251763716 AX-586011865 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 4 1 4 1 20000 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165877 Affx-1251763716 AX-606941286 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165966 Affx-1251763716 AX-606941375 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165996 Affx-1251763716 AX-606941405 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166291 Affx-1251763716 AX-606941699 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166392 Affx-1251763716 AX-606941800 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166562 Affx-1251763716 AX-606941970 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 38396401 Affx-122963014 AX-123266756 6 4157344 CTATGGGTTGAATGCTTGTGTCCCCTCAAAATTCC[C/T]AAGTTAAAGCCCTAATCCTCAAGGTGATGATTACA Y 2 1 2 1 201000 r 74 goat snp18698-scaffold189-729955 6 5101236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799258 Affx-122949001 AX-385286188 6 4204662 AAAGGTGATGTCTTCCTCTTACCTGAGGCAAACAC[A/G]ATTGGGAGTTGTGAAATTTATACTGATAACTAGAG R 2 1 2 1 101000 f 74 goat snp18697-scaffold189-682637 6 5147912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387095 Affx-122970679 AX-123257453 6 4270215 AAAATGAGACTGAGAGAGGCTCATTCTTGCCAGCC[A/G]CCTGATTCAACTGAGGTTGTAGAATAGCTTTCACT R 2 1 2 1 201000 r 74 goat snp18695-scaffold189-617084 6 5213448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446525 Affx-122925023 AX-123316861 6 4352051 ATAAGATCCAAGGCTGGAGACTTCCCCTTAGATGA[C/T]GGCGTTTTTCCAGTACTCTAAACCAGCGATTCTCA Y 2 1 2 1 201000 r 74 goat snp18693-scaffold189-535248 6 5295397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444853 Affx-122926295 AX-123315190 6 4440548 GTACATTGCATTAATATACATACATTTCTTTACCT[A/G]TCTTGTTTCTGAGCGAGTGAATTGTTTCTAGCTTT R 2 1 2 1 101000 r 74 goat snp18691-scaffold189-446751 6 5383860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396869 Affx-122963243 AX-123267224 6 4482379 AAGCATGGATCTCATCTTAAAAAGAAAAATCTGTA[C/T]GCCTTGGATCATAGAAACCTTGTTATCTGTTACAC Y 2 1 2 1 101000 r 74 goat snp18690-scaffold189-404920 6 5426581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789039 Affx-122979160 AX-385276052 6 4512913 AGTTTCTCTTAAATGTGTTTCCAAGGTTTTAGAAA[C/T]GGTAGAATCCAACCTATGGAGTACTAAATGCTCTA Y 2 1 2 1 201000 f 74 goat snp18689-scaffold189-374386 6 5456804 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446693 Affx-122924743 AX-123317029 6 4553960 GGAGGGAGAGAAGCACAAGGTTAATAAGCAACTCA[A/G]CCTCTTTTCCTTCTTTCTCTTCTGCTCAGCATCCT R 2 1 2 1 201000 f 74 goat snp18688-scaffold189-333339 6 5498985 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437917 Affx-122931647 AX-123308255 6 4600563 CAGCTGCGTGAGGCGTGGACACTCTGGTGACCTGT[A/G]CTCCCTGAGAACATGGTCACTGACCGTTAGGTAGA R 2 1 2 1 101000 r 74 goat snp18687-scaffold189-286736 6 5545798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410554 Affx-122952147 AX-123280904 6 4632624 TTAGTATTTTATTTAGAAAAAATCGAGGAACAGCT[A/G]TAGCATTTTGAATGGGAAAGAGACAGGGTGAAAGT R 2 1 2 1 101000 r 74 goat snp18686-scaffold189-254675 6 5579277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403332 Affx-122957818 AX-123273685 6 4665216 CATATTCATGAAGAAGAGGTAAGACTGTTTTGCTC[A/G]TAGACCAATGAGAATGTTGCCCCACCCCCCTCAAC R 2 1 2 1 201000 f 74 goat snp18685-scaffold189-222083 6 5612072 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453149 Affx-122919993 AX-123323482 6 4710077 TTGGCAAAGATAGGCACAGCCAGGCCTAGTGTGTG[C/T]AGCCGTTGACAGATAAACAAGGCCCGATGCTGCAG Y 2 1 2 1 101000 r 74 goat snp18684-scaffold189-177222 6 5657270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795444 Affx-122955881 AX-385282400 6 4753317 GCAAAGTAGTTGGTTGTTAGTAAATCATTCTCGAA[C/T]GACTTAAGCTTATATGCCTTTGTGAACTAGCTCTG Y 2 1 2 1 101000 r 74 goat snp18683-scaffold189-133982 6 5701045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438919 Affx-122930427 AX-123309256 6 4799509 GGTCTAAAAACACCTAATCCCTACCTCCCACACCT[A/G]CAGGGTTAGCCAAAGCTGTCAGGAGTCCTACGTTA R 2 1 2 1 101000 f 74 goat snp18682-scaffold189-87790 6 5747165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464411168 Affx-1110472562 AX-515884134 6 4876249 CTTGCTAGCTTTAGTTCTGTCCTTATTGTGTTAAT[A/G]GAGAGAGTGGCTTCCTATCCTTGAGATGCATTCTT R 2 1 2 1 201000 f 74 goat GoatD01.015342 6 4876249 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409757 Affx-122953004 AX-123280108 6 4909464 GTGAAGCCCTGCTCTGGTCACTCCTATAACTTCAA[C/T]AAGCAGCTCAACTTATTCTCTTTTTTAAATATAAT Y 2 1 2 1 101000 f 74 goat snp5510-scaffold1193-22066 6 5905384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779044 Affx-122973435 AX-385266150 6 5065035 ACAGTATGGAATTCGTGTCCTCAAAATGCACTTTT[C/T]GTACATTTTTCTAACATACTCAGGCTTCCCAGGTA Y 2 1 2 1 201000 r 74 goat snp5513-scaffold1193-177637 6 6065820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393089 Affx-122965595 AX-123263446 6 5128896 CCCTACGCCTAAAATACTAATTTACACAGAAATAA[C/T]GGTATTTAGTTCAGTTCAGTTCAGTTACTCAATTG Y 2 1 2 1 303000 f 74 goat snp5514-scaffold1193-241498 6 6131533 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395415 Affx-122963948 AX-123265770 6 5181687 CTGGGAAGCACATCTTTTAATTCTAATTGCTAAAA[C/T]GATAGCCATGTCTATTCTTCCTTTTCATATATTTG Y 2 1 2 1 101000 f 74 goat snp5515-scaffold1193-294289 6 6184536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765969 Affx-122956576 AX-385253393 6 5230594 AGGGTAAAATACCTTTGTGGAATTTGCATCCATTT[C/T]GTTCTTTTTGCTCAGACAGCCAGGGTGTAATTTAT Y 2 1 2 1 101000 f 74 goat snp5516-scaffold1193-343196 6 6233883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798592 Affx-122960460 AX-385285525 6 5266300 TGGCAAATGATTGAGGTATTAAAAGTCTTAAAACA[G/T]TATGTCACCAATGCGAGTCTCCGTGAGATCACTGT K 2 1 2 1 101000 r 74 goat snp5517-scaffold1193-378902 6 6268947 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273208 Affx-1111833508 AX-519546867 6 5343525 GAAGAACTTTTCTGTGACAAAATGCTGCCCAAGAT[A/C]TCTAAGGCTCCCTTCTCTTTAGACACAGAAGGTAG M 2 1 2 1 101000 f 74 goat 6_5343525_AF-PAKI 6 5343525 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416164 Affx-122948271 AX-123286513 6 5408209 CCTCTTTCCCCATTCACTGCTAGGAACTGGACAGG[C/T]GCTTTAAGACTTTTCTGCTGCTCCTTACATCTGTC Y 2 1 2 1 101000 r 74 goat snp17774-scaffold1844-6278 6 6415772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421412 Affx-122943971 AX-123291759 6 5474004 ATGTAGTTCATATATAAAAGATAGATTCAGAAACT[A/G]TTTCTGTTGACCCACAAGTAAAAACTATCAGAGGC R 2 1 2 1 101000 r 74 goat snp17776-scaffold1844-72073 6 6482275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787206 Affx-122933019 AX-385274232 6 5505913 GGTGAATGTTGGATCCTTGACATTCAGTTCCAGCC[A/G]TAGCCCACATTAACCCCTAGTGGTAGCATTAAAAT R 2 1 2 1 101000 f 74 goat snp17777-scaffold1844-103982 6 6514342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787611 Affx-122936299 AX-385274634 6 5571293 CATCTCAAATAAAACATGCATCTCAAGTAAACAAT[A/G]CATCAGCGTTACCTTTTTCTCTTGAAAAGTTTTGT R 2 1 2 1 101000 r 74 goat snp16164-scaffold170-20288 6 6578637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799486 Affx-122979041 AX-385286416 6 5614926 TTACCTTACCATGCTCACAGTTTCTATTGCCATCA[A/G]TGGAGGCAATAAAAGGCAATAGAAGCAAGCGCAGA R 2 1 2 1 101000 f 74 goat snp16165-scaffold170-63921 6 6622409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793490 Affx-122943896 AX-385280467 6 5662317 ATTTGAAGATCCCTATCACTGGGAACATCTTGTCT[A/G]TAGTCCTCGATTAATGTCAGTTCATCTCAATTCTA R 2 1 2 1 101000 f 74 goat snp16166-scaffold170-111312 6 6670641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278312 Affx-1111836357 AX-519551798 6 5668668 TGACACAGGACAGAGGTTTCCTTAAGATCTGGCAC[A/G]GCTGAAGGTGGGGCTTTCGGCACAGGACAGACATT R 2 1 2 1 201000 f 74 goat Random2.2K-634 6 5668668 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273612 Affx-1111833725 AX-519547225 6 5744939 CATGTATGTACTGATCAGGACTCCACCTAGTACAC[A/G]ACAAAGACTTCTGCAGAGCTCGGTCTGCACACCTC R 2 1 2 1 201000 f 74 goat GoatD01.002544 6 5744939 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404013 Affx-122957188 AX-123274365 6 5753451 TGGTGGAAGCAAAGAAATCTAGGAAGGGGAATCAA[C/T]AGAGTGGGGAGAGAACCCTAAAATCCCAGTTCTCT Y 2 1 2 1 101000 f 74 goat snp16168-scaffold170-202446 6 6762314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443876 Affx-122927504 AX-123314213 6 5795798 CCAAAAAGGAATGACAGCATTGCTTTGATCAATGG[C/T]AGTATGTTAAGCTGAAGAAGACAACTCCAATTTTA Y 2 1 2 1 201000 r 74 goat snp16169-scaffold170-244793 6 6804847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802030 Affx-122950926 AX-385288934 6 5842149 AATGATTGAAAGAGTCAGAGTTGACTTACTCTAAA[C/T]GGAGCTAAACAGCACTATAAGTGACAATTCTTCAT Y 2 1 2 1 101000 f 74 goat snp16170-scaffold170-291144 6 6851981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450439 Affx-122922965 AX-123320773 6 5876124 TTCATAGAATATATTATCTCCCATTCTTTTCTAAA[C/T]GTTGAAGGAACAAAACACAGACAATCATTTCTTCT Y 2 1 2 1 201000 f 74 goat snp16171-scaffold170-325119 6 6884527 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381756 Affx-122974315 AX-123252114 6 5932510 AATCAAGCTGAAACCCTTTAAGAACTGAGGCACAC[G/T]CAAAACCTCTATTGAGATTTCTCTGTGGTGTTTTA K 2 1 2 1 101000 f 74 goat snp16172-scaffold170-381505 6 6940901 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405046 Affx-122956353 AX-123275398 6 5988222 TGGTTAGGACGGTAGATTGTTTTCTGTGTTTTACC[A/G]CTATTGAAAATCATTTTAAAAGGAAAGAAAATGAG R 2 1 2 1 101000 f 74 goat snp16173-scaffold170-437217 6 6995308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398499 Affx-122961562 AX-123268854 6 6018234 GGTCTAAACATGTTCTTATGGTTGGGAGTAAGCAG[C/T]CCACCAGAACTGATTCAAGGAATCTTTAACGTGCC Y 2 1 2 1 101000 f 74 goat snp16174-scaffold170-467229 6 7025074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782039 Affx-122939979 AX-385269117 6 6054516 TTAGCTGCTTGGCTATTTGTCCTCGTCAGCTTCTT[A/C]GGAAGCATGAGTAACAGTCATCGGTAGCTGCACAA M 2 1 2 1 102000 f 74 goat snp16175-scaffold170-503511 6 7061825 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278314 Affx-1111836358 AX-519551800 6 6073225 TTCACTCTTGATTATGGAAGCAAAGAAGGAACCAC[A/G]AATGAAGAATTGAGGTCAAAGCCCCAGCAGCATCC R 2 1 2 1 101000 f 74 goat Random2.2K-635 6 6073225 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385005 Affx-122971877 AX-123255363 6 6085156 AGGATATCTCAACAGAAATCTCAAAAACTGAAAAG[C/T]AAAGGGAACAAAAATTGGGCGGAAAAAAGACTATC Y 2 1 2 1 201000 f 74 goat snp16176-scaffold170-534151 6 7092177 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395099 Affx-122964165 AX-123265454 6 6123549 ACCTAGTATTGGGAAAAATTTAAAAGTCAGCTAAT[A/G]CCAATGTTGGTTAGAATGAGGAGTCATGAGAAACT R 2 1 2 1 101000 r 74 goat snp16177-scaffold170-572544 6 7129135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405055 Affx-122956347 AX-123275407 6 6168905 GTAAAGAATATGGAAAAGCAAGAAGTACCAAATTT[A/C]TTTCTTTTTATCTACCTCATATAGGGCTTAACTTG M 2 1 2 1 101000 r 74 goat snp16178-scaffold170-617900 6 7174988 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378334 Affx-122977336 AX-123248693 6 6201455 ACACTGGGGTCCACTTTGGCTCAGCCAGTAGCTAT[A/G]CAGTGTTGAGTAGGACTCTTAACCCCCAGAGCTTT R 2 1 2 1 101000 r 74 goat snp16179-scaffold170-650450 6 7208182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794083 Affx-122930479 AX-385281050 6 6253918 TCTTTCAATGTAATAAAACTGTCAAACTTGCTGGT[A/G]TCCTTGAAGGTTTAGAAATGATATTTGCTTCATAA R 2 1 2 1 101000 f 74 goat snp11296-scaffold1408-4126 6 7264651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799883 Affx-122942096 AX-385286809 6 6285753 GTGAAAGTAAAGCATAGATCTGTTTTTTGTAAAAG[A/G]GAATTAAAGATATTTAGGAATACTTTTAGTCCTAG R 2 1 2 1 101000 r 74 goat snp11297-scaffold1408-35961 6 7297020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423638 Affx-122942359 AX-123293984 6 6316297 AATTATAATTCTTTCTAAATACTTCAGTGGATTTA[C/T]ATTTTTGCAAGCAGTTTTCACGGGCATTAGGCCTC Y 2 1 2 1 201000 f 74 goat snp11298-scaffold1408-66505 6 7327864 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448014 Affx-122923727 AX-123318350 6 6366163 GAATTGGACATGACTGAAGCGACTTAGCATCATCA[G/T]CAGCAGCAGGGATGGTCTGTAACCATTTACCTTCC K 2 1 2 1 202000 r 74 goat snp11299-scaffold1408-116371 6 7376953 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786578 Affx-122957417 AX-385273610 6 6399744 AAATCTGGTTCATATTTATAGATTTGGCTACTAGA[C/T]TTCTTTCTAGTTTTTCCAGTGTGCTTTTTAATTCA Y 2 1 2 1 201000 r 74 goat snp11300-scaffold1408-149952 6 7410410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767101 Affx-122933736 AX-385254388 6 6435512 AAGTAAAGACATCAGGAACTGTTGGGATGCAGTGA[C/T]AGTCAATACTCAAAACCTCTTATGGTATTTGGAGC Y 2 1 2 1 101000 f 74 goat snp11301-scaffold1408-185720 6 7444281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425080 Affx-122941249 AX-123295426 6 6474976 TCATCGCTACAGCCTCTCAAATCATCCTATCACTA[C/T]AGATTTGCCTTCTCAATCTGCCCTGCTTAGTAGGA Y 2 1 2 1 201000 r 74 goat snp11302-scaffold1408-225184 6 7483684 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798523 Affx-122959942 AX-385285456 6 6506807 GAGCTTTGAAGAGGGATGAAGAGAATAATAAAATG[A/G]ACTTATTGAGAGAGGTACTAAAATCAAAGATAATG R 2 1 2 1 101000 f 74 goat snp11303-scaffold1408-257015 6 7515664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783743 Affx-122969891 AX-385270799 6 6540871 CTGTTAATACTGATTTCATTGAGATCATTGTGTCC[A/G]TTAGATGGGAAATGCAGGTAAAAATGCTTTGAAAA R 2 1 2 1 101000 f 74 goat snp11304-scaffold1408-291079 6 7550758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776194 Affx-122943814 AX-385263322 6 6598573 AAGTGTGCTCCATAGATAAGCACTTAGTTGTGTAT[A/G]TAATCTGTAAGCCCTGAAAGTCACATTGTTTTTCC R 2 1 2 1 101000 f 74 goat snp11305-scaffold1408-348781 6 7606792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409751 Affx-122953009 AX-123280102 6 6631124 TGGATGTGCTACCAGTTCATAGTGTTGAGGCAGTA[A/G]ATGTGATATATAATTGATTCATGAAGCCTTTGCTG R 2 1 2 1 101000 f 74 goat snp11306-scaffold1408-381332 6 7639027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400464 Affx-122961307 AX-123270819 6 6664705 GATCCCTTGTCTCAAACAAGAACGAACTCAGTGCA[A/G]TTTGTGCTTCCTGGTCCCTCTTGGAATCAGGCTGA R 2 1 2 1 101000 f 74 goat snp11307-scaffold1408-414913 6 7672687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272421 Affx-1111834252 AX-519546147 6 6716692 GTTTTGCCACCATTCCCTTGGCCCC[A/G]CGAGAGGTAAGGTCACAAGGCAACCAGTAAAACAT R 2 1 2 1 101000 r 74 goat GoatD01.027587 6 6716692 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432903 Affx-122935324 AX-123303244 6 6718915 AATTCATGGACTCCCAAAGAGTAAGCACAAAAACC[G/T]AAGGATCTCCCAGATCTGGTCTAGGAGTGTTAATC K 2 1 2 1 101000 r 74 goat snp11308-scaffold1408-469123 6 7727335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278316 Affx-1111836359 AX-519551802 6 6751503 CCAGGTATTCCTATAGCAAGCGGTCTAGGGCCACA[A/G]TTAGAGAAGGACTGACTTAAAGGGGACCCACCACG R 2 1 2 1 201000 f 74 goat Random2.2K-636 6 6751503 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278318 Affx-1111836360 AX-519551804 6 6755014 AAGTCTGGTTAGAAACTCGGTTTCCATCCAGAAAA[A/G]AAATAGTTGTTTGTTCTCAAGCCAGACCACTTGAG R 2 1 2 1 201000 f 74 goat Random2.2K-637 6 6755014 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412578 Affx-122951307 AX-123282927 6 6790248 CATTGTAAGTTAACATGGCATGAGCTGTTGCTAAA[G/T]CTACCAGGGTCTCCTTCCACCCAGCATTGCCTCCC K 2 1 2 1 101000 f 74 goat snp46120-scaffold635-31540 6 7955787 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428283 Affx-122939393 AX-123298626 6 6850253 AAGTAAGTTATATACATTTTTGCAAGCATTTTCCC[C/T]ACTCTTTTCATAGTGACTTGTAACTTCTCCCATGG Y 2 1 2 1 101000 r 74 goat snp46122-scaffold635-91545 6 8016126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802068 Affx-122971097 AX-385288972 6 6888531 CTAGCAGCTAATGTATTCAACAGGGCAGATGCAGA[A/C]CATATCCATCGTGGCAGAGGGTTCTATTAGACTGT M 2 1 2 1 101000 f 74 goat snp46123-scaffold635-129823 6 8054263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771318 Affx-122926307 AX-385258476 6 6919777 GCAATGATATTCAAACAAAATGTGAAAAATTTGGG[C/T]TTATGTCCCTTACCTTTAGAAGATAATGGCACAGA Y 2 1 2 1 201000 f 74 goat snp46124-scaffold635-161069 6 8086484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795972 Affx-122960020 AX-385282924 6 6957551 TATCCATTTAAGCAAAAATATTGTGATTTAAGTTC[A/G]TTTTCTATATGAAATAGGAAGACTGCAAAATTCAA R 2 1 2 1 202000 f 74 goat snp46125-scaffold635-198843 6 8125994 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418578 Affx-122946376 AX-123288926 6 6993314 CTACCAAATGCATCAATCCATGGATTTCACTTTTG[C/T]GGCAATCGTCACTGATAGCTTTCTTGCTTCACAGG Y 2 1 2 1 101000 r 74 goat snp46126-scaffold635-234606 6 8162051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451235 Affx-122921952 AX-123321569 6 7042385 CTGAACCCTGCCGAGTTCCCTGGCTAGAACATGCC[A/G]TCACCTTGACCTTGCAGATGAACAAAGCCACTGGT R 2 1 2 1 201000 r 74 goat snp46127-scaffold635-283677 6 8211709 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764631 Affx-986696938 AX-385252273 6 7078329 TTGAGGCTGATAGGAAAAGCTTCAAGGAAGAAAAA[C/T]TGAAGTTATATCTTGAAGAGTAAGTAATACTAACA Y 2 1 2 1 600010 r 74 goat 6_7078329 6 7078329 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38375718 Affx-122978635 AX-123246077 6 7081190 GATGATTTGATGGCTATGTCCATATCCGAAAAGTG[A/C]ATCAAATTGTACACTCTAAGTTTGTACAGCCTCAT M 2 1 2 1 101000 f 74 goat snp46128-scaffold635-322482 6 8244296 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424971 Affx-122941919 AX-123295317 6 7215141 TTATATTTACCTTTTTCTTTGTGGAGTTATGCATT[A/G]TTGAAAAGCAGACTGTACTTGTTTTACGGAATTAA R 2 1 2 1 101000 r 74 goat snp46131-scaffold635-456433 6 8373232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425268 Affx-122940977 AX-123295614 6 7265184 ATTAAGTTTCATATACAGAGTAAACTTATTCATTT[A/G]TAAGGTTAAATCTAAAGTGTACATTTAGGGCAGAA R 2 1 2 1 101000 r 74 goat snp46132-scaffold635-506476 6 8423412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785295 Affx-122963980 AX-385272340 6 7297387 CATCTTTGAAAAATTTTAGACATTCACTCACCTCC[A/G]TTTGTAAATTTCACCTGCAAACTTTTAACCACATT R 2 1 2 1 101000 f 74 goat snp51700-scaffold760-12170 6 8472930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392873 Affx-122965747 AX-123263230 6 7357474 TTTGTTCTTACAGCCTTTAAACATATGTAAGGACA[C/T]GGCAATATACTCCAGTATTCATGCCTGAAAAATTT Y 2 1 2 1 201000 f 74 goat snp51701-scaffold760-72257 6 8533888 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384676 Affx-122972131 AX-123255034 6 7438269 GCTTTAGCTATTGTATCCATCTAGTGAGCAAGTCA[G/T]CAGATCACTGAAACATGCCACTTGTTTGGTTTCCT K 2 1 2 1 202000 r 74 goat snp51703-scaffold760-153052 6 8614338 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403123 Affx-122958118 AX-123273476 6 7508063 TAAAATTTGATTTCCCAACAACTAGCTTGTCTCAT[A/G]TTCACTTCCAGCACATGCACACACATATAGTACTG R 2 1 2 1 201000 f 74 goat snp51705-scaffold760-222846 6 8682586 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777000 Affx-122972447 AX-385264124 6 7565675 GTTGAGACTACTAGCATCTGGTGGTTAAAGGTCCA[G/T]TATGCTAGTCAGCTTTCTACATTGCATAGGACACC K 2 1 2 1 201000 r 74 goat snp51706-scaffold760-280458 6 8741030 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772867 Affx-122924284 AX-385260012 6 7598943 ATCTCAATGCTTTATAGTTTGTCTCAAATATAATC[A/G]TTGGATACTAAATGGTGTAAATATATTTATTACGT R 2 1 2 1 201000 r 74 goat snp51707-scaffold760-313726 6 8772725 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767739 Affx-122957449 AX-385254969 6 7613489 GCAATGGTACTTAAAGCTTCTGGATTTCACTTCTA[C/T]ACATATAATTGTCTATTAATTAAGAATTCTTTATT Y 2 1 2 1 101000 f 74 goat snp19454-scaffold1964-526 6 9268471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278320 Affx-1111836361 AX-519551806 6 7677794 GTGGTAGGAAATCATGGAGACAGTGAATTTTAATC[A/G]TATCTTGAAAACTGAATAGGATTTCAATTTTTAAA R 2 1 2 1 101000 f 74 goat Random2.2K-639 6 7677794 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444255 Affx-122927215 AX-123314592 6 7696943 GAGGAGATCTGTCTTTCCTGTTACAGGGAATATGA[C/T]GAAACCTCATTTTCTAAAATATGTAGTTAGAATTC Y 2 1 2 1 101000 f 74 goat snp19456-scaffold1964-83980 6 9352637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780598 Affx-122974551 AX-385267688 6 7732009 TCTTGCAGTTCTATTACGAATAGTTCTAGGGTTGT[A/G]TCCTCAGAGATTCCCAGCTGAGTTTAATAATGGGC R 2 1 2 1 101000 r 74 goat snp19457-scaffold1964-119046 6 9388916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780535 Affx-122936401 AX-385267626 6 7769818 CAACGACTCCAATTTTAGCGTAGTTTCTAAAAATG[C/T]AACTAATTTGGAATTAATGAAAATTTTCCTTTTAT Y 2 1 2 1 201000 r 74 goat snp19458-scaffold1964-156855 6 9428226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801655 Affx-122974228 AX-385288563 6 7836609 GTTAAACCACCAATCACATATGTAATAAACACTAA[C/T]TATTTTCCAAACATTAAGCTGAACTTGAATGGGGA Y 2 1 2 1 101000 r 74 goat snp19373-scaffold1958-302086 6 9549745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773041 Affx-122935378 AX-385260185 6 7873027 TTTAGTTCAAATCTGAAATACACATTCCGAAAGCA[C/T]GGTAAAATTTCTCAGAGAATGCATACTAAATATAT Y 2 1 2 1 101000 f 74 goat snp19372-scaffold1958-265668 6 9586619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770996 Affx-122932787 AX-385258158 6 7913627 TATGCTCCTTTTCTTAGGAAATTACTTTGTGTGAA[G/T]CTTTCATATTTCAGTAGGCAGATTATATGATTCTT K 2 1 2 1 101000 f 74 goat snp19371-scaffold1958-225068 6 9627998 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273278 Affx-1111833518 AX-519546924 6 7926323 ATTTTTACAAAGTGCAATTAATAGGCAAGGCAAAT[A/G]TAGGATGATAGAAGTTTTCCACAGAAAAAAATAAC R 2 1 2 1 101000 r 74 goat 6_7926323_AF-PAKI 6 7926323 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444610 Affx-122926946 AX-123314947 6 7946652 AATCCACTGATTCCTAGAATGTAGTATTCAGCATT[A/G]CATGAACTGTGAACTTCCAGATGTTCAAGCTGGTT R 2 1 2 1 201000 f 74 goat snp19370-scaffold1958-192043 6 9662177 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783160 Affx-122926017 AX-385270227 6 7976669 TGTATAACTTGAGTAGAAAGACTACTTGTTTGAGA[C/T]AACATGTACACGCAATGACTCATATCCTAGAGAAA Y 2 1 2 1 101000 r 74 goat snp19369-scaffold1958-162026 6 9692160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391137 Affx-122966791 AX-123261494 6 8034538 TATTTTGATCAGGAATATTTCCTATTGCCTTAATT[A/G]CATGCTTAGTCGCTCAATCATGTCCAACTCTTTGC R 2 1 2 1 103000 f 74 goat snp19368-scaffold1958-104157 6 9749336 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772951 Affx-122975422 AX-385260095 6 8077883 ATTAGTTTTATTCCACAATTGTTTTATCTACTTGA[G/T]CACAAAATTCAAACTCTTGATCATATCTTATTTAA K 2 1 2 1 201000 r 74 goat snp19367-scaffold1958-60812 6 9793076 T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432107 Affx-122936458 AX-123302448 6 8110392 CTACATTTTGTTTGTCCATTTCCTTATTGAAGGAC[A/G]CTTAGGTTGCTTCCAGTTTGGGGAAATAATCAATA R 2 1 2 1 303000 f 74 goat snp19366-scaffold1958-28303 6 9825323 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419238 Affx-122945674 AX-123289586 6 8144193 GATTATACAATGAGAAAAAGGCAACCACTGTTCAG[C/T]GTATTCTTGATCATTTTTCTACAAAGAAGTAAGAC Y 2 1 2 1 201000 r 74 goat snp31088-scaffold344-5399 6 9872044 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401618 Affx-122959604 AX-123271971 6 8175997 ATTCATGGGGTCACAAAGAGTCAGACATGACTGAA[C/T]GACTGAACTAACTAAATAAGCTACCATAATTGGCT Y 2 1 2 1 103000 r 74 goat snp31089-scaffold344-37203 NW_017216331.1 8391 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390750 Affx-122967905 AX-123261107 6 8226906 ATGGGCTTAGAACCCTATCACATTTTTATCTCTTT[A/G]CCACTGCATAGCAGATAGCTTCAGAGAAGGTGATG R 2 1 2 1 201000 f 74 goat snp31090-scaffold344-88112 6 9917478 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436310 Affx-122933264 AX-123306649 6 8311658 CCTACAACAGTAGATAGCACTATCTTTTGATTTTG[A/C]TTTAAAATAAGATTTTGACTTCTAGTTTACATTAA M 2 1 2 1 201000 r 74 goat snp31092-scaffold344-172864 6 10000394 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796529 Affx-122919710 AX-385283475 6 8341303 ATACTTCTGGCCATAGAGCAAGAAAATGATCAGCA[C/T]AGACTCCCCAGGGCAATGTTTTAACTATGACTCTC Y 2 1 2 1 101000 f 74 goat snp31093-scaffold344-202509 NW_017204024.1 1975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389658 Affx-122968724 AX-123260016 6 8395647 GTGTACAGCATAGAAGATGAATTCGTCATCCTCCA[C/T]GATGAATGAGGAACCTGAGGCTCTCTCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp31094-scaffold344-256853 6 10083795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438512 Affx-122931208 AX-123308850 6 8456089 CTTAAGATACCATCTAAGTTCTAGTAAATTTAGAC[A/G]TTAGACATCTCTTTTGAAGTCTGTGCTGTAAAATA R 2 1 2 1 101000 f 74 goat snp31095-scaffold344-317295 6 10144986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432512 Affx-122935571 AX-123302853 6 8487885 TTTCAATGCCCAGAACAACCTTATCATCATGACAT[A/G]TTGACATGGGCAGGTGGAAGAGATACAGGCTTTGC R 2 1 2 1 101000 f 74 goat snp31096-scaffold344-349091 6 10177177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774602 Affx-122962786 AX-385261736 6 8521311 ATTGAAGATAGTCTATAGATATTGAATATGCATGA[C/T]GACTTGAAAACTATAAGAAAGGAACATCACTAAGA Y 2 1 2 1 102000 r 74 goat snp31097-scaffold344-382517 6 10211421 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423270 Affx-122942663 AX-123293616 6 8563804 TCTGTCATTTTATGAGTCCTCTGTCTTCTATCAGA[A/G]TTTTAATTACATTGTTTTCATATTCTGATATAATA R 2 1 2 1 201000 r 74 goat snp31098-scaffold344-425010 6 10254371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791579 Affx-122975932 AX-385278570 6 8597302 ATATGATTAGAAATTTAGGTGCTCCAAATATAAAA[G/T]AACTGTGGAAATGTTTGCAGCCATTTATAATTCAG K 2 1 2 1 101000 r 74 goat snp31099-scaffold344-458508 6 10288420 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390975 Affx-122966919 AX-123261332 6 8630635 AGATAAATGAGCTGCACAGGTAGATCAGCTCAGTT[A/C]GGTTCAGTTGACCAGTCGTGTCCGACACTTTGTGA M 2 1 2 1 103000 f 74 goat snp31100-scaffold344-491841 6 10322023 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780959 Affx-122920555 AX-385268046 6 8671058 GACTTCAAAATAATCATTGGGAAAACTTGCCATAC[A/G]TTCACTAGAGTCCAGGGCATATCTGAGTCCATCTG R 2 1 2 1 101000 r 74 goat snp31101-scaffold344-532264 6 10362832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769781 Affx-122967168 AX-385256951 6 8722938 GTTTAGGCCAGCATCTGGATAAAGTAGACAATTCT[A/G]TCAGTGGTTAATATGCCTAGCAGAGATAGACTTAG R 2 1 2 1 101000 f 74 goat snp31102-scaffold344-584144 6 10414687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794522 Affx-122934736 AX-385281485 6 8774561 GAAAGTGACTGAATCCAGATGAATGTCAATTCATT[A/C]GTTTATTCAGAACCTATTTGTTACTCTCCTACTCT M 2 1 2 1 201000 f 74 goat snp31103-scaffold344-635767 6 10467125 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430560 Affx-122937015 AX-123300901 6 8805871 AGTGAAGTCATATTACAATTTTTTAATATATTGAT[A/G]CTGTCAAAATTATCCAGATATAGCAGTTTTGTTCT R 2 1 2 1 101000 r 74 goat snp31104-scaffold344-667077 6 10498408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387096 Affx-122970678 AX-123257454 6 8848750 TGGAATTGTAGGCTAGTATTTTTAATGTACACATC[A/G]TTTAAAAATAATATGTATAAGCATTCATAACCTAG R 2 1 2 1 103000 f 74 goat snp31105-scaffold344-709956 6 10541646 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397489 Affx-122962074 AX-123267844 6 8878779 CTTCCCAAGGGTAAATGAGAACTGCTACCCCTAAT[A/G]TAGAACAGAATACACTTGTTTGACTACCTATAATA R 2 1 2 1 101000 f 74 goat snp31106-scaffold344-739985 6 10572162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765632 Affx-122938417 AX-385253105 6 8912565 TGATTGTTTCAGCATAATCTTACTGCAAACAAAAA[C/T]AGAAGATTTTACCAACTACTCAACCTAACCAAGGC Y 2 1 2 1 201000 f 74 goat snp31107-scaffold344-773771 6 10607407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408848 Affx-122954010 AX-123279199 6 8948836 TATTGGCAAACATCTCTAAGCAATGTTGAAATTAC[A/G]TATTAATAGTAGAAAAATTAGAATTAAAAATAAAT R 2 1 2 1 103000 f 74 goat snp31108-scaffold344-810042 6 10643593 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429461 Affx-122938485 AX-123299803 6 9063008 CCGTGGTCTAGTTGTGGTCTCTGGCTCCCATATTA[C/T]GTCCTGTGCCCTAGGCTGTCTTTGTTGCTAACTCA Y 2 1 2 1 101000 f 74 goat snp31111-scaffold344-924214 6 10759124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793553 Affx-122968412 AX-385280529 6 9108911 ATCACCTCTCAGCCTAAAGGAGGTTTCCAGCCATC[A/G]CTGGCTAACTTTCAAACATCATATTCTTATACCAT R 2 1 2 1 101000 f 74 goat snp31112-scaffold344-970117 6 10805932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424793 Affx-122941391 AX-123295139 6 9202008 ATTTATTGCAGGTGTTTCTGTTTATAGTTTCTCAC[C/T]CTTTTATGAAATGGTATAGAAAAGCCCACTTGAGT Y 2 1 2 1 201000 f 74 goat snp31114-scaffold344-1063214 6 10900756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377630 Affx-122977876 AX-123247989 6 9256535 GCTTAGAAACATAAAAAGGAACACAGTAAATTTCA[C/T]GCATAAATGTAGTTATGGAAATCATATGTTTAAAT Y 2 1 2 1 303000 r 74 goat snp31115-scaffold344-1117741 6 10955166 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377496 Affx-122977493 AX-123247855 6 9289885 GCATATTTCTTTCTTATTGAATTATTATCTTTCTG[C/T]ATCCAGATGACACTTCAAAACCCTCACTATTAAGA Y 2 1 2 1 101000 r 74 goat snp31116-scaffold344-1151091 6 10988896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375534 Affx-122979106 AX-123245893 6 9334892 CATCATGACCTCATCACATATTGATATTTGCCTGC[A/G]CTGTTCCACACTTGTCAAATGCTAACATGCATTTC R 2 1 2 1 101000 r 74 goat snp31117-scaffold344-1196098 6 11034964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785440 Affx-122946328 AX-385272485 6 9382659 AAGCAGGCTGAGTGGTTGAATCAATAGCTGGAGTG[C/T]ACTCAGTAGAGATTTAAAGACGTGAACTAAATCAT Y 2 1 2 1 101000 f 74 goat snp31118-scaffold344-1243865 6 11083495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379808 Affx-122976233 AX-123250166 6 9441703 AACCACAGATATATTTTATAATCCTTTTTTCAGCC[A/G]TTCATCTAAAAATTGCCAATCACTCCAGCTTGGTT R 2 1 2 1 101000 r 74 goat snp31119-scaffold344-1302909 6 11137061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387430 Affx-122970391 AX-123257788 6 9492360 GTGTATTAATTGGAAACAATGTCACATAGGAAAAA[C/T]AGCTCCTTCGGTTTTCTTCCTTCTCTGATCCTAGC Y 2 1 2 1 201000 f 74 goat snp31120-scaffold344-1353566 6 11187013 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800657 Affx-122959783 AX-385287576 6 9521662 TAGAAAAAGTTGACTATTTAATTATATAAAGTCTC[C/T]AGTTTTAATGACTTCACAGCAATTTGCAAATTATA Y 2 1 2 1 101000 f 74 goat snp31121-scaffold344-1382868 6 11215972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415142 Affx-122949416 AX-123285491 6 9613372 ACTGACTTGTTGAGTGCTAGTTTATTCAGCTGTCC[A/G]TACTGGGTGAGTCACTACAGCTGTTCATTCAACTG R 2 1 2 1 101000 r 74 goat snp31123-scaffold344-1474578 6 11307853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769802 Affx-122940860 AX-385256972 6 9657796 AGGCACAAAAGTTAGTTCTAGTAAACAGGATGGGA[C/T]AGAAGCAGAGTGGTACGTGCAATTTCTCATTTACA Y 2 1 2 1 101000 f 74 goat snp31124-scaffold344-1519002 6 11360536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383221 Affx-122972769 AX-123253579 6 9705253 TGACATTCATATTAAAGAGTTTTGAACCGTAGAAG[C/T]GATGGGTGGCTGAGAAGCTCTACCAGCAAGAAAGG Y 2 1 2 1 201000 f 74 goat snp21377-scaffold2085-181875 6 11547361 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447159 Affx-122924437 AX-123317495 6 9752966 TTTCACTACTGTTGACCCATTCTCCTTGAATATGC[A/G]CTATCCTTAGGGATTACCTGAAATAGGCGAGATTT R 2 1 2 1 201000 r 74 goat snp21376-scaffold2085-134162 6 11595263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391249 Affx-122967378 AX-123261606 6 9828863 TATATTGTTGATGTTTAACTTCTTCTTCCTTCTTG[C/T]AAACTACTCCCCTCCGCATAATTTATTGACTGTTC Y 2 1 2 1 101000 r 74 goat snp21374-scaffold2085-58265 6 11671730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800704 Affx-122965385 AX-385287621 6 9870085 ATAATAAAGAGTGACTCCGCTTTTTTGATGTGTGA[C/T]GGTTGACAGTTTCTAAGCCCGCCTTTCTCTTTCTC Y 2 1 2 1 101000 f 74 goat snp21373-scaffold2085-17043 6 11713793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418725 Affx-122946277 AX-123289073 6 9888228 GACCACCAGGCTTGTGGTCAGACAGAGTCCTGGCA[A/G]TAGAATGAGGGTTGCTGTCAGCAAGCAGTGGGTGA R 2 1 2 1 101000 r 74 goat snp30882-scaffold340-3646604 6 11733550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476213 Affx-1251763718 AX-586011637 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 4 1 4 1 20000 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 539476467 Affx-1251763718 AX-586011867 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 4 1 4 1 20000 r 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562165396 Affx-1251763718 AX-606940807 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562165466 Affx-1251763718 AX-606940877 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 r 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562166125 Affx-1251763718 AX-606941533 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 38432794 Affx-122935415 AX-123303135 6 9937793 TATGGAGAGTATGTTGTAGACGAAAGCATGCCAGA[C/T]AAGAAGGGGAGTAAATGAAAGCCCTTTGTAGTCAG Y 2 1 2 1 101000 f 74 goat snp30881-scaffold340-3597039 6 11784174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403437 Affx-122957739 AX-123273790 6 9981762 TGCCCCAGGGCCTTTGCACTTAACTGTTCACTTGG[A/G]AGAAGTGGTCTTCTCCTAGAGGGCCACATTTCTTA R 2 1 2 1 303000 r 74 goat snp30880-scaffold340-3553070 6 11828141 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377776 Affx-122977335 AX-123248135 6 10035288 TGCCATTGTCAGGAAGGACCCTGTGTTATCACTGC[A/G]TATGTAATGTTGCCTTGAGCTAATTGCTCTTTACA R 2 1 2 1 201000 r 74 goat snp30879-scaffold340-3499544 6 11882255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394647 Affx-122964386 AX-123265002 6 10066724 TTACAGTGTTGTTTCTCAAAGCCCAGTACACAGAA[C/T]GTCTGCATTACTCTCTCTCCTGCAATCGACTGCCA Y 2 1 2 1 101000 f 74 goat snp30878-scaffold340-3468108 6 11914028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450558 Affx-122922468 AX-123320892 6 10114409 GGACCACATTTCTTTAGCATGAAAGTACCTAGATA[C/T]ACATTTTGAGGGCTTATTACCAATGTGAACTTTGT Y 2 1 2 1 101000 f 74 goat snp30877-scaffold340-3420423 6 11961236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435449 Affx-122933469 AX-123305789 6 10150733 GTCATATATGCACATCTGCATGCCTTTTAATTTCC[A/G]TTTATATTTATTAGCAATTTCGGTCAGAATTGAAT R 2 1 2 1 201000 r 74 goat snp30876-scaffold340-3384099 6 11997365 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401322 Affx-122959840 AX-123271675 6 10269756 GTCCAGTTTGCAGCTCAACCTCTCTGACCTGTTCT[A/G]TCATAGTGCTAGGATGGCTGCTGTGCCTCTGAACT R 2 1 2 1 101000 r 74 goat snp30874-scaffold340-3265076 6 12116601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450299 Affx-122922153 AX-123320634 6 10312514 ACCATCCTGGTGTAGCCAGTGTGAAAGGTGGTGGA[C/T]GAAAAGGGATGATTCTAATGAAGAAATTAGTAAAA Y 2 1 2 1 201000 r 74 goat snp30873-scaffold340-3222318 6 12160039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769763 Affx-122953251 AX-385256933 6 10345862 GAATTAAACCATGAGAGATCATACTTTCATTAGTG[C/T]AAAACAGAAATTAGTAGTAAAAGACCAATTTTGGG Y 2 1 2 1 101000 r 74 goat snp30872-scaffold340-3188970 6 12193214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404356 Affx-122956819 AX-123274708 6 10390058 GGCTGCTGCTTTCACAGATGAGGACACTGAGGTCC[A/G]CAGAGATGGCAATCTGCCTGGTCACACAGAACCAG R 2 1 2 1 101000 r 74 goat snp30871-scaffold340-3144774 6 12237490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797363 Affx-122940475 AX-385284302 6 10425954 CACTGTTCTAAATAACTCACAATGAAGACAAAATT[A/G]CTTCACTAGAGAATTACATTTCTTTTTAATCTCCA R 2 1 2 1 201000 r 74 goat snp30870-scaffold340-3108878 6 12273239 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411955 Affx-122951141 AX-123282305 6 10461641 TTAAGTCCTTTTCAAAAATGTACTGAGCAGATGCA[C/T]TGCTTTTCTGATAATATCCCTTGGAGAACAGAATA Y 2 1 2 1 101000 f 74 goat snp30869-scaffold340-3073191 6 12309347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440075 Affx-122929732 AX-123310412 6 10492869 TCCAGTAATAGAATGCACTGATAAGGGCCGTTCAA[C/T]AATGCTTATTTAGGCAAATTTTACTTGCATATTTA Y 2 1 2 1 101000 f 74 goat snp30868-scaffold340-3041963 6 12340047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272329 Affx-1111833488 AX-519546064 6 10513422 CACATTTAAGTTTTTTACATATGAAATGGTCAGTC[A/G]GATAGCATCACTGACTCAATGGACATGACTTTGGG R 2 1 2 1 201000 f 74 goat 6_10513422_AF-PAKI 6 10513422 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448706 Affx-122923856 AX-123319042 6 10541956 GGGCCATCCACGGCACAGCCCACACTCGGCATCAC[G/T]ACACAGTACAGCTTTTCCAGTCATCACACTGTCCA K 2 1 2 1 101000 r 74 goat snp30867-scaffold340-2992876 6 12389096 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800442 Affx-122921186 AX-385287363 6 10579073 AAAGCAGTATTAAGTAAATCCTGTGGCAGTTAATA[C/T]GTTAGAAAGCAAACTCAGAATAATTAGAATTGCAA Y 2 1 2 1 101000 r 74 goat snp30866-scaffold340-2955759 6 12426264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408351 Affx-122953743 AX-123278702 6 10616587 TCAAATAGCTAACTTATAGACCCACATTCTTTGCA[C/T]GATAATCCTCCATGCCCTATTTATTTGAAAGTTTT Y 2 1 2 1 101000 f 74 goat snp30865-scaffold340-2918245 6 12463407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401376 Affx-122959233 AX-123271729 6 10666512 AAAAATTTGCCACTCAGTTTGTGGAAAGTGTGATT[A/G]CCAGACAACCTGATAACCTCTCAGCTCCTTCAAAG R 2 1 2 1 101000 f 74 goat snp30864-scaffold340-2868320 6 12513254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446014 Affx-122925863 AX-123316351 6 10698272 GCTCTGCTTTGTGTGTTATCAAGAAGGAATCTACC[A/G]CCAGAGGAAATTCTACGGGGTATCTCTTTTTCAGG R 2 1 2 1 201000 f 74 goat snp30863-scaffold340-2836560 6 12544858 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447518 Affx-122924065 AX-123317854 6 10748673 GCAGTAATGACATCCACAGCCTCCCTCTGAGAGAA[C/T]GAACAGCAAGAGCAAGATTTAGCATCTCCAGCTCC Y 2 1 2 1 201000 r 74 goat snp30862-scaffold340-2786159 6 12596533 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448436 Affx-122923654 AX-123318772 6 10798863 CATACCTAGCCGGAGAGAGCAAGAGAGGGCGCACA[C/T]GAGGGAGAATGGTGTACTGCCTCCACATTATGACC Y 2 1 2 1 101000 r 74 goat snp30861-scaffold340-2735969 6 12646821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784465 Affx-122931148 AX-385271514 6 10829359 TATCCATTGTGAATGCTAATTAGAATGCTAATTGG[C/T]GAAAATATAATATTAGTTACCATTTGGAGTCTGTT Y 2 1 2 1 101000 f 74 goat snp30860-scaffold340-2705473 6 12677116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392977 Affx-122965671 AX-123263334 6 10892947 AACACATGACTATGAAATTATGCTGCTCTGTCTTT[A/G]TTCAAACAGTGATAACTCATAAAACTCACTATTCT R 2 1 2 1 101000 r 74 goat snp30859-scaffold340-2641885 6 12741165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430051 Affx-122937561 AX-123300392 6 10921784 CCAGCTTGTCTTTGAAGACCTTTGTACAGGAATAC[A/G]TATTACCTGTACTGTTCATTCATTCATCACACAGA R 2 1 2 1 103000 f 74 goat snp30858-scaffold340-2613048 6 12770304 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278490 Affx-1111836363 AX-519551973 6 10927851 TAATAATAAAAGGACCAATTCATCAACAAAATGGC[A/C]TACTAACCACAACCTGAGTTGTGAAATACACGATG M 2 1 2 1 101000 r 74 goat Random2.2K-643 6 10927851 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413596 Affx-122950570 AX-123283945 6 10952096 TCTGACAGCAATGCAAGCTTCCTCCGTGCCGCCAG[A/G]GCAGGCAACTTAGACAAAGTCGTGGAATATCTGAA R 2 1 2 1 101000 r 74 goat snp30857-scaffold340-2582736 6 12801008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375748 Affx-122978611 AX-123246107 6 10982097 CACTTATTAAAGAAGAAGTTCTAAGAGATACCTTA[C/T]AGAATTTGTCCTGGATCCTTAGGGGAGCTCTATCA Y 2 1 2 1 201000 f 74 goat snp30856-scaffold340-2552735 6 12830983 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402867 Affx-122958235 AX-123273220 6 11035696 GTGGGTAACTGAGAGGTTTGCGTGAAGACAAAGAG[C/T]ATTAGACCTTAAACTGTTGTTTTGGCATGTCCTTT Y 2 1 2 1 101000 f 74 goat snp30855-scaffold340-2499136 6 12884454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448897 Affx-122923183 AX-123319232 6 11096905 GGGAAATTCTCCCCACTCAAATAATGCTATAATGT[A/G]TCAGTATGAGTGTGTATATATGTCAGATTCTGTAA R 2 1 2 1 103000 f 74 goat snp30854-scaffold340-2437927 6 12945770 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397554 Affx-122962022 AX-123267909 6 11141619 AGAGTGTTTTATTCTCCCCATCCCAGGAGAAAACT[A/G]TTGCTCAAAGAAAAGAAAGAGCTCTGAAGGACTTT R 2 1 2 1 202000 r 74 goat snp30853-scaffold340-2393213 6 12989728 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278491 Affx-1111836364 AX-519551974 6 11149962 TCTGCATTGCAGGCAGATTCTTTACAATTTGAGCT[A/C]CAAGGAAGACCTACTTTTTGACATAAGTTCAAGGA M 2 1 2 1 201000 r 74 goat Random2.2K-644 6 11149962 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801729 Affx-122964522 AX-385288637 6 11171501 AAATATATTCTCTACAGATAATTTAGAAATATCCT[C/T]AGTTGATCTCTTCATGAAGTAAGAGATCTCTTCAT Y 2 1 2 1 201000 f 74 goat snp30852-scaffold340-2363331 6 13020321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275051 Affx-1111834565 AX-519548633 6 11193164 GTGAGTGACCCACCCTGCAGGGTTGCAT[A/G]GTCATTGGGCATGCTGGGCTCAGAGATATGTTTTA R 2 1 2 1 102000 r 74 goat GoatD01.041763 6 11193164 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392333 Affx-122966688 AX-123262690 6 11210940 GTAAGGCTTTGCATATTTAATTCTCTTTCCAGGCC[A/G]TTTTATAACTTTGTAGAGGTAGAAGTTAATTTGTA R 2 1 2 1 201000 r 74 goat snp30851-scaffold340-2323892 6 13060434 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438496 Affx-122931221 AX-123308834 6 11253242 CATGTACTTTTTTTTTGAGACCTTATCATGTTCCA[C/T]GTACTTTTCCAGCATAATCTTATCTTTGCATCATA Y 2 1 2 1 101000 r 74 goat snp30850-scaffold340-2281590 6 13102291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388170 Affx-122969443 AX-123258528 6 11284353 GTTTTTGTTTTATTTATTTATTTATTTTTGAGAAC[A/G]TATCATTGGCTTGTGTTATATAGAATGCAGCCTTG R 2 1 2 1 101000 r 74 goat snp30849-scaffold340-2250479 6 13133655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278493 Affx-1111836365 AX-519551976 6 11308338 CAATAAGAGGAAGAAATGGACTCATTATGTCTTAT[A/G]AAGTAGTCTATATGAGGGTTACTGGTACCTTTACG R 2 1 2 1 101000 r 74 goat Random2.2K-645 6 11308338 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450528 Affx-122922491 AX-123320862 6 11315450 AAACAGGAGATGTAGAATTCTGTTTACAAGGCCTC[A/G]TCTAGCAAGGGAGGTTGGGAGCTGTAGTCTGCTCA R 2 1 2 1 201000 f 74 goat snp30848-scaffold340-2219382 6 13164696 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448749 Affx-122923321 AX-123319085 6 11346351 TATATATGTGTCCCTAACAGTAGATGGAATTGTCT[C/T]TCATGTTTTAAAAGTTCATATAAATGATATCATAT Y 2 1 2 1 101000 f 74 goat snp30847-scaffold340-2188481 6 13195756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387886 Affx-122969623 AX-123258244 6 11376428 TAGAGGGGGGGGCATGCCAGCAAATTGTCAGATTT[C/T]AGTTCCCCAACCAGGGATTGAACCTGGCTCATGGC Y 2 1 2 1 103000 f 74 goat snp30846-scaffold340-2158404 6 13225850 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778137 Affx-122955934 AX-385265252 6 11420217 CACTTTTCCTTTATAATAGATGGTAGCTTGCCAAC[C/T]GCTTAGTATTAAAAATCAAACTCCAGGAAATGCAA Y 2 1 2 1 101000 f 74 goat snp30845-scaffold340-2114615 6 13269233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437207 Affx-122932045 AX-123307545 6 11451766 TTGTTTCTGTTACAGTTATAGCAATTTTCACAATG[C/T]GGCCTCCAAACTTGTAACAGATCAGAATGGTGTTA Y 2 1 2 1 201000 f 74 goat snp30844-scaffold340-2083066 6 13301964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785094 Affx-122949137 AX-385272142 6 11491575 GTTAAAAAAGAAGCTCCAGAAGTTTGTAAAGAAAG[C/T]AAAGGTATTTCTGACTTTATGTTTAGGATTAGATA Y 2 1 2 1 101000 f 74 goat snp30843-scaffold340-2043257 6 13342058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278495 Affx-1111836366 AX-519551978 6 11559350 CAAAAAATGGATGATCATTTTTATTATTTTTTGCG[A/G]TCACAGGATTATAGCTGTTATCTAATGAGAAAAAA R 2 1 2 1 101000 r 74 goat Random2.2K-646 6 11559350 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383969 Affx-122972939 AX-123254327 6 11560452 AGGAATTCAAAGGCTTGCAGTGATATTTGGATTGT[A/G]TTTTTCCTTTACTTTATAATCAAATCATACTAATA R 2 1 2 1 303000 r 74 goat snp30841-scaffold340-1974380 6 13410795 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424190 Affx-122942516 AX-123294536 6 11647114 GAAGAAAGGTGAAATAAATCACTGTCAAGAACAGA[C/T]TTTGTTCCAAAGAACAAAAATAGTCTCTACAAGAA Y 2 1 2 1 303000 r 74 goat snp30840-scaffold340-1887718 6 13498678 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442370 Affx-122928020 AX-123312707 6 11733391 AAGCAGTTACTGACCCATGATGTTCCCTAACATAC[A/G]CACTCACCTTTCTTAGGAATATATGAAATGATTAC R 2 1 2 1 101000 f 74 goat snp30838-scaffold340-1801441 6 13585034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437228 Affx-122932030 AX-123307566 6 11776663 TCAGTTCTGGGCTGGTGGTAGCTCCCTGTAGTACC[G/T]ACATCTTTTAGACTTTCGAGTTTCCTTCTAGAATT K 2 1 2 1 201000 r 74 goat snp30837-scaffold340-1758169 6 13628666 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278332 Affx-1111836367 AX-519551818 6 11809176 CACACTGATGCAAAGCACTTAAAGCAGTCTGGTGC[A/G]AAGGTACTTAATAATTTTTAGTGTAATTATTACAC R 2 1 2 1 101000 f 74 goat Random2.2K-647 6 11809176 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382925 Affx-122973389 AX-123253283 6 11825896 TTTTCTTCTCCTTCAGATTGCCCAGATTAAGAAAT[A/G]CTTCAGTAAGGTGGCAGATTTTTAGTAATTATTTT R 2 1 2 1 101000 f 74 goat snp30836-scaffold340-1708936 6 13678156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403629 Affx-122957541 AX-123273981 6 11857813 CTTATTATCATAAGATACTGCTAGAGAGGTTTACT[A/G]AACCTTTCATATATTTACTGAGCATCTGCATTTTC R 2 1 2 1 201000 f 74 goat snp30835-scaffold340-1677019 6 13710175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789957 Affx-122930699 AX-385276963 6 11891602 TTTGACAAAAGCTTTGTGCATAAATGTGCTCAATG[G/T]AAGTACTATACCTGTTTGCTTACCAGCCTGGAAGT K 2 1 2 1 101000 r 74 goat snp30834-scaffold340-1643230 6 13743803 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775832 Affx-122962088 AX-385262963 6 11926434 TAGGGAAGAAGAAGGCTAATTCTGATCATTCATTC[A/G]TCCTATCTCATATTTACGTTTCTTTTCTTCTCCAG R 2 1 2 1 101000 f 74 goat snp30833-scaffold340-1608398 6 13777942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801528 Affx-122932357 AX-385288437 6 11957800 AAGGATTCTAACAAATATTTGCACACCAAAGTTCA[C/T]AGCAGCATAATTCATAACAGTCAAAAGGTAGAACA Y 2 1 2 1 103000 r 74 goat snp30832-scaffold340-1577032 6 13809798 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782280 Affx-122960245 AX-385269358 6 11987875 AGCAGTTTTATTTCACAGGGTTTTTGCTCTGGGGG[C/T]ACTTGAATAGTATCAGGACTCTAATATTTAGTGTT Y 2 1 2 1 101000 f 74 goat snp30831-scaffold340-1546957 6 13840009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394585 Affx-122964436 AX-123264940 6 12017011 ATTCTCTCCTATGCTAATCATGTGAACTGCCATTT[A/G]GCATTGTTAGTAACTGTATCAAGACAAGTTGTTAT R 2 1 2 1 101000 r 74 goat snp30830-scaffold340-1517821 6 13868975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771123 Affx-122960157 AX-385258283 6 12049918 CCTACTAAAGTGAAAGTTTCTTATATCAGTGATTA[C/T]ATATTAGTCACCACTGTGTTCTCAGCAATCAATAC Y 2 1 2 1 101000 r 74 goat snp30829-scaffold340-1484914 6 13901585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420316 Affx-122945018 AX-123290663 6 12121843 TGTGGGCGATGAATTCCGCATTCGAACCCAGGTCT[A/C]GAGGCGGGCTTTGGGGGCGAGGGGCCGCGTTCCTA M 2 1 2 1 103000 f 74 goat snp30828-scaffold340-1412989 6 13973493 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420568 Affx-122945276 AX-123290915 6 12160387 CTAAAGCGGTTGAGCCTGAAGCCCCAGGGACCCAG[C/T]AGCAGCAGCAGAGATGATACACATGATACCAGCCT Y 2 1 2 1 101000 r 74 goat snp30827-scaffold340-1374445 6 14012807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793783 Affx-122967242 AX-385280755 6 12264321 GACTACAAGTAAATGGCAAGGGCTTTGACTCTAAG[C/T]GGATCTTCCTTCAAACCCTGTTCTGTCACATACTA Y 2 1 2 1 101000 f 74 goat snp30825-scaffold340-1270511 6 14116546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447695 Affx-122924619 AX-123318031 6 12293091 CAAGAATGTTAAACTCATGAGCCAGTTTTATTCTA[C/T]GCTACTCAATAAGTAAATATTGCACTAATGCTGCT Y 2 1 2 1 201000 f 74 goat snp30824-scaffold340-1241741 6 14145434 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412573 Affx-122951312 AX-123282922 6 12325594 CTCCAATATTATCAATAGAAAAACCAAAATTCTTC[A/G]CCTTAATACTAAGACATCCCTTTCATCTGATCCCA R 2 1 2 1 101000 r 74 goat snp30823-scaffold340-1209238 6 14178198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393998 Affx-122965027 AX-123264353 6 12402233 TTTACTGGCCAGATTGCATAAGGCTAAGTTATGGG[A/C]GCTCTAAAATAAAATAGACAGGAACATCAAGAAAT M 2 1 2 1 101000 f 74 goat snp30822-scaffold340-1132599 6 14254732 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774038 Affx-122928697 AX-385261176 6 12457921 TAGCACCATGCAAACAAGCCTATTTAAACATCTAA[C/T]ACGTTGCACTGTGGTACTATGTGTACTAGTATAGT Y 2 1 2 1 101000 r 74 goat snp30821-scaffold340-1076911 6 14310591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278334 Affx-1111836368 AX-519551820 6 12470889 AGGAAGTCAGGCTGAAATTTAGAACTCACAAAGTG[A/G]GTAATTCCAGAGGATAATTGAAAGTTGACTGTAGT R 2 1 2 1 101000 f 74 goat Random2.2K-648 6 12470889 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779427 Affx-122960637 AX-385266530 6 12506281 CTTGTCTTTATGTGTCTAAACTACTATATCTATGA[C/T]GAAAGGGACACATTTTTATTGCTGTATCTCCAACC Y 2 1 2 1 101000 r 74 goat snp30820-scaffold340-1028551 6 14358997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400814 Affx-122959808 AX-123271169 6 12552612 GCACCCACTTGATAAATAAGAACACATGCATTCAT[A/G]TTTTAGAATCATTTTGCAGCCCACAGAGCAAAACT R 2 1 2 1 101000 r 74 goat snp30819-scaffold340-982220 6 14405578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783935 Affx-122955158 AX-385270989 6 12581283 AGATGATAAATGTTAGCAGATCTATTATATTTAGA[C/T]TAACCAAACTAATTCAAGTTGATCAATGGAAGAAA Y 2 1 2 1 101000 r 74 goat snp30818-scaffold340-953549 6 14434277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393715 Affx-122965240 AX-123264070 6 12616734 GACTTTTCTATGAATTGCACTCTGAATTACAACTT[A/G]TCACAAAATTGTATTTTAATAATATTATAATATCA R 2 1 2 1 101000 f 74 goat snp30817-scaffold340-918098 6 14469982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410448 Affx-122952387 AX-123280798 6 12654988 AATCATTGTAATAAACTGCTATTTGATGAACCTAC[A/G]TCACTTTTGATCTGATACAAACAGTTCAGCTCCTG R 2 1 2 1 101000 f 74 goat snp30816-scaffold340-879844 6 14508198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785109 Affx-122929634 AX-385272155 6 12710384 ATAGGTTTCTGTCTGTCCTCTAATTATAGACTGCT[A/G]TCAACTGGTATTTAATTTTTCCAGTGTGCTTCTCT R 2 1 2 1 201000 r 74 goat snp30815-scaffold340-824448 6 14563391 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392679 Affx-122966422 AX-123263036 6 12759842 AATGTGATCAGAACTATTGAGCAGAAATATAGATA[C/T]CCAAGCCTTTTCCATAATCTGAGACATACTGATAA Y 2 1 2 1 101000 f 74 goat snp30814-scaffold340-774990 6 14613402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446165 Affx-122925747 AX-123316501 6 12795147 CCCCCACAAAAAAGAAACCTATATGACCCTGAAAA[G/T]CCTTCTGAATCGTTTGAGTAAAGTAAAATTTTGTT K 2 1 2 1 101000 f 74 goat snp30813-scaffold340-739685 6 14648765 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409685 Affx-122953062 AX-123280036 6 12845505 AACTGACTTATTTCTTTTGATAAGGAAGACAATTG[A/C]GAAAAAGTGTTTTTGACTTAGCTACTCATACATAC M 2 1 2 1 101000 r 74 goat snp30812-scaffold340-689327 6 14699890 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790962 Affx-122935453 AX-385277959 6 12878262 CGGAGTCACTCACGTCTTTCAGTAACTAGTGGCAG[C/T]ACTGGTGATGAAAATTCACCCACCATGGGACTATG Y 2 1 2 1 101000 r 74 goat snp30811-scaffold340-656570 6 14732934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779755 Affx-122925275 AX-385266855 6 12933674 GAGAAGCTCATCAGTGTGAAAGCCTGATCACCTTC[A/G]TGTAAAATGTGATCCTCTATGTCTGGTGAAAATAT R 2 1 2 1 101000 f 74 goat snp30810-scaffold340-601158 6 14788563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780195 Affx-122969089 AX-385267291 6 12973831 GGATATGATTTGTGTAAATATTTCACCATTTTATA[C/T]GGCCAATCTTAATTTCTTGTAGCACATATTTTTCC Y 2 1 2 1 303000 f 74 goat snp30809-scaffold340-561001 6 14828734 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272246 Affx-1111833494 AX-519545989 6 13015198 CCGTAGGATGGCACAGGTGATGCAGACAGTCTTCC[A/G]TAAATGTAATTCCCTCCATAAAACTTCCGTATGAG R 2 1 2 1 101000 r 74 goat 6_13015198_AF-PAKI 6 13015198 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38400290 Affx-122960081 AX-123270645 6 13045662 AATTATTCTGATCTTGAAAATTAAGGATGAGAATC[A/G]TGTTTTGTTTGTTGTTGAATCCTAGCACTTACTTT R 2 1 2 1 201000 f 74 goat snp30808-scaffold340-489170 6 14900689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380834 Affx-122975067 AX-123251192 6 13085229 ATCTTAGCAGTTCTTTGTGCGTCTGTGGTGTCTCC[C/T]GAGTGCCTGGTATCCTGCAGGCATTCTATTCATAA Y 2 1 2 1 201000 f 74 goat snp30807-scaffold340-449603 6 14938224 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408024 Affx-122954299 AX-123278375 6 13135455 ATTAATGAAATGCATAGATAAAATAAAGATGAGTG[C/T]ACTTCTAGGTTCCCTGTGCAAGATCGCAGAATTAT Y 2 1 2 1 101000 r 74 goat snp30806-scaffold340-399377 6 14988387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277621 Affx-1111835941 AX-519551120 6 13150743 AGTTGTCAGAGACCTGGCTTGCAAACAGATCTGGA[A/G]TTCTCTTGAATCCGAAGGAAACTGATGAATAAAGG R 2 1 2 1 101000 r 74 goat Random2.2K-649 6 13150743 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781236 Affx-122930389 AX-385268321 6 13173300 TAATTGGTCTGAGAGAGTGTGGACCCAGAAATATC[A/G]TTCCATGAATCTGTGACACTGTCTTAATGAACTGA R 2 1 2 1 101000 f 74 goat snp30805-scaffold340-361532 6 15026429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392910 Affx-122965720 AX-123263267 6 13254220 AAGTACTAAATATTAAATGAGAAATTATTACATCA[C/T]AGTCACTTATAATTTTTACACAAAGTAGTTTTGAA Y 2 1 2 1 101000 r 74 goat snp30803-scaffold340-280612 6 15107279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436081 Affx-122932690 AX-123306420 6 13284643 TTGGCTGTTCTAAATTTTCTCCCAGTCCAGGTCTT[A/G]TTTCCAAATTTATTCAGGAGGTCTGATCCTACCTC R 2 1 2 1 101000 r 74 goat snp30802-scaffold340-250189 6 15137588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388759 Affx-122968945 AX-123259117 6 13375737 CTATGGAGGATACAGGAAAAGAAACATTCTCCAAA[C/T]GAGTAGTAGTATTCTCTGTAAAGGGGTAGTCCAAA Y 2 1 2 1 101000 f 74 goat snp30800-scaffold340-159095 6 15228960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780172 Affx-122925725 AX-385267269 6 13404668 GAGCATGAGACATTTTAAGGGATGATGGTGGTAGT[A/G]TCATTTCAATGTAATTTCTAAAATGTTTCGTTTCC R 2 1 2 1 201000 r 74 goat snp30799-scaffold340-130164 6 15258535 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407414 Affx-122955237 AX-123277765 6 13454831 CTTCTCTTTTTTTCCTGTGTGTTTATAATTTGGAA[C/T]CGTTTAAGGTAGCATTTCTCAGAGTATGGAATACA Y 2 1 2 1 101000 r 74 goat snp30798-scaffold340-80001 6 15308985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387751 Affx-122969730 AX-123258109 6 13492644 TGGACCTTATTTTCATAAGAAGCAAAAGCTGTAAG[C/T]CATTGGAAGAAGGACAGCAGTCCTTCTCAGCCCTT Y 2 1 2 1 101000 f 74 goat snp30797-scaffold340-42188 6 15347345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378370 Affx-122976817 AX-123248729 6 13523916 ATAATTTGTGGTGCTACATTCCTTCTGGCTTTATA[C/T]GAACAACTTCTGAAATTATAATGGAAAGTGGTTGA Y 2 1 2 1 201000 f 74 goat snp30796-scaffold340-10916 6 15379583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398383 Affx-122961651 AX-123268738 6 13563202 CAGTGATCTCTCCCAGTCCCGAGGCATTGAATACC[A/G]TCTATAAACTGATGACTCTCCAAAGTATGTTTCTA R 2 1 2 1 101000 r 74 goat snp40297-scaffold5140-28271 6 15418511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453731 Affx-122919622 AX-123324064 6 13592048 ATTATTATTACTTATATGTTTATTTTATTTCCACC[A/G]TACTTTTCCTGATTTCTACTCACCCTGCTTTTTCT R 2 1 2 1 101000 r 74 goat snp40298-scaffold5140-57117 6 15448067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796871 Affx-122923760 AX-385283814 6 13604730 TGGATCAGTTTTTCCATGAATCCTGGTCTTAAATT[C/T]GGAATCTTAAAACAGATGTAGAGACTTGCAGAAAA Y 2 1 2 1 201000 f 74 goat snp18671-scaffold1887-1655 6 15460688 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764606 Affx-122942632 AX-385252249 6 13644975 AAAATCCAGGAAGAAAGGCATTCTGGCTTGCATCA[C/T]ATAAAATCTGAAAACTCTACAAATACTAAGTAAAG Y 2 1 2 1 101000 f 74 goat snp18672-scaffold1887-41900 6 15501584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417075 Affx-122947503 AX-123287423 6 13699662 TTCTCTCACAAACCTCTCACTAATCCTGGGCTCTG[A/G]CCTTGCTGCAAGGAAACCCCGGAGGGCCTGGCCTT R 2 1 2 1 101000 f 74 goat snp18673-scaffold1887-96587 6 15556296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426912 Affx-122940448 AX-123297257 6 13752968 TGTCTTCATTTTGAGAACCCTCAGGCCACCTCCTC[C/T]CTTGTCCAAACTGTTCGTGCAGTAACTCAGTTTAT Y 2 1 2 1 101000 r 74 goat snp18674-scaffold1887-149893 6 15609221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376565 Affx-122979084 AX-123246924 6 13784538 TGTAGGCTCAGCGGAAGTGCTATATCCATTTTTGC[A/G]TACTACCTTCCACAGCAGCAAATCAGTCCCCAATT R 2 1 2 1 101000 f 74 goat snp18675-scaffold1887-181463 6 15640971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783906 Affx-122919873 AX-385270961 6 13856347 ATATCCATCTCTCCACTTTTCATGTCAAAACTTAC[A/G]CATTTCTTCCAATCTGTCTTCTTTCCAAGCTTTTC R 2 1 2 1 101000 r 74 goat snp18676-scaffold1887-253272 6 15714153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778067 Affx-122931770 AX-385265183 6 13902634 GAATGGTTATTTAGATATTTTCATACCAAATTATT[C/T]GTATTTGTGAACGTATTTAATAAGAAGTTGCATTG Y 2 1 2 1 201000 f 74 goat snp18677-scaffold1887-299559 6 15760232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772725 Affx-122954571 AX-385259871 6 13956997 AAACATAGGAAAGAATACATTAGAGATTTAAATAC[A/G]TAGTGGCTTGTTTTTGCTACTGTTTAAATGACCAC R 2 1 2 1 101000 r 74 goat snp18678-scaffold1887-353922 6 15814509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404784 Affx-122956675 AX-123275136 6 13993039 AAGTGCAGTTTCCAAGACCCCAGGCTGCTGAATTC[A/C]TATTTGTAGAACCTAGTAGCCTCCATTTTAACAAC M 2 1 2 1 101000 r 74 goat snp18679-scaffold1887-389964 6 15851910 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407473 Affx-122954772 AX-123277824 6 14024090 CTGGAGCTTGTGAAACGGATGAACTGGTTCATGAA[C/T]GTAAAGAATGCCCTCTTTCTGCTGGTGAGCTGAGG Y 2 1 2 1 102000 r 74 goat snp18680-scaffold1887-421015 6 15882730 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788142 Affx-122965571 AX-385275162 6 14053165 ATTTTCTTACCTTGACTTCATATCCAGTTGTTCTA[A/G]CAAACTTTGACTTTAGATCTAATAATTTTCAATTA R 2 1 2 1 101000 f 74 goat snp17583-scaffold1822-2306 6 15915782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766606 Affx-122947490 AX-385253959 6 14090958 GAAATAAGATGATTTCATGTTGTCCTTTTTAAAGG[C/T]AGGACAGAGTTTAGACAGAAAATTATTATCAAAGT Y 2 1 2 1 101000 f 74 goat snp17584-scaffold1822-40099 6 15954215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395148 Affx-122964123 AX-123265503 6 14127197 GGTGAAGTCTTCACTTAGAAGTATGTTTGTTTTCC[A/G]TAAAATTTAAAATATACATATATGCCCAGAAGGAG R 2 1 2 1 103000 f 74 goat snp17585-scaffold1822-76338 6 15990382 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776241 Affx-122967967 AX-385263369 6 14198094 AAAATTTCTATGGGAGGTGCCTTTCAGATAAGAAC[A/G]TTTACCAATTGTTTGCTCCTTATCTAAGCTAATTA R 2 1 2 1 101000 f 74 goat snp17587-scaffold1822-147235 6 16062071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799931 Affx-122974735 AX-385286857 6 14250043 TTTCTGAAACGAAATTTCAGGTTTATGGTCACATT[A/G]CTGTCAGTCTCTCTAATAAAAATGCACACTCGTAT R 2 1 2 1 201000 r 74 goat snp17588-scaffold1822-199184 6 16114494 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784108 Affx-122978389 AX-385271160 6 14305053 GGAAAACTCCACCTTGCATCATTTCACTAACACAT[A/G]CTGCAGTTGATATTCCTAACAGATAACATATTAAA R 2 1 2 1 101000 f 74 goat snp52911-scaffold795-18975 6 16169314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393146 Affx-122965546 AX-123263503 6 14338814 TGCGATGCGGAGGACGAGGCACCTTGGAAAGATCC[C/T]GGGGTGGATCCCACAGCATGAGGGGCGGGAGGAGC Y 2 1 2 1 101000 f 74 goat snp52912-scaffold795-52736 6 16202958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391823 Affx-122967016 AX-123262180 6 14375460 CACTTTTAAAATAAAGTAGAAGTTGGAGGCAAAAA[C/T]AATGATTGTTGCTATTTCTTGAGCACCTATGAAGC Y 2 1 2 1 202000 f 74 goat snp52913-scaffold795-89382 6 16240035 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397347 Affx-122962297 AX-123267702 6 14405683 TACGTTAATTTCTGATGTGTAAACTTTTATATTTT[A/C]GTTACTGATCTTAAGAAAACAGAGTTTCTCCATCA M 2 1 2 1 202000 f 74 goat snp52914-scaffold795-119605 6 16270771 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441436 Affx-122928814 AX-123311773 6 14436373 CTGCAAGGAAAGGATACATGAATGTTCCTTTGGAG[C/T]AAGTAAACCCGTCAGGATTGGGGACAGAGGAATAG Y 2 1 2 1 101000 f 74 goat snp52915-scaffold795-150295 6 16301985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771764 Affx-122951203 AX-385258921 6 14471222 AGAAATTACACACGTAAAGGAACTAGGGCCTTTAT[A/G]TTCTTGCATAGTTTCCTTCTGTGCATAGTTATTTA R 2 1 2 1 101000 f 74 goat snp52916-scaffold795-185144 6 16337058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442881 Affx-122927659 AX-123313218 6 14513321 ACACATCAGGAATCTGTACAAATGAATTAAAGTCA[C/T]GGAGGTAGTTTTCTGGGGGTAAGATTGGGGTTACT Y 2 1 2 1 303000 f 74 goat snp52917-scaffold795-227243 6 16379349 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391117 Affx-122966804 AX-123261474 6 14557602 CTGTTGGGTGACATCCATTTCCTTGATGTCCTGTA[C/T]GGTCTTGGATGTGATTGTTGAGTGAGTTTTACCTG Y 2 1 2 1 101000 f 74 goat snp52918-scaffold795-271524 6 16423690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776575 Affx-122949900 AX-385263702 6 14594614 CTATGCCACTGAATACCTTTAGCTCATCTTATACG[C/T]TGTAACTAAAAATATGCATACTGTCACACACTCAT Y 2 1 2 1 101000 f 74 goat snp52919-scaffold795-308536 6 16459877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448590 Affx-122923400 AX-123318926 6 14635436 TTGAATTCCCCTCCAGGCAAACCATCCAGGAGCTG[C/T]TGCAGTGGCATATGGCTTGATAGCAGGCAATGTTT Y 2 1 2 1 101000 r 74 goat snp52920-scaffold795-349358 6 16500436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446741 Affx-122925340 AX-123317077 6 14669593 ATTATTAGCAACCTTGACTTCAATTTGGTAATACG[C/T]ATTCATCTTTTAAAAATGTCGGTCCCTAAGGCTGA Y 2 1 2 1 101000 f 74 goat snp52921-scaffold795-383515 6 16534455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442741 Affx-122927845 AX-123313078 6 14701121 CAATTTGTAAATTGGGGAACATCTCATCTAGTAGA[C/T]AGAAAGGGACTCTGAGGAACTGCACAAAATGGAAA Y 2 1 2 1 201000 f 74 goat snp52922-scaffold795-415043 6 16565611 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386435 Affx-122970798 AX-123256793 6 14731837 GGGTGGCACGTCCCTTCTTCCTATTTGACTACCTT[A/C]TGTCCAAACACTTAGTTGTGTGGCTAAATTCCTAA M 2 1 2 1 101000 f 74 goat snp52923-scaffold795-445759 6 16597354 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428522 Affx-122938753 AX-123298864 6 14772125 ACTGAATTTTAACTATGTAACAACTTCTTTGGGGA[A/G]TTTTCAAGCATATTTAAAAGGAAGAGAAAATAGTG R 2 1 2 1 101000 f 74 goat snp52924-scaffold795-486047 6 16637583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412845 Affx-122950454 AX-123283194 6 14814363 ATAATGATATGACAGGCATATATCTGTAATTTTTT[A/C]GCCACATATGGTAATCATAAAAGTTGCAGCTGATG M 2 1 2 1 101000 r 74 goat snp52925-scaffold795-528285 6 16680176 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393732 Affx-122965229 AX-123264087 6 14853214 TTTAAAACTGTCACATATATGCTTATGAAGACTGC[A/G]TATTCTTTCTTTTTCCAAAGGAAGTATGCAATTTC R 2 1 2 1 303000 r 74 goat snp52926-scaffold795-567136 6 16718907 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407726 Affx-122955001 AX-123278077 6 14893863 CTATTTGTATAGATATTCCACTAAATAACCTACTA[C/T]GCCCCTTAAATAAATGTAAAAATCATTTCACTTGA Y 2 1 2 1 101000 f 74 goat snp52927-scaffold795-607785 6 16759520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795349 Affx-122933248 AX-385282305 6 14938062 ACTATTCTTTCTACCCTAAGTAACAACTCTGGTTT[A/G]CTCGGTGACTATCATACAGTAGAGATTTCTGTAAT R 2 1 2 1 101000 f 74 goat snp52928-scaffold795-651984 6 16803224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464424506 Affx-1110475942 AX-515897336 6 14978606 GGGATCAACCTCTGGGGCAGTCACTGCAGATGCTT[C/T]AGTACTGAGAGTCTGGGCTAACACAGGACTCAGTA Y 2 1 2 1 202000 r 74 goat GoatD01.012043 6 14978606 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788782 Affx-122961739 AX-385275797 6 15013908 AAACAGTATAATGCTTGGCACGTGATAAACATGCC[A/G]CAAATGATTACTTTTCCACCTGTGTCCGAGTAGTG R 2 1 2 1 101000 r 74 goat snp52930-scaffold795-727830 6 16880306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393445 Affx-122965856 AX-123263801 6 15059911 ACTCTGTCCTTGGCTTTAGAGAAATGAACCTGTAG[C/T]CTTTGACCCCCTACAGGTAGGCACTGCCAGACTAC Y 2 1 2 1 101000 f 74 goat snp52931-scaffold795-773833 6 16927196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425499 Affx-122941479 AX-123295845 6 15124236 GAGGAAAGCATTTTATTTATCACTATTATTGCTGC[G/T]AAGTTGCTTCAGTCGTTTCCGACTCTGTGCGACCC K 2 1 2 1 101000 f 74 goat snp52933-scaffold795-838158 6 16991272 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602979 Affx-1002479330 AX-413837225 6 15156394 TTCGTCCATGAACTGCATGAAAGGCCCGCTGCACT[G/T]GGAGCATCGAGCAGCAGGGACCAAGCTGTTGGCTG K 2 1 2 1 202000 f 74 goat UniBern-var1 6 15156394 T G 2 neutral Goat_IGGC_65K_v2 candidate gene ou candidate region PITX2 PITX2-variant SNP in PITX2 gene multi-breed 350602981 Affx-1002479331 AX-413837227 6 15156423 TGCACTTGGAGCATCGAGCAGCAGGGACCAAGCTG[G/T]TGGCTGCCTCCTCGTCCTCCTCCTGTCACCATCCT K 2 1 2 1 202000 f 74 goat UniBern-var2 6 15156423 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles PITX2 PITX2-variant SNP in PITX2 gene multi-breed 350603093 Affx-1002479332 AX-413837291 6 15156447 GGACCAAGCTGTTGGCTGCCTCCTCGTCCTCCTCC[C/T]GTCACCATCCTCAGCCGCTGGCCATGGCTTCGGTC Y 2 1 2 1 202000 r 74 goat UniBern-var3 6 15156447 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles PITX2 PITX2-variant SNP in PITX2 gene multi-breed 320801596 Affx-122975172 AX-385288505 6 15162737 TTAAAAAATAAATCTCAGTAGGAGAACTCAGAAGC[A/G]TTTTGGAACACAAATTGGAAGCTACTTATTAAACA R 2 1 2 1 101000 f 74 goat snp52934-scaffold795-876659 6 17029945 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412064 Affx-122951707 AX-123282414 6 15216748 CTGAAGATGATCAAGGGATTGAAGGAAATACTCCC[A/G]CATTCACTACTGCTATAGCAAGCTCCCACTGCTGT R 2 1 2 1 101000 r 74 goat snp52935-scaffold795-930670 6 17083708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796056 Affx-122971452 AX-385283008 6 15263557 GGCTAATCTGGTTATTTTGAAAGTCTGAATTTTCT[C/T]ATAAGATTTCTTAAAGACAGCACAACTGTTGTTTA Y 2 1 2 1 101000 r 74 goat snp52936-scaffold795-977479 6 17130760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445385 Affx-122925400 AX-123315722 6 15305231 AGGGAGAATGTCTATGACCATCCCAAAGACGAAGG[A/G]AGTTAAAAAACATGTTCTGAGCACAGATGACAACG R 2 1 2 1 101000 f 74 goat snp52937-scaffold795-1019153 6 17172602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439875 Affx-122930046 AX-123310212 6 15368104 CCTCACTTCCAAGGACATGCTAATCACTCTGCAGA[C/T]GTTTAGCCTCCTGAACTCCGACAATGGAAACTGCG Y 2 1 2 1 101000 r 74 goat snp52938-scaffold795-1082026 6 17235578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776079 Affx-122972037 AX-385263209 6 15449693 ACCCACAAGGCCAATGAAAAATCTGAATTTAAGTA[C/T]AGTCATCGGGAAGCGGCTCTTCTGTAGACACATGA Y 2 1 2 1 101000 f 74 goat snp52940-scaffold795-1163615 6 17316787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772286 Affx-122938234 AX-385259441 6 15490196 AAGGTACATGACTATCTCAGGTCACAGTACATCGC[A/G]TTAGGACCAGAATCTAAGTGACCAAGACAGGTGGC R 2 1 2 1 101000 r 74 goat snp52941-scaffold795-1204118 6 17357273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426068 Affx-122941090 AX-123296414 6 15548252 GAAGCAACTTAGCAGCAGCAGCAGGATGCTTTCTG[C/T]AACTTCAGCTATCACTGCCGTCACTGGCACTCAGA Y 2 1 2 1 101000 r 74 goat snp52942-scaffold795-1262174 6 17415336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768017 Affx-122943350 AX-385255231 6 15586763 CAAGTGTCAGTCTCAAAGACAGCTATAATCATCCT[A/G]TTAGCAACTGTCTAGGCAGTAGACACATGGCTGCG R 2 1 2 1 101000 f 74 goat snp52943-scaffold795-1300685 6 17453875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785309 Affx-122949963 AX-385272354 6 15626125 GAAAATTGGAATTTTTCTCATTGAAATTGCATTTT[A/G]CTATAATTCCATTGAAGTTTTAGAAATGCTTCAGT R 2 1 2 1 101000 f 74 goat snp52944-scaffold795-1340047 6 17493059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272336 Affx-1111833495 AX-519546068 6 15642402 CTCAGGGGAGTGAACCTGGATGCGCTGCAGGGTTG[A/G]CAGTAGAGCTCAGCCTTCTTCCTCTGGCTTCTGTG R 2 1 2 1 202000 f 74 goat 6_15642402_AF-PAKI 6 15642402 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408731 Affx-122953412 AX-123279082 6 15701965 GCTGGGATGATTACTATAATGGTCACAAGAAATGA[C/T]AGAGACATTAAAGTACTTAGAACAGAAAAAAAGTG Y 2 1 2 1 101000 f 74 goat snp52946-scaffold795-1415887 6 17567697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422285 Affx-122943487 AX-123292631 6 15738674 ATGAATTTTCCCAAATGATATTCAGGCCTTTCTTG[C/T]CAGAAAAGGGAATACTTTCTGCTTCATCCATCCTA Y 2 1 2 1 101000 f 74 goat snp52947-scaffold795-1452596 6 17605017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423700 Affx-122942890 AX-123294046 6 15810347 GGAACAGATGAATTCTTTTCTTTACCCAGCTTCAA[C/T]AGGACAGACACTATCAGACAAAGGGAGAGATATTA Y 2 1 2 1 201000 f 74 goat snp52949-scaffold795-1524269 6 17669579 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776589 Affx-122978726 AX-385263716 6 15865931 TGCTTTCTGTATGAAGGTATTCAGACATGTAATAT[A/C]TACTATATCAGTCATCATCTTTACAACTTTCTAGT M 2 1 2 1 101000 f 74 goat snp52950-scaffold795-1579853 6 17724808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392213 Affx-122966275 AX-123262570 6 15965178 TTTATAATCTTGACGCTAAGCCCAGATCCGGGAAC[A/G]CAGTAGATATTTAGAACACAGTAGACATTTGTTAA R 2 1 2 1 201000 r 74 goat snp52952-scaffold795-1679100 6 17824226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420972 Affx-122944578 AX-123291319 6 16016156 GCTCTGTTAATGCAGGACACCCACAGGCAGCTTCT[A/G]GAGAGGGGCTACCGGCGCCCTGTCCTTCTCCTTCA R 2 1 2 1 101000 f 74 goat snp52953-scaffold795-1730078 6 17875056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407996 Affx-122954319 AX-123278347 6 16055561 GCTTAAGCTGTTCACCCAGTCAGTTCACCTTTGAC[A/G]CCACACTGAGTAACAAGAGGGGACCACGTAGTTAT R 2 1 2 1 101000 f 74 goat snp52954-scaffold795-1769483 6 17914871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419364 Affx-122945630 AX-123289712 6 16151131 AACCCCAAACATATTTATTCTTTCTCACCAGGTCA[C/T]GGTGACTTTGTTTTATTCATTGAGGGTGAGAAAAA Y 2 1 2 1 101000 f 74 goat snp52956-scaffold795-1865053 6 18010768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430826 Affx-122937445 AX-123301167 6 16193298 CTTTAAGAGAACAGCATAAGAAGAGGGTCATGAGC[A/G]TGAAAATGAGTAAGACAGCTATTAGGTCATTAGGA R 2 1 2 1 101000 f 74 goat snp52957-scaffold795-1907220 6 18054099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392607 Affx-122966048 AX-123262964 6 16230871 TTTATTTTGAAGGAAGTTTTCCTAAAGTCAGAATG[C/T]CTCCTGAACTCTGCCTTCCCAGTAATTAAAAAATG Y 2 1 2 1 101000 r 74 goat snp52958-scaffold795-1944793 6 18091733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800898 Affx-122964834 AX-385287813 6 16291289 CATTTGAATTGAGTGAGTGGTACAAACTTTCAGAC[G/T]ATAGCAGGTATCTTTGTTCATGAGTATAGACTCAG K 2 1 2 1 101000 f 74 goat snp52959-scaffold795-2005211 6 18153848 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443898 Affx-122927057 AX-123314235 6 16361903 AGTGCTATAAAAAAACTTCCCAAACTACAAGAAAA[C/T]GGAGGATGACATGTCCATGCCTCAGGGCTTAACAA Y 2 1 2 1 201000 f 74 goat snp52961-scaffold795-2075825 6 18224216 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424884 Affx-122941323 AX-123295230 6 16398458 ATGATTTGATAATCCTGTCATTAAAAGGAATTATC[A/G]TTGATATTATCACTCCCAATGCACGTAAAGTATGC R 2 1 2 1 101000 r 74 goat snp52962-scaffold795-2112380 6 18260353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785333 Affx-122927137 AX-385272378 6 16437041 CATATTTCGCCTTTTGGATCTTACTGGAATTTTTT[A/G]TCCAAATATTTTTGGTTTGTGGCTAGTTGAATCAG R 2 1 2 1 101000 r 74 goat snp52963-scaffold795-2150963 6 18298877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411571 Affx-122951630 AX-123281921 6 16521448 GCATGTCATAGCAAGTTAGGCTAAGCAGGGCAGGG[C/T]GTTTACGACATCTACTATATTGATTTCTGTTACAT Y 2 1 2 1 101000 r 74 goat snp52965-scaffold795-2235370 6 18383693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385173 Affx-122971738 AX-123255531 6 16714746 CCCTGCAGGCTTTCTTCTGCCTGCCCAGCTGACGA[C/T]GTTTTTCTGGCTCCAGAAAACTTCCAAGATTGTTA Y 2 1 2 1 102000 r 74 goat snp52970-scaffold795-2428668 6 18579548 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451244 Affx-122921946 AX-123321577 6 16747718 GTCCTTGTTAGAATAATGCAGCTTCAAAGGTCCCC[A/G]CTTACCTCTCCAGTTTCCTGCTCAGTTACTATTTA R 2 1 2 1 201000 r 74 goat snp52971-scaffold795-2461640 6 18612548 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413095 Affx-122950948 AX-123283444 6 16795691 GAAAAGTAAAGCCACAGATTGGGAGAAAATATTTG[C/T]AAAACACATATGCAACGAAGAGATTGAATCCAAAA Y 2 1 2 1 303000 r 74 goat snp52972-scaffold795-2509613 6 18661580 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391163 Affx-122967443 AX-123261520 6 16898004 GAAAGAGAGTTGGAATCTCATAGATATTTACCTCC[A/G]GAGTGTTATGCATGTGTGCTCAGATGTGTCCAACT R 2 1 2 1 201000 f 74 goat snp52974-scaffold795-2611926 6 18764181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383504 Affx-122972646 AX-123253862 6 16931847 GACGGGTGGATTCTTTACCACTGAGCCACCTGGGA[C/T]ACTCCTTTCCTCTTTGCATCTGAATAATTTCCTCC Y 2 1 2 1 101000 r 74 goat snp49773-scaffold710-2455417 6 18811896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441214 Affx-122929522 AX-123311551 6 16971547 AGTAATAGTAGCTCTTTTTGCTTTTGTCTTGCACT[A/G]TTGGTTAACTCATGAAGCCAAGTCTAAACAACTAT R 2 1 2 1 101000 r 74 goat snp49772-scaffold710-2415717 6 18852009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403698 Affx-122958044 AX-123274050 6 17043213 TTCTCACAACTCTGGGCTCTGAGGGGTTACGAGGA[C/T]GTAGGTTTCCAAAAAAGCATACTTTTAGCAGGGGA Y 2 1 2 1 101000 r 74 goat snp49770-scaffold710-2344051 6 18923158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414457 Affx-122949571 AX-123284806 6 17108455 GCTGTGAACCTGCTGCACTCTTGCTGTCATATTGG[C/T]GAGAGCATATTTTGTACCCCCCTCTCTAGAGTTCA Y 2 1 2 1 201000 r 74 goat snp49769-scaffold710-2278809 6 18989323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798230 Affx-122950977 AX-385285165 6 17138984 CATCCAGATTGCCTGTGTTACCATGTCTCCCTTTT[C/T]TCATACACCGATGCAACCCCAGTCAACAGGATTTA Y 2 1 2 1 101000 f 74 goat snp49768-scaffold710-2248280 6 19020032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772886 Affx-122968659 AX-385260031 6 17198078 GAATATCTAGCATTACTTTAACCAATTCTCCTACC[A/G]TCTCTCTTTTAACAAAGGAATATGTTGATGTTTAG R 2 1 2 1 101000 f 74 goat snp49767-scaffold710-2189186 6 19083602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403569 Affx-122957583 AX-123273922 6 17232625 ACAGTCTACTATGGAGGGGAAAGCTATTGAACTAG[C/T]ATAATAATTCTTTATAACTTTTTCTATGGTTTGTC Y 2 1 2 1 101000 f 74 goat snp49766-scaffold710-2154639 6 19118319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389024 Affx-122968634 AX-123259382 6 17286854 AAAGATTAACCCCCAACATATAATAGCAGCAATAA[C/T]AACAATAGTGATAACAACTGTACTTTGTGGCTATG Y 2 1 2 1 101000 r 74 goat snp49765-scaffold710-2100410 6 19172415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438241 Affx-122931430 AX-123308579 6 17331182 GCCCAAATAATAAACAGGATTTCACCTGTTCATCT[G/T]TACAATGTCAGTGCAAAATCCTGCAGGATATGAGA K 2 1 2 1 101000 r 74 goat snp49764-scaffold710-2056082 6 19216857 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784341 Affx-122949329 AX-385271392 6 17404152 TAAAGCTAAGATTATATCCAAGGACATTATAATTC[C/T]TTACAGTGAATAAGGAAAAGCTCTCCTCAAGGGTG Y 2 1 2 1 101000 r 74 goat snp49763-scaffold710-1983112 6 19289823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410830 Affx-122952631 AX-123281180 6 17459324 AAAAAAGGAATTATGGATACCTACTGAAAATACTC[A/G]TGTTAAGAATCCTTTGCCTTTTGCTCATTATAGAG R 2 1 2 1 101000 f 74 goat snp49762-scaffold710-1927940 6 19345046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793349 Affx-122955753 AX-385280327 6 17529643 ACAAGGGAAAAAAGGAAACCCAGTAATACTTTAAA[A/G]CATGCTGTTGTGCTAAGTCATCATTGTTGCTAAAC R 2 1 2 1 103000 r 74 goat snp49761-scaffold710-1857621 6 19413771 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779187 Affx-122925779 AX-385266291 6 17562497 AAGTAACTTACCTACAAACTGGAACTCAACTTGCT[A/G]CAAATTAGAGATTTCAGCAAATGTGCTGAAGTTCT R 2 1 2 1 101000 f 74 goat snp49760-scaffold710-1824767 6 19446810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375763 Affx-122978598 AX-123246122 6 17607424 ATGGGTTACAGTCAACAAACACTTTTCCATTTATT[A/G]TCTCATTTGGCCTCATTGGATAACATACAATTCCC R 2 1 2 1 101000 r 74 goat snp49759-scaffold710-1779840 6 19490953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412542 Affx-122951336 AX-123282891 6 17668475 CCAAGTAGCTCTACAATTGTGAGCAAAATCTTAGC[A/G]TTGCAATTAATAATAGGAAAGTAATTCCTGTTCTG R 2 1 2 1 101000 f 74 goat snp49758-scaffold710-1718789 6 19551628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406877 Affx-122955642 AX-123277228 6 17703937 ATATAAAACGCACACCTAGAGTTTGATTTTACTTT[A/G]CTAGTTCTAAACCTCATTTCCTCCTACCGTCCCCC R 2 1 2 1 101000 r 74 goat snp49757-scaffold710-1683327 6 19587633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425028 Affx-122941875 AX-123295374 6 17751202 TTCTCCATGTAATACGTTTGTGTATGTTTATCATG[C/T]GTCTCTGTAGAATTTAAGCTCCAAGCAGTCTGTTT Y 2 1 2 1 101000 f 74 goat snp49756-scaffold710-1636062 6 19635606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390448 Affx-122967622 AX-123260805 6 17792438 CCAAAGACTCAAATGCCAGTGTTAGTTTCTTTGCC[A/G]CTTGATGGCTCCATTTAATAGCAGCATTTGTGACT R 2 1 2 1 101000 r 74 goat snp49755-scaffold710-1594826 6 19677127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771203 Affx-122945491 AX-385258361 6 17873200 ACGTTTTGTTCTTTTTCTGCCTAGGTAATTATCTG[C/T]AGGAAACTTTCTGGAAAGCTGGTAGAATTTCCACT Y 2 1 2 1 101000 r 74 goat snp49753-scaffold710-1514064 6 19757890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785758 Affx-122977009 AX-385272798 6 17946415 TTCAGTTATTAGCCAGTACCAAACTGATTATACAT[A/G]CCATATTCCATAAAACAGGTGTGTGTTCACACAGA R 2 1 2 1 101000 r 74 goat snp49752-scaffold710-1440849 6 19831079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790564 Affx-122966800 AX-385277567 6 18002158 TTTGATCATCAAATTAGAAGCTTAAATTACATTTC[C/T]ACATTGAGGTCAGGGCAGTAATATCCAACTGTGGG Y 2 1 2 1 101000 r 74 goat snp49751-scaffold710-1385106 6 19887362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438147 Affx-122931469 AX-123308485 6 18031353 ACTTCCTCTCAGCCATCTACCCACTTCAGTTATTC[A/G]TGTATCTAGGGTACACAGTTTTTAGCAAAGGAACC R 2 1 2 1 101000 r 74 goat snp49750-scaffold710-1355911 6 19916905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275283 Affx-1111834701 AX-519548858 6 18059400 GACTGCCAGTATTCACAAGGCTGAGACAGTGCAGC[A/G]CCCACAACAGTGTGCTTCATAAGACCACACAACAG R 2 1 2 1 202000 r 74 goat GoatD01.046794 6 18059400 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381002 Affx-122974666 AX-123251360 6 18078211 ATCTCCTTTCATGGCGTTCCATCCATTCTGGCTTA[C/T]ACTTCTACCCCATCACTGAAGCTGCTTTTGAAAAG Y 2 1 2 1 101000 f 74 goat snp49749-scaffold710-1309053 6 19963419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428022 Affx-122939147 AX-123298365 6 18115742 ATATCATTAGTCATCAGGAAAATGCAAATGAAACC[A/G]CAATTAAATACCATTACAATGTTCAGTAAATGGTC R 2 1 2 1 303000 r 74 goat snp49748-scaffold710-1271522 6 20001871 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433552 Affx-122934989 AX-123303893 6 18150523 AGCCTTCAGTGACGAAGCCCAGGATCCGGTCACAC[A/G]GGACCTTGCAACAGTAAGAGCAGAACCTGGCATGA R 2 1 2 1 101000 r 74 goat snp49747-scaffold710-1236741 6 20036705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272252 Affx-1111833497 AX-519545994 6 18150704 TCTTCTGAAACAATCCACTTCTCTCTTAACCTGTT[A/G]CCACTACCATGGTCTATGTATATGTAGTTTCCTCT R 2 1 2 1 101000 r 74 goat 6_18150704_AF-PAKI 6 18150704 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449110 Affx-122923582 AX-123319445 6 18192066 ACTGGGCAGCCACGAGTTACTGTTCAAAATTAATG[A/G]AGCAATAAACATATTTTGAAGTGTAATACCTAGAG R 2 1 2 1 101000 f 74 goat snp49746-scaffold710-1195198 6 20078195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415756 Affx-122948933 AX-123286105 6 18223823 CTCAAAACCTTTCAATGGTTCCATCTTACTCAGAA[C/T]AAGAAATGAAATTCTTAAAATAATCATTACAGGGT Y 2 1 2 1 101000 f 74 goat snp49745-scaffold710-1163441 6 20110012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398988 Affx-122960954 AX-123269343 6 18279840 CAAAAATAAAAACTTTTTTTCCTTGAATATAAGAG[A/C]TAACACATTTACTGTAGAAAGTTAAACGACATAGA M 2 1 2 1 101000 r 74 goat snp49744-scaffold710-1107424 6 20167260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417003 Affx-122947983 AX-123287351 6 18313417 CTGGAGATTCAAATGTGGGAATCATCAGCATGAGA[C/T]GATGTTAAAACCACTAGACTAGATAAAATCGCCTA Y 2 1 2 1 101000 f 74 goat snp49743-scaffold710-1073847 6 20201001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415839 Affx-122948873 AX-123286188 6 18352201 TGAGATGTGATGATTTAATGTTACTATAATAAGGG[C/T]ATTCAAGTAACTAAAACATACTCAGATTTTAATAT Y 2 1 2 1 101000 f 74 goat snp49742-scaffold710-1035063 6 20239572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439280 Affx-122930978 AX-123309617 6 18384358 GGAGACACAGTCTGCTGTTGAAAGTAGGTTTTGCA[C/T]AGATTGACTGTTTTTCTTAAAAATTTTAGCTTTAA Y 2 1 2 1 101000 f 74 goat snp49741-scaffold710-1002906 6 20271800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796926 Affx-122968573 AX-385283868 6 18412881 TCCTATTAGAATACAAAGGTCACAATGATATGATA[C/T]GCACAACTGACATTGATATGAAAAACTGTGAATTT Y 2 1 2 1 101000 r 74 goat snp49740-scaffold710-974383 6 20300362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443087 Affx-122928114 AX-123313424 6 18444762 GAAGGTGAGTTTTATACATGGAAATATAAAATGCA[C/T]CATGCCTATAAAAATAATGTATATAATTTCTTAAA Y 2 1 2 1 303000 r 74 goat snp49739-scaffold710-942502 6 20331587 T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771964 Affx-122961834 AX-385259120 6 18487124 CATTTCTCCTGGCTCAGAAACTTGTTGCGCAATGA[C/T]ATTTAATCATCTCCAACAAACATATATTTGTGAGG Y 2 1 2 1 101000 f 74 goat snp49738-scaffold710-900140 6 20373960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447270 Affx-122924940 AX-123317606 6 18519376 TTGACATGGTGTTCCTGGGAATGACACAGATGGCC[A/G]TCTGCCTAGAGAAAAAAATCAAGGGCTGGTGAGCA R 2 1 2 1 101000 f 74 goat snp49737-scaffold710-867888 6 20405778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794595 Affx-122962241 AX-385281557 6 18563565 AATATGTTTATAAAATGATTGACAAATCCTGACTA[C/T]ATTCCAAGGACACAAAGATGAGGAAGATGTGATCC Y 2 1 2 1 101000 r 74 goat snp49736-scaffold710-823699 6 20451972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394889 Affx-122964744 AX-123265244 6 18609494 GTTTTCTAGACAATATAGCAAGCACCATTCTATGA[A/G]TTCAGCATTTCCTCAGCTCCCCGCTCCCACTCCTT R 2 1 2 1 101000 f 74 goat snp49735-scaffold710-777770 6 20498822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775071 Affx-122969837 AX-385262203 6 18638933 GAAAAACTGAAACCCTACTTATGTAAGCCTCTACT[A/G]CTTGCAATTTTTGATACTTGCAGCCAAAGCAGCCT R 2 1 2 1 101000 f 74 goat snp49734-scaffold710-748331 6 20528183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396287 Affx-122963100 AX-123266642 6 18668608 ATTGATCCTTATGATTGTTAGAAACCTTCTATTTT[A/G]TCATGCTTTAAAAATTATATCTGAATCAGCATCTT R 2 1 2 1 201000 f 74 goat snp49733-scaffold710-718656 6 20558094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433951 Affx-122934278 AX-123304292 6 18702260 CTCAATATTTTTAAAATCTGCCCAGTTTACATTTT[A/G]CTTAAAGTACTGCTAACCTTGAAACTAAATTGAAA R 2 1 2 1 101000 r 74 goat snp49732-scaffold710-685004 6 20590027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402261 Affx-122959123 AX-123272614 6 18769652 AGGTGTGCAGAGCCTTTGAACCATAATACATAGCT[A/G]ATATGTAGAGAAGAAATAAAAGGAAGGGAGAAAAA R 2 1 2 1 101000 f 74 goat snp49730-scaffold710-617612 6 20657521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798964 Affx-122921038 AX-385285894 6 18856555 CATCATTTCATTAATCCTCATTCAGGGAAGGGGGC[A/G]TTATGTACAAAATCTCAACAGGAAAGGGAAGAGAA R 2 1 2 1 101000 f 74 goat snp49729-scaffold710-530709 6 20745509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781363 Affx-122969887 AX-385268448 6 18900142 TCGAAAATTAAACTATAATCACATACTCCCATTTA[C/T]AGGTTTTACTTATTTTCACATGGTTATTCAGTATG Y 2 1 2 1 201000 r 74 goat snp49728-scaffold710-487122 6 20789804 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453094 Affx-122920037 AX-123323427 6 18954537 CACTTTTCTGTAAGAATGTCATTTCTCTCCTTTTC[A/G]TCTTCAGATTTCTCCTTTAATTGGTTTGGTAGACA R 2 1 2 1 201000 r 74 goat snp49727-scaffold710-432727 6 20844275 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451458 Affx-122921149 AX-123321791 6 18988897 ATACAGTTTTACATCAAGTAACACAAGCTTTGGCC[A/G]TTTTCCAAATTTATACTTTCTTTCCATAGGTACTG R 2 1 2 1 101000 f 74 goat snp49726-scaffold710-398367 6 20878915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429319 Affx-122938594 AX-123299661 6 19033479 CACTGTGATTGGTGCACCAACAGCAACAAGCAGTG[A/G]ACATTAGAACTTTATGGTGCCAACTTCTTTCTAGC R 2 1 2 1 101000 r 74 goat snp49725-scaffold710-353785 6 20923847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774826 Affx-122969146 AX-385261960 6 19066422 CTAATTTACAGTGGTTTCCTAGTCATCAAATCCTG[C/T]GGACCTGTCTCAGATCTCATCAGTCTCTCTGGCAT Y 2 1 2 1 202000 r 74 goat snp49724-scaffold710-320842 6 20956884 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416598 Affx-122947642 AX-123286946 6 19110806 TTTAGAATTGTTCTTTGCAAAACTTAATTTGGTCT[A/C]GGCCATTTCTTATTTTTTCACTCCTCGTTATATAA M 2 1 2 1 101000 f 74 goat snp49723-scaffold710-276458 6 21002010 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768815 Affx-122922240 AX-385255992 6 19145196 TGGAACCATATAAATGATTTCCAAGATATAATACT[A/G]TGTTCTACATTTCTTGTAGTTTATGAAGCAGCAAA R 2 1 2 1 201000 r 74 goat snp49722-scaffold710-242068 6 21036346 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785025 Affx-122931497 AX-385272072 6 19180571 GTCTGATTCTCCAACTTTACTGTTTTTAAGTATTA[C/T]ATTCATCCATGGCAGAGGCTGCTGTATGTTTATTA Y 2 1 2 1 201000 f 74 goat snp49721-scaffold710-206693 6 21071971 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400483 Affx-122961293 AX-123270838 6 19211445 CACAGTTAAGCTGCTCTGCTCTACACTCAAATAGC[C/T]GTCCACAACTGCTGAAAATTGATTTATCCCCAGAT Y 2 1 2 1 101000 f 74 goat snp49720-scaffold710-175819 6 21102981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422320 Affx-122943465 AX-123292666 6 19268603 AACTGCATCCACACAAGGTAAGTATTTTGAAGTTG[C/T]GCTAATTATTTTTGTTTTTAATATACTGTTCCTGT Y 2 1 2 1 101000 f 74 goat snp49719-scaffold710-118661 6 21160026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416956 Affx-122948021 AX-123287304 6 19375398 CCAGATACAACTCCAATTTTTAAAGATAGAGTTCA[C/T]AATTTTTATTCAACTTATCCCTTAAATGCAATAGC Y 2 1 2 1 201000 r 74 goat snp49717-scaffold710-11866 6 21267109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375622 Affx-122978708 AX-123245981 6 19439848 CACCAAACAACTGAAAAATTAAAGCTCAGTAGGGA[A/C]TAAAAATAGAAAAACATTAATGATATCAGCAGAAG M 2 1 2 1 102000 f 74 goat snp42243-scaffold553-586410 6 21360351 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445075 Affx-122926215 AX-123315412 6 19571776 TTTACTATTAGGACTGCAGGTTCTATGAACTTTTG[C/T]GTACAAGTTTTCCTGTGGATGTATTTTCAAAGGTA Y 2 1 2 1 101000 f 74 goat snp42241-scaffold553-454482 6 21492259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400845 Affx-122959784 AX-123271200 6 19625267 TCAAGCAAGTATTGGACTTTTTGTTTTTGTCTCTC[A/G]GAGTGTTATTTTTATAGATTATACTCCACTAAATG R 2 1 2 1 201000 r 74 goat snp42240-scaffold553-400991 6 21545111 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382362 Affx-122973867 AX-123252720 6 19666966 TTCAAGGCAGGGATAGGTAACTGTTCCACACAAAA[C/T]GAGAAGACAGAACAATGTTTCAAATGAAAGAACAG Y 2 1 2 1 101000 f 74 goat snp42239-scaffold553-359292 6 21588071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439698 Affx-122930569 AX-123310035 6 19696217 GTACAGAAAGAAAACTTTAAGCCTATTAACTTTAT[A/G]ATGGAGGAGAAGAGGGAAACAAAGCCAGCATCAGT R 2 1 2 1 303000 f 74 goat snp42238-scaffold553-330041 6 21617396 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792237 Affx-122929969 AX-385279221 6 19729867 CCACATTCATTCCTTGTAACAAAATATCATATTCA[A/C]AAAATTTTAGTTTTTGTCCCCTTTTCATATAAAAT M 2 1 2 1 202000 r 74 goat snp42237-scaffold553-296391 6 21651093 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789953 Affx-122967347 AX-385276959 6 19763188 CTATGTTGAATACAATTAAATTAACACTTGAAACT[G/T]AAAAACCAAGCTGTTGTGGTAAGCTTGAGATAAAA K 2 1 2 1 101000 r 74 goat snp42236-scaffold553-263070 6 21683723 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379110 Affx-122976753 AX-123249469 6 19799432 TATCTTGAAGGTGTGCATACTTTGTTTTTTTGAAA[C/T]GGCATAAATCTGGAATATTTGAGATTATTCTTTTC Y 2 1 2 1 101000 f 74 goat snp42235-scaffold553-226826 6 21720480 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449293 Affx-122923014 AX-123319628 6 19828038 CGTTACTGGCCAGAAAACATGAGTGAAAGAAAAAA[C/T]ATAGTAGTTCAATTCCCAATGTATATTTTTTTGTT Y 2 1 2 1 101000 f 74 goat snp42234-scaffold553-198220 6 21746391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382252 Affx-122973949 AX-123252610 6 19871886 CCTCAATTTTTGCTGTTACCATATCACTGTACATT[A/G]CAATATTGGTATTTTCAATGACATCTCGGTAGTAT R 2 1 2 1 101000 f 74 goat snp42233-scaffold553-154372 6 21793053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442455 Affx-122927952 AX-123312792 6 19905684 CAGATGCTTAATATTTTGAGTAATCAGAGTGTTTA[C/T]GTGTTAGAATACTGAATCACCATGGCAACCTAACT Y 2 1 2 1 201000 f 74 goat snp42232-scaffold553-120574 6 21827301 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413922 Affx-122949817 AX-123284271 6 19994814 TAGTGCTAGATCTTTAAATACTCATGGCCTGCCAA[A/G]TTTTGATATATAACTGGTTCTAACTTGAGGAGGAT R 2 1 2 1 201000 r 74 goat snp42230-scaffold553-31444 6 21919284 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433960 Affx-122934269 AX-123304301 6 20043700 TTGTAAACCACATTAAGGGATTTGAACTTTGAATT[G/T]TGCTAAAAACAAGGAAAAGCCTTGTATAGAACGTA K 2 1 2 1 201000 r 74 goat snp34149-scaffold4002-17343 6 21968147 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375738 Affx-122978619 AX-123246097 6 20136449 AATGCAGAGGTTGAAATGTTTTAGTGACAGAGCAG[G/T]AACTACTTCTCAGAACTATTTGCAGCAGTTTTTCA K 2 1 2 1 101000 f 74 goat snp34151-scaffold4002-110092 6 22061563 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416271 Affx-122947952 AX-123286620 6 20221291 GGAGCCATTGGGAGTAAAGTAAATTTCTCAAAAAA[G/T]ACAGTGATAAGAAAAAAGGCATAAGGCAGAATCCC K 2 1 2 1 201000 f 74 goat snp46532-scaffold645-27823 6 22146662 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436476 Affx-122932974 AX-123306814 6 20274837 GTTCCCATTCTACTATCATGCTGTTGTCACCCTAC[A/G]CTTTTGTTATTTTTAATGGGAAAATATTTCTAAAA R 2 1 2 1 101000 f 74 goat snp46533-scaffold645-81369 6 22200997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431695 Affx-122936776 AX-123302036 6 20306887 CTTATTCTTCTATGGTTATATCTTTATATTTGCCC[A/G]TGGTTTTGTTTGCCTTTTTTTTTTTTGGCCCATTT R 2 1 2 1 101000 f 74 goat snp46534-scaffold645-113419 6 22233365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379917 Affx-122975753 AX-123250275 6 20438646 ATTCAGAACTGCAGATATGGAGGGCTGACTTTGAG[C/T]ATCAGTAGATTTTGGTCCTGGATTTTGGTCTTGGT Y 2 1 2 1 201000 r 74 goat snp46537-scaffold645-245178 6 22364493 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787191 Affx-122962933 AX-385274217 6 20498961 AAACAGAAGTTTAGGAAGAAGATAATAGAAAAGTT[A/C]TCCTTAACTTTTGGGGCACTAAACTGTTATAGTCA M 2 1 2 1 102000 r 74 goat snp46538-scaffold645-305493 6 22426963 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442360 Affx-122928027 AX-123312697 6 20537176 ATACAGAAAATCCTTGTTGCTTATCTGTTTTATGT[A/G]TAATAATGTGTATCAGTTAATCCCACATCCTGCTT R 2 1 2 1 103000 r 74 goat snp46539-scaffold645-343708 6 22465380 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778130 Affx-122938442 AX-385265245 6 20574224 ATAAATATAAATAGAGCATCAGGAATATAATTTCT[A/G]CTCTCCACAGGAAATAATATTTTGGGGGAAAGAAG R 2 1 2 1 102000 r 74 goat snp46540-scaffold645-380756 6 22502168 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403400 Affx-122957769 AX-123273753 6 20624381 AGCAGCAGAGAGAAGCCAAATGACAGTGTCAGCTC[C/T]GAATCCAGTGGGCTTTGAAGCTAGCTAGCTTTTCC Y 2 1 2 1 101000 r 74 goat snp46541-scaffold645-430913 6 22552318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774478 Affx-122971958 AX-385261614 6 20673371 TCTGAAATTCACTAGAACAATAATTTATTAAAAAG[C/T]ACCCCGTATGGGTCAGAATAAAAGCTGGTTGTAAG Y 2 1 2 1 303000 f 74 goat snp46542-scaffold645-479903 6 22600590 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272339 Affx-1111833498 AX-519546071 6 20695624 TTTGCAACACAATATAGTTGTACAACTTTTTCATC[A/G]TCCCCACAAATCTCCTAGTGCCCATTTTGGCCAAT R 2 1 2 1 201000 f 74 goat 6_20695624_AF-PAKI 6 20695624 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389243 Affx-122969038 AX-123259601 6 20748728 TACTTCATCTGTTTAAAATTAAATTTCAAGCCCCA[C/T]AAATTGGATACAAAACCATAGCATGATAAACTCTT Y 2 1 2 1 101000 r 74 goat snp46543-scaffold645-555260 6 22675562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779020 Affx-122929069 AX-385266127 6 20777997 GGGAAAAAAGCCCTCAAATAGTGTAACTGAGTGTA[C/T]GATCTGAATATATAAACAGGCAATTAAAATATAGC Y 2 1 2 1 101000 f 74 goat snp46544-scaffold645-584529 6 22705189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781048 Affx-122929929 AX-385268135 6 20810439 GCCGCTAAGGTGAGAGTTTGAACTCTAACACAGTT[A/G]TGAAGAGAGGGCTAGTAAACTTTCCCCCTTAATGA R 2 1 2 1 101000 f 74 goat snp46545-scaffold645-616971 6 22737729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391177 Affx-122967433 AX-123261534 6 20854750 AATACAGGGATTCTTACTAAACTGACTTAGCATGA[G/T]CCCTGCTACAACTGGACTCTGTACACTGGGGCAAA K 2 1 2 1 201000 r 74 goat snp46546-scaffold645-661282 6 22781684 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778289 Affx-122962193 AX-385265404 6 20886101 TCTTAGTCTGTTTAGACTTGCTATAGCAAATACCA[C/T]GCACTGAATAGGTTATAACCAGCCAAAATCTATTT Y 2 1 2 1 101000 f 74 goat snp46547-scaffold645-692633 6 22812845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762425 Affx-986696956 AX-385250571 6 20905116 CTCAAGTCCCAGGAAATGCTAAGTACTTCTCAGTC[A/T]TGGATCTTAAAGATGCCTTCTTTTGCATTCCTCTC W 4 1 2 1 600010 f 74 goat 6_20905116 6 20905116 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320764663 Affx-986696958 AX-385252298 6 20906937 CTCAAGCCTATTCTCTACCATCCCCAGCTGGCTAA[A/G]GTTGTTAGACAGGTCACACAGAATTGTGATACCTG R 2 1 2 1 600010 r 74 goat 6_20906937 6 20906937 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38421255 Affx-122944757 AX-123291602 6 20924241 CTCAGATTAGATTTTAAAATGATGATTGTTAGGCA[A/G]GAGAATCAAATAACTGTATCTCCATGGAAACATAG R 2 1 2 1 101000 r 74 goat snp46548-scaffold645-730773 6 22851841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414348 Affx-122950023 AX-123284697 6 20957981 TTTCTCTTTTGGTTTTCAGAACATTTTTAAAAGAT[A/G]TAAATTCAAGATATGAGTCTTCTTTTGACTCTATG R 2 1 2 1 103000 r 74 goat snp46549-scaffold645-764513 6 22885652 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395084 Affx-122964176 AX-123265439 6 20998285 GAGCACACTGAAGGAAATATCCCAAGGGCACCCAG[C/T]GATAAACATCAGAGCTAGGATTCATATTGAGACCT Y 2 1 2 1 101000 r 74 goat snp46550-scaffold645-804817 6 22926326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450142 Affx-122922750 AX-123320477 6 21065820 GAAAGCTTTATACATTTTAAGCATAAAATGCATAA[C/T]GTTTATAGGAGACAACTAGAAAATTCATGTTATAG Y 2 1 2 1 101000 r 74 goat snp46551-scaffold645-872352 6 22994317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383150 Affx-122973240 AX-123253508 6 21098116 CTTTGACTAATAGTCTATTTTCTAGAGAATGTGAA[C/T]AGGAGAAAATTATGGAGTTAATCCAAAAAACCTAG Y 2 1 2 1 101000 f 74 goat snp46552-scaffold645-904648 6 23026678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394027 Affx-122965004 AX-123264382 6 21144389 TATCTTACACTGACATGAAGTTGTTGTTTCAAAGA[C/T]TGTGTGAGTTTCTTTTCTCCTTCAGAGACTAACAT Y 2 1 2 1 201000 f 74 goat snp46553-scaffold645-950921 6 23072803 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781471 Affx-122959325 AX-385268556 6 21181931 ACACAGCAGTGAGAAGTGCTGCCTTGGGAAATAAG[C/T]ACCTTTCTTATTAAAGTATAGATTTAACAACATTT Y 2 1 2 1 101000 f 74 goat snp46554-scaffold645-988463 6 23110465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775650 Affx-122950241 AX-385262781 6 21224685 AGATCTAGGTAAAATCCTATTTCCTTCAGGAAACA[C/T]AGCTTGAAAAATAATGTAGCTTTTCTTTAAAATTC Y 2 1 2 1 101000 f 74 goat snp46555-scaffold645-1031217 6 23153401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433278 Affx-122935217 AX-123303619 6 21257572 AGTTTCTGTGTATTGTTTTAAACTGTATTCAGTGC[C/T]GAGGAATGAACAGGAAGGCGCTAATCTCAGAGGTT Y 2 1 2 1 101000 f 74 goat snp46556-scaffold645-1064104 6 23186553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771178 Affx-122966769 AX-385258338 6 21290469 TTTTTAAAATTCTACATGGCAAAATGCGTATACTG[C/T]GCTTCTGCTACCTACTCAAGTTTAGTAATCATCTC Y 2 1 2 1 101000 r 74 goat snp46557-scaffold645-1097001 6 23220147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409322 Affx-122953084 AX-123279673 6 21327560 TCATCACCCAGGCTCCCAAGCCCACTCCAATGGAA[C/T]ACCAGAAGGGGAAGGACAGGAACGATAGGGTTATT Y 2 1 2 1 303000 f 74 goat snp46558-scaffold645-1134092 6 23258180 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413235 Affx-122950243 AX-123283584 6 21399397 CAGGATCATAGAATAGCCTAATCGGTTGCACCCCT[A/G]AACAGGGCCACAGACTGGCCATAAATGAGTCTCCT R 2 1 2 1 202000 r 74 goat snp46560-scaffold645-1205929 NW_017213563.1 6258 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440815 Affx-122929821 AX-123311152 6 21429594 GTTAGTCAGTATTTATAGAAAGGTTTTTGTCTCTA[G/T]ATCATGAAGGGGCTATAAGGCAGGAACTGCAATGT K 2 1 2 1 201000 f 74 goat snp46561-scaffold645-1236126 6 23361905 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399872 Affx-122960228 AX-123270227 6 21487719 CATGTCATACCTCATATTTATAAAATGTTAAAAGT[A/C]TCACAATATCAAGGGTTGGCAAAAATATAGACTAA M 2 1 2 1 201000 r 74 goat snp30519-scaffold337-29243 6 23417569 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798196 Affx-122934648 AX-385285131 6 21529605 CAATTGGACATATTTAAAAAAGTCCAGTCAGAGAT[A/G]CTTCTCAAAATTAGACAGAAGGAACAATGCACAAC R 2 1 2 1 202000 r 74 goat snp30520-scaffold337-71129 6 23459796 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768829 Affx-122958132 AX-385256006 6 21564361 GGGAAGTACTAAAGAGAAAGGCTTAGGAGTATAAA[C/T]AGAGTTACAGGGTTTACAAGTGTAAATAGGTTTGA Y 2 1 2 1 101000 r 74 goat snp30521-scaffold337-105885 6 23494025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394412 Affx-122964609 AX-123264767 6 21593545 TCAAAATGGACAGATTCCTTAACTAAACAGTTACC[A/G]CAAAACTGGTGTTTCAAGAAAACAAACTGATAACT R 2 1 2 1 101000 f 74 goat snp30522-scaffold337-135069 6 23521611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379474 Affx-122976482 AX-123249832 6 21644035 CACAAACGTGAACATTTTCATATGAATAACACCTG[A/G]ATAGACATTGGAAATAGTCAAACTACCACCTACTG R 2 1 2 1 101000 f 74 goat snp30523-scaffold337-185559 6 23572583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781134 Affx-122955245 AX-385268219 6 21806238 TGATCTTTGAACATTAATAAAGTGAATGGCCAGTC[A/G]TCCAATCCAACAGCTAAAAATCATTCATGAATGTT R 2 1 2 1 101000 f 74 goat snp30526-scaffold337-347762 6 23735925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403693 Affx-122958048 AX-123274045 6 21837736 TCCCGGTCATCTGCCCCCTGCCTCTCTCTGCTCCT[A/G]CCCCTTCAGTACCTCCTGAAGCATCTTTGTTGCCT R 2 1 2 1 101000 r 74 goat snp30527-scaffold337-379260 6 23767528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393983 Affx-122965038 AX-123264338 6 21881015 TCTCTTGTTTTCCTGTGTGACCTTGGTGTGTCCCT[A/G]TAGGTGTGCTGTTGGGTCTCCTCCGTTTGCCTGGG R 2 1 2 1 201000 r 74 goat snp30528-scaffold337-422539 6 23810865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789296 Affx-122977490 AX-385276307 6 21913344 AGAATTCCCATGTAATATGGGCTCCATAATTTAAA[G/T]ATAGGTTATTTTATGTCTACGAGGGAGAATGAAAA K 2 1 2 1 201000 f 74 goat snp30529-scaffold337-454868 6 23843624 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441446 Affx-122928771 AX-123311783 6 21996682 GGCTTGTGATCAAATAATTTTTGAAAACACTTCCT[A/G]CAGCACAAAACCTTGTACAGACTTTGCATTGTTCA R 2 1 2 1 101000 r 74 goat snp30531-scaffold337-538206 6 23927977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436010 Affx-122933491 AX-123306349 6 22080615 CAGAGTTGTTATAAGTCCAAGGTTTGTAAAACAGT[A/C]TCTCTATAATTGTTTGATCTCAAGTGGCATGTTTA M 2 1 2 1 101000 f 74 goat snp30533-scaffold337-622139 6 24011885 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408980 Affx-122953907 AX-123279331 6 22126042 GGAAAAAGAAAATGAGGAAGCTGCTAGCCAGTCCT[A/G]TCCCTGAGGATCATTTGGCTTTATTTTGATCCACA R 2 1 2 1 101000 f 74 goat snp30534-scaffold337-667566 6 24057337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383764 Affx-122972434 AX-123254122 6 22160699 ACCACCAGAAATGGGCTGAGCATCCTCTGAGCAAG[C/T]GTATTTTGGAATCTTCATTGTATCTCAGCTTTACC Y 2 1 2 1 101000 r 74 goat snp30535-scaffold337-702223 6 24090592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791217 Affx-122924498 AX-385278211 6 22199744 TCCAGATACAACTCAAAAACTCAGTAAGATGTACT[A/G]AAGAGCAATTTTATAGGCTCTGGACATCAGCAACA R 2 1 2 1 101000 r 74 goat snp30536-scaffold337-741268 6 24130107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786662 Affx-122933702 AX-385273694 6 22235092 CTAAACTTTGAGTAGCAGGAATTGGGGGACTTTTA[A/G]TCTCATATAAGGCCATGAGCTTCTTACACAAAATG R 2 1 2 1 201000 r 74 goat snp30537-scaffold337-776616 6 24165778 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273667 Affx-1111833760 AX-519547280 6 22254481 CACGGAGAGACACTGCAGACAGACATGAAGATAAG[A/C]TCAGGGGGCCGCCAAGTCCCAAGATGCGGCCTCAC M 2 1 2 1 101000 f 74 goat GoatD01.003754 6 22254481 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320768352 Affx-122979051 AX-385255532 6 22294690 CTCGCTCATGTTACGCCCTGGGTCAACTTGATGGC[C/T]TATTTTGTCTTCGTGCTGAAACCCAGGATGAAAGA Y 2 1 2 1 201000 r 74 goat snp30538-scaffold337-836214 6 24225528 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384140 Affx-122972809 AX-123254498 6 22339433 AGCTTTTCTGAGAAAAGCAATGGTGAGCTTGGTCT[A/G]TTTAAACCATTTTCTCCCTTTTAAAATGCTACTTA R 2 1 2 1 101000 f 74 goat snp30539-scaffold337-880957 6 24270361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400212 Affx-122960174 AX-123270567 6 22370829 AATATTCCCTGCCCTCATGGAGCTTTAAGAAAGAC[A/G]TAAAACCTAAAGAGCACTCAAGATATTTTAGTACC R 2 1 2 1 201000 r 74 goat snp30540-scaffold337-912353 6 24302281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419664 Affx-122945947 AX-123290012 6 22393820 CCAGGGCAAAGCAACTGATGAGACATCTAGCTAAA[C/T]GATCCAGGGCCAAGTGTGAGGGCCAGGGTCAGAGC Y 2 1 2 1 103000 f 74 goat snp38133-scaffold476-899162 6 24326176 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395094 Affx-122964167 AX-123265449 6 22472014 CCTCAGTATTTGTTTTTATAGATAAATAGATTCAG[C/T]AATCAAACTTCTTTGCTGTGGCTTTTCCAATCATT Y 2 1 2 1 201000 f 74 goat snp38131-scaffold476-820968 6 24404951 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799317 Affx-122923998 AX-385286247 6 22505773 TATTTGTTGGAAGATCTGTGAATTTGCAGCTGAGA[C/T]GTTCTCCCAGGCAGCGTTTAACTTTGAAGGGTCAC Y 2 1 2 1 101000 f 74 goat snp38130-scaffold476-787209 6 24439041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440310 Affx-122930212 AX-123310647 6 22534569 ATTTGCTGCAAATTACTATTAGCTGATACTAGGTC[A/G]TCTACCTATCCCTATCATCTCCTCTGCTACAGTTT R 2 1 2 1 101000 r 74 goat snp38129-scaffold476-758413 6 24467883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409475 Affx-122954062 AX-123279826 6 22578745 GATGAATTAGAGTATTCTTTATTTGTGGGTACATA[C/T]GGACATCCTTATAATAAAAATTTTAAAAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp38128-scaffold476-714237 6 24512457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444942 Affx-122926691 AX-123315279 6 22657235 TGATTTTGTTAGATTACTACCGCATGTCATCTGGA[C/T]ATCACTTCATTGGGACAGGTGACTGGCAAGCAGGA Y 2 1 2 1 101000 f 74 goat snp38126-scaffold476-635747 6 24590099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444943 Affx-122926691 AX-123315280 6 22657235 TGATTTTGTTAGATTACTACCGCATGTCATCTGGA[C/T]ATCACTTCATTGGGACAGGTGACTGGCAAGCAGGA Y 2 1 2 1 600000 r 74 goat snp38126-scaffold476-635747 6 22657235 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790870 Affx-122972158 AX-385277868 6 22703219 AGAATATGTACTATGATAATCATGTTACAAAATCA[C/T]GAATATAGAAAAGATAGAAAGACTACAAAATATAC Y 2 1 2 1 201000 r 74 goat snp38125-scaffold476-589763 6 24636644 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796969 Affx-122954872 AX-385283910 6 22777508 CTGTAATTAACTTATGTCTTCCTTTTGGAGAAAGC[G/T]AAACTCAAGAAGTCTTTGTAAGATCATCAAAATTT K 2 1 2 1 101000 f 74 goat snp38124-scaffold476-515474 6 24711581 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409846 Affx-122952933 AX-123280197 6 22823578 TATTTAAAAAGAAAGCTACTGTGTCTAGTTTGTTT[G/T]TCTGATTTCCCCCCAAAATAATTATTCTCTTTTCA K 2 1 2 1 102000 r 74 goat snp38123-scaffold476-469404 6 24757650 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389151 Affx-122968539 AX-123259509 6 22873428 TAAGCCAAAGAAATAAATTCTTAGTCTGTTATGAA[C/T]GTATGATGGTGAGTGTAGGCTGGTCTCTTTCCTCT Y 2 1 2 1 101000 r 74 goat snp38122-scaffold476-419554 6 24807268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382823 Affx-122973553 AX-123253181 6 22928411 GGCATTGGCAACCAATAATGACTGAAGACTTGCCC[A/G]TTAATAAAACAAAGTAAAGCAAAACAAAACCCCTT R 2 1 2 1 103000 f 74 goat snp38121-scaffold476-364571 6 24861987 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394627 Affx-122964404 AX-123264982 6 22958415 ATATCAAGTTGGCCCCACACAGCTGTTCTTATTGG[C/T]AGGGACATCAGAGGTAGAAAATCCTGCCTGAATCC Y 2 1 2 1 201000 r 74 goat snp38120-scaffold476-334567 6 24892495 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437580 Affx-122931874 AX-123307918 6 22991430 TATTGTCTAGGTTTCATGACTCATCAGTGGTGGTA[C/T]AGGAGGAAGGTAGAAAATATTTATTGTTACCCAGG Y 2 1 2 1 101000 f 74 goat snp38119-scaffold476-301552 6 24925487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388455 Affx-122969253 AX-123258813 6 23023108 AAGAAATACCACCTAGCACAGTGTTTTCTCAAACT[A/G]TGGTCTGCCTACAGAGTAATTTCCTTGAGTGTTTG R 2 1 2 1 201000 r 74 goat snp38118-scaffold476-269874 6 24956614 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780666 Affx-122977461 AX-385267756 6 23060812 CGGTCTACCCCTAGAGGGCTTGGAGTGAGACGATA[G/T]TCTTTAATCAAATCATAACCCGTGTCTTTCTGGAG K 2 1 2 1 101000 f 74 goat snp38117-scaffold476-232170 6 24994400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401005 Affx-122959689 AX-123271358 6 23123714 ATATACAAATGAAAGTTAGTGATTGTACTCGTTTC[A/G]TTCACTTTTCCTAAGCCACTTTATCTTCCTCACAC R 2 1 2 1 101000 r 74 goat snp38116-scaffold476-169268 6 25057312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797778 Affx-122970439 AX-385284717 6 23164075 AGCAGACATTAGGACACACTGATTTAGAAAACAGA[G/T]AGCTCAGAGACCTATGTAGAAACTCCCTCTGCCTT K 2 1 2 1 101000 r 74 goat snp38115-scaffold476-128907 6 25097753 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433793 Affx-122934467 AX-123304134 6 23208482 TTCATCCTTCCCTTTCCACAGTTGATAGCACATTG[C/T]AATGTAAGCCTTTGTCTGATGGTTTTACTGGTGCT Y 2 1 2 1 201000 r 74 goat snp38114-scaffold476-84500 6 25140318 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38412109 Affx-122951112 AX-123282459 6 23252906 GTGATGAGTCACCCAGCAGAACCTGAGGCAGGGAG[C/T]GGAGCTGTTTACATGAGTTTGGCCACTCACTGAGA Y 2 1 2 1 101000 r 74 goat snp38113-scaffold476-40076 6 25184541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272340 Affx-1111833499 AX-519546072 6 23269461 CAGAGAGGCATACAGTGGCCAAAATGTTAAGCTTT[A/G]GAGTCAGTCTGTCATGGAGTCCAATTGGGCAAATA R 2 1 2 1 101000 f 74 goat 6_23269461_AF-PAKI 6 23269461 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412930 Affx-122951472 AX-123283279 6 23287643 CAATACCAGCATAGGAAAAAAATTTGTAGAAAAAA[G/T]AAATTGGCCTTTTTCAAGTGAGGTCAATTTCCAAC K 2 1 2 1 103000 f 74 goat snp38112-scaffold476-5339 6 25219293 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411711 Affx-122951532 AX-123282061 6 23302356 ACAGCCAACACCTGCCCCAGGGGGCCAGGCAGCAT[A/G]CAGAGCTGTGAGCATGACCTCCGGTTTAAAGAAAT R 2 1 2 1 101000 r 74 goat snp14188-scaffold1567-424418 6 25233462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411704 Affx-122951538 AX-123282054 6 23336625 ACCAAAGAGTTTGCCAAATTTCCCATAAGAGAAGT[A/G]TTTAGCAGGCCAGATTAAACTTTGCCTTGGCACTA R 2 1 2 1 101000 r 74 goat snp14187-scaffold1567-390149 6 25267769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393640 Affx-122965298 AX-123263995 6 23368884 GTCCTAGTTATTTTCATCAGAAGCCACTTCAGGTT[A/G]CCACAAAACTTGAATTTTAGTATATTCCGACATCA R 2 1 2 1 101000 f 74 goat snp14186-scaffold1567-357890 6 25300005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772984 Affx-122964379 AX-385260128 6 23407559 AGAGACCTTTAAATGGGTTACTGTAATAGAGTACT[A/G]AGAATAAAGCAACAAGAGTCAGTGGACGTCAATAT R 2 1 2 1 101000 r 74 goat snp14185-scaffold1567-319215 6 25338666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786023 Affx-122922013 AX-385273059 6 23437356 ATATCTGCTCCTCGGTTTGAAAGCAAAGGCAGCCA[C/T]ATTTCAGCTAGAAATGGAAGCTGTTTTCTAGTCAG Y 2 1 2 1 102000 f 74 goat snp14184-scaffold1567-289418 6 25368248 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449328 Affx-122922989 AX-123319663 6 23476329 CCACACACAGAGTCAGCCTCAGGGAGGGAGGAAGC[A/G]CTCTTGAATACAAACTACCAGGCACACCCAGGCTA R 2 1 2 1 101000 r 74 goat snp14183-scaffold1567-250445 6 25408166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391050 Affx-122966857 AX-123261407 6 23504923 TTTTCAAAACCTAATTCAACTTATTTTGTAACAAG[C/T]GCTTTTTAAAAATATTTACATTTGAATCCAAAAAG Y 2 1 2 1 101000 f 74 goat snp14182-scaffold1567-221851 6 25436859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389179 Affx-122969086 AX-123259537 6 23571234 CACTTGCTGATGTAGAGAACACAGTAGTGCATGGA[C/T]GCATACATGCCTGAGTCAGGCAGGAAGGGGGAAGA Y 2 1 2 1 101000 f 74 goat snp14180-scaffold1567-155540 6 25503606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799260 Affx-122963947 AX-385286190 6 23646279 AAACACTTCATCCCTAAAGGTATGCTAGCTGGAGC[A/G]TACTGACATTTGTCAAGAAATGATATAGAAAGGCT R 2 1 2 1 101000 f 74 goat snp14179-scaffold1567-80495 6 25577999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440837 Affx-122929266 AX-123311174 6 23755627 TTCCCCCACTGCAGGTTATCAAGTGCAAGGCTGCA[A/G]TTGCCTGGGAGGCTGGGAAGCCTCTTTCTATAGAG R 2 1 2 1 201000 f 74 goat snp34814-scaffold415-28754 6 26016615 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437918 Affx-122931646 AX-123308256 6 23866747 TTGAGGAATTTCTTACCTAAGGAATGATTTCTTCT[A/G]TTTCATATATGACCAGTGTTTACAGATACCTATGA R 2 1 2 1 101000 r 74 goat snp34816-scaffold415-139874 6 26128154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385607 Affx-122971196 AX-123255965 6 23902087 TGCTGGAACTCAAACCCAGGTTCTGTCTACAAGCT[G/T]TATTACTACACTTAGAAAAAACAAACTAAAATTCA K 2 1 2 1 101000 f 74 goat snp34817-scaffold415-175214 6 26163649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381609 Affx-122974783 AX-123251967 6 23938613 ACTGACTTCCTTCCTTGCTTGCTTGTAATTTTTGC[A/G]TTCACAGTTTCCCAGTGTAAATTGTAGTCTTATCT R 2 1 2 1 201000 r 74 goat snp34818-scaffold415-211740 6 26200227 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433524 Affx-122935009 AX-123303865 6 23970185 TTGCTGAGCCACTGGGGAAGCCCTATCTCTTTAAA[C/T]ACAGAGAAAAGAACTATCGAGTTTGAAGTATGTTT Y 2 1 2 1 101000 r 74 goat snp34819-scaffold415-243312 6 26232406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414390 Affx-122949992 AX-123284739 6 24028808 TTTGTGCCGCTGTGTCAGTCTTGATTCAATAGAAG[C/T]ATTTCATTCCACAGAGACAGTGGGTAGCAACTGTT Y 2 1 2 1 101000 f 74 goat snp34820-scaffold415-301935 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392756 Affx-122966003 AX-123263113 6 24059620 AAGAATGGAATGTTTTCCTGCTTTCTTGCCTTAGA[C/T]ATCTTTAAGTTGGTATATATCTTGAATTTGAGGAG Y 2 1 2 1 201000 r 74 goat snp34821-scaffold415-332747 6 26312981 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407814 Affx-122954551 AX-123278165 6 24088676 TAGGCCAGACCAGGGACCCTTGCCTGCACTCTTAG[A/C]GTTCCCTGCAGTTTTTCTTTCTACCAAATAGCACA M 2 1 2 1 201000 f 74 goat snp34822-scaffold415-361803 6 26342268 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397763 Affx-122962522 AX-123268118 6 24120521 GCATTGTCCCCTTTGTCCATCCATTCATCCGTTCC[A/G]TCATGATTGTAGTGTATGCAGACCTGCCTTGATTG R 2 1 2 1 201000 r 74 goat snp34823-scaffold415-393648 6 26374279 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432562 Affx-122935534 AX-123302903 6 24153390 TGGACATATTTAAAAGTCAAATTCCTGGGTGAGGC[A/G]TTTTGATTTTATCTGAACTTGAAACTTTCATGACT R 2 1 2 1 201000 r 74 goat snp34824-scaffold415-426517 6 26406992 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418757 Affx-122946204 AX-123289105 6 24206396 ACCTGTTTGTCTTCTTTGGAAAAAATGTCTCTTCA[C/T]GTCTTCATCCTTCTTAATACTAGAGTGACGGAGGG Y 2 1 2 1 101000 r 74 goat snp34825-scaffold415-479523 6 26460006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426916 Affx-122940444 AX-123297261 6 24241996 TTACAAAGTGGAAAATAGCTGTAGCAGAATCCCTG[C/T]AGTAAACACAATAAGGACTTTTTTCCTGTAATATT Y 2 1 2 1 101000 f 74 goat snp34826-scaffold415-515123 6 26496008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388202 Affx-122969421 AX-123258560 6 24293081 AAGGGAGAGGTGGACCCTGGTTCAGATGGGAAATA[G/T]CCTGTTTACAAGTCTGGACTTTATCTGCCATGCCA K 2 1 2 1 101000 r 74 goat snp34827-scaffold415-566208 6 26546758 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419909 Affx-122945335 AX-123290257 6 24398707 GTCCATGTGGCAAATACATTATCATAAGAGTATGC[C/T]AGAGAGATTTCAGGAACCAGAAAAGAGAAATGAAC Y 2 1 2 1 101000 f 74 goat snp34830-scaffold415-671834 6 26653528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426636 Affx-122939949 AX-123296982 6 24491012 CAGTGGTACAGTTTGTAAAATTGTACTTCACATAA[C/T]GTCAAAAGACCTTTTCACTGAGAGTTCAAGAATTA Y 2 1 2 1 101000 f 74 goat snp34832-scaffold415-764139 6 26746134 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792018 Affx-122971355 AX-385279006 6 24548865 CTCCCAAATTAGAAAGCTCAGAGCCATTCTGCATT[C/T]CTCTCTCTTACCCAATCTATATATAATTGACTTTC Y 2 1 2 1 101000 f 74 goat snp34833-scaffold415-821992 6 26804333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423925 Affx-122942266 AX-123294271 6 24583397 GAGGTTTGAATGACAATATAGATAAGACAGTTAGT[A/G]TGATTCCTCTTGCTCAGTCACCAAGTTGTCTTTGT R 2 1 2 1 303000 f 74 goat snp34834-scaffold415-856524 6 26839243 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788450 Affx-122942994 AX-385275467 6 24710053 TTTTCATCTTTATAGAAGGAAATGGGATGAGACAC[A/G]TTATGACACAGGTACCTACTAAAAGCCTAAAGTCA R 2 1 2 1 101000 f 74 goat snp34837-scaffold415-983180 6 26964833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779028 Affx-122929138 AX-385266135 6 24752999 CAACTAGACAACTGTTCAGAACAGGAGGCAAGTAG[C/T]AGTAGTCCCTGTTTGTCAGTAGCTAATTATTTTTT Y 2 1 2 1 101000 f 74 goat snp34838-scaffold415-1026126 6 27008185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788090 Affx-122931215 AX-385275110 6 24814748 TCTGTTTTGTATTTTCCCATTCTAACCACCATCCT[A/G]CTGCTTTTTCCCTACACTGGGATCTTTTTCAGTTT R 2 1 2 1 101000 f 74 goat snp34839-scaffold415-1087875 6 27070068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454219 Affx-122919679 AX-123324552 6 24862427 AATCCATAGAGGCTTGCTTTATTTTTCAGTTTCAC[A/G]AATCAGGTATATTACCAACTTACAGGTCCATTTTA R 2 1 2 1 201000 r 74 goat snp34840-scaffold415-1135554 6 27117745 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432522 Affx-122935562 AX-123302863 6 24903743 CCTGCTGTCCTTACAGGTCCACTGTCTTAGTGTAG[C/T]GGGCAGAGGCTTAGACTGTTTTTACAGGTAGTCCT Y 2 1 2 1 101000 f 74 goat snp34841-scaffold415-1176870 6 27158856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414682 Affx-122949293 AX-123285031 6 25000003 ATTAGCAGAGAAATTGTTACTGAAAACTCTGTCCA[C/T]GTCTGTGATGCTGAATGAGAATGAGGAGGCCAAGT Y 2 1 2 1 201000 f 74 goat snp34843-scaffold415-1273130 6 27257290 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787202 Affx-122944833 AX-385274228 6 25052954 ATTCACATAGCACTTTCCAGAGTTTGTGTGCTTTC[A/G]TTAATCATATTTCACTTATAAAGTATCCTTTTGTC R 2 1 2 1 101000 f 74 goat snp34844-scaffold415-1326081 6 27310294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380231 Affx-122975473 AX-123250589 6 25087845 AGTTTTTGCCTTCTGAGAGAACCCTGATTTGGATA[C/T]GGATACAAGAAGAGAAAACCAATTTGGCTGCAGTG Y 2 1 2 1 101000 f 74 goat snp34845-scaffold415-1360972 6 27345209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391438 Affx-122966748 AX-123261795 6 25118173 CCAATATGTGTGTGTGTATGTGCGTGTGTGTGTAC[A/G]TGTGTATGGAACCAATACCAAGGAATGACAGCGTG R 2 1 2 1 201000 r 74 goat snp34846-scaffold415-1391300 6 27375870 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779731 Affx-122973038 AX-385266831 6 25167678 TAAATCATTCCTAGGACATAATAGTTTTTTCTGTT[A/G]GCATTCAACCATTATTTGAAAGTAAAAAGGTTTCT R 2 1 2 1 101000 r 74 goat snp34847-scaffold415-1440805 6 27426069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765162 Affx-122944064 AX-385252713 6 25200092 TGTAGGGGTTGATAGAAGAGGATAAAGTCAGATAT[C/T]CATTTACAAATACTGTAGCTAATTATCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp34848-scaffold415-1473219 6 27458857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779193 Affx-122945303 AX-385266297 6 25233743 AATTATTGTATTTATGAATAATATAATTAATACAT[A/G]TTATTCTTTTGTTTGACTACTCATAGCTCAGTCCA R 2 1 2 1 303000 f 74 goat snp34849-scaffold415-1506870 6 27492535 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409790 Affx-122952974 AX-123280141 6 25279461 ATCAGGCTGAGCTATAGAGCCAATCGCTATGAGCC[A/G]GACTATGGGGAAAGACCATCTCTTTTTTGTACAGG R 2 1 2 1 201000 f 74 goat snp34850-scaffold415-1552588 6 27539918 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381369 Affx-122974399 AX-123251727 6 25318673 AAAATATACTTTGGCTTTAAAAATTTCATGACTTA[C/T]GGCTATTTTGTAAATACAACTGCTTTGTACATTGT Y 2 1 2 1 101000 r 74 goat snp34851-scaffold415-1591800 6 27579191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437325 Affx-122931959 AX-123307663 6 25359030 TTTTCATTATCTGGTTGAAGACTATCCTACGGTAG[C/T]ATGACAATTATTTTGAGCTGAAGACATTAGAGTTC Y 2 1 2 1 101000 f 74 goat snp34852-scaffold415-1632157 6 27612703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432969 Affx-122935274 AX-123303310 6 25395390 TCGCTTGGAAGCTGGGGTGTTTTGAAATAAATCTT[C/T]AGGAGTTTGCTGTTTGAATATCTCAATCACTGCCC Y 2 1 2 1 101000 f 74 goat snp34853-scaffold415-1668517 6 27648984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386335 Affx-122970876 AX-123256693 6 25453429 TGTGAGTTCATAGACAGGGCGAAATAGATTGCTGC[A/G]GCTGTGTCAAATCTGTGCAGAATACAGATTTGCTG R 2 1 2 1 101000 f 74 goat snp34854-scaffold415-1726556 6 27708244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784489 Affx-122942420 AX-385271538 6 25515545 CAAGTGACTGAATTTTGACAATAATGCAAAGTGTG[A/C]TGCTTACAGAGGTGACCCATAAAAGATTGAGTGTA M 2 1 2 1 101000 f 74 goat snp34856-scaffold415-1788672 6 27770384 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418548 Affx-122946400 AX-123288896 6 25592179 TTGCTATAAAGTGGACTTGAGGCCCAAGTATAGAC[A/G]CTTAGGTATTCCTATCCAGAATTTTGATTTCTGTG R 2 1 2 1 101000 f 74 goat snp34858-scaffold415-1865306 6 27847844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425330 Affx-122940931 AX-123295676 6 25629079 TGTACAAACTGGCATCTTCTCACCTACTTTGTACT[A/G]CTTTATCCCATCCTCATGCACTTGACTTTTGCTGT R 2 1 2 1 101000 r 74 goat snp34859-scaffold415-1902206 6 27884880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450570 Affx-122922040 AX-123320904 6 25668680 AGAGATATAATATCTTTCAACTGTGACAAATTTGG[C/T]AACAGAAAAATTTAAAGGAAAACAACTCACAGTTT Y 2 1 2 1 103000 f 74 goat snp34860-scaffold415-1941807 6 27924974 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799250 Affx-122972350 AX-385286180 6 25705039 AGTAGGGAATGGAGGCTTGGAAACCTGTACTTACA[C/T]GGATCTGCTGGTTTAAATCACTTCAAACCTCCCCT Y 2 1 2 1 101000 f 74 goat snp34861-scaffold415-1978166 6 27961577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801897 Affx-122958190 AX-385288805 6 25737878 ATACATGAAGTCCACAAAGGCAGGTGTGATACTTG[C/T]TACTCTCAGCAGTGGCACTGTATCTGTTACACAGA Y 2 1 2 1 101000 f 74 goat snp34862-scaffold415-2011005 6 27994435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394958 Affx-122964281 AX-123265313 6 25774149 ATATGAGAGAACTAGGTTTGGTTTGGATATCAGTT[A/G]TAAATGCATTATTTAAAAAACAGCTTAATAATTAA R 2 1 2 1 101000 f 74 goat snp34863-scaffold415-2047276 6 28030977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409261 Affx-122953130 AX-123279612 6 25804972 TTATTTGGGCCTAATGTAATAAATTTTAAGTGACG[C/T]AAGTCAGTCTAAAAATCTTGATCCAATGACACTGC Y 2 1 2 1 101000 r 74 goat snp34864-scaffold415-2078099 6 28062018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272341 Affx-1111833500 AX-185174181 6 25825036 GGAAAAGACTCTGATGCTGGGAGGGATTGGGGGCA[A/G]GAGGAGAAGGGGACGACAGAGGATGAGATGGCTGG R 2 1 2 1 103000 f 74 goat 6_25825036_AF-PAKI 6 25825036 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38405705 Affx-122956538 AX-123276057 6 25837598 GAAAGCACAGGGACAGAGGGACCCTGAAATCTAGC[A/G]TCATTAAGACCAATCTCTTATTTTTCTCTCATATT R 2 1 2 1 101000 f 74 goat snp21589-scaffold211-12629 6 28095951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433053 Affx-122935755 AX-123303394 6 25898159 ATAAGATAAAATACATTTTCCAAACACAGGCATAA[C/T]GATGTCACCTGAAAATTCTGGTTAGACATAAGCCA Y 2 1 2 1 101000 r 74 goat snp21590-scaffold211-73190 6 28156599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452960 Affx-122920166 AX-123323293 6 25935818 CTATACATATAAGAGATATCATCCAAGAACTAAAT[A/C]AAGAAGGAGTTGTCTTAGAGTAATGTGGTCTGTAT M 2 1 2 1 101000 r 74 goat snp21591-scaffold211-110849 6 28194306 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771394 Affx-122939718 AX-385258552 6 25969563 AGCTTTGCATAGGGCAGACACACAAGTATGTGTTC[A/G]TTGAAAGTAACAAACATTGAAAAGTAGTACTTAGA R 2 1 2 1 102000 f 74 goat snp14498-scaffold1580-21386 6 28226848 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442364 Affx-122928024 AX-123312701 6 26003679 GGCTGATAATAAATATTTTCTTCCTTTATAATCAC[A/G]TAAACTTTTGAATATATGTACATACATTTATACAT R 2 1 2 1 103000 f 74 goat snp14499-scaffold1580-55502 6 28261829 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449778 Affx-122922434 AX-123320113 6 26058676 ATTAACATCCTATTTTTCAAAGTGATATGCCCGCT[A/G]TATACAAACATTTTAACTGATCCTACTGAGATACT R 2 1 2 1 201000 r 74 goat snp14500-scaffold1580-110499 6 28317795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792819 Affx-122950159 AX-385279797 6 26094911 CTTAGATGACCTGTTTCTGGAGGACAGACATGATG[C/T]TTAATAAAATGTAGAACAGACACACAGTTAATCAT Y 2 1 2 1 101000 f 74 goat snp58966-scaffold968-13458 6 28354282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396481 Affx-122963547 AX-123266836 6 26139009 CAATAGATATTGACTTTTTTCAAGGTTCTAGTGGT[A/G]TACTTGTACAAACAAAGCCTTTGCTCTCAAGAAGC R 2 1 2 1 101000 r 74 goat snp58967-scaffold968-57556 6 28396204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782415 Affx-122919934 AX-385269491 6 26177943 GTCAGATTCCTATTATTACATAATGGAAGAAGTGG[A/G]ATTCCTAGGAACTTTCTTAATGTGGCCAGATATCG R 2 1 2 1 101000 r 74 goat snp58968-scaffold968-96490 6 28441253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772657 Affx-122929443 AX-385259804 6 26215353 TTGAAAAGGCAAAATGGACATTGCCGAGAGTGCCA[C/T]AAGGATGTTGACTGTTTTAGCTCGTTTAACGTGTC Y 2 1 2 1 101000 f 74 goat snp58969-scaffold968-133900 6 28479368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793445 Affx-122966889 AX-385280422 6 26287037 TTCTTAGTATAAGTTTTCTCCTCCCATACACCTAG[C/T]AATTTTTCTCATCCCATGGGAGATTAACTTGAAAC Y 2 1 2 1 101000 f 74 goat snp58970-scaffold968-205584 6 28551663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778200 Affx-122945282 AX-385265315 6 26331733 AAATATAAATATTAACCTAATTATGGTAAACATTT[A/G]TGAAAATGTCTTTGAGCTCAATATTGTATCTTACC R 2 1 2 1 201000 f 74 goat snp58971-scaffold968-250280 6 28596618 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428978 Affx-122938864 AX-123299320 6 26364955 AGTATACTTTCCCCAAATGTGCTCATGCTAAGAAC[A/G]TGAATAGACATTGTTCCTCCTGGATTTTCTATTCT R 2 1 2 1 202000 r 74 goat snp58972-scaffold968-283502 6 28630370 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409794 Affx-122952971 AX-123280145 6 26419337 TGGTTAATTTTTCTTGGTGTCTTGCTTAACTTGGT[A/G]TCCTGTGACTAACTGCAAACAACCAGACAGACTTT R 2 1 2 1 201000 r 74 goat snp58973-scaffold968-337884 6 28686137 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786582 Affx-122929695 AX-385273614 6 26469670 TGAAACTAAAATCATAGTAGGTTCTTCTGCTGGGC[A/G]TCAGGGACAAGGATGTGGTGTAAAGTATGTGCAGT R 2 1 2 1 101000 r 74 goat snp58974-scaffold968-388217 6 28736494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777885 Affx-122943257 AX-385265001 6 26507871 AAGTGTAAAGTTGATTCAATCTGTTCTTGATACTC[A/G]CCTTCATATTCACTTTTCTGCCCGCATAATCCCAT R 2 1 2 1 101000 r 74 goat snp58975-scaffold968-426418 6 28773976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799613 Affx-122961662 AX-385286543 6 26544694 AACCCTCTGCATCTAAAAAATTGGGTAAAAGCCGT[A/G]CTTAAATCATATAGCTGTTGGGTAAATATAACAAG R 2 1 2 1 101000 f 74 goat snp58976-scaffold968-463241 6 28811120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278338 Affx-1111836370 AX-519551824 6 26559855 GTACTCAGCTTTGAGTGAGACAGTAAATGCGCTGG[A/G]GGGCTTGAAGTAGAGACGCGACAGGATTCTGCCTT R 2 1 2 1 101000 f 74 goat Random2.2K-660 6 26559855 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443081 Affx-122928119 AX-123313418 6 26637729 CACAGTCACACTGACATTCACTGACGCAGTGTTCT[A/G]TAGTTTAGCTACTATGCCTTAGCCACTGTCAGCTT R 2 1 2 1 201000 r 74 goat snp58977-scaffold968-556276 6 28903049 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387878 Affx-122969629 AX-123258236 6 26696231 AAATATAAGAGGCATGGGTCTCCAAATGATTATAT[C/T]GAACAGTTCACTTGAAAACACAGACACACACAGGT Y 2 1 2 1 201000 f 74 goat snp58978-scaffold968-614778 6 28962901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418460 Affx-122946468 AX-123288808 6 26759285 CTACGCTGCAATCAAGTCTCAATCAGATCCACTCC[A/G]CCCACAAGCTGCTCACTGTTTCTGAAAAAAGAGAA R 2 1 2 1 201000 f 74 goat snp58979-scaffold968-677832 6 29025606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801176 Affx-122976709 AX-385288088 6 26790439 AATCCTCATAAGATTTCAGGTAGCCTCCAGCTATG[C/T]TGAAACACTTTTCATACCGTTTCAAAGCTTCCATC Y 2 1 2 1 201000 r 74 goat snp58980-scaffold968-708986 6 29056730 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415782 Affx-122948914 AX-123286131 6 26820944 ATCATTAAAAAATAATCTGTAATTTGATTAACATC[A/G]ATAGGTTATTTAAAAAGTAGTGACTTTTTTCTTGT R 2 1 2 1 201000 f 74 goat snp58981-scaffold968-739491 6 29087661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798782 Affx-122974820 AX-385285713 6 26849679 GCCTCATAAATAGCAGCACTGTGATAGTGTACCAG[C/T]ACTCTTCAGCTTCTAAGTGCATCAGATATAAACTG Y 2 1 2 1 101000 f 74 goat snp58982-scaffold968-768226 6 29117050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448107 Affx-122924313 AX-123318443 6 26902957 CTGCTCTGTTAAACATCATGTTTTATTTGGAAAAA[C/T]AGTCATTCTAACTGGTTCTAGCATCAATATTAAAT Y 2 1 2 1 201000 r 74 goat snp58983-scaffold968-821504 6 29170732 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428461 Affx-122938800 AX-123298804 6 26936028 CTGCATCAGATACCTAGTATACCTGATATATTTAA[C/T]ATGAACAAACCCAAATTCTTGGTTTCCTACCCTAA Y 2 1 2 1 201000 f 74 goat snp58984-scaffold968-854575 6 29203826 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766857 Affx-122954846 AX-385254178 6 27042661 TCCCTATCACCAGAGACTAGGAGTCAACACTGAAA[C/T]GGATCTATACAGACTCACTAAAATAATACTTATCT Y 2 1 2 1 101000 f 74 goat snp58986-scaffold968-961208 6 29312449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784195 Affx-122924022 AX-385271246 6 27076659 ATAAGAGAGCATGAATTGCAGAGAGGTAAGGATAA[A/G]GTGGTTGGGTTAGTGCCTCATTATCCTTGCATCTC R 2 1 2 1 101000 r 74 goat snp58987-scaffold968-995206 6 29346523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795826 Affx-122923435 AX-385282779 6 27107543 GATCACAGAAGGAGAGACAGTTTTAAGAGCAACAG[C/T]AATAGAGTCACGTCTGGACATGCTGAGTCTCAAGT Y 2 1 2 1 101000 r 74 goat snp58988-scaffold968-1026090 6 29377452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772098 Affx-122973888 AX-385259253 6 27147319 AGGGCCGAAAATTGTTAGGAATGAAGTACTTCAAA[G/T]CAATATGTTTCCAATTTCCTAAAGGCACCTTCTTC K 2 1 2 1 201000 r 74 goat snp58989-scaffold968-1065866 6 29417869 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377414 Affx-122977556 AX-123247773 6 27205314 TAAAATTATTTGAGGGGGAAAGAGTTGTTACTACT[G/T]AAAGAATATAAAAAATTTAATTCTGCATAGAGGGA K 2 1 2 1 101000 f 74 goat snp58990-scaffold968-1123861 6 29475856 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376201 Affx-122978814 AX-123246560 6 27250020 TGGTGGGCTATAGTCCATGGGATCACAAAGAGTTG[A/G]ACACAACTGACTGGACATATGCACCCACTCTTGTC R 2 1 2 1 303000 r 74 goat snp58991-scaffold968-1168567 6 29520557 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780236 Affx-122951983 AX-385267331 6 27337276 TGAGAAGTAAGTTTGCTTTGAACTTTCTGATTCTT[A/G]TTTTAGATGAAATATCAAATAATAGATAGGCTTCT R 2 1 2 1 102000 f 74 goat snp58993-scaffold968-1255823 6 29607878 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443490 Affx-122927808 AX-123313827 6 27388755 AAGTATTTTTAGTGTATATTACTCTAATCTATGTT[A/G]TTCTCCATGTCAGTTCTACTACTTAATACTTGAGG R 2 1 2 1 101000 r 74 goat snp58994-scaffold968-1307302 6 29659340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765182 Affx-122938997 AX-385252731 6 27431574 AGATTAGAGCCAAGGAAAGATTTGGCAGCCTTAAT[A/G]CTTGTGTAGTATTCATATTTGGAATGGAATGCTTT R 2 1 2 1 101000 f 74 goat snp58995-scaffold968-1350121 6 29702490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794741 Affx-122969223 AX-385281700 6 27487166 TTAAACCTGTCTTTTGAAGTACAGGCCTCTGATGT[A/G]TGGTCACCATTCTCACTTAGGAAACAGTAATTTTC R 2 1 2 1 101000 f 74 goat snp58996-scaffold968-1405713 6 29759230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787424 Affx-122968083 AX-385274449 6 27543511 GTATTTTTTATCTTGTACTCTTCTACATTCTAACT[A/G]CATACTGACTCCCACGTTTAGAAATACACTAAGCA R 2 1 2 1 101000 r 74 goat snp58997-scaffold968-1462058 6 29815950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787614 Affx-122970445 AX-385274637 6 27590453 CTTAAACCACCTCAAAACTAGTGTGACCTACATTT[C/T]ATGTTTTTAGGACCATGGTCTCTGAAATTAAATTA Y 2 1 2 1 101000 f 74 goat snp58998-scaffold968-1509000 6 29863156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278340 Affx-1111836371 AX-519551826 6 27612120 CACAAGGAAGGGGTGCTTCAGACACAGTGGCAATG[A/G]AGTCAGCAGGGGCAGGGGGAGGGTAATGGCGCCAG R 2 1 2 1 102000 f 74 goat Random2.2K-662 6 27612120 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385575 Affx-122971841 AX-123255933 6 27619461 GAGAAGTTAGCGCCATTTAAAGAATAGAAACTCCA[C/T]AAAGAATGAAACGGCACTTCACAAAGACCGTTCAC Y 2 1 2 1 101000 f 74 goat snp58999-scaffold968-1538008 6 29892139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440722 Affx-122929891 AX-123311059 6 27703450 TACAGACCTCACTGAACTGGGAGATGACAGCCTTT[C/T]TATAGCAAAAGCAGCCTGAGCAGTATCAATGCACA Y 2 1 2 1 201000 r 74 goat snp59001-scaffold968-1621997 6 29976369 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431116 Affx-122936599 AX-123301457 6 27748058 CCAAGATTCTGTCTCTTAAGTCCTTCTCTCATTTC[C/T]ATGCACCAAAGGCCCTTTTCTTCCTTTGCTCCAGC Y 2 1 2 1 101000 f 74 goat snp59002-scaffold968-1666605 6 30020914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801447 Affx-122928263 AX-385288357 6 27800859 CTCCAAGACAGGAGGGGCAAGGTGATCCTAAAATC[A/G]CCCTACCAGAAGGATTTCTGTCAGCTAAAAGGAGA R 2 1 2 1 101000 f 74 goat snp59003-scaffold968-1719406 6 30073666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411682 Affx-122952001 AX-123282032 6 27866327 TTGGCCCCTCAGAATTCAAAACGTAGGGAAAATTG[C/T]AGCAAAACTGACAGCAGAAATGTTGCCAATGGTTA Y 2 1 2 1 101000 f 74 goat snp59004-scaffold968-1784874 6 30139356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772464 Affx-122949116 AX-385259615 6 27897570 AATAGTGACAGAAACTAGACTTTTGCTGATGAGCC[C/T]ACTATAGAGTATACAGGTGTCAAATTATACTGTTG Y 2 1 2 1 101000 f 74 goat snp59005-scaffold968-1816117 6 30170250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413239 Affx-122950239 AX-123283588 6 28008827 CTTAAAGGTGGCACTGATACACCTTCACCGACACA[C/T]GTACTTCCTTCAAGAGGCAGGTTCTAAGGGAAAAT Y 2 1 2 1 101000 f 74 goat snp59007-scaffold968-1927374 6 30282274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802228 Affx-122946174 AX-385289132 6 28058251 AAACATCTATAAGTGCATTATATCATAGAAATGCA[C/T]AAAGGAATGAAAACTGTCTAGATTCAAGTCATATC Y 2 1 2 1 102000 r 74 goat snp59008-scaffold968-1976798 6 30332531 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389819 Affx-122968191 AX-123260176 6 28102440 CAGGCACTTCATACAACACAGCGACAAAAACAAAA[C/T]TATCTTGCAACCAGAGTGAAATAGCAGAATTGTGA Y 2 1 2 1 101000 f 74 goat snp59009-scaffold968-2020987 6 30380872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382478 Affx-122974202 AX-123252836 6 28162984 GTAGTCCTTGAAAATGGTACCATGAATACCGCTTT[C/T]GTTATAATCATTTTTAAACATAACGCTGTTTTGAA Y 2 1 2 1 101000 f 74 goat snp59010-scaffold968-2081531 6 30441024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408339 Affx-122953750 AX-123278690 6 28204085 CCGCTTCAGAAAGGGAAATATAATTATAAATCTAA[C/T]GCTTTTGCTAAGGACAAAGAAGCTTGAAGAATTAA Y 2 1 2 1 101000 r 74 goat snp59011-scaffold968-2122632 6 30482438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402870 Affx-122958232 AX-123273223 6 28263130 AGTTTACAGAGACAATGATGAAAATTAGAAAGAAA[C/T]CACTGATTAGGTACTTACACGGTGCCAGGGTTACT Y 2 1 2 1 201000 f 74 goat snp59013-scaffold968-2181677 6 30541734 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436881 Affx-122933232 AX-123307219 6 28316337 GGAACAAATTCAATGGCAAAAATTCTTACTGTGGT[A/G]TATTTGAAAAAGTAAAATGAACTTTTAGACAACAG R 2 1 2 1 103000 f 74 goat snp59014-scaffold968-2234884 6 30594292 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798205 Affx-122938016 AX-385285140 6 28397609 CATTTTTCAATTTCAACAGACAGTAAATTTAAAAA[G/T]ATGCAACTGTTCCCTACAATCACGGGGGATTTGAT K 2 1 2 1 102000 r 74 goat snp59016-scaffold968-2316156 6 30673494 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476215 Affx-1251763720 AX-586011639 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 4 1 4 1 20000 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 539476469 Affx-1251763720 AX-586011869 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20000 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 560378495 Affx-1251763720 AX-605230910 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20000 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165618 Affx-1251763720 AX-606941029 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165755 Affx-1251763720 AX-606941164 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165991 Affx-1251763720 AX-606941400 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562166248 Affx-1251763720 AX-606941656 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562166361 Affx-1251763720 AX-606941769 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 38421562 Affx-122943855 AX-123291909 6 28433270 TGGGTATGAAGATATTTGCTAGTGGCTTAAATATG[C/T]AATGTGATTTTTTATTTAGGCCATATTTTTCAGTA Y 2 1 2 1 101000 f 74 goat snp59017-scaffold968-2351817 6 30709494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785938 Affx-122970788 AX-385272975 6 28471829 CAGAGTTCTATGTGCTGTACAGTAGTAAAAATATA[A/C]TGCTTAGTTTGGTGTAAATGATACCATACTATATT M 2 1 2 1 101000 f 74 goat snp59018-scaffold968-2390376 6 30747854 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420749 Affx-122944724 AX-123291096 6 28511349 TATTAGCTAAGTAATGTAAGTATGATTTTTTCCCC[A/G]TATTTCACCATTTAAGGATTATGCTCTCTGTGTGT R 2 1 2 1 101000 r 74 goat snp59019-scaffold968-2429896 6 30788852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431507 Affx-122936238 AX-123301848 6 28554042 GCATGTTATTTACTCTTCATCACACAGTATGCTTC[A/G]CTAAGGCATCACAACTTGTGTCAGCTTTATTTGGG R 2 1 2 1 101000 f 74 goat snp59020-scaffold968-2472589 6 30831884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389702 Affx-122968689 AX-123260060 6 28596607 TGTTAGTTTAGAATTTAGATCTAAGTAGTGATACA[C/T]TGTCAATGAATGTAAGACATCAGTTTCATTTCTCA Y 2 1 2 1 101000 f 74 goat snp59021-scaffold968-2515154 6 30874462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448550 Affx-122923428 AX-123318886 6 28639865 TAAAAGAGAGATGCTAATAATCACAGGATTAATGT[A/G]CACATAAAATTAGAAGATATATATTAAGAATTTAA R 2 1 2 1 101000 f 74 goat snp59022-scaffold968-2558412 6 30918054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428121 Affx-122939070 AX-123298464 6 28669076 AATGTGACTTCTAGAACTTGAAACCTCTATTAACT[A/G]CTGTTAACAATTTAAGGGATTAAAAATAATGAATA R 2 1 2 1 101000 f 74 goat snp59023-scaffold968-2587623 6 30947311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766687 Affx-122947551 AX-385254031 6 28763035 GGTTCCAGACAGTTTATCATAGCTTTGAGTTTCAG[A/C]TTTCTCTTCCATTGACAATTAAAGCAATGCTTTGC M 2 1 2 1 101000 f 74 goat snp59024-scaffold968-2681582 6 31041030 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464427210 Affx-1110480594 AX-515900025 6 28776552 CCCAGTCAGAGATAATTCTTTCCTATTAAACATCT[C/T]TAAATTTATTTTATAGTATTTATCACAGACTTCCT Y 2 1 2 1 101000 f 74 goat 6_28776552_AF-PAKI 6 28776552 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449433 Affx-122922679 AX-123319768 6 28792431 AGCAGAGGAAAACTATGTCTAATACTACAGATAAT[A/G]CAATCCATCTAGTAGGGGTTTCCATAAAAATCTGA R 2 1 2 1 201000 f 74 goat snp59025-scaffold968-2710978 6 31070854 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797747 Affx-122920175 AX-385284686 6 28830290 TTCTCCGCAAGAACTTTGATTCACTATTAAATTCC[G/T]TCTAATGAAGATGACTTTGCCATCCCACGGCCATC K 2 1 2 1 101000 r 74 goat snp59026-scaffold968-2748837 6 31108765 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413997 Affx-122950277 AX-123284346 6 28844432 TATTCAGGACATTCTGCTGATGCGGACTAGAAATA[G/T]ACTAAGGAATTGAGATTACAAATACCATCCGAAAG K 2 1 2 1 101000 f 74 goat snp12505-scaffold148-5556 6 31122826 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779499 Affx-122927863 AX-385266602 6 28878176 TAAGGGTCTTCATAAACCTCAGTGATTAGTTGCCT[A/G]CCGGAATATACTATGCAAAGGTAATTTATACACAA R 2 1 2 1 101000 f 74 goat snp12506-scaffold148-39300 6 31156496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789866 Affx-122944286 AX-385276873 6 28912296 GTGTTACAAGGTATTTGAGGTGATTTTGGCTCTTC[A/G]TTGATTAAAATGAGATTCCTTTGGTAGAGCTCATA R 2 1 2 1 101000 f 74 goat snp12507-scaffold148-73420 6 31190970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400299 Affx-122960074 AX-123270654 6 28973752 TTAATAAGGTAGATTCCTGGGCCCCTACTAAATCT[A/G]CCAAATCCACTTTTTGAAAGGAACCGAGGACTTGT R 2 1 2 1 101000 r 74 goat snp12508-scaffold148-134876 6 31252563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443676 Affx-122927181 AX-123314013 6 29006880 TTATTTGAATTTTTTAAAAGTGTAATATGTTCCGT[A/G]TTACTCTAATGGGGATAGAAAAATACGGGGCTATG R 2 1 2 1 103000 r 74 goat snp12509-scaffold148-168004 6 31285442 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392247 Affx-122967567 AX-123262604 6 29052799 AAAGACTCAGGAAAAAATTTTGACCGTCCCCATAA[C/T]TGCACCCAAAAATTTAGATCGAAGGTCTGTTTCTG Y 2 1 2 1 201000 r 74 goat snp12510-scaffold148-213923 6 31331006 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431962 Affx-122935961 AX-123302303 6 29101223 AAAAGGGGAGGAAGAGCTCATGTTATATCAAACAG[C/T]GAGCAGTAAAGTTTTTTATTTCTTTATCCAGAATC Y 2 1 2 1 103000 f 74 goat snp12511-scaffold148-262347 6 31383681 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378412 Affx-122976786 AX-123248771 6 29165070 TTCCATGAATGAGAAATAGCTTTTTTCAAGTCATG[A/G]ATACTTTGGGCTGTTTGCTACACAGAAAAGGTGAC R 2 1 2 1 101000 r 74 goat snp12512-scaffold148-326194 6 31448495 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432166 Affx-122936413 AX-123302507 6 29207870 TACAGGAAAGCCTACTGATGTTGCAAGCGATCAGT[A/G]TGGGGTGGCAAAGCCAGAGCCTTGAAAGAAATGTC R 2 1 2 1 201000 f 74 goat snp12513-scaffold148-368994 6 31491328 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417915 Affx-122946729 AX-123288263 6 29237567 CCAATACATTTATGGCTCAGGGCCTCCTTTTCTTC[A/G]CCAACGAAATGCAGGAGTTGCTATTTAATGAACTG R 2 1 2 1 101000 f 74 goat snp12514-scaffold148-398691 6 31521126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431209 Affx-122937160 AX-123301550 6 29276768 CACATTTGAGCCTTGTTGTGTGGAATGTTCACCAA[C/T]AAATGACAAGAGTGAGCTGCCAGCTCTAGTTCTGG Y 2 1 2 1 201000 f 74 goat snp12515-scaffold148-437892 6 31560558 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798433 Affx-122957194 AX-385285367 6 29329297 CTTGAAGATTAAGTATAGCCTCAATGGATGAACTG[C/T]ACATCTTTTTCAAAAGAAGGTTTTCTGGAGGATAA Y 2 1 2 1 101000 r 74 goat snp12516-scaffold148-490421 6 31613602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802089 Affx-122940165 AX-385288993 6 29368528 TTGTTGACTTGCTCTTTGCTGAGTGGTGAGAGAAA[C/T]AAGTATTTTTATAAAACCCTAAATTGTGAAAGAAA Y 2 1 2 1 101000 f 74 goat snp12517-scaffold148-529652 6 31653471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785664 Affx-122962148 AX-385272705 6 29401236 CTACATAAGAATCAATGGGAAAAATTAGTTTGAAC[A/G]TTTCATTTTCTCATTTCATGCCACTGGCAATGGTT R 2 1 2 1 303000 r 74 goat snp12518-scaffold148-562360 6 31686224 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439617 Affx-122930632 AX-123309954 6 29432519 TTTTCAAAAAGGAATGGATTAGAATTCTTGGTAAT[A/G]ACAGACTATGTGGAAAGAAAAAGAAACCACATGGA R 2 1 2 1 201000 f 74 goat snp12519-scaffold148-593643 6 31715754 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278508 Affx-1111836372 AX-519551990 6 29479803 AATGCAAGTGTCAATTATAAAATACATAACAGTTT[A/G]GGTATCTTAATTTACCTTTTTGCCTATATTATAAC R 2 1 2 1 101000 r 74 goat Random2.2K-663 6 29479803 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429511 Affx-122937854 AX-123299853 6 29482007 AATACATATTTTCATTTTAAATAAAAAATGATTTA[C/T]AAGTCATTACACATTTGGCTCTTTCAAACTCACTA Y 2 1 2 1 103000 r 74 goat snp12520-scaffold148-643131 6 31765153 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788964 Affx-122925776 AX-385275977 6 29569382 TCCCTTCTGTCTAAATCATTTTAATGTTGCCATGC[A/G]TAAGTAACATTGAAGTATCAGGTATCTTCATGGAT R 2 1 2 1 101000 f 74 goat snp12522-scaffold148-730506 6 31851817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777531 Affx-122931359 AX-385264650 6 29604633 GCAAAAAGTTTATTTGTACCCGTTTCTGTCAAAAA[G/T]TTATCTCATATTCCAAGTCAGTATTGTCTCTGTTA K 2 1 2 1 202000 r 74 goat snp12523-scaffold148-765757 6 31887118 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788902 Affx-122928333 AX-385275917 6 29657406 AGTGGTATCATTCTCTGAGTTCAAGGAGAAAAATA[C/T]ATCACTATATGAGGAGGCAAGAAAATCAACTTATT Y 2 1 2 1 101000 f 74 goat snp12524-scaffold148-818530 6 31940001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278510 Affx-1111836373 AX-519551993 6 29663534 AAAAACCTGCTTACCCAAAGTGTTCCTGAAAACAG[A/G]CAGGCTTTCAATTCACTTATGAAGCTGCTTGCTTT R 2 1 2 1 101000 r 74 goat Random2.2K-664 6 29663534 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415019 Affx-122949026 AX-123285368 6 29706746 GTATAAAATAAGTAGGGGGCATCTGTAAAACAAAG[A/C]GTATGGAGGCTGATAAAGGCACTCTGTGAGGAGAT M 2 1 2 1 101000 r 74 goat snp12525-scaffold148-867870 6 31990015 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377402 Affx-122977564 AX-123247761 6 29757929 CTCAAAACTGTTAAGTAATTTGCAGGCATCACACG[A/G]CCAGAATGTGACTGGCGTGGTCTTGCACCTGTGTG R 2 1 2 1 101000 f 74 goat snp12526-scaffold148-919053 6 32041452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765726 Affx-122952529 AX-385253187 6 29808067 TACAGAAGATACTCAATGCCTACCACTGAATTGCC[A/G]GAGTTTATTCCCCTGCCTATTGAGGCTATGTGACT R 2 1 2 1 101000 f 74 goat snp12527-scaffold148-969191 6 32091506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464434283 Affx-1110480925 AX-515907038 6 29847420 ATATTGCATGCCAGGGGACTGCAGGTCTGACAGCG[C/T]CCCAGCCCAGCAGGCAGTGGTCTCCCTTCTGTTCC Y 2 1 2 1 303000 r 74 goat GoatD01.042824 6 29847420 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397793 Affx-122962501 AX-123268148 6 29907050 AATGAAATAAGCTAAGTTTTCCTGACATCAGCATT[A/G]TCTGGGCTAGGCAAAGTCAGCATGCTTACTTCTAT R 2 1 2 1 101000 r 74 goat snp12528-scaffold148-1068174 6 32191213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377804 Affx-122977318 AX-123248163 6 29956156 TAGCAGCAGCAGCAGAAGCAATGCCTAACTACCTG[C/T]AGAAATAAATAACCAATGTGGTGCACACTGTAAAC Y 2 1 2 1 201000 r 74 goat snp12529-scaffold148-1117280 6 32243636 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378316 Affx-122977350 AX-123248675 6 30061341 TAAGAAAAAAGTCAGTTGAAGGTACTATTGAGCAT[A/G]GAGGAAGAATGCATAGGTCAGGTTGGGAGCAATAA R 2 1 2 1 201000 f 74 goat snp12531-scaffold148-1222465 6 32349183 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385278 Affx-122972068 AX-123255636 6 30114680 TTGCACACATAGCATCCCCCACAGTACAAGGACCA[C/T]GACACAGAAAAGGGTCAAGATATGCAGCACGACGG Y 2 1 2 1 101000 r 74 goat snp12532-scaffold148-1275804 6 32402952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787416 Affx-122941147 AX-385274441 6 30175051 AAACCTCATAACAGCCATTTTTATTAAGGAGAATA[C/T]TTGTCAGACATTTCCTCTTAATTAGGTAATGCTAA Y 2 1 2 1 101000 r 74 goat snp12534-scaffold148-1336175 6 32464266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793307 Affx-122923933 AX-385280285 6 30215114 CAGAGAGATAGTAAACTACACTGATTAACAGTACA[A/C]AATCTGAAGTTGAACTCTCTTGGGTTCAAAAGACA M 2 1 2 1 101000 r 74 goat snp12535-scaffold148-1376238 6 32502437 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789392 Affx-122944230 AX-385276402 6 30246187 GCTATACACAATAGTTGTGTACAATATATAAAGTA[G/T]AACACAATAAACTACCATTAAGAAGAATCAAAACA K 2 1 2 1 101000 r 74 goat snp12536-scaffold148-1407311 6 32533499 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434039 Affx-122934207 AX-123304380 6 30292433 TTTGATAGTCCTTTGTTTTCAAATAGAATCATTTG[C/T]GACTCTATGGTATAAATCTTCCCTTATACTCTTCT Y 2 1 2 1 101000 r 74 goat snp12537-scaffold148-1453557 6 32579773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409825 Affx-122952949 AX-123280176 6 30322182 GACAGTCTTGATGCACATATTTTATAATATTGTCT[A/G]TTTTGTCCAGCCTGGAAACTTTCATATAAATAAAC R 2 1 2 1 102000 r 74 goat snp12538-scaffold148-1483306 6 32609503 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774844 Affx-122973404 AX-385261978 6 30351434 ATTATAACTCAAATATTCCTTGATTTCTTTGACCA[C/T]AGAATTGATTCCTGAAGGAAAAATTGTGATATCTG Y 2 1 2 1 201000 f 74 goat snp12539-scaffold148-1512558 6 32639307 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436764 Affx-122932277 AX-123307102 6 30386478 AATATATAATTGTTGATGGAATAAATAAATGCAAT[A/G]TAGTAAATGCTTTAACAGAAGCACTTATTCAATCA R 2 1 2 1 101000 r 74 goat snp12540-scaffold148-1547602 6 32674653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803155 Affx-122939468 AX-385290018 6 30441516 CTCTTATCTAGAAGGTTGCCACTTCATTTCAGTAA[C/T]GGTTTATTTGCTGTGCAGAAAGTTTTTTTTTTTTT Y 2 1 2 1 201000 r 74 goat snp12541-scaffold148-1602640 6 32730351 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404348 Affx-122956825 AX-123274700 6 30470196 GTATTTCATTTAAGGAAAATAATTAATATATGAAC[C/T]CTTAGGATTGCAAGTACTGTTTGGTAATCTCATTT Y 2 1 2 1 101000 r 74 goat snp12542-scaffold148-1631320 6 32759204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435433 Affx-122933483 AX-123305773 6 30532259 AAATAAATTAAATAATTTTTTAAAAAAGAGAGAGA[G/T]ATCAGCAGTATTTCCATTGGTTCATTGAGTAACTC K 2 1 2 1 101000 r 74 goat snp12543-scaffold148-1693383 6 32820796 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775833 Affx-122961538 AX-385262964 6 30609415 TTTTTAAGTGCATATTACTTCAGCTGTAATTTATA[C/T]GCTACGTGCAACATTTCTGATCATTTCAAAACAGT Y 2 1 2 1 102000 r 74 goat snp12544-scaffold148-1770539 6 32898786 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278345 Affx-1111836374 AX-519551831 6 30628118 ATGGTATAAATACCGAGAGAAGAAACTTTACTCAT[A/T]GGTTTTTAATTGCAAATTATTTCATGGACTTGTTT W 4 1 2 1 101000 f 74 goat Random2.2K-665 6 30628118 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378908 Affx-122976455 AX-123249267 6 30674858 AAATAAGTCCAAAATCTCTGATTTCTAATTCTTCA[C/T]AACTCATTTCCGCTGTTTCAGCTCTTACTGTTCTG Y 2 1 2 1 101000 r 74 goat snp12545-scaffold148-1835982 6 32965897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802609 Affx-122976911 AX-385289511 6 30704753 GTGTGTGCATGTATACATAAAGGTATGCAAATGTG[C/T]ATGGTTCTTTGCAACAATAGCACAATTAGGAGAAT Y 2 1 2 1 201000 f 74 goat snp12546-scaffold148-1865877 6 32996417 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776135 Affx-122930093 AX-385263265 6 30755045 TAGTAGTTTGTAACTTCATCCATGAGTTTTGTGGT[A/G]CATCTCAGTTTGAACTTGCAGCTGTCTCCTTTCTA R 2 1 2 1 101000 r 74 goat snp12547-scaffold148-1916169 6 33045438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395654 Affx-122963766 AX-123266009 6 30852258 TTTTTATTTAACTTCTCCAAATCCTGGTGTGAGTG[C/T]GGCTAGAGCTCAGTGGAGACCATCAAGGATTCTAA Y 2 1 2 1 201000 r 74 goat snp12549-scaffold148-2013382 6 33143559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796837 Affx-122950015 AX-385283780 6 30884819 ATTAATTAAAGAGAGATACTAATATTATCTACTCC[A/G]TGGATTGTAATGAAGAGCAAATCTTTGCTACATGT R 2 1 2 1 101000 r 74 goat snp12550-scaffold148-2045943 6 33176060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778565 Affx-122957954 AX-385265677 6 30922133 ACAAGTAGAATATGTTGCTTGCAAACCACTGCATA[G/T]AAATAAGATTTGCTCCTCTCATTGTAACTTCCCAT K 2 1 2 1 101000 f 74 goat snp12551-scaffold148-2083257 6 33213605 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447512 Affx-122924070 AX-123317848 6 30957233 AAATGATTACTTCAAATTCATTATAGAAATTTGGT[A/G]CATTGTTGTATACAGTTACCTAAGTGAACACTAAG R 2 1 2 1 101000 r 74 goat snp12552-scaffold148-2118357 6 33249084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428591 Affx-122938702 AX-123298933 6 30993315 TCCCTATCCTTCTTGCAAATGATATTAACGTGTTT[A/G]TAAGGACGTCTGGTCAAGCTCGTGAGATGTCACAT R 2 1 2 1 101000 r 74 goat snp12553-scaffold148-2154439 6 33285478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768622 Affx-122944605 AX-385255802 6 31037872 TTTTAAAGGGATGAAAGCTTTCATGCAATGAATAA[G/T]AAATTTAAATTTTTTGGTGCTAGTATCATTATAGA K 2 1 2 1 202000 r 74 goat snp12554-scaffold148-2198996 6 33330782 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381997 Affx-122974080 AX-123252355 6 31066648 GTTAGAGAACTTGTTGGAATTCTAGAGTTTCTGGC[A/G]CTATAGATTTCAACTGATTTGTTTTATGCAGAGGG R 2 1 2 1 201000 r 74 goat snp12555-scaffold148-2227772 6 33359675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799586 Affx-122951191 AX-385286517 6 31122766 AACAGTAACTAAATATGGAGAAAGATTATTCCACT[A/G]CTTCTTGACTTACATTGTCTCTTTTAGGAAGTCAG R 2 1 2 1 101000 r 74 goat snp12556-scaffold148-2283890 6 33416372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384110 Affx-122972831 AX-123254468 6 31180994 ATAAGTTCAAGCTGAAAATGATGACAAATGCTTTC[C/T]AACTCCACTCAGAAATAGCCATGAAAGAATGAAAA Y 2 1 2 1 201000 f 74 goat snp12557-scaffold148-2342118 6 33475320 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427516 Affx-122939523 AX-123297859 6 31221691 GTAAACCCATTATTCAGAGGTTCTCGATAAGAGAC[A/G]TTTCTCCTCTCTCCCAGGGCTATATAGAAATACTG R 2 1 2 1 101000 f 74 goat snp12558-scaffold148-2382815 6 33517310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789984 Affx-122956580 AX-385276990 6 31253764 GGATTCTATACTTATTGATCTAAACATCAATAATT[A/G]TTCTTAAAAGCTTTGGAAGGGTTAGTGTTCTGGTT R 2 1 2 1 201000 f 74 goat snp12559-scaffold148-2414888 6 33550043 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415201 Affx-122948987 AX-123285550 6 31291349 AAATCATCTCTTTGGTCTACTCTATTTGTACCCAT[A/G]TCAACTCCCCCTCAGTTTGGTGCCTGTCAGCCTCC R 2 1 2 1 201000 f 74 goat snp12560-scaffold148-2452473 6 33587806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404786 Affx-122956674 AX-123275138 6 31363126 AACATTTAAATTTTCACACACTGGACACACTCCTC[A/G]TACTTTGTTAGACTTTGGGGAGAAAATATTTCTAA R 2 1 2 1 202000 r 74 goat snp12561-scaffold148-2524250 6 33660412 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797985 Affx-122920837 AX-385284921 6 31398437 CTTTTCACAAAAATCATATAGTGGCCAAAAAGCAC[A/G]TGAAAAGTTATTCAATACTGCTATCTATTAGAGAA R 2 1 2 1 201000 r 74 goat snp12562-scaffold148-2559561 6 33696024 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794947 Affx-122923280 AX-385281907 6 31466344 TTCCCATCTAGTGAAATTTAGCCTTTAATTTTATT[A/G]TGTCTGAATATTGAATCAATTTAGAAAACATTTCC R 2 1 2 1 201000 f 74 goat snp12564-scaffold148-2627468 6 33765092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784900 Affx-122960340 AX-385271947 6 31522657 TTTAAAGTACTGAGCATCTTGTGAGTATGGGAAAA[C/T]AGATTCTAAAGTTTTCATATGTATGCACAGATAAA Y 2 1 2 1 201000 r 74 goat snp12565-scaffold148-2683781 6 33821640 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391133 Affx-122966794 AX-123261490 6 31561561 CCACCAAGTGGAAGAAATTAACTACCTGATGACCA[C/T]GAGCATTTAGGTCTGGGAGCCTTAGGAATGATAAT Y 2 1 2 1 201000 r 74 goat snp12566-scaffold148-2722685 6 33860778 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774279 Affx-122977609 AX-385261415 6 31617551 ATCTGCTAAATGGGCAACCCTAGGTACACTGGTCC[A/G]TTCTAACCTTAGAGACTTACATTATATATGCAATG R 2 1 2 1 101000 f 74 goat snp12567-scaffold148-2778675 6 33917687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377163 Affx-122978214 AX-123247522 6 31664274 TCTCTCCTCTCAAAAGAAAAACAATTAACAAAAAG[C/T]AAACCCAGAATATTTTATTTATTCATATCTTCCAT Y 2 1 2 1 103000 f 74 goat snp12568-scaffold148-2825398 6 33964506 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377488 Affx-122977498 AX-123247847 6 31710162 ATCTTGTTCAAATGGCTTTGCATATTCAAGCTCTT[C/T]TAGTGTTCACAATAACCCTATGAGGTAGATATTGT Y 2 1 2 1 201000 f 74 goat snp12569-scaffold148-2871286 6 34009617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775293 Affx-122976332 AX-385262424 6 31754679 TGGGATTCAGGAATTTCTATGATTATGGCTAATCA[C/T]ATGGGCAAAGAATGACTGTAGACCAGTTCCCACTG Y 2 1 2 1 101000 r 74 goat snp12570-scaffold148-2915803 6 34054242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436135 Affx-122932641 AX-123306474 6 31793838 TCTTCCTACTTTGGTTTTCATTGGCCCAATCCGCT[A/G]CCCCAGGTTCCTTCTTAGACTCGGATTACTTCCTT R 2 1 2 1 101000 f 74 goat snp12571-scaffold148-2954962 6 34093601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783080 Affx-122953316 AX-385270147 6 31838348 ATGTCAAAGGGTGCTAGTTCCCCTATGGTGAGTTT[C/T]TATCCAAGATCCAAACCCACACTTCAAGGTTGGTA Y 2 1 2 1 102000 f 74 goat snp12572-scaffold148-2999472 6 34138098 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395948 Affx-122963575 AX-123266303 6 31880169 CATGTCAATACTATGCAAATAACATTTCATTTTGT[A/G]GGCTGCACCTGAGTAGTTTGTCTTCCAAGTCTTTT R 2 1 2 1 101000 r 74 goat snp12573-scaffold148-3041293 6 34179940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452532 Affx-122920542 AX-123322865 6 31912928 CTAGCACAGCTCAGAGTGCTGTACTCACATGATCA[C/T]ACCTCATCTTGGGATTTTTTACTATGATTACCACC Y 2 1 2 1 101000 r 74 goat snp12574-scaffold148-3074052 6 34212443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771534 Affx-122976194 AX-385258692 6 31955976 TTTATTATAATGCAGAACTAGACAAAATGAGTTTA[C/T]GCTTTTATGCTAGGCATACATTAAAAACATGAAAA Y 2 1 2 1 101000 r 74 goat snp12575-scaffold148-3117100 6 34257575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397360 Affx-122962288 AX-123267715 6 32005652 TGGTCCCTGTTTCTTTGATTTCTAGAATATTTTAG[A/G]TCAGAATCGATTTTGACTTTACCCTTTCCTTTTTG R 2 1 2 1 101000 r 74 goat snp12576-scaffold148-3166776 6 34307394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776422 Affx-122944063 AX-385263549 6 32084419 GGCCAGTTGTATAGCTTGATAGGCTTGTTATATAC[A/G]TCAGCTTATCAATACTTAATTTAATAAAATGGCTT R 2 1 2 1 101000 f 74 goat snp12577-scaffold148-3245543 6 34386561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394576 Affx-122964442 AX-123264931 6 32116034 TTTACTATCTAAATCAGGACCAACTCTTTAGACTT[A/C]GACTAAGTTCAGCAAGCTTACCAATTTTCGTCACA M 2 1 2 1 101000 r 74 goat snp12578-scaffold148-3277158 6 34418818 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768759 Affx-122929558 AX-385255936 6 32146770 AAACCTGACCCTCTCCTAAGTATTTGGATTCCTGC[A/G]AGTTTTCTCAGCTGGCGGTATCTCTGTCTTCAGCA R 2 1 2 1 101000 f 74 goat snp12579-scaffold148-3307894 6 34449796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399752 Affx-122960320 AX-123270107 6 32181272 TCCCAGAGGACTATTGAAAGTTAATGTTGCTTAAA[C/T]AGCAAAAGAGTCATGGAAATATACTTCCCTCCCCT Y 2 1 2 1 201000 f 74 goat snp12580-scaffold148-3342396 6 34484359 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405643 Affx-122956585 AX-123275995 6 32222609 CGATTATCACCATTATCTTCATTGACATTTTCATC[A/G]TTTATAACATGATTAGAGTGCCTTTTATGTGACAC R 2 1 2 1 303000 r 74 goat snp12581-scaffold148-3383733 6 34526728 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377457 Affx-122977520 AX-123247816 6 32252416 TCTGCAGGACTGGCCCTTGGCCAGCTCCTGGGAGA[C/T]GAGTTCTGAGTCCTTAGAATATCTGTAAGATAAGA Y 2 1 2 1 101000 r 74 goat snp12582-scaffold148-3413540 6 34557816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774738 Affx-122970210 AX-385261872 6 32296635 TCCTCACAAAGCTACTAAAGAAATTTAAGCAATAA[A/C]ATTTCACATATATCAGCTGAAGATAATTCCCTTAC M 2 1 2 1 201000 f 74 goat snp12583-scaffold148-3457759 6 34602486 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431932 Affx-122935984 AX-123302273 6 32365703 TCTCCCAACTCCAATCCTCCTCCAAAAGCTGTGGC[A/G]GAGACTCAAATTTAGGCCACAGTTCTCTCCACAGA R 2 1 2 1 201000 r 74 goat snp12584-scaffold148-3526827 6 34671206 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429687 Affx-122937640 AX-123300028 6 32420831 CTTTTCAGCTAAATATAAATATTTACTTCTTTAAT[A/G]TTTTCTTCATTATTAACTCCTGTTCAGAGAATTAT R 2 1 2 1 103000 r 74 goat snp12585-scaffold148-3581955 6 34726977 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401879 Affx-122958854 AX-123272232 6 32449737 TGGCTTGAGATGAACATGGTAACATGGAAAAGAAT[A/G]CTGTCACAATTAAAATTCTTGGAAATCTAGTATTT R 2 1 2 1 101000 f 74 goat snp12586-scaffold148-3610861 6 34755798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378621 Affx-122976562 AX-123248980 6 32525693 CCTTCAAACAGTGTGTAACATATATCCAGGGCACA[C/T]AGCTAGCACTGGGTTCAACTGAAAATTCACTTTGC Y 2 1 2 1 101000 f 74 goat snp12587-scaffold148-3686817 6 34831119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799914 Affx-122925246 AX-385286840 6 32588064 ATTTCCCTCATGTTCTGAACTCAACCCAACAATAC[A/G]TTTTTCAGTGAAGAGGCAAAGTTATGCATATTTGG R 2 1 2 1 101000 f 74 goat snp12588-scaffold148-3749188 6 34893977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426922 Affx-122940439 AX-123297267 6 32617738 CCACTTCAGAGAGCTATATCTGGTGTATATAAAAG[A/G]CACAGTGAAAAATAAGCACAGTCCTAAGCTCTCAA R 2 1 2 1 101000 f 74 goat snp12589-scaffold148-3778862 6 34924471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388200 Affx-122969423 AX-123258558 6 32660121 TAAGATGCAATAATCTATTAGCAGTCATTAAAACC[A/G]TAAAGAATATTAATTTATCAGATTATCAGAGCAAA R 2 1 2 1 101000 f 74 goat snp12590-scaffold148-3821245 6 34967343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424608 Affx-122942197 AX-123294954 6 32720242 TGTGGAAGATGGAGAGGAATAATTTGTATATTTCC[A/G]TTCAGTCTAGATCTGATACTCCATCATATTTACTC R 2 1 2 1 101000 r 74 goat snp12591-scaffold148-3881366 6 35030673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445043 Affx-122926615 AX-123315380 6 32769306 CTGCTTATATTCCAAGCACTAGTTTAAGCATTACA[C/T]GTATAATAGCTCTAATCTCAAAATAACATAGCAAG Y 2 1 2 1 101000 r 74 goat snp12592-scaffold148-3930430 6 35079732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447874 Affx-122923878 AX-123318210 6 32870210 AGAGACTCTGTCTCTTCCGTTCATTCAACTTCAGA[C/T]GTTTAGAACTCAAAGAGGGAACAGCATAGGAAGAG Y 2 1 2 1 101000 f 74 goat snp12594-scaffold148-4031334 6 35181318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420222 Affx-122945534 AX-123290570 6 32921837 CTGGCATAATTTTTTATTTATTTGGAGGAAGAAGA[C/T]AATCTGTAGCTTGTGGAAAAGTGTATGCATTTAGA Y 2 1 2 1 101000 r 74 goat snp12595-scaffold148-4082961 6 35233924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411600 Affx-122951607 AX-123281950 6 32976660 TTTTAATAAGATTACCTCTTGCATGCAAATCCTTC[C/T]GAAATAAAACTCAGAAAGCCCACTGTTTCTACCTC Y 2 1 2 1 101000 f 74 goat snp12596-scaffold148-4137784 6 35288662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441723 Affx-122929143 AX-123312060 6 33009159 TCAGTCTTGAAGAATAATGTTTGCAGAGTCTTGAA[C/T]AAAATACTGTTCTTTCAGAATTAATGACTGACAGT Y 2 1 2 1 101000 f 74 goat snp12597-scaffold148-4170283 6 35321910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795904 Affx-122923744 AX-385282856 6 33039929 TGATGGTCAATATCAACTGGATATGAGGCTTGGGG[A/G]AGAAGGTGTTTGTAGATATGAGAAGAAATACTTGT R 2 1 2 1 101000 f 74 goat snp12598-scaffold148-4201053 6 35353321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788390 Affx-122948664 AX-385275408 6 33080776 TATTATAAGGGTAAATAAATGATTAAGGTAATAAC[C/T]TCAGCAGTTAATCGGAGAGAGAATTGGTTGCTTTT Y 2 1 2 1 101000 r 74 goat snp12599-scaffold148-4241900 6 35394526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437957 Affx-122931614 AX-123308295 6 33111604 TCTCAGAGGTGTGGTAACCACCTGAGACAAGAGTG[A/G]GCCCAGAGCCTGGCACAAGAGAGTTTCATAGTTGC R 2 1 2 1 101000 f 74 goat snp12600-scaffold148-4272728 6 35425838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441370 Affx-122928864 AX-123311707 6 33161232 CTGACTTTGAGATCCTGAAGGCCAGGGATAGCATC[C/T]TATTCTTCCTGGAATTTCCAACCCTTTGTGCTGTG Y 2 1 2 1 101000 r 74 goat snp12601-scaffold148-4322356 6 35476169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423983 Affx-122942122 AX-123294329 6 33190439 AAAAAAGGGATAGAAAAGTCACATCAAAAAAGACT[A/G]CCAGCACTTTAAAAGGTTAGGGCAAAAGAGGAATA R 2 1 2 1 101000 r 74 goat snp12602-scaffold148-4351563 6 35505421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777771 Affx-122957945 AX-385264889 6 33231230 CTGTTAAGTTCAGACAGAAGCTGAGAGTGGGACTG[A/C]TATTGTGAACTTCCCCCCAAGCAAAGCAAGAATAA M 2 1 2 1 101000 f 74 goat snp12603-scaffold148-4392354 6 35546251 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776078 Affx-122938011 AX-385263208 6 33261404 AGACATATATCCTGGGGATATGATTATTCTCATAG[C/T]GCAAATTCTAAATCAGGCCAAATAAAGATAAGCCC Y 2 1 2 1 101000 r 74 goat snp12604-scaffold148-4422528 6 35576733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389771 Affx-122968233 AX-123260128 6 33293819 AGATAGCTACTGATCTAGGTCTCATGCAAGCCTTA[C/T]AGTAGGAAAGATGAGGAAAACAAAAGAGCAGAATC Y 2 1 2 1 101000 f 74 goat snp12605-scaffold148-4454943 6 35610683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799162 Affx-122976330 AX-385286092 6 33328019 CCTCAGAATCAGTTCATTCAATCTCTCACAGAGAC[A/G]TCTCCGATGATTTGATGAGATATTTCCCCCTTCTT R 2 1 2 1 101000 f 74 goat snp12606-scaffold148-4489143 6 35644361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391407 Affx-122966775 AX-123261764 6 33370611 AAGACCAGGGCTTGAACCCAGGAGAGCCACACTCC[A/G]TCAGAGTCTCCAAGAAAATGTGGAGAAAAGGCATA R 2 1 2 1 101000 r 74 goat snp16801-scaffold1760-13796 6 35688215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434878 Affx-122934351 AX-123305219 6 33415791 TAAAATGAAAATTATGTGACAGTTATTTTCCTACT[A/G]TATGGATGTGCTTGGAACTATACCCTGGAAAACAA R 2 1 2 1 101000 r 74 goat snp16802-scaffold1760-58976 6 35733825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797864 Affx-122926237 AX-385284802 6 33468388 GGAAGTAAGCTACTTTATGATAAAGGGAGTTCCAC[A/G]TTTCAGAAAGAAATATTCCTAGTTGGGAATGTATA R 2 1 2 1 101000 r 74 goat snp16803-scaffold1760-111573 6 35785321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443641 Affx-122927284 AX-123313978 6 33502535 TGATTGATCATGAGGTTTAAGAAACCTCTTCCAGA[C/T]ACATGTTCTTGTTCTCTTACCTCTTGATCTGGAGA Y 2 1 2 1 201000 r 74 goat snp16804-scaffold1760-145720 6 35819359 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402804 Affx-122958283 AX-123273157 6 33547730 CTAAATTTTTTTCTTCTTTCTTTTCTTAAATTACT[A/G]TTTGCTAACCATTCCCTCTCTAGAACAATAGCTAT R 2 1 2 1 101000 r 74 goat snp16805-scaffold1760-190915 6 35859016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278347 Affx-1111836375 AX-519551833 6 33583530 TTCTTGGTTCTTTTTGCACCAGTTATTTCTGAGCT[A/G]CCTTCCTGGAAGGGATGTTTCTTTCCACTTTGGGG R 2 1 2 1 101000 f 74 goat Random2.2K-668 6 33583530 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433495 Affx-122935030 AX-123303836 6 33584091 TCTTAAGTACATGAGTGTGGGACATTATGGGTGTG[C/T]CATAAGGAAAGAAACTGTAGTCTCTTTTTGTCATG Y 2 1 2 1 101000 f 74 goat snp16806-scaffold1760-227276 6 35896333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437594 Affx-122931864 AX-123307932 6 33612630 TGTTTTCACTTTTTCCTCAGCATCTAGACCAGCAC[C/T]GTCCACTAGAAATGTAATGTGAGCCACATATGTAA Y 2 1 2 1 101000 f 74 goat snp16807-scaffold1760-255815 6 35924453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796045 Affx-122921153 AX-385282997 6 33642909 TTAATTTACTTATTCATTCTCCTGGGTTTTTTATT[A/G]TGGTTAGAAAAAACATGCAACATGAGATATACCCT R 2 1 2 1 201000 f 74 goat snp16808-scaffold1760-286094 6 35955623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395817 Affx-122963638 AX-123266172 6 33704350 TCTCTGCAGAGCCCTGGTGAATGAGCCCATCTCTG[C/T]ATGTTTGCCCCTACTTGCAGAACTTCGTAGCCTTG Y 2 1 2 1 101000 r 74 goat snp16809-scaffold1760-347535 6 36018389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388045 Affx-122969542 AX-123258403 6 33737096 CATAGCAAATGAAAAGGTAAAAATGCCAAATATGA[C/T]GAATTACATATAAGAAAAAATATGTTTGAAACAAA Y 2 1 2 1 102000 f 74 goat snp16810-scaffold1760-380281 6 36051052 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452228 Affx-122920795 AX-123322561 6 33765608 GTACATACCTTGTATGAATTATCTAAATTCTCAAA[G/T]CAGTGGAAAGCAGGAAGAAGAAACAGTCGTTCAAA K 2 1 2 1 201000 f 74 goat snp16811-scaffold1760-408793 6 36079594 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375889 Affx-122978494 AX-123246248 6 33846824 CTGCCACCTTGTGTGCTGTGCCTATCAGCATCGTT[A/G]CTTCCCATTCTCATCTCTAGAATACTAACCAGAAA R 2 1 2 1 201000 r 74 goat snp16813-scaffold1760-490009 21 2183902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778671 Affx-122938987 AX-385265781 6 33884847 AACAACTTTGTGAGTTAGCTTTGTGTCATGATTAT[C/T]ACACTGAAACAGCTTACAATATGTTAGTTTGGATT Y 2 1 2 1 101000 r 74 goat snp16814-scaffold1760-528032 6 36199742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797199 Affx-122978979 AX-385284138 6 33917093 TTTTAAGAAGCATAGAAAAGATCCTAGAAGTAAAT[A/G]TTAAATGTTTCTGGGTGTCCTCTGTTATTCTTTTG R 2 1 2 1 101000 r 74 goat snp16815-scaffold1760-560278 6 36232621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438228 Affx-122931440 AX-123308566 6 34043869 TTCCCTAAAGAAAGGAGAATGGATACTAGGAATGC[C/T]AAAACATCAGTTGTCTACCCTGGTGCTATTGAGAC Y 2 1 2 1 101000 f 74 goat snp16817-scaffold1760-687054 6 36360840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392207 Affx-122966280 AX-123262564 6 34112365 AATCATGCAAGACCTAGAGAACACCATTAAACAAA[C/T]GAATATACATGACTGAGAAGTCCAAACAGGAGAAA Y 2 1 2 1 101000 f 74 goat snp16818-scaffold1760-755550 6 36429649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410457 Affx-122952220 AX-123280807 6 34149710 AAGGCCAAATCAAGAGATGAGATACATCTAAGATA[C/T]GTATTCACCAAAAGTTGGTTCAACCACAAGCAGCC Y 2 1 2 1 101000 r 74 goat snp16819-scaffold1760-792895 6 36467345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801434 Affx-122941275 AX-385288343 6 34180737 TAATCCTCCCAGTAACCCATAAAGTAGTAATTATT[A/G]TTATTAATATTCTCATTTGAACATGAGGAAAATGA R 2 1 2 1 202000 f 74 goat snp16820-scaffold1760-823922 6 36498331 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273199 Affx-1111833502 AX-519546858 6 34193381 GGTTTCAGGACTAGCAACGGTGGAAATTATTCTAC[A/G]GAAAGAGAGAACACTCTAGATCAAGGGTAGGGGAT R 2 1 2 1 101000 f 74 goat 6_34193381_AF-PAKI 6 34193381 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38442974 Affx-122928202 AX-123313311 6 34261735 AGTTGATTTTTTTCCCCCTGTTTTGGAATGCAAGC[A/G]CTTTTACTGTGAAAGCATCAACTTCAAAGATAGCT R 2 1 2 1 201000 r 74 goat snp16822-scaffold1760-904920 6 36578566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794414 Affx-122934191 AX-385281377 6 34297163 CTATTTACGGACCATGACAAATCTCAAAGTCCTTA[C/T]ATTCTGTTCAGGATAAGAAAAGCAGAGGTTGTTTG Y 2 1 2 1 101000 f 74 goat snp16823-scaffold1760-940348 6 36614070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771156 Affx-122966944 AX-385258316 6 34328116 ATTAAATTTGGTTAATCCACCCACTTTCTTAGAGA[A/G]AGGAATACTTCAGACTGTACTACTTGTGGACACAA R 2 1 2 1 102000 r 74 goat snp16824-scaffold1760-971301 6 36645232 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411570 Affx-122951631 AX-123281920 6 34349154 GGCATTTTTTGACAATAAAAGTATATTTTATTTCT[A/G]ATCCTTTCACAAGAAGCAATTTAAGATCTTTAGAA R 2 1 2 1 101000 r 74 goat snp26732-scaffold281-14273 6 36663600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433755 Affx-122934498 AX-123304096 6 34377762 ATTCACCAGGGTGCCATCTGCAGATTTTTGCTATC[A/G]CTGGCCTGCAAGGGTTTCACTTCCTTTTTCAGCTG R 2 1 2 1 101000 f 74 goat snp26733-scaffold281-42881 6 36692047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443947 Affx-122927017 AX-123314284 6 34418705 TAGATGAGCAACACTGACCTGAGTTAAGACAATGG[C/T]GGCAGAAATGAGGATGAGGAGAGATCTATGAGAGA Y 2 1 2 1 101000 f 74 goat snp26734-scaffold281-83824 6 36732997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448970 Affx-122923124 AX-123319305 6 34450752 TATTCTTAAACATGCTGAGATGAAGGAGCTGGGAA[G/T]CATGCAGGTAGACACAGGCTACGTAGGAAAAGCGG K 2 1 2 1 101000 f 74 goat snp26735-scaffold281-115871 6 36764986 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399302 Affx-122960533 AX-123269657 6 34481947 GATATTTCTTCTGAAATTTTGAGTTCTTATAAAAA[C/T]GTTTCAGTGTATTTTCTTTTTCCAAGTAACAATCT Y 2 1 2 1 303000 f 74 goat snp26736-scaffold281-147066 6 36796108 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771963 Affx-122929449 AX-385259119 6 34522041 TATTTTAAGTCACTATGCTTTGGGATGGTTCATTA[C/T]GAAGCATTTCTGTAGCCAAAGGTAACTAACTAATA Y 2 1 2 1 101000 r 74 goat snp26737-scaffold281-187160 6 36835936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435056 Affx-122933742 AX-123305396 6 34556008 TCCTCTGACTTTCCAGCCCTGAACAGTGAGAACAG[C/T]GAATCCTCTGCTCAGGAAGCGATGGGCAGGGAGCC Y 2 1 2 1 101000 f 74 goat snp26738-scaffold281-221127 6 36870150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411159 Affx-122951874 AX-123281509 6 34602233 CTGGTTCATAATTAGAAGCTATTCAAAGAGTGACT[A/G]CATTCCAATGATACCACTAACACCCTCAGTGTAAA R 2 1 2 1 101000 r 74 goat snp26739-scaffold281-267352 6 36917015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384638 Affx-122972156 AX-123254996 6 34634824 AATACTACCTACATCAAAGGGCTTTTATGTGGTCC[A/G]CCTGTAATGCAGGAGACCCCAGTTTGATTCCTGGG R 2 1 2 1 101000 f 74 goat snp26740-scaffold281-299943 6 36949865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771989 Affx-122965283 AX-385259145 6 34667347 CTGAGGGAAGTTTTGTAGTGGAGAACCAATGGTTA[C/T]TGGCAGATAGGTTAAAAATTATTGTAGGAGATATT Y 2 1 2 1 101000 f 74 goat snp26741-scaffold281-332466 6 36982281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397222 Affx-122962382 AX-123267577 6 34708150 GTCCTGTTTGAATTCTAGCCCAGAGGAAAGAGGAA[A/G]CAGGAAAGAGCATTCTAGGTTTCTAAGAAATATTG R 2 1 2 1 101000 f 74 goat snp26742-scaffold281-373269 6 37023063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428194 Affx-122939015 AX-123298537 6 34745411 TCCATTGTCTGGCCATTGTCAGAGCTCTCATAACA[C/T]AGGGAGGAAAAAAATGTCTTAAGAAGATCAGGTAA Y 2 1 2 1 101000 f 74 goat snp26743-scaffold281-410530 6 37060549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392380 Affx-122966231 AX-123262737 6 34779914 TCTCTCCCTGTCAGTCCCTCTGATACACTACTTAC[A/G]TCATCTTCAGATGGGTTATAGTCTCCTATTTGGCT R 2 1 2 1 101000 r 74 goat snp26744-scaffold281-445033 6 37095270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767539 Affx-122943065 AX-385254794 6 34811407 ATAGGAAATAACTGTTAAAGAAATGCAATCTGTAT[C/T]ACTTCTGTAGAAGACAGCTTAAAAAGGTTTTTTTG Y 2 1 2 1 101000 f 74 goat snp26745-scaffold281-476526 6 37126708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388263 Affx-122969775 AX-123258621 6 34882078 GGAAATGCACAACTCCTATTTTTCTTCATCTGGTT[A/G]CTACGTTCTATTGCCATATTACAAATTTCAGGCAT R 2 1 2 1 101000 r 74 goat snp26747-scaffold281-547197 6 37198076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379518 Affx-122976075 AX-123249876 6 34966172 GGGAGGGCTTTTCCAAATATTTCCCTCTAATTTAT[A/G]CTGAATTCCTTACTTTTGTTGATGTGATTCAATTC R 2 1 2 1 101000 f 74 goat snp26749-scaffold281-631291 6 37282758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786056 Affx-122930734 AX-385273092 6 35049865 TTCTTTTCTTTAATAACTAGTATGTTGACATGCAA[C/T]AGTGAAGGCAAGACAAAAGATACCTTTTATATTAG Y 2 1 2 1 101000 r 74 goat snp26750-scaffold281-714984 6 37368764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400567 Affx-122960417 AX-123270922 6 35081977 GTTATATTGCACCTTCCTGAGTTGAACTTTGAAAA[C/T]GGTAGCCACGCAAAATCCCAGAAGGGGTGAACTCA Y 2 1 2 1 101000 f 74 goat snp26751-scaffold281-747096 6 37401587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414798 Affx-122949221 AX-123285147 6 35111079 GAAAATCTTTTAAAATACATGGAACTTATTTTTCT[C/T]GAAATCTGATGAGCTGGCATCAGGAGATGATGTCC Y 2 1 2 1 201000 f 74 goat snp26752-scaffold281-776198 6 37430746 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418294 Affx-122946991 AX-123288642 6 35140586 TAGAGTCAAAGAGATGAATAGGAGAAACCAGCTAT[A/G]TTAAAATGTTCCCTGACCCTGCCAAAAATCAGGCC R 2 1 2 1 201000 r 74 goat snp26753-scaffold281-805705 6 37459874 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448369 Affx-122924108 AX-123318705 6 35210909 CCTTCCCCAGCATTTATTGTTCCTGGATGTTTAAA[C/T]GGTAAGCACTCTGACTGGTGGGTAATGATACCCTG Y 2 1 2 1 103000 r 74 goat snp26755-scaffold281-876028 6 37531231 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779528 Affx-122945617 AX-385266631 6 35249288 TATGAAATAGGTCAACAAGACCTACTGAATTATCA[C/T]GGGGAATTGGATCAGGAGGCTTTAATAATGTCTAT Y 2 1 2 1 102000 r 74 goat snp26756-scaffold281-914407 6 37570018 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416412 Affx-122947846 AX-123286761 6 35289058 TTTCACAGATTTGATGTTTTACATCTAAACCAAGT[A/C]GAGTGCACCCAAAGGATGGCGGATACTCTGGGCTA M 2 1 2 1 201000 f 74 goat snp26757-scaffold281-954177 6 37608512 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448441 Affx-122923651 AX-123318777 6 35334226 AGCATAGATTATAATAATCATAATCAAAGCAAACC[A/G]TGGTGTGAAATAATTTGTAAACTATTTGAGACTAA R 2 1 2 1 101000 r 74 goat snp26758-scaffold281-999345 6 37653431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771510 Affx-122932247 AX-385258668 6 35384267 TCACCTTATGCCAGTCAGAAACTGGCAACTTTAGA[G/T]TTCTTGATTAAACACCTAACTGATAGCATTTTAGA K 2 1 2 1 101000 f 74 goat snp26759-scaffold281-1049386 6 37703575 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420188 Affx-122945559 AX-123290536 6 35426330 GGAATGGAGTGAAAAGTCTGCTCTCAATCGGCCTT[A/G]TTATTTATATCTCTCTTGACTCACTGAAATGCTCT R 2 1 2 1 201000 r 74 goat snp26760-scaffold281-1091449 6 37746029 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774999 Affx-122940570 AX-385262131 6 35459451 TGTTGCCTGACTATACATATTGTCAAACAAAGGCA[C/T]GGAATATTAGGTAACATTCTTGAGGTTCTGGGGTT Y 2 1 2 1 101000 r 74 goat snp26761-scaffold281-1124570 6 37779121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789266 Affx-122936447 AX-385276277 6 35496829 AGTGAAAGAAGTTAAATTATATAACATTTATACAA[C/T]GGGATATTTTTAACACAACCATTAAAATTATGTTG Y 2 1 2 1 202000 f 74 goat snp26762-scaffold281-1161948 6 37816650 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429344 Affx-122938575 AX-123299686 6 35578781 GGTATGGGTGACAGAAGACCTCAAGAGCCTGTTGA[C/T]GTCAGGGTGCGCTCTGATGAGCAGCATCCTGGAGG Y 2 1 2 1 101000 f 74 goat snp26764-scaffold281-1243900 6 37898873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377020 Affx-122977718 AX-123247379 6 35646796 GATCAGAAAATGATATAGTGGAAGGTAAGAAGGGA[C/T]GTCTTACAGCACTACTGACAGTGTACAGTTCTTGC Y 2 1 2 1 101000 r 74 goat snp26766-scaffold281-1311915 6 37966873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770292 Affx-122953010 AX-385257458 6 35696664 CATCTTGGGTTATCAGTAGGCAATTAAGTATAATG[A/C]TGTTTCTGATCTGAACGAGGACAGCAGGTTTAAAA M 2 1 2 1 101000 r 74 goat snp26767-scaffold281-1361783 6 38016838 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401339 Affx-122959263 AX-123271692 6 35771847 AGGTTCCAATGGTTACTGAAAACCACTGTTATTTT[C/T]CCTAAATTATTTGCTTTTGTTTGTTTTTCAGGCAA Y 2 1 2 1 101000 f 74 goat snp26768-scaffold281-1436966 6 38091565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790242 Affx-122925351 AX-385277246 6 35825633 TTCATCATCGTATATGAAATTGACACTTGATATAG[C/T]CAGAGTCAGGTTAAAAATGCAACCCAAGGTAGAGC Y 2 1 2 1 101000 r 74 goat snp26769-scaffold281-1490752 6 38144878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771696 Affx-122948406 AX-385258853 6 35865814 ACTTTATCTAAGACACCTTCTGAAAGGTGTCTTTA[C/T]AGATTCTAATAACACCTTCTGAAAGGTTCTCTGCA Y 2 1 2 1 101000 f 74 goat snp26770-scaffold281-1530933 6 38185434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770636 Affx-122943207 AX-385257800 6 35908910 ATCAAATAAATAGAAATCAGATTGGTGGTCAGGGA[C/T]GGGATTTTGATTTTAAAGGGTCACAGCAAATTTTG Y 2 1 2 1 201000 r 74 goat snp26771-scaffold281-1574029 6 38228930 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397016 Affx-122963128 AX-123267371 6 35954378 CATATCGTCAGGGAAAGTATCGCTAACCACCAAGC[A/G]TCTTTCCTTTTTCTTTGTATTTATCACTTATCCTA R 2 1 2 1 101000 f 74 goat snp26772-scaffold281-1619497 6 38274307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412002 Affx-122951755 AX-123282352 6 36006994 AGGCTGTCATGGGCAAAGCTTTCATACCATTGGCT[A/G]CAGTTCTGTCACATGATCACATATAGCTGCAAGAA R 2 1 2 1 101000 f 74 goat snp26773-scaffold281-1672113 6 38327501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390051 Affx-122968422 AX-123260408 6 36050641 AGTGGTACAATAATACCAATGCCAAATAAATGCCC[A/G]TAAGTGTGAAAACCTATACCAGTCAAGGGTCATGT R 2 1 2 1 101000 f 74 goat snp26774-scaffold281-1715760 6 38371444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800610 Affx-122968765 AX-385287529 6 36080167 CCCTCCTCTTCTTCCTTTTTAGTTAAAATCAAAAT[A/G]TCTATTGAAGTTTAGAATTGACATCTTGGTGCTTA R 2 1 2 1 101000 f 74 goat snp26775-scaffold281-1745286 6 38400840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278518 Affx-1111836377 AX-519552002 6 36101662 CAAAATGAAAAAGTTATTTGGGGAAACACAACATT[A/G]GACTGGCATATTTTTTCTCAGATCTGTGGTAATGT R 2 1 2 1 101000 r 74 goat Random2.2K-670 6 36101662 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447986 Affx-122923749 AX-123318322 6 36109438 AATAAATGAGTGGCAGGGCAGGGATGAAATGGGGA[C/T]GTCCACGAAACCAGGCACCACTGGGCAATTTTTCT Y 2 1 2 1 201000 r 74 goat snp26776-scaffold281-1774557 6 38431246 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790339 Affx-122966025 AX-385277342 6 36151709 AGAGCCTTCTTCTGGCAACCTTAAGTTGGTGACCA[A/G]CTGTTAGAAATTGTGGACAACAACCTGGATTTAAT R 2 1 2 1 101000 f 74 goat snp26777-scaffold281-1816828 6 38473627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416502 Affx-122947784 AX-123286850 6 36184782 TTTAACCATTAAGCTATAAATGCCCCATGAAATTT[A/G]CTTCCTTTTAAAGCAGCTATTTTACTATTAGTATG R 2 1 2 1 101000 r 74 goat snp26778-scaffold281-1849901 6 38506633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774542 Affx-122936789 AX-385261676 6 36236213 ATAAGGTCACCTCCTCTATCCACCTTATCAACCCA[A/G]TCTCATTAATTGGCACTTCAGCTCTTCTGTGAAAT R 2 1 2 1 101000 f 74 goat snp26779-scaffold281-1901332 6 38558109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441925 Affx-122928593 AX-123312262 6 36269170 TTGCAGAAGTGAGGGGTGTCTTCAAAGGCATGAAG[G/T]GTTCTTACAAGGAAGAGAGGTGTAGTGGACACTTG K 2 1 2 1 101000 r 74 goat snp26780-scaffold281-1934289 6 38590195 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436699 Affx-122932327 AX-123307037 6 36334988 TAAGTGTTTTGAATGCGGTGTCTAATTTTAGTTTT[A/C]GTCTCCTTAGAAACAAGAATTGATAAATTCTAATA M 2 1 2 1 101000 f 74 goat snp26782-scaffold281-2000107 6 38657369 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376883 Affx-122977819 AX-123247242 6 36374073 ATTTCCAATATCTAAATGAGTGGCTGAATTCAACT[C/T]GAAGGATGCTCATTTGGGTAATTTAAATTTTTTTA Y 2 1 2 1 101000 f 74 goat snp26783-scaffold281-2039192 6 38696985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375758 Affx-122978601 AX-123246117 6 36421332 GTGAATGTTCTCTGCAGTTTCTTCCAACTCTAATG[A/G]GCTGAGATTAAAAGAGTAATGAATTTTACAACTAG R 2 1 2 1 101000 r 74 goat snp26784-scaffold281-2086451 6 38742182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389575 Affx-122968789 AX-123259933 6 36451847 GTGAGCCTGTTGTCCTGATTAGATATTCTCCTTGA[C/T]CAGCTGATAAGCTTCTAACACATCCCAGAAAGCTT Y 2 1 2 1 101000 f 74 goat snp26785-scaffold281-2116966 6 38772709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278353 Affx-1111836378 AX-519551839 6 36491607 TGGAGTATTAAAAATCACCAAGATAGTATAATGGT[A/G]AAAATATTATGACAATATTTAATTCATAATTTTGC R 2 1 2 1 101000 f 74 goat Random2.2K-671 6 36491607 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390990 Affx-122966906 AX-123261347 6 36551034 AGGAGGTACCACTGAGTTTACTTTTACGTGTGAAG[C/T]ATCTTTAGGGAGAACAACATATTAGAAACTCAAGA Y 2 1 2 1 101000 r 74 goat snp26787-scaffold281-2216153 6 38874180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774177 Affx-122939821 AX-385261314 6 36589460 ATCCAAAACCCACATTATGCACAGTGCCTGGGATC[C/T]ATGATAATATTTAGCACAGTTTCCATGAAGACTAT Y 2 1 2 1 101000 f 74 goat snp26788-scaffold281-2254579 6 38913406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435705 Affx-122933312 AX-123306044 6 36643389 TCAAAGATAACCTTGGCTGATTTTTGTGTCTTGTC[A/G]CTGTGGCATCTATCATAAAACCTAACACACTCTTC R 2 1 2 1 201000 r 74 goat snp26789-scaffold281-2308508 6 38967139 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424498 Affx-122941747 AX-123294844 6 36674413 TTTATGGGTATATGCACAAACTTTTAAGAAGTGTT[A/G]CCTTGACACACACTTTGTGATATGCTTGGCTACTA R 2 1 2 1 101000 r 74 goat snp26790-scaffold281-2339532 6 38998199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464437918 Affx-1110482789 AX-515910643 6 36707177 AGCTTGAATATGCACCAAATATTTTAACTCAGGAC[C/T]GGAGTTTGGTTAAATGCTAATAAGATAACCACCAA Y 2 1 2 1 101000 r 74 goat 6_36707177_AF-PAKI 6 36707177 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398937 Affx-122960993 AX-123269292 6 36732355 TTAGTGGGCACAAAGTCAAGAATAAGAGCAGGTGC[A/G]TAAGCCACTGTGGCCTCTTTCCCTAGATCTTTATG R 2 1 2 1 201000 f 74 goat snp26791-scaffold281-2397474 6 39056220 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423602 Affx-122942385 AX-123293948 6 36794061 CCTGACTGTGCTGTGCACAGCCTCTGACTCTTGCT[A/G]CATCTGCAATCTAAACCATTTAATTAGTAATAGGA R 2 1 2 1 201000 r 74 goat snp26792-scaffold281-2459180 6 39118052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394357 Affx-122964651 AX-123264712 6 36827041 ATAGGCATTATTTGTTTCTCTAGGCATGAATAGGT[A/C]TTTGAATAATAGTGATTTCTAAAGGTAGAAACAAC M 2 1 2 1 201000 r 74 goat snp26793-scaffold281-2492160 6 39150759 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785273 Affx-122938672 AX-385272318 6 36864248 CAAATAAAATAAAGCATGTGTTTAACATATGTAAC[A/G]TAAACATTACATATAGCCTGGTTTTTTTGATAGAG R 2 1 2 1 101000 r 74 goat snp26794-scaffold281-2529367 6 39187840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795434 Affx-122941109 AX-385282391 6 36919135 TATAAAGTAGTTTCTTGGCTTATGAAAAAGCCAGT[A/G]TTGTCTTTCACTGGAAGCACCCCAGTAGTGCCTCT R 2 1 2 1 101000 r 74 goat snp26795-scaffold281-2584254 6 39243101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788283 Affx-122951591 AX-385275301 6 36971395 CATTCTCCGCATGTTACAATAGGATGACTAGAGTT[G/T]GAATTACTCATTCTAAATAGTGATGAGACCTCAAT K 2 1 2 1 101000 f 74 goat snp26796-scaffold281-2636514 6 39295173 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448652 Affx-122923349 AX-123318988 6 37073419 CAGGACTTATGAGAATCAAGTAAAGAAGCTGTGAA[C/T]AGACCATCACTGATAAAAGAAGCTTAGACATAAAG Y 2 1 2 1 101000 f 74 goat snp26798-scaffold281-2738538 6 39397002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431336 Affx-122937062 AX-123301677 6 37113211 TTAAGGATGTTAAACAAATTGAAAAATTCCTCTAG[A/G]GCACCATTCTTTCAGTTTCATAAAACTATTGATGC R 2 1 2 1 101000 r 74 goat snp26799-scaffold281-2778330 6 39437063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762454 Affx-986696984 AX-385250583 6 37135587 TCTCTCCTTTCATTATGCATATTTATAAAATGTCA[C/T]ATGGGTTTATCACTGGGAGATAAGGAGGCAATATG Y 2 1 2 1 600010 f 74 goat 6_37135587 6 37135587 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320788852 Affx-122944169 AX-385275867 6 37190104 TGCCAAGAGCATTGTACCTTGGTTATATCTGAAGA[C/T]AATATTTTGAAACCTCTATTATTTGCATTATTGCA Y 2 1 2 1 101000 f 74 goat snp26801-scaffold281-2855223 6 39514043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793297 Affx-122954394 AX-385280275 6 37248152 TTTATTTAACCATTATTGATTCATCATCTGCTATG[C/T]GTCAGTTCCAAAGCCAAGATTAGAAGGAGAGTGGT Y 2 1 2 1 101000 r 74 goat snp26802-scaffold281-2913271 6 39573331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432799 Affx-122935410 AX-123303140 6 37325914 CTACAAAATTCCCTCTAGAATTGGCTGAAGATGTC[G/T]CTGTGACTGTTTACATTTTACCGTATTCTCCTGCT K 2 1 2 1 101000 f 74 goat snp26803-scaffold281-2991033 6 39651303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434467 Affx-122934638 AX-123304808 6 37374272 GAGAAAGTGAAATGACTTGCTGTTTAGCAATGATA[C/T]ATAAAGTACTAAATCTTCATTTTCTATCAACCTTC Y 2 1 2 1 101000 f 74 goat snp26804-scaffold281-3039391 6 39700586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768783 Affx-122944354 AX-385255960 6 37407402 AGCACAATGTAAGAAGTGCCATTCCAGAGGTGAGC[G/T]CAGTTCATGTCAGTAGCACATGTACGAAAGCAGAG K 2 1 2 1 101000 f 74 goat snp26805-scaffold281-3072521 6 39733758 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395164 Affx-122964113 AX-123265519 6 37437326 TAAATTCTAGAAACTTGACAACTAGTATTTTTAGA[C/T]GCTGCTTTGGAAGTGACTCTGAGCTCTCCCTGTTT Y 2 1 2 1 201000 f 74 goat snp26806-scaffold281-3102445 6 39764156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448577 Affx-122923408 AX-123318913 6 37505405 AACTGAAGCCATCAGGGCCTCCCAGGTGGCGTTAG[C/T]GGTAAATAACCCACTTGCCAGTGCAGAAAACTTAA Y 2 1 2 1 303000 f 74 goat snp26807-scaffold281-3170524 6 39829276 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse498 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320782828 Affx-122949614 AX-385269899 6 37550096 GCATTTCATAGCATCACATCTCAAAGGGATAATGT[A/G]ATTCTGAAGTTTCATCAATGTCAAACCCAATTTAG R 2 1 2 1 101000 f 74 goat snp26808-scaffold281-3215215 6 39874411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse499 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320767580 Affx-122925286 AX-385254832 6 37588975 TTATTTAGTTGGATATTTTTACACTGGAAGAAACA[C/T]AGCAAGATGTAAAATTGCTAGTAATCTAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp26809-scaffold281-3254094 6 39913786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779486 Affx-122925811 AX-385266589 6 37659068 CTTCTGAGAATAAGTTAAAAGATTTGGACTATGAA[C/T]AGGGAAGATATCTGTCTTCATGGGAACAAAGCTTC Y 2 1 2 1 101000 r 74 goat snp7248-scaffold1268-14447 6 39985135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse500 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38417728 Affx-122947435 AX-123288076 6 37700309 GACTGTGGTATGAACTGGTTGACTAAATCTCTCTG[C/T]GAAAATATTTTGCCAACTGTGCAGGGCTACAGAAA Y 2 1 2 1 101000 f 74 goat snp7249-scaffold1268-55688 6 40026095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse501 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38446840 Affx-122925269 AX-123317176 6 37749287 TTATTACTGAGAGACTATATAAAAGTCATCATTGA[C/T]AGCAACAATTGACATCTAAATTCCGATACTAATAT Y 2 1 2 1 101000 f 74 goat snp7250-scaffold1268-104666 6 40075174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790713 Affx-122972448 AX-385277714 6 37840604 GCAATTTGCCTTCACAAAGTAAGGATAGAAACTCA[C/T]ATACACGGTCTAGTCAAGTTTCATACTGCCTTTCA Y 2 1 2 1 101000 r 74 goat snp7252-scaffold1268-195983 6 40166627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse502 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38411895 Affx-122951188 AX-123282245 6 37883816 TAGACATCTCTTAAATCCATCCACTTCTGTCCATC[A/G]CTTTTACCACCATCCTAATGCACTCTCCCATTGTC R 2 1 2 1 201000 r 74 goat snp7253-scaffold1268-239195 6 40209422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse503 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 538942931 Affx-1251531516 AX-585490051 6 37923911 GAGAAAAACTTACCTAGTTGGTATTTTGAATAATA[G/T]TTTGCCATTTGTCCACTGTTGCAAGACTGTCGTTT K 2 1 2 1 400000 f 74 goat SNPs_040 6 37923911 G T SV-TF-chip candidate gene ou candidate region LCORL 538942936 Affx-1251531517 AX-585490055 6 37923960 CACTGTTGCAAGACTGTCGTTTATGTCTTTTTGTT[C/G]ACATTTCTGTGGTCTTCCACGGTGGTCTTTTTCTT S 4 1 2 1 400000 r 74 goat SNPs_041 6 37923960 G C SV-TF-chip candidate gene ou candidate region LCORL 538942862 Affx-1251531495 AX-585489986 6 37924983 GAGACTGTGTTTCTGTTGTTTGCATAAACCAGGTA[C/T]AGAGTTCATTCAAATCATACTTTTTCTGAAAAAGC Y 2 1 2 1 400000 r 74 goat SNPs_042 6 37924983 C T SV-TF-chip candidate gene ou candidate region LCORL 538942793 Affx-1251531472 AX-585489927 6 37924999 TGTTTGCATAAACCAGGTACAGAGTTCATTCAAAT[C/CATACTTTTTCTGAAAA]AGCATTTTTACCGGTGAAACCTCAAGTTCTAAAAG - 2 1 2 1 400000 r 74 goat ins-del_001 6 37924999 CATACTTTTTCTGAAAA C SV-TF-chip candidate gene ou candidate region LCORL 538942829 Affx-1251531476 AX-585489958 6 37925099 GGACTTGCTATTTTGAAGTTATCATTTTCAATGGG[T/TTC]TCTTTTTCTATGAACAGAATTTTCAGCTTCATCTC - 2 1 2 1 400000 r 74 goat ins-del_002 6 37925099 TTC T SV-TF-chip candidate gene ou candidate region LCORL 538942824 Affx-1251531473 AX-585489953 6 37925378 TTGGAAGCTATTTTAATCCTTGACTGCTTATGTTT[G/GTCC]TCCTGACTTTTACCTTTCTGCAAATGGAGCTTATA - 4 1 2 1 400000 r 74 goat ins-del_003 6 37925378 GTCC G SV-TF-chip candidate gene ou candidate region LCORL 538942864 Affx-1251531496 AX-585489988 6 37925811 TCGGTCGAATAATATTCTTGGAAGGTTGAGGTATC[A/G]CAGGCTTGTTCTTGAAAGGTCTAACATATTCAAAG R 2 1 2 1 400000 r 74 goat SNPs_043 6 37925811 A G SV-TF-chip candidate gene ou candidate region LCORL 538942857 Affx-1251531497 AX-585489981 6 37926205 GTCAGTTTTAGGTTTCGGTGGTCTTCCAATTGGTC[A/G]CTTTATCTGTTTCACAACCTGGGGACCTATTTTTT R 2 1 2 1 400000 f 74 goat SNPs_044 6 37926205 G A SV-TF-chip candidate gene ou candidate region LCORL 538942826 Affx-1251531474 AX-585489955 6 37926262 GGGACCTATTTTTTTAGGTCTACCTGGTTTTCTTT[T/TA]AAAGATGAATCAATCATACTGCTTGAATACTCTTT - 4 1 2 1 400000 r 74 goat ins-del_004 6 37926262 TA T SV-TF-chip candidate gene ou candidate region LCORL 538942868 Affx-1251531498 AX-585489992 6 37926529 TGGTTGCTTTTCAGAAGAAAAATCACGATTTGATT[C/T]GGAATTACCAACTGAAGTTAAAGTATATTTGACTC Y 2 1 2 1 400000 r 74 goat SNPs_045 6 37926529 C T SV-TF-chip candidate gene ou candidate region LCORL 538942915 Affx-1251531479 AX-585490038 6 37926957 AAGACTTTTTGGCCATATTTATTGTATCTTCCAAA[C/T]GTTCCACAACAACTTGTAAATTAGAATTCATTGCA Y 2 1 2 1 400000 r 74 goat SNPs_046 6 37926957 T C SV-TF-chip candidate gene ou candidate region LCORL 538942855 Affx-1251531451 AX-585489979 6 37927192 GGTTCTGCTCAAAAGTCCAGGGATATCACTTTTCA[A/C]AGGAGTTTGAGTATTCTCTAATTTTGGATTCTCTT M 2 1 2 1 400000 r 74 goat SNPs_047 6 37927192 A C SV-TF-chip candidate gene ou candidate region LCORL 538942804 Affx-1251531470 AX-585489938 6 37927338 TTTTAAAGCTTTCTGAAAATGCATCAAAAGCCAAG[C/T]TAGTTTCTAAATTATTTAGAGGTAGTTTCAATGAC Y 2 1 2 1 400000 r 74 goat SNPs_048 6 37927338 T C SV-TF-chip candidate gene ou candidate region LCORL 538942827 Affx-1251531475 AX-585489957 6 37927485 GTCTTTGGCAATGATAGAATTGCTCTTTGTCTGCT[G/GAA]AAGAGTTCATCATTGCGCAAAAACTTCCTTGGATT - 2 1 2 1 400000 r 74 goat ins-del_005 6 37927485 GAA G SV-TF-chip candidate gene ou candidate region LCORL 538942794 Affx-1251531452 AX-585489928 6 37927656 AGCTGTGCATTGCAAATAAGGTTTCTTGACGCTTT[C/T]GAAATCTTGTCTGAATAATTTTATTTTCTATCTTT Y 2 1 2 1 400000 f 74 goat SNPs_049 6 37927656 C T SV-TF-chip candidate gene ou candidate region LCORL 538942806 Affx-1251531471 AX-585489940 6 37927681 TTGACGCTTTCGAAATCTTGTCTGAATAATTTTAT[C/T]TTCTATCTTTTTATCATGTTGACTCAGCAATTCCA Y 2 1 2 1 400000 r 74 goat SNPs_050 6 37927681 T C SV-TF-chip candidate gene ou candidate region LCORL 538942918 Affx-1251531484 AX-585490040 6 37927782 GCAAAAGAGAGGTTATTAAATCTCTCAATTTTAAA[C/T]CATTATCTGTATTGCAATCACTGCTAGATAATTTT Y 2 1 2 1 400000 f 74 goat SNPs_051 6 37927782 T C SV-TF-chip candidate gene ou candidate region LCORL 538942920 Affx-1251531485 AX-585490042 6 37927785 AAAGAGAGGTTATTAAATCTCTCAATTTTAAATCA[C/T]TATCTGTATTGCAATCACTGCTAGATAATTTTATA Y 2 1 2 1 400000 f 74 goat SNPs_052 6 37927785 T C SV-TF-chip candidate gene ou candidate region LCORL 538942818 Affx-1251531491 AX-585489949 6 37927850 TTTATAAGGTTTGTCATATCTATTGTTTCTATTGA[C/CTTTAA]TTTTTCATTAATACGATCCATTAAATCTTGAAAAA - 2 1 2 1 400000 r 74 goat ins-del_006 6 37927850 CTTTAA C SV-TF-chip candidate gene ou candidate region LCORL 538942913 Affx-1251531478 AX-585490036 6 37927924 AATTATAGTAGTTTCACCCTTTTCATGATTTGTAG[C/T]ACAATTATTGCTGTCTTCTAAGAGCAAAGAATCAG Y 2 1 2 1 400000 r 74 goat SNPs_053 6 37927924 T C SV-TF-chip candidate gene ou candidate region LCORL 538942807 Affx-1251531477 AX-585489941 6 37928059 TGCTGGTGTCAGAGATGGAGGCTGGTTAATATTTG[C/T]TTCAAGTCTATTATTTTCTAAGGCTGAACACTCCG Y 2 1 2 1 400000 r 74 goat SNPs_054 6 37928059 T C SV-TF-chip candidate gene ou candidate region LCORL 538942928 Affx-1251531488 AX-585490049 6 37928172 GTGATAATGGTGGGGGTGAGGGACTTCGAGATCTA[C/T]AAACATCTTGAAGATTTACCGAAACATCACATATT Y 2 1 2 1 400000 r 74 goat SNPs_055 6 37928172 T C SV-TF-chip candidate gene ou candidate region LCORL 538942925 Affx-1251531489 AX-585490046 6 37928266 AAAGCCTGATTTTGTGGAATGAATGTCTGCTAACA[C/G]TCCAGAACAGAACCTGTGAGAATTGTAACTGTCTG S 4 1 2 1 400000 f 74 goat SNPs_056 6 37928266 G C SV-TF-chip candidate gene ou candidate region LCORL 538942823 Affx-1251531486 AX-585489952 6 37928641 TATGCACAAAGATTCCAAAACTTTGCTTAATGCTG[A/AT]TTTTCCTTTTTCCATTTTAGTAGCTTCCTCTGATT - 2 1 2 1 400000 f 74 goat ins-del_007 6 37928641 A AT SV-TF-chip candidate gene ou candidate region LCORL 38392238 Affx-122967574 AX-123262595 6 37929411 CTTCATCTCAGAACAATTTTCTGTTCTGTGAAGAT[A/G]CAGTAAGATATTTCAGAGTGGGAGGAGGGTTTGTA R 2 1 2 1 202000 r 74 goat snp7254-scaffold1268-284790 6 40254822 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779802 Affx-122978701 AX-385266902 6 37967374 TCCTGATGTGTTCAGGAGTTTTGAGGGAAATTCTC[A/G]CACTGGTTTGTACTGAAGCAGAAGACATACCAGTA R 2 1 2 1 101000 f 74 goat snp7255-scaffold1268-322753 6 40292732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse504 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320769058 Affx-122959291 AX-385256233 6 38014967 TTTCAGTGACTTCAAAGAAGATGACATTTGGTGGA[C/T]AAAGAGAAGTGATTTAGCGCATAAGAAAGGATTAT Y 2 1 2 1 101000 f 74 goat snp7256-scaffold1268-370346 6 40340257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse505 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449893 Affx-122922342 AX-123320228 6 38071340 CAAATTTAGTAAAAATCTTATTTATCTAGAGACTA[C/T]GCTTCATTTAATTTCAGTTCTGGCCAAACCCCAGG Y 2 1 2 1 101000 r 74 goat snp7257-scaffold1268-426719 6 40396508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419723 Affx-122945903 AX-123290071 6 38101262 TTAAATATCAGTCTCCAATTGGGTATTTTCTTATA[C/T]AGGAATATGTTATTGTTTCCTCCCTCCAATGCATG Y 2 1 2 1 101000 f 74 goat snp7258-scaffold1268-456641 6 40426392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse506 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320775893 Affx-122941715 AX-385263024 6 38131017 GAATTTAAATTGCTATCCTGTATTTTGAAAGACAC[A/G]GTGTTTCCTGGTGTAAGATTTGGTTTACTCACCTA R 2 1 2 1 101000 r 74 goat snp57869-scaffold935-9613 6 40455979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse507 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783562 Affx-122923374 AX-385270624 6 38160849 TTGAAATATGTAATATTTCTACTAACACCATGATT[C/T]TAACTTTGTTATTACGTTTATCTTACTGATCTCAG Y 2 1 2 1 101000 f 74 goat snp57870-scaffold935-39445 6 40485606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392797 Affx-122965973 AX-123263154 6 38199574 GAGAGTTAAGATGTATGTGGGAGCAAGACTGTTCT[A/G]GACCTAGAAGGAAACTGCTCAAATCCTGATCATAG R 2 1 2 1 101000 f 74 goat snp57871-scaffold935-78170 6 40524279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse508 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380620 Affx-122975241 AX-123250978 6 38247412 CCCTCCAAAATGTCTTGTTCTCCCTCTAGTTATTT[A/G]TTTAATAGCAGCAAGAACTGATTACATACATTTGT R 2 1 2 1 201000 r 74 goat snp57872-scaffold935-126008 6 40572138 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse509 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447272 Affx-122924939 AX-123317608 6 38279583 CTCATCCTTAGTGCCAAACAAGCTTTCCTTCTGCT[A/G]TCTCCTCAGCTGGCTATAAGTAATTGACCATCATG R 2 1 2 1 201000 r 74 goat snp57873-scaffold935-158179 6 40604765 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419950 Affx-122945210 AX-123290298 6 38333801 GAATGAGAGGAAGAATGACAGAAAGACAGTCAAGG[A/C]TGTGTTCATCACAGGTCACTGCTGCGGACGATTGA M 2 1 2 1 101000 f 74 goat snp57874-scaffold935-212397 6 40658741 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse510 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449794 Affx-122922422 AX-123320129 6 38364658 TAATTCCCTCAGGAAGGGGCATGTCATGATAAAAA[G/T]AAACTGATAAGAGTCAAATTTTTTGCTTTGAAATT K 2 1 2 1 101000 f 74 goat snp57875-scaffold935-243254 6 40689544 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse511 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320801944 Affx-122924529 AX-385288849 6 38395125 GTCTGCAGGATGAGTTCCTAGAGGTGGAACTTCTC[A/G]GTCAAAAGATTTGAACATTGATAAATTTTATATAC R 2 1 2 1 101000 f 74 goat snp57876-scaffold935-273721 6 40719722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781262 Affx-122938833 AX-385268347 6 38420676 GAACTCTTCTTTGCACATCATATTTGATGTGAGCT[A/G]TCAGTACAATATTAACAACCTGGAATTTGGTAAAC R 2 1 2 1 101000 f 74 goat snp7617-scaffold1273-10351 6 40745285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse512 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320795710 Affx-122975719 AX-385282663 6 38482775 TAGAAGTCAGGAAGAAAGGCTAGTTCTACTTTTGG[C/T]AAAATACGTAAGATGTCTGGATTGCAGGCATAATA Y 2 1 2 1 101000 f 74 goat snp7619-scaffold1273-72450 6 40807481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse513 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38429952 Affx-122938077 AX-123300293 6 38513140 TTAGCCATCTCAAAATCTCATCAAGACAGAGAGTC[A/G]TACCCTACCTTGATCTAGCAATCCCACTTCTGGGT R 2 1 2 1 101000 f 74 goat snp7620-scaffold1273-102815 6 40838651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382168 Affx-122974029 AX-123252526 6 38550093 TTGATTTTATTTTTTCTGTTAAGACCAGGCTTTTA[A/G]CCAGTTAAATTGCTCTCATTTTTATTGAGTTTTGG R 2 1 2 1 101000 r 74 goat snp7621-scaffold1273-139768 6 40875771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse514 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38430999 Affx-122936683 AX-123301340 6 38591591 AGATGGCAAACAACAAAATGGTACTGCTAATTAGA[C/T]ATCCAATGAAATGTCACATGGAAAGGTTAACTATT Y 2 1 2 1 101000 f 74 goat snp7622-scaffold1273-181266 6 40917327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse515 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38443044 Affx-122928148 AX-123313381 6 38624908 ATTTGGATATGTGTCCATAAATATTTATTGGAAGA[C/T]GGCCACACCCATCTATTTTTATACCCTTTGTGCTG Y 2 1 2 1 103000 r 74 goat snp7623-scaffold1273-214583 6 40948616 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789255 Affx-122955599 AX-385276266 6 38658929 ACTTGCTCTTGACCAATTTTCAAATCAGACCTTTA[C/T]GATTATTAACCCTAAGTGTCTCCCTTCAAGAGCCC Y 2 1 2 1 101000 r 74 goat snp7624-scaffold1273-248604 6 40982644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse516 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798588 Affx-122946462 AX-385285521 6 38714374 GGTAATTGTTTTCCCTCATGAAATATTACTACCAC[A/G]TACTTGTCACTAGATGATGTAGCCAAGAAGTCAGA R 2 1 2 1 101000 r 74 goat snp7625-scaffold1273-304049 6 41037445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse517 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425817 Affx-122940688 AX-123296163 6 38722193 ATTGGCAATCACTGGTACTGACAAATAATTTTTTC[A/G]TTTATGTTGAGTTTCCTAGTTTTTGATGTTTCACG R 2 1 2 1 201000 r 74 goat snp54015-scaffold821-1251869 6 41045116 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428796 Affx-122938402 AX-123299138 6 38751371 CAAGTCAACAAAGACAGCTTCGTTTACAGATACTA[C/T]GTTCTTAAAGAAAATGCATTATGTTTTGGTAGGCT Y 2 1 2 1 101000 f 74 goat snp54014-scaffold821-1222691 6 41073728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse518 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410094 Affx-122952838 AX-123280444 6 38828723 CTGCCAGTGCCAAGAGTCTCCCCACTGTTTACAAA[G/T]AAGTGTTTTCTGATGAATTTTCTTTAGCCATAATA K 2 1 2 1 201000 r 74 goat snp54013-scaffold821-1145339 6 41150643 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse519 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384604 Affx-122972572 AX-123254962 6 38857480 CCCAGAGGAACCACTTACTTGCTACACTCCTAATA[G/T]AAGTTACTTAGCCTCTTAAGCCTTGGGCTCCTTAT K 2 1 2 1 201000 f 74 goat snp54012-scaffold821-1116582 6 41179776 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769228 Affx-122925711 AX-385256402 6 38915386 ATTTAGTTGCAGGACTGTTGTGTTGTACACAGGAT[A/G]CATGGTATAAAAATAACTCTAGTAGAGATTTTAAA R 2 1 2 1 101000 f 74 goat snp54011-scaffold821-1058676 6 41238907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse520 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278523 Affx-1111836379 AX-519552006 6 38932564 TCTTATGAAAATTTATCATAGGGTTTTATTGCAAT[A/T]CATTTCAATTAACGATTTCTCAGAGAACTAGGTTT W 4 1 2 1 101000 r 74 goat Random2.2K-674 6 38932564 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415214 Affx-122948976 AX-123285563 6 38962409 CTGTGCAGAACACACAGAGTTTTTTGCATACAGCC[A/C]GTTATTGTTTCTATAAAGTTGTCAGAGCAATTTTT M 2 1 2 1 101000 f 74 goat snp54010-scaffold821-1011653 6 41285688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse521 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320800817 Affx-122973666 AX-385287733 6 39059889 ACTTGTTATAATTATGTTTGAAACCAATCTAGATA[C/T]GTTAAATATGTGAATCATTTTAATCTCCACAGCCA Y 2 1 2 1 101000 r 74 goat snp54008-scaffold821-914173 6 41385076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379202 Affx-122976295 AX-123249561 6 39124666 TTCTACTGTAAAATAAAGGGTGGAGACTAAGGGTC[G/T]ACAGACTAAGTCTAAGGAGTCTTTGCTCTTTACTT K 2 1 2 1 101000 r 74 goat snp54006-scaffold821-849396 6 41450679 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse522 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381297 Affx-122974457 AX-123251655 6 39155448 TAATGGACCTGATTCCCTCTGGGGTCTCAATAATT[C/T]TGCTATTTCAAATGAATGAAGTACTGCCTTCCAAG Y 2 1 2 1 101000 f 74 goat snp54005-scaffold821-818614 6 41481388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse523 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376234 Affx-122978788 AX-123246593 6 39188065 CATATATTTGTCAAATAAATATAATCTATTAAGAG[A/C]TTTCTAGGAAGGAAAATAGGAAACTACTTTATTCA M 2 1 2 1 103000 r 74 goat snp54004-scaffold821-785997 6 41514012 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273249 Affx-1111833503 AX-519546901 6 39213717 GATAAAAATTTCTGTCTCTTCTTCCTGCTGCTGTG[A/G]ACAAATGCATTAAAATGTATCTTTCTTTCTTTTCT R 2 1 2 1 201000 r 74 goat 6_39213717_AF-PAKI 6 39213717 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446134 Affx-122925772 AX-123316470 6 39280982 TATGTTATTAGGGCAGTTTCTGTCCTGATAATCAA[A/C]TTTTAAAGTGAAAATTAGTTTCATATGTAATTGAA M 2 1 2 1 303000 r 74 goat snp54002-scaffold821-693080 6 41606728 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse524 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38407756 Affx-122954978 AX-123278107 6 39314505 AAGAGAAGATAATGGAAAGCAGGAAACGGACTGGG[C/T]AGCATTTCTAGGTCAGCAGAGGGGTAGCATCATCT Y 2 1 2 1 101000 f 74 goat snp54001-scaffold821-659557 6 41638377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse525 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320768633 Affx-122961434 AX-385255812 6 39360271 TATGTCATTGAACAAACACAAGGAAGTTTAAAATC[A/G]TACCACAAATTTTTGACTTCCTGTGATGTACAGGG R 2 1 2 1 101000 r 74 goat snp54000-scaffold821-613791 6 41684168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440272 Affx-122930643 AX-123310609 6 39404274 CAAAGAATTTTATGAAGGTGGTAGATGGTTGTGAC[A/G]TCATAAACTGTAAGCATTGAATCCAAAATCTAGTG R 2 1 2 1 101000 r 74 goat snp53999-scaffold821-569788 6 41727639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse526 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320778208 Affx-122946430 AX-385265323 6 39434354 TCTTTGAGACAATGTAAAGGCTTTTGAGTCTGGCT[A/G]TTGAGGGAACAACTGCTTCATTGCTCGCCCCAGGA R 2 1 2 1 101000 f 74 goat snp53998-scaffold821-539708 6 41757720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse527 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783109 Affx-122926499 AX-385270176 6 39498305 ATAAATCAATCTACAATGTTTATATTATTATGGCT[A/G]TAAACCTTGATGTCTGGAGATCCATGAAATTATAT R 2 1 2 1 101000 r 74 goat snp53997-scaffold821-475757 6 41821698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785720 Affx-122933787 AX-385272761 6 39549491 CAATGTTCTCTCTGTTTGTCTACATATAATTTAGC[A/G]TCTTTAAAATGATTCCTTGTATCATATTTTGTTTA R 2 1 2 1 201000 r 74 goat snp53996-scaffold821-424571 6 41873350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse528 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38438929 Affx-122930421 AX-123309266 6 39578923 ATATTTAAATAACTGGCTAGAGGTCACACAGCTGG[C/T]AAGTGATGCAGCCAGAATGTGAACTGACCACTAAG Y 2 1 2 1 201000 r 74 goat snp53995-scaffold821-395139 6 41902850 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse529 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38394446 Affx-122964590 AX-123264801 6 39641943 AGAGAGGAAGAGGGTGGGATGATTTGGGAGAATGG[C/T]ATTGAAACATGCACATACCTTTTAAAAGCAGAGTA Y 2 1 2 1 303000 r 74 goat snp53993-scaffold821-332119 6 41965951 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791744 Affx-122929727 AX-385278735 6 39681920 AAACATGCTGGGAAGAGTAATGTCATATCTAAAAG[A/G]TTTTGATCCTAGTAGCCTCTTGTGAAGGCATTTCT R 2 1 2 1 201000 f 74 goat snp53992-scaffold821-292142 6 42005965 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse530 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320766380 Affx-122926300 AX-385253759 6 39713419 GCTCAGGATTATTCAAAGAGGAATGCCAGAGAATC[G/T]AAAGTTAATCTTTGACATTCTGGTTTGTGTTGGCC K 2 1 2 1 101000 f 74 goat snp53991-scaffold821-260643 6 42037438 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse531 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320778915 Affx-122957180 AX-385266022 6 39754097 ATGAGGCTGTCTTTCATCTAAACATATCATATGTT[A/C]TGCATCCAAATGAATGTCTTTAAAATCATATACTT M 2 1 2 1 101000 r 74 goat snp53990-scaffold821-219965 6 42078273 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450867 Affx-122922224 AX-123321201 6 39784459 GCTTTGAGCAGTTAAATTACATGAAGATCCATGTG[C/T]GGCAAATCATAGGTTGAAGATGTGTTTTAGCCTGA Y 2 1 2 1 101000 r 74 goat snp53989-scaffold821-189603 6 42108554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse532 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380030 Affx-122975587 AX-123250388 6 39818505 TTGGAGTCCCTCCAGTGAATTCATTCATGCGATCA[C/T]GACAGCAGAGAATGTCTTTGTGAATCCAGAGGACT Y 2 1 2 1 101000 r 74 goat snp53988-scaffold821-155557 6 42143763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse533 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377692 Affx-122977415 AX-123248051 6 39856451 GCTTTTGTTCTAGTAGGGGTTATTTTTGTTTAATC[A/G]CTAAGTGGTATCTGACTCTTTGTAACCCCACGGAT R 2 1 2 1 201000 f 74 goat snp53987-scaffold821-117611 6 42181641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450074 Affx-122922802 AX-123320409 6 39913225 GAAATACAGTAGACTACCCAAACCTCTTTTCTACC[A/G]TATCAGATTTCTTAACCTCAGTCTGCTTCGTATGG R 2 1 2 1 101000 f 74 goat snp53986-scaffold821-60837 6 42239414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse534 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38451339 Affx-122921267 AX-123321672 6 39985100 GTTGTAATCACCTTGCAACTGTGGCTGAAACCACC[A/G]TTGGTCTTTGTTAACTAAAGGGGAGATACTGGCTT R 2 1 2 1 101000 f 74 goat snp5610-scaffold1199-10939 6 42311182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse535 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392361 Affx-122966248 AX-123262718 6 40015507 TTATGCTGTGAGCTCTAGTCCAGGCAGGTGAGACA[C/T]GAGAAGCCTTCTTGAAGCTTGCACTTTACAGGAAT Y 2 1 2 1 101000 r 74 goat snp5611-scaffold1199-41346 6 42342544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376965 Affx-122977759 AX-123247324 6 40045993 TAGATATATGGAGAAATGTGGGAACCAACAAAATA[G/T]ATTTGTCTTAGTTGTATGACTTCAATTTAGCTTTT K 2 1 2 1 101000 f 74 goat snp5612-scaffold1199-71832 6 42373274 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse536 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445296 Affx-122925449 AX-123315633 6 40117924 ATTCCTTGTGAAATAATCTTGACTCCGAAAACTAC[A/G]TAATTGATAAATTAAAATTTTCTGAAATCCTCATT R 2 1 2 1 101000 f 74 goat snp5614-scaffold1199-143763 6 42445683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse537 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320802915 Affx-122953937 AX-385289812 6 40187660 GATTTTGAGCCTGATTTTTAAGCTGAAATTCATGA[C/T]GAACCTACTATGCATTAATTGAGTGTATTTGCACA Y 2 1 2 1 101000 r 74 goat snp5616-scaffold1199-213499 6 42515861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397194 Affx-122962403 AX-123267549 6 40218526 ATACAATGTGCATATGAACTGAGTTAGTCCATCTG[C/T]CTATCTTCCAACTCAGACACATCAACTTTCCCCAC Y 2 1 2 1 101000 r 74 goat snp5617-scaffold1199-244365 6 42545736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415032 Affx-122949017 AX-123285381 6 40295190 GGCAGAAAGAAGCAATATCTGATCTGGGTCTCTCT[A/G]TCTCTAAAAACCATGGTCAGGCTAATCTATTTTAG R 2 1 2 1 201000 r 74 goat snp5619-scaffold1199-321029 6 42622661 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442833 Affx-122927697 AX-123313170 6 40450653 AGGAATCTAAACTGGGCTGGGAAACCAATCAAGAT[A/G]ATCACAAGGAAGATGGCAGCATGCTTGTGATGAAG R 2 1 2 1 101000 f 74 goat snp5623-scaffold1199-476492 6 42778317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397371 Affx-122962280 AX-123267726 6 40484715 AATAGCAATTGGATTCCTACACTTTTACTTACTTA[A/G]TTCAGTAGCTCAGTCGTGTCCGACTCTACGATGCC R 2 1 2 1 101000 f 74 goat snp5624-scaffold1199-510554 6 42812309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787130 Affx-122936387 AX-385274156 6 40548323 ACAATATAAATCCTTAACAAGGTAGATACCATGGT[A/G]TCTGTTTTACTATGAAAGAAACTGAGGTCTTGGAG R 2 1 2 1 201000 f 74 goat snp5626-scaffold1199-574162 6 42875832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772324 Affx-122974473 AX-385259478 6 40591830 CTAGGACCTGCTAAGTTAGTCTGAGTTCCCGTCAT[C/T]TCTGAACTTGAAGCTCAGTTGTGTGAAGAAGGGGA Y 2 1 2 1 101000 r 74 goat snp5627-scaffold1199-617669 6 42919478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389366 Affx-122968457 AX-123259724 6 40628318 GAGTGTTATCACTTAATAACCTTGCTACCTTCTTT[A/G]TGACATGGAGGTTGGCTTCCCTTGAGAGCACAGAA R 2 1 2 1 101000 f 74 goat snp5628-scaffold1199-654157 6 42955958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785673 Affx-122932496 AX-385272714 6 40732605 ATTAGAATTGCTGGGTAGAATACTATAAACAACAT[A/G]CCTAGTTAAGAGGTAGAATTCACTAGAATTTTAGT R 2 1 2 1 101000 r 74 goat snp5630-scaffold1199-758444 6 43061877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278357 Affx-1111836380 AX-519551843 6 40751543 TGACCTGAAGATGCAGGAACTTACGTGAAAAGAAA[A/G]GGGCCTCTCTCATGGCTCAGACAGTAAAGAATCTG R 2 1 2 1 101000 f 74 goat Random2.2K-676 6 40751543 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440299 Affx-122930219 AX-123310636 6 40830947 GCTATGTGGATCCAGCAGTCCAAAGTCATTCTAAA[C/T]ACTCCAAACCCTTGTTTCCCTGGCAGTGAAAAATC Y 2 1 2 1 102000 r 74 goat snp5632-scaffold1199-856786 6 43160722 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408223 Affx-122953841 AX-123278574 6 40874418 CCGACTCAAAAAGTGCTGACTTCCTCTGGTAGGTC[A/G]TCTTATAGGTCTACCTTATACTGCATAAGAGTGTG R 2 1 2 1 202000 r 74 goat snp5633-scaffold1199-900257 6 43204571 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388660 Affx-122969105 AX-123259018 6 40904297 GGCACAAAAGGATGGACTGTTACTCACAGAGCATC[A/G]CCCTTCACAAGGAAACACATGGGCAGGGGATGAAT R 2 1 2 1 101000 f 74 goat snp5634-scaffold1199-930136 6 43235619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795518 Affx-122948665 AX-385282473 6 40956702 TTATTCTATGTGTAGGGTATTGGGACTGGGACAGA[C/T]AGATTGAAAACCATTCCTCAAGGTTCCATTGACTA Y 2 1 2 1 101000 f 74 goat snp5635-scaffold1199-982541 6 43288081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782436 Affx-122921908 AX-385269512 6 41257845 AAACAAAGGGGTCAGGTGTTTTTATTCTGCTGTGA[C/T]GCCCTTGAAAAATTGAGATATTCCTTTGAGAGTCA Y 2 1 2 1 101000 f 74 goat snp5641-scaffold1199-1283684 6 43589749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784047 Affx-122938001 AX-385271100 6 41292834 TTGGAGGAGAGAATTGGCATGGCTGGGAAGAGATA[C/T]GGAAGAAAGGTTTTATCTCTGGGACTAGACAGCAT Y 2 1 2 1 101000 r 74 goat snp5642-scaffold1199-1318673 6 43624691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419110 Affx-122945771 AX-123289458 6 41520851 AAAGACTTAGCACCACGAGGTATGTGGGCAAACCA[C/T]GCAGCTGCAGATGTCTCACACCTGGATCTATATGG Y 2 1 2 1 101000 f 74 goat snp5648-scaffold1199-1546690 6 43853896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420862 Affx-122944639 AX-123291209 6 41592699 TGCAAATGGCATTATCTCATTCTTTTAAATAAATG[C/T]AATCATCTTCCAAAGGAAAAATTTGTGTGCCCTTG Y 2 1 2 1 102000 r 74 goat snp5650-scaffold1199-1618538 6 43925687 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381048 Affx-122974630 AX-123251406 6 41666037 AGAATAATTTCACGTCTAGAAATGGTTTAACCCAA[C/T]AATGTAGCAAAAATTCTGGCTTATATGTAATTATT Y 2 1 2 1 201000 r 74 goat snp5652-scaffold1199-1691876 6 43998891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795859 Affx-122974611 AX-385282811 6 41698185 TATTAGCCAAATCTGAGGTCAAATTATGGTCACTC[A/G]CCTTATTAGTCCTAATTCTTGGGCACATCTATAAC R 2 1 2 1 101000 f 74 goat snp5653-scaffold1199-1724024 6 44031201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794753 Affx-122966705 AX-385281713 6 41837813 ACTATACATCAGGCAATTCCAGAACATTTAAATAG[C/T]AGGGCAGAGGTACCACTATAAGAAGCCACTGTGGG Y 2 1 2 1 101000 r 74 goat snp5656-scaffold1199-1863652 6 44170141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402806 Affx-122958282 AX-123273159 6 41891566 TTACAGGAAAAAAAAAATATTCTACTTTCTGGTAA[G/T]ACAGCAGATGGTCCAGTGGTGAGCACTGAACTGTA K 2 1 2 1 101000 r 74 goat snp5657-scaffold1199-1917405 6 44223969 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770793 Affx-122927426 AX-385257957 6 41958478 TAACAGGTGAGACACTTAAGGCTTCAATAAGATAA[A/G]TATTGTGCCCAGTGTCACGTTAACTAGTCACAGTT R 2 1 2 1 201000 f 74 goat snp5658-scaffold1199-1984317 6 44290824 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278359 Affx-1111836381 AX-519551845 6 41988264 TCAGATGAGGTACATGTGTATAGCATCCTGCACCA[A/G]CTTTGGTACATAGTAGATTCTCAATAAAGGTTAGT R 2 1 2 1 101000 f 74 goat Random2.2K-677 6 41988264 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391501 Affx-122966675 AX-123261858 6 42023440 TGTACCCCTCAGAGCTACTACTTAGAGTCCTGTGA[C/T]GCAGGCACTGATGTAAGCACTTTGTGTAATTATTT Y 2 1 2 1 101000 f 74 goat snp5660-scaffold1199-2049279 6 44356183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273202 Affx-1111833504 AX-519546861 6 42035155 ACACACTTGCCAGTGCAAGAGACATAAAAGATGTG[A/G]GTTCAATCCCTGGGTCAGGAAGATACCCTTGAGCA R 2 1 2 1 103000 f 74 goat 6_42035155_AF-PAKI 6 42035155 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784667 Affx-122955399 AX-385271715 6 42063129 CATCTGCAGAACACCGTGTTTACGAAAACCTGTTG[A/G]TCTTTTTGATCAGCCTCCTTGCTCCCTTTATACCA R 2 1 2 1 101000 r 74 goat snp5661-scaffold1199-2088968 6 44395361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411450 Affx-122951815 AX-123281800 6 42092794 TTGACCTACAAAAAGCTAGTGAGTTTTATTTGGGA[C/T]GTATAGAATTAAAGGTGACTCTGGATATTCAGATA Y 2 1 2 1 101000 r 74 goat snp5662-scaffold1199-2118633 6 44424892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394779 Affx-122964829 AX-123265134 6 42392481 GGAAGCAGCAGGAAGGCTGAAGAAATGTGCTGAAG[A/G]TTACTGAGCTAGTAAATTGCAGATTTGAGGTTTAG R 2 1 2 1 101000 f 74 goat snp5669-scaffold1199-2418320 6 44723975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416122 Affx-122948300 AX-123286471 6 42427557 CTTTTATTTGAACAAGGCTTTGAAACTGATCAAAT[A/G]CCTGGATTATCTCATTCATTGCTCATCACCCTTTG R 2 1 2 1 101000 r 74 goat snp5670-scaffold1199-2453396 6 44759620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411884 Affx-122951195 AX-123282234 6 42467230 CATTCATCCCATTTGACTGGTCTCATAACAGGAAG[C/T]AAAGTATCCCAAGGGACCAAATGGCCCTCTTATAA Y 2 1 2 1 101000 f 74 goat snp5671-scaffold1199-2493069 6 44799485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400192 Affx-122960188 AX-123270547 6 42644423 ACTTTAACTGGAACCGTAAATTCAGAGGCATCGGC[A/G]TGGCCAGGCAGTGGGTTACAGCAGGTGATTTAAGA R 2 1 2 1 101000 f 74 goat snp5675-scaffold1199-2670262 6 44976665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786720 Affx-122929917 AX-385273751 6 42710009 CTAAATGTGATCAAGACTATAATGGACCCAATGCC[A/G]CATAAGAGGTACTAAGTATTTGTTCAGAGATCTGT R 2 1 2 1 101000 f 74 goat snp5677-scaffold1199-2735848 6 45042013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422271 Affx-122943990 AX-123292617 6 42760768 GTAGCTGCTGGGTTTGACTTAGCAGCACAGTGATG[C/T]AAAGGTGGTTCTCCTTTTCTTCCCTCATGATTGTA Y 2 1 2 1 101000 f 74 goat snp5678-scaffold1199-2786607 6 45092988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278361 Affx-1111836382 AX-519551847 6 42808051 ATGCACAGTCCCACTCATCATGTACAAAAGGATTG[A/G]TTCATGCACTAAGCTGGGGGATAAAAACGATGCCC R 2 1 2 1 101000 f 74 goat Random2.2K-678 6 42808051 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784063 Affx-122945048 AX-385271116 6 42824957 ACCCTACTGTCTTAAAAAACACCTACTCAGATAAA[C/T]TGTTTCCATCTCCCTGTTGCAGCTAGTTCACATGT Y 2 1 2 1 101000 r 74 goat snp5680-scaffold1199-2850796 6 45156751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402234 Affx-122959145 AX-123272587 6 42860198 ACGTTAGTTGAGATGGGTTAGGTTTCACTGTGCCT[A/G]CAAACAATCCCCAAATCAGTGGAATTTTATTTAAA R 2 1 2 1 101000 f 74 goat snp5681-scaffold1199-2886037 6 45192284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421750 Affx-122944367 AX-123292097 6 42922711 CTGTTTAGGACCAGTATCAATGGAGTATGTATGTG[A/G]AACCATTCACTTTATTCCGTCTCTGATTCAATTCT R 2 1 2 1 101000 r 74 goat snp5682-scaffold1199-2948550 6 45255805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403145 Affx-122958101 AX-123273498 6 42959257 ATAACTTTGTGTGTCGGGACTGAGTCATAGGATGA[C/T]GGCAGTGACGCTCCACCTACAGTCTGGCTGATGGC Y 2 1 2 1 101000 f 74 goat snp5683-scaffold1199-2985096 6 45293384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775803 Affx-122938664 AX-385262934 6 42997376 AATTTGTCATAGCAAATTGTACCTTTTTTATAATA[C/T]AATTTTACTCTCATGGAGTCCTCTCTGAATCTGTT Y 2 1 2 1 101000 r 74 goat snp5684-scaffold1199-3023215 6 45331924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388702 Affx-122968988 AX-123259060 6 43036116 ATAAATAGCCTTAGACTGTAAAGAGATCTGTAGCT[A/G]TTGGAGTTGCTGATTGGAAAATGGGTTTAAAATAA R 2 1 2 1 101000 r 74 goat snp5685-scaffold1199-3061955 6 45370898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798573 Affx-122953453 AX-385285506 6 43076360 GGAGCCAGCTATTGTTTTAATTTACAACAAGAGCC[A/G]CTATTGCTTCTGGAAGTATTAAATATTTTCAGTTC R 2 1 2 1 101000 f 74 goat snp12879-scaffold1498-8679 6 45415346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775315 Affx-122977432 AX-385262446 6 43115323 TTTTATAATGAGATGATGGCATCTCTACAAGAGAT[A/G]CTAATTTTCCATTTGTGGTGGTGACACTATTTATT R 2 1 2 1 202000 f 74 goat snp12880-scaffold1498-47642 6 45452774 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440762 Affx-122929859 AX-123311099 6 43157354 AGGACAAATTCCTAGAAGAAACTTTGAGTCAGAGT[A/G]TATGCTCATTTCTAAGACTTTTGATGTATTTTGCT R 2 1 2 1 201000 r 74 goat snp12881-scaffold1498-89673 6 45494802 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386556 Affx-122970713 AX-123256914 6 43210112 CAAAATTCAACTTACTCCGAATGACCTGGAGCATC[A/G]CCATGAAGGGTAGAGGGGGAGGGTGACTGGACTGC R 2 1 2 1 101000 f 74 goat snp12882-scaffold1498-142431 6 45547890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443315 Affx-122927453 AX-123313652 6 43258334 TCCCCATTCTGTTCTCCAGGGATTATCTTTGTGAC[A/G]TTTAGAGGAAGTTGAAGGAAAGTAACCACCATCCT R 2 1 2 1 201000 r 74 goat snp12883-scaffold1498-190653 6 45596465 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397813 Affx-122962488 AX-123268168 6 43288657 ATGCTTTTGATAAGAAATATCTTACTGAATTTTCT[A/C]TTTATCTACAAAAACAGCATAGAGTCAGTACTCCC M 2 1 2 1 101000 r 74 goat snp12884-scaffold1498-220976 6 45625400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787656 Affx-122923700 AX-385274679 6 43330064 GTGCTCTACCTGGCAACAAATTTAGGGACGGGACA[G/T]AATTTGCATGAGGAAAATTTATCAGCCAGCATGCT K 2 1 2 1 101000 f 74 goat snp12885-scaffold1498-262383 6 45666818 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442857 Affx-122927677 AX-123313194 6 43385988 GGAGGGGATTGAAAATCTGCAAAAGGGCAAGAAAA[C/T]GAAAGGAACAACACTGTCATCAAATGCCCGTGGAT Y 2 1 2 1 101000 f 74 goat snp12886-scaffold1498-318307 6 45722762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439859 Affx-122930057 AX-123310196 6 43444445 CAAACTCTCAAGAGGGAAAGAAAACAATTCTCTTC[A/G]GCACTTCCTTATCCACCTCCCCCCATCCTCACCCC R 2 1 2 1 101000 f 74 goat snp12887-scaffold1498-376764 6 45780116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376956 Affx-122977765 AX-123247315 6 43490419 GTGATCAGATTCAGCCTTTCCAGGCATCTCTGACT[A/G]TATCTGGCGGAGGGGCCGGAAGGGCCAAGGTTGAA R 2 1 2 1 101000 f 74 goat snp12888-scaffold1498-422738 6 45826049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386939 Affx-122969992 AX-123257297 6 43527601 AGTGTTTTTTCAGTGTTTTGCCATTTCACAAAGAT[A/G]TATTTTTATTCACTGTGTTGGGCATTCCAAGGGTC R 2 1 2 1 101000 r 74 goat snp12889-scaffold1498-459920 6 45863398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441222 Affx-122929516 AX-123311559 6 43583813 AGAGCTGGTGGTCTCTCTGGCCGTCCACCTGGAGA[C/T]GACCTGCGTTCCCCCAAAGGGGCAGTTATATAGCC Y 2 1 2 1 101000 r 74 goat snp12890-scaffold1498-516132 6 45919970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437672 Affx-122931779 AX-123308010 6 43627970 ACAATGGAAAATAAGATTCCAGAGGGAAAGCATGA[C/T]GAACGACTCAACAAACTGTTCAACTGAAGAAACAC Y 2 1 2 1 101000 f 74 goat snp12891-scaffold1498-560289 6 45963557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798694 Affx-122963064 AX-385285626 6 43637248 GAAAGAATTCAGAGGTGGGTATAAGGAAGGGATAA[C/T]GTTTAGGAAAACCTTGCCAATGTGTTTTCAACTTT Y 2 1 2 1 101000 r 74 goat snp52104-scaffold771-4330 6 45972755 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779257 Affx-122954257 AX-385266361 6 43665773 GTGGCTAATTTGGTGTCCCTTTTCTGCAATATGGC[A/G]TTGAAAGTCATTCCTATAAACGAAACCTTCCCAAT R 2 1 2 1 101000 f 74 goat snp52105-scaffold771-32855 6 46001930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428610 Affx-122938690 AX-123298952 6 43696657 TGCCCGCAATGTGCCCCACAGGCAGACCCCAGTTT[A/G]CATCTAAGCCCTTCTCAATTCCCAAGGAAAATAGG R 2 1 2 1 101000 r 74 goat snp52106-scaffold771-63739 6 46033200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418170 Affx-122947085 AX-123288518 6 43754531 TCCCTGGTGGGAGAACTAAGGTCCCACATACCTTG[C/T]AGTGTGGCTAGAACAGAACAAAAACTTGAGCACAC Y 2 1 2 1 103000 r 74 goat snp52107-scaffold771-121613 6 46090905 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385670 Affx-122971146 AX-123256028 6 43877924 ATAAATCTGGTCATCAGATGACCAGAATTTATTTC[G/T]CTTACATGTTTGGTCTTGTCCACAGTTCCTGACTC K 2 1 2 1 101000 r 74 goat snp52109-scaffold771-245006 6 46214946 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396721 Affx-122962806 AX-123267076 6 43912067 AAATGAGAACACATATAAACACATACATTCTGTTT[A/G]TTGTGTGCTTGTCTTTTATTGCATGAGGCTAGTTT R 2 1 2 1 101000 r 74 goat snp52110-scaffold771-279149 6 46249736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777416 Affx-122937781 AX-385264537 6 43944582 CATGCTTTGGTGGACAAGGCTGCTTATGGAGGAAC[A/G]TGAAAGATTTTTTTGGGTTGGCTTGAAAGGTAATA R 2 1 2 1 101000 f 74 goat snp52111-scaffold771-311664 6 46282589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445097 Affx-122926200 AX-123315434 6 43974295 CCTGGCGAGAACCTGCAAGACTGGACAGTTACTTG[C/T]GGTTCATGTGTTAAGGATAAAGTCGTCTGTGTGCC Y 2 1 2 1 101000 r 74 goat snp52112-scaffold771-341377 6 46312352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445654 Affx-122926152 AX-123315991 6 44007285 GTCAGGAGTTTTCTGCTTGCTTGGGAAACCTCCAG[A/G]TTGCTTCTACTGCATAATGAGCAAAAATCAACAAC R 2 1 2 1 201000 r 74 goat snp52113-scaffold771-374367 6 46345544 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411865 Affx-122951212 AX-123282215 6 44055931 TCCTTTATGCTGGAAACTCCCTGTGGCAGAGACCA[G/T]CTAGATGTTCACTGACCCAGATTCCACTTCCTAGA K 2 1 2 1 101000 r 74 goat snp52114-scaffold771-423013 6 46394446 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802695 Affx-122928223 AX-385289594 6 44094303 TTTTTCTAATGCCTAGAAATTAATAATGTAGAAAA[C/T]GATTTTCATAGATGTTCAGAAGAACTTCTTGCAGA Y 2 1 2 1 201000 f 74 goat snp52115-scaffold771-461385 6 46430025 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428058 Affx-122939121 AX-123298401 6 44124080 GCTGGTGAGCAGGTCAGATGGAAATGGGGAGTGTT[A/C]TACTTTCATCCTCCACTTCATTCCTTCCTATATTC M 2 1 2 1 101000 r 74 goat snp52116-scaffold771-491162 6 46459707 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789285 Affx-122943050 AX-385276296 6 44161902 GATGAGTCTTTTACACCCTACTGGTAATTCAGGTG[C/T]AAACTAGCAGTCTATACATTTTCAATAAACAGTGT Y 2 1 2 1 101000 f 74 goat snp52117-scaffold771-528984 6 46496239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781599 Affx-122920730 AX-385268682 6 44217076 CTTTAAAAAAGTATCATTAGGTTGTAACACATTAT[A/G]TAGTAATTTGAGACTTTTATAATGAGCTTAAGGCA R 2 1 2 1 101000 f 74 goat snp52118-scaffold771-584158 6 46551483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425540 Affx-122941451 AX-123295886 6 44285145 AAAAGGAGAAGGGTGGATAAAGAAGAAAATAAATC[A/G]CAGGAATTGTCTGGTAAAATAAAGATTCATCTTGT R 2 1 2 1 101000 r 74 goat snp52120-scaffold771-652227 6 46619342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784166 Affx-122936522 AX-385271218 6 44314748 CTTAATAAAGATTAGTGCTCGAGTGTTGGGCAGAT[A/G]TTTATATTGGTTCAGGGTGTGATTGGTGATGTAGA R 2 1 2 1 201000 r 74 goat snp52121-scaffold771-681830 6 46649320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388152 Affx-122969460 AX-123258510 6 44359112 CTTCTTGACACTTGCTAATCCTACCTTCAGCAACT[A/G]TTCTTGACTGGTTTCACTGTTGCAGATTTAAGGAT R 2 1 2 1 101000 r 74 goat snp52122-scaffold771-726194 6 46693889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379493 Affx-122976470 AX-123249851 6 44410192 GATTAGTGGGAACTTCTTGAGGTGACAAGGACAGC[A/G]TGTTTTGTGTGGGTGGGAGAATAAGTGGGAGTAAA R 2 1 2 1 303000 r 74 goat snp52123-scaffold771-777274 6 46744954 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421205 Affx-122944144 AX-123291552 6 44438872 TGTTGACTTTGGGAACAGACAGAAAATTGGGAGGA[C/T]GAGGGGGTCTCTAGCATCATGGACAAATTGGAATT Y 2 1 2 1 101000 f 74 goat snp52124-scaffold771-805954 6 46773590 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393638 Affx-122965300 AX-123263993 6 44476857 TCTAGAAAACAGTAGGCTTTCTTGAACATCTTACC[A/G]TTCTTTCTTTCCTTACCCCACCAATTGGGAACCAG R 2 1 2 1 101000 f 74 goat snp52125-scaffold771-843939 6 46810675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800723 Affx-122949222 AX-385287640 6 44519341 GCAATGCAGTGAGAACAGTTTCATGATGTGAAAAT[A/G]CACTGTGGTATTGCCATGTGAGAACAAGGAGGGAA R 2 1 2 1 101000 f 74 goat snp52126-scaffold771-886423 6 46853080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442970 Affx-122928205 AX-123313307 6 44569251 TGCCTTATCTGTAGGTTCTCCATCTGCTGACAGAA[C/T]ATGCAGATGCAGAGGGCGGCTGTGAATTTCCATGG Y 2 1 2 1 201000 f 74 goat snp52127-scaffold771-936333 6 46902404 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793268 Affx-122939536 AX-385280246 6 44606058 ATTCTTTTGCAGATGTAAAAGTGTACTGTAAAGCC[A/G]TATCCTAGGATGTAGACAGTGTACTGTAAAGGTTG R 2 1 2 1 101000 r 74 goat snp52128-scaffold771-973140 6 46939046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439194 Affx-122931043 AX-123309531 6 44649197 GGTAACTCAACAGTGCAGTAAGGGAGATAGATATG[C/T]ATGTATTCAGGTGTAATAAATTATTGAAAACTGAA Y 2 1 2 1 101000 f 74 goat snp52129-scaffold771-1016279 6 46982221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464443080 Affx-1110485489 AX-515915757 6 44694785 CAGAGCAGAGCTAAAATTCTCTCAGATCCATAACA[A/G]GCTACATGAATACCCTTCCATTCTCTGGAACATGG R 2 1 2 1 101000 r 74 goat 6_44694785_AF-PAKI 6 44694785 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427730 Affx-122939268 AX-123298073 6 44699431 AGGTTTGAGAAGCATTCTTTAAAGACATTGAAACT[A/G]TTTTCCCTTTACCAACAGGGCCTCAGTAGCATACA R 2 1 2 1 101000 r 74 goat snp52130-scaffold771-1066513 6 47032712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799890 Affx-122921439 AX-385286816 6 44732416 GATCAGTTGGCAATGACTTTCCGGAGCATTGTCTT[A/C]TGAAGGCTTCTGATGGTGTGTTTAGATTCAACAGT M 2 1 2 1 101000 r 74 goat snp52131-scaffold771-1099498 6 47065959 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402374 Affx-122959035 AX-123272727 6 44774781 CCAGGCAAGAGTCACAGCCATTCCGAAAACTTTAA[C/T]GGTTTGACAAATGAGCAATTTATAATCAGCTGCAC Y 2 1 2 1 101000 f 74 goat snp52132-scaffold771-1141863 6 47108866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770772 Affx-122942684 AX-385257936 6 44806084 GAACAGAATCTAGCACACAATTGGTCCTAAACAAA[C/T]GTGAGTTTCATTTTTACCTTCCTTTGGATCAACAT Y 2 1 2 1 201000 r 74 goat snp52133-scaffold771-1173166 6 47140009 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418561 Affx-122946389 AX-123288909 6 44836351 AAATCCAATACTTTCTCACTCAGCGGGCAGCTTCA[C/T]TGGAGGACCCTGATGGGGTTGCAACTCTCTAATTT Y 2 1 2 1 201000 f 74 goat snp52134-scaffold771-1203433 6 47170181 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379308 Affx-122976199 AX-123249667 6 44886217 GTCTTAATAGTGAAAGAGGATAGTAAGTGACTGCC[A/G]CAATGGATGAAAAAGACTTGCACTTAGGCAAATCA R 2 1 2 1 201000 r 74 goat snp52135-scaffold771-1253299 6 47218095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773504 Affx-122963673 AX-385260645 6 44925511 GCACCTTTTCTTATGTTCTTGTGACACTCCCTGTG[C/T]GATTCCTTTGCTGTTTGATACTCAATGCTTTTAGC Y 2 1 2 1 101000 f 74 goat snp52136-scaffold771-1292593 6 47257398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383249 Affx-122972747 AX-123253607 6 44957766 ATAATAAGTTAAATTTGTGGGCGAGCATATTAAAA[C/T]GACGAAATAGAACAGAATAGAAACTCATTGCATGT Y 2 1 2 1 202000 f 74 goat snp52137-scaffold771-1324848 6 47289467 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786900 Affx-122956865 AX-385273929 6 44995471 AAAGTCTAGAGAATAAAATGAGCTAAAGGCCAACC[A/G]TGAACATTGACACACAGAATAAAACAATAGCTTAA R 2 1 2 1 101000 f 74 goat snp52138-scaffold771-1362553 6 47327222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409829 Affx-122952946 AX-123280180 6 45024541 AATGTCTAGATAAAATTGTGTCTTTCGACTAATGG[C/T]GCTTGGAATTTAACTTGAGGTTTTACCACAATAAT Y 2 1 2 1 101000 f 74 goat snp52139-scaffold771-1391623 6 47356219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438119 Affx-122931492 AX-123308457 6 45064774 TGATTAATTTGGTCAGTATGCCACGTCTCCTCCTC[A/G]GTTAAGGGCTTACACTTTCAGCCTTCTTCACGGGC R 2 1 2 1 101000 f 74 goat snp52140-scaffold771-1431856 6 47396256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801858 Affx-122975882 AX-385288765 6 45098816 TTCTTATTTCTAAAGGTATTTTATGCTATTCATCT[A/G]GTACTGCTTGAAATGAACTTGCAGGAAAGTAAGTA R 2 1 2 1 101000 r 74 goat snp52141-scaffold771-1465898 6 47430369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278365 Affx-1111836384 AX-519551851 6 45098894 AAGGAACTCCTAGAATGGAAGTGGGAAGCATAGGC[A/G]TGCGTGCTAAGTCACTTCAGTCATGTCCAACTTTT R 2 1 2 1 202000 f 74 goat Random2.2K-680 6 45098894 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783078 Affx-122957729 AX-385270145 6 45145304 TCAATATTTGAATCCCTGTAACTTGTGAATATGTT[A/G]TCTTATTTGATAAAAGGATTTATAGACATGATTAA R 2 1 2 1 101000 f 74 goat snp52142-scaffold771-1512386 6 47478200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794532 Affx-122943291 AX-385281495 6 45176457 TGAAGGATGATATCATCTTCAAGTAGGAAAGACCC[A/G]TCTAAGATTCAGAAAACAAATCAACCCCACAAAAG R 2 1 2 1 303000 r 74 goat snp52143-scaffold771-1543539 6 47509245 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770276 Affx-122971871 AX-385257442 6 45237340 GCATACAGAACAGCAGAAATGACAGTATACATAGT[C/T]ATCTCCCTCCTGTTGAAAGGTACAGAAAAAAGTTC Y 2 1 2 1 101000 f 74 goat snp52144-scaffold771-1604422 6 47570784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787645 Affx-122949223 AX-385274668 6 45292403 GCCTGTATTAACAAAATCAGTCAGAATAGTGCTGA[A/G]TTCCTGGAAGCAAATGACAATGGAAGCTAAAGTGA R 2 1 2 1 101000 r 74 goat snp52145-scaffold771-1659485 6 47626274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384302 Affx-122972285 AX-123254660 6 45345134 AATAAGTCCTATAATTTTGTACATGTTGTTTCCTC[A/G]TCAGTCACACATTTTTCCTTATCATTTACCTACTT R 2 1 2 1 101000 r 74 goat snp52146-scaffold771-1712216 6 47681649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414210 Affx-122949650 AX-123284559 6 45382106 AACTTTACAATAGCACTTATTTTTCATTAATCTCA[A/C]TTTCACTGAGACAGGTTCCATTATGTGAGTTACTC M 2 1 2 1 201000 f 74 goat snp52147-scaffold771-1749188 6 47718157 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432205 Affx-122936382 AX-123302546 6 45399891 TTTCTCTGTCATCAGCATCCACATGCCCATAGTTG[C/T]ACCATTCATTCCCTAAATGATACCCAAGAGGTAAA Y 2 1 2 1 101000 r 74 goat snp23942-scaffold241-2178809 6 47735751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767237 Affx-122949104 AX-385254518 6 45442328 ATGAAGCTGGAGATGGGACTCTGAAAATTACCTTT[A/C]TCCTTTGCCAGCTAATATACTATTAGGTTGTTCAA M 2 1 2 1 101000 f 74 goat snp23941-scaffold241-2136372 6 47779383 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384538 Affx-122973026 AX-123254896 6 45483029 AAACTGAGATTCCCTGAGGTCATCTTGTTCCAAAC[A/G]CATAGTTATTTATTCTCATTTCACTGCAGTGATTT R 2 1 2 1 101000 f 74 goat snp23940-scaffold241-2095671 6 47820057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764716 Affx-986696988 AX-385252335 6 45532325 CATGATGAGATGTTTGATGGAGCTGGGAGGTCAAT[A/G]AATGCGTTGTTTACAATTTTTATTAGTGGGTGAGT R 2 1 2 1 600010 r 74 goat 6_45532325 6 45532325 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320775208 Affx-122948376 AX-385262339 6 45534923 GTTCCACTGAAAGTTGGATTTGCTTAAAATTTCAC[G/T]TATGTTAAGAAAGTATCATTATCTGGTGAGCAATT K 2 1 2 1 201000 r 74 goat snp23939-scaffold241-2043777 6 47871724 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428397 Affx-122938949 AX-123298740 6 45581506 AAATAACATATAATAAAATAACAAAATGCCTCATG[C/T]GGAGTTTTTTGTTATAATAGGATCTATAAAGCAGA Y 2 1 2 1 103000 r 74 goat snp23938-scaffold241-1997194 6 47918132 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799385 Affx-122940454 AX-385286315 6 45636938 TAGGATGCAGCTTAAGATGATTAAAATAACAAGAA[C/T]GCCTGTTGAGGTCTGTTCTATTACAGCAAGAAAAA Y 2 1 2 1 101000 r 74 goat snp23937-scaffold241-1941762 6 47972912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376616 Affx-122979044 AX-123246975 6 45666511 TCTGACTCTGTTCTGACATATTAGGAAATGTGTCA[C/T]ATTTGCACCCCAGGCCATTTAAATATCCTTTATCT Y 2 1 2 1 101000 r 74 goat snp23936-scaffold241-1912189 6 48002111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437402 Affx-122932426 AX-123307740 6 45704214 ACTAAAACCTTTTGGATTTCCTGACAGATATGATC[A/G]TCTTTTGTTATTCATAAGAATTCATTTCTGAACAC R 2 1 2 1 101000 f 74 goat snp23935-scaffold241-1874486 6 48040408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770172 Affx-122976340 AX-385257340 6 45738088 CCAGTTAGATAACATTCTTCAGTCAATATCATTAT[C/T]TATCAGTGTTATTGTTTGTTTTGTAGCAAGATTTA Y 2 1 2 1 101000 r 74 goat snp23934-scaffold241-1840612 6 48074647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777926 Affx-122972431 AX-385265042 6 45785263 TTCACTTCAAATGGACATGAAAATGTTTTTGAGAT[A/C]GATAAAAAGCTTAGAGATTTTTACAGAAAGCAGTC M 2 1 2 1 101000 f 74 goat snp23933-scaffold241-1793437 6 48122015 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395599 Affx-122963823 AX-123265954 6 45821587 TTCAAAAATGTCTTCCAGTGCCTTTGATCTTATTG[C/T]AGTTTTCACAGTGTCCAGTGACAACCAGATGATAA Y 2 1 2 1 101000 r 74 goat snp23932-scaffold241-1757113 6 48158333 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408316 Affx-122953766 AX-123278667 6 45854605 TTTCTTAGAGAGAAAGAGAGGATCTCTGTATCTCC[A/G]TTAGAAAGAGGACTTGAGAAATAAAAGCACTGAGA R 2 1 2 1 102000 f 74 goat snp23931-scaffold241-1724095 6 48191533 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782246 Affx-122930624 AX-385269323 6 45910545 TTTCCAGTCCAGATAGTCACACTTCATTAAAAAGA[C/T]TGTGTTGCTTCTCAACTGAAAACATAACAGGAGAA Y 2 1 2 1 101000 r 74 goat snp23930-scaffold241-1668155 6 48247362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387789 Affx-122969702 AX-123258147 6 45952024 TATTTGCAATTGAAATATAGGCTACATACTGCACA[C/T]AGCAAGTTTAATATTTCAATTTCAGGCATCATAGC Y 2 1 2 1 101000 r 74 goat snp23929-scaffold241-1626676 6 48289571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404413 Affx-122956776 AX-123274765 6 46062932 ACAAATTCAGTGGACACTTAGCAGGCTGTGGGGCA[C/T]CTCATATACTAAAGCTACTTCCTCTCATAACCACT Y 2 1 2 1 201000 r 74 goat snp23927-scaffold241-1515768 6 48402508 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449372 Affx-122922722 AX-123319707 6 46109977 TCTGAAAAATATAGTTCCCTGACTGATCTACAAAA[C/T]AAGGGTGCTGTAGGCTAGGTGAATTATGTGGCCCC Y 2 1 2 1 101000 f 74 goat snp23926-scaffold241-1468723 6 48450528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424885 Affx-122941322 AX-123295231 6 46183819 ACTGATCAATGTTTTCCAATATGATTGTACCATTG[C/T]ACCTTCCCTTCACAGTGTAAGAGAGGTCCCCATGG Y 2 1 2 1 201000 f 74 goat snp23925-scaffold241-1394881 6 48525038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416792 Affx-122948149 AX-123287140 6 46215203 GTTTCTCTTTGATAAGGTTACAGACAGGAAATAGG[C/T]AGTTAACAAATCAAACTGAAGAATATAATTATTCT Y 2 1 2 1 101000 f 74 goat snp23924-scaffold241-1363497 6 48556914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421021 Affx-122944547 AX-123291368 6 46250563 CTCTGTTTGCATTACATTTATTTTGCTCATTTTCT[A/C]GTTTTGGGCAATAGAAACTCAGACTAAGACCTTTC M 2 1 2 1 101000 r 74 goat snp23923-scaffold241-1328137 6 48592679 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278367 Affx-1111836385 AX-519551853 6 46273708 TGTACACCTCAAATTGGATTTTTGTCACTTGTAAA[A/C]TCCAAATAATAAAGGTTCCAACATGAACTGTCTGC M 2 1 2 1 101000 f 74 goat Random2.2K-681 6 46273708 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430882 Affx-122936880 AX-123301223 6 46297424 TTTAGACTTTAAAACCTAACAAATAAGGCTGAGAA[C/T]GGTTTTGAGTGAGGAAAAACTTAAGATTTTACTTT Y 2 1 2 1 101000 f 74 goat snp23922-scaffold241-1281276 6 48639789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439420 Affx-122930236 AX-123309757 6 46331477 TTTCTACTTTGTTTTATTGCTCAAGATTTCTCAGG[A/C]TATCTTATGACTATATATATCTATACACTTTCCTT M 2 1 2 1 101000 f 74 goat snp23921-scaffold241-1247223 6 48674011 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399359 Affx-122961348 AX-123269714 6 46374762 CCATTTCTGTTTCAAATTGTCTCCTCAGCAAGAAA[C/T]GATTCATCAATAGTGATATTTCTAGGATGTGAGCT Y 2 1 2 1 101000 r 74 goat snp23920-scaffold241-1203938 6 48718119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390424 Affx-122967641 AX-123260781 6 46425740 CATGTGCCACCATCATTTAAATTACTTGGGATAAA[C/T]AAAATTTTGAAATGTCATTTCTAAAAAATAGACTC Y 2 1 2 1 103000 f 74 goat snp23919-scaffold241-1152960 6 48768998 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385547 Affx-122971232 AX-123255905 6 46487389 TGTCACCCTATCATTTTCAGGAGATTATGCTTTCT[A/G]CTTACTCCCTGGTGGTGTGCTGCAGTCCATAGAGT R 2 1 2 1 201000 f 74 goat snp23918-scaffold241-1091311 6 48830478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796334 Affx-122962460 AX-385283284 6 46527009 TGAACACGCACTCTCAGTGAGACACTGCTTCATCC[A/G]CACAAACTAGAAGATTGATGCAGGATAGACAAATC R 2 1 2 1 202000 f 74 goat snp23917-scaffold241-1051691 6 48870197 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434271 Affx-122934784 AX-123304612 6 46566578 TAATCATTCAGCACTGTGATTTTATTCTGTGAGGT[A/G]TAGAAAAAACTTTTAATTCATATTCGTATTTTAGC R 2 1 2 1 303000 r 74 goat snp23916-scaffold241-1012122 6 48909801 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381944 Affx-122974122 AX-123252302 6 46616471 AATTAGGATGGAAGACATGAAAAACAGACAGACGG[C/T]AATACTAAAACATTTTTCTATGTCTATGCCCCGAC Y 2 1 2 1 101000 f 74 goat snp23915-scaffold241-962229 6 48959996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799528 Affx-122965175 AX-385286458 6 46652528 ATATATTTGTTTTTAGAGTTAGGAGATGAATGTAC[A/G]TTCCTTAGAAGAGCTACAGAAATGCTTGTGCTTGA R 2 1 2 1 102000 r 74 goat snp23914-scaffold241-926172 6 48997331 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449162 Affx-122923544 AX-123319497 6 46688925 ATCCTTGAAATGTTTTCTTCATGTGGCTTCCAGTA[C/T]GCTTCACTTTTTTGTTTCATTTTTTTCTATTTTAT Y 2 1 2 1 303000 r 74 goat snp23913-scaffold241-889775 6 49034714 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801842 Affx-122947634 AX-385288749 6 46724222 TTCCACCTAACTACAAATGAAGCTGAAATGTGTAT[A/G]TTTTAATTGTGTGCTATGGACAAAGAGAAACTCTC R 2 1 2 1 101000 f 74 goat snp23912-scaffold241-854478 6 49069398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801931 Affx-122921887 AX-385288836 6 46760284 CTGGAAATCAAGCAGTAGGAGTCATACCACTGTTA[C/T]GTCTCTCTTACTTAAATTTAGGGCTCCTTCTCTAG Y 2 1 2 1 201000 r 74 goat snp23911-scaffold241-818416 6 49105764 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420885 Affx-122944621 AX-123291232 6 46808531 GCGCTTTACTGCTAAAATGATTCTAAATCAAAATG[C/T]AAAGAAGAGGTATTCCTTATTGACCTTTAAATATC Y 2 1 2 1 101000 f 74 goat snp23910-scaffold241-770169 6 49149953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444886 Affx-122926267 AX-123315223 6 46857254 GCGTTCCTCATGATGTTCTCTGCATAGAAGTTAAA[C/T]AAGCAGTGATAATCTCACCTCACTCTAAAGAGCAA Y 2 1 2 1 303000 r 74 goat snp23909-scaffold241-721446 6 49198696 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409091 Affx-122953328 AX-123279442 6 46908337 GATGTGCTTTAACTGGTGAATAACAATTTTAAACG[A/G]TGTTCTGATGGAAGCAAAGCAGTCTCTTTCCCATT R 2 1 2 1 101000 f 74 goat snp23908-scaffold241-670363 6 49250504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400945 Affx-122959706 AX-123271298 6 46966084 TCTCCAGTATTTAGTTACTGCTGTGTCTGTGCTGC[C/T]TTTTGGGACTAGACTTCTGAAACGGTTTCTTTGGT Y 2 1 2 1 101000 r 74 goat snp23907-scaffold241-612616 6 49308749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440132 Affx-122929691 AX-123310469 6 46997627 TCCCAGTTCATTCTTCTTTAGACCAATAAGAAAGT[A/G]CAATATACCTAAGTGTCTACACAAAGGTATGTTTG R 2 1 2 1 101000 f 74 goat snp23906-scaffold241-581073 6 49340865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784121 Affx-122968865 AX-385271173 6 47044407 AATTAGCCGTTCATCTCGGAGTACACATAACTTGC[A/G]TATATATTGCGTGTCAAGCATTACATCTTCATATG R 2 1 2 1 201000 r 74 goat snp23905-scaffold241-534293 6 49388576 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784769 Affx-122922081 AX-385271816 6 47092218 TATGACTTCAAGTTGTGCTTTGACATAAAAATCTT[A/G]TTTATTTTCTTCATATACATTGTATTGCTGTAAAT R 2 1 2 1 303000 r 74 goat snp23904-scaffold241-486482 6 49434549 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395123 Affx-122964144 AX-123265478 6 47127534 TTGGACATTTACTGGCTATCTGATTTTGAATGATA[C/T]GTGTGATTTGTTGGAGATTCCTCTTTTTGTTATAT Y 2 1 2 1 201000 r 74 goat snp23903-scaffold241-451166 6 49470441 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381194 Affx-122974537 AX-123251552 6 47164315 TGTATTAAAGCCAGAGAGCAAAGAAACAAAGCAAC[A/G]CTCTTCAGAAGAATAGAATTCAGAGTCTCACAAAT R 2 1 2 1 101000 f 74 goat snp23902-scaffold241-414385 6 49507882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409155 Affx-122953210 AX-123279506 6 47237570 TTCTGTAAAAGTCTTTGCTGAGTAAAGGATATAAT[A/G]AAAGTGATGTTGTGATAGGTGTATCCTAATGGGAA R 2 1 2 1 101000 r 74 goat snp23901-scaffold241-341130 6 49581486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273252 Affx-1111833505 AX-519546904 6 47260010 GTAAACAGAGCAATTCCTTTCATAAATATCAAAAC[A/G]CTAAACAGCTACCCTAGTTCCTAATGTTGAATTTG R 2 1 2 1 101000 r 74 goat 6_47260010_AF-PAKI 6 47260010 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774314 Affx-122943230 AX-385261450 6 47282510 CATTAGCACTTTATTACCAATAATATGGTTACAAA[C/T]ATTTTTGGTGTCTTGGTAATCATTTGGTCTCTTTG Y 2 1 2 1 201000 f 74 goat snp23900-scaffold241-296190 6 49627140 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784547 Affx-122939131 AX-385271596 6 47316985 AGGTCTCAAACTTTTAGATTCTGGTGGGGAGATAT[A/G]GGGATATACTCATCTTGTGGCCGCCTAAGACAAGT R 2 1 2 1 101000 r 74 goat snp23899-scaffold241-261715 6 49662691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384491 Affx-122973063 AX-123254849 6 47353748 TTTTGGAGAACACTAATTGGTACTATTGAAATACT[A/G]TATGCTAGTAATAATGTCCTTTTCTTTTTCATTGA R 2 1 2 1 101000 f 74 goat snp23898-scaffold241-224952 6 49699434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762462 Affx-986696992 AX-385250589 6 47355852 AAACATCAACTCAAGCCTCCAATCAACATAAAATA[C/T]AGCTAAAACACAAGAAACTAGTGCTTATGTATAAG Y 2 1 2 1 600010 f 74 goat 6_47355852 6 47355852 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38402200 Affx-122959167 AX-123272553 6 47396994 ATAAATCTTTGCAAAAAATAATAAAATGAGATGAA[A/C]TGCAAAGTAGATTGTCTCTGTGTTTTGCCATTTTT M 2 1 2 1 103000 r 74 goat snp23897-scaffold241-181706 6 49741962 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782418 Affx-122978740 AX-385269494 6 47437508 TTCATGCAATGCAAGAATTGGCAAACTATAGAACA[C/T]GTCAAAGCAGGCAAGCCTCCTATTGTATTTTAGTG Y 2 1 2 1 101000 r 74 goat snp23896-scaffold241-141192 6 49780747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792858 Affx-122932686 AX-385279836 6 47480381 AGTAAAAGATGAAACTCTGAGAGGTCAATAAACAC[A/G]TTCAAACTTACACGATTTAAAGATGTCAGATCCAG R 2 1 2 1 101000 r 74 goat snp23895-scaffold241-98319 6 49823477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400932 Affx-122959717 AX-123271285 6 47528553 TGAAAGATACTCCATGTGATACTGAACAAGCTAGA[C/T]ATCTTCTCACTATAAACCTCTGTGGGTTGTTGAGT Y 2 1 2 1 101000 r 74 goat snp23894-scaffold241-50147 6 49872061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382095 Affx-122974898 AX-123252453 6 47561162 TTCATGGAACAGACCTCTCTCCTTGTTAATCATCC[G/T]ATTTCTCTTGCTAACAATGCCTGGTACTCAGTGTC K 2 1 2 1 101000 r 74 goat snp23893-scaffold241-17538 6 49904342 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786022 Affx-122926498 AX-385273058 6 47587889 AGTCAAAACCCTATTTTTAAGTATCAGTGTGACAT[A/G]CACTATGTTGTAAGGTTTCTTTATACTTGCTTCCA R 2 1 2 1 101000 r 74 goat snp26647-scaffold2790-4489 6 49941106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390687 Affx-122967951 AX-123261044 6 47608548 CCAATGGGTGGTGAAGGGATATATTACAACTCGGT[A/G]ACTTATTAATGTTGGCAAAGAATTATTCAGGAAAA R 2 1 2 1 101000 r 74 goat snp17112-scaffold1789-313255 6 49975308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775992 Affx-122959144 AX-385263122 6 47647066 ACTAGTACAATATGATTATAACATAGCAGAGCATC[A/G]TTTTCCTGTCTTTGTTAACTTCATGTTTATAGCAG R 2 1 2 1 101000 f 74 goat snp17111-scaffold1789-274737 6 50014925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425614 Affx-122940910 AX-123295960 6 47724195 GCAGCTGCCTTACCCTTTTATTCCTATTCTAGTCC[A/G]TGCCCTGCATTGTGGCCTAAGTGATCTTCCTAATG R 2 1 2 1 101000 f 74 goat snp17109-scaffold1789-197608 6 50092811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780261 Affx-122942221 AX-385267356 6 47839202 GAAATGACAATGTGCTGCTCTGTAATAGGTCTTCT[A/G]CTTTCTTCACAATAGTCTTTTTATATCGGTGGCCC R 2 1 2 1 101000 f 74 goat snp17107-scaffold1789-82601 6 50208812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432337 Affx-122936286 AX-123302678 6 47881611 TATCAAACCAGTGACTTTTCAGATACCTCTGATTC[A/G]TTTAATGTAGATTCATTTAGCTTCTAACAAGTGCC R 2 1 2 1 201000 r 74 goat snp17106-scaffold1789-40192 6 50252133 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416521 Affx-122947770 AX-123286869 6 47921348 AAGGTGAAAGTAAAGAAATTTAATGTTACTGGATG[C/T]AAATTTACTCACTAAATTAATTTTTTGGAATATAT Y 2 1 2 1 103000 f 74 goat snp17105-scaffold1789-455 6 50291991 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779638 Affx-122921512 AX-385266740 6 47944843 GTCTTTATTTTGCAGGAAGAGAGAAAAATTCAACT[A/G]TAACAGTGTGTTAGGATGAGACCTACACGGACAGA R 2 1 2 1 101000 f 74 goat snp41819-scaffold544-267102 6 50316301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417849 Affx-122946781 AX-123288197 6 47993414 TAGAAGTTATAAGCCAGGGAGGTTCTGACATATTT[C/T]GATTTGTGCTGATTTCTCTTTGAGAAGATCATATT Y 2 1 2 1 101000 f 74 goat snp41818-scaffold544-218531 6 50364437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770409 Affx-122961368 AX-385257575 6 48027579 GAAATGAAAAGGTGGATACTTAATGCTGTCAACGA[G/T]CCCCATTTTTCTCAATTAGACACATTATTTAGTTG K 2 1 2 1 201000 f 74 goat snp41817-scaffold544-184366 6 50398957 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439726 Affx-122930547 AX-123310063 6 48059256 CTTGAGCCTGACAAGATTTATTGTTTCCAACTACT[A/G]TCTCCTGCATTGGGTGTGAATTTCATTCCCATTAA R 2 1 2 1 101000 f 74 goat snp41816-scaffold544-152689 6 50430663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438416 Affx-122931278 AX-123308754 6 48094016 ACACATCATCAACAAATGGTTCACTGATTTATGGT[C/T]AAGGATGAATTATTAAAACTATCCCCTTCAAAAAT Y 2 1 2 1 101000 f 74 goat snp41815-scaffold544-117929 6 50465490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786733 Affx-122949231 AX-385273764 6 48139017 ATATCATTTGCTTTCTCAATTTATTATTGTACACA[C/T]ATGGATTTTACTGTTAGGTAACTAGAAAAATAAAG Y 2 1 2 1 101000 f 74 goat snp41814-scaffold544-72928 6 50510087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412652 Affx-122950788 AX-123283001 6 48194883 AATCACCAGCTGTTTGTTTAGTTCTCTCTTTGACA[C/T]AAATTCAGCAAAAATAAAAATAAGGCCTGCTATTA Y 2 1 2 1 101000 f 74 goat snp41813-scaffold544-17062 6 50566064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445322 Affx-122925428 AX-123315659 6 48249709 CCAAAATGGTATTTTCATGTAAAATCCAATACAAA[C/T]CCTGATTAAAACCTAACCAAGCAAAACACTGCAGA Y 2 1 2 1 101000 r 74 goat snp35094-scaffold42-2458825 6 50617818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425860 Affx-122940656 AX-123296206 6 48278785 CTGTGGTTTTCGTATGTTACAGAGGAGGAAACCCG[C/T]GCTCCCTGGGAAGTTAAATATTGTTAACTGGCAAA Y 2 1 2 1 201000 r 74 goat snp35093-scaffold42-2429749 6 50646915 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788217 Affx-122966466 AX-385275236 6 48312591 TAATTTTATAATCATCAGCCTAGTAATCTCTATTA[C/T]CAACATTCTAACCTAGTTAATCACTGTATTATATG Y 2 1 2 1 101000 r 74 goat snp35092-scaffold42-2395943 6 50680795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787139 Affx-122971103 AX-385274165 6 48341490 GACAAGACACAAAATGAACAGGGGGCCAAAGAGAC[G/T]TCTTTGAAGTGACATTTACCTGCAAACTAAATGAT K 2 1 2 1 101000 f 74 goat snp35091-scaffold42-2367044 6 50710104 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397661 Affx-122962599 AX-123268016 6 48375102 ATGCTCCTAGAAAAGAGAGTGCCCTCTGGCTCTAC[A/C]TGTCGTCCCCTGTACACGCATACACACAGATACAC M 2 1 2 1 101000 f 74 goat snp35090-scaffold42-2333432 6 50743833 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396873 Affx-122963240 AX-123267228 6 48407107 CAGTCTTTTTTTGTGCCCTACAACGATCAGCAACT[A/C]GTTCTTATGAGGACTGCATAATTATTGTTGTATGT M 2 1 2 1 101000 f 74 goat snp35089-scaffold42-2301427 6 50776156 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405004 Affx-122956386 AX-123275356 6 48438026 CTGTTGGGACCAGGAGCTTTACTTTTATTAAAAAA[G/T]AAATATACTGAAATCATTTTTTGAAAAATAAATAT K 2 1 2 1 103000 f 74 goat snp35088-scaffold42-2270508 6 50806887 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435499 Affx-122933427 AX-123305839 6 48491269 CTATTACAATAAATGCATTAGCCTTCTAGACCAAA[G/T]GAAGCAGCCTATATAAATTTTGTTTTATGAATGAA K 2 1 2 1 101000 f 74 goat snp35087-scaffold42-2217265 6 50860064 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792542 Affx-122974940 AX-385279523 6 48532149 TTTGCATTTTTGTCTAGCATACATATGTATATTCA[C/T]CTATGCCCCAAGTTCTATTTTCCCACTAATGCTTC Y 2 1 2 1 201000 f 74 goat snp35086-scaffold42-2176385 6 50899654 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384274 Affx-122972306 AX-123254632 6 48577994 GGTTAATTTTTTTTTTTACTTTTAATAGATGAATT[A/C]GTTTTGCATCAGAAAGAAGCATTACTGAAAAAAGA M 2 1 2 1 103000 r 74 goat snp35085-scaffold42-2130540 6 50946281 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278368 Affx-1111836386 AX-519551854 6 48594228 GCTCATACACAGAGAGATGTGTCATGCTAAACCTC[A/G]ATAATAAACAAAGCCACTTAAGGTAAGCAGATGAC R 2 1 2 1 101000 f 74 goat Random2.2K-683 6 48594228 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409346 Affx-122954179 AX-123279697 6 48640453 CCATTCAGCTTTTTAACAATGGCTAATAGCAATTT[A/C]GTTGATTTTCAGTTTAGTTCTGCAGCCATTTATTG M 2 1 2 1 201000 f 74 goat snp35084-scaffold42-2068081 6 51009317 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768465 Affx-122927647 AX-385255645 6 48671241 GATACAGTCATTAGCAATATTCAGAAATATTCTGA[C/T]AGCTTTCACTACAATTTCCTTTCCTTTTGTTTAAA Y 2 1 2 1 102000 r 74 goat snp35083-scaffold42-2037293 6 51040169 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391721 Affx-122967501 AX-123262078 6 48737586 TTAATGTAAACCAAATCTACAAGTTCCCTACATCC[A/G]TAGAGCTCCTATTTTAGTGCGAGAAGCCAGATCAC R 2 1 2 1 101000 r 74 goat snp35082-scaffold42-1970948 6 51107813 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395590 Affx-122963830 AX-123265945 6 48833493 CATATTTATTCTCAACTGACTAGTTAATGCGGCTG[C/T]GTCCTGTCTGTCCTCTCTAAGGCCATGTTGAAATT Y 2 1 2 1 201000 f 74 goat snp35080-scaffold42-1875041 6 51204738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801417 Affx-122930071 AX-385288326 6 48883723 ATTCAAGAAAATTGAATTTCAGTGACTTCATGGTT[A/G]CAAAGTCTCATTATTCAGTTAGAAGTGTGCTTTAG R 2 1 2 1 101000 f 74 goat snp35079-scaffold42-1824811 6 51254637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433772 Affx-122934483 AX-123304113 6 48913083 CTATGGTAATTGAGATAATGTATAATTCTAGAAGA[C/T]GGCTGATTATTAATAACTTGACAATATAATTATGG Y 2 1 2 1 101000 f 74 goat snp35078-scaffold42-1795451 6 51285255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438677 Affx-122930876 AX-123309014 6 48948203 ATGGACTTAATGATAGATGGCTTATAAGATTATTG[C/T]GAGAATAAATTTTAAAATTCAAATCATCCAGCATA Y 2 1 2 1 101000 f 74 goat snp35077-scaffold42-1760331 6 51320397 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787050 Affx-122921666 AX-385274078 6 48994843 ATGGTCCAAAAAGTATTGGAAAGCTGCAATCAATA[C/T]TTATATTTAAATAAAAGGGAGATGTGAGGCACAGC Y 2 1 2 1 201000 r 74 goat snp35076-scaffold42-1713691 6 51367433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386598 Affx-122970685 AX-123256956 6 49042195 GGCTTGTGTCTCTGTGTGCTATAAACTCTAATTCA[A/G]TTTCATATAGGGAACATTCACTCCCCTGCTGAGTG R 2 1 2 1 101000 f 74 goat snp35075-scaffold42-1666339 6 51415707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790469 Affx-122937943 AX-385277472 6 49084596 GGAGTGAAATTACTGAAGAATTTCATGTAGTGGAA[C/T]GATATGGCCTAATGTACACTTCAGAAACAAATTTA Y 2 1 2 1 101000 f 74 goat snp35074-scaffold42-1623938 6 51453989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445383 Affx-122925402 AX-123315720 6 49120348 AGCTAGGGGAAAAAAAGAAGCAATAAAAACAAAAA[C/T]AGCAACCAGCAATAAGCATGATGAAGCAATATACT Y 2 1 2 1 101000 r 74 goat snp35073-scaffold42-1588186 6 51489807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413182 Affx-122950333 AX-123283531 6 49159217 CATCATTTATTTGAATCAGCCAATGTAACCATGTA[C/T]GAACTTAAAAGGGTCAGAATCAGAAAAGGTGATAT Y 2 1 2 1 101000 f 74 goat snp35072-scaffold42-1549317 6 51529013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381391 Affx-122974381 AX-123251749 6 49197917 AAATGATGAGAAAGGCAAAGCAAAGAACTTAAGCA[A/G]AAGAAATCAAAGGTAAACAAATATATGACATATAA R 2 1 2 1 101000 f 74 goat snp35071-scaffold42-1510617 6 51568641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772749 Affx-122927732 AX-385259894 6 49231999 TACTCCTATATTGACAAGGATATTGTGTCTTTATG[C/T]GGAAAAGTTACCTAGTATACTTAAGTATAGATATT Y 2 1 2 1 101000 f 74 goat snp35070-scaffold42-1476535 6 51603714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799501 Affx-122946492 AX-385286431 6 49277224 CTTCCAGTCCACAATAGCTATAATTAGAGTTGACT[A/C]TGTTCTCCATTTGACCTTGAAGAACCAATAAATGT M 2 1 2 1 101000 r 74 goat snp35069-scaffold42-1431310 6 51648777 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798659 Affx-122943236 AX-385285591 6 49312264 GATTAGAACCCAGATCTCCAAAAACTTGGTTGTCA[C/T]TATTTTGTTTATAAATTCAACTTTGGAAAATATTT Y 2 1 2 1 201000 r 74 goat snp35068-scaffold42-1396270 6 51683946 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774030 Affx-122959483 AX-385261168 6 49371788 ACAGAAAGAATTCTTGAGGGTTTAAATCAGATAAT[A/G]TCATTCTAAGCTTTATAGTAATATGAAGGTCCTCA R 2 1 2 1 101000 r 74 goat snp35067-scaffold42-1336746 6 51745089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790258 Affx-122970045 AX-385277262 6 49404101 AAAACCAGTTTTAATGATTCTAATCTCCTCTTCAT[A/G]TCTGTTTGGATGTAGCTCACTGATAGCCCAAAGTG R 2 1 2 1 101000 r 74 goat snp35066-scaffold42-1304433 6 51777890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388177 Affx-122969439 AX-123258535 6 49441678 CATCCTATGGAATATCACCAAGAAAAAAATGTAGT[C/T]AAAGCAAAATAATCACATTTTTGACCCAAAATATC Y 2 1 2 1 101000 f 74 goat snp35065-scaffold42-1266856 6 51815100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799283 Affx-122948200 AX-385286213 6 49501236 ATTTATTATTCATATGAGAGGTTTAGTAAAACCAC[A/G]CTTTCTGGGTCTTTGGAAAGATTCCCAGCCGGCAG R 2 1 2 1 102000 r 74 goat snp35064-scaffold42-1207298 6 51875509 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418769 Affx-122946194 AX-123289117 6 49591082 TCAAACAATTAACATCCCTGTCATCTCACACAGTT[A/G]CCACTTTATTTCTTTTTAAGCTGTTGTGAGAACAC R 2 1 2 1 101000 f 74 goat snp35062-scaffold42-1117452 6 51966254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388715 Affx-122968977 AX-123259073 6 49625187 ATATACATAAGTGATAATTTAATTCAAAAAAGTTA[C/T]AAAAGAATAAGTATAAAAATTCAGTGTGGAGGCAG Y 2 1 2 1 201000 f 74 goat snp35061-scaffold42-1083347 6 52000487 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445783 Affx-122926056 AX-123316120 6 49656694 GAAGAAATACAAAGGTTTAGAGAGATTGGAATGTT[A/C]GAAAGGACTATTTAAGACCTGTTACACATCCTGAG M 2 1 2 1 101000 r 74 goat snp35060-scaffold42-1051840 6 52032569 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786934 Affx-122930924 AX-385273963 6 49733929 CTTTTTGCCTGAAGCAGAATCTCCAAGGTGCCAAT[G/T]CTGATACAACTTGTAGGGTAATTTCCTTTAGAAAA K 2 1 2 1 101000 f 74 goat snp35058-scaffold42-974605 6 52110326 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273205 Affx-1111833506 AX-519546864 6 49830191 ACAAACATTAAAGCCCTAGGTGTGTCACAGCTCTC[A/G]GGTCTTGGACAGACCGTGTTATAGCTCTTAGACAA R 2 1 2 1 103000 f 74 goat 6_49830191_AF-PAKI 6 49830191 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398829 Affx-122961390 AX-123269184 6 49858790 TATCATTCCTTAAAATATAAATACATTGACCCAGA[C/T]ATCCCTGGAAATAACAAAAGACTTTGCAAGGTCAT Y 2 1 2 1 201000 r 74 goat snp35056-scaffold42-849744 6 52236308 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448691 Affx-122923867 AX-123319027 6 49898737 CTACAGATAGCTGCCTTATGGCCATATTCTAATGT[A/G]TATGTAAGTATATGTACACATACATGTACTGTTAC R 2 1 2 1 103000 f 74 goat snp35055-scaffold42-809797 6 52276570 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783227 Affx-122926202 AX-385270293 6 49929963 CGTAATGGTGAATGAACAGACAATTGAATGAAAAT[A/G]TCAACAGTGTGATTCCAATTGTATAAAGTTTGAAA R 2 1 2 1 101000 f 74 goat snp35054-scaffold42-778571 6 52308869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791047 Affx-122975019 AX-385278042 6 50011448 GTCAGTTTCATATGATAACAGGATATCCATGTCGT[A/G]TAAAGGGATAGAGACTTGGGTTTTGAGTCTGAGGA R 2 1 2 1 101000 r 74 goat snp35052-scaffold42-697086 6 52392203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779827 Affx-122965500 AX-385266927 6 50040174 CTGTGTGATATGGCCTTCTACCTCAACCTAAAGCT[A/G]TTTACGAATGTCTCATCATTAATAAAAGTGAGTCT R 2 1 2 1 101000 f 74 goat snp35051-scaffold42-668360 6 52421450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391985 Affx-122966508 AX-123262342 6 50087916 CCCACAAAGCAGAATCCTCTTTACTTAACATGAGG[C/T]AAACCTCTTCAACTCACTGTCAGAAAGTTAGAAAG Y 2 1 2 1 101000 f 74 goat snp35050-scaffold42-620618 6 52468657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383931 Affx-122972968 AX-123254289 6 50130394 CTATAACAAATATTGTTGAGAGGTTGAGGGAGAAA[C/T]AGATTATAATATGTTCCCTGGATTACATATCTAAG Y 2 1 2 1 101000 f 74 goat snp35049-scaffold42-578140 6 52509132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443000 Affx-122928182 AX-123313337 6 50186340 CCAATTATCTAAGGATGCATTTCTACTCTTAAAGT[A/G]CAATAAACTATATTTGGACACACAAAACTCAAATC R 2 1 2 1 101000 f 74 goat snp35048-scaffold42-522194 6 52573873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802563 Affx-122920526 AX-385289465 6 50221252 GTATATATGAAAGGTTTACAGCACATGCATATTAG[A/G]TAGCTTTTCAGGCATTTAATATTAAGAAGTGATGT R 2 1 2 1 101000 r 74 goat snp35047-scaffold42-487282 6 52609400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792142 Affx-122970875 AX-385279127 6 50267089 TCAGTAACTCTGTGGTGTCATAACCATAAGTGTTA[C/T]TTCCTAATAGCCCCAAACCCAGAAATATTAATTAT Y 2 1 2 1 201000 r 74 goat snp35046-scaffold42-441445 6 52655928 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386316 Affx-122970890 AX-123256674 6 50309445 AATATAATTTTAGCAGTGGATCATATAAAAGAAGC[A/G]CAGTTTCTTTCAAGTCACAACTTCACAGTTAGTAA R 2 1 2 1 101000 r 74 goat snp35045-scaffold42-399089 6 52698895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769372 Affx-122939594 AX-385256543 6 50343195 GCATTTGTCAAAGTTTTAATAAATTTCACATGGGT[A/G]GTATAGGTACTCCAGGTCAGCATAATAGTCTGAAA R 2 1 2 1 201000 f 74 goat snp35044-scaffold42-365339 6 52732905 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385838 Affx-122971007 AX-123256196 6 50375724 CACAAGCATAGATAGTTTTCATCAAGTATGACTTG[C/T]GGTCCAACTATGCTCCGAAGAATTTTAAGAACATG Y 2 1 2 1 101000 r 74 goat snp35043-scaffold42-332810 6 52765988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395020 Affx-122964220 AX-123265375 6 50408417 CTAATTTTGTCCTTGTGGATGATACTGTCCCTTCT[A/G]TGAATATACTGTGGTGACTTTGACCTTTCTATCTG R 2 1 2 1 101000 r 74 goat snp35042-scaffold42-300117 6 52798943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383897 Affx-122973116 AX-123254255 6 50450877 TAATATGTTCAAGGGGTTCATTTTCCACCATTTGT[A/G]TGAGTGTGTTTTAACATAATGCCTCTCATCCCTTT R 2 1 2 1 201000 r 74 goat snp35041-scaffold42-257657 6 52840374 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450026 Affx-122922841 AX-123320361 6 50495230 CACATGAACCTGGGGCCTTGAGCATATTCTATTTC[A/G]CAGCTGCATCAAATGTGACTCTGATGTGATTTTAG R 2 1 2 1 101000 f 74 goat snp35040-scaffold42-213304 6 52882205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801307 Affx-122921900 AX-385288219 6 50525121 AGTATAAAAGTTTACATCTAGTGAGCATTAAAGAT[A/G]CTAAAACTAAACATCAGTCTTCATACTTGTTTCAC R 2 1 2 1 101000 r 74 goat snp35039-scaffold42-183413 6 52913027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416472 Affx-122947806 AX-123286820 6 50576791 CTTGTGTTGTTCACAATATAGCAAGCAGTTTATTA[C/T]TGGCAAATAAATAATTTCACTTTTGAAAACTGAAG Y 2 1 2 1 101000 f 74 goat snp35038-scaffold42-131743 6 52954327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440177 Affx-122930716 AX-123310514 6 50622421 TACCCACACTCAGCATCTGTGCATAGACACTGATA[A/G]GGGTAATTGTCATGGCAGCCAAAAATGGCAAACCC R 2 1 2 1 101000 f 74 goat snp35037-scaffold42-86113 6 52999944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798471 Affx-122953881 AX-385285404 6 50656116 CTGCATTTGAACTGCCACCCTCTTATGCAGGAGAT[A/G]CAATAACTTTCTGAGGCTTCTGCAGCTTTATATTA R 2 1 2 1 201000 r 74 goat snp35036-scaffold42-52418 6 53033351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446953 Affx-122924670 AX-123317289 6 50699551 GTAGACCTTGTTTTTCACTCAGGTGGCATATAAAC[A/C]TTCTATCTTAATCAGTCCAGCTGCTGTAACAGAAC M 2 1 2 1 101000 f 74 goat snp35035-scaffold42-8983 6 53077308 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413938 Affx-122949805 AX-123284287 6 50722833 CCTCTGCCCCAGTATTCAATAGCACTGAAGTGGGA[C/T]ACCATTATACATACATCAGTGATGATACCATGTGC Y 2 1 2 1 201000 r 74 goat snp41643-scaffold541-3277890 6 53100757 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407059 Affx-122954923 AX-123277410 6 50786453 TAGAGAACAAAATAATAGATAAAATCATTCTTACT[A/G]GGCAAATTATCAAGGAATTATGCAATTTTGTCAGA R 2 1 2 1 101000 r 74 goat snp41642-scaffold541-3214270 6 53165865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791591 Affx-122968289 AX-385278582 6 50830298 CAGCAAAAAATAACTACACATTTCTCTGCAGCTCC[A/G]TAAAATGGTATATCACCAAAATAATGCATCATACT R 2 1 2 1 101000 f 74 goat snp41641-scaffold541-3170425 6 53209655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393687 Affx-122965260 AX-123264042 6 50861509 TATTGGAGAATTTTTGACAAAAAAATTAAAATGTG[C/T]CCCAAAGTGTCATGTGAGTACTGCCTAAAGATATC Y 2 1 2 1 101000 r 74 goat snp41640-scaffold541-3139214 6 53240554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423600 Affx-122942387 AX-123293946 6 50890395 GCAAAGCAATCCCTCCTCCTCGGGATGACAGCACA[A/G]CAGCACTGCATATCTGACAGGTGTCTTTGTAGGAG R 2 1 2 1 101000 r 74 goat snp41639-scaffold541-3110328 6 53269689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454044 Affx-122919404 AX-123324377 6 50938792 TTAAAATCTCATTCTCCCCAGGAGATAGGCAATAT[A/G]CATATATATTTTTATTAATTTTTTTGGATTATAGT R 2 1 2 1 103000 f 74 goat snp41638-scaffold541-3061931 6 53315909 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799298 Affx-122977042 AX-385286228 6 50987327 TAAAGGAAACACTCAATAAAGCTTTATTAAATTAA[C/T]GCAGTATACTTGACTTTTGACTCAAAAGCACTTAG Y 2 1 2 1 201000 f 74 goat snp41637-scaffold541-3013396 6 53365364 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400152 Affx-122960695 AX-123270507 6 51027616 TTCAGTGCTTTGCCCTATTAAAAAGTTAATGCTGA[C/T]AGAATGATATGCTAATTGACATTTTCTAACTGATA Y 2 1 2 1 101000 r 74 goat snp41636-scaffold541-2973107 6 53406821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425787 Affx-122940711 AX-123296133 6 51099723 AATATTTCACAGGATAACACTATTTATTATAGGAG[C/T]ACTTCAAAATTGTATGGCTATAGTATACCTTGTAG Y 2 1 2 1 101000 f 74 goat snp41635-scaffold541-2901000 6 53479250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440016 Affx-122929777 AX-123310353 6 51162173 TACTCACCAGTAGAATACACAGATCAAAGACCCCC[G/T]AGGACCATGCTCACAACATGACCACTAATGCCCAA K 2 1 2 1 201000 r 74 goat snp41634-scaffold541-2838550 6 53541545 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398977 Affx-122960962 AX-123269332 6 51215058 GGTCTACTGAACCCAGTCTATCTTCTCTTCTAAAA[G/T]CCAATGCCTATTCTTAGTTCTAATCTTACTTAAAC K 2 1 2 1 101000 f 74 goat snp41633-scaffold541-2785665 6 53594183 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435790 Affx-122932859 AX-123306129 6 51253701 TGTCTCCAATGAACTTAAATAAAATCTTTTTGGCT[A/C]AGGCCCTGGATTCTTCATTTTAAACAAACTCCACT M 2 1 2 1 101000 r 74 goat snp41632-scaffold541-2747022 6 53633692 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278538 Affx-1111836387 AX-519552020 6 51254728 AGTTACTAGAAGAAATAATCCCTTCGACTTGGAAT[A/G]CAGTCAATGCAGTGTCAAGTTTTGACCCTGCCACT R 2 1 2 1 101000 r 74 goat Random2.2K-684 6 51254728 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384089 Affx-122972849 AX-123254447 6 51291749 ATTTCATGTCAATCTGAGGCAGAAGATAGATGGGC[A/G]TCCAGCCTCCAGGGTAAAGTGGGAAGATGGGCCCT R 2 1 2 1 303000 r 74 goat snp41631-scaffold541-2708974 6 53671465 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414686 Affx-122949290 AX-123285035 6 51325949 GTTTGATACTTTGAAATATAATTAAAATAATAATT[A/G]CCATCCTGAGGTCATGGCTGTCAGAATAAATTTTG R 2 1 2 1 103000 r 74 goat snp41630-scaffold541-2674774 6 53705830 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765227 Affx-122941304 AX-385252766 6 51379885 CTTGGCCCTAAATTCCCTGTTTCTGGTGATAAGGA[C/T]GTCTCTTCCTCCCACTATAAGGAAAGACCTTTCAC Y 2 1 2 1 101000 f 74 goat snp41629-scaffold541-2620838 6 53759652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385001 Affx-122971880 AX-123255359 6 51438137 TTAGTAAAACATGATTAATTTCTCACTGATTAGCA[C/T]ACTTTGGCTTTTATTTTTTTCATTTGAAAAACCAA Y 2 1 2 1 101000 f 74 goat snp41628-scaffold541-2562586 6 53818604 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794459 Affx-122941390 AX-385281422 6 51471168 TATTAAAAATGAAATAAGCAGCCCAAAATGAAGCC[A/G]CTTGTACAAAATATCACCAAGACTTAATACCTAAC R 2 1 2 1 101000 f 74 goat snp41627-scaffold541-2529555 6 53851670 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781934 Affx-122930114 AX-385269015 6 51500436 ATCCTCACATTTAATTGTGTAAATACTTTAATGAT[C/T]GTGGCTTAGCACACCAATTGACAATTACCCTGAAA Y 2 1 2 1 101000 r 74 goat snp41626-scaffold541-2500287 6 53881355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453811 Affx-122919564 AX-123324144 6 51530904 TATATTTCTCCTGGTTTCTTTTATATTTTTGGTCC[A/G]TGTTAAAGTTATTGAAGGAAACTTATTTATGAGAG R 2 1 2 1 201000 r 74 goat snp41625-scaffold541-2469819 6 53911675 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401191 Affx-122959343 AX-123271544 6 51581437 TGGAATGAGCTGTCACCTTGGAAATACCAACTGGA[A/G]ACCTCTGTGTTGCCATCCTCTAGCCAAGATAATAA R 2 1 2 1 101000 f 74 goat snp41624-scaffold541-2419286 6 53962817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782337 Affx-122930530 AX-385269414 6 51629229 CAAGCTTTGAGCCCAGGTCGTGGAGCCACTACTTG[C/T]AAATGTCTGAGATCATCAGACTAGTTAATTTCTGA Y 2 1 2 1 102000 f 74 goat snp41623-scaffold541-2371494 6 54010666 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440700 Affx-122929906 AX-123311037 6 51698717 ACTTCAAATCAGCCCCACGCTGAGCTAAAATGTCC[A/G]TATATTTTATATCCTCATTTTCATCTATTGGTCAT R 2 1 2 1 201000 r 74 goat snp41622-scaffold541-2302006 6 54078643 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798689 Affx-122921971 AX-385285621 6 51738487 AAAATTCCAGTATCATTTTGGGACTCAGTATCAAG[C/T]ATTGCATAATAAGATGTCACCATTTATAAGTCACT Y 2 1 2 1 101000 f 74 goat snp41621-scaffold541-2262236 6 54119339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449956 Affx-122922894 AX-123320291 6 51797469 TCCTTAATCCTTTTCACACATTAGTAAAGAATCAC[A/G]TGATTAAAATCTTGATTCCTCCATCTGACCTACAA R 2 1 2 1 101000 r 74 goat snp41620-scaffold541-2203254 6 54178733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795856 Affx-122941068 AX-385282809 6 51833576 AGAAAGGAATTCAACCCTACTGACACTTATTTTAA[G/T]ACAGAAATCAGCTTTCCAACTCATGGAACTATAAG K 2 1 2 1 201000 r 74 goat snp41619-scaffold541-2167147 6 54218216 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801946 Affx-122969713 AX-385288851 6 51864328 TTTTTATTCAAAATTTCATATTTCAAATCAAATAG[C/T]ATGATTTCAGCTACGATCAAGTTCCTTTTTCTGTC Y 2 1 2 1 201000 f 74 goat snp41618-scaffold541-2136395 6 54248886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415876 Affx-122948488 AX-123286225 6 51897112 GAGGAGGGAAAAAAACCCCCAAGTGTTAAAGATGA[C/T]ATCAAGGTTTAAGAGTGCTGGCTGGAAATACCAAA Y 2 1 2 1 201000 r 74 goat snp41617-scaffold541-2103611 6 54282477 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379205 Affx-122976293 AX-123249564 6 51981535 AGACATTGACGTTCAGTGGGAAGATGGTCATATGA[C/T]GAATTGGAGTTATGCACCTGTAAACCAAGCAACAC Y 2 1 2 1 101000 r 74 goat snp41615-scaffold541-2019188 6 54366134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768888 Affx-122965207 AX-385256065 6 52033228 TATTTTCCTTTTAACATCTAAGAATTTTCTTTCAT[A/G]TCCATTGAAATCCCTGACCTAAAATACTTCTGAAA R 2 1 2 1 101000 r 74 goat snp41614-scaffold541-1967495 NW_017198690.1 18956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402609 Affx-122958415 AX-123272962 6 52070615 ATTGGTTGTTCTAATTTTAAAACCATTTTATAGCA[C/T]GTAATTGATCCCATTTCCTTCTCTTTGTGATCTCT Y 2 1 2 1 101000 r 74 goat snp41613-scaffold541-1930108 6 54453522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775017 Affx-122941098 AX-385262149 6 52115224 CAAAACTATCTTTATAAGAGATTGTTTGAACTAGC[A/G]TTTTCATTTCCCTGGAGGAAGTTTTCCTTCTGAAA R 2 1 2 1 201000 r 74 goat snp41612-scaffold541-1885499 6 54498594 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770073 Affx-122962818 AX-385257240 6 52158086 AAATAGTAGGAGCATGCCATTTGAATTTAATGACT[A/G]TACAACTTCAATCACCAATACTTTCTCAAATTCTC R 2 1 2 1 101000 f 74 goat snp41611-scaffold541-1842637 6 54541395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432375 Affx-122935862 AX-123302716 6 52193617 ATGAGCACATTTGTTTTTCTCCAGAAATTAACCTT[A/G]TGCTATAATTAAGCAATGCTCCTCAGATTTCCCAA R 2 1 2 1 101000 r 74 goat snp41610-scaffold541-1807106 6 54577700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795058 Affx-122957317 AX-385282017 6 52242276 ATGGAGATGTATGATGGGAATAGATTGACATATAC[A/G]TTCTATAGAAGAAACCTTGACAGTGAATAGAATCT R 2 1 2 1 201000 r 74 goat snp41609-scaffold541-1758447 6 54627135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406214 Affx-122956126 AX-123276566 6 52274759 TGCACATCCATGCTTTTTCTCACATCAGGAGGCAG[A/C]TATTATTTTCTCTGTCCTGAATCTGGATAGGTCTT M 2 1 2 1 201000 r 74 goat snp41608-scaffold541-1725964 6 54659249 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791244 Affx-122967322 AX-385278238 6 52323275 AATAAATTATATATACTATTTCACTTTGAAAAAAT[A/G]CTGACTTTAAGTTTAAGGTAATGTGTTTACATATT R 2 1 2 1 202000 f 74 goat snp41607-scaffold541-1677448 6 54707039 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273207 Affx-1111833507 AX-519546866 6 52338101 AGCAAATTTGGAAAACTCAGCAGTGGCCACTGGCT[A/G]GAAAAGGTCAGTTTTCTTTCCAATCCCAAAGAAAG R 2 1 2 1 103000 f 74 goat 6_52338101_AF-PAKI 6 52338101 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783697 Affx-122959991 AX-385270755 6 52380151 GTAGGGTATTTTGCTGGAGGATGCCTGGGTTTACA[A/G]CAATCTGAAAGTGAATGTAGTGTTTTGTCCTCTTT R 2 1 2 1 101000 f 74 goat snp41606-scaffold541-1620572 6 54762668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777225 Affx-122967562 AX-385264348 6 52450805 TTCAATTTAACCTTCAGGAAATGGATTTCATAGGG[A/G]CATTAAGCTACCATTCATGTTCATACTTTCTAAAT R 2 1 2 1 101000 f 74 goat snp41604-scaffold541-1549918 6 54833362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785299 Affx-122932253 AX-385272344 6 52483058 AACACTGAAATATGTTACCACTCTCCTTGATCTGA[C/T]GCTGGATGTCCTATTAATATACTTTTCATAGAACT Y 2 1 2 1 101000 f 74 goat snp41603-scaffold541-1517665 6 54865614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476218 Affx-1251763723 AX-586011642 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 4 1 4 1 20000 f 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 539476472 Affx-1251763723 AX-586011872 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20000 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562165589 Affx-1251763723 AX-606941000 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562165628 Affx-1251763723 AX-606941038 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 f 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562166556 Affx-1251763723 AX-606941964 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 38382390 Affx-122973843 AX-123252748 6 52519995 AACTGAAAATGACTCCACCCCTCACTGGGCTTCCC[A/G]TGTGGCTCAGTGATAAAGAACCAGCCTGCTAAGGC R 2 1 2 1 103000 f 74 goat snp41602-scaffold541-1480728 6 54903232 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790235 Affx-122951638 AX-385277239 6 52576661 GTAACAGATATGTGTTAGGCACTTAAAACAAACCA[C/T]GAAATGTGAAGTGACTTTCAGTCATTCATTCAGCA Y 2 1 2 1 101000 r 74 goat snp41601-scaffold541-1424062 6 54960045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400466 Affx-122961305 AX-123270821 6 52616699 GTGGATTTTTAAATAACATTAGTATAGAGCATCAA[C/T]ACAGACTTAAATTCAGTTTTTGATTGGGATTATTA Y 2 1 2 1 101000 f 74 goat snp41600-scaffold541-1384024 6 54999837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441036 Affx-122928937 AX-123311373 6 52653114 TCAAAGTGAACAAACACCAAGTGAGAGCCAGGCTC[A/G]CAAAGCCAATTGACTGAACCCAGTCTAACAGTCAA R 2 1 2 1 101000 r 74 goat snp41599-scaffold541-1347609 6 55036616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430098 Affx-122937527 AX-123300439 6 52700026 AATTAACCAAGCGAGTATAAGTCATACAATTGGTA[G/T]AAAAGAAAAAATAATATGCAATGAAGTTGTCTTAA K 2 1 2 1 103000 f 74 goat snp41598-scaffold541-1300697 6 55084024 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444429 Affx-122926565 AX-123314766 6 52731753 AGAGACAGAGGGTACCTCTATGATCTCATACATTA[C/T]AGAAAAGTTTTAAAACACAGAAATGTTAGAAGAAC Y 2 1 2 1 101000 f 74 goat snp41597-scaffold541-1268970 6 55116497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770866 Affx-122944179 AX-385258030 6 52764918 CACACAAGATAATGATTCAAAGAACTGTAAAAGAA[G/T]AATCAAAAGAGTAGTATGTTCCTTAAACCAACCTA K 2 1 2 1 101000 r 74 goat snp41596-scaffold541-1235805 6 55150320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416957 Affx-122948020 AX-123287305 6 52824662 ACCATAATGATACTAAACAGTATCTCAAGGTAGTA[C/T]GGCTATTAATTGTATGTTAGATCAATAAATATATA Y 2 1 2 1 201000 r 74 goat snp41595-scaffold541-1176061 6 55209895 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773088 Affx-122968942 AX-385260231 6 52876347 TTCCAAATGATGTGTAATGTGAAATATGATAGTAG[C/T]GACTGATTTTAAAAATGGCAGTGCTCAGATATAGC Y 2 1 2 1 102000 r 74 goat snp41594-scaffold541-1124376 6 55263647 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784506 Affx-122942132 AX-385271555 6 52943748 AGACAGAAAGAGAGATTTCTCATATAAGATATTTC[A/G]TATTATTTTTCAAGTTCTTACCAAACTTGAAGTTC R 2 1 2 1 101000 f 74 goat snp41593-scaffold541-1056975 6 55331994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393287 Affx-122965443 AX-123263643 6 52973230 TTACTGACAGCTGATTTTGACATGTAACTTGTGGT[A/C]TCTCACCTAGAAGGACTGAACTTTACTTTCCATTG M 2 1 2 1 101000 r 74 goat snp41592-scaffold541-1027493 6 55361506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787937 Affx-122949440 AX-385274959 6 53007147 AGAAAAACTTACCCTAGACATCAAATTATTTACTA[C/T]AAAGATTGTACAAACCCAATATCTTACACATTAAA Y 2 1 2 1 101000 r 74 goat snp41591-scaffold541-993576 6 55395509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387952 Affx-122969613 AX-123258310 6 53071152 GACATGAAAGTTACAGGAAGTCTCTTCTCCACACC[A/G]TTTAATCTCAGAATGTGGAGTATGTACATACTCCA R 2 1 2 1 201000 r 74 goat snp41590-scaffold541-929571 6 55460282 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391728 Affx-122967495 AX-123262085 6 53109337 AAATTGTTTGTTATTTATTGTTGAGTTGACTTTTA[C/T]GGTATGTTTATTTTCTCTTTCAGTTCAAGCACCTT Y 2 1 2 1 201000 f 74 goat snp41589-scaffold541-891386 6 55498619 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410955 Affx-122952031 AX-123281305 6 53152837 ATACAAAAAGTGGCTTGGAATTTTTAAAATGCTTC[A/G]TCCCTGAAACAGGTTAGAAGTTTATCTATTTTTGA R 2 1 2 1 103000 r 74 goat snp41588-scaffold541-847886 NW_017215591.1 16929 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786953 Affx-122963228 AX-385273982 6 53209067 CAGATGGTAGACTATGATGAAGTGCAGTCAGGCTG[C/T]ACTTCAGATACATATAGTTTTGGTAGGGTTTTTCA Y 2 1 2 1 101000 f 74 goat snp41587-scaffold541-791656 6 55599306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412657 Affx-122950785 AX-123283006 6 53264333 TGTTCATGCCTGGTAAAATCTCTTCCCCCCATTTG[C/T]GGTAGGACCTCTGACCTGTTTTTTAGACAATGGCA Y 2 1 2 1 101000 r 74 goat snp41586-scaffold541-736390 6 55655227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782317 Affx-122974633 AX-385269394 6 53299463 CTAATCTTGTGCCTGAGTTTCTCTAGTTTCATATA[C/T]TTCTATGTCTTGCCTTGCTCTCCAGACTCTAGGGG Y 2 1 2 1 101000 r 74 goat snp41585-scaffold541-701260 6 55690449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780322 Affx-122962916 AX-385267417 6 53331946 AAATACTGACTGCCATGATTAAAATTGGTGACTAA[C/T]AATCTAACCAAGGGTTACTTTGTATTGGCCTCCAT Y 2 1 2 1 201000 f 74 goat snp41584-scaffold541-668777 6 55722849 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792556 Affx-122965149 AX-385279537 6 53364486 GCTTATGTGGCATCTGTCTTAGTTTCTATTAAGTA[C/T]AGCTGTGGGCACATACTAACAGATTTTGGTGTGGG Y 2 1 2 1 101000 r 74 goat snp41583-scaffold541-636237 6 55761187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383489 Affx-122973432 AX-123253847 6 53401539 GGTAGCTACTTTGCCTTTTTTCCTTCCTCACTCTG[C/T]AGCCTTGTATTAAATCAAGGGGTTGATATTCATTT Y 2 1 2 1 303000 r 74 goat snp41582-scaffold541-599184 6 55798620 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770117 Affx-122955263 AX-385257284 6 53443902 TGCAAGAGAAAGAGATTCTCTGACATGCAAGGACA[C/T]GAAAATTATACCACCTAAGTAGTTATCCTGAAAAA Y 2 1 2 1 101000 f 74 goat snp41581-scaffold541-556821 6 55841000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770787 Affx-122977043 AX-385257951 6 53486622 CAATGACTAGAAACACAGTATAGGAGGGTGGTTTA[C/T]GTGTTATGGACAGCATACATTGCTCTGATGATCAG Y 2 1 2 1 201000 f 74 goat snp41580-scaffold541-514101 6 55883702 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445711 Affx-122926111 AX-123316048 6 53516848 GACCAGTAATTATTTTTTTTTTTGCCAAAGATACA[G/T]ATGTTTTTGTTTCTGATTAATTTGTTTCTTTTAAT K 2 1 2 1 303000 r 74 goat snp41579-scaffold541-483875 6 55913943 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378996 Affx-122976385 AX-123249355 6 53565271 TTAGTTTGGGCACTAAGCATCTTTCCAAAGGACAA[C/T]AATAATAGCATCCTCGGGACAACCCTGCTTATAGT Y 2 1 2 1 101000 r 74 goat snp41578-scaffold541-435452 6 55963060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422654 Affx-122943689 AX-123293000 6 53634775 CATATATAGACATAGCATTATCCAGAAAAATCCAC[C/T]GTTTGATCCATTTTCACTGAGTTTTCATGGAAATC Y 2 1 2 1 101000 f 74 goat snp41577-scaffold541-365948 6 56033687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789748 Affx-122930607 AX-385276756 6 53676109 AGGTAACATTTCTTTGGAATTCAATTAGGTGAAAA[C/T]GAAACATTTTTCAAAAGGTCATAAAATAAAGATAA Y 2 1 2 1 202000 r 74 goat snp41576-scaffold541-324614 6 56075898 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768196 Affx-122938223 AX-385255386 6 53722722 ATATGAGTTACCTCTAATGAAAGATGTTTTATATT[A/C]TTTATATATGTGCAATATGCTTATGATCAATAAGG M 2 1 2 1 201000 f 74 goat snp41575-scaffold541-278001 6 56122592 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786399 Affx-122949053 AX-385273433 6 53824162 GAATGGTATGGGAGATGGAGGACACAAAACAAATG[C/T]ATAATTGAAAATTCTCCTAAGTGCCATTAAGTAAA Y 2 1 2 1 101000 f 74 goat snp41573-scaffold541-176561 6 56222491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791413 Affx-122969944 AX-385278405 6 53853016 GGCAAATGTACGTTCACATCTGTAATGCCAACTAT[A/G]TATTCTCTAAATGTGCACTGTATATATATATCATG R 2 1 2 1 101000 f 74 goat snp41572-scaffold541-147707 6 56251331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449541 Affx-122923253 AX-123319876 6 53900353 CTAAGACTATAGTGGTAATCATATCACAGTAAAAA[A/G]TACATCAAATCAACATACTGTACACCTTAAACTTA R 2 1 2 1 101000 f 74 goat snp41571-scaffold541-100370 6 56298754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775554 Affx-122953604 AX-385262685 6 53957192 ATCTCTAAACAGACTTTCATTGAGAAAAATCCTAT[A/G]TAAACCTCTTAATTTTCTAGCTTGGCTAATTTGAC R 2 1 2 1 101000 f 74 goat snp41570-scaffold541-43531 6 56355481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802761 Affx-122973023 AX-385289660 6 53987778 TTTATGAACAAGATACACATAAAAGTCCTTCTGAA[C/T]TTCACCCCTGTTTGGGAAAAGTCCTGAATTGCATG Y 2 1 2 1 101000 r 74 goat snp41569-scaffold541-12945 6 56386380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798211 Affx-122953268 AX-385285146 6 54001940 ACTAGAGATTCAGGACATCTGACCCACAACCTAAC[A/G]CTAATGCTTTCACATATGTCAGAAGGCAGTAGCTT R 2 1 2 1 101000 f 74 goat snp221-scaffold1005-54720 6 56407385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783846 Affx-122938749 AX-385270902 6 54042701 TGTTTGGTTGTTGTCATGTTCTAAATAGTTCAGCA[G/T]CAAGATTTTAAACCACTATCCCCATTAACTGGAGA K 2 1 2 1 101000 r 74 goat snp220-scaffold1005-13959 6 56448194 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385549 Affx-122971231 AX-123255907 6 54059823 TACCTGAAGTGTGTTTACATTCATGTAACTCACTC[A/G]TGAACTGGGGAAGGACAGATATTGATTGGCAAATT R 2 1 2 1 202000 r 74 goat snp27054-scaffold289-3064 6 56475731 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395021 Affx-122964219 AX-123265376 6 54089115 CCTTTGGCTCTTCCTTTACTTCCCCTAAATATCAC[C/T]AAGTCCTTTAGATTTAATGACCTTATCCCCGTACT Y 2 1 2 1 201000 r 74 goat snp27055-scaffold289-32356 6 56505117 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450293 Affx-122922158 AX-123320628 6 54143030 AAATAAAATTTATTTTTGGTTTTGCAGTAAACAAA[C/T]GGGCTTCAGAAAGGGAAAAGATATTAGTATTAAGA Y 2 1 2 1 103000 r 74 goat snp27056-scaffold289-86271 NW_017196821.1 4209 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771397 Affx-122931438 AX-385258555 6 54194612 AGGGATGTATCAACATGATTGCTAATTTCCTTTTA[C/T]GGAAATGTTTAAATCTCATTGCTTTCCTTCTATGG Y 2 1 2 1 202000 r 74 goat snp27057-scaffold289-137853 6 56613395 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444745 Affx-122926396 AX-123315082 6 54233109 TATGGCTCAAATCAGCAATAATTTAACATTTTTAT[A/G]TTTATGTAATAAACTTTTATGCCTTTACAATTTAA R 2 1 2 1 201000 r 74 goat snp27058-scaffold289-176350 6 56649292 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773430 Affx-122945689 AX-385260572 6 54263982 GGGTGATGTCAGATATGCCATCTCTGAGCTTGAGT[A/G]TGTCATCTCTGAGCCCTAATACTCACTTGATTTAG R 2 1 2 1 102000 f 74 goat snp27059-scaffold289-207223 6 56680140 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381742 Affx-122974324 AX-123252100 6 54321366 ACTCTCTATGAAGCAAAATAGACTTTATTCAAGGA[A/G]ACAGGCCCTTGATAATGTTGTAAATAGTTAATTAC R 2 1 2 1 101000 f 74 goat snp27060-scaffold289-264607 6 56738762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419297 Affx-122946235 AX-123289645 6 54384851 CCAACTCTGATTCTACTCATACTCAACTCCAATTG[C/T]GTTTGCTACTACATCAATATCTTGAGTTTAAGAAT Y 2 1 2 1 101000 r 74 goat snp27061-scaffold289-328092 6 56803216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771572 Affx-122919781 AX-385258730 6 54456831 TTTTGCTTGAAAGCAATAGGTATAGAATCTCTGAG[A/G]AGTTGAACTGTTTACAAGAACACTGCCTGAGGGGA R 2 1 2 1 101000 r 74 goat snp27063-scaffold289-400072 6 56875390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392973 Affx-122965674 AX-123263330 6 54519683 GCTTAGGATGGCCACATTACTGAATTCTGGCCAAC[A/G]TTATGTAACAGAGGTATGATTTGAAACTTATGACA R 2 1 2 1 201000 r 74 goat snp27065-scaffold289-462924 6 56939051 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802016 Affx-122926009 AX-385288920 6 54556698 TCCAGGCTTAATCTAATACTTTGTGGTTATTGATT[A/G]TCCAATTTATGAGAATTAATCCACCATAGGTCCTT R 2 1 2 1 101000 f 74 goat snp27066-scaffold289-499939 6 56976047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783295 Affx-122920891 AX-385270360 6 54586820 TGTGAAGCCCATGCATTGGCTTGCTTTATGAAATT[A/G]CTAGTTTTCTCCTTGTGTAAGTATGCCTTTTTTAA R 2 1 2 1 101000 f 74 goat snp27067-scaffold289-530061 6 57006151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798546 Affx-122961337 AX-385285479 6 54628693 CCTGAAGGATTTGAGACATAAAGTTTATGTCATAA[A/G]AAATACATTTGGGAGAATAGATAAAGGCCAAAACA R 2 1 2 1 101000 r 74 goat snp27068-scaffold289-571934 6 57046273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396923 Affx-122963200 AX-123267278 6 54684985 AAGGTGTTTCTAGCACACTCTAGCTTCTGAATTCC[A/G]CCTGAGACTACACCTAAGTTCCATAACTTTGTTTT R 2 1 2 1 101000 f 74 goat snp27069-scaffold289-628226 6 57104020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407394 Affx-122955254 AX-123277745 6 54723965 ATCAAATCTTCTAGTTACATCAATTACATCATGAG[C/T]GGGTAAAAATAGGCCTTTTCATCACTACAACTATG Y 2 1 2 1 101000 f 74 goat snp27070-scaffold289-667206 6 57143518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432694 Affx-122936032 AX-123303035 6 54783680 TGTTTGGGATAGAGGAAAGTAGAGAGGAGGCATGA[C/T]GAGAAGGGGGAGATGGAGCTCTTGAGTGAATCAAC Y 2 1 2 1 101000 f 74 goat snp27071-scaffold289-726921 6 57202628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380848 Affx-122975446 AX-123251206 6 54857972 CACTGGTCCCTGTCACTCTGTTGAGCTGCCGCTGC[A/G]TCTCAGACTCTCAGGACTGGTTGTTTGCCTCTCAA R 2 1 2 1 101000 r 74 goat snp27073-scaffold289-801213 6 57277219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773492 Affx-122954089 AX-385260633 6 54890815 GGAAATAATAGTTACCTGCCTCCTGGTGTCTTTCT[A/G]AGGATGAAATTAAATTACAGGACACTTTTTACAGT R 2 1 2 1 102000 f 74 goat snp27074-scaffold289-834056 NW_017190901.1 5064 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273210 Affx-1111833509 AX-519546869 6 54905847 AATAGCAAGGAGAGGTAAGAAAGTCATAGTCAGTG[A/G]ACAATGCAAAGAAATAGAGGAAAACAATAAAATGG R 2 1 2 1 103000 f 74 goat 6_54905847_AF-PAKI 6 54905847 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454165 Affx-122919319 AX-123324498 6 54931769 CCTATGGTGCTTTTTATTCCCCTTTTCTTTAAAGT[A/G]TGTGCTTTGAAGTCTAGATATAGAGAAAAGAAGAA R 2 1 2 1 201000 r 74 goat snp27075-scaffold289-875010 6 57349745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272476 Affx-1111836388 AX-519546198 6 54952728 TCCCATATATTGTTTCTTAAATTATACTTTTGAAG[A/G]TGAGTGGTTTTGAGTATTATACCTACATGGAAACT R 2 1 2 1 101000 r 74 goat Random2.2K-687 6 54952728 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426193 Affx-122940573 AX-123296539 6 54983172 AGCCAAGAGGTACCTGTTCTCAGGTAATTTTGTAT[A/G]CATCTTCAGTAAACTGAGGAATTGATCGTTAATAG R 2 1 2 1 101000 f 74 goat snp27076-scaffold289-926413 6 57402187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452917 Affx-122920198 AX-123323250 6 55018728 CAGGAGGAGGACCAGGGGAGGTGGCAGAAGGTATT[A/G]TGCTGGGTCTTTTAGGTTACATACTATAATCTGAC R 2 1 2 1 101000 r 74 goat snp27077-scaffold289-961969 6 57437726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803404 Affx-122950789 AX-385290235 6 55049569 TCTCCTTAACCATATGATCATGTATTATTGTGTTA[C/T]AATTTTCTTATATCTTAAGTTAAGCTAACTCCCAG Y 2 1 2 1 101000 r 74 goat snp27078-scaffold289-992810 6 57468649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275123 Affx-1111834706 AX-519548702 6 55128708 AGATGTCTCTAGCTTGAAAAGCTCTTGAATGGACC[A/G]GA R 2 1 2 1 101000 f 74 goat GoatD01.047087 6 55128708 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453609 Affx-122920133 AX-123323942 6 55136928 AGAGCAAGACCAGTGCCAACTTGGAGCCAGTAGGG[C/T]AGTGCTGGAAACAGGCACTAAACAAGTGAACACCT Y 2 1 2 1 201000 r 74 goat snp27079-scaffold289-1080169 6 57554828 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766058 Affx-122963835 AX-385253475 6 55177801 CCTGAGCCTAGAAATTAAACTATAAATTATAAGTT[A/G]TAGCCAGAGTCTCATGTAAAATGGAAACTTTTTTT R 2 1 2 1 102000 f 74 goat snp27080-scaffold289-1121042 6 57595684 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438122 Affx-122931490 AX-123308460 6 55222086 TGGACTACCTCACTCATCTTTATAATAAAAATATG[C/T]ATTTTACGTACATTCATAATGAACCACCAAGACAG Y 2 1 2 1 102000 r 74 goat snp27081-scaffold289-1165327 6 57640646 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800550 Affx-122977121 AX-385287469 6 55266307 TATCCAGTGTCTTTTATCCTTCATCACAATCTGAG[C/T]ATCTTACCTAGGAAAGACTATAGACATGTTCATTG Y 2 1 2 1 101000 r 74 goat snp27082-scaffold289-1209548 6 57681279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788885 Affx-122978733 AX-385275900 6 55319895 ACCTATGTACTTTTTGCTCTAAGATCATAAAGTGA[G/T]AGAAGGTACCACAGTTTAAACATAAAGAGGCTGGC K 2 1 2 1 101000 r 74 goat snp27083-scaffold289-1263136 6 57728823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415519 Affx-122948678 AX-123285868 6 55350592 TCTCCTGCATTGCAGGCAGATTCTTTACCATCTGA[A/G]CCACCAGGAAAGCCTCTCTTTGTTGGAATCAGCAT R 2 1 2 1 103000 r 74 goat snp27084-scaffold289-1293833 6 57758106 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450503 Affx-122922510 AX-123320837 6 55386602 GCTTCTGTCTTGATCATTCCACTGATGGCTCCTAC[A/C]TGTCAGCAGTCCCTTGTAGCTTGTGAAATCTGGTT M 2 1 2 1 101000 f 74 goat snp27085-scaffold289-1329843 6 57793927 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437214 Affx-122932041 AX-123307552 6 55419535 TTATAAAAAGTAAAAAAGAAATTGCCCTCTCCATC[C/T]TACTGCTGGAACATGTGCACCCTTCCCCAGTTTTC Y 2 1 2 1 101000 r 74 goat snp27086-scaffold289-1362776 6 57827231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390685 Affx-122967952 AX-123261042 6 55451660 TAGTGGCATCTCCTCCAGCCAGCGACAGGACACCA[A/G]ACAGGAAGCTGAAGGTGGGGCTTGGAGGCCCAGGT R 2 1 2 1 201000 f 74 goat snp27087-scaffold289-1394901 6 57859371 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375673 Affx-122978670 AX-123246032 6 55514155 ACAGTTCACCCATTTAAAGTATACAGTATATTTTT[A/C]TGTATTTATAGGGTTGTGGAACCATCGCTGCAGTC M 2 1 2 1 101000 r 74 goat snp27088-scaffold289-1457396 6 57921757 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792830 Affx-122978517 AX-385279808 6 55553261 GGAGATGGCTGAGCAGCCCTTTCTAGAGTTCCTGT[A/G]GGTCTGTTATAAATGAAATTGACTCTCTGGTTCAG R 2 1 2 1 101000 f 74 goat snp27089-scaffold289-1496502 6 57960681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446164 Affx-122925748 AX-123316500 6 55591293 CTCTGGTATTTCAGAGAATGAAGAGGCTGGAGATA[C/T]GCTTCCTTTGGCAAAGATGTGTCCATTGTTCTTCC Y 2 1 2 1 201000 r 74 goat snp27090-scaffold289-1534534 6 57998777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404208 Affx-122957666 AX-123274560 6 55626053 CTTGAAAAAGAATTTCTTAACATTTCCTTCCTCTC[A/G]AACACTGAGTGGTATTTTGCTAAGGGAATGACTAT R 2 1 2 1 101000 r 74 goat snp27091-scaffold289-1569294 6 58033222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391618 Affx-122966586 AX-123261975 6 55690601 ATGCTTTGAGGCCCAAGGCCCCTTCCTCTGTGCAG[A/G]CTTTTCCCAGTGTCTGCCTGGATTTCTGTAGAAGC R 2 1 2 1 101000 r 74 goat snp27092-scaffold289-1633842 6 58098874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381978 Affx-122974097 AX-123252336 6 55739558 GGCTGGAGTAGTCCATCCTAGTTCCTAGGGGCTGT[A/C]ATACTCACCCCTAGGATTCACTGGGTCTCTAGCAT M 2 1 2 1 101000 r 74 goat snp27093-scaffold289-1682799 6 58147630 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441874 Affx-122928632 AX-123312211 6 55792130 TTGGGTGGAAATGCAGATTCCTGAGTCCTACCATA[G/T]CCCTGTTGAGTTCCTGGGGGTGGGTAGGCTGGAGT K 2 1 2 1 101000 f 74 goat snp27094-scaffold289-1735371 6 58200652 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408503 Affx-122954402 AX-123278854 6 55862952 TATGAGAAATAGCTAATAAAATGGGATAGAGACAC[A/G]CCCAATTTAAGTGCAAACAGCTGTAAAACAACAAA R 2 1 2 1 101000 f 74 goat snp27095-scaffold289-1806193 6 58271760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383121 Affx-122973262 AX-123253479 6 55921565 TCCCTCCCCTATTATTGAAATCACAACTATATACC[C/T]TCACTCTCAGTAGGTGGGAGGGAAAAGCCATCCTT Y 2 1 2 1 201000 f 74 goat snp27096-scaffold289-1864806 6 58330787 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783149 Affx-122947310 AX-385270216 6 55982686 AATACAACTTGTATTGTACTCAAGCAGAGTACAGT[A/G]TGCATTCAGTCATTTGAGGGAGACTGAACTTGAAA R 2 1 2 1 101000 r 74 goat snp27097-scaffold289-1925927 6 58390681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796051 Affx-122938940 AX-385283003 6 56015974 TCATGTGAAAACAGCAGCAAGCTGATGCGACTCTG[C/T]TGCATCAAAGTACTATATTGCTAAATTTCCTTTTA Y 2 1 2 1 101000 f 74 goat snp27098-scaffold289-1959215 6 58424208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453923 Affx-122919901 AX-123324256 6 56045128 AGGCTTCCCCATCTTAGTAAACAACAGCTCTATTC[A/G]TCCAGCTGCTCAGACCCAAAACCTTGACTCATTTT R 2 1 2 1 101000 r 74 goat snp27099-scaffold289-1988369 6 58453359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413924 Affx-122949815 AX-123284273 6 56092650 CACATGACACTTTTCTGCCTTCATAATTTGGTCCA[C/T]CATCACACAAGGAGAAGAAACTTTCCTGGGAGGAA Y 2 1 2 1 201000 f 74 goat snp27100-scaffold289-2035891 6 58501198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428464 Affx-122938797 AX-123298807 6 56129710 GGCGCCGTGTTAATAAAAGTGAGTTGTAGGGACTG[C/T]GCACCTAAGAGATCCCGCTTATCAGCCCTCGGATC Y 2 1 2 1 101000 f 74 goat snp27101-scaffold289-2072951 6 58538376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443812 Affx-122927074 AX-123314149 6 56185911 TAACCCAAAGTCCATTCCATGAAAGTTCATTGAAC[A/G]TCTTTTCTGAACCATGGACTGAACAAACTGCTGCT R 2 1 2 1 101000 r 74 goat snp27102-scaffold289-2129152 6 58594485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771473 Affx-122962249 AX-385258632 6 56230874 TGTTCGCATCACTGCATATGTCTATATCAGGTTTA[C/T]GTTTCTCTACATAATTACTCGTTTTCATTTATGTT Y 2 1 2 1 101000 f 74 goat snp27103-scaffold289-2174115 6 58638358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397046 Affx-122962743 AX-123267401 6 56266918 ACTTTCACAGATACAGATAATACTCTTAGTTCCTA[C/T]GTGCATATTTCCTCATGCCAGGTGAAAGATCCATG Y 2 1 2 1 101000 r 74 goat snp27104-scaffold289-2210159 6 58674096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788966 Affx-122963904 AX-385275979 6 56301284 CCCTACATCTTGGAGTAAATGGGGCTTTTAAGCAT[A/G]CATCTAATGTACAAATGTGTGTTTGTGCAGATGTT R 2 1 2 1 101000 f 74 goat snp27105-scaffold289-2244525 6 58708410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407325 Affx-122955303 AX-123277676 6 56330049 GCAAGTATTTAGATAGAATATTAGAGGGATTACAA[C/T]ACAGTAGACCCCCAGGACTGCACTTTAAAATCTAC Y 2 1 2 1 201000 f 74 goat snp27106-scaffold289-2273290 6 58736621 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802407 Affx-122953436 AX-385289311 6 56365383 GTAATATTTAGTCTCTAACCTCAGCTTGTCCTTCC[A/G]AAGTAATTCTTGATTCCCACTGAGTAACAGAAATT R 2 1 2 1 101000 f 74 goat snp27107-scaffold289-2308624 6 58772977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424539 Affx-122941717 AX-123294885 6 56396058 GCTAGAATATGCTCTCTTGCCAGTGAATACCAATG[C/T]GGAGTTATTACAAGTCCCAAATACCATTAAAGAAG Y 2 1 2 1 101000 f 74 goat snp27108-scaffold289-2339299 6 58803620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776090 Affx-122944421 AX-385263220 6 56428994 ATAACTTGTGTAGATAAGTTGGGGATACAAAGTCC[A/G]TAAAATATTAATTTAGCTGATTTTTAAAAATGTTA R 2 1 2 1 202000 r 74 goat snp27109-scaffold289-2372235 6 58837011 A G 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38407123 Affx-122954870 AX-123277474 6 56468903 CCATCAAATAGTAGAAGGCTTTGGGCAGCAGAGGT[A/G]TGTGGATTTTTAAGGAGTGACCGTTTTGCCATGCG R 2 1 2 1 101000 r 74 goat snp27110-scaffold289-2412144 6 58877044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783018 Affx-122926623 AX-385270086 6 56512164 TAAATGAAGATATCGTCTTCCTTTATGAATTTAGT[A/G]TAATTATTCTACTATCAATGGATATGTTTTTAGTA R 2 1 2 1 201000 r 74 goat snp27111-scaffold289-2455405 6 58920674 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797820 Affx-122934184 AX-385284759 6 56609110 TCCCAAATTTCCCTCCCAAACAGCATGTTAAGCAC[G/T]GAAAGCACATGTCCTATGTGTTCGGAAAGATTAAA K 2 1 2 1 101000 f 74 goat snp27113-scaffold289-2552351 6 59017819 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778959 Affx-122951292 AX-385266066 6 56688892 AGGGCCTCAGAAGATATGTGAATCCCTTTAAGTGG[C/T]GTATGTATGTCCTTACATATTTCTGTGAGCAGCAA Y 2 1 2 1 101000 f 74 goat snp27115-scaffold289-2632133 6 59096273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433818 Affx-122935167 AX-123304159 6 56721738 TTGTATGCTTCCTTGTTTTACCTTTAAATATGAAC[A/G]TGTTATTCTGGAGTAAAAAAAAAAAACTAAACATT R 2 1 2 1 101000 f 74 goat snp27116-scaffold289-2664979 6 59129005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376740 Affx-122978950 AX-123247099 6 56779588 CTCTGGTCCATTCCGATGGCTGTGGCCACCTCTTC[C/T]ACATCAGCTCCTGTTGCTTCACAGAGGGCACTTAT Y 2 1 2 1 101000 r 74 goat snp27117-scaffold289-2722829 6 59187339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428872 Affx-122938341 AX-123299214 6 56816888 CAAGTGAAGCCACCATGGAAATAGTTTTAAAGAGA[C/T]AATACCCAAATCAAATGAGAAAGAAAACAAGTATA Y 2 1 2 1 101000 f 74 goat snp27118-scaffold289-2760129 6 59224499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395387 Affx-122963968 AX-123265742 6 56871621 GAATCAGCTACAGGAAGATCTGGGAGAAGACTGAA[G/T]CCACAAGGAAGAGCAAGTGCAAATGCCCTGAGGCA K 2 1 2 1 101000 f 74 goat snp27119-scaffold289-2814862 6 59279248 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781340 Affx-122977784 AX-385268425 6 56927977 TAACTACAAGAGTTTCTTATAGATCATTATGAGGA[A/G]TCAGGAGGTGCTTCATCAGCATTAAGCAATTCTTC R 2 1 2 1 101000 r 74 goat snp27120-scaffold289-2871218 6 59336246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446307 Affx-122925643 AX-123316643 6 56976082 GGATGTGTTAGCCGATGCTGCCCCAGGAAAATACC[A/G]TAGACTGGGTGGCATAAACAACAGAAGTTAATTTT R 2 1 2 1 101000 f 74 goat snp27121-scaffold289-2919323 6 59384174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411302 Affx-122952291 AX-123281652 6 57028161 AACCATTGACTTTGAAAATTTGCATTTCCATTCTT[C/T]TAGTACTAGTTTAAAATAAATGCTTAAATCAGCTG Y 2 1 2 1 101000 f 74 goat snp27122-scaffold289-2971402 6 59436378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801772 Affx-122960144 AX-385288680 6 57088355 AGGTGAATCATATATGGAACTACATACTCAGGCAA[C/T]AGTGATAATAATTTCTCTAGAGTGAAAACATTATT Y 2 1 2 1 101000 f 74 goat snp27123-scaffold289-3031596 6 59496880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793026 Affx-122948338 AX-385280004 6 57121687 TAACTGATAATTCTGACTAAAGTCTTATTTAAACA[C/T]GATATGTCTAAACATGCAGAAAGTGATTTCTGAAC Y 2 1 2 1 101000 r 74 goat snp27124-scaffold289-3064928 6 59530692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436416 Affx-122933017 AX-123306754 6 57176344 TCTAATATTTGTAATCTCCAAAGGCTGAGGACCCT[A/G]TATTTAGGCATGTCTGTAACTGTATAGAAGTGTAC R 2 1 2 1 101000 r 74 goat snp27125-scaffold289-3119585 6 59585654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779764 Affx-122975009 AX-385266864 6 57219985 AGAGGTGGTTTTCCCACTATGGTAACAATGGGCTT[A/G]GGTTTTTAACAAGGACTTGACATCTCATGAGGCAG R 2 1 2 1 101000 f 74 goat snp27126-scaffold289-3163226 6 59630010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423796 Affx-122942818 AX-123294142 6 57305061 ATAAAAAAATCATACGATGAAGCACAAATTGGGCC[A/G]TTTTCTCTGGGACTGAATTTGAAGGAAATTATTAG R 2 1 2 1 101000 r 74 goat snp27127-scaffold289-3248302 6 59715678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398931 Affx-122960997 AX-123269286 6 57338998 GTTTCCAATCCTTTATTTTGTCCTTTTAAAATTCA[A/C]GTGTTTTGTATGCTTAGAAAAAAAGACGTGTATAA M 2 1 2 1 101000 r 74 goat snp27128-scaffold289-3282239 6 59749954 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398266 Affx-122962179 AX-123268621 6 57370521 TTGGTTTACCTGTGATATTATTTCCAAGGCTGCTT[G/T]GCCGTGGAGACGCAGATGCCTCGCGCTCAAAGCTG K 2 1 2 1 101000 f 74 goat snp27129-scaffold289-3313762 6 59781433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378283 Affx-122976869 AX-123248642 6 57404371 AGGCACACACCACTCCTACAATACATGAACTAAAA[A/C]CAAAATTCTAGTATCTCACCATTCTAACACAAATG M 2 1 2 1 101000 f 74 goat snp40155-scaffold511-5493595 6 59802430 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273212 Affx-1111833510 AX-519546871 6 57406488 GGGAGAAAACAGAATGCTGAGAGAAAAAGCTGTTA[A/G]TGAAGCTTATAGTCCAGTGGAGGATGGCAGACATG R 2 1 2 1 101000 f 74 goat 6_57406488_AF-PAKI 6 57406488 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789166 Affx-122934239 AX-385276178 6 57455903 TACCTCGAGCAGTTGCCTAAGTTGTTCACTGCACA[A/G]AAGTACTCAGCCAATAAGTGAGTGGTAGCTACATT R 2 1 2 1 101000 f 74 goat snp40154-scaffold511-5442063 6 59853974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431373 Affx-122937030 AX-123301714 6 57495022 CACTTCTAATCTAACCTGTATCCAGTTGTTTGTTT[A/G]CAATGGATACGTGTTAGACTAACACCTCTCAAATG R 2 1 2 1 101000 r 74 goat snp40153-scaffold511-5402944 6 59893165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399200 Affx-122960614 AX-123269555 6 57538917 ATTTCTCAAGATCCTGGGGAAGGGAAAATGCTGTT[A/G]CTCCTCACTGTGGACAGCTGCTCCAGGCTGTTTCA R 2 1 2 1 101000 f 74 goat snp40152-scaffold511-5359049 6 59937162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792290 Affx-122952637 AX-385279272 6 57572037 TAAGGGTTGACGGGTGTTAACCATGTGTTATTCAC[A/G]ATGGTTCTGTTCTTTAAACGCTCGACCTCTCCTTA R 2 1 2 1 101000 f 74 goat snp40151-scaffold511-5325929 6 59970295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413812 Affx-122949897 AX-123284161 6 57612087 TAAATACATAGAGTGATTTGTCATTTCTGTTGTAA[A/C]AGAAATTTTCATTTTCTACTCCCAAACTGGGGTAT M 2 1 2 1 102000 r 74 goat snp40150-scaffold511-5285879 6 60010410 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784585 Affx-122960910 AX-385271633 6 57723513 AATGTCAGATTCAAACCCTAGATATCATTATCCAA[C/T]GCTCCACATATTATGGATTCATGATCAGTGAATGC Y 2 1 2 1 101000 r 74 goat snp40148-scaffold511-5174453 6 60121532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438599 Affx-122930940 AX-123308936 6 57769091 TAAGCTTCATGAGGATAGAAATTTTTATCTGTTTT[A/G]TTCACTTCTATCTTCCTAAGGCCCAGACAATAGTT R 2 1 2 1 101000 r 74 goat snp40147-scaffold511-5128875 6 60167482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378102 Affx-122977151 AX-123248461 6 57825135 TGGGAGTCAAAATGACTACACAGGGTCTCATAGGT[C/T]ATATCAGGGAGTGTCAACTCTATCCCCTAAGCAAT Y 2 1 2 1 101000 r 74 goat snp40146-scaffold511-5072831 6 60223017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765310 Affx-122920351 AX-385252834 6 57887916 GAAAGTGTGTGCGTATTTTCTGTGAAAGGATGCCA[A/G]TGTTTTACCTGATATTGTAGTGACACTTCAGTTAT R 2 1 2 1 101000 f 74 goat snp40144-scaffold511-5010050 6 60286526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401288 Affx-122959865 AX-123271641 6 57938636 ACATTTTTAGGCACTTCAATGTTTTTTTTCTCTCT[A/G]CCAGTTAAACTTGAAGGTAATGTAGTGCGTATTCA R 2 1 2 1 101000 r 74 goat snp40143-scaffold511-4959330 6 60337471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423335 Affx-122943168 AX-123293681 6 57975561 CTGAGCCACCAGGGAAGCCCGTATGTCACCAGGCA[C/T]GGCCTAGATCAGATTTGTTGAAAATTCAGAGATAC Y 2 1 2 1 101000 r 74 goat snp40142-scaffold511-4922405 6 60374479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408372 Affx-122953727 AX-123278723 6 58015918 TTTAGGGGCAAGAAATTAAATTTCCTCTCAACTCC[A/G]TGGCTCTTATTTTCTCATGTTATTTTACTGTTTCA R 2 1 2 1 101000 f 74 goat snp40141-scaffold511-4882048 6 60415118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408728 Affx-122953415 AX-123279079 6 58050059 TGGGAAGGAAAAGAAATAAGGGTTTTCAGCACAAA[C/T]GCAGTAGGAATATCACCCTTGGGTCAGGTCTGGTT Y 2 1 2 1 101000 f 74 goat snp40140-scaffold511-4847907 6 60449142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453429 Affx-122919877 AX-123323762 6 58114278 AAAGTTTAAAAAAATTAGATTTTTTTGTTGCTCAG[C/T]ACAGAAAATCTCATGTCTTCTTTCAAGCTTTTCAA Y 2 1 2 1 103000 r 74 goat snp40139-scaffold511-4783688 6 60513524 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411966 Affx-122951132 AX-123282316 6 58171057 CTCAGTTCCATGAGGGCAGGGATCTGGTTTAGTGA[C/T]GTATCTCTAGCACCTCGAATGGTGCCTGCTAAATA Y 2 1 2 1 201000 r 74 goat snp40138-scaffold511-4726909 6 60570178 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422497 Affx-122943307 AX-123292843 6 58200356 CATTCTGGACTCCAGAGTGCTCCTCTGTCCAGTAA[C/T]GGACTGCTGTGACCTCCTTGTTCTGACTGAGCCAA Y 2 1 2 1 102000 f 74 goat snp40137-scaffold511-4697610 6 60599450 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443507 Affx-122927795 AX-123313844 6 58258121 CTTGTATAAAGGACCTAGAGATCTGGCCTTTCAAA[G/T]CTCTATAGCTGTGGTTCTTGGGGTGGGGGGTGGGT K 2 1 2 1 101000 f 74 goat snp40136-scaffold511-4639845 6 60657059 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436660 Affx-122932474 AX-123306998 6 58320961 CCACAGGAGTTGCCAATGGTCTGCTTCATGAAGTA[C/T]ACCTTGGGACTGACTTCTTGTCCCTTCAGCTCTTC Y 2 1 2 1 201000 f 74 goat snp40135-scaffold511-4577005 6 60719838 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448857 Affx-122923284 AX-123319192 6 58354882 TCACATTTGCAAAGGGCTTTAATTGTTTGCATGAA[C/T]GTCTCAAATGTGTAGCTCCATCCTCTGAATAGGGA Y 2 1 2 1 101000 f 74 goat snp40134-scaffold511-4543084 6 60754247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771109 Affx-122943955 AX-385258269 6 58409934 GTTGGTTGCAACAGAACAGTTAAGTTTAATTTTGC[G/T]AACTAAAACACACAAAAGAATGTTTGAATGAAAAA K 2 1 2 1 202000 r 74 goat snp40133-scaffold511-4488032 6 60809883 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376712 Affx-122978970 AX-123247071 6 58452914 CCTTTTCTCATGCTAAAGATCTGGCTGTGTCCAGT[A/G]TCGTCCAGCCAAGAAGGTCAGGCAGAAGACAGAGA R 2 1 2 1 101000 f 74 goat snp40132-scaffold511-4445052 6 60852528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388326 Affx-122969365 AX-123258684 6 58494380 GGAGAGTCAGTTGGCATAATCAGTTTGAGAAGCAA[C/T]GAACTGATGAAAATCTAGAAAGCCTGGAGATAACA Y 2 1 2 1 101000 f 74 goat snp40131-scaffold511-4403586 6 60894165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774476 Affx-122941380 AX-385261612 6 58530060 TTACTGGCTCTCCTCTTAAATTCTATCACCATACC[A/G]TCTAACCCAACAGACATTGTCTCCTTTGATCTGAA R 2 1 2 1 101000 f 74 goat snp40130-scaffold511-4367906 6 60929835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785637 Affx-122924751 AX-385272679 6 58562735 TTCATGAATGCACTTAATTTTAACCATGAATTTAA[C/T]CTTCTTAAAAAGTGGGGGTTTTATAGCTTATCTTG Y 2 1 2 1 202000 r 74 goat snp40129-scaffold511-4335231 6 60962593 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795348 Affx-122976152 AX-385282304 6 58591614 TTTTTATAACACAGTCAGTCCATTGCTAATACTTC[A/G]TGTCAGCAAATTTAACCAAGGTAACAGTTGGGTCA R 2 1 2 1 101000 r 74 goat snp40128-scaffold511-4306352 6 60991451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447103 Affx-122924482 AX-123317439 6 58695102 AAATGAAAGCAAAGTCTTGACACTTCTGAAGAATG[C/T]GAAATTTGTAGGAAAACCCAAAGAGGAAATAAAAA Y 2 1 2 1 101000 f 74 goat snp40126-scaffold511-4202864 6 61095251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396018 Affx-122963482 AX-123266373 6 58726236 TCACTGTTCACATCCTTAGGGCTCCTTTTTAGTGG[C/T]GTGGGAACATGCAGTCCTTACCAAGGTAAAGGGAT Y 2 1 2 1 101000 f 74 goat snp40125-scaffold511-4171730 6 61126366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787120 Affx-122940821 AX-385274146 6 58770780 TATCCATAAAAAGAGTCTTTCCTTAACTATCTAAT[A/G]AAAGTTCTGCGATTCCTGCTGTTTGGACCATTCAT R 2 1 2 1 101000 r 74 goat snp40124-scaffold511-4127186 6 61171028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396024 Affx-122963478 AX-123266379 6 58813389 AATGACCTTCAGTAAATTCTCCCAGACAACATTAC[A/G]TAAACAGTGGCATTAATTTTGATGGTCTAAAATGC R 2 1 2 1 101000 r 74 goat snp40123-scaffold511-4084577 6 61213935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436366 Affx-122933058 AX-123306705 6 58844002 CACAGGGCACTTAAGGCCTTTTCTGCTTCTGACTG[A/G]CCAGACCACATCTGCTATCATCAACTTGCCACCCC R 2 1 2 1 201000 r 74 goat snp40122-scaffold511-4053964 6 61245036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433706 Affx-122934533 AX-123304047 6 58887167 GTTTTGATTATCCCATGCTGATGCTCAGTGTGGAG[C/T]GAGATGGATTCTCCACAGGAAGGCTTCTCTCTATT Y 2 1 2 1 101000 r 74 goat snp40121-scaffold511-4010799 6 61288659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423337 Affx-122943166 AX-123293683 6 58929851 ATTTTGTTTGTGTATTTAAATAAGGCTGTAGATAG[C/T]GGCATTCATATTCTTTTTATTTTTAATTCTTTTAT Y 2 1 2 1 101000 f 74 goat snp40120-scaffold511-3968115 6 61330588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400427 Affx-122959973 AX-123270782 6 58962278 ATAAAATTTTTTAAAAATTGAAGGGTTAGGTTAAA[C/T]AGGTGATCTTGGAAGGAAAAAAGTTGTCCACCTAG Y 2 1 2 1 101000 r 74 goat snp40119-scaffold511-3935688 6 61362996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379427 Affx-122976107 AX-123249785 6 59004675 CTACTTGAGGAAAGAGTGCCACCTACTGCTCATCA[A/G]CATAACTGGTTACTTTCTCCCTTGAGGTTTTCACC R 2 1 2 1 101000 f 74 goat snp40118-scaffold511-3893291 6 61405346 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395168 Affx-122964110 AX-123265523 6 59038753 ATGTAGTCCACATTTGCATCAAAGTGGTAGAAAAG[C/T]ATATTTGTCTCTACTCTTGTGTGGCCCTGTCTCCC Y 2 1 2 1 101000 r 74 goat snp40117-scaffold511-3859213 6 61439681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416115 Affx-122948305 AX-123286464 6 59081246 AAAAACAGCTTTGTGCATTAGTCCAAGACATACAG[A/G]AAGAAATAACACAGATTTTTTTAAAGTTTTATATG R 2 1 2 1 101000 f 74 goat snp40116-scaffold511-3816720 6 61482648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412814 Affx-122950477 AX-123283163 6 59112809 TGAGTGTGGCCGGAGAAAAGATGTAACCCTGGGAC[A/G]TGCCAATTCTTGGAGGTAAGGGAAATGAGGAATAA R 2 1 2 1 101000 r 74 goat snp40115-scaffold511-3785157 6 61514355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278373 Affx-1111836389 AX-519551859 6 59118528 AAAAGATTTTCATCACTATGAAAGTCGACAAAGAA[A/G]CTATGGCATTTCCTTCCTTATTTATATATAAGTTA R 2 1 2 1 101000 f 74 goat Random2.2K-688 6 59118528 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420120 Affx-122945080 AX-123290468 6 59157831 CGGTACTTTCAGGTATAAAAGGGGGACAGGAAGGC[A/G]CCAGCCCTCACCTCAAGGAAGGAGACTGGGAAGAG R 2 1 2 1 101000 f 74 goat snp40114-scaffold511-3740135 6 61559529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405366 Affx-122956314 AX-123275718 6 59222392 GTCTAACACCACTTCAGTCCGTTATGTAATCCCCA[A/G]TTTTCCCCCATTTTGACTGTCTCTGCTGTTTATTG R 2 1 2 1 201000 r 74 goat snp40113-scaffold511-3675574 6 61624572 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398874 Affx-122961040 AX-123269229 6 59262193 AATGTGTAGTTGAAAGCATCCAATGAACCAGGTTT[A/C]GGGAGAACTGAATAACTGAACTGCTCTCATTGTCT M 2 1 2 1 101000 f 74 goat snp40112-scaffold511-3635773 6 61664468 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433926 Affx-122934298 AX-123304267 6 59292351 ACAACCTTGACTAATACACCCAGAGAATCTCTACC[G/T]AGCCTGAGAGGGCTTCCCCTGAGTCATCAAGTGTT K 2 1 2 1 102000 f 74 goat snp40111-scaffold511-3605615 6 61694511 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386251 Affx-122970960 AX-123256609 6 59343911 GTTTTGTTTTTCTGTGTGAACTTTAATGTCAACTT[A/G]CCTAGTTCCAGAAAAAAAGACTTATTGGTATTTTT R 2 1 2 1 101000 f 74 goat snp40110-scaffold511-3554055 6 61746078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400169 Affx-122960681 AX-123270524 6 59436416 GGAAAAACATATTTGGGAGCCTAGTGGTTTGTTCT[C/T]GTACAACATGAGTGCAAAACAAATAATACTTGATG Y 2 1 2 1 101000 r 74 goat snp40108-scaffold511-3461550 6 61838586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445247 Affx-122925484 AX-123315584 6 59518377 CCTCATGGCAGGCTCTATGTGAGGCCTGAGAATCC[A/G]TGGTAAACATAATAGTCCTGACGCTCTATTTGTAC R 2 1 2 1 201000 r 74 goat snp40106-scaffold511-3379589 6 61920274 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406626 Affx-122955828 AX-123276978 6 59608807 AGTTCTGTCTTCCTATGATTGTGTTGTGGTGAAAT[C/T]AATGGGGTTACCTTTCTGCAAGCATTTTTACCAAC Y 2 1 2 1 101000 f 74 goat snp40104-scaffold511-3289159 6 62010755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779522 Affx-122925608 AX-385266625 6 59670026 TTGGCTCCTTCACCAATCCACGATCATCTGTATTT[C/T]ATTTTCTCTAGCTGGAGATCCTCACCATTCCCATC Y 2 1 2 1 101000 f 74 goat snp40103-scaffold511-3227940 6 62072989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429616 Affx-122937699 AX-123299957 6 59715756 AAAATTGGCTTATAATTTTCTTTTATTGCCTTTAC[A/G]TGATTTTGGAGTCAATACTTCACTAATCTCATCAA R 2 1 2 1 101000 r 74 goat snp40102-scaffold511-3182210 6 62119745 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385165 Affx-122971744 AX-123255523 6 59747039 CATGTACTTCTTCCAAAGAGAGTTTTCCATGATCC[G/T]AAACAACTCAGAGCTTTCTCACAGTTTTTGCAGAT K 2 1 2 1 101000 f 74 goat snp40101-scaffold511-3150927 6 62150968 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402501 Affx-122958576 AX-123272854 6 59818152 GATGCTCCTTTCTTCCACACTGCTGGCTGAAACAG[A/G]ATTCCTGATTCCACATCCAGAAAATGCAAAAGGCT R 2 1 2 1 201000 r 74 goat snp40099-scaffold511-3079814 6 62222870 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274832 Affx-1111834444 AX-519548417 6 59834165 GCTCTCTGCAGGACTATGGAAACTGAGGTCAAAGG[A/G]GAAAGCTTTATAGCCTGCAGCACACTTACAATTGC R 2 1 2 1 101000 r 74 goat GoatD01.036251 6 59834165 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395446 Affx-122963925 AX-123265801 6 59885446 TTTAATATAGAGTTCAAGGTTACCCCCATAATAAC[A/G]TCACACTCACATTCTAGCTTTTGAAATGTTCTCCT R 2 1 2 1 101000 r 74 goat snp40098-scaffold511-3012520 6 62289903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446157 Affx-122925754 AX-123316493 6 59935930 AAGGTATCAAAGAAAACTGAGATTTGGAGTCCGAG[C/T]GACTGGAAGAATTGTGGGGTCATTTATCAAAACCA Y 2 1 2 1 201000 r 74 goat snp40097-scaffold511-2962036 6 62339949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791734 Affx-122953234 AX-385278725 6 59981954 CTCTGGTCTAAAGCCTTGCCACTGTAAGAAAAGGA[C/T]AGTAAATGCATTTTGATTCACATGTGAATTCTGAT Y 2 1 2 1 101000 f 74 goat snp40096-scaffold511-2916012 6 62386041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452662 Affx-122920330 AX-123322995 6 60034963 TGAAGCACTGCTTCAGACCGATTTCAAGAGGGTGC[C/T]AGCCCTTGAAGGGTGCCAGACTGCAAGAGGACACC Y 2 1 2 1 101000 f 74 goat snp40095-scaffold511-2863003 6 62438828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378626 Affx-122977115 AX-123248985 6 60087151 TTGAATTTCCATCATCCCAGAAAAATTAACTGTTA[C/T]GATCTAATCATTGTTAGGGTCAAGCAACATGAAAG Y 2 1 2 1 101000 r 74 goat snp40094-scaffold511-2810815 6 62491347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771304 Affx-122925280 AX-385258462 6 60194889 AAACAGCCTTGAACTAGCTTTCTCGCTTCGCCCAT[A/G]CAAATCCATGAATAACATGGTAATCTCTATTCTGC R 2 1 2 1 102000 f 74 goat snp40092-scaffold511-2703077 6 62598454 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273214 Affx-1111833511 AX-519546873 6 60205735 TTAGTTCCTCCTCGCTATGTGACATCTTCCAGGAC[A/G]AGGGGTCAAATCTGTGTCCACTGCATTGGCGGTGG R 2 1 2 1 102000 f 74 goat 6_60205735_AF-PAKI 6 60205735 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446261 Affx-122925677 AX-123316597 6 60242274 TCAGTTATGTGATCCCTGTAGGCCAGGTCTCATAG[C/T]AAACCATATGCCATTATTCAACCAGACTACTGGGA Y 2 1 2 1 101000 f 74 goat snp40091-scaffold511-2655692 6 62643472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432488 Affx-122935590 AX-123302829 6 60307831 TCTATTTACCATAAAAGCAGTTTCAAGTCACAAAG[C/T]AAAACTCACCTTCTAAAATATATCATTTTTAACAA Y 2 1 2 1 101000 f 74 goat snp40089-scaffold511-2590135 6 62710047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394945 Affx-122964292 AX-123265300 6 60356655 ACCTATAGAATTTTGAATGTTTATAATGCACTTGT[A/G]TTAACCTGCCTGGTTGTACTCCCTTTTAGTACATT R 2 1 2 1 101000 r 74 goat snp40088-scaffold511-2541311 6 62749473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390939 Affx-122967070 AX-123261296 6 60389433 TAATAAGATTTTAAAGTTTATGCTGTGAAATGGGA[G/T]CAGTATTAACAAGAGAGAAACTTGTTTGTCTCATA K 2 1 2 1 101000 r 74 goat snp40087-scaffold511-2508533 6 62783220 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777354 Affx-122974368 AX-385264476 6 60440291 CAAATTTGTGGTAGAATGTGGATGGAACACTGAGT[A/G]CAATCCTGTTTCAGTGAAATACAAATTTCTAGCCC R 2 1 2 1 101000 r 74 goat snp40086-scaffold511-2457675 6 62834521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391251 Affx-122967376 AX-123261608 6 60483823 GAGACTATTATTCAGTTTAGCCTCTGGGGGCCCAG[C/T]GGTCTGGAACTTGTCAGAATATCCAGCACACTTTG Y 2 1 2 1 101000 r 74 goat snp40085-scaffold511-2414143 6 62878413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379214 Affx-122976285 AX-123249573 6 60523238 TGATCAATTATATTCAAAAGTTCAAAAGAGAAAAA[C/T]ATAGGTTGAAAAGTTTGATATGATGCTGGCTGATG Y 2 1 2 1 101000 r 74 goat snp40084-scaffold511-2374728 6 62917823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391701 Affx-122967515 AX-123262058 6 60553915 TAAACTGAATACAGAGGATGACCTAAATCAGAATG[C/T]ACCTCCCACTCCCAGTCCTTTTGTATGTCATGAAC Y 2 1 2 1 201000 f 74 goat snp40083-scaffold511-2344051 6 62949329 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392464 Affx-122966156 AX-123262821 6 60588680 ATAGGTGCATAATAATCTTTTTCACTTCTAAGAGA[G/T]CTCCAGAAAGGGACTTTAAACTCTATCTTGGCATC K 2 1 2 1 101000 r 74 goat snp40082-scaffold511-2309286 6 62985051 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398003 Affx-122961791 AX-123268358 6 60617536 TATTTGGCTAACTGTACCTTCATCTTAGATATTGA[C/T]GTCAAGAAGGAGAGCTCTCCTTTTACCAAAATTTG Y 2 1 2 1 101000 f 74 goat snp40081-scaffold511-2280430 6 63013941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789638 Affx-122954130 AX-385276647 6 60657087 ACATACAGTTTGACTTTCAGGTAAAATAAAGACAG[C/T]CATATAGCATTAGCTGCAGTAGGAAACTGATGAAA Y 2 1 2 1 101000 r 74 goat snp40080-scaffold511-2240879 6 63053735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775187 Affx-122950131 AX-385262318 6 60713965 TTATTTTTCAGCATTTGATAGCATTTCCATCATTT[C/T]GGAGAGTTTTGTTGGATATGAAAGTAAGGATAGAG Y 2 1 2 1 101000 r 74 goat snp40079-scaffold511-2184001 6 63110211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793447 Affx-122949070 AX-385280424 6 60759247 TTGAATTGATACCATAGTAACACCTTATATTGTTG[C/T]AACTGTCTTTCTTAGTGAATTCCATTTTTCATTGG Y 2 1 2 1 101000 f 74 goat snp40078-scaffold511-2138719 6 63154609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403641 Affx-122957531 AX-123273993 6 60855435 TAAACAATCCTGCAATCTCTAGGTTAAATTGTCCC[A/G]ATTTTGTATTTTTCAGGAAGGACTTTGCTATTCCT R 2 1 2 1 101000 f 74 goat snp40076-scaffold511-2042531 6 63249483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434541 Affx-122934145 AX-123304882 6 60905890 ATAGGCAAAAATTGCATCTTTTTCATTTGATCTGC[A/G]ACAGCACCTTTGTGTATTTGCCCAAGAAGTAGCAA R 2 1 2 1 101000 r 74 goat snp40075-scaffold511-1992076 6 63298730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793186 Affx-122962552 AX-385280164 6 60948298 CTCAAAAATTAGCTCAATCTCTTCACATTCATTAC[A/G]TGAACTGAGCTAGTAGACACCTTTTTTTCCCCTAA R 2 1 2 1 101000 r 74 goat snp40074-scaffold511-1949668 6 63341408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385315 Affx-122971673 AX-123255673 6 60990865 GTATTTTCAAATTCAAGAGAGAGCCTTAGAAGAAT[A/G]AGAAAGAAGAAAAATGCAGAAGGCAGAATGTAGAG R 2 1 2 1 201000 f 74 goat snp40073-scaffold511-1907101 6 63383763 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445576 Affx-122925135 AX-123315913 6 61049316 AGAGATATCCTTTCTCTACTATCTTTTCTCTGCCT[A/G]CTGACTGGACACTGAGGTCAAAGCTGATCTTGAAG R 2 1 2 1 101000 r 74 goat snp40072-scaffold511-1848650 6 63442701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795303 Affx-122957708 AX-385282261 6 61092351 GAACAAGCTGTTACACTTTAAATTGAGAATAAAGT[A/G]CCAGACCATGTTTCATCATTCTACTTGTGTCCAAT R 2 1 2 1 201000 f 74 goat snp40071-scaffold511-1805615 6 63486112 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783230 Affx-122936404 AX-385270296 6 61152023 GGCAGAACTAAATAAACATAGGAATGAACTAGTGA[C/T]GGTATTATACAAAAGTAAAGACAGCACTGACCTGA Y 2 1 2 1 101000 r 74 goat snp40069-scaffold511-1745943 6 63545248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447154 Affx-122924441 AX-123317490 6 61203225 TTATTGTAGTCACTTCTGCATTGTCATGTAGAAAA[G/T]AATATGGATTATGGAATAAAGACCACTTTCTATTC K 2 1 2 1 101000 f 74 goat snp40068-scaffold511-1694741 6 63597105 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448042 Affx-122923705 AX-123318378 6 61254371 TATTTGTCTCTGATTCATCCTAGGGACTGAAGACC[A/G]TTAACCCTGCTCTATTTTAAACTATTTTAACTTAC R 2 1 2 1 101000 f 74 goat snp40067-scaffold511-1643595 6 63651501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410002 Affx-122953267 AX-123280352 6 61310517 TCAGGTGTACTTTCCAGGGATATTTGTACCTAAAG[A/C]GATGTTTGTGGCCTCCAAAATTCATATGTTGAGAT M 2 1 2 1 201000 f 74 goat snp40066-scaffold511-1587449 6 63707127 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411753 Affx-122951503 AX-123282103 6 61357685 ATGAGATTTCTGCAAAGTCCGTGTTGATATAGCTT[A/C]TTTTAGAATTTATGTAACTCTTCCAGAAAAGTCTT M 2 1 2 1 101000 f 74 goat snp40065-scaffold511-1540281 6 63754510 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435381 Affx-122933574 AX-123305721 6 61390566 AGGGCTGGGGTACATGTGAGGTTTGCTCAGGGGAA[G/T]GAGTGTATTCTGCAAATGAGAGAAGTAGACATGAT K 2 1 2 1 101000 r 74 goat snp40064-scaffold511-1507400 6 63787490 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393123 Affx-122965564 AX-123263480 6 61425323 CATCCAGTTAAATGTCAAGTAAAATGTTACTCTAA[C/T]ACATGAAAGTTATTTGAAATTGTCACTATTTTCCA Y 2 1 2 1 101000 f 74 goat snp40063-scaffold511-1472643 6 63822282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440634 Affx-122929953 AX-123310971 6 61474508 CCACTTATTAAAATATCGGCATCACATACTTAGCC[A/G]CCACCATTTTGCCCCTGGACTACTACTGCAAACTG R 2 1 2 1 201000 f 74 goat snp40062-scaffold511-1423458 6 63870488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402938 Affx-122958180 AX-123273291 6 61508159 AGTTCTGCCTAAAAGAGATGAGATATAGGGTGTTA[C/T]AATTGATCTAGGCCCTGTTGTAAGGGGATCAGAGC Y 2 1 2 1 101000 f 74 goat snp40061-scaffold511-1389807 6 63903819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272533 Affx-1111833898 AX-519546251 6 61540367 AGATGGCAGTACTTCCCAGACTGATCTACGAGTCC[A/G]TTGCAGTTCCTGAGCAAATCTCAGATGACCTCTGC R 2 1 2 1 101000 f 74 goat GoatD01.009857 6 61540367 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320791018 Affx-122978607 AX-385278014 6 61543789 GGATTGCAGACAGATTGAATACAGGGTGTAAGAGA[A/G]AGAGTGGAGTCAAAAATGAGAGCAAGATTTGAAGC R 2 1 2 1 101000 f 74 goat snp40060-scaffold511-1354177 6 63939465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380033 Affx-122975585 AX-123250391 6 61585161 TAGAGAGAGAGAGATAGGGAGTTATATAAACCTAG[A/C]TGGGTTCTCAAAGACATTTATCTAGTTGGTGATTG M 2 1 2 1 101000 f 74 goat snp40059-scaffold511-1312805 6 63981514 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420943 Affx-122944986 AX-123291290 6 61616541 CATTCAGTAAACATAAGCAAAGAACTAAGTATCAA[C/T]AGAGATGATTCAGGGATCTCTTTATATGGAAAAAG Y 2 1 2 1 101000 f 74 goat snp40058-scaffold511-1281425 6 64013030 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397043 Affx-122963104 AX-123267398 6 61685992 AGCATTTGAAAGGTTCTTAATCATCTTAACTACAG[C/T]AATAGAAATCAAACTGTTGAACAAGTTACTCTTGA Y 2 1 2 1 201000 f 74 goat snp40057-scaffold511-1211974 6 64083343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774618 Affx-122971634 AX-385261752 6 61719617 ACACAGAACTACAGCCTTTCAAATACACAAAGAAA[G/T]CTAAAAGATGCTCTATAGTACCTTTCAAAGACACT K 2 1 2 1 101000 f 74 goat snp40056-scaffold511-1178349 6 64119866 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387194 Affx-122970605 AX-123257552 6 61752544 TCATGACGGAACACCCGTATTTTGTATCCTTCCAC[G/T]CAAGGCAAAGCAAGTTATCAAAGTAATAATGGAAC K 2 1 2 1 101000 f 74 goat snp40055-scaffold511-1145422 6 64152774 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376948 Affx-122977770 AX-123247307 6 61796926 AATATTTTATTGTGTGATTGTGTCAATTAAGTCAG[C/T]GGTAATGTCCTGTTGCTAAACATTTAGTTTCTATT Y 2 1 2 1 101000 r 74 goat snp40054-scaffold511-1101040 6 64197436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382090 Affx-122974903 AX-123252448 6 61826989 TACTGATGGTGAAACCAACCAGATGGCAGCCTTTT[A/C]TGCTGGATGTAGGTGACCTCAAGGCTAGGGCTTTG M 2 1 2 1 101000 f 74 goat snp40053-scaffold511-1070977 6 64228064 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771163 Affx-122971733 AX-385258323 6 61855567 AAACAGAATGCATTTAATTCAGATTAAGGACAAAA[C/T]GAAGAGCATTAATTCAGGCACTTAATATTCCAGCC Y 2 1 2 1 101000 r 74 goat snp40052-scaffold511-1042399 6 64256839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401463 Affx-122958970 AX-123271816 6 61903603 CCCTTTTTTTTTTTCTTTCAGGTAGTGTTGACTAA[C/T]ATAAATTATTTCTTAATTTCTCAAAGCAGTTATTT Y 2 1 2 1 303000 r 74 goat snp40051-scaffold511-994363 6 64305304 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398867 Affx-122961046 AX-123269222 6 61942014 AATATTAAAAATAGTTTGATCTTTTTTTGCTTTAT[C/T]CTGAATGATCTACCACACAGAATTAATATCTCTGT Y 2 1 2 1 101000 r 74 goat snp40050-scaffold511-955952 6 64343943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278542 Affx-1111836390 AX-519552024 6 61957289 CCTTTATTTTGCACAAAGCCAATTTTAACTTGAAG[A/G]AAGGTGAGGGAACGGAAACAGATCCCCTAATCTTG R 2 1 2 1 101000 r 74 goat Random2.2K-689 6 61957289 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437772 Affx-122931705 AX-123308110 6 61984096 AATGAGAGATGTTTGTTTAATTAAAAGGAAATAGC[A/G]TGTTCATATGTCTTCAAGACTAAATACAGGAATGC R 2 1 2 1 101000 r 74 goat snp40049-scaffold511-913870 6 64386057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402008 Affx-122958758 AX-123272361 6 62051060 TCACCCTCAAGGCACCACAGCCCATGTTTCTGTAC[A/G]TGAGCTTGTCTCAGTTTATCTCCCCATTGTCTTTG R 2 1 2 1 101000 r 74 goat snp40047-scaffold511-846906 6 64453604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772812 Affx-122969520 AX-385259957 6 62125742 AACACTCATCTGTAAAATCCTATTTCTCCAGAATT[A/G]CTCTTGAGATAAAACTGTGTATTAATACAGTCTCT R 2 1 2 1 101000 r 74 goat snp40046-scaffold511-772224 6 64528513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383353 Affx-122972671 AX-123253711 6 62157956 TTTACTAGGACAGAAAAGTTGGGGAAAAAAGATTC[A/G]CAAACATATCCATCCTCTGTGGCCTCTGCTAGATC R 2 1 2 1 101000 r 74 goat snp40045-scaffold511-740010 6 64561782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446527 Affx-122925021 AX-123316863 6 62201240 AGAGATACTATATTTCCTTACCTCCAACGCAAATA[C/T]AGGAAAAAGTCAACAATTAGTAAAGAAGCTTCACT Y 2 1 2 1 101000 f 74 goat snp40044-scaffold511-696726 6 64605093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396633 Affx-122962871 AX-123266988 6 62231019 CCAATCAGTAGAACACTGTACTCCAATGTTCATCG[C/T]AGCACTGTTTACAATAGCCAGGACATGGAAACAAC Y 2 1 2 1 103000 f 74 goat snp40043-scaffold511-666947 6 64633642 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421829 Affx-122944308 AX-123292176 6 62365821 TTCTGGAATCAGTAACAGAGGTCTTTGTATTTTTT[A/G]CCCTTAAAGAACCAAGTTTTAAATTATTGCTTTCA R 2 1 2 1 102000 f 74 goat snp40040-scaffold511-532145 6 64769030 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770131 Affx-122954624 AX-385257298 6 62416878 AAATCAAGACATGTCTTTCTGAATCATGAAACAAG[C/T]TTACTTGAGGTCATGAGAATTTGTAGTGACAGAAA Y 2 1 2 1 101000 f 74 goat snp40039-scaffold511-481088 6 64820842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766977 Affx-122929081 AX-385254276 6 62464431 GAAGAAATTTCTAGCAAAAGTGTTAAAAATATATA[C/T]AGTTGCCACTTTATGGTCTTTGCATTTCCAAAAAA Y 2 1 2 1 303000 f 74 goat snp40038-scaffold511-433535 6 64868681 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445388 Affx-122925398 AX-123315725 6 62494048 TAAATTTTTGTTTACCTTAAATTCCATTTCTCTAA[C/T]GAGAAATATCAGATATTCAGTTTCCATTTTGTTCT Y 2 1 2 1 303000 f 74 goat snp40037-scaffold511-403918 6 64902752 T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768367 Affx-122932444 AX-385255547 6 62542890 AGAGTTCTGCCTTTTAGTGAATAATTCACACTTGT[G/T]AAGATCAAAATGCACTTTGAGTGAGTACAAATAGA K 2 1 2 1 201000 r 74 goat snp40036-scaffold511-355076 6 64951977 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451977 Affx-122920940 AX-123322310 6 62575456 GTTATCTACTATTACTGTATGTATCCATCCATAGA[C/T]AACATATTTATGTAGCTTTTTTTTTTGCATATTTT Y 2 1 2 1 103000 f 74 goat snp40035-scaffold511-322510 6 64983461 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424572 Affx-122942222 AX-123294918 6 62633076 AAACAGTGCAGGAGATGTTCAGATAGGGAGCATGG[A/C]TGTTAAAAATGAGTTTTCTCTCATTTACATGTGGT M 2 1 2 1 101000 f 74 goat snp40034-scaffold511-264890 6 65042221 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453965 Affx-122919461 AX-123324298 6 62661739 ACTGGCCTGGGGACAGAAAGGAATGGCATCTGCAT[A/C]TGTCAGGCTTCATTTATTGGGCAACTCAGCACAGG M 2 1 2 1 101000 r 74 goat snp40033-scaffold511-236227 6 65071262 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797754 Affx-122937366 AX-385284693 6 62691874 AACATACTATCATTTCAAAACTACATTAACAAAGT[A/G]ATAAAGTGAAGCCAAATTGCCCTTGGGATAGATGA R 2 1 2 1 101000 r 74 goat snp40032-scaffold511-206092 6 65101680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278545 Affx-1111836392 AX-519552027 6 62719218 TTTTCTTAATCATGGAGACAAACTGAAAATTTTTG[A/C]TTGTTGGCAGCACTAAAAGGAATTGGAATTTTTCA M 2 1 2 1 101000 r 74 goat Random2.2K-690 6 62719218 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431918 Affx-122935996 AX-123302259 6 62728701 ATATAATTGTTCATTCATCAAATATTTATTAAGGA[C/T]ACCCAGGTTCTAGGTACTGTTCTAGAATAGCTATT Y 2 1 2 1 103000 r 74 goat snp40031-scaffold511-169265 6 65138555 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273215 Affx-1111833512 AX-519546874 6 62742869 GGATGAGATAGTTGGATCGAATCACCAACTCAAGG[A/G]GCATGAGTTTGAGAAAACTCCAAGAGATAGTGAAG R 2 1 2 1 101000 f 74 goat 6_62742869_AF-PAKI 6 62742869 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386473 Affx-122970770 AX-123256831 6 62765353 CCTCAACTTTGAATGAATTGGTTGTTGTGGGTGGT[A/G]TATATTTGGTTGGTGGTGAGTGAGGGGTTGCATGG R 2 1 2 1 202000 r 74 goat snp40030-scaffold511-132613 6 65175792 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396651 Affx-122962859 AX-123267006 6 62810304 CTAAAGGAATGTAACAAACAAACAAACCAGGAAAG[C/T]ATGGTGTCATGATGCCAAGTATTTTGAGAAAGAGA Y 2 1 2 1 101000 r 74 goat snp40029-scaffold511-87662 6 65221196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396430 Affx-122962992 AX-123266785 6 62937396 TTCACAAATTAGCAGTTATTAGTCAGACTGTACAA[C/T]GCAAAACAAAACAAGTTTAATGTTGCTATACATCT Y 2 1 2 1 101000 f 74 goat snp57966-scaffold94-39331 6 65348867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449901 Affx-122922335 AX-123320236 6 62991870 TTTTTGGCCACATCCATTTTTATGTCCTTGTTTCA[A/G]TAACTGGCAAATTTTGAAATAGGTATCTAAGAAGA R 2 1 2 1 101000 r 74 goat snp57967-scaffold94-93805 6 65404262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413041 Affx-122950988 AX-123283390 6 63023019 AACCCTAGATCAGAAATCTTGATATGATTTCAAAG[C/T]GTCCATCGTTTAAGCTCTAACCCTAATACTTATCA Y 2 1 2 1 101000 r 74 goat snp57968-scaffold94-124954 6 65443071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278547 Affx-1111836393 AX-519552029 6 63038504 CATATCTGCCAATGGTTACTTTGCAGAAATATTTA[A/G]ATTACATAAATTAAAGTGCCTGGTATATAATAAAT R 2 1 2 1 201000 r 74 goat Random2.2K-691 6 63038504 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435875 Affx-122932792 AX-123306214 6 63081852 TCAGCCCTCCAAGGGATTTCAATTTGCTAACATCC[A/G]CTGGATCATCAAAAAAGCAACTATCTACTTCTGCT R 2 1 2 1 103000 f 74 goat snp57969-scaffold94-183787 6 65503377 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776622 Affx-122937901 AX-385263749 6 63152755 CATAGGCAAAATTTGGTGAAAAGGAAAAAGGGAGC[G/T]ATTCTTTGCAGAGAACACAGTATACACAGTCACTA K 2 1 2 1 101000 f 74 goat snp57970-scaffold94-254690 6 65573768 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420088 Affx-122945105 AX-123290436 6 63189415 TCTGACAACACCCAGTCCAGTTGGAGTTGGACTGA[A/C]GGAAAAGAGCTCAGAAGGGTCAGATGCAAAGCTAA M 2 1 2 1 202000 r 74 goat snp57971-scaffold94-291350 6 65612806 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414731 Affx-122949258 AX-123285080 6 63227939 GGTCAATTGTTGGTTTCATTTTCCACACCTCACCT[C/T]TCCTGGGACCCTCCCTGACAAGCGTACACACCATT Y 2 1 2 1 101000 f 74 goat snp57972-scaffold94-329874 6 65652075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397401 Affx-122962258 AX-123267756 6 63265842 CCTAGTATAATAGCCCTTTATTCATAATCTGAATA[C/T]GAGAATAAGCAACCTATATACTAAAGCATTGGTAA Y 2 1 2 1 101000 r 74 goat snp57973-scaffold94-367777 6 65690075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449011 Affx-122923095 AX-123319346 6 63295688 GCTGCAGAATATTTCTTTCAATAAATAATTGAATA[C/T]ATATGATTCCATTTTCTATCAAGGTGTATAGGCAA Y 2 1 2 1 103000 r 74 goat snp57974-scaffold94-397623 6 65720216 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424301 Affx-122941971 AX-123294647 6 63349990 GAAGTAGGGTTTTAGAGATAGGATTCATCAGCTCC[A/G]TAATTTCTTTGTGAAAGTATATTACCTCCCACAGA R 2 1 2 1 101000 f 74 goat snp57975-scaffold94-451925 6 65775410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800995 Affx-122967341 AX-385287909 6 63402028 AGGAACTGAAGTCACGGCCCTTGTTCTTAAAAATC[A/G]TATAAGGGTCCCAAATCAAAGTAAGAACAATGAAT R 2 1 2 1 101000 f 74 goat snp57976-scaffold94-503963 6 65827615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411530 Affx-122951662 AX-123281880 6 63456147 CCACTTTGGGGTTACATTAGTTTACATTAACTTAG[C/T]AATACTAACAAAACTGAAAATGGGCATTCCTTAAA Y 2 1 2 1 101000 f 74 goat snp57977-scaffold94-558082 6 65880435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443345 Affx-122927430 AX-123313682 6 63502180 TTTGAACACTTTACTTCAATACTCTCATTACTGAG[C/T]ACTGATATCTATGCCTTTTTTTCTAATAAGTGACT Y 2 1 2 1 101000 r 74 goat snp57978-scaffold94-604115 6 65927141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408742 Affx-122953405 AX-123279093 6 63538337 AGCATCAAATTATGAAGAAAAGGTAAAAGGTATTT[A/C]GGTCAAACCCTCACTCTGTGGCATTTGACATCATG M 2 1 2 1 201000 f 74 goat snp57979-scaffold94-640272 6 65963323 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412412 Affx-122951436 AX-123282761 6 63611702 AAACTCAGCATCTACAAAACACAATGACATGAAGC[A/G]CACACACACAAAGAAAACTAAGGTATATCTGTACC R 2 1 2 1 101000 f 74 goat snp57980-scaffold94-713637 6 66036890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387873 Affx-122969633 AX-123258231 6 63659235 CCAAGGAGGCATCTACATCATCTTTCTAAACCATC[A/G]AAGTTGCTTAGATATGAGTTCTCCACAATATCTCT R 2 1 2 1 101000 r 74 goat snp57981-scaffold94-761170 6 66083493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398465 Affx-122961588 AX-123268820 6 63695650 CAATTAATTAGCACACGTTAAGTATATCACACAGT[A/G]CCTGACACAATGTAAAAGTCTGAGGAATTTTAGTC R 2 1 2 1 101000 f 74 goat snp57982-scaffold94-797585 6 66115772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410522 Affx-122952171 AX-123280872 6 63726709 TGTCTTAGAAGTGGTTGAAGCAAAAGACAAGCTGC[C/T]TGACTAAGGTTTTAAAGAGTCAAGTGTGAGTTCTG Y 2 1 2 1 101000 f 74 goat snp57983-scaffold94-828644 6 66146654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792864 Affx-122929509 AX-385279842 6 63759347 TGAAAAATGAAGACAGTTTTACCAGAGTTTAAAGA[C/T]GTCAGGTATAAATGACTTAATAAAAGGCTTACCAC Y 2 1 2 1 101000 r 74 goat snp57984-scaffold94-861282 6 66181148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401646 Affx-122959585 AX-123271999 6 63793467 AAGAATTGCCCTCCACTTCAGAATTCTCTAAACGG[A/G]AGCAGGCATCAACCCCTGGAAGGGGGAAGCATGCC R 2 1 2 1 103000 f 74 goat snp57985-scaffold94-895402 6 66214156 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781496 Affx-122958863 AX-385268581 6 63825837 TATCACACGCTTCGAAATAAATTTTTAGAGAAACC[A/G]TGTGAGATACTTTGCTCCACTTTCTCCTTTTGTTA R 2 1 2 1 201000 r 74 goat snp57986-scaffold94-927772 6 66247096 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786664 Affx-122928193 AX-385273696 6 63866821 AAGAACACTTTTCACAACTTCTCACAAATGATTTG[A/G]CTTTATTAAAAGTTTCTGGGGGAAAACAGTGCAAA R 2 1 2 1 102000 r 74 goat snp57987-scaffold94-968756 6 66288209 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401997 Affx-122958766 AX-123272350 6 63962235 ACAATCTGCTTCTCCTCTAAAAGCATGGAGAAGCA[G/T]CAAATTATTCTTCCATTCATTTCTTCCATGGAACC K 2 1 2 1 101000 r 74 goat snp57989-scaffold94-1064170 6 66376585 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778761 Affx-122971780 AX-385265872 6 64004559 AGCAAGTAATTCATACCTAACAAACTGAATTTATG[C/T]ACCAACCCATGAATTCTAGCCCTAAATTTGTCTTC Y 2 1 2 1 101000 r 74 goat snp57990-scaffold94-1106494 6 66419574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445672 Affx-122926139 AX-123316009 6 64035395 TCTCAATGCATACAAGGATAAGTCATAAACAAAAT[A/C]TTTTATTTTAAATATTTTGTGTGGGAAATCTTATA M 2 1 2 1 103000 f 74 goat snp57991-scaffold94-1137330 6 66450372 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396650 Affx-122962860 AX-123267005 6 64068425 TAAACTAAAAAGACTAAACTGGCAATAAAATACAA[C/T]ATCTGATCCTTGATTCAATTCTGAACTGTTCAAAA Y 2 1 2 1 101000 f 74 goat snp57992-scaffold94-1170360 6 66483982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278382 Affx-1111836394 AX-519551867 6 64081724 AACTCAAAGGATTATTCTTGGTAGGGTTTTAAGTC[A/G]TTCCTTTCAAATATTTCAAATGTTTGACAGAACAG R 2 1 2 1 101000 f 74 goat Random2.2K-692 6 64081724 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396032 Affx-122963471 AX-123266387 6 64097851 TGAATGTTATCAAGATATGGAATTCAGTCATTTTA[C/T]AAGAATGAAAATAAAACATTTACATAAGACTTTAC Y 2 1 2 1 201000 f 74 goat snp57993-scaffold94-1199786 6 66513997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795048 Affx-122941911 AX-385282007 6 64154072 TTTCACCTGGAGATTTCTTATTCAATGGTTGAAAG[C/T]GAAGGTGGAGTGCTTGGAAAGCCATCTTAACTCCT Y 2 1 2 1 101000 r 74 goat snp57994-scaffold94-1256007 6 66570681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434141 Affx-122934912 AX-123304482 6 64213476 TGTGTCTGTAAGCATAAATAAATTAAAAAGAAGAC[G/T]AAAGGTTTAGCAAGATATTAAAAATAATGGGCACT K 2 1 2 1 201000 f 74 goat snp57995-scaffold94-1315411 6 66629991 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278551 Affx-1111836395 AX-519552033 6 64290890 CACCCTGGTAGTAAAAAGCACAGATCTTTGTTTCT[A/G]ACACCATTCTCCTATGAGAGAAACTAGTAATAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-694 6 64290890 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382166 Affx-122974030 AX-123252524 6 64320710 AAACCAACTTGGTGCCAGCTTGACCAGTATTAAAA[C/T]GAGAGAGATTGAGAAAGAGAAAGAGAACAGAGTAG Y 2 1 2 1 101000 f 74 goat snp57997-scaffold94-1422645 6 66737838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431467 Affx-122936269 AX-123301808 6 64369900 ACTGGGGAGAACGTAGTGGGGAGGAGCAGCTGTGC[C/T]TGTGTGGCTGTTGGCCTTTGTCTTTTCTCATAGGT Y 2 1 2 1 101000 r 74 goat snp57998-scaffold94-1471835 6 66787294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403330 Affx-122957819 AX-123273683 6 64408843 CATTCACATTTCTTTGGTCCAAGCAAGACACAGCC[A/G]TGCTTAATTTCAAGGTAGTGGGGAAATGCAGTTCT R 2 1 2 1 101000 f 74 goat snp57999-scaffold94-1510778 6 66826462 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424614 Affx-122942192 AX-123294960 6 64491727 GTATGGTTGTAGGGCAAATTCAAGCAGAGTTCCAA[C/T]GTAATTGGTTCACACTGACCTAACAATAACAACAA Y 2 1 2 1 101000 f 74 goat snp58001-scaffold94-1593662 6 66909519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413541 Affx-122950610 AX-123283890 6 64625727 CTTCTGAAATGTATATCCTAGAGGCCTTTGTCTAG[C/T]GCATATCTATGAACATATAACCACAGAAGGAACTA Y 2 1 2 1 101000 r 74 goat snp58004-scaffold94-1727662 6 67042652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782222 Affx-122941824 AX-385269300 6 64661550 CACATTATCTCTTACAAGGGCCCTTAGTAAAACCC[A/G]ATATAATTGTACTGGTGGCAAACTGGCAATAGAAA R 2 1 2 1 201000 r 74 goat snp58005-scaffold94-1763485 6 67078272 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427113 Affx-122939664 AX-123297456 6 64716700 CAGCTTAGCCCAGTAATCACATTTGTCTACCCAGA[C/T]AGCTAGTCTAATCTCTCAAGCTCCAGGAACCTGGC Y 2 1 2 1 101000 f 74 goat snp58006-scaffold94-1818635 6 67135632 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383571 Affx-122972596 AX-123253929 6 64780940 TCAGAATCAGCAAAGCCAGGTGCTTTTTCAAATCA[G/T]CATCTTCCATACTACAAACCCAACATGGCCTGGTC K 2 1 2 1 101000 r 74 goat snp58007-scaffold94-1882875 6 67199278 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400173 Affx-122960677 AX-123270528 6 64810238 GGAAAGGAAATCAATCCTTAAAGACCTAATGCATG[C/T]GGGGGTGGTGTTTCCCCATCACATCCTCATTTAAT Y 2 1 2 1 101000 f 74 goat snp58008-scaffold94-1912173 6 67228672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407503 Affx-122954746 AX-123277854 6 64852528 TCATACATTTATTCATTCACTCAGCTCGTCAACAG[A/G]TATTTATTGGTGCCAACAATATGCCAGACTCTATG R 2 1 2 1 102000 r 74 goat snp58009-scaffold94-1954463 6 67271501 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801622 Affx-122958384 AX-385288530 6 64885120 AGGCCCCACCTCAGACCTATTGAATCAGAACCTGC[A/G]TTTTAACAAAGGCCGCAGGTGATTGTACATGCATT R 2 1 2 1 303000 f 74 goat snp58010-scaffold94-1987055 6 67304117 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384452 Affx-122973095 AX-123254810 6 64968894 GGAAAAAAAAAAAAATTCAATGACACTGTCACAGA[C/T]AGCTGGTTCGGCAGGCTTCATTCAGCACCACTGTG Y 2 1 2 1 201000 r 74 goat snp58012-scaffold94-2070829 6 67387931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408546 Affx-122953684 AX-123278897 6 65020904 GCTCTGCAACCCTGGGTGAGGAACTCAACCTCCTT[A/G]TCCTTCAGTTTCCTCATCTGTAAAATGGAAATGAT R 2 1 2 1 303000 f 74 goat snp58013-scaffold94-2122839 6 67440911 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796563 Affx-122965315 AX-385283509 6 65060425 GATTGTGAATTACCAAACAAGAGGACGGTAAGGAA[C/T]ATAGTAATTAAGAAACCCTAGTTGTCAGGGTAGAG Y 2 1 2 1 101000 f 74 goat snp58014-scaffold94-2162360 6 67480466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382209 Affx-122973998 AX-123252567 6 65111552 TATGACTTCTTTGAGAGAGGGACTCCCTTCTTACC[A/G]TATATCCACATGGCTTCATAAAATTCATATATTTA R 2 1 2 1 201000 r 74 goat snp58015-scaffold94-2213487 6 67530818 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410552 Affx-122952148 AX-123280902 6 65156571 CACACGGGCTTTCTCTAGTTTTGGTGAGGGAGGAA[C/T]AATCTTCATTGAGGTGCCTGAGCTTCCCATTGCAG Y 2 1 2 1 101000 r 74 goat snp58016-scaffold94-2258506 6 67576147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768248 Affx-122939800 AX-385255429 6 65200898 GTCTAATCCATTTAACATTAGGATTTTGACCATTT[A/G]TTTTTCCTCTGCTGATTAGATCACAGTACACTTGC R 2 1 2 1 101000 r 74 goat snp58017-scaffold94-2302833 6 67620539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803172 Affx-122969389 AX-385290035 6 65259550 AGATTTCTGTTTACTTGCTTTGGGACAGTTATTTC[A/G]CAGGCCTCCTTTGGCATTCTTCTTGATTTTTCACT R 2 1 2 1 101000 r 74 goat snp58018-scaffold94-2361485 6 67679002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403682 Affx-122958054 AX-123274034 6 65308475 CAAACCCAAGCAGAGGATGCTGTCTACGTGGCAAC[A/G]TGTACACACTGGGGACAGTTTATTAATGGAAACAC R 2 1 2 1 101000 f 74 goat snp58019-scaffold94-2410410 6 67728132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425307 Affx-122940948 AX-123295653 6 65368690 TAAGGAGCCACAGTGATTGTACAGCATATTAAAAA[C/T]ACCAGTCTATGACTATAAAAATACATTGAATGCAT Y 2 1 2 1 101000 f 74 goat snp58020-scaffold94-2470625 6 67788573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775982 Affx-122965885 AX-385263113 6 65399463 TGTATCATTTTTATTCCTATGAATCTATAGAATAA[C/T]GCCTTTTTAATACCCCAGAATTATAGCCAAAAGCA Y 2 1 2 1 101000 r 74 goat snp58021-scaffold94-2501398 6 67819418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781911 Affx-122968275 AX-385268992 6 65442263 GAACACAGTGTATGCTATTTATTTTAAACAATGAC[A/G]TGTTTACTCTGTTTCACGATCCAACATTGCGTATT R 2 1 2 1 201000 f 74 goat snp58022-scaffold94-2544198 6 67862134 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436674 Affx-122932463 AX-123307012 6 65542763 TCTTTTCAAGTCCTGTGATTACATTAGGTCCACCT[G/T]TTTCTAAAACCCTCACAACTCCATTTGTGCATGCT K 2 1 2 1 201000 r 74 goat snp58024-scaffold94-2644698 6 67962508 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791359 Affx-122948237 AX-385278352 6 65572523 GTCCCATCAAGCACAGCCTTGCAAACAGTTCAAAG[C/T]AGAATTTTATTATACTCATTTGTTGAGAGTCCTTT Y 2 1 2 1 101000 f 74 goat snp58025-scaffold94-2674458 6 67992875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273218 Affx-1111833513 AX-185498070 6 65673512 GGCTTAAAGCTCAACATTCAGAAAACGAAGATCAT[A/G]GCATCTGGTCCCATCACTTCATGGGAAATAGATGG R 2 1 2 1 303000 f 74 goat 6_65673512_AF-PAKI 6 65673512 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386877 Affx-122970057 AX-123257235 6 65683835 AAGGACTCTATTGTGGAATTGCTTTGGAAAATTCT[A/G]CAGACCAATTGCACTGCCCAGCCCCTTGGAGACTC R 2 1 2 1 201000 f 74 goat snp58027-scaffold94-2785770 6 68104101 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796133 Affx-122932881 AX-385283084 6 65716444 TGAGCCCACAAAGCTTTAGCCTAAAACTTTGTATG[C/T]ATTTTACAGCACTGTCTGTAGCTTACCCCTATTTG Y 2 1 2 1 101000 f 74 goat snp58028-scaffold94-2818379 6 68136961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384553 Affx-122973015 AX-123254911 6 65749403 GGGACTTCAGATACTTCCTAAGAAGATGAAACAAC[A/G]TTGTTTTTCGCAGAGTCTGAAGGGATTCTTACACA R 2 1 2 1 101000 f 74 goat snp58029-scaffold94-2851338 6 68170435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765178 Affx-122973043 AX-385252729 6 65800812 GTTTCTGGGGAAATCTATAGCCCTAGCTCCTCTTC[A/G]CATCCAGCTTACTGGGTAGAGAAGGTATACAGATT R 2 1 2 1 101000 f 74 goat snp58030-scaffold94-2902747 6 68222016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407579 Affx-122954665 AX-123277930 6 65833543 ACACATAAATGCTTGCTGTATGTTAGAAATGGGCC[A/G]TGTATTTTGGCTCTCAGCTTCCTAGTGGCCAAAAT R 2 1 2 1 101000 f 74 goat snp58031-scaffold94-2935478 6 68254822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781782 Affx-122957749 AX-385268864 6 65865489 CATAGTGTAAACACTTACATAGTATTAGAATTTAT[A/C]TGTTTTTCATGTTTACATCTTGAAAGCATGACTCT M 2 1 2 1 101000 r 74 goat snp58032-scaffold94-2967424 6 68286770 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392427 Affx-122966193 AX-123262784 6 65903443 TTTTTAAGGGGAAGAAGAGCCAGAAGTAATAAGAT[A/G]TTTTTTCATAAAAATCTCCCTAAGTTACATAAGTT R 2 1 2 1 101000 f 74 goat snp58033-scaffold94-3005378 6 68324908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398119 Affx-122922353 AX-123268474 6 65934485 GGAGGGATGGTCAGCAGTTGGCCAACAGGAAAATC[A/G]TGGAAGAGCCAGGTAAGCTGTGGTAAGGATGTGGG R 2 1 2 1 201000 f 74 goat snp58034-scaffold94-3036420 6 68356453 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452787 Affx-122920240 AX-123323120 6 65967118 GTCTACTATCTGCAGAGCACTTACTATAACTGTTT[A/G]TGCTGAGAGATGATGACTTAATTGAAACGGCTTCA R 2 1 2 1 201000 f 74 goat snp58035-scaffold94-3069053 6 68389462 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769861 Affx-122954482 AX-385257030 6 66001059 ACACTTTACTTATCACTCCAGTTGGCTAAAGTTAG[C/T]ATTATCCTAGACCAGCAGTTTTCAAAGTATGGGCT Y 2 1 2 1 101000 r 74 goat snp58036-scaffold94-3102994 6 68423518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436510 Affx-122932949 AX-123306848 6 66095987 TGAAGACTCAGAAGTTAGAAATGGATATCCAACTG[C/T]AAATCATTCTATTGGCCCTTGGTAAGGTTATAACC Y 2 1 2 1 101000 r 74 goat snp58038-scaffold94-3197922 6 68515529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394483 Affx-122964563 AX-123264838 6 66199879 CTTAAAGACCTCCCTGGCTGCTGTGTGGAGAATAC[A/G]TGAGAGGTAAAGACATCAGGGTAACCAGTCGGAGG R 2 1 2 1 201000 r 74 goat snp58041-scaffold94-3301814 6 68616641 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393502 Affx-122965813 AX-123263858 6 66235138 TGCTCTGCATTTTCTTTCTTTTTCTGTTAACCTTT[A/G]TGTGGATAATCCACAGAGACACAACTTAATATTTA R 2 1 2 1 202000 r 74 goat snp58042-scaffold94-3337073 6 68651909 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442708 Affx-122927868 AX-123313045 6 66300361 GTCTCCAAATTTTTTTTTTCCAGTTTCTTGCGCCA[C/T]ATCTCAGGACTGGGGTGTGAAGATGAGGTTATTGG Y 2 1 2 1 101000 f 74 goat snp58044-scaffold94-3402296 6 68717757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402103 Affx-122958689 AX-123272456 6 66351834 TGCCACGACCATGAGCCCGAAAGCTCTAGAACCCA[C/T]GTGCTGCAACAAGAGAGGCCAGCGCAGTGAGAAGC Y 2 1 2 1 103000 f 74 goat snp58045-scaffold94-3453769 6 68769734 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391563 Affx-122966625 AX-123261920 6 66385058 TGCTATTCTTCAGGTTGTCTACCTTTCCTCAGATC[A/G]TATTAACCTAGTTTGTTCCTAGGGGATTTAAAGAT R 2 1 2 1 101000 f 74 goat snp58046-scaffold94-3486993 6 68802867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400691 Affx-122959940 AX-123271046 6 66489189 TAGGGTATTCTCGCGCGAAAAATTTGAAAAACCGG[A/C]GCTTCGGGGTTGGGAGACGTCTAATTGGTTACCTT M 2 1 2 1 102000 f 74 goat snp58049-scaffold94-3591124 6 68906739 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407968 Affx-122954341 AX-123278319 6 66517734 GAGCAGTATCATTTATAATACTATTGCTAGTTGTG[C/T]TGAATTGTCTTATAAATCACATGAAGTAAGTGGCT Y 2 1 2 1 101000 r 74 goat snp58050-scaffold94-3619669 6 68935210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430873 Affx-122937411 AX-123301214 6 66549834 GAAACTACGTACGGAGCTACCAAAGTATGCTAACA[A/G]CATGACGGACTCCAGAGGCTTATCTGGTTCTGTAA R 2 1 2 1 101000 f 74 goat snp58051-scaffold94-3651769 6 68967104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423770 Affx-122942839 AX-123294116 6 66582754 ATGTGTCTATACTCACTGTCTCCAAGCCTCCTCTC[A/G]TTTTTCCTCAGCCTACTTGCATCAGGCTTTTTGTT R 2 1 2 1 201000 r 74 goat snp58052-scaffold94-3684689 6 68998343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777391 Affx-122974125 AX-385264513 6 66622844 AGGGAAAGAGATAGTTTCTAGAGGCAACCTGAGGT[A/G]TCTGCCACTATCTGCATGGTGGAAGAAATGTAGGC R 2 1 2 1 101000 f 74 goat snp58053-scaffold94-3724779 6 69045830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417261 Affx-122947263 AX-123287609 6 66659560 CAGTCCCCTCCCTTCCGCTTCTTGGGATCCCCTCC[C/T]ATGTAAAGTCTGCTTGCGGCCTCCTGTTTCAGGCT Y 2 1 2 1 101000 r 74 goat snp58054-scaffold94-3761495 6 69082559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420513 Affx-122944844 AX-123290860 6 66695600 CAAAGGGGGCCTTATATGGAGACCGTTCTCGGAAA[C/T]GGTTCTATTTCTTTTTGAAACTTATAATAGATGGA Y 2 1 2 1 101000 f 74 goat snp58055-scaffold94-3797535 6 69118877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446135 Affx-122925771 AX-123316471 6 66724861 AATAAAACCGAGGGGACAGAATTCCTTATCGACAG[A/G]AAGTTATGCTTCCACTAGGACATGGCTTTCTCACA R 2 1 2 1 101000 r 74 goat snp58056-scaffold94-3826796 6 69148066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800927 Affx-122930179 AX-385287842 6 66755919 CCCTGCTGTAATTTGAGGCTTTTAGGCTTCTCATA[G/T]GGTATAAACATCCCTCTATTAATTGAAAACAGTGC K 2 1 2 1 101000 f 74 goat snp58057-scaffold94-3857854 6 69178964 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777493 Affx-122929188 AX-385264612 6 66787974 AATTCTCTGTCAGCAGGAAAACTCCACCGGGCTTA[C/T]GATGTGCAGTTTTCACGCTTGGAGTTTCCTTTATT Y 2 1 2 1 101000 f 74 goat snp58058-scaffold94-3889909 6 69211220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403298 Affx-122957844 AX-123273651 6 66817302 GACCCAAACATGAACACAATGGTCCTTGGCTTTCA[C/T]GACTCCTCACTCCTTAAGGAATAAGGTGACTCTGT Y 2 1 2 1 101000 r 74 goat snp58059-scaffold94-3919237 6 69241329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276050 Affx-1111835139 AX-519549604 6 66848642 CAGTGCCTTTTAAGCTGCAAGAGGGAGAAGTACGC[A/G]TTATTTCTCTGGAGCAGTGTCAGTCCTACTTTGAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656019149 6 66848642 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276124 Affx-1111835252 AX-519549674 6 66850943 AATAACCTAGACCACCCATCAACATTCATGCAGAT[A/G]CGCCTTGTGAAGACCATCATCCTGCATCCTCGCTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs668167322 6 66850943 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38427819 Affx-122939747 AX-123298162 6 66853002 CTCAGGTTTCATTTTATGTTTATATTTTTAAGAAG[C/T]ATTGCCATTTGTAATAACCAGGTTCTCTCTGTGTT Y 2 1 2 1 101000 r 74 goat snp58060-scaffold94-3954937 6 69276901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275668 Affx-1111835025 AX-519549237 6 66864627 AGGCAGAGCAAAAGAAAAGGTGCAGCTTACCCCTC[A/G]AAGCAGTGGGCGACCGTCAGAACCCATTTCTTGGC R 2 1 2 1 102000 f 74 goat ilmnseq_rs642326566 6 66864627 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276083 Affx-1111835233 AX-519549635 6 66864837 AAGGAGCAGGACAGAGGACAGACAGATGTGACTCA[C/G]CGCCAAACCCAACTGGGTGCCTGCATCTTCGCTGT S 4 1 2 1 102000 f 74 goat ilmnseq_rs666783461 6 66864837 C G 1 neutral Goat_IGGC_65K_v2 Illumina 468276140 Affx-1111835260 AX-519549690 6 66864838 GACAGCGAAGATGCAGGCACCCAGTTGGGTTTGGC[A/G]GTGAGTCACATCTGTCTGTCCTCTGTCCTGCTCCT R 2 1 2 1 102000 f 74 goat ilmnseq_rs668594959 6 66864838 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275949 Affx-1111835167 AX-519549507 6 66867979 GGAACAGGAGCAAGACCAACAGTGGCTTACATTAC[A/G]CTCCAACTGGGAGAGCCTTAATGCAACAACTTTGC R 2 1 2 1 201000 f 74 goat ilmnseq_rs658741356 6 66867979 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275990 Affx-1111835189 AX-519549546 6 66891894 GCCCTCTGAGAAATTCATCAGGGCTACAAACTACT[A/G]ACCTTACCCTAAACCCATCTGCTTGCAGGCCAGCT R 2 1 2 1 101000 f 74 goat ilmnseq_rs661850269 6 66891894 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275729 Affx-1111835056 AX-519549296 6 66891976 TCCTGCCAGCCATCCGCACACACGTGGTGTTCCAC[C/G]GCAGATCTGTGAGCCATCAGGAATGAGGAGGAGTT S 4 1 2 1 202000 f 74 goat ilmnseq_rs645776058 6 66891976 G C 2 neutral Goat_IGGC_65K_v2 Illumina 468275895 Affx-1111835138 AX-519549453 6 66891983 AAACGTGAACTCCTCCTCATTCCTGATGGCTCACA[A/G]ATCTGCCGTGGAACACCACGTGTGTGCGGATGGCT R 2 1 2 1 102000 f 74 goat ilmnseq_rs656001291 6 66891983 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276340 Affx-1111835288 AX-519549873 6 66892020 CCCCTCCTTTTTTTCCCCACTCAGTGACCCTCTCT[A/G]CAAACGTGAACTCCTCCTCATTCCTGATGGCTCAC R 2 1 2 1 201000 r 74 goat ilmnseq_rs672467829 6 66892020 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275867 Affx-1111835050 AX-519549428 6 66893157 TGAGCTAGAATGTGCAAACCACGAGTGTGTGCCAC[A/G]TGACCGGTGGTGTGACGGTGAAGCCGACTGTATAG R 2 1 2 1 202000 r 74 goat ilmnseq_rs645120099 6 66893157 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276147 Affx-1111835263 AX-519549697 6 66893161 CTGATGAGCTAGAATGTGCAAACCACGAGTGTGTG[A/C]CACGTGACCGGTGGTGTGACGGTGAAGCCGACTGT M 2 1 2 1 101000 f 74 goat ilmnseq_rs669194710 6 66893161 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275888 Affx-1111835134 AX-169484688 6 66894545 GTCATCTGTGATGGGTTTCCAGACTGCCCTGATAA[A/C]ATGGATGAAAAAAACTGCTGTAAGTACTTATTGGG M 2 1 2 1 101000 f 74 goat ilmnseq_rs655677263 6 66894545 T G 1 recommended Goat_IGGC_65K_v2 Illumina 468275746 Affx-1111834987 AX-519549312 6 66894611 ATGACTGTGTGCTTCAAACACTGTTTACTGGATGG[A/G]CATTCCCAAAGATCTCTCTCCTTACATCCTGGAGA R 2 1 2 1 101000 r 74 goat ilmnseq_rs636938375 6 66894611 A G 1 recommended Goat_IGGC_65K_v2 Illumina 38448573 Affx-122923411 AX-123318909 6 66903127 AGATCTGGTGTCTCACCCCCAAAGACTCAGCTGCA[C/T]ACTGCCCTCCAGTGCCTGGACTTGGCCCCTTGTTG Y 2 1 2 1 201000 r 74 goat snp58061-scaffold94-4005062 6 69326777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276087 Affx-1111835235 AX-519549639 6 66904929 AATGCTCACCTAGTCACTTCAAGTGCAGCTCAGGA[A/C]GGTGTGTTCTGGCTTCCAGAAGATGTGATGGCCAG M 2 1 2 1 101000 f 74 goat ilmnseq_rs666917056 6 66904929 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468276115 Affx-1111835248 AX-519549666 6 66909345 CTCATGTTCTTTGCTTGCACCATCTTGGTACCAAA[A/G]TGTGACGAGGATACACACCAGCGTATCCCACCTTG R 2 1 2 1 101000 f 74 goat ilmnseq_rs667768032 6 66909345 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276035 Affx-1111835130 AX-519549589 6 66909408 GCATCCATCAGCTGGGAGTCTTCTCTTTTCCCTGC[A/G]CTTGTTCAAACCAACTGTTACAAATACCTCATGTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs655252822 6 66909408 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275865 Affx-1111835122 AX-519549426 6 66909489 GTCCTGTGGCCAAGGTAATTCGGAAAATTTGTATG[A/G]TTGTAGGGCAAATTCAAGCAGAGTTCCAATGTAAT R 2 1 2 1 101000 f 74 goat ilmnseq_rs654723024 6 66909489 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275915 Affx-1111835073 AX-519549473 6 66909520 TATGGTTGTAGGGCAAATTCAAGCAGAGTTCCAAT[A/G]TAATTGGTTCACACTGACCTAACAATAACAACAAC R 2 1 2 1 201000 r 74 goat ilmnseq_rs647482533 6 66909520 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275906 Affx-1111835069 AX-519549464 6 66917415 ATTCATGTGGTGGTAACTCTCTTTGTGACCCCAGC[A/G]ACAGTGTGAATAATTGTAGTAAGTACAGCCTCTGA R 2 1 2 1 201000 r 74 goat ilmnseq_rs647207540 6 66917415 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275782 Affx-1111835007 AX-519549347 6 66923570 ACGGGGACCACGACTGCGTGGATAAGTCCGATGAA[A/G]TCAATTGCTGTGAGTGCCCTGAAGGTTTTCATCTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640229792 6 66923570 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276150 Affx-1111835193 AX-519549700 6 66923604 ACTTCATCGGACTTATCCACGCAGTCGTGGTCCCC[A/G]TCACACACCCATTCAATGGCAATGCAGCGCCCGTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs662161074 6 66923604 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275878 Affx-1111835129 AX-519549438 6 66923637 CCGTCACACACCCATTCAATGGCAATGCAGCGCCC[A/G]TCTCCACAGCGATGCTCCTCTACGGGGTTGCAATC R 2 1 2 1 202000 f 74 goat ilmnseq_rs655197517 6 66923637 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468276214 Affx-1111835224 AX-519549764 6 66923660 TTCCTGAGTGCTTGCTTCCTCCAGATTGCAACCCC[A/G]TAGAGGAGCATCGCTGTGGAGACGGGCGCTGCATT R 2 1 2 1 202000 r 74 goat ilmnseq_rs665735605 6 66923660 C T 2 neutral Goat_IGGC_65K_v2 Illumina 320768479 Affx-122962420 AX-385255659 6 66974514 GTCTTTCAGACCTCGAAGTCCAACCTTTTCCTAAA[C/T]AGCACTCCTTCCGTTTAGTCACTTCCCATTCTATG Y 2 1 2 1 101000 f 74 goat snp58062-scaffold94-4076449 6 69398775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275875 Affx-1111835054 AX-519549436 6 66992449 AGGATTTGCTTCTCACCACAGCAGGAAAACGAAAA[A/G]CAATGTAGGTGTCTGCATTTTGTTGCATTTTTTAA R 2 1 2 1 201000 r 74 goat ilmnseq_rs645564281 6 66992449 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275969 Affx-1111835178 AX-519549526 6 66992454 TCAGCAGGATTTGCTTCTCACCACAGCAGGAAAAC[A/G]AAAAGCAATGTAGGTGTCTGCATTTTGTTGCATTT R 2 1 2 1 101000 f 74 goat ilmnseq_rs660329608 6 66992454 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275846 Affx-1111835113 AX-272252796 6 66992496 TCAAGTGTTCACAGTTTAGAAACCAAAGTGAAAAC[A/G]GCAATGTCAGCAGGATTTGCTTCTCACCACAGCAG R 2 1 2 1 201000 f 74 goat ilmnseq_rs653783895 6 66992496 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275822 Affx-1111835027 AX-519549386 6 66992578 CAGGAGGCATTCACCATTCCCAGGACTGACTCACA[C/G]CCCTCTTTTGCAGACTCACAGAAGGATCTACAAGG S 4 1 2 1 102000 r 74 goat ilmnseq_rs642396302 6 66992578 G C 1 neutral Goat_IGGC_65K_v2 Illumina 38412492 Affx-122951377 AX-123282841 6 67013525 AAACACAGAAATAAAAACAAGTCAGGCAGGACAAC[A/G]GGACCGAGGAGCATGTTCCAAATGAAAGAACAAGA R 2 1 2 1 101000 r 74 goat snp58063-scaffold94-4115460 6 69437616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275839 Affx-1111835036 AX-519549402 6 67018683 CTGCAGCCTGGCCTTTCCCAAGTGCATCAGGGATG[A/G]TGCTGACAGGTATTTTGGAACCAAAAGCATTCAGT R 2 1 2 1 101000 r 74 goat ilmnseq_rs643218186 6 67018683 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275952 Affx-1111835169 AX-519549510 6 67018732 TCACGTACCTCCATCGCCTCGGTTGCTATCAACAT[A/G]TCATGCTTTTTGGCTGCAGCCTGGCCTTTCCCAAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs658807116 6 67018732 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276287 Affx-1111835261 AX-519549829 6 67018807 TGCCCTACTACACCACACTGACATCTCCCCTCTCC[A/G]TTGTCAAAAGCATGGAAATGGAGAAGTTCCTCAAA R 2 1 2 1 101000 r 74 goat ilmnseq_rs668716411 6 67018807 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275898 Affx-1111835065 AX-519549456 6 67018887 ACTGGCTGTGGGTGATGTTCATGCAGGCACCTGGG[A/G]AGGTAAGAAAATTACATTTAGGAGAAGACACATAA R 2 1 2 1 201000 r 74 goat ilmnseq_rs646887981 6 67018887 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468275987 Affx-1111835187 AX-519549543 6 67054675 GTGTCTGATGTTATTCTTAATACAATTCATAATGA[C/G]GAGAGCACTGTGACATCTGCTGCCCATCCCACCCA S 4 1 2 1 101000 f 74 goat ilmnseq_rs661663919 6 67054675 G C 1 recommended Goat_IGGC_65K_v2 Illumina 468276052 Affx-1111835140 AX-519549605 6 67070142 GCAGGACAATGAGAGCACAGATACATGGAATCAGG[A/G]CCAGCAAGAGGAAACGAAGAATATTCACAGTCGTC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656037355 6 67070142 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276307 Affx-1111835270 AX-169459686 6 67070170 ACATGGGTGATGGCTGCTCTCAGAAGCTGACGACT[A/G]TGAATATTCTTCGTTTCCTCTTGCTGGTCCTGATT R 2 1 2 1 101000 r 74 goat ilmnseq_rs669469752 6 67070170 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276049 Affx-1111835217 AX-519549603 6 67072103 ATTCTCTGTGGGAGACATTACTTGAATGAACATAC[A/G]ATGTTAGCTTGAGAATGGCTTGATTTCCTAGATTA R 2 1 2 1 201000 f 74 goat ilmnseq_rs664532560 6 67072103 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275991 Affx-1111835108 AX-519549547 6 67072123 GCATGGATCAGTAAAGGTGTTAATCTAGGAAATCA[A/C]GCCATTCTCAAGCTAACATCGTATGTTCATTCAAG M 2 1 2 1 102000 r 74 goat ilmnseq_rs652837066 6 67072123 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275963 Affx-1111835175 AX-519549521 6 67072134 ATACGATGTTAGCTTGAGAATGGCTTGATTTCCTA[A/G]ATTAACACCTTTACTGATCCATGCCTTTTGAACCT R 2 1 2 1 103000 f 74 goat ilmnseq_rs659659872 6 67072134 G A 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275834 Affx-1111835033 AX-519549397 6 67072148 TGAGAATGGCTTGATTTCCTAGATTAACACCTTTA[C/G]TGATCCATGCCTTTTGAACCTGGTTTAATCGACCC S 4 1 2 1 101000 r 74 goat ilmnseq_rs642934508 6 67072148 C G 1 recommended Goat_IGGC_65K_v2 Illumina 468276090 Affx-1111835161 AX-519549642 6 67072178 TATATTAAGTATGAGGGATCTCACATTGGTGGGTC[A/G]ATTAAACCAGGTTCAAAAGGCATGGATCAGTAAAG R 2 1 2 1 201000 r 74 goat ilmnseq_rs657769287 6 67072178 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276253 Affx-1111835244 AX-519549800 6 67072203 CCTCCAAAATGGTGCCAATTATTTGTATATTAAGT[A/C]TGAGGGATCTCACATTGGTGGGTCGATTAAACCAG M 2 1 2 1 102000 r 74 goat ilmnseq_rs667545042 6 67072203 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275802 Affx-1111835016 AX-519549366 6 67072209 TAATCGACCCACCAATGTGAGATCCCTCATACTTA[A/G]TATACAAATAATTGGCACCATTTTGGAGGAGGTCA R 2 1 2 1 201000 r 74 goat ilmnseq_rs641001499 6 67072209 A G 2 recommended Goat_IGGC_65K_v2 Illumina 320782259 Affx-122959535 AX-385269337 6 67072258 GAGAGATAGATGGTTTCTGGAGTTGAATCAGTGAT[C/T]TGAATATAGCAGAGTCAAGGTGTCTTGAGTTCTCT Y 2 1 2 1 101000 r 74 goat snp58064-scaffold94-4174193 6 69496944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276144 Affx-1111835262 AX-519549695 6 67072263 TCTGATTGCCTGAGTCCTGCTCATGGGTCAATGTG[A/G]TGGGTCACATCCTTTCCATGACCTCCTCCAAAATG R 2 1 2 1 202000 f 74 goat ilmnseq_rs668953752 6 67072263 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275779 Affx-1111835080 AX-519549344 6 67072558 AACTGCCACCCAGCAATCTGGAATGATCTACTGCC[A/G]GGAGCCAGCATGGGGAATCCCACCTGTGGCAAAGG R 2 1 2 1 102000 f 74 goat ilmnseq_rs648835223 6 67072558 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275959 Affx-1111835173 AX-519549517 6 67072583 TGCCTGTCAGGCCTCTTCCTCATGACCTTTGCCAC[A/G]GGTGGGATTCCCCATGCTGGCTCCCGGCAGTAGAT R 2 1 2 1 103000 f 74 goat ilmnseq_rs659491889 6 67072583 T C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276191 Affx-1111835286 AX-519549741 6 67072608 TTCCCTCGAGGCCTGATCTCACCTTTGCCTGTCAG[A/G]CCTCTTCCTCATGACCTTTGCCACAGGTGGGATTC R 2 1 2 1 103000 f 74 goat ilmnseq_rs672305404 6 67072608 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 38443318 Affx-122927451 AX-123313655 6 67141213 AGCAGCCTGCCTCTGAGATCACATGTGGCACACAG[A/G]CCATACACAGCCATGCAGGCAATAGGAGGCATCCG R 2 1 2 1 101000 f 74 goat snp58065-scaffold94-4243148 6 69566353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416273 Affx-122947951 AX-123286622 6 67198796 AAGACAGTCACAACACACTTTACAAATTTATTCCA[C/T]GCAGGACCCATGGGAGACTTTAACAGGACTTATTA Y 2 1 2 1 201000 f 74 goat snp58066-scaffold94-4300731 6 69624021 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432852 Affx-122935365 AX-123303193 6 67250236 AGCATAATGATACTAGTTAATGAGGAATCTGAAAA[C/T]ACCAGATGACTCATGTGTTAACGTGAGTATGCTGG Y 2 1 2 1 201000 f 74 goat snp58067-scaffold94-4352171 6 69675969 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417281 Affx-122947247 AX-123287629 6 67297634 GATTGTCAGGAAGGGGACGAAGCACTCGCTGAAAG[A/G]GGGTGGTGGCCTTGGTGGCTAAGCACCCAAAGAGC R 2 1 2 1 101000 f 74 goat snp58068-scaffold94-4399569 6 69723126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427053 Affx-122939815 AX-123297398 6 67333034 TGTAAGTCCATTTGTTTCCCCTCTGAGCTCTGTTT[A/G]TATGGATCACTTCCCTATCCAGTGGTTCTGCTTAA R 2 1 2 1 201000 r 74 goat snp58069-scaffold94-4434969 6 69758437 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791985 Affx-122966369 AX-385278973 6 67371713 AAGTAAAGGATAAGCATAGCTTATGCTGAGTGGAA[C/T]GTGGATGAGAATTCCTTCTTAGTCCAGAGATCCCG Y 2 1 2 1 101000 r 74 goat snp58070-scaffold94-4473648 6 69796564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384420 Affx-122972189 AX-123254778 6 67403838 CTCAGTGCTGGTCCTTTTCTCCCCGACCCAGCTGC[C/T]AAAACTTGGCAGATACTGCTAACCATGAGGATTTT Y 2 1 2 1 101000 r 74 goat snp58071-scaffold94-4505773 6 69826676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409627 Affx-122953539 AX-123279978 6 67492603 CAAGGAAAGGTAATAAGTAATCTGGATACTTTGCC[A/G]TATAATTTGATATTTTACTAAACATATTTCATTTG R 2 1 2 1 201000 r 74 goat snp58073-scaffold94-4594538 6 69916501 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426249 Affx-122940337 AX-123296595 6 67568572 TCCAGCTTTAACTCTCTCCTTCCTGACACACACTC[A/G]TCCAAAAAAATCGGCAGAAACCCTTGGTGGACAAA R 2 1 2 1 201000 r 74 goat snp58075-scaffold94-4670507 6 69993297 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383639 Affx-122972534 AX-123253997 6 67622550 CCCCAAGAGTTTGAACCTCAGACCTTTCAATCCCT[C/T]GGCTGAAGCTATAAACCACAAATGTGCTTCATGAT Y 2 1 2 1 101000 f 74 goat snp58076-scaffold94-4724485 6 70048414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275364 Affx-1111834856 AX-519548938 6 67741693 CTGCAGTGTCTCAAATGTCACAAAGCCTATTCTTC[A/G]CCACGTAACCCCTAATGCACAGCTGATTGGTTCTC R 2 1 2 1 201000 f 74 goat GoatD01.056687 6 67741693 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439957 Affx-122929985 AX-123310294 6 67753278 TAAGTTTAAAACTGTATGTGGGTTTTTTTTTAAGC[A/G]CATGTCATTTCCCTTTCTCTGTCTTTCAGAACCAG R 2 1 2 1 101000 r 74 goat snp58078-scaffold94-4855213 6 70179795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419512 Affx-122945448 AX-123289860 6 67825438 TCTACCCCTCCCCTCCAAAGATGTGGCGTGGAGCT[A/G]TTTCTGATTCAGAATGATTGCAGTGTTTCAGCCAG R 2 1 2 1 101000 r 74 goat snp58080-scaffold94-4927373 6 70253358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427639 Affx-122939337 AX-123297982 6 67868642 CTGTACACTTGCTATTACAACCACACGCAGATGGA[C/T]GAGAACGAGATCGAGGGCAGACATATTTACATCTA Y 2 1 2 1 201000 f 74 goat snp58081-scaffold94-4970577 6 70297210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447471 Affx-122924352 AX-123317807 6 67957639 AAAACTTTGGGCTCTGTCGTAATAGAAAACTCTTG[C/T]GGGTAGTTGACTGAACTTTCTGCCTGTTCCTAATT Y 2 1 2 1 101000 f 74 goat snp58083-scaffold94-5059574 6 70386549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445260 Affx-122925475 AX-123315597 6 67996322 GCCCTGTGTGATCTGAGGCAAGCTGTTTCACCTCA[A/G]TAAGCCTCAGTTTCCCCCTCCTTCAAGGCTATTGT R 2 1 2 1 201000 f 74 goat snp58084-scaffold94-5098257 6 70425574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436808 Affx-122932243 AX-123307146 6 68025618 AAATTTGAATGAGAGCAGCACTGGAGCTCAGGCAG[A/G]CACCCTTTTATTGAGGCATCTCAAAGAAGTGCTGA R 2 1 2 1 101000 r 74 goat snp58085-scaffold94-5127553 6 70454815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409956 Affx-122952855 AX-123280307 6 68066850 TTTTGCTTAGTTTTGTTGGTTTTGTCCTTTCATTT[A/G]TTTATCTTACAATATTTATTGAGTACCTCCTGTAT R 2 1 2 1 101000 r 74 goat snp58086-scaffold94-5168785 6 70496212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413920 Affx-122949819 AX-123284269 6 68096669 ACCAAAGAACTAGAGGGTTTCCTGTTTTTGGTTTT[C/T]AACATGGATTTTCAATTTTTGGAGAACGAGAAAAC Y 2 1 2 1 201000 r 74 goat snp58087-scaffold94-5198604 6 70525889 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397736 Affx-122962540 AX-123268091 6 68129743 CACGAGGATCCTTTCTGATTTGGTTCTTGGTCTTA[C/T]GCTGGCTTTAAGGCCAGGCTATCCTGCAGAATGAA Y 2 1 2 1 101000 f 74 goat snp58088-scaffold94-5231678 6 70559150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411854 Affx-122951220 AX-123282204 6 68162012 ACAGCAAAGTCCCCTAGACACTCTTGAACAGCCCC[A/G]CGAGATGGGGGCTGCTCAAGATTATGCCCCTTGCT R 2 1 2 1 303000 r 74 goat snp58089-scaffold94-5263947 6 70591611 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387739 Affx-122969741 AX-123258097 6 68196811 ATCTGTGTGCCTAGACCATAAAAGACCATAAAGTA[C/T]AACAATCATTTATTAAAATGCTAATTATTCAGGGG Y 2 1 2 1 101000 f 74 goat snp58090-scaffold94-5298746 6 70626559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421471 Affx-122943926 AX-123291818 6 68241922 TGTTAAAGGACTCAGTTTGCACAGAGAGCTATGCA[C/T]ACACAAACAATTTGATTCACCACCACCTCTGGGTT Y 2 1 2 1 101000 f 74 goat snp58091-scaffold94-5343857 6 70672374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273270 Affx-1111833514 AX-519546918 6 68304402 TCTTTGAAAACTAAAAAAAGATTAAAATTAGGCTA[A/C]CTTTAGAAGTCAGAAAAGGCTTCTTTAAGGAACTG M 2 1 2 1 101000 r 74 goat 6_68304402_AF-PAKI 6 68304402 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278552 Affx-1111836396 AX-519552034 6 68305243 TCAGAGACTGATGGTGGGGACGTGTCAGAACGACA[C/G]TGGAGGGACAGTTGTGCACCATAAAGAATGAGGAC S 4 1 2 1 102000 r 74 goat Random2.2K-696 6 68305243 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425590 Affx-122941412 AX-123295936 6 68327191 TGTAGAAAACTCCGGAGGAGCTAGTATTTTATTCA[C/T]GATGATTGTGACAGAAATCAGTGCAAGTAATATTG Y 2 1 2 1 101000 f 74 goat snp58093-scaffold94-5429126 6 70758177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382273 Affx-122973932 AX-123252631 6 68357949 CTTCATATTAAGGAAGTTTTCCAAAAGCTGTCATA[C/T]AATACTTAGTGGCCAAAACCAAGCCACATGGCTGT Y 2 1 2 1 101000 r 74 goat snp58094-scaffold94-5459884 6 70788868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438371 Affx-122931315 AX-123308709 6 68403067 AAAATAATCACCAGGCACTCTGATCCTACAAGGGT[A/G]TGTGCTCTGTCCATACACATGCCCCTGTGGGTTTC R 2 1 2 1 101000 f 74 goat snp58095-scaffold94-5505002 6 70834128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442630 Affx-122928461 AX-123312967 6 68443348 GTTGAGTTAGATTTTATGGTGCCTAGAATATAGTA[C/T]GGAGAAGGCAATGGCACCTCACTCCAGTACTCTTG Y 2 1 2 1 101000 f 74 goat snp58096-scaffold94-5545283 6 70874215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450917 Affx-122921783 AX-123321251 6 68495816 ATGCATAGTCTGAGGAAACCTTTGGGTCTTCTTTC[A/G]TTTTTTTTCAATTACATCAGAGTAGGGTGGAGGGG R 2 1 2 1 102000 r 74 goat snp58097-scaffold94-5597751 6 70927567 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444622 Affx-122926938 AX-123314959 6 68528130 CACTTCTGCCTGAAAAATACATTGCTAATGGATCA[C/T]AGCACAGTGCTCTGCAGAGTCAACGCTTCAGGACC Y 2 1 2 1 101000 f 74 goat snp58098-scaffold94-5630065 6 70959830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774289 Affx-122953111 AX-385261425 6 68557747 ACATATGTATCCTTGTTCTCCAGCCAGGGGTCATA[G/T]AGTCTCATTGTCTTTGTCATTCACAAGACACCCCT K 2 1 2 1 101000 f 74 goat snp58099-scaffold94-5659682 6 70990195 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799510 Affx-122942960 AX-385286440 6 68612251 GTGTTTCTAAATATTTCTTCAGAAAGCAAATTCAG[C/T]AATATTCCATCTCATGTCTTGTCTTCCCCCAGAGG Y 2 1 2 1 101000 f 74 goat snp58100-scaffold94-5714186 6 71044898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452526 Affx-122920547 AX-123322859 6 68666685 AGCAAACTGATCTCAGGAGGGCCAACCCTGCACCT[C/T]TTAGGGACTAACCCTTCATAGGGACGGCTGTACAA Y 2 1 2 1 101000 r 74 goat snp58101-scaffold94-5768620 6 71099110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436263 Affx-122932545 AX-123306602 6 68697752 AGGATAAAGGCCAAAGGTCAAATTATAATCTACAA[C/T]GGATAACTAAAAATACCAAAAATATATTTACTTCT Y 2 1 2 1 101000 f 74 goat snp58102-scaffold94-5799687 6 71130474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779836 Affx-122928253 AX-385266935 6 68731943 CAAACAATTCTTCTCTCTCAACTTTATTTACAATT[C/T]GTGACACTTCCTTTTCCACGTCTCACTTAAGAAGA Y 2 1 2 1 101000 r 74 goat snp58103-scaffold94-5833878 6 71164653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389687 Affx-122968701 AX-123260045 6 68784341 AAATCTTGTAATAGGGAGTAATATTATTAGCCTAA[A/G]TCCTGCTTTGGGGCCCAGAGTTATGGTTTAAAAAG R 2 1 2 1 201000 f 74 goat snp58104-scaffold94-5886276 6 71210057 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435682 Affx-122933329 AX-123306021 6 68898128 ACACGTAAAGGACATAAAGATCTTTCTGGTCACTC[C/T]CTAGTTCCACAAAGAAGCGCAGCAATGAAGCCAAG Y 2 1 2 1 201000 r 74 goat snp58106-scaffold94-6000063 6 71325965 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401755 Affx-122959505 AX-123272108 6 68938118 TCTTTTCCCGTTTCAGGAGTGGTCATTCACTGTAA[C/T]CACCGAATCCCTTTTGGAGACTGGTTTGAATACGT Y 2 1 2 1 101000 f 74 goat snp58107-scaffold94-6040053 6 71366099 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476219 Affx-1251763724 AX-586011643 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20000 f 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 539476473 Affx-1251763724 AX-586011873 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 4 1 4 1 20000 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562165381 Affx-1251763724 AX-606940792 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 f 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562166276 Affx-1251763724 AX-606941684 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562166475 Affx-1251763724 AX-606941883 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 38402786 Affx-122958298 AX-123273139 6 69033849 CTTTGAAAGTTTTGAAAATTGTAAGTTTCACCACA[C/T]GTGAACATGTAAAATATAACAGGACTAAGAAAGCT Y 2 1 2 1 101000 f 74 goat snp58109-scaffold94-6135784 6 71459875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412921 Affx-122950396 AX-123283270 6 69069888 TTTAAATCTAAAACAGACAGCAAAAACAAGAAACA[C/T]ATCCTAAATCAAAGTCTCACAATCCAGACCTCTTA Y 2 1 2 1 101000 r 74 goat snp58110-scaffold94-6171823 6 71495883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448931 Affx-122923156 AX-123319266 6 69117144 GTTTCTCTCTCTCTTTTTTTTTTTTTTACTTTATG[C/T]ATCTGCAAGGAACTGGAAAGAAATACAAACAATAG Y 2 1 2 1 101000 r 74 goat snp58111-scaffold94-6219079 6 71543593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394309 Affx-122964687 AX-123264664 6 69161017 TTGAATCACTTTAATACAATGTTACAATTTCTGCC[G/T]TAAACAATTATAATGTCTTTTAAGAAAATTAAGAA K 2 1 2 1 101000 f 74 goat snp58112-scaffold94-6262952 6 71587897 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783346 Affx-122939374 AX-385270410 6 69198397 ATACAATGTTGTAGCACAACTTTATGTAAACTTTA[C/T]GTTTATTTGTATGTAAATCACTAGTACTTGCTATA Y 2 1 2 1 201000 f 74 goat snp58113-scaffold94-6300332 6 71625921 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420161 Affx-122945581 AX-123290509 6 69241950 GAAGTCCACAGAAATGTGGCACCTCTGACTCCCAG[C/T]GCACATGAGAGGTCACATCGCTATGTCCACCCTCT Y 2 1 2 1 201000 r 74 goat snp58114-scaffold94-6343885 6 71669928 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426179 Affx-122940584 AX-123296525 6 69283954 ATTCTGTATCCAAAGAGAGCAGGGAATGTCTAGCA[C/T]GTAGGACATGGCAAATACCCAATAAAAGTTTGTAA Y 2 1 2 1 101000 r 74 goat snp58115-scaffold94-6385889 6 71712561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464457978 Affx-1110493026 AX-515930543 6 69317455 AGACTGGGACTTCTGTTATTCTTGAATGAGTCCCC[A/G]GTAACTTCATACAAAAGGTCCTCTGTAAAATGTAT R 2 1 2 1 201000 r 74 goat GoatD01.005815 6 69317455 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777139 Affx-122934098 AX-385264262 6 69326638 GCCAGATTTTTGGCTTTCTGGGAGACATAAATTTG[A/C]TGTTGACTTGCATTCCTTCTATCAAGACTTTTTAA M 2 1 2 1 101000 f 74 goat snp58116-scaffold94-6428573 6 71755407 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424913 Affx-122941300 AX-123295259 6 69369235 TCCAAGACCTACTTGTATGAGGATGGACAAAACCA[C/T]GACATTTTGCTGAAGCGAAAGGGCTTTGGGACGTG Y 2 1 2 1 101000 f 74 goat snp58117-scaffold94-6471170 6 71797566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386823 Affx-122970098 AX-123257181 6 69409654 CACTTTGAGAGGAATCCAGGAGAGGAAGTGAAAAA[C/T]GGCAATTCACTTCTCAACTCTGAAGAGGGCTGTAA Y 2 1 2 1 101000 f 74 goat snp58118-scaffold94-6511589 6 71838503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379597 Affx-122976024 AX-123249955 6 69450147 ATATCACATTTTCTTGTAAAAATAGAATCCTTTAA[C/T]TATTTGATATATGTAGGGTTTGTCCAGACATATTG Y 2 1 2 1 101000 r 74 goat snp58119-scaffold94-6552082 6 71879090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791268 Affx-122919915 AX-385278262 6 69508413 AAGAGTGATTTAGAAGGTGTAATCTCTAAAATTTA[A/G]TGATGGATAAATTTAGTAAACTTGGGATGTAGAGG R 2 1 2 1 201000 f 74 goat snp58120-scaffold94-6610348 6 71937412 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387506 Affx-122970329 AX-123257864 6 69538323 AGTACTGGCTGAATGATTTAGTAAATAAAAAAAGG[C/T]CTACAGCAGAGTGACTTTTTCAATGAAATATATAA Y 2 1 2 1 101000 r 74 goat snp58121-scaffold94-6640258 6 71967098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418263 Affx-122947017 AX-123288611 6 69568217 GGTGTTAACCGTGATTTGTGGCCCTCCGAAGGACC[A/G]CAGTACATTAACAGTGTATCTGTGTATTAAAATTT R 2 1 2 1 201000 r 74 goat snp58122-scaffold94-6670152 6 71996981 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391330 Affx-122967313 AX-123261687 6 69598991 TTAATTGAAATTAATATGAAATCCTCCAGGGTAGG[A/G]GACTTCCCTGGTGGTCCAGTGGTTAAGACTTGGTG R 2 1 2 1 103000 f 74 goat snp58123-scaffold94-6700926 6 72027672 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427351 Affx-122940109 AX-123297694 6 69723260 TGATGTGATTTGGGGTCCAAGACTGACTTTATCAC[A/G]TATGCCCACCAGATTCTTCCCATTTCCGGCAACTG R 2 1 2 1 201000 f 74 goat snp58126-scaffold94-6825195 6 72152395 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434465 Affx-122934639 AX-123304806 6 69763017 AGTTAGGAGAATAAACCTTTCATTCCTTGATGGTG[A/G]ACTGGATGGAATACCCACCACCACCTATACCATTA R 2 1 2 1 101000 f 74 goat snp58127-scaffold94-6864952 6 72192177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433185 Affx-122935648 AX-123303526 6 69860768 ATGTCTCTGCAATTTCACCATCCGCCATGTAAAGC[C/T]GAGGGGGAGTTGGGTGAAGGTGGATTTGATACTCT Y 2 1 2 1 101000 f 74 goat snp58129-scaffold94-6962703 6 72290258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451054 Affx-122921434 AX-123321388 6 69906314 GGTCACAAAGAGTTGACCACCACTCAGGAACTTAA[C/T]GACAAATGTTTATGACCTTTTATCTTATGGTGAGT Y 2 1 2 1 101000 f 74 goat snp58130-scaffold94-7008249 6 72335146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413163 Affx-122950347 AX-123283512 6 69937288 TACCATTTTCTTTTCTAAAAACACCTCAATAAAAC[A/C]AAAAACTATGGAAAACACAAAAGTCAAGTCAGAGA M 2 1 2 1 101000 f 74 goat snp58131-scaffold94-7039223 6 72366121 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375642 Affx-122978693 AX-123246001 6 70017021 TGTTTCTGCTTCCTTTTTGTCCTCATCTCCTATTG[C/T]TGCTTCCCCTTCACTCCACTCCAGCTTCACAAGCC Y 2 1 2 1 202000 r 74 goat snp58132-scaffold94-7118956 6 72446014 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447509 Affx-122924073 AX-123317845 6 70067940 GCTTGGATTTGATCATTCAAATTCATGCCTGTTTC[A/G]CTCACTTTCTCTTCTACAACTTGCAGGGTTCAATA R 2 1 2 1 101000 r 74 goat snp58133-scaffold94-7169875 6 72497088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375896 Affx-122978489 AX-123246255 6 70103888 AGCTATTCTGAAGGACCCTTGCACATCCCCAGTCC[A/G]TGTAAGACTGAGGACAATAACACTAGGCCCAGAAC R 2 1 2 1 101000 r 74 goat snp58134-scaffold94-7205823 6 72533307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278388 Affx-1111836397 AX-519551873 6 70135434 ACTGTCAAACACCACACATCTCGTAGCTAAAGGGT[A/G]CAAAGGTCCTCACTTCAAAATCTACGATCTTGTGG R 2 1 2 1 101000 f 74 goat Random2.2K-698 6 70135434 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438504 Affx-122931214 AX-123308842 6 70169162 GATCTAAGAAGTCCTTTGAAGTATGACAACCTCAA[C/T]GGCTTTAGTGCTTAGGCACCATCCAGGCCTCAAAA Y 2 1 2 1 101000 f 74 goat snp58135-scaffold94-7271097 6 72599015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770095 Affx-122961350 AX-385257262 6 70231525 GCTCTTCTCCAAATCAAGGAGCAAAACCTAACCCT[A/C]TTGTTTGCAATTTTGGGCCAAACATGTCTGATGGT M 2 1 2 1 101000 f 74 goat snp58137-scaffold94-7333460 6 72661900 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402047 Affx-122958730 AX-123272400 6 70265439 GCACAGAGTCTTAACCAAGTACCTGTCCTGAGCTC[A/G]TATCACACTGGCCATTGTGTTGTTACAGAGCTGGA R 2 1 2 1 101000 r 74 goat snp58138-scaffold94-7367374 6 72695645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275609 Affx-1111834994 AX-519549179 6 70300890 CGGCATGGGATGATGACTGAATCTTCGTCCTCCAC[A/G]ATGACCAAGGAATCTGTCATTCCTAGAGGTACGAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs638012483 6 70300890 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275841 Affx-1111835037 AX-519549404 6 70302479 AAACTTGATCTGGAAATGGAATCTCCTAAGACTGT[A/G]TATAAGGCAGGCGAATCGATTGTGGTCACCTGCAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs643256510 6 70302479 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275833 Affx-1111835107 AX-519549396 6 70305708 GTTAAAGTCAGTTTTCCTCCCCTTCTGCTGTAGAA[C/G]GGCAAAGGCATCACGAGGCTGGAGGAAACCAAGTT S 4 1 2 1 102000 f 74 goat ilmnseq_rs652546920 6 70305708 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468276146 Affx-1111835191 AX-519549696 6 70305714 GTCAGTTTTCCTCCCCTTCTGCTGTAGAAGGGCAA[A/G]GGCATCACGAGGCTGGAGGAAACCAAGTTCCCGTC R 2 1 2 1 202000 r 74 goat ilmnseq_rs662035189 6 70305714 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275580 Affx-1111834981 AX-519549150 6 70308752 TTATCTTTATCTGGCTCTTACAAACCTTGAGTCAA[A/G]AGTTCAAAAGTATAGCTCTTCACATCATCTTCATT R 2 1 2 1 101000 f 74 goat ilmnseq_rs636417098 6 70308752 C T 1 recommended Goat_IGGC_65K_v2 Illumina 464452875 Affx-1110493423 AX-515925478 6 70312019 GCAGTCCTGGTGTTGTTGGTGATTGTAATCATCTC[A/G]CTCATTGTCCTGGTCGTCATTTGGAAACAGGTAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs672064024 6 70312019 G A 1 recommended Goat_IGGC_65K_v2 Illumina 464452878 Affx-1110493424 AX-457120230 6 70312056 TCATTGTCCTGGTCGTCATTTGGAAACAGGTAGAT[A/G]TTTTTTTAAAGAACTAAAAATCCTTACTGATACGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs660380088 6 70312056 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275923 Affx-1111835077 AX-519549481 6 70312347 CATCTCGAGTCATAAGGCAGCTGCATCGGGTCCAC[A/G]TAAATGTATTCATGTCCATCAGGGCTGATTGATTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs647814964 6 70312347 T C 2 recommended Goat_IGGC_65K_v2 Illumina 320769512 Affx-122951241 AX-385256682 6 70314508 CCAGTCTTCCCTCCTCTTGGATGATATATTAGGAA[C/T]GACCTTAAGGTAACTGATCTCTAGACAGGAATTTC Y 2 1 2 1 101000 f 74 goat snp58139-scaffold94-7416443 6 72745375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276137 Affx-1111835258 AX-519549687 6 70314690 GGATTAAGTCGGTCTCAACCTGTCATGAAAGTAGC[A/C]GTGAAGATGCTAAAACGTGAGTGCTCCTTTTCTGG M 2 1 2 1 101000 f 74 goat ilmnseq_rs668543709 6 70314690 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468276193 Affx-1111835287 AX-519549743 6 70315120 CAGCCACAGCCAGATCCAGTGAAAAACAAGCTCTC[A/C]TGTCTGAACTGAAGATAATGACCCACCTGGGGCCG M 2 1 2 1 101000 f 74 goat ilmnseq_rs672371467 6 70315120 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468276044 Affx-1111835215 AX-519549598 6 70316692 GGTGACTACATGGACATGAAGCAAGCTGACACTAC[A/G]CAGTATGTCCCCATGCTGGAGAGAAAAGAGGTTTC R 2 1 2 1 101000 f 74 goat ilmnseq_rs664392780 6 70316692 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276133 Affx-1111835256 AX-519549683 6 70320163 AGGCCAAAGTCACAGATCTTCACGATTTTCCCTTG[A/C]GCCAGGAGGACGTTGCGAGCCGCCAGGTCCCGATG M 2 1 2 1 101000 f 74 goat ilmnseq_rs668425158 6 70320163 T G 1 recommended Goat_IGGC_65K_v2 Illumina 468276064 Affx-1111835147 AX-519549616 6 70320229 AATGAGGTAGGGGCACGTACACTGCCTTTGGACAC[A/G]TAGTTCGAGTCATGCATGATGTCTCGGGCCAGGCC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656670959 6 70320229 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275992 Affx-1111835190 AX-519549548 6 70324679 ACAGGGTCGATGTCGGGCAGAGGGATGATGTAGCC[A/G]CTATCTGCACTCAGCCTCTGCTCGTCGAGGCCACC R 2 1 2 1 102000 f 74 goat ilmnseq_rs661931429 6 70324679 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468275660 Affx-1111835021 AX-519549230 6 70331382 ATCGACATGATGGACGACATTGGCATAGACTCCTC[A/G]GATCTGGTGGAGGACAGCTTCCTGTAACTGGCAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs641692739 6 70331382 G A 1 recommended Goat_IGGC_65K_v2 Illumina 320772234 Affx-122957088 AX-385259389 6 70353895 TGATGTACACATTTTAGTAAATCCAAGGGAGTTAG[C/T]ATACTAAACCAGCAGTCATCTAAACCTGTTAGCTT Y 2 1 2 1 101000 f 74 goat snp58140-scaffold94-7455830 6 72784911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273475 Affx-1111833641 AX-519547093 6 70403831 ACATTGAGTTTGTAACTTGCATCCATACCCAGAAT[A/G]TGACTTTTCTGCAGGCCATCAGAGCCCAAGAGAGA R 2 1 2 1 101000 f 74 goat GoatD01.000208 6 70403831 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320772092 Affx-122977024 AX-385259247 6 70404839 CTAAATCTGGCCATAGAATAGAGAAGCCAACAGAA[C/T]GGAACTAATATAAAGTAGCCAGCCCACAAGTATGT Y 2 1 2 1 101000 f 74 goat snp58141-scaffold94-7506774 6 72836279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421697 Affx-122944406 AX-123292044 6 70435882 GGTTTTCAAAATCCAGCTTGTAATGTATACAAGCT[A/G]CACCTTCTCCCTTTCTCTCCCATGTCCAGCTTTTG R 2 1 2 1 303000 f 74 goat snp58142-scaffold94-7537817 6 72867672 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388472 Affx-122969240 AX-123258830 6 70549917 GATGATTTACAGGAGAAAGAAGTAGCTTATTGTTC[C/T]ACATATACGCACTGTGAAATTCATCCATCAATGAT Y 2 1 2 1 101000 f 74 goat snp58144-scaffold94-7651852 6 72982256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447462 Affx-122924359 AX-123317798 6 70580335 AAATATTTGATTCTGTTTGGGAGACTGTCCCCTCC[A/G]TTGGTTATCTGAAGTTACTTTCAAAGACCAGACTA R 2 1 2 1 101000 r 74 goat snp58145-scaffold94-7682270 6 73013074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799039 Affx-122952037 AX-385285969 6 70612857 GGATGAATCCCTTCAGTTGAATTCTGTCCCAAAGC[A/G]TTAGTCTTGGGAAAGTCATAGAAAATAGAAAGCAA R 2 1 2 1 101000 f 74 goat snp58146-scaffold94-7714792 6 73045717 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391361 Affx-122967288 AX-123261718 6 70665009 CAGCAGCAGTAGCTCACTGCCTCTGTCCATGTCCT[A/G]TGAGCTGCTGCAGCAATCTCCAGTAGCCTCTTAGG R 2 1 2 1 201000 r 74 goat snp58147-scaffold94-7766944 6 73098798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769859 Affx-122949434 AX-385257028 6 70710315 GCATGTGACAGGTGTTTACATTATTAAGTAAAAGC[A/G]TTTAAACAGCGACCTCCTTCGTATAAGGGTGAAGG R 2 1 2 1 101000 f 74 goat snp58148-scaffold94-7812250 6 73143653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428718 Affx-122938460 AX-123299060 6 70739283 ATAACAGAATTCACGTTAGGATTTCTTTAAATTGC[A/G]AAGTCCCTTGCTGGATTAAGGACATTACTGAAACA R 2 1 2 1 101000 r 74 goat snp58149-scaffold94-7841218 6 73172491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276296 Affx-1111835265 AX-519549835 6 70744246 GGGGCACACACAATCTGGGCCATAGCACTTCTCTT[A/G]CTCTTGGTGCTCGGTAACATGTGATGACTAATTCA R 2 1 2 1 101000 r 74 goat ilmnseq_rs669256409 6 70744246 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276003 Affx-1111835114 AX-519549558 6 70747255 GAGAAAGCAGAGGCCACAAATACAGGCAATTACAC[A/G]TGCACCAATAAAGGCGGCTTGAGCAGTTCCATTTA R 2 1 2 1 101000 r 74 goat ilmnseq_rs653927630 6 70747255 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275831 Affx-1111835106 AX-519549394 6 70750521 CGGGGTGTGAGGGGAAACCTCTCCCCAAGGATTTG[A/G]CGTTTGTGGCTGACCCCAAGGCAGGCATCACAATC R 2 1 2 1 102000 f 74 goat ilmnseq_rs652137856 6 70750521 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468275873 Affx-1111835053 AX-519549434 6 70756107 GATTTCTTTCTTTCCCTCCCCTTCTGAGAGCAGCA[A/G]AGTAAAGCACAGACGAAGAAGAATAGCTGGCATCA R 2 1 2 1 202000 r 74 goat ilmnseq_rs645259857 6 70756107 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468276334 Affx-1111835285 AX-519549867 6 70756206 CCAAAAGTATTATTGGCGTAACACATGAACACACC[A/G]GAATCATTCACTCTTGCTGAGCTGATAGTCAGCCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs672280002 6 70756206 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276058 Affx-1111835144 AX-519549610 6 70763252 GTCCCTTTTAATCTGGTTAGATGAAGTTCATTTAC[A/G]TATCTACAAAAAAAGAACAACCCATCAGTCACCTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs656209566 6 70763252 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276327 Affx-1111835281 AX-519549860 6 70763304 GGAAGAATTGACATCAGAATTGGACACGTGAAATG[A/T]GTAAGTGCCTCCTTCAGTCCCTTTTAATCTGGTTA W 4 1 2 1 101000 r 74 goat ilmnseq_rs671664904 6 70763304 A T 1 recommended Goat_IGGC_65K_v2 Illumina 468275714 Affx-1111835048 AX-519549282 6 70763355 ATTCTGATGTCAATTCTTCCGTGACATTTAATGTT[A/T]ACGTGAACAGTGAGTAGAACAAATGGTTCCTTATC W 4 1 2 1 101000 f 74 goat ilmnseq_rs644724711 6 70763355 T A 1 recommended Goat_IGGC_65K_v2 Illumina 468276313 Affx-1111835273 AX-519549846 6 70777648 TCGATGGTTGGCTCCGGGAACCCTGCAGCCACGCA[A/C]TGTAGCATGCCATTCACCAGCCTGTCATGTGTCAG M 2 1 2 1 201000 r 74 goat ilmnseq_rs669741195 6 70777648 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468276099 Affx-1111835166 AX-519549650 6 70779463 GAATGTGCTGTCATCAATGGTGCTATAAACCACTA[A/G]TTTTCCAAATGGTGAGACAGATGAGTTTTGGATCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs658674363 6 70779463 C T 1 recommended Goat_IGGC_65K_v2 Illumina 464458934 Affx-1110493535 AX-515931490 6 70781581 TTTTTCTAAAATAAGATGTTTTTAATTTTAGCAAG[C/T]GCCCATTTAACAGAACGAGAAGCCCTAATGTCTGA Y 2 1 2 1 101000 r 74 goat ilmnseq_rs668535829 6 70781581 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276280 Affx-1111835257 AX-519549822 6 70785270 AACAACCTCATTGACTCAGAGTTTCTCATACCACC[A/G]TGGAATCTAACATGATTCCTGGTAGTAACCGGTTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs668445864 6 70785270 G A 2 recommended Goat_IGGC_65K_v2 Illumina 38446269 Affx-122925672 AX-123316605 6 70785589 TCTCCCACTCAGTTGCAATTCCTGGTCTTCTGGAT[A/G]TCTGTTAGAACACTGGGCTAACTCATTTCTAGGGC R 2 1 2 1 101000 r 74 goat snp58150-scaffold94-7887524 6 73219811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275759 Affx-1111835070 AX-519549324 6 70785717 AAGAGACGTGACTCCTGCTATCATGGAAGATGATG[A/G]GCTGGCCCTGGACCTGGAGGACTTGCTGAGCTTTT R 2 1 2 1 101000 f 74 goat ilmnseq_rs647214940 6 70785717 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276173 Affx-1111835204 AX-519549723 6 70790523 TTGCAGGTATGACATCATGAAGACCTGCTGGGATG[A/C]AGATCCCTTGAAAAGGCCAACATTTAAGCAGATTG M 2 1 2 1 101000 r 74 goat ilmnseq_rs663369828 6 70790523 C A 1 recommended Goat_IGGC_65K_v2 Illumina 468273223 Affx-1111833515 AX-519546880 6 70844830 TTTTAATATTTTGAGCTCTGGGAAGTCAAAACCAC[A/G]CTCTTTATCAGGAAAGAGCACGTCATTAACAATAT R 2 1 2 1 101000 f 74 goat 6_70844830_AF-PAKI 6 70844830 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425158 Affx-122941066 AX-123295504 6 70886354 TCCATCATTATTATCATGATAAATCCTCTAGGTCT[A/G]TGACTTCAGCAGACAGCATGTATGCTTATAGAATT R 2 1 2 1 201000 f 74 goat snp58152-scaffold94-7988289 NW_017203438.1 15998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778738 Affx-122962366 AX-385265849 6 70944700 ACTTAAGTACAATCTAAATGGGCTCTTTGTCAAGC[C/T]GATTCCTATTTGTATAGCTCTGTGCAGTAAACAGA Y 2 1 2 1 101000 f 74 goat snp58153-scaffold94-8046635 6 73379964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398042 Affx-122961760 AX-123268397 6 70983425 AAATGATTGACTTGATCGTCCTCAGGGAAAAATCC[A/G]TGCTTACCTTGGCATGTGCTTGTGTCTTAGATAAA R 2 1 2 1 101000 f 74 goat snp58154-scaffold94-8085360 6 73418501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781933 Affx-122957615 AX-385269013 6 71017703 TGTAGCATATTTTTCTTCAACTAAATTTCCTATGA[G/T]TCTCACTTCTTTTCTCCCAATCTTCTATAAACAGT K 2 1 2 1 101000 r 74 goat snp58155-scaffold94-8119638 6 73452743 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782778 Affx-122940500 AX-385269850 6 71104781 AATATTTTTGAATGACTCCTTTTCCTTTAACACCC[A/G]CTTATACTCATGCTATTCCCAAATACATTTGATTA R 2 1 2 1 101000 f 74 goat snp11743-scaffold1432-949027 6 73540579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276105 Affx-1111835243 AX-519549656 6 71116760 TCAAGTGTTGTTCTTTCCACCACCAGGAAGTAGCC[A/C]CATTTGATTTTCATTTCAAAAAAAGGACCTCAGAC M 2 1 2 1 202000 f 74 goat ilmnseq_rs667531652 6 71116760 T G 2 neutral Goat_IGGC_65K_v2 Illumina 468275891 Affx-1111835136 AX-519549450 6 71116801 CTTCCTGGTGGTGGAAAGAACAACACTTGAAAATC[C/G]GAGCAGCACCTCTCGTGTGATTTCCAGGACTGGGG S 4 1 2 1 102000 f 74 goat ilmnseq_rs655911882 6 71116801 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468276222 Affx-1111835228 AX-519549772 6 71116802 TTCCTGGTGGTGGAAAGAACAACACTTGAAAATCG[A/G]AGCAGCACCTCTCGTGTGATTTCCAGGACTGGGGG R 2 1 2 1 201000 r 74 goat ilmnseq_rs666141385 6 71116802 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275845 Affx-1111835039 AX-519549408 6 71116917 CCAGAGTCAGGCTGGAGAATCGGAGCTGCACTGCC[A/G]ACCTGCGGTCCAATCTCCATCAGCTTTAAAAGTTC R 2 1 2 1 101000 r 74 goat ilmnseq_rs643588602 6 71116917 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275708 Affx-1111835045 AX-519549277 6 71116980 AAAAGTTCAGCCTCCTCGCTGGAGTACACAGTGGT[A/G]TCCGTGTCATCAGAATGGTATCCCGACTGGTAGCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs644176015 6 71116980 G A 1 neutral Goat_IGGC_65K_v2 Illumina 464453391 Affx-1110493681 AX-515925988 6 71117080 CAGACTCCTTGCTTTTGCTGGGCATCAGTCCACTG[C/T]GGAAGAGATGGCAACCAAATAAGTTGGCAGAGAGA Y 2 1 2 1 202000 f 74 goat ilmnseq_rs669554547 6 71117080 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468276016 Affx-1111835120 AX-519549570 6 71123023 TCCAGCATCGCATTTGGCACTTCCATCACACATAC[A/C]TGACTTCATCAACTCTCAGCACCATATGCAAAGCA M 2 1 2 1 101000 r 74 goat ilmnseq_rs654438626 6 71123023 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468272472 Affx-1111835231 AX-519546194 6 71127128 AATATTTCCCAGAGCAGGACACCAAAAGACCACAC[A/G]TCACTCTGAATTGTGTACACTCGGTCAAAAATCGT R 2 1 2 1 201000 r 74 goat ilmnseq_rs666644397 6 71127128 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468276148 Affx-1111835192 AX-519549698 6 71127430 CACAGGGACCTGGCAGCGCGAAACATCCTCTTGTC[A/G]GAAAAGAACGTGGTTAAAATCTGTGACTTTGGCTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs662070915 6 71127430 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275621 Affx-1111835000 AX-519549191 6 71129960 CTCACCTTCCGTGATGCCAAAAACTCCATGCCCTT[A/G]GCCACTTGGAAGCTGTAACAGATGAGATGCTCCAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs638944036 6 71129960 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275787 Affx-1111835009 AX-519549352 6 71137849 TGATTGCCATGTTCTTCTGGCTACTTCTTGTCATC[A/G]TTCTACGGACCGTTAAGCGGGTAACAGAATAATTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640423402 6 71137849 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275850 Affx-1111835042 AX-519549412 6 71137868 TTAACGGTCCGTAGAACGATGACAAGAAGTAGCCA[A/G]AAGAACATGGCAATCACTGCAGTGCCTACTAGAAT R 2 1 2 1 202000 r 74 goat ilmnseq_rs643706093 6 71137868 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275785 Affx-1111835008 AX-519549349 6 71140310 TTTTCCCCCTTTCTCAGGCATTGTGCTAAAAGATG[A/G]GAACCGAAACCTAACTATCCGCAGAGTGAGGAAGG R 2 1 2 1 201000 r 74 goat ilmnseq_rs640409229 6 71140310 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275641 Affx-1111835011 AX-519549211 6 71143988 TGAATGCCACCATGATCTCTAACAGCACTAATGAC[A/G]TCTTGATCATGGAGCTGCAGAATGCATCCTTGCAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs640585759 6 71143988 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275775 Affx-1111835078 AX-519549340 6 71144140 TGTACCACGTGAGGTTCTCAAACATAGTTCTGTCC[A/G]CGGAGCACCACAGAGACACACTCTCCTGCTCGGTG R 2 1 2 1 102000 f 74 goat ilmnseq_rs648134856 6 71144140 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276326 Affx-1111835280 AX-519549859 6 71144187 AGAGACACACTCTCCTGCTCGGTGGGCTGGGTGCC[A/G]GGTTGCAATGTGATTTCAGGACCCCCTGAAATGTA R 2 1 2 1 102000 r 74 goat ilmnseq_rs671110083 6 71144187 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276006 Affx-1111835197 AX-519549561 6 71146873 CTGGCAGCTGGAGACAGAGTGCACCTACCAGCCCA[C/G]GTGAGTAGGACCATGCCCTGTGCCCCTGCTGTTCT S 4 1 2 1 202000 f 74 goat ilmnseq_rs662787102 6 71146873 G C 2 neutral Goat_IGGC_65K_v2 Illumina 468275840 Affx-1111835110 AX-519549403 6 71146947 CAGCGAATGTGACTTGGGGGAGGAACGGCATAGAC[A/G]GTGCACGTCAGTGTCTGGGAAGTGCCGTACTGGTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs653334871 6 71146947 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276149 Affx-1111835264 AX-519549699 6 71148937 ACAGGAAATTACACTGTCATTCTTACCAATCCCAT[A/T]TCAAAGGAGAAACAGAGCCACATGGTATCTCTGGT W 4 1 2 1 201000 f 74 goat ilmnseq_rs669227336 6 71148937 T A 2 recommended Goat_IGGC_65K_v2 Illumina 468275965 Affx-1111835176 AX-390134760 6 71149239 TTTATTTTCTTCCAGAAAAGCCGTTTGTTGCTTTC[A/G]GTAGTGGCATGGAATCCTTGGTGGAAGCCACCGTG R 2 1 2 1 101000 f 74 goat ilmnseq_rs660192572 6 71149239 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38446094 Affx-122925805 AX-123316431 6 71150072 AAGGAATAGTCATAATGACAAAGATTCCAGATAAG[C/T]AATTTGTCAGAGGTTTTCGTTTCATAGGAAAAAAG Y 2 1 2 1 101000 f 74 goat snp11742-scaffold1432-903736 6 73586334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275591 Affx-1111834986 AX-519549161 6 71150662 TTTCAAGGCAGAGCATAATTCTGAAGGCAATCTTC[A/G]CTTACCATGTACCCGGACGAACGTGCTGTTCTTCT R 2 1 2 1 101000 f 74 goat ilmnseq_rs636924423 6 71150662 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275722 Affx-1111834975 AX-519549290 6 71150677 TAATTCTGAAGGCAATCTTCGCTTACCATGTACCC[A/G]GACGAACGTGCTGTTCTTCTTGGTCATCAGCCCAC R 2 1 2 1 202000 r 74 goat ilmnseq_rs635694893 6 71150677 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275767 Affx-1111835074 AX-519549332 6 71152749 TTCAGACCTCAATGTGTCACTTTGTGCAGTAAGTT[A/G]CATCTTCTTCCATCATCTCTTACCTTTAATTTTTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs647673929 6 71152749 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275885 Affx-1111835059 AX-519549446 6 71152867 GACATTCTCATCTAGATTACAGGTCTCCGTTTATT[A/G]CTTCTGTTAGCGACCAGCATGAAGTTGTGTACATC R 2 1 2 1 101000 r 74 goat ilmnseq_rs646143562 6 71152867 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276183 Affx-1111835282 AX-519549733 6 71155674 ACATAAACAGTGGAGGCCATGTCAGTGTCCTGGTA[A/G]AAGCACTTGTAGGTTCCAGTATCATTTCCAATCAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs671747138 6 71155674 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275796 Affx-1111835013 AX-519549360 6 71155675 CATAAACAGTGGAGGCCATGTCAGTGTCCTGGTAG[A/G]AGCACTTGTAGGTTCCAGTATCATTTCCAATCACT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640680613 6 71155675 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276038 Affx-1111835132 AX-519549592 6 71155807 TCTCAGAGCTGCTCTGATTGTTGGGCCAGAGCCAG[A/C]GCAAGTCCCTCTGACCCCTGAAAAATTCATTCCAA M 2 1 2 1 101000 r 74 goat ilmnseq_rs655505473 6 71155807 C A 1 recommended Goat_IGGC_65K_v2 Illumina 468275780 Affx-1111835006 AX-519549345 6 71161708 CTAGGAAGTGGGCTCCTTACCCACAGAGGCAGCCC[A/G]GGTCTCCACGCAGAGCCACAGAGCAAGGGCCAGCA R 2 1 2 1 202000 r 74 goat ilmnseq_rs640054948 6 71161708 G A 2 neutral Goat_IGGC_65K_v2 Illumina 38433506 Affx-122935020 AX-123303847 6 71202037 AATGTCAGGATCTACGCATGATTTATTTAATACCA[C/T]GGAGCCTATTTTTACAATAAAAAAAGGCTTTAGGT Y 2 1 2 1 101000 f 74 goat snp11741-scaffold1432-851771 6 73638431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376995 Affx-122977736 AX-123247354 6 71252243 ATCTCCAACTTTACATTTTCAAAACTGAAATTCTT[A/G]CATCCACATCTTGCCAAGTTCCAAATCTCAGTTGG R 2 1 2 1 101000 r 74 goat snp11740-scaffold1432-801565 6 73688563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407212 Affx-122955390 AX-123277563 6 71295395 GGCATAAGTTATATAGTCTGACGTAACTGGAAGAC[A/G]TGTTTCTTTCCTTTATAATATCAAGCTAGTTACTT R 2 1 2 1 101000 f 74 goat snp11739-scaffold1432-758413 6 73731904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387360 Affx-122970474 AX-123257718 6 71336157 GTAGTGCATTTCTATCTTTGCTTTGGAAATATTCA[G/T]AGTTAGAAAGACGGTTCTCAGAACATCTAAAAAGA K 2 1 2 1 101000 r 74 goat snp11738-scaffold1432-717651 6 73773180 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398863 Affx-122961049 AX-123269218 6 71372917 CATCTCAATGTCTATTTCGTTGTTTAACCCAAAAG[A/G]AAAGCCTCCAGCAACAATAATACTTAAGAAGCAAA R 2 1 2 1 101000 f 74 goat snp11737-scaffold1432-680891 6 73810194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383950 Affx-122972954 AX-123254308 6 71404857 TTATGACTGAAACATAAGTGCCTTTCTAAATGTTT[A/G]TGGAGACAGCTAAGCTGACCTTTCAGCAGGAAATT R 2 1 2 1 201000 f 74 goat snp11736-scaffold1432-648951 6 73842137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278556 Affx-1111836398 AX-519552038 6 71421015 ATATTAAAATCCATCTAAAGTCCTTAAATATAGGC[A/G]GAACAATGTATAAATACTGCAAACTCTTCTGCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-699 6 71421015 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779880 Affx-122962879 AX-385266979 6 71458917 TCACTAGAATACCCATGGGATTGTGATTGTATTAG[C/T]GTTCTTCTTCCTCTCCAGACCATACTAGCCAAAAA Y 2 1 2 1 101000 r 74 goat snp11735-scaffold1432-594891 6 73896533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452174 Affx-122921236 AX-123322507 6 71493644 CATGTATGATGGTAAAAAGCACTTTGCAGTCAAAC[C/T]GCCCACTAACCTTAGAGTTTTCCCTTACTAACTGG Y 2 1 2 1 101000 r 74 goat snp11734-scaffold1432-560164 6 73930843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389844 Affx-122968164 AX-123260201 6 71525518 GAGAGATTTTTCTCTTATTTCCTTACTTAGAGCAA[C/T]CCAAGAAGCATTAATATTCCTCATGTATTACATAA Y 2 1 2 1 101000 f 74 goat snp11733-scaffold1432-528290 6 73962627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384432 Affx-122972179 AX-123254790 6 71559439 ACATATTAGATGCTTATACACAACAACTGAAAACC[A/G]CATAAAACAAAGCAAGAAACAAGAAAGTATTGTAA R 2 1 2 1 101000 f 74 goat snp11732-scaffold1432-494369 6 73996870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436795 Affx-122932252 AX-123307133 6 71595243 TGCTCAAAAGAAGAAGAATCAGTACAGATGAGAAG[C/T]AACTACTATTTTTCCTTGTAAATTTCCAAAAGTTT Y 2 1 2 1 101000 f 74 goat snp11731-scaffold1432-458565 6 74033216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792931 Affx-122956594 AX-385279909 6 71641904 AGAATATAGATAAGTCAATGCTGAGGTCTTTACAT[A/G]TATTCACCTGAACAAGCAGGTTGTAGTATTATGCT R 2 1 2 1 101000 r 74 goat snp11730-scaffold1432-411904 6 74080084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446694 Affx-122924742 AX-123317030 6 71698967 CTGAGATGTTTCTCTCTGGTGTATCATAGAGTTGC[A/G]GAACACACAATGTGCCCCAGCTATGCTGTGTTCCT R 2 1 2 1 101000 f 74 goat snp11729-scaffold1432-354841 6 74138059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274573 Affx-1111834302 AX-519548162 6 71739524 ACGAATGCCTGCAGGAAAGATTTTGGACG[A/G]AGTCCAGTTATTAGTAACAGAAAGGTTAAAGTTAG R 2 1 2 1 101000 r 74 goat GoatD01.029542 6 71739524 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389772 Affx-122968232 AX-123260129 6 71797251 TTCCTGCCTCCTGAGTAAGACTGCTGTGATAAACA[G/T]CTAGTAATGTTTCATGCTTCTTCCAGGTGCTCATT K 2 1 2 1 101000 r 74 goat snp11727-scaffold1432-256557 6 74237862 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409601 Affx-122953558 AX-123279952 6 71885307 TACCGTTCAGGAGGGCAATATTGACTTTATGTGGT[A/G]CTAGTTCCCAGGTGTTTTACCATCTCTTATCAGAT R 2 1 2 1 201000 r 74 goat snp11725-scaffold1432-168501 6 74334337 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278562 Affx-1111836401 AX-519552042 6 71916920 CTTGGCCTTTCTGGTGGCCAGCCCCATCCTGCAGC[A/G]ATGGAGAGTCCTGCTGGAGTCATCTCATTCGAACA R 2 1 2 1 101000 r 74 goat Random2.2K-701 6 71916920 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776946 Affx-122935229 AX-385264070 6 71933661 TGTTGTTCTTTAAATACCTAAGTGGAATAAAAATT[A/G]TTGAGCATAATGAACTTAAAGAGCAAATACAGTGG R 2 1 2 1 201000 f 74 goat snp11724-scaffold1432-120147 6 74383233 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768938 Affx-122948130 AX-385256113 6 71978511 GTCCCAAGCACTGCAGTGAGAGTAAATCCACAGGT[A/G]TAGGTGAAGGAGTCCTACCTGGAGATTATGGGGGA R 2 1 2 1 101000 f 74 goat snp11723-scaffold1432-75297 6 74434229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377976 Affx-122977618 AX-123248335 6 72021377 TTGCTTAGGATCAGATAATCCATGAGAGGTGTATT[A/G]ATTTTTCCTCAGGATTGTAAAGACTACTGAAAATT R 2 1 2 1 101000 f 74 goat snp11722-scaffold1432-32431 6 74474818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402284 Affx-122959108 AX-123272637 6 72145463 AGTGGCAAACACTTCATGCAATATACAACAAATAT[A/G]CCTTTACAGGACATTGATTCAAGGAAAACATCACC R 2 1 2 1 101000 r 74 goat snp2158-scaffold1066-91556 6 74589910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450885 Affx-122922210 AX-123321219 6 72184942 TGAAAAACTGTCCTTGACCCTTTGTGCTAAGACCA[C/T]GAATGAATTTGAAAATGTATCTATGAATTAAATGC Y 2 1 2 1 101000 f 74 goat snp2159-scaffold1066-131035 6 74629157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434250 Affx-122934823 AX-123304591 6 72225383 CACTTGGCATTTTTCTCTTGGCTTAAGCTACTCCT[A/G]TGTCTTCACTTTGCACTGAGGAAGTTTGAATGTAC R 2 1 2 1 101000 f 74 goat snp2160-scaffold1066-171476 6 74670320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445188 Affx-122925531 AX-123315525 6 72256280 AACTGTGAACATTTTCCAAAGCTAACAGTGGCTTT[A/G]TTCACTTTGTCTATATACACAGAAAAATATCAATT R 2 1 2 1 201000 r 74 goat snp2161-scaffold1066-202373 6 74701544 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766520 Affx-122951850 AX-385253881 6 72305696 TCATCTGTGATTTTTTTCACTCTCAAGAAACTCTG[C/T]ACCTAGCCTCCAACAATTAATCTAAATTGCCATTT Y 2 1 2 1 101000 f 74 goat snp2162-scaffold1066-251789 6 74751248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417547 Affx-122946922 AX-123287895 6 72337990 ATTTCATTTCAACACAGATTAAATTAAAAATGGAG[C/T]GACTGAGTAAAGTTATAACCAGGCAATGACAAGGG Y 2 1 2 1 101000 r 74 goat snp2163-scaffold1066-284083 6 74784159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442615 Affx-122928472 AX-123312952 6 72371834 AATGTATATACATGCATATATCTTTATTCCTACTG[C/T]GGGGAGCAGATCATTACATGCATAAGACAAAATTC Y 2 1 2 1 103000 r 74 goat snp2164-scaffold1066-317927 6 74818685 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380244 Affx-122975460 AX-123250602 6 72421104 TGTGTGTGTGTGTGTGTGTACATTCCCCCAAAACA[C/T]AATTTTTTTGAAGACTAATCTGGAGTGTGTGGTAA Y 2 1 2 1 201000 r 74 goat snp2165-scaffold1066-367197 6 74868090 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428678 Affx-122938639 AX-123299020 6 72451605 CCTAACTCAAAGTCAAAATGTTTCCTTTTTTCTAC[A/G]TGTTCTTATATAACTTTTAAAGTCTACCACTTATG R 2 1 2 1 103000 f 74 goat snp2166-scaffold1066-397698 6 74898573 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425283 Affx-122940965 AX-123295629 6 72488188 GCACTGAGCCATGGTCACTATGTGAAAAGCAGTAC[A/G]TAAGTTTAAAAATTTTGTATATATACCATGAAGCT R 2 1 2 1 101000 f 74 goat snp2167-scaffold1066-434281 6 74935322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476220 Affx-1251763725 AX-586011644 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20000 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 539476474 Affx-1251763725 AX-586011874 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 4 1 4 1 20000 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165271 Affx-1251763725 AX-606940683 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165322 Affx-1251763725 AX-606940733 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165612 Affx-1251763725 AX-606941023 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165715 Affx-1251763725 AX-606941124 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165916 Affx-1251763725 AX-606941326 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562166346 Affx-1251763725 AX-606941754 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 320798489 Affx-122925534 AX-385285422 6 72518254 AGATCTGTATATCACATGAATAGTGGCATCTTAGA[C/T]AGGGAAGGGTTTAATGAAATTTACAAATCTGGAGA Y 2 1 2 1 101000 r 74 goat snp2168-scaffold1066-464347 6 74966540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398468 Affx-122961586 AX-123268823 6 72556353 ATAAATAGCTTAGTCCTTGAGGAGTACATTTAATC[A/G]CTATTGCATATATTTTGTTTTGTTTTCCTTATAAC R 2 1 2 1 101000 f 74 goat snp2169-scaffold1066-502446 6 75005606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793960 Affx-122961028 AX-385280929 6 72588110 CCAATGAGGGATAATTGAATATCATATGTTCAGAT[A/G]CAACATCATTTCACTTGTGTAGAACTTTTTTAGGA R 2 1 2 1 101000 r 74 goat snp2170-scaffold1066-534203 6 75037649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402240 Affx-122959141 AX-123272593 6 72650873 CTCCTAACCAGAACCCCAGGTCCTGAAAACCCAGT[A/G]AGCAAAACTTCTGTAGACAAGTAAAACCTCCTGAA R 2 1 2 1 201000 r 74 goat snp2171-scaffold1066-596966 6 75100819 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794630 Affx-122943229 AX-385281591 6 72710549 TAAAAATCTCATGTTTGGACTCTGGGGTAAATTGG[C/T]AAGGGTAGAATTTGATTCAGTCACAACTGTTAATG Y 2 1 2 1 101000 f 74 goat snp2172-scaffold1066-656642 6 75160735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392127 Affx-122966339 AX-123262484 6 72748977 TGGAGTATGAAGGGCAAGACTATCATGAAAAAACA[C/T]AAAGTGGGAATGTATAATGGGAGAAATTTCTGCAC Y 2 1 2 1 101000 f 74 goat snp2173-scaffold1066-695070 6 75199259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803047 Affx-986696144 AX-385289920 6 72764602 TGGTACGTATTTTGAGAAAATGGCCGAATGCCTAT[G/T]TCAGTCAGGAATGCCGCGGCCGAGGCCGGCGCTGG K 2 1 2 1 600010 f 74 goat 6_72764602 6 72764602 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320781597 Affx-122974146 AX-385268681 6 72791056 GAGATTTATGTTTCAGCAAATTGTTGAATATATTG[C/T]AACAATAGCAATTTCTTATACAGCCATGACACTCA Y 2 1 2 1 201000 f 74 goat snp2174-scaffold1066-737149 6 75241459 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787336 Affx-122961674 AX-385274361 6 72820512 ATAGAACAAGACATGTTTTATCACAATTACTAGAC[A/G]GAATAAGCCAGACTGTCCCAGATCTATGAGTACTA R 2 1 2 1 101000 r 74 goat snp2175-scaffold1066-766605 6 75270886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785131 Affx-122961433 AX-385272177 6 72855662 AATCCAGACTTTACACACTCTTTTCTTCTAAGCAT[A/C]AGTTGCATTCTCCAACCAATGAACAGAATTGGCAT M 2 1 2 1 101000 r 74 goat snp2176-scaffold1066-801755 6 75306006 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798962 Affx-122933932 AX-385285892 6 72899284 CATATGTATATATCATGTATCATTATATATTTAAG[C/T]TTTTCTGGATTCTCTCAAGTCTATAAGCTCTTTAA Y 2 1 2 1 202000 f 74 goat snp2177-scaffold1066-845377 6 75350335 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787225 Affx-122951616 AX-385274251 6 72981945 CCTAACTGTATATCTAATAGTCTAAAATATCGACT[A/G]TTGATGTCAACTGAAGTTTGTAGATGGTAGAGCCA R 2 1 2 1 101000 r 74 goat snp2178-scaffold1066-928038 6 75435551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452326 Affx-122920662 AX-123322659 6 73067507 AACCAGCTCCTATTGTTAATACTGGGTCTAATGTT[A/G]CCAGAGTGTCTGACATTTCCAGATAATCTGCAAAG R 2 1 2 1 101000 f 74 goat snp2180-scaffold1066-1013600 6 75521317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785180 Affx-122923946 AX-385272226 6 73102041 AAACACATTTGGAGAATTACCTGGTAATACTGTTA[C/T]AGATTCACATGTTTCTTAGAAAGATTTCACACTCT Y 2 1 2 1 101000 r 74 goat snp2181-scaffold1066-1048134 6 75556022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769821 Affx-122977980 AX-385256991 6 73133711 TAGTGAGAATGTGAATTTAGTTTAATCTACTTCTA[A/G]TTGAGTAATAAGGACTTCAATCCAAATCTAGTAAA R 2 1 2 1 101000 r 74 goat snp2182-scaffold1066-1079804 6 75587774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800056 Affx-122963133 AX-385286979 6 73165497 TTATTATTATTGATCACAATATCACAAGAAAGGGC[A/G]CAATGTCTATAACAATAGTAGTAATCTCAGGGTTA R 2 1 2 1 101000 r 74 goat snp2183-scaffold1066-1111590 6 75620791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426067 Affx-122941091 AX-123296413 6 73196968 GGTAGGGGAATGATGTTGGCCAGGACACCGTGCTT[A/G]CAGTGCTTGGTGACATCTACCACAGTTCAAGATTT R 2 1 2 1 101000 r 74 goat snp2184-scaffold1066-1143061 6 75652448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785870 Affx-122938710 AX-385272907 6 73247952 TGAAAAGATTGAATAAAGTTATGCACAATACTTAA[C/T]ACTTATTTACAGACATTAATTCAAGCAACTTCCTA Y 2 1 2 1 101000 f 74 goat snp2185-scaffold1066-1194045 6 75704398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408378 Affx-122953724 AX-123278729 6 73291427 ATCCTTTGGCATTTCTAGTATAATCAATATTCCTC[A/G]TGCCTATTTCAGTAATTATTATTGCTTTTATTTCC R 2 1 2 1 101000 f 74 goat snp2186-scaffold1066-1237520 6 75747830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375792 Affx-122978574 AX-123246151 6 73334083 TCCGCTTAAGGTTAATAGTCATGATTATAATGTGA[C/T]GTCATCAATCATAAATTATTTTGCTAGTCAACTAT Y 2 1 2 1 101000 f 74 goat snp2187-scaffold1066-1280176 6 75790588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768218 Affx-122930158 AX-385255403 6 73406759 CTAGAAACCCTTACCTCAAATTTCTTAAGAAAACC[A/G]CAAGTTGAACTTCCACTTCATATTATTTAATCATA R 2 1 2 1 101000 f 74 goat snp24425-scaffold248-45659 6 75864969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447140 Affx-122924453 AX-123317476 6 73441268 CTCTAAGCTACGTCCAACTAAAATGTGATATGATG[C/T]AAATAATTTATTCATCCAGGAGTCTAGCCATATAT Y 2 1 2 1 101000 f 74 goat snp24426-scaffold248-80168 6 75895912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400170 Affx-122960680 AX-123270525 6 73473843 TCCCTGACAATTTTTAATTGGATATTCATATTGTG[C/T]TCTGCTTGTAGACCAATGCTCTTTAAGGGTTGAGA Y 2 1 2 1 101000 r 74 goat snp24427-scaffold248-112743 6 75929191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275196 Affx-1111834759 AX-519548775 6 73482924 GTTCATGGCTTTAAAGCCTTTTAGCCTGCAGTGCC[A/G]AAA R 2 1 2 1 101000 f 74 goat GoatD01.051768 6 73482924 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417709 Affx-122947449 AX-123288057 6 73511410 AATCTACCTTTTTACCCCTCCCATTTGACTCTCTT[A/G]TGGCAATATTATATTGATAAACTACTCTACACTAT R 2 1 2 1 201000 r 74 goat snp24428-scaffold248-150310 6 75966731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442033 Affx-122928403 AX-123312370 6 73571711 ACAGATACAATTGGTACATATATCATTTGCAAACC[A/G]TAAGTAAAGAAAGTGACCTCTGAGGTTGCCAGGAG R 2 1 2 1 101000 r 74 goat snp24429-scaffold248-210611 6 76028190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772745 Affx-122952028 AX-385259890 6 73605540 CAAAAGTGAAATACAAACCCCCTTAGTTAGAATGG[C/T]ATGTTTCATTACATTTCTAAATTGTGGGAAATATT Y 2 1 2 1 102000 f 74 goat snp24430-scaffold248-244440 6 76062710 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444195 Affx-122927261 AX-123314532 6 73652781 GTTTTTTGTTACTGTTTTTTAAATCACATCCATAG[C/T]AGCTTGCTCAAAATTTGCATTTAATTCATATTAGG Y 2 1 2 1 101000 r 74 goat snp24431-scaffold248-291681 6 76107667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775558 Affx-122930263 AX-385262689 6 73750979 TAGCAGGAAATATGAAAATGAAGCAGTACTTTCTT[A/G]CATAATCTCTAATTCCCCAAGATATGAAGAAAGTT R 2 1 2 1 101000 f 74 goat snp24433-scaffold248-389879 6 76208155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382588 Affx-122973724 AX-123252946 6 73782112 TATCAATAAATTCCTAAAATAAATTTGAAGTTAAG[C/T]TGTTATCCTTAGGCCATAATATAATTACACTGTAT Y 2 1 2 1 101000 r 74 goat snp24434-scaffold248-421012 6 76239682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435140 Affx-122933678 AX-123305480 6 73872499 AACATAGTAATGTAGTACATGTCTTCCTCTCTAAT[C/T]TCATCTTGCATCAGTCTACACTTCATAATATTTAC Y 2 1 2 1 101000 r 74 goat snp24436-scaffold248-511399 6 76331912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402950 Affx-122958171 AX-123273303 6 73926154 AGACCCGAAGCATAAACTGAAAACCAAACTTAAGA[G/T]AAAAACCAGCACTTTGTAATGAGAGAAACCTAGAA K 2 1 2 1 101000 f 74 goat snp24437-scaffold248-565054 6 76385839 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395717 Affx-122963715 AX-123266072 6 73977587 TGGATTGAAGAAGATTTAATATCTTAATATATCTT[A/G]CTCTAGTTGCTGTTTTTTTTATGCCTACCTGGGAT R 2 1 2 1 101000 r 74 goat snp24438-scaffold248-616487 6 76422624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771134 Affx-122923240 AX-385258294 6 74025207 TCTTCCTTACTGTAAACAGTTGAGTCTATGACTCT[A/G]CATGTCAGTTGGTTCTCAAGCTAGAGGAAACATAG R 2 1 2 1 201000 f 74 goat snp24439-scaffold248-664107 6 76470244 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774959 Affx-122936574 AX-385262092 6 74088079 TTAAATTGCAATTCTTGACTTTTATTAATATCACT[A/G]TAGTTCAAAGTCCAAGTGAAAGTGATGAATGGAAA R 2 1 2 1 101000 r 74 goat snp24440-scaffold248-726979 6 76532305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450864 Affx-122922226 AX-123321198 6 74125585 ACTCTTGGTTTATATAGGCAAGCAAGGCGGTTTTG[C/T]GAGGGACTTTCTATAGTTGCACCAATCACGTTAAA Y 2 1 2 1 103000 f 74 goat snp24441-scaffold248-764485 6 76569926 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790777 Affx-122930999 AX-385277778 6 74168996 TAATATAAGGATTTTCTGTGAGTAGGTATAAAACA[C/T]AAATCTTTCTTAGATATGTTGCCAGCTAATGGCTT Y 2 1 2 1 201000 f 74 goat snp24442-scaffold248-807896 6 76613648 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403538 Affx-122957608 AX-123273891 6 74226660 ACTCCTTTAAGTACTCAATTCACTATCAGTTTAAA[C/T]ATCCATTTACTTACCTACTCACAAACACAGAAACA Y 2 1 2 1 101000 r 74 goat snp24443-scaffold248-865560 6 76669568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405428 Affx-122956062 AX-123275780 6 74284963 TACAAAATGAAATGACACACTAAGAATAGAGAGAG[A/G]CATTTTTATAAAAGGAAATTCTTTTAAGTGATAGT R 2 1 2 1 201000 f 74 goat snp24444-scaffold248-923863 6 76729100 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391363 Affx-122967286 AX-123261720 6 74328557 CTATATAATTTCCTAGAGTGATCACTTTAAAAATA[C/T]GGAGAGATGGCAACATTCTCCTCACAGCCTACTAC Y 2 1 2 1 201000 f 74 goat snp24445-scaffold248-967457 6 76776276 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787387 Affx-122922579 AX-385274412 6 74378188 AGCAAGATTGGCTTTGAGTTGATAACTATTGAAGA[C/T]GGGTGATGAATCCATTTCAGCTCATCACATCATGT Y 2 1 2 1 101000 r 74 goat snp24446-scaffold248-1017088 6 76826473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794564 Affx-122921233 AX-385281526 6 74441930 GATTTTTGAGCCAGTCTTTAATATTAGCATAGTAC[A/G]CAACTCTCCTTCCCAGAAAAGGTGGTACTAATCTA R 2 1 2 1 101000 r 74 goat snp24447-scaffold248-1080830 6 76891418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383733 Affx-122972456 AX-123254091 6 74477995 TCACAAGAAATAGGCTTGAAATAAAAGAGCTGAAG[A/C]GCTTTCATTATGAATGATATCTGGATCTCTTGGTC M 2 1 2 1 101000 r 74 goat snp24448-scaffold248-1116895 6 76927267 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795568 Affx-122950751 AX-385282523 6 74513269 TATAAGCCTCTGTAATTTTGCTATATGTGACAATG[C/T]AGACCTCAGAAGTATGATGTAAATATTTTTTCAAA Y 2 1 2 1 101000 r 74 goat snp24449-scaffold248-1152169 6 76963216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434888 Affx-122934342 AX-123305228 6 74555146 TCCTAATTTGTTTTTAATTCTTTTCTGTTATTTAT[C/T]ATGTAGGACATTGGACACTCCCTAGAGAGCTACAA Y 2 1 2 1 103000 r 74 goat snp24450-scaffold248-1194046 6 77005946 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777206 Affx-122957620 AX-385264329 6 74599630 AACTAGCTAGCTAATGACTAGACAGAAGATATAAA[A/C]TCTTTTCTACTTAAATCACTGCAACAATATCTTAA M 2 1 2 1 201000 r 74 goat snp24451-scaffold248-1238530 6 77050458 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420685 Affx-122944801 AX-123291032 6 74646716 TTAATTAAATTGTGATTAGAAATAGATTTGGGTGA[C/T]ATTGGAGGAATAGCTACTTTAAACACTTCAAAATA Y 2 1 2 1 101000 r 74 goat snp24452-scaffold248-1285616 6 77093453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400965 Affx-122960110 AX-123271318 6 74678146 AACACTGATACTTTAAGTTAGCTAGACCCTGTGTA[C/T]TATCAAATTGTTGGTCTCTAAAGGAATGTATCATT Y 2 1 2 1 101000 f 74 goat snp24453-scaffold248-1317046 6 77124764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453124 Affx-122920013 AX-123323457 6 74707367 GCATGATTATGCATATGTCAAGACACACAGAATTA[C/T]ACATAACAAAGACTGAACTTTCCTGTGTGCAAATT Y 2 1 2 1 101000 f 74 goat snp24454-scaffold248-1346267 6 77154443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446359 Affx-122925601 AX-123316695 6 74762491 TAACAAACATCAACAATAGACAAATAAAATTATAC[A/G]TTTGGTATTTACCTAACATCTGCATGTCTATAAGC R 2 1 2 1 101000 r 74 goat snp24455-scaffold248-1401391 6 77209530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793521 Affx-122957662 AX-385280498 6 74799772 GATGGCCACATTAACCTTGTAGTGCAAGTAAGACA[G/T]ATTTTTGAAATACTAATTTCTCCAATAAGGAAAAC K 2 1 2 1 101000 f 74 goat snp24456-scaffold248-1438672 6 77246736 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785170 Affx-122955850 AX-385272216 6 74829520 TTATAATTAGGTAATAGTTACCAAAATTATTGGCA[A/G]TTTTGAGAAAAAATTATACAGTTGGTATGCATAAT R 2 1 2 1 101000 f 74 goat snp24457-scaffold248-1468420 6 77275965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404489 Affx-122956717 AX-123274841 6 74882325 TGTCAAGGAAGAGTATCTCCTTTGAAAAAGAGTAA[C/T]GTCTATATTGAATATTTGCCATGTGATAAGCGAGG Y 2 1 2 1 101000 f 74 goat snp24458-scaffold248-1521225 6 77329260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421460 Affx-122943933 AX-123291807 6 74987343 CTATTTGACTATGGAGCCTCACACACTTAATTTCT[A/G]TTTGCAGAACTTGACTCACATTGACCACACATTTG R 2 1 2 1 101000 r 74 goat snp24460-scaffold248-1626243 6 77439194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476221 Affx-1251763726 AX-586011645 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 4 1 4 1 20000 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 539476475 Affx-1251763726 AX-586011875 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20000 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165428 Affx-1251763726 AX-606940839 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165766 Affx-1251763726 AX-606941175 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165908 Affx-1251763726 AX-606941317 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562166448 Affx-1251763726 AX-606941856 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 38453799 Affx-122919575 AX-123324132 6 75038743 GTAATGGAAGCAAGCAGTTGTTTGCTGGCTTTGTT[A/G]CCAAAAATTGTGAATGGCTAGATTTTTATAAAACA R 2 1 2 1 201000 r 74 goat snp24461-scaffold248-1677643 6 77490672 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381528 Affx-122974849 AX-123251886 6 75072253 TTTAATATTCTGTGTGGACTCAGGATCAAGGAGAG[C/T]GAATTGGTTATTGCTAATTTTTTTACTATTAATGA Y 2 1 2 1 101000 f 74 goat snp24462-scaffold248-1711153 6 77524371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778870 Affx-122957164 AX-385265978 6 75116041 CAAAGTTTAATGTTGGCTTTGCAATGACTTAGAGA[A/G]ACATGCATATATTGCTTGTTTAGTAATCATAAATG R 2 1 2 1 201000 r 74 goat snp24463-scaffold248-1754941 6 77566884 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776687 Affx-122924857 AX-385263813 6 75170597 AAAACTCTTAAGTATCTATACAATTCATGTTTACA[A/C]AGTCAGTCTAAAATTGTACTAGTAGAGCAAGGTAG M 2 1 2 1 101000 r 74 goat snp24464-scaffold248-1809497 6 77622385 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408082 Affx-122954725 AX-123278433 6 75201248 AGACTTGAGCATGGAGAGATCAGTTAGGTTATTGC[C/T]CTAGGGCAGAAGGTAATGAGTGTCTGAATTGAGGA Y 2 1 2 1 101000 f 74 goat snp24465-scaffold248-1840148 6 77652852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431350 Affx-122937050 AX-123301691 6 75237432 CTATCCTGTCATTTATTAATTCTAAACTCAGGCCT[A/G]CCATCTTGAGAATTTATTTATTACTCATAAGATGA R 2 1 2 1 101000 r 74 goat snp24466-scaffold248-1876332 6 77688803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413865 Affx-122949858 AX-123284214 6 75267130 CCAATGTGCCTGAGGCCAGCATCTCACCACCAACC[A/G]TTCCTGTGGATTCAACACTTATGCTCTAAGGAAGC R 2 1 2 1 102000 r 74 goat snp24467-scaffold248-1906030 6 77718518 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782012 Affx-122942865 AX-385269091 6 75297704 AACTATGATAAATTTAATTTGATAGTAAAGGTCCA[G/T]TCCAAGGATGAGTATTAACAAGCAATCAGAACGGT K 2 1 2 1 101000 r 74 goat snp24468-scaffold248-1936604 6 77749744 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442432 Affx-122927971 AX-123312769 6 75342927 TTCTAAGAAATGTGAATCTTTCTAATTTTGAAAAT[A/G]TTTCTTTCTTTGGAGAATGAACAAACAACGAAATC R 2 1 2 1 103000 r 74 goat snp24469-scaffold248-1981827 6 77795365 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444492 Affx-122926519 AX-123314829 6 75395713 GAACATAAAAAGTGTAATTGTTAAAGGAGGTCAAG[C/T]GTGCCCAGGCTTTGTTATTTGATATCACAGCACAT Y 2 1 2 1 201000 f 74 goat snp24470-scaffold248-2034613 6 77847993 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785633 Affx-122936705 AX-385272675 6 75437604 CCACTTTAGAATACTCTGCTTCTATCCATATTACC[A/G]TAGGTAAGTGAGAACTGACTTTATTACATAGTAAA R 2 1 2 1 201000 r 74 goat snp24471-scaffold248-2076504 6 77889923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423823 Affx-122942796 AX-123294169 6 75535467 GTCTTAAGTGTTTATGTTTTTCTTAATTCCTTGAT[A/G]GTGAGAAATGATTAACTAAAACATTTGTTAATGAA R 2 1 2 1 201000 r 74 goat snp24472-scaffold248-2174367 6 77987320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse271 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278564 Affx-1111836402 AX-519552044 6 75555731 TGCCTAAGCCTTAGTATGGTCATCAAAATACTGAT[C/G]ATCTGAATTCAGACTAGATGTTTCTAAACCGGTGG S 4 1 2 1 101000 r 74 goat Random2.2K-703 6 75555731 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394643 Affx-122964390 AX-123264998 6 75566667 TAGATAGTGAAGCTGAGTACACACATCTTGAAATT[A/G]ATGTTTTAAAAACATTTTCCTGTTTATGGAAGCCA R 2 1 2 1 101000 f 74 goat snp24473-scaffold248-2205567 6 78018184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377918 Affx-122977230 AX-123248277 6 75597316 CTGTTCAACTTCGGTTCAAAACTGTAGTTAAGTTC[A/G]TTTCTTTGGAACCAAATAAAATGAAAAAGTAACAT R 2 1 2 1 103000 f 74 goat snp24474-scaffold248-2236216 6 78048833 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476222 Affx-1251763727 AX-586011646 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20000 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 539476476 Affx-1251763727 AX-586011876 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 4 1 4 1 20000 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165370 Affx-1251763727 AX-606940781 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165377 Affx-1251763727 AX-606940788 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165409 Affx-1251763727 AX-606940820 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166203 Affx-1251763727 AX-606941611 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166339 Affx-1251763727 AX-606941747 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166457 Affx-1251763727 AX-606941865 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 38442491 Affx-122927923 AX-123312828 6 75648175 TTATTATATCATCATTTCATCACCCAGGAACCTGC[A/G]TTGAGCATGAGATTCTCACTGTATGCAGTATATAA R 2 1 2 1 101000 f 74 goat snp24475-scaffold248-2287075 6 78099933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394652 Affx-122964383 AX-123265007 6 75676925 TTCAGATTTCTAGTTATAAATATATTTAAGGGCTA[C/T]AACATCTCACAGAGCTTCTGTGTTAGAAGCAGACT Y 2 1 2 1 103000 r 74 goat snp24476-scaffold248-2315825 6 78128675 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771069 Affx-122940947 AX-385258229 6 75720398 GGGAGATGGAGTGACAATACAATTTTTTTACAAAA[C/T]GATTTGATATTGAATATGCAGAATTAATAAACCGT Y 2 1 2 1 201000 r 74 goat snp24477-scaffold248-2359298 6 78172617 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417396 Affx-122947688 AX-123287744 6 75756138 TTAATTTCAAACAAGCTAGAGGGGAGACCATCATA[A/C]AGAAATGATGCAAATCTTTAATTAGAAAAAATTAA M 2 1 2 1 101000 f 74 goat snp24478-scaffold248-2395038 6 78208246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443874 Affx-122927506 AX-123314211 6 75812828 GTTTAGTAAAGAGGTTTCTCTGGAGCTGTTGTACT[A/G]CTTGGTTGCTCCATCTTCTTTTGAGGAAGAGGCTT R 2 1 2 1 101000 r 74 goat snp24479-scaffold248-2451728 6 78265646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446796 Affx-122925300 AX-123317132 6 75852226 TGTGATTAGTCTTTTTTAAGAAACAGAAGAAAACA[C/T]AATGAGTAATATGGAAACAGGTAAAATTTTTTTGT Y 2 1 2 1 101000 f 74 goat snp24480-scaffold248-2491126 6 78305644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376942 Affx-122977774 AX-123247301 6 75894354 AGTAAAACTTAAAAATGATAAATTTTGGGAAAATA[G/T]CCAAACCTCTGAAGTAAAACTCAAGTGACAAGTAT K 2 1 2 1 101000 r 74 goat snp24481-scaffold248-2533254 6 78348338 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408723 Affx-122953420 AX-123279074 6 75943148 TGCAGTGTTCTATTCTCTATGTTTTCAGATATTTT[C/T]CAGAAAGAAATGATAACCAAAATAGCAAAACACAT Y 2 1 2 1 101000 r 74 goat snp24482-scaffold248-2582048 6 78398367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794987 Affx-122953654 AX-272333284 6 75977807 TTAATTTAAGCACTCTTGTGGTCTAGAAGAAAACT[A/G]CTTTGCCTCAGTACTCAAATGTATGACCTCCAGAA R 2 1 2 1 101000 r 74 goat snp24483-scaffold248-2616707 6 78433050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781425 Affx-122940110 AX-385268510 6 76062429 CAAAGATATATAATAAGGATAATATGCTTAATAAC[G/T]AAAAGAAGTCTACTTTGATAGAATCCTAAGTGAAT K 2 1 2 1 101000 r 74 goat snp24484-scaffold248-2701329 6 78517278 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796797 Affx-122971844 AX-385283740 6 76116354 CTACTGAGACTGTATAAGATGGAACTTCACTAATG[C/T]CCGTTTATTTTATTTGGATTGAATTGGCCTACAAC Y 2 1 2 1 101000 r 74 goat snp24485-scaffold248-2755254 6 78573134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428333 Affx-122938999 AX-123298676 6 76199241 TGGGAGTCGGGACTGGAAGCAGAGGGGCTGGAGCC[A/G]GAGCCAGGTATGAACTAGGGTTTCTATGCTCAGTG R 2 1 2 1 101000 r 74 goat snp24486-scaffold248-2838141 6 78657310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273225 Affx-1111833516 AX-519546882 6 76212340 CGTATGCAAAGAGTTGACTCATTGATGAAGACTCT[A/G]ATGCTGGGAGGGATCGGGGGCAGGAGGAGAAGGGT R 2 1 2 1 103000 f 74 goat 6_76212340_AF-PAKI 6 76212340 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274740 Affx-1111834468 AX-519548326 6 76218877 AGATGAGGAAATAGGGTGAGACTGGTGAGTGACAG[A/C]ACAGGCAGAAGCCTGCAGAATGGGATTCAAAGCAG M 2 1 2 1 201000 f 74 goat GoatD01.037030 6 76218877 G T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423400 Affx-122943119 AX-123293746 6 76237641 AACTACAGGTTGTAGTTTTAAAAAATTAATAAGCT[A/G]CTATGGCAGGGGCTGACATCTTAAAGAAGAACTTC R 2 1 2 1 103000 r 74 goat snp24487-scaffold248-2876541 6 78692249 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447345 Affx-122924882 AX-123317681 6 76268797 ATTTATTAATTTTTTTCCCATTTCAGTAGTTGAAC[A/G]TCAGAACACATGGCTTAAAGCAGTACATTTTAGTT R 2 1 2 1 101000 r 74 goat snp24488-scaffold248-2907697 6 78723789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432195 Affx-122936391 AX-123302536 6 76307936 AACTGAAATATAATGAAAAAGATAATTCTCATTTT[A/G]CATTGATATTTTCTTATAAAATTAATGTATACTAG R 2 1 2 1 103000 r 74 goat snp24489-scaffold248-2946836 6 78763081 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431399 Affx-122936542 AX-123301740 6 76360010 TCAGACACAGCTGAGCAACTAACATACATATTCCC[A/G]TGAGAGAACCGAGATTAGTTAATCCCATCTCCCGG R 2 1 2 1 101000 r 74 goat snp24490-scaffold248-2998910 6 78816057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801184 Affx-122934108 AX-385288097 6 76446487 TTGAAATCTGGAAGCCATAGAAAGAATACTGAAAC[C/T]ATTATCAATTGGATTACTTCATATCTCTCTACAGC Y 2 1 2 1 101000 f 74 goat snp24492-scaffold248-3085387 6 78903196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790586 Affx-122942415 AX-385277589 6 76519217 AGAAATGCCTGAGATGTTAGGTCTTTCCTTAAGTA[C/T]AAATTTACTATTTTAGTCTGATGCAACAATAATAA Y 2 1 2 1 201000 r 74 goat snp24493-scaffold248-3158117 6 78976441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395320 Affx-122964051 AX-123265675 6 76622277 ACTAATAATTCAATGCTGGAATTTCAAAAGGAGCT[A/G]TACAACAAAGCAGGTCTTTGTGAAACAGAGTACAA R 2 1 2 1 101000 r 74 goat snp24495-scaffold248-3261177 6 79080650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802722 Affx-122947892 AX-385289621 6 76668935 AACAATCATTATGGAGGTGATACACAGTACTGAAG[C/T]ATCATAGTTTCAAGTCTTTGCAGAGGACAAAGCTA Y 2 1 2 1 101000 f 74 goat snp24496-scaffold248-3307835 6 79128493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772122 Affx-122927064 AX-385259276 6 76749714 ATATAGTCCCTAACAAGAAAGATGAATTTAACATC[A/G]TTATAGTAGATTAAGAAATACAGTAACCCCAAAAC R 2 1 2 1 101000 f 74 goat snp24497-scaffold248-3388614 6 79209818 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786156 Affx-122942076 AX-385273192 6 76801029 TATTGTCCGATAGATATGTAAAGTCTGCCAAATAC[A/G]TAATTTTTAATTTTCTGGTACATTAATATTTCTGC R 2 1 2 1 303000 r 74 goat snp24498-scaffold248-3439929 6 79262166 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444435 Affx-122926561 AX-123314772 6 76921365 TTTTAACAAATAAATGATGCAACAGGTTTCTTCAG[C/T]CTAAGTTTTTAACAGCTATTAAGTTTTTGGTGGTT Y 2 1 2 1 101000 r 74 goat snp24500-scaffold248-3560265 6 79383630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782964 Affx-122961223 AX-385270033 6 76974481 CATATACCATGATCAAGAAAGATTTATTCCAGGGA[C/T]GCAAGTAATTTTCATTACCTGCAAATCAATTACTG Y 2 1 2 1 201000 f 74 goat snp24501-scaffold248-3613381 6 79437999 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413018 Affx-122951004 AX-123283367 6 77011193 ACACTCTCACCAGGACTTTAGCTACATATTGCTAA[C/T]AAAAAGTTAGAAAACATTTGTAACTGATTGGTTTT Y 2 1 2 1 202000 r 74 goat snp24502-scaffold248-3650093 6 79474329 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433229 Affx-122935613 AX-123303570 6 77047398 AAATAAAATGCATACTGTTAGAAGAGAAGGAATGA[G/T]CAGATGAAGAAAGACAAGAAACAAAAATAAATCCA K 2 1 2 1 101000 f 74 goat snp24503-scaffold248-3686298 6 79510603 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440333 Affx-122929674 AX-123310670 6 77096243 AATGAAAAATTAAAAATAAAATAGTTGCTTTATTA[C/T]GCTTACATCATTTGTAAGTCATGGTGATGAATTTC Y 2 1 2 1 103000 r 74 goat snp27941-scaffold30-18900 6 79560290 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432643 Affx-122935473 AX-123302984 6 77134685 GGGAAGATGGAGTGGATGTGCTTTACTTATTTCTC[A/G]CACTAAGAACAACTAAAAATATTTGACATGGTAAA R 2 1 2 1 101000 f 74 goat snp27942-scaffold30-57342 6 79599228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425178 Affx-122941050 AX-123295524 6 77174216 AAGTATTACTGGTGAGAATTTTAAAACATGTAAAA[A/G]TGATGACAGTGGAAAAGAGAAAGTGAAAAGTTTGT R 2 1 2 1 201000 f 74 goat snp27943-scaffold30-96873 6 79639059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437470 Affx-122932377 AX-123307808 6 77391292 TGTCACAGCAGGGTGTGCATATTATCAAGATATTT[A/G]TTATTGGTTATATTAACATTGGCCACTGGTTAAGA R 2 1 2 1 101000 r 74 goat snp27947-scaffold30-313949 6 79902177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791404 Affx-122969506 AX-385278396 6 77424068 TCCATACCAACACAAGCATATATACATTACCTTGT[A/G]CTACTTATGGATTATTAGATGAAAGATAAATAAGC R 2 1 2 1 101000 f 74 goat snp27948-scaffold30-346725 6 79935318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779448 Affx-122928222 AX-385266551 6 77473818 GAAACACTGAGGTATAGGATGAAATGAGAGAATAA[C/T]GGAAACCATTTCAGATGTCTTATTAAAAAATATAT Y 2 1 2 1 101000 f 74 goat snp27949-scaffold30-396475 6 79986173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse272 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377842 Affx-122977289 AX-123248201 6 77510393 AAGACCAAGTATTCTTAGACCATCCTTGTGAACAC[A/G]TACATCACAAAATGAAGCATGAACATATAAAAATG R 2 1 2 1 101000 f 74 goat snp27950-scaffold30-433050 6 80013238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416841 Affx-122948109 AX-123287189 6 77545118 AAAAGAAAAGAAACCTAGATAAAGTAATACAAGAT[A/G]TTTATTGGCTCATGGAATTTAATTTAGGTCAGAAA R 2 1 2 1 101000 r 74 goat snp27951-scaffold30-467775 6 80048034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785635 Affx-122952925 AX-385272677 6 77591033 TCATTTTCTTAATGGGCTATGGAATTAATAAACAT[A/G]CAATGTTAAATAGCCCTTCAAGGTTAAAGTCTGAA R 2 1 2 1 101000 r 74 goat snp27952-scaffold30-513690 6 80078674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788036 Affx-122925070 AX-385275057 6 77626938 CTTTCAACACTATTAAGGACAAATAATACACATTT[A/G]TGGAACAAATCAGTTTGCAGCATCTGATTTTGGTA R 2 1 2 1 101000 r 74 goat snp27953-scaffold30-549595 6 80114517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422622 Affx-122943714 AX-123292968 6 77656918 TATAGAAAAAGGATAAAAGATAAAACATCTTTAAA[C/T]ATTGATATAGTAACTGACTTGAAAATCTGGATTTA Y 2 1 2 1 303000 f 74 goat snp27954-scaffold30-579575 6 80144179 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406383 Affx-122955404 AX-123276735 6 77688838 TTTAAAAAAGAATTATAATAATTTTTATACAATGC[A/G]TGGACTTACTATCATTCAACCCTTCAGTTATTCAG R 2 1 2 1 101000 r 74 goat snp27955-scaffold30-611495 6 80176716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386791 Affx-122970917 AX-123257149 6 77733863 TTTCATCCATTCCCAAGGGTCGATGTGTGTGTACC[C/T]GTGTGTGTATCTGTGTTGAGATGAATTCTTATTTC Y 2 1 2 1 102000 f 74 goat snp27956-scaffold30-656520 6 80221731 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408834 Affx-122954020 AX-123279185 6 77811218 CAGTAAACCTGATAAAAATTTCTTATTCTGTGTTG[A/G]CTTTGACCTGATAGTTTATCTTAAATCATTTCTTT R 2 1 2 1 101000 r 74 goat snp27957-scaffold30-733875 6 80298430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse273 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320796807 Affx-122925325 AX-385283750 6 77848033 GTACATTGTAGTTCTTTCATACTTCTAAAATCTAA[C/T]GAACATGAAACATTTTCCCCAGAGGAGCCCATAGA Y 2 1 2 1 102000 r 74 goat snp27958-scaffold30-770690 6 80336432 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447713 Affx-122924607 AX-123318049 6 77877528 TCTGTGGAAACCATATTTTATTACATATTTCTGTT[A/G]CAGCCATTCACTGCTTTCTAATTTGTATTACACAT R 2 1 2 1 101000 r 74 goat snp27959-scaffold30-800185 6 80364362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383463 Affx-122973449 AX-123253821 6 77907284 CAGAATAGTTTACTTTCCTTTAAAATGAGCAATAG[C/T]ACAGAACTTCAGTTTTTGTTTTTTTCTAGAATTAT Y 2 1 2 1 101000 f 74 goat snp27960-scaffold30-829941 6 80394184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783110 Affx-122964039 AX-385270177 6 77953101 GTCCATCTGCAGAATGATAAATTATATTTGAAAGG[C/T]AAAATAGCCCAAGGCTTCTTCAAGTAAGCTTTAAA Y 2 1 2 1 101000 f 74 goat snp27961-scaffold30-875758 6 80439756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440908 Affx-122929217 AX-123311245 6 78000019 GATTCAAGAGGCCATGTATTTTTCCATTCTTTTTG[C/T]GAACACCCTGAACAGCACCTTGTAACAGAACCTAA Y 2 1 2 1 101000 r 74 goat snp27962-scaffold30-922676 6 80487198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429412 Affx-122938522 AX-123299754 6 78041848 AAAAATCTAGGCAAATGTCACATAGGCTGAGAAGA[C/T]GAGCACTGAAATTTTGCCTCCTGACTATGGCCCCA Y 2 1 2 1 101000 f 74 goat snp27963-scaffold30-964505 6 80529767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423133 Affx-122942768 AX-123293479 6 78074634 GAGAAGTAGGATGTTTTCGGCAGCACAATTCACTG[C/T]GGTGATAAAAAAATAATAATAACTGAGATAAGCTC Y 2 1 2 1 101000 f 74 goat snp27964-scaffold30-997291 6 80562582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse274 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320780542 Affx-122928955 AX-385267633 6 78130338 CGTTAGTTTTAACATCCATTATTCCATAATCCATT[A/G]TTAGATGATTGTCACAAAATGATAACCGTCATTTT R 2 1 2 1 101000 f 74 goat snp27965-scaffold30-1052995 6 80618555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394069 Affx-122964972 AX-123264424 6 78178268 TCACTATTTTGTCTAAAAATTAATTTTTACTGCTT[A/C]TATCTTATGTGTTTCTCCCCATTCCATGAAACAAA M 2 1 2 1 101000 r 74 goat snp27966-scaffold30-1100925 6 80666948 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787290 Affx-122933253 AX-385274315 6 78232492 GAGACAAGTTACTTGACTGCAAATCTCATTTTTTC[A/G]TTGTTTTATTTATCATAGTGTTAATAATATTAATC R 2 1 2 1 202000 r 74 goat snp27967-scaffold30-1155149 6 80722486 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382046 Affx-122974939 AX-123252404 6 78264337 TGATGCAGTGCCTTTTGTATTCAGAGAATATACAT[A/G]CATAGTTTTACGTGTGCACACAAATTAACATTTAT R 2 1 2 1 101000 f 74 goat snp27968-scaffold30-1186994 6 80754569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse275 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783861 Affx-122932383 AX-385270917 6 78379861 ACTTAATTTTTGTAATTTTTGAGTAAATTCCAAAA[G/T]CCTACTGCTAACCTTATGGACCAAAATATGGCAAG K 2 1 2 1 202000 f 74 goat snp27970-scaffold30-1302518 6 80871249 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420500 Affx-122944854 AX-123290847 6 78436051 TCTTCTTTATCTCTCGTTAAACTTTACAAATTTCC[A/G]TTACTATAAGCCTAGACATGACCAACCATATGATG R 2 1 2 1 101000 r 74 goat snp27971-scaffold30-1358708 6 80928252 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447973 Affx-122923758 AX-123318309 6 78468711 AAGTAAGTTTGACAAAGGAGGCTGTATGGTATGAT[A/G]TTAAGAATAGAGTCTATGAAATTAGATATATTGTC R 2 1 2 1 201000 r 74 goat snp27972-scaffold30-1391368 6 80961287 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse276 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783008 Affx-122927470 AX-385270076 6 78506979 AGAGCATGAACTGAGTATAGAAAAGACCCAGTTCT[A/G]CTCCCAAACATTGGTACTCCTTCACTTTGCTTCAT R 2 1 2 1 201000 r 74 goat snp27973-scaffold30-1429636 6 80999545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407769 Affx-122954969 AX-123278120 6 78563952 ATCTGATTTTTTTTAACTGTATCTGATTTTTCACC[A/G]TGAAATTAGTATTGCCAACATGTATAGCACTACCC R 2 1 2 1 101000 r 74 goat snp27974-scaffold30-1486609 6 81048838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787836 Affx-122954349 AX-385274859 6 78597373 GAAAGTAACATTCACTAAACAAATACATGATGAAT[A/G]CCTACTTAAATGAATGTTTCTTTGATTAAGCAAGT R 2 1 2 1 101000 r 74 goat snp27975-scaffold30-1520030 6 81082930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788955 Affx-122922009 AX-385275968 6 78634160 AAGGTTGCAAAGCAGGGAGTGGAGAATTTTGACAG[C/T]ACTAAATAATTCCTGTTTATCTTATGTTAACTCTG Y 2 1 2 1 101000 f 74 goat snp27976-scaffold30-1556817 6 81119678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406686 Affx-122955781 AX-123277038 6 78708653 CAAAATTCCTAAACAGGGAAGTTTGGGCCATTTCT[A/G]TGTATTAAAAACTTTCAAGGGGCCTTGAGAATTCA R 2 1 2 1 202000 f 74 goat snp27977-scaffold30-1631310 6 81184265 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse277 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273227 Affx-1111833517 AX-519546883 6 78750467 TCAGACTCATTTACAAGGTAAAGTTTGGATCAATC[A/C]GACAGTTCAACATCTTTCTCACTCTTTTTTGACCT M 2 1 2 1 201000 f 74 goat 6_78750467_AF-PAKI 6 78750467 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389224 Affx-122969052 AX-123259582 6 78758991 ATGGCCATTGCAGTGGCATATTTGTAAAGTAACTA[C/T]ATGTATAGGTTTGTTTCCTAATTCTCTCTTGGTTT Y 2 1 2 1 101000 f 74 goat snp27978-scaffold30-1681648 6 81234384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449570 Affx-122923234 AX-123319905 6 78819485 TCTTACTTGTATTTTTTCCAGATGGCCTTCTGAAG[A/G]CCATCATTTTTCAGCTGTTTGTGAAACAAATGCTA R 2 1 2 1 101000 r 74 goat snp27979-scaffold30-1742142 6 81296323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse278 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38385641 Affx-122971171 AX-123255999 6 78852104 CCATCCATATATTCCATGATTTTCTCTCTATCTAA[C/T]GGTTAGCTGATTCAATAGCAACTCTAATTCCACTG Y 2 1 2 1 101000 r 74 goat snp27980-scaffold30-1774761 6 81329129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278399 Affx-1111836403 AX-519551884 6 78889128 GACCTTTTTATGTGAAGCACCTGATTTTGATAAAG[A/G]TCAGGACTGCTGACCCCCGCGTGACTCTGTATTCA R 2 1 2 1 303000 f 74 goat Random2.2K-708 6 78889128 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767054 Affx-122975088 AX-385254344 6 78893700 CATTAAGGGCAGTAGCTCTTTTCAGGAAGAGATTA[C/T]GCTAGAACTATTATAAGGGTAAATTCAAGTATTTG Y 2 1 2 1 101000 f 74 goat snp27981-scaffold30-1816357 6 81371504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379048 Affx-122976346 AX-123249407 6 78924159 AAAAGAGACAGGGTGCACATAGGATGAAAAAAGAA[C/T]AGGAAAAATAATTAAAGCAACCTACCTGGTCCTTC Y 2 1 2 1 201000 f 74 goat snp27982-scaffold30-1846816 6 81401376 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407859 Affx-122954514 AX-123278210 6 78971556 ATCCATAGTAGCACAGGTGTCTTCCTTCATCAAAT[A/G]TATCTTGGTTCTATTGGCATTTAGAGCATTCTGAA R 2 1 2 1 201000 r 74 goat snp27983-scaffold30-1894213 6 81446998 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799033 Affx-122928306 AX-385285963 6 79009002 GAACACATCATTTCCGGTAAAGCAGTCTCTTTTCA[C/T]AAGCTATCTCAAAATTAGGTTAAACAAACTTTGGG Y 2 1 2 1 101000 f 74 goat snp27984-scaffold30-1931659 6 81484507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785247 Affx-122970847 AX-385272292 6 79060435 ATTAAAAAGCAAGCAAATTTCACTACTTCTAATGA[C/T]ATATTTTCACTATATGAAAAGCTAAGATCTCACTA Y 2 1 2 1 201000 f 74 goat snp27985-scaffold30-1983092 6 81536993 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425906 Affx-122941619 AX-123296252 6 79129246 AGTTGTTTATACAGGGGTTGTAATACTGAAATAGA[C/T]AAAAGGAAATACTGATGTATTTCACTGGTAGATCC Y 2 1 2 1 101000 f 74 goat snp27986-scaffold30-2051903 6 81606037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797870 Affx-122940888 AX-385284808 6 79168154 CCAATGTACTTCTCTAGGAAGCTAGCTAGCACAAA[C/T]GCTAAATGCTTGTTCAATTAGTTGACCAAGATCTG Y 2 1 2 1 201000 r 74 goat snp27987-scaffold30-2090811 6 81645057 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387589 Affx-122970261 AX-123257947 6 79210762 GCAAAGAGTCGGACATGACTCAGCGACTGAATTGA[A/C]CTGATAATGCTCTCAGAATAATTCTTCCTGTTTTA M 2 1 2 1 202000 r 74 goat snp27988-scaffold30-2133419 6 81688698 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772438 Affx-122960821 AX-385259589 6 79266060 AAAGTAGACTTTGTTTTAGACAAAAACATTACATT[A/C]TAAATGAAGAAATACAACTACCTAGACTCTAAAAT M 2 1 2 1 101000 r 74 goat snp27989-scaffold30-2188717 6 81745130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380566 Affx-122975277 AX-123250924 6 79318962 CAGTTCTGGCAGCTGTCCTGTCCGGATGTATATAA[C/T]GTGCAGTGGAATACATGAAGGATTCATGAAGCATA Y 2 1 2 1 101000 f 74 goat snp27990-scaffold30-2241619 6 81804650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425980 Affx-122941157 AX-123296326 6 79377086 ATTTTTGAGTTCATTCAAGCTGAGCAGTACTTCTT[A/C]TCTTTTGAAATGTCAGGTGGTTGGTCTGAGGAAAA M 2 1 2 1 201000 f 74 goat snp27991-scaffold30-2299743 6 81862810 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795666 Affx-122939027 AX-385282621 6 79418719 AGCTTTCTTTCCTAATAATTCAACAGATTAGGAAT[A/G]TAAAGGAATTTCATCAACATCATAAAGAGCATCTA R 2 1 2 1 201000 r 74 goat snp27992-scaffold30-2341376 6 81904295 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799798 Affx-122956206 AX-385286724 6 79469448 TTCAAAATAGAAGATCCAACTTTTCAAATTGCCTC[G/T]CCCTACTGAGTGCCAGGTGAGACATTAATAATTAA K 2 1 2 1 101000 r 74 goat snp27993-scaffold30-2392105 6 81955740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780209 Affx-122927013 AX-385267305 6 79507804 GAGGTCTGGGGCTAAACTGGGGATGGAGATCTGAT[C/T]CAGTGTACATATACAATGAAGGAGTCTAAATTTTG Y 2 1 2 1 101000 f 74 goat snp27994-scaffold30-2430461 6 81996285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse279 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376586 Affx-122979069 AX-123246945 6 79579734 CTATGCATAAAATATGTGAATAAATGTAACTACAA[G/T]CAGAAAGCAAAGGAACAAATCAGAGCTTGAAAGAG K 2 1 2 1 201000 f 74 goat snp27995-scaffold30-2502391 6 82067071 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786422 Affx-122927258 AX-385273456 6 79624781 TGTCCTTGTCTGTTGGGATACACAAATAAACAATG[C/T]AGTTTTCTAGTACTTTCCTGAACTATGACATTATC Y 2 1 2 1 101000 f 74 goat snp27996-scaffold30-2547438 6 82113961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445678 Affx-122926135 AX-123316015 6 79699474 AAATGGGGATTGTGAAAATTACAGAAAACTAAGGA[C/T]TAGAGATAATGTAAAATGTGTAATGACCTGAGATG Y 2 1 2 1 101000 r 74 goat snp27997-scaffold30-2622131 6 82190647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792863 Affx-122978220 AX-385279841 6 79728463 TATTAGCCTAAGATCTTTCCCAATATTAAGTAATG[C/T]ATCTTTTTTCTCTTGTTGTATCTATATTGGTAGAC Y 2 1 2 1 101000 f 74 goat snp27998-scaffold30-2651120 6 82219569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767064 Affx-122955456 AX-385254353 6 79746635 AGAAATCAAGTTTAAAGATAGCAGTGTTGATACTC[A/G]TCCTCCTGAATGTAATAATAAATACTGTAAGATTG R 2 1 2 1 101000 f 74 goat snp36190-scaffold433-12605 6 82237885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse280 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320772159 Affx-122969673 AX-385259315 6 79802352 TCTAATTATGAATATCTAGTAATAAGATAAAATGA[C/T]ATCAAATAATAAGATAAGATGGCATCTAGGACTTG Y 2 1 2 1 101000 r 74 goat snp36191-scaffold433-68322 6 82294794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770311 Affx-122922966 AX-385257476 6 79832023 ATCCCTCTTTAACTCCATGCTGAAAATGTGGAGCT[C/T]AAAATGGGACTACTCTTAGAATGTAATATGAGTTC Y 2 1 2 1 102000 f 74 goat snp36192-scaffold433-97993 6 82324888 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801797 Affx-122951479 AX-385288705 6 79871327 TTCCTTTTCAATGGTGAAAGGAATATCACATATTA[C/T]GCTCTATAAAGACATGAGTAGTAGAGAAATAACAA Y 2 1 2 1 101000 f 74 goat snp36193-scaffold433-137297 6 82364176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379150 Affx-122976722 AX-123249509 6 80011267 ACTAAGCCAAAAAGAGGAACTGAATTGGAGGACCC[A/G]CATACCAGATTTTTAAAAATTGTTATACAGGCCAT R 2 1 2 1 101000 f 74 goat snp36196-scaffold433-277237 6 82505537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse281 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421457 Affx-122943935 AX-123291804 6 80079001 CTGATAATAACTGCCTTATAAACTTGTAACCAAAG[C/T]AGGATTATCCAAATGTTTGGTTCTGGGCCTGGGTT Y 2 1 2 1 101000 r 74 goat snp36197-scaffold433-344971 6 82574479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451786 Affx-122921501 AX-123322119 6 80132082 CCATGTTCTGTCTATCCATATTGTTCACCTACAAT[C/T]TGAGCAAAAGCTATTTAAATTGGGGGAAGTCAGTG Y 2 1 2 1 201000 f 74 goat snp36198-scaffold433-398052 6 82628656 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795990 Affx-122953924 AX-385282942 6 80162527 AATAAGCCTGTGCAAAGTTTTCAGAACTCCACTTA[C/T]ATCAGTTTTTTTTAGACTTAATGTCTATGATTCAA Y 2 1 2 1 101000 f 74 goat snp36199-scaffold433-428497 6 82659561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791953 Affx-122952024 AX-385278943 6 80201296 TTTAACCAGCCCATACAGAGTTTTAAGGCCAAGAA[C/T]GGAGAAGAATTGTATGTAGATAAAATGAGGACTTG Y 2 1 2 1 101000 f 74 goat snp36200-scaffold433-467266 6 82698836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438403 Affx-122931288 AX-123308741 6 80245600 TTGACTATTACTTGACTATACTATTACTATTACTT[A/G]TTTGGCAGAGTAATGCCTCTGCTTTTCAACACACT R 2 1 2 1 201000 f 74 goat snp36201-scaffold433-511570 6 82743388 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440987 Affx-122928975 AX-123311324 6 80294542 GTTTGACTTAGCTGATGAGAAAAAGCAAGTAGGCT[A/G]TTTTCAAAAGACCAACCATTATTCAATCCCTGACT R 2 1 2 1 201000 r 74 goat snp36202-scaffold433-560512 6 82794061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403780 Affx-122957985 AX-123274132 6 80390108 GAAAAGGAAACCAAAATTAAGATTCAAAAAATGAC[A/G]CAGGAATAACCTTCAAAGAACATAGACACATCAGC R 2 1 2 1 101000 r 74 goat snp36204-scaffold433-656078 6 82889736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376800 Affx-122977942 AX-123247159 6 80422272 GCTAAAAGTATACCTACAAAATAACCTGCAACCCT[A/G]CTCCTGAAGGAAACCACAATTCCAAAAGACATATA R 2 1 2 1 101000 f 74 goat snp36205-scaffold433-688242 6 82922388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse282 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38389958 Affx-122968078 AX-123260315 6 80482270 GTTGACTGGATTCCCCTACGATCCACTTAGTTGTT[A/C]TCACTTTTTGGCTACAATGGCTTATCTTTTTTCTC M 2 1 2 1 201000 r 74 goat snp36206-scaffold433-748240 6 82981447 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385706 Affx-122971113 AX-123256064 6 80521898 GTCACTGCAAAGCATTCACAGTGTATCACTTTCCA[C/T]CCTTGTTATATTCTTTTTCAGAAAAATGAGATATT Y 2 1 2 1 101000 f 74 goat snp36207-scaffold433-787868 6 83022313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421376 Affx-122944041 AX-123291723 6 80553631 CCCAATTATAGAAAGGCAGTGTTTAAAAAAAAAGG[C/T]AGTCAAATTGACCAGTTTGATAGATGTCCACTATA Y 2 1 2 1 101000 r 74 goat snp36208-scaffold433-819601 6 83054831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436250 Affx-122932554 AX-123306589 6 80594073 CTTAGCACTTGCAGCCTGTTCTACTTCAGGCCTCT[A/G]CAGTCAGAAGGAGCCTTTAGGTACTTTCATTAACA R 2 1 2 1 201000 r 74 goat snp36209-scaffold433-860043 6 83096251 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407995 Affx-122954320 AX-123278346 6 80625907 GGGACATACCTGACAAAGCACAAGACACATCACAC[G/T]TGCTTGCGTGTTAAGTAGCTTCAGCCATGTCAAAC K 2 1 2 1 102000 r 74 goat snp36210-scaffold433-891877 6 83127761 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405196 Affx-122956917 AX-123275548 6 80705169 CATAATGAGGTCAAGGCAGCAATCAATGTCTGCTG[C/T]GCTGTCTCCTGTTTCTTGAAAGTACAACTGCTTTT Y 2 1 2 1 201000 r 74 goat snp36211-scaffold433-971139 6 83207820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse283 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38448446 Affx-122923647 AX-123318782 6 80758174 ATATTCAAAACACATGCATCCAGGATTACATTGAG[C/T]AACAATCTGCACATAAAGTTAAACACTGGAGACTT Y 2 1 2 1 101000 r 74 goat snp36212-scaffold433-1024144 6 83262094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775593 Affx-122935287 AX-385262724 6 80787787 CCTTTTTATGAATACTCCTTCTGATCCTTTTTTTC[A/G]TCTTTTGTTAGTCCCATTATATGTACATTATATAT R 2 1 2 1 101000 f 74 goat snp36213-scaffold433-1053757 6 83291850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse284 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449431 Affx-122922680 AX-123319766 6 80837359 GTTCAGTATTTCCCAGGAAGCATACATGATGGGCT[A/G]TGGGAAAGGCAATCTTTCAGTGTTTTCAATAATAA R 2 1 2 1 101000 f 74 goat snp36214-scaffold433-1103329 6 83341218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785054 Affx-122941330 AX-385272101 6 80896456 TGCCAATATCTTGAAAGAAAATGCCAGAATCAATA[A/C]TTAAGCATTCTTTAACCTCTATAAGATAAACCATT M 2 1 2 1 202000 f 74 goat snp36215-scaffold433-1162426 6 83400743 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764962 Affx-122962516 AX-385252541 6 80926961 TTAGTTGAGCTTTTGCCCATTTCTCTTTGTCAGTG[C/T]GTTCAACCTGCAACTCAACAAACATCTCATTTTCA Y 2 1 2 1 101000 f 74 goat snp36216-scaffold433-1192931 6 83432946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402037 Affx-122958735 AX-123272390 6 80985023 AGGTTTTTTGTGTGTGTGTAATTTCAAGGCTACTG[C/T]GGTTGAACAGCTACTTTGATAGCTTAGCAGTTAAA Y 2 1 2 1 201000 r 74 goat snp36217-scaffold433-1250993 6 83490974 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409766 Affx-122952992 AX-123280117 6 81014570 CCATCAGTTTGATCCCCAAACAATGAAATGCATAG[C/T]ACAAAAAGAGCTTAACTCTGCACATTTGATCTCAA Y 2 1 2 1 201000 r 74 goat snp36218-scaffold433-1280540 6 83520284 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422354 Affx-122943438 AX-123292700 6 81044577 CTCTTTCCAGTAGTTCATTTCCACAAATTGCAGCC[G/T]AGGGAGCAGGAAAGACCACAGGCGGACCCAGAGAG K 2 1 2 1 101000 f 74 goat snp36219-scaffold433-1310547 6 83550716 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420729 Affx-122944769 AX-123291076 6 81074637 CAGTAGTATCATTATTTTGTAGCTAAGGAATATGA[G/T]CATGGGGGCAGTGATGGCTCATCTAGTCAGAATGG K 2 1 2 1 202000 f 74 goat snp36220-scaffold433-1340607 6 83580897 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393196 Affx-122965509 AX-123263553 6 81108353 AGGCTTTTAATAAGACCAGGCAGATGAAGGTTCAA[G/T]CTCCTGTGCTCTGGACACTTACTTCCTTATATCAC K 2 1 2 1 101000 f 74 goat snp36221-scaffold433-1374323 6 83615197 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse285 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38390611 Affx-122967172 AX-123260968 6 81142637 ATAGTAGACAAAAGGTTAATGTTTGCTTGTAAGAA[C/T]GACACAAAATAGAAAACAGGTATTGACTAAGTGCC Y 2 1 2 1 201000 f 74 goat snp36222-scaffold433-1408607 6 83649734 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse286 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320794914 Affx-122936440 AX-385281874 6 81176060 TTCTGAACAAAATCCTCTCCTGCTGGCATGTTTAT[A/G]ACTCACTAGCATTACCTCCTGTATGCCAGAGATAT R 2 1 2 1 101000 f 74 goat snp36223-scaffold433-1442030 6 83683464 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38431431 Affx-122936515 AX-123301772 6 81206252 TACAAAATTTTGTCCTGAATTCAAGAATTTGAGCA[A/G]TCCTTTGACTACGCATATGATCTTTTCTCAAATAT R 2 1 2 1 101000 f 74 goat snp36224-scaffold433-1472222 6 83714089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406546 Affx-122955114 AX-123276898 6 81239014 AGAAATTAATCACTTCCTCCTACAAGTCTCTCAAT[A/G]TCTTCAACTATCTCCACCCTTCTTGCTTGTTGCGG R 2 1 2 1 101000 f 74 goat snp36225-scaffold433-1504984 6 83747651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273279 Affx-1111833519 AX-519546925 6 81250711 AACAATTTTATAATGAAATGTCAAGCAGTTAAGTG[A/G]TGTGTGCAATAGAATCAAGATGACTTTTGCTGTAA R 2 1 2 1 101000 r 74 goat 6_81250711_AF-PAKI 6 81250711 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396173 Affx-122963774 AX-123266528 6 81297166 ATTCACTGCTTGCCAGGCTAACACCCATCAATTTG[A/G]AAAACTCTGAAATCCTTCTTGACTTTATGCAAGAA R 2 1 2 1 101000 f 74 goat snp36226-scaffold433-1563136 6 83805503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439212 Affx-122931030 AX-123309549 6 81328007 AATGTCAAGTGAAAAAAGCAACTCCTAGAAGACTG[C/T]ATATTTGGTTTAGCGCCCTTTATATACTCTGCTGC Y 2 1 2 1 101000 r 74 goat snp36227-scaffold433-1593977 6 83836778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436960 Affx-122933168 AX-123307298 6 81407294 TAATAAAAGACCTAGGTACACTTATTTATCTTAAG[C/T]GTACCTTACTTACATGTAAAAATAGAGCTAATACA Y 2 1 2 1 101000 r 74 goat snp36228-scaffold433-1673264 6 83917206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427221 Affx-122939577 AX-123297564 6 81458232 ATTTAACATCACAAATACAAGAGAAATGAATAAAG[C/T]ACAGCAACATGAATGATTATGTTAAACAAAACAAA Y 2 1 2 1 101000 f 74 goat snp36229-scaffold433-1724202 6 83969304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379070 Affx-122976328 AX-123249429 6 81547288 CTGGGCTTTTGGTAAAAATTTCCTTCCCCACCTCA[C/T]GTTTTCATTACTCTATGTCTTTGGTTATTTTTAAC Y 2 1 2 1 201000 r 74 goat snp36231-scaffold433-1813258 6 84058501 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391033 Affx-122966871 AX-123261390 6 81585781 TTTCACCACGAAAAGGATTTATCAGGCAAAAAATT[A/G]TTTCCCACCTTGGAATTTAGATGACTTAAAGTTGA R 2 1 2 1 101000 f 74 goat snp36232-scaffold433-1851751 6 84097842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423824 Affx-122942795 AX-123294170 6 81614567 AGTACTGAGTCCTGAGGTCAGGCCTTCATGAACAT[G/T]GTTGGAAAGCAGCCAACCTACTGAGTTTTGGAGCA K 2 1 2 1 101000 f 74 goat snp36233-scaffold433-1880537 6 84126949 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764734 Affx-122938656 AX-385252351 6 81678042 TCTCAGGATCAAGCCACATGAAAAAGGTGTGTTCT[A/G]TTAACATGATTTATATCTCAGCATTAGCCAGTTAC R 2 1 2 1 101000 f 74 goat snp36234-scaffold433-1944012 6 84191264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442777 Affx-122927735 AX-123313114 6 81714484 AACTATCTTGATTCACAAATGTAAAATTATGGTTC[A/G]TTAATAAAAATTTAAAGGCAAATAAACTTTATTTC R 2 1 2 1 103000 f 74 goat snp36235-scaffold433-1980454 6 84227696 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386255 Affx-122970956 AX-123256613 6 81748393 GAGAGCTAAAAAAGAAAACTGAGAAGAAATAACTG[A/C]GAAGTAAAAGGAAAATCAAAGTGTAGAGGGTTATG M 2 1 2 1 202000 f 74 goat snp36236-scaffold433-2014363 6 84262013 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse287 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421792 Affx-122944335 AX-123292139 6 81819089 TTCGTGTTTATTTTAGGTTTATTTTCTCTTCTTTT[A/C]TAGTGTCTTAAAAGGAGAGCTTTCTTATTTTATAA M 2 1 2 1 103000 r 74 goat snp36238-scaffold433-2085059 6 84333659 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794111 Affx-122921129 AX-385281077 6 81848962 GGAAGTCTGAAAGGCTGACAAGTATATGGCAGTGA[C/T]GCACAATTGAAATATGCAATAGAAAAATGCAAATT Y 2 1 2 1 101000 f 74 goat snp36239-scaffold433-2114932 6 84363690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431351 Affx-122937049 AX-123301692 6 81884920 TCTTAGCTGTGATCACATAGTTACATGAAGGATAA[C/T]GTTAGATTTAAACTTGGGATTCCTCACCACCTGGG Y 2 1 2 1 101000 f 74 goat snp36240-scaffold433-2150890 6 84399935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse288 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38429793 Affx-122938204 AX-123300134 6 81977976 AAGGTAAAAATAAACAAAAGATCCATGCTTAGACA[C/T]GATCAATTGCTTGTCCCCTTCCTCCAGGAAATCGA Y 2 1 2 1 101000 r 74 goat snp36242-scaffold433-2243946 6 84494753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773242 Affx-122936106 AX-385260385 6 82024869 GGTTAGACTAAGCAGGTGTTTGAACAAAATTACTC[A/G]TCAAATATCAGTTATTAATTTCCGAGTCTGTAAAA R 2 1 2 1 201000 r 74 goat snp36243-scaffold433-2290839 6 84550454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779534 Affx-122949776 AX-385266637 6 82061120 ATGTCTCTATCATTTGAGCACTGAAATGAATGGTT[A/C]TGTCATTTACTTATATCTCAAAAGCAATGTTCTTT M 2 1 2 1 101000 f 74 goat snp36244-scaffold433-2327090 6 84587097 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse289 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38431202 Affx-122937165 AX-123301543 6 82103759 CCTTACTGGTTAATATTCAAGGTCCTTAGAATGCC[A/G]TTTCTTTTTACCAATACTGTTCCATTATAGCGTGC R 2 1 2 1 101000 r 74 goat snp36245-scaffold433-2369729 6 84630329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789356 Affx-122963438 AX-385276366 6 82144111 CAGAAAAAAAGGTCTCAGCTCAGCTATTGCACAGG[C/T]AGAAGCCTTGGAGGTTCTAATTTAAGAAAATGTTA Y 2 1 2 1 101000 f 74 goat snp36246-scaffold433-2410081 6 84670923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392211 Affx-122966277 AX-123262568 6 82192038 ACAAACTACCCAAATTATGTCTGTCTCCACCCTCA[A/G]TTTCCCATACATTCTGAAATTATCTTCTCTTCCTT R 2 1 2 1 201000 r 74 goat snp36247-scaffold433-2458008 6 84718350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778852 Affx-122940132 AX-385265960 6 82230438 GTTGCCAAATGGCCCTTACACATCCTCTTGTGTAT[A/G]CACAAGCTCTCATTATGTGTGACAAACGCAGAATG R 2 1 2 1 201000 r 74 goat snp36248-scaffold433-2496408 6 84756937 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse290 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38403876 Affx-122957918 AX-123274228 6 82275459 GTGGCTAATTCTGGGCCTTGGTTTTAGTCTTTCTG[C/T]TATACAAATTAGCAACCATCAATAACTACTGTCTT Y 2 1 2 1 201000 r 74 goat snp36249-scaffold433-2541429 6 84803252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449740 Affx-122922462 AX-123320075 6 82332256 AAGCAGTGTCTTTTAGATAACAGATGATGATGATA[C/T]AGGGGAAACTTCATTTAAACTGCTTTCAGAACTCA Y 2 1 2 1 201000 f 74 goat snp36250-scaffold433-2598226 6 84859302 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432712 Affx-122936019 AX-123303053 6 82377438 TTATTTTTAAATCACTTCATGGGATATCTGCTTTC[G/T]AGGATTTTGCTGGAGAGCATGATCTTGATGTGTTA K 2 1 2 1 101000 r 74 goat snp36251-scaffold433-2643408 6 84905253 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428657 Affx-122938655 AX-123298999 6 82423194 ACATCTTTACAGCTTTGTTGCCTCATGAAATTGCC[A/G]TTCCTTTATCCTCTTCCTTAAATTTTTAGGTACTC R 2 1 2 1 101000 f 74 goat snp59410-scaffold980-39769 6 85723685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409208 Affx-122953168 AX-123279559 6 82559703 TGGTCACTTTTTCTTCTCTATTTCCATATATTGAA[C/T]ATACTGATATTATTTTATATATTTTAGTATTTTGT Y 2 1 2 1 103000 f 74 goat snp59413-scaffold980-176278 6 85861248 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse291 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320776654 Affx-122933865 AX-385263781 6 82612388 CCAATAAACAGGCATCCGTGATTCTTAGCAAAGTC[A/G]TATGGGAAAGAATGTTTCTTCGGAGAACAACAGAG R 2 1 2 1 101000 f 74 goat snp59414-scaffold980-228963 6 85913548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794276 Affx-122977634 AX-385281241 6 82646152 CATATAAAGGGACATGATAGTATTACTATCTGTTA[C/T]GATAATAATTTTACTGTCTTTGTTTTTTTCTGAAA Y 2 1 2 1 201000 r 74 goat snp59415-scaffold980-262727 6 85946764 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383903 Affx-122973111 AX-123254261 6 82677412 TAGCTCAGAAGCAAAAGTCTGCCATCACCTTGATC[A/G]TCAACCCAGCTTGCTGCTTCTTCCCAGTCTTGGGT R 2 1 2 1 102000 f 74 goat snp59416-scaffold980-293987 6 85978529 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse292 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320798890 Affx-122967647 AX-385285820 6 82678598 AAAACCTTACTATTACTTTCAGGATCAAATGCTTT[A/G]CTTTGAAGTGTAGTAAGATATTGATATTTCTTATC R 2 1 2 1 201000 r 74 goat snp59417-scaffold980-295173 6 85979715 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse293 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603665 Affx-122931499 AX-413837802 6 82678888 CATCCTTACCTGTCTTGTGGCTGTTGCTCTTGCCA[A/G]GCCTGTGAGTACAGTAAAGAATTTAGAAGATTCTA R 2 1 2 1 400000 f 74 goat snp59418-scaffold980-295463 6 85980005 A G GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38404336 Affx-122957000 AX-123274688 6 82679453 ATGAAAGCAAAAAGTGAAAGAGAAGTCTCTTAGTC[A/G]TGTCCTACTCTTCGCGACCCCATGGACTGCAGCCT R 2 1 2 1 103000 f 74 goat snp59419-scaffold980-296028 6 85980570 A G 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 532567209 Affx-122945173 AX-579205702 6 82680594 TTGCATTTTTTTTTTAACAGAAACATCCTATCAAT[A/C]ACCAAGGACTCTCTCCAGTGAGTGTTCTTTTCTGT M 4 1 2 1 303000 f 74 goat "snp59420-scaffold980-297169;snp59995-CSN1S1-ex3-1;SNPs_063" 6 85981710 "A;C" "A;C" 3 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320781563 Affx-122965474 AX-385268648 6 82681499 TTTACAATTCACAATTTAATTCCTACAGGAAGTCC[C/T]CAATGAAAATTTACTCAGGTTTGTTGTGGCGGTAA Y 2 1 2 1 201000 r 74 goat "snp59421-scaffold980-298074;SNPs_064;UniBern-var4" 6 85982615 "C;T" "C;T" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 320798954 Affx-122966240 AX-385285884 6 82681531 TCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG[A/G]TAAGTATTATCTACTTCTTCTTCAATGACAAATGT R 2 1 2 1 202000 r 74 goat "snp59422-scaffold980-298106;SNPs_065" 6 85982647 "A;G" "A;G" 2 neutral GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 320780399 Affx-122957941 AX-174390636 6 82686324 GAAGTACATTCAAAAGGAAGATGTGCCCTCTGAGC[A/G]TTACCTGGGTTATCTGGTAAAATTTTATTAAAAGT R 2 1 2 1 101000 f 74 goat snp59424-scaffold980-302899 6 85987327 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320785113 Affx-122950393 AX-385272158 6 82687681 ATATATTTTTCTCTTTGAATAGGAACAGCTTCTCA[A/G]ACTGAAAAAATACAACGTGCCCCAGCTGGTAATGT R 2 1 2 1 201000 r 74 goat "snp59425-scaffold980-304256;SNPs_068;UniBern-var7" 6 85988705 "A;G" "A;G" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 38385044 Affx-122971835 AX-123255402 6 82690713 ACATTGCTGGTTCCAACATTGCTATGAAAGATCAG[A/C]TCTAAGTTGCCAAAGGAAATGAAAGAACAATTCTA M 2 1 2 1 101000 f 74 goat snp59426-scaffold980-307288 6 85991743 A C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse294 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38412851 Affx-122950450 AX-123283200 6 82692557 TGGTCCTCTAGTCTAGCTATATTTAGACACATTAC[A/G]CTTAGATAATATCAATAATTAAATTGGCTTCAACA R 2 1 2 1 101000 f 74 goat snp59427-scaffold980-309132 6 85994216 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse295 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320771066 Affx-122973645 AX-385258226 6 82693835 ACTGTTTATAGAATATTTTCCATGTGAACATGGAT[A/G]TGGCTGCAGAGAGAACAACAGTGTAGTAGTTGTGG R 2 1 2 1 102000 r 74 goat snp59428-scaffold980-310410 6 85995496 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse296 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320778614 Affx-122969566 AX-385265725 6 82693948 TGCAGGACTTGTTGGAGCCCAATCCATTTGATTAT[A/G]CTTGAGTTTATAACTAGGTAGATTATAAAATAAAC R 2 1 2 1 101000 f 74 goat snp59429-scaffold980-310523 6 85995609 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse297 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320782209 Affx-122969125 AX-385269287 6 82694478 TGGACCTGGCAGAAGTTAATGGAGGGTGCAGATTC[A/G]TACGTCTTCATAAAATGTATCTCCCAGCTTCTGTC R 2 1 2 1 101000 f 74 goat snp59430-scaffold980-311053 6 85996139 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse298 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320796084 Affx-122960451 AX-385283036 6 82694935 CTATTTTAAAGGCCAAATGAGGAAGTGGAATAATG[A/G]TGTAATTCACTATCTTTTAGTCTTTGCATCTTTTA R 2 1 2 1 101000 f 74 goat snp59431-scaffold980-311510 6 85996594 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse299 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320774639 Affx-122925923 AX-385261773 6 82694972 GTAATTCACTATCTTTTAGTCTTTGCATCTTTTAG[C/T]GTTCAACAGCTGTAATTCCCCCATAAATGCAAATT Y 2 1 2 1 101000 r 74 goat snp59432-scaffold980-311547 6 85996631 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse300 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320798536 Affx-122952944 AX-385285469 6 82706793 TAGAGACTGTGCCTGGGCAAAGGGGTGGATTTTAT[G/T]CTGGAGTTCATCCTGGAAAGAAGGAAAAAAAATCT K 2 1 2 1 201000 r 74 goat snp59437-scaffold980-323368 6 86008407 G T 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320789717 Affx-122966021 AX-385276725 6 82707198 AAAAGACTTAAAAAGTTACTCTGAGGTTTATTTTT[A/G]TTTGTTTTAATGGAAACTAAGTCTTAATATGTGTT R 2 1 2 1 202000 f 74 goat snp59438-scaffold980-323773 6 86008812 A G 2 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse302 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38402573 Affx-122958444 AX-123272926 6 82707736 AATTTACAGGTGAAGAAAATGATGTACAGAGAAAC[A/G]TGGAGCCAAGGTTATACAGCTGATAAATGATCAAA R 2 1 2 1 101000 r 74 goat snp59439-scaffold980-324311 6 86009350 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse303 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38397388 Affx-122962267 AX-123267743 6 82708253 TATAAAAATCAAACACAAAATTTTTAAAAATGTAC[A/G]TTTAAATATGAAGGTTTTACCTTATTGATGTGTGT R 2 1 2 1 103000 r 74 goat snp59440-scaffold980-324828 6 86009867 A G 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38391027 Affx-122966875 AX-123261384 6 82708778 CAACTTTGCATGCATACCTGTCCCTCAATCACCCT[A/G]TTTTCTCCTTAGGAAAACAAATGATCTCTGATATT R 2 1 2 1 202000 r 74 goat snp59441-scaffold980-325353 6 86010392 A G 2 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse304 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38444710 Affx-122926423 AX-123315047 6 82748317 GTCATAAAAACAAAAGCAGCCCCAGTTTAAGAAGT[A/G]CAGCCTGGTGTAGCTCTCTTAAACTGTACTCATTT R 2 1 2 1 102000 r 74 goat snp59442-scaffold980-364892 6 86050148 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438782 Affx-122931376 AX-123309119 6 82774413 CAGACGGTAAAGCATCTGTCTAAAATGCAGGAGAC[C/T]TGGGTTCGATCCCTGGGTCGGGAAGATTACCTGGA Y 2 1 2 1 103000 f 74 goat snp59443-scaffold980-390988 6 86076276 T C 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38418052 Affx-122946626 AX-123288400 6 82779273 GAAAATTGGAAGTGCAACCACAACGAAAAAGTATA[G/T]AGAGAGGAATAAAGACCAAAAATCTACACATTCAA K 2 1 2 1 101000 f 74 goat snp59445-scaffold980-395848 6 86081135 T G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38454002 Affx-122919436 AX-123324335 6 82782072 GAGAACCATAGCCTCGGCTCAGAGCCTTGAGGCTG[A/C]GCCTGAAGACTTCCTGCTTAACATCTAGGAAGCCT M 2 1 2 1 101000 r 74 goat snp59447-scaffold980-398647 6 86083934 A C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse305 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38398635 Affx-122961462 AX-123268990 6 82782776 GTTAATCCTCCTTTTCTTCCCTGAAGGAATCTGCT[A/G]AAGTTGCCCCAGAGGTAACTAATTTTCATTCAAAT R 2 1 2 1 201000 r 74 goat "snp59448-scaffold980-399351;SNPs_077;UniBern-var13" 6 86084638 G A 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 538942989 Affx-122973451 AX-585490104 6 82783272 GTATCCGTATCAAGGTCCAATTGTTTTGAACCCAT[A/G]GGATCAGGTTAAGAGAAATGCTGGCCCCTTTACTC R 4 1 2 1 400000 r 74 goat "snp59449-scaffold980-399847;SNPs_079" 6 86085134 G A wobble probeset GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 38390323 Affx-122967706 AX-123260680 6 82784092 CAGAACAAATATGTACACATTGAAGGATACAAAGA[C/T]TGGATCTGTGCTCGTATACTTTGTCAAAATGCTGT Y 2 1 2 1 101000 r 74 goat snp59450-scaffold980-400667 6 86085957 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38402145 Affx-122958659 AX-123272498 6 82786023 TGATCCCTGGCTTGAGAAGATTGCCTGAAGAAGGG[C/T]ATGGCAACCCATTCCAGTATTCTTGCCTGGATATC Y 2 1 2 1 103000 f 74 goat snp59451-scaffold980-402598 6 86087888 C T 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38383623 Affx-122972548 AX-123253981 6 82786136 CAAAGAGTCACATAGGACTGAAGTGACTTAGCATG[A/G]AGGGAGGCACAGCCATTAAAAAAACAATGGTTTTC R 2 1 2 1 201000 r 74 goat snp59452-scaffold980-402711 6 86088001 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38400335 Affx-122960047 AX-123270690 6 82786576 CTGATTTTCTTTTTTTTTTCCATAAGGAATCAACA[A/G]AAGTATTCACTAAGGTAAGTAATTTCCTATCAAAC R 2 1 2 1 201000 r 74 goat snp59453-scaffold980-403151 6 86088442 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320772971 Affx-122961824 AX-385260115 6 82786730 GAAGAAGAAAAGAATCGCCTAAATTTTCTGGTAAA[C/T]TTTTATACAAACATGTGAGCACACTCAGACTCAGC Y 2 1 2 1 102000 r 74 goat snp59454-scaffold980-403305 6 86088596 T C 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse306 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320776854 Affx-122959763 AX-385263978 6 82791242 GAAAAAAAATAATAACATTCTGCTAAACTAGTATG[A/G]ATGAGTATGTGTGGGTTCTGTATACAGACATACAT R 2 1 2 1 101000 r 74 goat snp59455-scaffold980-407817 6 86093184 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse307 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320767829 Affx-122921209 AX-385255051 6 82791406 CACTTTACTTCATACAACCAGCATGTTTGGGGTGG[C/T]GCATCAATAAGACAAATCGCAGAGTATTTCCTGAA Y 2 1 2 1 101000 f 74 goat snp59456-scaffold980-407981 6 86093348 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320782988 Affx-122960441 AX-385270057 6 82817980 TTTAGGACAATCTTTCAGCTGCTGAAAAAATAGCC[G/T]CATAATAATCTCAACCCTTTAGAAATTTGTTGTCT K 2 1 2 1 101000 f 74 goat snp59458-scaffold980-434555 6 86118792 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse308 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433337 Affx-122935152 AX-123303678 6 82852913 AGTGATCTAACACATTTTTTTTTAATTCTAACAGA[C/T]GCCATTCTATACTGAATTTGGATATATTCCACAAG Y 2 1 2 1 101000 r 74 goat snp59459-scaffold980-469488 6 86155434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse309 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320788579 Affx-122968481 AX-385275596 6 82896008 GTGTGTGCTCTTTATCAAGCCTGAACTTCTAACTC[C/T]GTGACCCTAGTCTGTAAAACTCAGTTTGCAGGTTT Y 2 1 2 1 101000 r 74 goat snp59460-scaffold980-512583 6 86198530 C T 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38442876 Affx-122927663 AX-123313213 6 82898948 GGAGAAATAGCAATAACCTCAGATATGCAGATGAC[A/G]TCACCCATATGGCAGAAAGCAAAGAAGAACTAAAG R 2 1 2 1 303000 r 74 goat snp59461-scaffold980-515523 6 86201470 G A 3 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38399057 Affx-122960902 AX-123269412 6 82900719 CATTTTTTGATAAACCTTTAAAAGTTAACAATAAA[A/G]AACAAACATTTCATGATATAACCAATGATTGTTTT R 2 1 2 1 201000 f 74 goat snp59462-scaffold980-517294 6 86203242 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320800979 Affx-122970898 AX-385287893 6 82901201 CACCTTTTGTAAGTTTTAAAGCTTCATATAGATAT[A/G]CCTGGAGACTACTTTCTCACTCCTGATTTCCTATG R 2 1 2 1 101000 r 74 goat snp59463-scaffold980-517776 6 86203724 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320798338 Affx-122976794 AX-385285273 6 82901438 TTTCTCCCCTTCTTTTTAGCAATATATATTCAATA[C/T]AAATTGAATATAGGTTGTTCATGTTCTTCATTTAA Y 2 1 2 1 102000 f 74 goat snp59464-scaffold980-518013 6 86203961 C T 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38443804 Affx-122927082 AX-123314141 6 82905902 TTTTTGCAGTGCTGTGAGAAAGATGAAAGATTCTT[C/T]GATGACAAAATAGCCAAATATATCCCAATTCAGTA Y 2 1 2 1 101000 r 74 goat "snp59465-scaffold980-522477;SNPs_083" 6 86208883 C T 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38449622 Affx-122923196 AX-123319957 6 82905977 CTGAGTAGGTATCCTAGTTATGGACTCAATTACTA[C/T]CAACAGAGACCAGTTGCACTAATTAATAATCAATT Y 2 1 2 1 101000 f 74 goat "snp59466-scaffold980-522552;SNPs_085" 6 86208958 "C;T" "C;T" 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38434729 Affx-122933924 AX-123305070 6 82905979 GAGTAGGTATCCTAGTTATGGACTCAATTACTATC[A/G]ACAGAGACCAGTTGCACTAATTAATAATCAATTTC R 2 1 2 1 201000 r 74 goat "snp59467-scaffold980-522554;SNPs_086" 6 86208960 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320793820 Affx-122972546 AX-385280791 6 82906006 TTACTATCAACAGAGACCAGTTGCACTAATTAATA[A/G]TCAATTTCTGCCATACCCATATTATGCAAAGCCAG R 2 1 2 1 201000 f 74 goat "snp59468-scaffold980-522581;SNPs_087" 6 86208987 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320777525 Affx-122955707 AX-385264644 6 82906041 ATCAATTTCTGCCATACCCATATTATGCAAAGCCA[A/G]TTGCAGTTAGGTCACCTGCCCAAACTCTTCAATGG R 2 1 2 1 201000 r 74 goat "snp59469-scaffold980-522616;SNPs_090;UniBern-var17" 6 86209022 "A;G" "A;G" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320778152 Affx-122921659 AX-385265267 6 82906078 TGCAGTTAGGTCACCTGCCCAAACTCTTCAATGGC[A/G]AGTTTTGCCAAATACTGTGCCTGCCAAGTCCTGCC R 2 1 2 1 102000 f 74 goat snp59470-scaffold980-522653 6 86209059 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38402882 Affx-122958222 AX-123273235 6 82906116 TTTTGCCAAATACTGTGCCTGCCAAGTCCTGCCAA[A/G]ACCAGCCAACTACCCTGGCACGTCACCCACACCCA R 2 1 2 1 102000 f 74 goat "snp59471-scaffold980-522691;SNPs_091" 6 86209097 "A;G" "A;G" 1 neutral GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38379413 Affx-122976117 AX-123249771 6 82906203 CCATTCCACCAAAGAAAGATCAGGATAAAACAGAA[A/G]TCCCTGCCATCAATACCATTGCTAGTGCTGAGCCT R 2 1 2 1 201000 f 74 goat "snp59472-scaffold980-522778;SNPs_093;UniBern-var18" 6 86209184 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 532567196 Affx-122933267 AX-579205689 6 82906784 CTTAGAAAAAAATCATATAGGCTATGAGTTTAAAT[A/G]CATTTTAATTGTATACCAGTGTTGTTGCACTCTAC R 4 1 2 1 101000 r 74 goat "QTLcaseins6.16;snp59473-scaffold980-523359" 6 86209768 A G 1 wobble probeset "not_recommended;recommended" GoatSNP50 chip candidate gene ou candidate region 10.1371/journal.pone.0086227 320772265 Affx-122925726 AX-385259421 6 82907013 ACCTACTTATTAAGAGGAAACTTTCAGAACTTTAA[C/T]GTAAAATATGTCTATTTATTATTTGGATCAATGGA Y 2 1 2 1 101000 r 74 goat snp59474-scaffold980-523588 6 86209997 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38437282 Affx-122931990 AX-123307620 6 82965046 TTATGCCACAGCTCATATAATTTTCCTAAATGATT[A/C]TGGGAATCAGGAAGGGAAGGGAAGTAGGATGCTTC M 2 1 2 1 201000 f 74 goat snp59475-scaffold980-581621 6 86266392 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse311 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38391193 Affx-122967421 AX-123261550 6 82995053 ATATTCCATAGTTCTTCTAAGTATTACAAAGTTGC[A/G]CCAGTTGTCAAAATGAAAAAAGGCATCATAACAAA R 2 1 2 1 101000 f 74 goat snp59476-scaffold980-611628 6 86296958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776969 Affx-122926575 AX-385264093 6 83033912 CTTCAAATCCTGATCATTTATATGCAACTTCTTAT[A/G]TGGAAGAGGAGATAAAACTAAAATTTCTATTTCCA R 2 1 2 1 101000 r 74 goat snp59477-scaffold980-650487 6 86335455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774150 Affx-122968702 AX-385261288 6 83102610 AGAACTTTTCCTGATCCTCTTGGCCTCATCCAAAG[A/C]TTGGAGACTTTTTATGTCATCAAGAAGAAGAGGTC M 2 1 2 1 102000 f 74 goat snp59478-scaffold980-719185 6 86403944 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse312 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771575 Affx-122973607 AX-385258734 6 83140158 ACTGATATGAACAAGTGATGCATTGTTCCTTTTCC[C/T]GTGACTGACTTGATTCTTGCTTTCCCTTTCTGAGA Y 2 1 2 1 201000 f 74 goat snp59479-scaffold980-756733 6 86441696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783016 Affx-122975938 AX-385270084 6 83189194 CCTGTAGTTGAATATGTTCCTGTTACCTTATTTTC[A/G]TACTGGCCAATAGGAGGAAAGAAGGGTCAACTCTC R 2 1 2 1 101000 r 74 goat snp59480-scaffold980-805769 6 86490795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378141 Affx-122976983 AX-123248500 6 83228568 GTTACTTTCAACTTTTATGACATGATCATGAGACC[C/T]GCTGCAGGGGAAAAAAATCGACTTCATCAATTTTA Y 2 1 2 1 201000 f 74 goat snp59481-scaffold980-845143 6 86530449 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse313 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418905 Affx-122946095 AX-123289253 6 83280940 GAGAAAGCGAAAGTTCTTCATCCTGCCTCAGGAGG[C/T]AGGAAAGGCTTTTCAGGTGACATTTAAAGTCAATC Y 2 1 2 1 202000 f 74 goat snp59482-scaffold980-897515 6 86583042 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389915 Affx-122968109 AX-123260272 6 83315589 TCTAAACTGGAGGCTCCTCCTTAGGCAGCAGTGGC[C/T]CTCAAGTTTCTTGTTCTGCCCAGCAAAGCCCTATT Y 2 1 2 1 101000 r 74 goat snp59483-scaffold980-932164 6 86617703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439487 Affx-122930155 AX-123309824 6 83421411 ACCTCTGGATACAGAGGGCTGACTATCAGACTTGA[G/T]CATTCATGGATTCTGGTATCCATGACGCGTCCTGG K 2 1 2 1 303000 r 74 goat snp59485-scaffold980-1037986 6 86723586 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse314 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38413996 Affx-122950278 AX-123284345 6 83451593 TCTTCCTGCCCACTATGGGCTTTATTTTACTAAGT[C/T]TCTTTGTCCTGTACTCAAATAGAATGATTGGTGTG Y 2 1 2 1 101000 r 74 goat snp59486-scaffold980-1068168 6 86753883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382344 Affx-122973881 AX-123252702 6 83485578 TGGAGGTAGAGTCCACCAGGGTCGCAAAGAGTAGG[A/G]CACAACTGAGCATTTAAGCAGTAGTAAACCATTAA R 2 1 2 1 103000 r 74 goat snp59487-scaffold980-1102153 6 86788148 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398074 Affx-122961734 AX-123268429 6 83518784 TCACTGTGCCAGAATCTCAGGTGCCTGCTTCTGAG[C/T]ATTCCTTGAAAAAGAGGTATTGGGAAGTAAGGACA Y 2 1 2 1 101000 r 74 goat snp59488-scaffold980-1135359 6 86822427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451496 Affx-122921122 AX-123321829 6 83553692 TCCGTGCTAAAGCTGCACATGTCAGGGTCTGTGGT[A/G]TTATAAAGAGAAAATTAGTATTATGACTGTTAAAG R 2 1 2 1 201000 r 74 goat snp59489-scaffold980-1170267 6 86858086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787442 Affx-122953134 AX-385274467 6 83601195 CCATTATCTAGTGGGAGAATTCCTACATTATTAAT[C/T]TGATATAGGGATCTACCCTTCTGTGGGTAAACAGC Y 2 1 2 1 201000 f 74 goat snp59490-scaffold980-1217770 6 86905715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394629 Affx-122964402 AX-123264984 6 83648311 GGGTTAGAATATCTTTATAAGGACTTTTTAAGACA[C/T]GAAAGAAAGACATCATGATACAATGGGAAAGAATA Y 2 1 2 1 101000 f 74 goat snp59491-scaffold980-1264886 6 86946899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385744 Affx-122971081 AX-123256102 6 83691916 GCGAGAAGAAATGAGATGTTGGCCGTATTCCAAAT[A/G]CTATAATCGTCCCATGAATAAATGAGAGTTGATGC R 2 1 2 1 101000 r 74 goat snp59492-scaffold980-1308491 6 86990478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377051 Affx-122978300 AX-123247410 6 83727693 ATTTCTCTTCTCTTAGTCAAATGAGATGATATTTT[A/G]TCTAACGATCCTAGTTGATTTTGCAAAGGTCATTG R 2 1 2 1 101000 r 74 goat snp59493-scaffold980-1344268 6 87026491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse315 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38414578 Affx-122949375 AX-123284927 6 83761149 TTAGGGTTAGGGACCTAAAGCTTGCAGAAGTGAGT[A/G]ACTCTCCTGACATTACATGGTTGGCAAGTGGTATT R 2 1 2 1 101000 f 74 goat snp59494-scaffold980-1377724 6 87059365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse316 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381750 Affx-122974319 AX-123252108 6 83792644 GATCATTTCAGATGTTGCTCCAGTTCTTGACACAT[A/G]CTTAAAACTCTGCTCTCTCAGATTAAAATGGAGAA R 2 1 2 1 101000 f 74 goat snp59495-scaffold980-1409219 6 87091435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273234 Affx-1111833520 AX-502851688 6 83819304 CAGCTTTGTTCACAGTCCAACTCTCACATCCATAC[A/C]TGACCACTGGAAAAACCATAGCCTTGACTGGACAG M 2 1 2 1 103000 f 74 goat 6_83819304_AF-PAKI 6 83819304 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439591 Affx-122930067 AX-123309928 6 83926387 TTTCAACCACAGAAATGTAATGTTTACTCTAATTC[A/G]TTAATAAAGAAAAAAAGCTTCTGGTTAAAAATAAC R 2 1 2 1 103000 f 74 goat snp59498-scaffold980-1542962 6 87224612 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409487 Affx-122954053 AX-123279838 6 83981411 GGGTCATTCTCTAGAAAATGAGATTCAGAAAAAAA[C/T]AGGTTGACATCTCTTTTCATGAGATTGAGCTCAGT Y 2 1 2 1 303000 f 74 goat snp59499-scaffold980-1597986 6 87277378 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378805 Affx-122976561 AX-123249164 6 84037381 TTCAAAGGACTCCTGAAGCAACTTAACTCAATATT[C/T]CAGCCTTTGAGTAGATAAAACTACCTGTACCTTCA Y 2 1 2 1 101000 r 74 goat snp59500-scaffold980-1653956 6 87333480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792150 Affx-122937329 AX-385279135 6 84079917 TGTTCTCAAACGATGTAATTATTTCACATCACACA[C/T]GTGGCTCTAAGCAATGGAACCCAGAGCAATTTGCA Y 2 1 2 1 101000 r 74 goat snp59501-scaffold980-1696492 6 87375339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382012 Affx-122974066 AX-123252370 6 84137740 TAAAAATCTCAGTGGCTTGTAGGGCAGTCATTAAG[C/T]ATCCTTTGTAGGTGTGAGGAGGAGCTGGGCTGAAC Y 2 1 2 1 101000 f 74 goat snp59502-scaffold980-1754315 6 87432628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441000 Affx-122928963 AX-123311337 6 84192693 AAGACAGATGGCATGCTTCTTGCATGGGCAAGGGG[C/T]ATTACAAGGTAACCTGTCCCTGAGCTGACTTAAAT Y 2 1 2 1 101000 r 74 goat snp59503-scaffold980-1809268 6 87486240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772929 Affx-122932069 AX-385260073 6 84227645 AATTAATAACAGAAATGATGAACAGCTCTTTGAAG[C/T]GAGTTTGTTTTGTCCTAGAAATATTGAAATGGAGT Y 2 1 2 1 101000 f 74 goat snp59504-scaffold980-1844220 6 87520973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427405 Affx-122940071 AX-123297748 6 84268596 ACTATCAATACTGCAGGCTGCTTTGTGCAACATGA[C/T]TTTTGTTCCTGCAAAAACAATGCTTTTGGAATTCC Y 2 1 2 1 201000 r 74 goat snp59505-scaffold980-1885171 6 87562196 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389576 Affx-122968788 AX-123259934 6 84313021 CTTGAACAGAAAAAGGCTGTTTCATAGTAATGGAA[A/C]TTTTGCTCTAGTACACAGGAAACTGGAAAACACAT M 2 1 2 1 101000 f 74 goat snp59506-scaffold980-1929596 6 87607436 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426647 Affx-122939941 AX-123296993 6 84346966 AAACAATCTCTGAAGAGAAAACAAATAGCCAAAAA[C/T]TCAAAGCTGAACTTCAGAATTGGTAACTTGTCTTT Y 2 1 2 1 101000 r 74 goat snp59507-scaffold980-1963541 6 87643025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404988 Affx-122956397 AX-123275340 6 84380353 CTTTTATGAACAAAACAAGTTTGTTAGAAGCTTTT[C/T]CTTCTTTGTGTTTACATGAAGTCTGGTGATGTGAT Y 2 1 2 1 101000 r 74 goat snp59508-scaffold980-1996928 6 87676522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375789 Affx-122978576 AX-123246148 6 84422150 ACCATATTGGAAAGAGAGAAAGAAAATAAATACAG[C/T]AAATGTTAACAAGTGTGGAATTTGGGTGATATTCT Y 2 1 2 1 103000 r 74 goat snp59509-scaffold980-2038725 6 87717740 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774428 Affx-122971253 AX-385261564 6 84465351 TTACCTAAGATAACTGAGCTTGGCTACTAGTCTAC[A/G]TGGTTGACTATTTTTCCTATAGTTCACTGTGACTT R 2 1 2 1 101000 f 74 goat snp59510-scaffold980-2081926 6 87763555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476223 Affx-1251763728 AX-586011647 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 4 1 4 1 20000 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 539476477 Affx-1251763728 AX-586011877 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20000 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 560378499 Affx-1251763728 AX-605230914 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20000 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562165719 Affx-1251763728 AX-606941128 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166039 Affx-1251763728 AX-606941448 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166531 Affx-1251763728 AX-606941939 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166558 Affx-1251763728 AX-606941966 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 38400305 Affx-122960069 AX-123270660 6 84501582 TTTCCCTGCCTCCAGTGGAGAGGAGATGAGAGAAG[C/T]GCAGAGAAATTCCTCCCACGTGTTCAAGTGGCCAT Y 2 1 2 1 201000 r 74 goat snp59511-scaffold980-2118157 6 87799841 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439437 Affx-122930189 AX-123309774 6 84559123 GCATAGCTATTTGAAACTTCTCCCCTGGTGGTTCA[G/T]CGGGTAAAGAGCATGCCTGCCAATGTAGGAGACAC K 2 1 2 1 103000 f 74 goat snp59512-scaffold980-2175698 6 87856692 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420770 Affx-122944709 AX-123291117 6 84588611 CCCCTTTTCTCTAAACATGAATATGAGCAAAGGCT[A/G]TCACTGGCATCAAGGAGGAGCATATATCAAATCTT R 2 1 2 1 201000 r 74 goat snp59513-scaffold980-2205186 6 87885937 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430131 Affx-122937399 AX-123300472 6 84621575 AGTTGACTTTTCATGGTTTCATTTACCAGTGGTCA[C/T]CTGCACTGGTCCAAAAATGTTAAAAGGCAAATTCC Y 2 1 2 1 101000 f 74 goat snp59514-scaffold980-2238150 6 87918880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403531 Affx-122957614 AX-123273884 6 84650125 CTAGACATTTCTTTTATTACATCTTCATTGTCACC[A/G]TAAAACTGACTCTAGCTTTTTTAGCCCCCATAAAA R 2 1 2 1 101000 f 74 goat snp59881-scaffold996-25451 6 87947726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768903 Affx-122971413 AX-385256080 6 84681534 AATTTCTTGTTTTCAACTATGAAGTGTTACTATTG[C/T]GAGAGAATTCTGTCTAGGCTAGCTCCATTGTGGAG Y 2 1 2 1 101000 r 74 goat snp59882-scaffold996-56860 6 87977497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453645 Affx-122919733 AX-123323978 6 84721124 ACAATCTTGTTTTTTTAAATAGGCCACCCCATCTA[C/T]GTGAATGGCACCATTATCCAGTAGTATTCAAACCA Y 2 1 2 1 201000 r 74 goat snp59883-scaffold996-96450 6 88017071 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404368 Affx-122956810 AX-123274720 6 84762610 CTAGTAGAAATCTAAACTGGTGAAAACAGTGCAAT[A/G]TTGATGCAAAGGCTGACAAAGAGGCCAGTGGGAGA R 2 1 2 1 201000 f 74 goat snp59884-scaffold996-137936 6 88058923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434637 Affx-122933995 AX-123304978 6 84799567 GCTGGAAGACTGGGAAGGGAAAGGAAAGTAGCTGT[C/T]AGATACTAGGATTGTTGCACCAAAAATATAAAGAG Y 2 1 2 1 201000 r 74 goat snp59885-scaffold996-174893 6 88098811 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395243 Affx-122964471 AX-123265598 6 84831381 GCAAGTTGGCATCAGGGTCAGTGCCTCACACAGCA[A/C]TATTTCTCAAACTTTAAAGTATAAATGAATCAGCT M 2 1 2 1 101000 f 74 goat snp59886-scaffold996-206707 6 88129197 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437048 Affx-122933101 AX-123307386 6 84865479 CAGAAAGTAGCTAAACATCCTGTCATAAAGCAAAG[A/G]CTAAATATATTTGGAATATTCAATTAAGATCAAAA R 2 1 2 1 101000 f 74 goat snp59887-scaffold996-240805 6 88163608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448129 Affx-122924296 AX-123318465 6 84895433 TAGGAAATTTTCAACCTACAGGCTTGGCAAAATGA[A/G]TTGATCAACTCTGGAATGATTAAGGGGTCATCAAA R 2 1 2 1 101000 f 74 goat snp59888-scaffold996-270759 6 88193969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382384 Affx-122973848 AX-123252742 6 84943872 TGACACCAAATGGCCTGAAGTCCAGACTGGCTCTA[C/T]GAACACATGCTCCATTACCCAAGTCAGAGACTGGG Y 2 1 2 1 201000 r 74 goat snp59889-scaffold996-319198 6 88242668 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764711 Affx-986696985 AX-385252331 6 84985928 GAGCTGGACATTTTGATAATAAACTGCTTTTCTGA[G/T]GTACAGTTTTCATCAGTACCTTCAGATTGTTTTCA K 2 1 2 1 600010 r 74 goat 6_84985928 6 84985928 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320762459 Affx-986696989 AX-385250587 6 84994018 TGCAAAATTCAGATTTGAATTGAAGAAAGACTTAA[A/G]TTGAAAGCGGGGAAAACCGCTAAGCCATTCAGGTA R 2 1 2 1 600010 f 74 goat 6_84994018 6 84994018 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 38417180 Affx-122947325 AX-123287528 6 84997830 AATCCTCGCTGTGAGCTTAGTCAGGCAACGCCGTG[A/C]GGTCCTAACCGTCTGGGGCTCAGGTAGTGACACTG M 2 1 2 1 101000 f 74 goat snp59890-scaffold996-373156 6 88296909 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764721 Affx-986696991 AX-385252339 6 85018808 ACTGCTGCTGCACTGGGGCTACACTGGTGTGACCC[A/G]TGGTTATGTTACATGAGATTATGCTATGGCTAGGT R 2 1 2 1 600010 r 74 goat 6_85018808 6 85018808 Ancestral_priority_1043 ancestry 0.662 neutral IMAGE 10K 10K ancestral 320762463 Affx-986696993 AX-385250590 6 85018832 TGGTGTGACCCATGGTTATGTTACATGAGATTATG[C/T]TATGGCTAGGTTATGGTTATGTTATGGCTGCTGCT Y 2 1 2 1 600010 f 74 goat 6_85018832 6 85018832 Ancestral_priority_1043 ancestry 0.638 neutral IMAGE 10K 10K ancestral 320762465 Affx-986696995 AX-385250592 6 85018881 TGGTTATGTTATGGCTGCTGCTACAGGTACTGCAT[C/T]AGCCAGGAGAGAAGCTGTTTTATGGCTGCCGTGCC Y 2 1 2 1 600010 f 74 goat 6_85018881 6 85018881 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38390030 Affx-122968440 AX-123260387 6 85063923 CAGAAGTCAGGATTTCTTGTAATACCATAATTGGC[C/T]AAGTATGTATTATGGTGAATTTAATAACTTAGCCC Y 2 1 2 1 101000 f 74 goat snp59892-scaffold996-439249 6 88364237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422352 Affx-122943440 AX-123292698 6 85070017 CTTTGTATAAGATGTAGATGACTGTTTATGCACGT[A/C]CAGCATGTTTATAGTTATTTGGGAGGTTAATGATC M 2 1 2 1 101000 r 74 goat snp7871-scaffold1281-3251602 6 88369661 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 353791386 Affx-293815452 AX-416972589 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 2 1 2 1 400000 r 74 goat snp-genphyse672 - G INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 99229977 Affx-293815454 AX-180660630 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/A/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 6 1 2 1 600000 f 74 goat norsk01 6 parentage parentage 99229978 Affx-293815454 AX-180660631 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/A/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 4 1 2 1 600000 r 74 goat norsk01 6 parentage parentage 38440660 Affx-122929936 AX-123310997 6 85112368 TAAATGAAAGTGTTATAAATATGTAGCAGATTTTT[A/G]TTAAATATTTGGGGATGGTGAGGAAAATCAGAGTG R 2 1 2 1 102000 r 74 goat snp7870-scaffold1281-3209251 6 88414059 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454275 Affx-122919279 AX-123324608 6 85175103 TTCTCCTGATTTTATAAAGAGGACTCATTTAGTGG[C/T]ACTGTACTTAGTTTCAAAGATATAAAATCAGGTGG Y 2 1 2 1 201000 f 74 goat snp7869-scaffold1281-3146516 6 88477979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803053 Affx-986696147 AX-385289926 6 85219931 AAATTGAAATTTTATGATTGATAGTTATTTAAAAA[A/G]TGAAAATGGAAGGTCATGTGGGAAACTTCAATCTT R 2 1 2 1 600010 f 74 goat 6_85219931 6 85219931 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320764746 Affx-986697006 AX-385252361 6 85219957 ATTTAAAAAGTGAAAATGGAAGGTCATGTGGGAAA[A/C]TTCAATCTTTTCTACCATAGGAATTGATAAGAGCC M 2 1 2 1 600010 r 74 goat 6_85219957 6 85219957 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320762478 Affx-986697008 AX-385250602 6 85220005 TACCATAGGAATTGATAAGAGCCATTCCAAACACT[A/G]TAAGTTGGACAGTGGAAAGGAGAGTTCAGGATGAT R 2 1 2 1 600010 f 74 goat 6_85220005 6 85220005 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320764752 Affx-986697010 AX-173410846 6 85220034 AACACTGTAAGTTGGACAGTGGAAAGGAGAGTTCA[G/T]GATGATGTTCTTGTGGAAGTATAATAGAACAGAGT K 2 1 2 1 600010 r 74 goat 6_85220034 6 85220034 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 320782413 Affx-122927275 AX-385269489 6 85251808 TTATAGCATGTCAGCATACATTGGGTGAAATTTTT[A/G]CTAAATAGAGTATTTTTCTTAGCTGGTATAGAAGT R 2 1 2 1 101000 r 74 goat snp7867-scaffold1281-3069811 6 88548104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394847 Affx-122964776 AX-123265202 6 85285880 AGTCCAAGGAGTTGCAGAGTTGGACATGACTGAAT[A/G]ACTTTTACTTTCACTTCACTTTTCTGTATCATATT R 2 1 2 1 303000 r 74 goat snp7866-scaffold1281-3035739 6 88582504 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409577 Affx-122953579 AX-123279928 6 85328311 ACCAGCTGTTTGTAGAAAATAAATATTGGAAAGTT[A/G]CTAGCAGGGAATTAGTATTCTAAAAAATGATTTAA R 2 1 2 1 201000 r 74 goat snp7865-scaffold1281-2993308 6 88625439 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772599 Affx-122921192 AX-385259747 6 85374944 TTATGTATTCCAGTTAGATAAGATGTGCAGGTGAT[C/T]AGTTTAAAACGGTACCCAGATATCTTGTTATTGCT Y 2 1 2 1 101000 f 74 goat snp7864-scaffold1281-2946675 6 88672148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406344 Affx-122955439 AX-123276696 6 85415881 CTTTTGTTTCTCTCCTCACCCTTGCCACTAATACC[A/G]GTAAAATTTTCTTTCTGATCGTGAAATAATTCTAT R 2 1 2 1 201000 r 74 goat snp7863-scaffold1281-2905738 6 88713141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780298 Affx-122958292 AX-385267393 6 85453625 TTATAATATCCTGAGAACAGATTGTTATAATCTCC[A/G]TAACAATTACTTTACCTGTCTGGAAGTTAGAGAGC R 2 1 2 1 201000 f 74 goat snp7862-scaffold1281-2867994 6 88751536 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786479 Affx-122929630 AX-385273513 6 85533016 TCATTTATGATCATCTGTCACTCAGATGAGGAACT[A/G]TTTTTGAGAAAGTTTGTGGATTATTTAAAAGTCTA R 2 1 2 1 102000 f 74 goat snp7860-scaffold1281-2788603 6 88831292 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409491 Affx-122954051 AX-123279842 6 85577331 TGGCAAAGTGGAACTTAACCTTTGGTTCAAAGCCT[A/G]CCTATTCATTCATATATTCACATGCTCTGCTATGC R 2 1 2 1 101000 f 74 goat snp7859-scaffold1281-2744288 6 88875543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402967 Affx-122958159 AX-123273320 6 85611834 AGAGCTTTCTCCCACTTAGTTGGTAAGCTTAATAA[C/T]AATAGGGGCCATGTCTGTTTTTATTCACTACTGTA Y 2 1 2 1 101000 f 74 goat snp7858-scaffold1281-2709785 6 88910304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442187 Affx-122928800 AX-123312524 6 85651866 GGTTACCTGATAGGCATCCAAGATTTCAAGTAGGC[A/C]TTTGGATATATAAATTTAAACCTCAAAGGAGAAGC M 2 1 2 1 101000 f 74 goat snp7857-scaffold1281-2669753 6 88950363 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770818 Affx-122950717 AX-385257981 6 85688160 ATTCAGAGGTTGCTTCTTTGGTTCATTTTGACTTT[A/G]CCTTAAAATTGTGAGCATATTCCTGGGAAATATCG R 2 1 2 1 101000 f 74 goat snp7856-scaffold1281-2633459 6 88987300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773824 Affx-122928387 AX-385260964 6 85747726 ATTCCATACGAGTGTTTGAGTATAAACATGAGCTG[C/T]ACCTACCTCTTCTGTAAAGCAGACTTCCTGCTCTT Y 2 1 2 1 101000 r 74 goat snp7854-scaffold1281-2573893 6 89046546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416311 Affx-122947923 AX-123286660 6 85782574 GCACTTTTGATGTGGAATGGAGGGAGAAAAGAACC[A/G]CTGTTGCTGATGCCTTGGCCCATTCCCCCCTTTCT R 2 1 2 1 101000 f 74 goat snp7853-scaffold1281-2539045 6 89081487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410714 Affx-122952720 AX-123281064 6 85835455 GCCCACTTTATCTTTTAGCAGGCAGAACAGGTTCA[C/T]ATAATTTACTATTCAAACAAAGAAAATGCCTGTAG Y 2 1 2 1 101000 f 74 goat snp7852-scaffold1281-2486164 6 89131907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403769 Affx-122957993 AX-123274121 6 85867782 ATATAGTTTTACTTCCTGCCTCTGCCTAGAAGCCT[A/G]CTTGCTTCTCTATATCCACTTGCTAGACTCTTCCA R 2 1 2 1 201000 r 74 goat snp7851-scaffold1281-2453837 6 89164238 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418908 Affx-122946094 AX-123289256 6 85931620 TGATGACAACTGATATGGATTTAGAGTGGGGCGGA[C/T]GGGTTAGTTAATCCCTGCTTGTTCACTGGAGGCCT Y 2 1 2 1 101000 r 74 goat snp7850-scaffold1281-2389999 6 89228465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772097 Affx-122921474 AX-385259252 6 85974307 GGCACTTATGGTGGATCTATTTTCTTTGCCATTAG[C/T]GGTTATGAAAAGAAGCTCTATAGAGCCTGAATGAG Y 2 1 2 1 101000 f 74 goat snp7849-scaffold1281-2347312 6 89271507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601393 Affx-1002479923 AX-413835815 6 85980078 TTCTTGTTTGAAGTCATTTCAAATGCAATTTGATG[-/CAA]CGTCTCATCAAGTGCAAGACATTGCAGTTGTAAAG - 2 1 2 1 201000 r 74 goat QTLcaseins6.1 6 85980078 - CAA 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601926 Affx-1002479924 AX-413836309 6 85981181 TGCTAAACCCTAAGCATCAAAAGAAGGGAATATCT[A/G]GACAGTAAGTTACGAAAAAAGGATCCAAGTTCTTC R 2 1 2 1 201000 r 74 goat QTLcaseins6.2 6 85981181 G A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942825 Affx-1251531511 AX-585489954 6 85982608 TTTCACTTTTACAATTCACAATTTAATTCCTACAG[-/GAAGTCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG]GTAAGTATTATCTACTTCTTCTTCAATGACAAATG - 4 1 2 1 400000 f 74 goat ins-del_021 6 85982608 GAAGTCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG - SV-TF-chip candidate gene ou candidate region CSN1S1 350601928 Affx-1002479925 AX-413836311 6 85984028 AGCAATATATCTGCTCCAAGAATGTTTTACATAGT[C/T]CAATTTGATCAAGGTTGTTTTTCAAAGTTTTAATA Y 2 1 2 1 201000 r 74 goat QTLcaseins6.3 6 85984028 C T 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942836 Affx-1251531512 AX-585489964 6 85986404 CTCAGAGGCAGTAACAATGATTCTCTTTCTTTTAG[-/CAAATGAAAGCTGGAAGCAGTTCGTCAAGTGAG]GTATACCATTTTTATGTTAATTAAGTATCCCAATT - 2 1 2 1 400000 r 74 goat ins-del_022 6 85986404 CAAATGAAAGCTGGAAGCAGTTCGTCAAGTGAG - SV-TF-chip candidate gene ou candidate region CSN1S1 539241947 Affx-1251531560 AX-585780888 6 85986426 CTCTTTCTTTTAGCAAATGAAAGCTGGAAGCAGTT[C/CC/T]GTCAAGTGAGGTATACCATTTTTATGTTAATTAAG - 4 1 2 1 401000 r 74 goat "CSN1S1-F-allele-1-2;ins-del_008;snp59423-scaffold980-301989;SNPs_066;UniBern-var5" "0;6" "0;85986425;85986426" "c;C" "-;CC,T;g;T" GoatSNP50 chip candidate gene ou candidate region CSN1S1 10.1371/journal.pone.0086227 532567200 Affx-1002479337 AX-579205693 6 85987197 TTTTTTTTTTTAAGGAAATTGTTCCCAATAGTGCT[C/G]AGGTGAGATATATTTACTAAATTTAAAATATATTA S 8 1 2 1 101000 r 74 goat "QTLcaseins6.4;SNPs_067;UniBern-var6" 6 85987197 C G 1 wobble probeset "not_recommended;recommended" Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603035 Affx-1002479360 AX-413837256 6 85987976 TGGGAAGATCCCCTCGAGGAGGGCATGGCAACCCA[A/C]TCTAGTATTCTTGCCTTGAGAATTCCATAGACAAA M 2 1 2 1 103000 f 74 goat CSN1S1-GAFO2O3B2 6 85987976 c a 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603033 Affx-1002479359 AX-413837255 6 85988024 GCCTTGAGAATTCCATAGACAAAGGAGCCTGGAGG[A/G]CTATATCCATAGGATCACAGAGAGCTGGGTACAAC R 2 1 2 1 303000 f 74 goat CSN1S1-O1Ac 6 85988024 g a 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603036 Affx-1002479361 AX-413837257 6 85988066 CCATAGGATCACAGAGAGCTGGGTACAACTGAGGT[G/T]ACTTAGCACAGCACAGAAAGCAAATCTGTTTTCAA K 2 1 2 1 202000 f 74 goat CSN1S1-EBC 6 85988066 g t 2 neutral Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 539241943 Affx-1251531567 AX-585780884 6 85994929 AAAATTCCATGCTTTACATGTCTTTTCATCTATCA[T/TC/TG/TT]GTCAAACCATTCTATCCAAAGGCTTCAATTGCTGT - 6 1 2 1 401000 f 74 goat "CSN1S1-A-allele-1;CSN1S1-A-allele-2-2" 0 0 "-;C" "C;G" Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 468273457 Affx-1111833630 AX-413837314 6 85994929 ACAGCAATTGAAGCCTTTGGATAGAATGGTTTGAC[A/G]TG R 2 1 2 1 103000 f 74 goat "CSN1S1-A-allele-1;CSN1S1-A-allele-3" 0 0 "-;T" C 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 539241949 Affx-1251531570 AX-585780890 6 85995009 GGACAACCTCAAATTGAAGGCACTCTTTCTTCTTG[A/CTTCCTAAATTCCATATATATGTGTTAGTATACTGTATTGGTGTTTTTCTTTCTGGCTTACTTCACTCA/T]GTTCTCCACTGTATTTTAGATTGTGTAACATCCTT - 6 1 2 1 401000 r 74 goat "CSN1S1-E-allele-2-2;ins-del_025" "0;6" "0;85995009" A "CTTCCTAAATTCCATATATATGTGTTAGTATACTGTATTGGTGTTTTTCTTTCTGGCTTACTTCACTCA,T;T" Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 350603024 Affx-1002479354 AX-413837250 6 85997730 TACAAGTGAGTAAAAGAAATGATTGTGAAAATCTT[A/T]CTGAGGATGAACTGACAAATGCATGCATTCTCTTC W 4 1 2 1 201000 f 74 goat CSN1S1-O1-allele-1 6 85997730 A T 2 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350601852 Affx-1002479927 AX-413836236 6 85998059 GAGATTAGGAAAGAATAGTGTAGTAGGAAAATTAG[C/T]TGGAGAAAAGAGGCTGAATAACTTGGTTTACACAG Y 2 1 2 1 303000 f 74 goat QTLcaseins6.5 6 85998059 T C 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601854 Affx-1002479928 AX-413836238 6 85999129 TGCACGAGCAGATCCAGCGAGGCTCCCTTAAGGCC[A/C]CGACTCGCCTTTGCCTGTCGGGCCCCTTAACCGCA M 2 1 2 1 303000 f 74 goat QTLcaseins6.6 6 85999129 C A 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601856 Affx-1002479929 AX-413836240 6 86002527 ATAGCACTAGTACCTGAGAGAACTTTCTCAGATTC[C/T]CCTGTCAAGTTCTTCCTTCTCTCAGATAACCAGTA Y 2 1 2 1 201000 f 74 goat QTLcaseins6.7 6 86002527 C T 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942927 Affx-1251531514 AX-585490048 6 86006394 ATATTTCCAAGTTAAAATTGAACTTTTATGCTAAT[A/G]TTGAATTAACATTTTGAAAGTATATGGTTTATGAC R 2 1 2 1 400000 f 74 goat SNPs_070 6 86006394 G A SV-TF-chip candidate gene ou candidate region CSN2 350601858 Affx-1002479930 AX-413836242 6 86006797 AATGTCTGCTGAATCATGATCACAAAAAGATGTAT[A/T]TTCTTTAAGAATATCAAAACTATATGCTATTCCCC W 4 1 2 1 201000 f 74 goat QTLcaseins6.8 6 86006797 T A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 532567219 Affx-1207771851 AX-579205712 6 86007342 TGAGGAGGGGGCATTCACTTTGAAATCCTCTTAGA[A/C/G/T]CTTAAAAATTAAAAAAATAAAATAAGTGAATGAAT N 8 1 2 1 401000 f 74 goat "snp59433-scaffold980-322303;snp59999-CSN2-ex8-2" 6 86007342 A G GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532567214 Affx-1207771851 AX-579205707 6 86007342 TGAGGAGGGGGCATTCACTTTGAAATCCTCTTAGA[A/C/G/T]CTTAAAAATTAAAAAAATAAAATAAGTGAATGAAT N 8 1 2 1 304000 r 74 goat "snp59433-scaffold980-322303;snp59999-CSN2-ex8-2" 6 86007342 A G 3 GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 350601940 Affx-1002479931 AX-413836323 6 86007588 GTTTGTTATTCTTAGCCAAGTGAGATTATCAAGTT[A/C]CAATTCTGGCTTTATTGTAACTTAATCCCCTTCAT M 2 1 2 1 201000 r 74 goat QTLcaseins6.9 6 86007588 C A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 532567205 Affx-1207771856 AX-579205698 6 86008016 GAAAGGCCTGGATGGGCATATCTCTCTGGGGCACT[A/C/G/T]CTTTCTGGGGAACAGGCAGAACTTTGGGCTGAGAA N 8 1 2 1 201000 r 74 goat "snp59434-scaffold980-322977;SNPs_071;UniBern-var9" 6 86008016 "A;C" "G;T" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942982 Affx-1251531575 AX-585490097 6 86008047 CACTACTTTCTGGGGAACAGGCAGAACTTTGGGCT[A/C/G/T]AGAAAGGGACAGCACGGACTGAGGAGGAAACATGA N 8 1 2 1 401000 f 74 goat "snp59435-scaffold980-323008;SNPs_072" 6 86008047 "C;G" "A,C,T;T" GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942990 Affx-1251531580 AX-585490105 6 86008049 CTACTTTCTGGGGAACAGGCAGAACTTTGGGCTGA[A/C/G/T]AAAGGGACAGCACGGACTGAGGAGGAAACATGACG N 8 1 2 1 401000 r 74 goat "snp59436-scaffold980-323010;SNPs_073" 6 86008049 G A,C,T GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942822 Affx-1251531493 AX-413835719 6 86008403 AGACTAGAGACTGTGCCTGGGCAAAGGGGTGGATT[T/TT]ATCCTGGAGTTCATCCTGGAAAGAAGGAAAAAAAA - 4 1 2 1 400000 r 74 goat "ins-del_009;snp-genphyse673" 6 86008403 "-;TT" "A;T" SV-TF-chip candidate gene ou candidate region CSN2 350602998 Affx-1002479339 AX-413837236 6 86013169 TTCAACATTTTTTTCTGTATTTACCTCTCTTGCAA[G/T]GGCCAGAGCCACCAGACAGGCAAGGATGAGGACCT K 2 1 2 1 202000 f 74 goat "SNPs_074;UniBern-var10" 6 86013169 T G 2 neutral SV-TF-chip candidate gene ou candidate region CSN2 38446381 Affx-122925586 AX-123316717 6 86013256 CGTTCACAGTTGGCTTCCTCTGCAGGCTCCACTGC[A/G]ATGAATTCCTGAGGGGTGACTCAGTAGAAATTCCT R 2 1 2 1 202000 f 74 goat "GoatD01.029085;snp7848-scaffold1281-2308363" 6 89311060 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350601942 Affx-1002479932 AX-413836325 6 86054630 GCTGTTGGCATGAAATCATCTAAATAGAAACCAAT[A/C]CTCTTGCCTTTCTCTTTAACTGTACTTATCGAAGA M 2 1 2 1 201000 r 74 goat QTLcaseins6.10 6 86054630 C A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601865 Affx-1002479933 AX-413836249 6 86074665 GACATAATCACATGCCTATATTATTACAGTAGGCT[C/T]TCAAATTGATCATATTTCTTCTCTTGCCCCTTCAG Y 2 1 2 1 201000 f 74 goat QTLcaseins6.11 6 86074665 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603000 Affx-1002479340 AX-413837237 6 86079098 ATCTATTTCACAGGACCAAGTAAGTATGAAGTTCT[C/T]CATTTTTACCTGCCTTTTGGCCGTTGCCCTTGCAA Y 2 1 2 1 201000 f 74 goat "SNPs_075;UniBern-var11" 6 86079098 T C 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 539241946 Affx-1251531586 AX-585780887 6 86080969 ACTGTATTTGCTTTTGTTTGTAGAAGATGGAACAT[A/C/G/T]TCTCCTCCAGTGAGGTAAGATACTCTTAGTATCAA N 8 1 2 1 401000 f 74 goat "snp59444-scaffold980-395682;SNPs_076;UniBern-var12" 6 86080969 G "A;A,C,T;T" GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 350603109 Affx-1002479342 AX-413837305 6 86085104 GTTTTATCAGAAGTTCCCCCAGTATCTCCAGTATC[C/T]GTATCAAGGTCCAATTGTTTTGAACCCATGGGATC Y 2 1 2 1 201000 r 74 goat "SNPs_078;UniBern-var14" 6 86085104 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 350603111 Affx-1002479343 AX-124387046 6 86089401 TGGGATAATGGAATAATTATAATTTCCCTAGAAAA[A/T]AATCAGCCAGTATTACCAGAAATTTGCCTGGCCCC W 4 1 2 1 201000 r 74 goat "SNPs_080;UniBern-var15" 6 86089401 A T 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 38438173 Affx-122931837 AX-123308511 6 86096704 ACTGAGTGACTAAGCACACATACACACCATATGTG[C/T]TATGCAGATTTTTTTGAAGTCATATAGCCATTCAG Y 2 1 2 1 101000 r 74 goat snp7846-scaffold1281-2224915 6 89392434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444169 Affx-122927280 AX-123314506 6 86139194 ACAGAGTGCAACGTCTCCATTTGTAATTATTCATA[C/T]AGTGCCCTTCTCTAGTCCCAGGGGCACTAAGGCAG Y 2 1 2 1 102000 f 74 goat snp7845-scaffold1281-2182425 6 89433842 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601867 Affx-1002479934 AX-413836251 6 86157760 TTCTGCTGTGGACCCAATTATTACCACAGAGCTAA[C/T]TGGAAAAGAAGGTAATCAAAGATTCTTTTTATGAA Y 2 1 2 1 201000 f 74 goat QTLcaseins6.12 6 86157760 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601948 Affx-1002479935 AX-413836330 6 86159168 ATGTAGTTTTATTTCTTTTTAAGCAATTTAGAAAA[C/T]TATCTCAGGAATTTTATAGAAAGCAGTCTAATGAT Y 2 1 2 1 201000 r 74 goat QTLcaseins6.13 6 86159168 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38411113 Affx-122951909 AX-123281463 6 86174593 TGTAAATAAATAAGTGGAAGAACCCTGCTAAGAGA[C/T]GTTCAAACATATTAAGCCTGATCCAGGTGGCTTTA Y 2 1 2 1 101000 r 74 goat snp7844-scaffold1281-2147026 6 89469265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 538942848 Affx-1251531447 AX-585489971 6 86199773 TTTAAGGTGCAATGATGAAGAGTTTTTTCCTAGTT[A/G]TGACTATCCTGGCATTAACCCTGCCATTTTTGGTA R 2 1 2 1 400000 r 74 goat SNPs_082 6 86199773 G A SV-TF-chip candidate gene ou candidate region CSN3 350601871 Affx-1002479936 AX-413836255 6 86201554 AAGTGAAAGAAGAGAGTGAAAACGTTGGCTTAAAG[A/C]ATCAACATTCAGAAAACTAAGATCATGGCATCCAG M 2 1 2 1 303000 f 74 goat QTLcaseins6.14 6 86201554 A C 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601873 Affx-1002479937 AX-413836257 6 86208101 AATATATAATACAGTGTATAATACAATTTATAATA[A/T]ATATATGATTATATAATATACAGTATTAATATATC W 4 1 2 1 303000 f 74 goat QTLcaseins6.15 6 86208101 A T 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603008 Affx-1002479344 AX-413837240 6 86208947 TTCAGTATGTGCTGAGTAGGTATCCTAGTTATGGA[C/T]TCAATTACTATCAACAGAGACCAGTTGCACTAATT Y 2 1 2 1 201000 f 74 goat "SNPs_084;UniBern-var16" 6 86208947 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 538942842 Affx-1251531448 AX-585489967 6 86209003 CCAGTTGCACTAATTAATAATCAATTTCTGCCATA[C/T]CCATATTATGCAAAGCCAGTTGCAGTTAGGTCACC Y 2 1 2 1 400000 f 74 goat SNPs_088 6 86209003 C T SV-TF-chip candidate gene ou candidate region CSN3 538942844 Affx-1251531449 AX-585489968 6 86209011 ACTAATTAATAATCAATTTCTGCCATACCCATATT[A/G]TGCAAAGCCAGTTGCAGTTAGGTCACCTGCCCAAA R 2 1 2 1 400000 f 74 goat SNPs_089 6 86209011 A G SV-TF-chip candidate gene ou candidate region CSN3 538942854 Affx-1251531450 AX-585489978 6 86209098 TTTGCCAAATACTGTGCCTGCCAAGTCCTGCCAAG[A/G]CCAGCCAACTACCCTGGCACGTCACCCACACCCAC R 2 1 2 1 400000 r 74 goat SNPs_092 6 86209098 A G SV-TF-chip candidate gene ou candidate region CSN3 538942796 Affx-1251531453 AX-585489930 6 86209222 CCTGCCATCAATACCATTGCTAGTGCTGAGCCTAC[A/G]GTACACAGTACACCTACCACCGAAGCAATAGTGAA R 2 1 2 1 400000 f 74 goat SNPs_094 6 86209222 A G SV-TF-chip candidate gene ou candidate region CSN3 538942884 Affx-1251531454 AX-585490008 6 86209263 CAGTACACCTACCACCGAAGCAATAGTGAACACTG[C/T]AGATAATCCAGAAGCTTCCTCAGAATCGATTGCGA Y 2 1 2 1 400000 f 74 goat SNPs_095 6 86209263 T C SV-TF-chip candidate gene ou candidate region CSN3 350603011 Affx-1002479345 AX-413837242 6 86209296 TGTAGATAATCCAGAAGCTTCCTCAGAATCGATTG[C/T]GAGTGCATCTGAGACCAACACAGCCCAAGTTACTT Y 2 1 2 1 201000 f 74 goat "SNPs_096;UniBern-var19" 6 86209296 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 350603117 Affx-1002479346 AX-413837312 6 86209304 ATCCAGAAGCTTCCTCAGAATCGATTGCGAGTGCA[C/T]CTGAGACCAACACAGCCCAAGTTACTTCAACCGAG Y 2 1 2 1 201000 r 74 goat "SNPs_097;UniBern-var20" 6 86209304 T C 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 38415823 Affx-122948884 AX-123286172 6 86226008 CTTTTTACAGGTGGCCTGTGAAGAAGATGGAGTCT[A/G]TAATCCTCCATGAGTGGGAAAAAAAGCATTTGAAC R 2 1 2 1 101000 f 74 goat snp7843-scaffold1281-2095611 6 89521127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394288 Affx-122964705 AX-123264643 6 86289421 TTCTACACTTAAGGGAGAAAATGAAGATGGCTGAA[C/T]AAGTTACTAGATCCTAAGATCTCCCATCCTTCTAA Y 2 1 2 1 201000 r 74 goat snp7842-scaffold1281-2032198 6 89585747 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381873 Affx-122974176 AX-123252231 6 86340201 TGGAAACTCTATAGGAGGAAGCAGGGAAGTGAGGA[C/T]GCCAGTGAAGAGGCTAGTGTGGAATCTCAGGCTTG Y 2 1 2 1 101000 f 74 goat snp7841-scaffold1281-1981418 6 89636586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403418 Affx-122957754 AX-123273771 6 86376826 GGCATTACAAGACATAATATCCCCAATATCCTACC[A/G]TGAGTACTTCTACCTTAGGAACAGTGGGATGGGAG R 2 1 2 1 201000 r 74 goat snp7840-scaffold1281-1944793 6 89673395 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793387 Affx-122968205 AX-385280365 6 86412606 AACAAAACAAAGACTACTACACTGGCTTGATCTGG[A/C]GTCCCCGTCTTGGCTGTAATTCTGATAATATTCCA M 2 1 2 1 101000 f 74 goat snp7839-scaffold1281-1909013 6 89709558 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379052 Affx-122976343 AX-123249411 6 86463530 GAAATTATTTTTATATGGAAAAATAGTAATAACCA[C/T]AGGCAGTATCCATTAAATACTTACTACTTGCCAAG Y 2 1 2 1 101000 r 74 goat snp7838-scaffold1281-1858089 6 89760335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381069 Affx-122974615 AX-123251427 6 86532152 AGGAAATTAGGTGTGTCAGTCTTCCAGCTTCCATC[A/G]CCAAAGCATTTGTTCATCTTCCTTTTTTATAGTCC R 2 1 2 1 101000 r 74 goat snp7836-scaffold1281-1789467 6 89828187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278401 Affx-1111836405 AX-519551886 6 86545603 ACTGACAAGGTCCTGACCAAACAAAGGTTTCTACC[A/G]ATATCCTTCTCTAAATATGCTGTGATTTGACTCAC R 2 1 2 1 101000 f 74 goat Random2.2K-716 6 86545603 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390479 Affx-122967598 AX-123260836 6 86574829 ACCACCATCTGGGAAGGAAATCTATTTACTGCTTG[C/T]ACTTCTTACAGGGATAAAACAAAACATTGTGTTAA Y 2 1 2 1 201000 r 74 goat snp7835-scaffold1281-1746790 6 89871280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273236 Affx-1111833521 AX-519546889 6 86592865 AGGGAAACACTTAATGTTCACACGTTACTAAAGGA[A/C]ATGATCTGGAGGAGGATATGGCAACCCACTCTAGT M 2 1 2 1 201000 f 74 goat 6_86592865_AF-PAKI 6 86592865 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425607 Affx-122940917 AX-123295953 6 86609696 GATAAAAGGGGGAGGATTATCCTATAGAATGATAA[C/T]AACAGTATCCAAGAGCAGAGATAGAGTAGCAGGCT Y 2 1 2 1 201000 f 74 goat snp7834-scaffold1281-1711923 6 89906524 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787031 Affx-122920784 AX-385274059 6 86639307 GGAGCCACACTGTGTGTTGAAATGATCTGATGACC[A/G]TGGCAACACATGCCTGACCACGTGTAGTTATGCCT R 2 1 2 1 101000 f 74 goat snp7833-scaffold1281-1682312 6 89936278 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770979 Affx-122936848 AX-385258142 6 86669870 TCACCCATGGACAGCTATGCTTCATAAACAAAATA[C/T]GAATGTCTCTGAGACAAGGATCACAAGTGACTTTC Y 2 1 2 1 101000 f 74 goat snp7832-scaffold1281-1651749 6 89966827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278571 Affx-1111836406 AX-519552051 6 86679141 TATTCTCAGTCTATAAATAGCCTCATCCCCCAGGT[A/C]AAAATGAACACACCCAAAGGCTTTTTGTGGGGGTC M 2 1 2 1 201000 r 74 goat Random2.2K-718 6 86679141 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781522 Affx-122929163 AX-385268607 6 86698998 ACACTATACCTTAAATGTTTTATGATAGAGATTGT[A/G]TATTATTTGTTTTGTATCCTCTGTGACTGACACAC R 2 1 2 1 101000 r 74 goat snp7831-scaffold1281-1622621 6 89996745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401099 Affx-122959413 AX-123271452 6 86774741 TGGGTATTTAGATTGCCTACTCTTGAAAAGTCTCA[A/G]TTTTGTTAATCTACCAATTTGCATGAAAGGCTATC R 2 1 2 1 201000 r 74 goat snp7829-scaffold1281-1546878 6 90073686 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772361 Affx-122942675 AX-385259514 6 86834481 GTCACATTATTTTGAGAATCTTAAATTACCAATTG[C/T]AAACTAATTTGAAAGAATCCATTTGCACATACTCT Y 2 1 2 1 101000 r 74 goat snp7828-scaffold1281-1487138 6 90133710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393520 Affx-122965800 AX-123263876 6 86868879 CAGACAAAATAGACTTTGAAATAGAGGAAGAACTG[C/T]ATTTCGAGGATGCCTTTCCAAAGTAATGTACAGGA Y 2 1 2 1 101000 r 74 goat snp7827-scaffold1281-1452740 6 90168070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394900 Affx-122964736 AX-123265255 6 86902576 AGCACAGATGTGGAGGTCATAAGGGGAAGCTGGGA[G/T]AATCTGCAGCATATTAATGTGCAGTAATAACATGC K 2 1 2 1 101000 r 74 goat snp7826-scaffold1281-1419043 6 90201821 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802438 Affx-122941037 AX-385289342 6 86934578 CCCCCAAAATGTGACCACTTCCTATCTACCTGCCC[A/G]TACTATCAAAGAAAGATATTCTTACTTCTGGTCCC R 2 1 2 1 101000 f 74 goat snp7825-scaffold1281-1387041 6 90233787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452152 Affx-122921661 AX-123322485 6 86968766 TTCTTACTTTTCTCCCCTTTGTAACCAATACATAG[A/C]TTGCAAAATAACATAACTCTAATAACTGAATAATT M 2 1 2 1 201000 r 74 goat snp7824-scaffold1281-1352853 6 90267974 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432691 Affx-122936034 AX-123303032 6 87002714 TGCCCATGTTTAAAAACATTCAGTTTCTTCTAGTC[A/G]CAGGCTATATTAAGAAAAAATTCTAAGATGAACAT R 2 1 2 1 101000 f 74 goat snp7823-scaffold1281-1318905 6 90301669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787404 Affx-122974748 AX-385274429 6 87035438 GAGCTCTCTAACTAATAGCCAGAGAGGTCTGTCTC[A/G]CAGTCTGGCTCTCCACAAAGTTTCCCGAGCTGATA R 2 1 2 1 202000 r 74 goat snp7822-scaffold1281-1286181 6 90334276 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422231 Affx-122944019 AX-123292577 6 87077159 GAAGGACATTTGAGATGTTAGTTACCTGAAGAATG[A/C]TGTTACAGGCGCAAAACACAAATAGGCTCTCGAGA M 2 1 2 1 101000 f 74 goat snp7821-scaffold1281-1244460 6 90376567 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407844 Affx-122954527 AX-123278195 6 87118368 CCACCCTGTGACCTGCTCAGAACCAGGGAGATGCA[C/T]GTAATCATTGCCCTGACTCACCTGTGCACAGTCTC Y 2 1 2 1 101000 r 74 goat snp7820-scaffold1281-1203251 6 90417624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441666 Affx-122929187 AX-123312003 6 87174077 TGAGCTGTGTCATGCTGGGTCATCAAGTTTCTTGA[C/T]GGAAGGAACAAGATATTTCTACTGAGGAGTCATGT Y 2 1 2 1 101000 r 74 goat snp7819-scaffold1281-1147542 6 90473272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413813 Affx-122949896 AX-123284162 6 87203481 CTATGGAAAAAGCTCACTGAGTAATTGCAGAAAAA[C/T]GAGAGACTTTAAAAAATTGAAACAAAACAAAAAGT Y 2 1 2 1 101000 f 74 goat snp7818-scaffold1281-1118138 6 90502388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795836 Affx-122936757 AX-385282789 6 87260833 CTATGCTAAAATTTCAGACTGAAATTCTTATTCCA[C/T]ACCAAGATGAAAATTTATATGTACTATTTTTACAG Y 2 1 2 1 101000 r 74 goat snp7817-scaffold1281-1060786 6 90559594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419931 Affx-122945318 AX-123290279 6 87304858 TAAAAACTGGATTGTGAGTTAACAGGAGGTGGGGC[A/G]TGAGAGTGAAGGAGTTCAGCGAAAAACAACCTTCA R 2 1 2 1 101000 r 74 goat snp7816-scaffold1281-1016761 6 90604237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768869 Affx-122963643 AX-385256046 6 87342788 ATTACCACCTGGACAAATATAACAGGATTTCAAAC[C/T]ATCAGCGGACAGTAGGCACTGTCAAGATTTCTCTT Y 2 1 2 1 101000 r 74 goat snp7815-scaffold1281-978831 6 90642617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385346 Affx-122971651 AX-123255704 6 87372435 ACAAATATGTATTGAGACCTACTCTATGTCAGGCA[C/T]AAGAGGAAGCAGCAGTGAACTCTCAGACAAGCGCT Y 2 1 2 1 201000 f 74 goat snp7814-scaffold1281-949184 6 90673332 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387702 Affx-122969809 AX-123258060 6 87411509 ATTCTTCAAGTGGGAGTCAGCATCCTACTCTGTTT[A/G]GAAATCTGTATATGCTATATAGTGAGATGTTTACT R 2 1 2 1 201000 r 74 goat snp7813-scaffold1281-910110 6 90713008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408860 Affx-122954001 AX-123279211 6 87441654 AAGCATAAGTCCTTAAAGTGTTCTCTTTTTCTGAC[C/T]GAATATCCTCATGTTCTTCTTGCGGATTTGCTGGC Y 2 1 2 1 101000 r 74 goat snp7812-scaffold1281-879965 6 90743655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423325 Affx-122943177 AX-123293671 6 87510728 CTAGGGAACATGGAAACTATTTATTAAACCCCCCT[A/G]TTTATGATGCCCACCATATTTGCTAAAGCTAGAAG R 2 1 2 1 101000 r 74 goat snp7810-scaffold1281-810891 6 90814164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781465 Affx-122959503 AX-385268550 6 87556576 TTCTTGTCTGACATATAAGAAACATATTAATGTTC[A/G]TTATTACATTTAGTAAGTTGGTATTGTTTCCTTTG R 2 1 2 1 101000 f 74 goat snp7809-scaffold1281-765043 6 90863494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378192 Affx-122976943 AX-123248551 6 87656043 AACATATTAGTCTCCCAGTCTGGCGTTGTCAAGCT[A/G]TGTGATTTTGGATTTGCACGGACACTGGCAGCTCC R 2 1 2 1 101000 f 74 goat snp7807-scaffold1281-665576 6 90964681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410770 Affx-122952681 AX-123281120 6 87702846 TTGACATCAGTTGTTAACAGTAGTATTAAATGTAC[A/G]TAATTTCCACGTTTTTGTTGTTTTATAAAATTTTA R 2 1 2 1 101000 f 74 goat snp7806-scaffold1281-618773 6 91011237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802399 Affx-122939551 AX-385289303 6 87745801 CAATGTCTGTGTAAGTGTGGTGTGGTGACTTCTCA[C/T]GATCTTTGGTGATAAGAATGTTCTTTGGTTGACTT Y 2 1 2 1 101000 f 74 goat snp7805-scaffold1281-575818 6 91054091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780038 Affx-122946473 AX-385267137 6 87777342 ACTTTGCCTTCATGAGGTTTAAAACATAGTTATAA[A/C]TTCTTTTGAGAGAACTTCCCTAACTATGACTATAG M 2 1 2 1 201000 f 74 goat snp7804-scaffold1281-544277 6 91085634 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791372 Affx-122978344 AX-385278364 6 87821686 TTAATTCTTTAGGTAGTACTCAAAGCTATAAGATA[C/T]GAGTAAGCTCCTCAAGCAGTTTAGATTTTCACTCT Y 2 1 2 1 101000 r 74 goat snp7803-scaffold1281-499933 6 91129975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430266 Affx-122937299 AX-123300607 6 87867416 GTGTTGCCTCCATGCTGATTGATGTATGTGAGTGC[A/G]TTCTCAGTCACTTCAGTTGTGCCCAACTCTGCAAC R 2 1 2 1 101000 f 74 goat snp7802-scaffold1281-454203 6 91176157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392708 Affx-122966402 AX-123263065 6 87899462 ATCTCTTGTCTGAGTGAACACCACCGTTCTCAGTG[C/T]GCAACTGATTTAGATTCTTCTCTTTTTGCAAATAA Y 2 1 2 1 201000 r 74 goat snp7801-scaffold1281-422157 6 91208098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430912 Affx-122936856 AX-123301253 6 87931309 ATTATCAGACAAACTAAGTTAGAAATCAAAGTCAG[C/T]ATAAATCTAGTGGGAAAAGAACACAAGAATATTTA Y 2 1 2 1 101000 r 74 goat snp7800-scaffold1281-390310 6 91239611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429650 Affx-122937672 AX-123299991 6 87976824 CCATGGGGTTGCGAAGAGTCAGACATGACTGAAGC[A/G]ACCTTAGCATGCTCGCATGCTTTATCTGTTTTCAC R 2 1 2 1 103000 r 74 goat snp7799-scaffold1281-344795 6 91285169 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436497 Affx-122932958 AX-123306835 6 88022077 TGGGTTCCTAATTTTCTCTATTCTGTCCTTCCCTC[G/T]AGGCCAGCAGAGTAATCAATTATTAAGTGAAAATT K 2 1 2 1 201000 r 74 goat snp7798-scaffold1281-299542 6 91331202 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796596 Affx-122946821 AX-385283542 6 88077411 ATCCTGACTCCACTTGACAAGTGTTCCTCGCAAGA[C/T]AGATGATGCAGAGATTAAGCCAATAAAACTAAAAT Y 2 1 2 1 101000 f 74 goat snp7797-scaffold1281-244208 6 91386844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433776 Affx-122934479 AX-123304117 6 88112743 ATGTTCTCAAAGAATTAATCCTCCCCATGTGATAA[C/T]AGAAAGTGTTTAGGTCAGAAGAAGTCATAGGGTTA Y 2 1 2 1 201000 r 74 goat snp7796-scaffold1281-208876 6 91422189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381431 Affx-122974351 AX-123251789 6 88147358 TGGAAATTATCACCGTCCAAAGACCAGCAGGATAA[A/G]ACACGTCAGGAAAGGTGAGAGACCACTAGAGGGCA R 2 1 2 1 201000 f 74 goat snp7795-scaffold1281-174261 6 91457367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397697 Affx-122962571 AX-123268052 6 88263412 TGGAAGAGACCCTTAATACATGAATTTAGAATTTC[A/G]CCTTGACCAGAAGTTGGAAGAATTCCTGTTTTTTG R 2 1 2 1 201000 f 74 goat snp7793-scaffold1281-58207 6 91571351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395924 Affx-122963593 AX-123266279 6 88316143 AAGAGGAGAGAGAAAAAGGATGAAAATCAAATGAG[C/T]AGGTTGGGCTAATTGTGAGAAGCTTAGTAACATAA Y 2 1 2 1 101000 r 74 goat snp7792-scaffold1281-5476 6 91624233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385404 Affx-122971341 AX-123255762 6 88338374 TAAGGCAGTTATGAGGAGGACCATGTCTCCACTTG[C/T]GCCGGGGACAGAGGGTGGCAGTCTCCACAGTTTCC Y 2 1 2 1 103000 f 74 goat snp42034-scaffold549-16656 6 91646745 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388876 Affx-122968868 AX-123259234 6 88382855 TGTGCTGAGCTGAGCTGAGTGTGAATTAATCTAGG[C/T]ATTTCTGATGATATGCAGCTACCTTCCAAAGTCCA Y 2 1 2 1 101000 r 74 goat snp42035-scaffold549-61137 6 91691362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375735 Affx-122978622 AX-123246094 6 88443477 ATACAAAACACAAACATACACACTCTTCAAACAAT[C/T]AGCTCCCTCCGTTTACCTTGTGTTAATGAGCCACA Y 2 1 2 1 101000 r 74 goat snp42036-scaffold549-121759 6 91751464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409251 Affx-122953138 AX-123279602 6 88485041 AAAGCTGTGTCCTGAGTATGCCCTGCTGTTTCAGG[A/G]CCCTCCTTTATTTACACTCTTTTTCTTCCTCCTTT R 2 1 2 1 101000 r 74 goat snp42037-scaffold549-163323 6 91793057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438925 Affx-122930423 AX-123309262 6 88516711 AAAAGGCAAATACTATAAGGGACAGAAAAGATAAC[A/G]CATTTGATTTGAAAATATTTATATGGCAAAAGCTC R 2 1 2 1 101000 f 74 goat snp42038-scaffold549-194993 6 91824722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773131 Affx-122938837 AX-385260274 6 88548133 TTTTAATGAAAAGGTCTCTAAAGATCAAACAGCCT[A/G]GCCTAGATCTAGGACCCAGTTTGCTGCTAGGTGAG R 2 1 2 1 101000 r 74 goat snp42039-scaffold549-226415 6 91856045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400513 Affx-122961271 AX-123270868 6 88595695 GATGGTTGTCAGGATTAAGTAAATGTTTAGAAAAA[C/T]GCCATTTAGAAAATACCCAGTAATTCTTAATTTCT Y 2 1 2 1 201000 r 74 goat snp41450-scaffold539-1889731 6 91905025 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431761 Affx-122936723 AX-123302102 6 88672175 TTTCTTCAGCAATTCCATTAGGCTTTCTCACTGGT[A/G]TCACTTGGCTGAGTTGCACAATGCCTCAGCCACGT R 2 1 2 1 101000 f 74 goat snp41448-scaffold539-1813251 6 91981444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601297 Affx-1002479939 AX-413835727 6 88683688 TTAGAGGGAAAAAATAATTAATTCTACATTTTAGA[-/GA]GAAAAAAAACACTAAGTCTTGGGGACCCCAACTAC - 2 1 2 1 202000 f 74 goat QTLcaseins6.17 6 88683688 GA - 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38401878 Affx-122958855 AX-123272231 6 88700790 TTCCGGGTTGTCTGCGTTACTCATGACCTAAAACT[C/T]CTCCCTCCTCAAGAGGTTAGGTCACTTTGAGGATT Y 2 1 2 1 101000 f 74 goat snp41447-scaffold539-1784636 6 92010631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601956 Affx-1002479940 AX-413836337 6 88701993 GGTTATGTGACTTTGGGCAAGTTACTTCACCTTTC[C/T]CGTGCCTCCCACTCTCCACCATAAGATGGGGATAA Y 2 1 2 1 202000 r 74 goat QTLcaseins6.18 6 88701993 C T 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601957 Affx-1002479941 AX-413836339 6 88708206 GACGCACGAGGCAGGAAAGTCCCACCTTTCCCACG[A/C]CGGCACTGAGCAAGCCTACTGCGCAGACACGAAAC M 2 1 2 1 102000 r 74 goat QTLcaseins6.19 6 88708206 C A 1 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601880 Affx-1002479942 AX-413836264 6 88709540 CTATTCCTCAAATTCCTAAGACTTCCTTCTGTGGA[G/T]TTCGTACTCAGGAGTTGAAGCTGGAACTTCAATGA K 2 1 2 1 202000 f 74 goat QTLcaseins6.20 6 88709540 T G 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320802989 Affx-122970034 AX-385289872 6 88747021 TACACAGCAATAGAAAATTCGGCAAACTGTTCTCT[A/G]TATGAGCTAGGAGTAAGTTCCCTCACTTGGTCCTT R 2 1 2 1 101000 r 74 goat snp41446-scaffold539-1738405 6 92056817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427517 Affx-122939522 AX-123297860 6 88786160 CTCACCATCTGGTGTCCCTTCCACAGTTGGGCCTC[C/T]GCATTTAACCTTCTAAAAGCCTGTAACACGGCCAT Y 2 1 2 1 101000 r 74 goat snp41445-scaffold539-1699266 6 92095669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449702 Affx-122922542 AX-123320037 6 88822373 CACCCTTCTCCCACCTCCCTAGGCCGATCATGTAA[C/T]GAAATGAGTTCAAGGCTCTCCAGGCTAAGGTACTG Y 2 1 2 1 101000 r 74 goat snp41444-scaffold539-1663053 6 92131912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441433 Affx-122928816 AX-123311770 6 88868406 GGCACTTTGAAGGTGAGTTTGAGGAGGCCTGTTCC[G/T]CTAGCCCAGCCCACTGGCCCTCCTTTTTTTCTCCC K 2 1 2 1 101000 f 74 goat snp41443-scaffold539-1617020 6 92178768 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381482 Affx-122974964 AX-123251840 6 88916010 ATGTGGCATCTGCGGTGTGGCAGCCTGAGGTGGTG[C/T]GGAATAAGGTGAGGATGGAAAGGGAATTTAAGGTC Y 2 1 2 1 101000 r 74 goat snp41442-scaffold539-1569416 6 92226541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392989 Affx-122965663 AX-123263346 6 88949370 TAATAGTGTTTGCTTCTGTGAGAGGGCATATGGGG[C/T]AGGTGTGGGCCAAGTTAATAAACACTGTGGGCACC Y 2 1 2 1 201000 r 74 goat snp41441-scaffold539-1536056 6 92260024 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438042 Affx-122931550 AX-123308380 6 88990668 CTTGAAAAATTTACATTTCATAAAACCATTATTTA[C/T]GTCAACAGGCAATACAATTATTCTCACATAAAATG Y 2 1 2 1 102000 f 74 goat snp41440-scaffold539-1494758 6 92299933 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436047 Affx-122932718 AX-123306386 6 89025642 GTTAACTTCAGCCGCACATTGCTTTCCTGAAGCTC[A/G]TAACTTCTGGCTTTTAACCGGACACCTGGTTCATT R 2 1 2 1 201000 r 74 goat snp41439-scaffold539-1459784 6 92335367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393528 Affx-122965793 AX-123263884 6 89058318 GCCACTCTGAACAGGCATAAATGGCAAGTCATTTG[C/T]GTTTCCAGAAACAAAGTCCCACTGCACATAGCTTT Y 2 1 2 1 101000 f 74 goat snp41438-scaffold539-1427108 6 92367977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770666 Affx-122922367 AX-385257830 6 89112534 CCAAGCCTCCATAGTCATGAACCAATTTCTTAAAA[C/T]AAATCTCTCTCAAAATCCCTCTATGTATATAGAAA Y 2 1 2 1 201000 r 74 goat snp41437-scaffold539-1372892 6 92422056 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273284 Affx-1111833522 AX-519546928 6 89127917 CTTGAATAACAATGTCGAATAAACATGAAGATGGA[A/G]ATAGACATTGTGAAAACTGTAAGGACATCAGGTCA R 2 1 2 1 101000 r 74 goat 6_89127917_AF-PAKI 6 89127917 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395231 Affx-122964478 AX-123265586 6 89157290 AGAGACAATGGCACTAGTCAGCAGGTACCTCCTTC[A/G]CAGAGATCTGGCTCCTAGCCTAAAGGGCTCCTGTT R 2 1 2 1 101000 f 74 goat snp41436-scaffold539-1328136 6 92467252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427466 Affx-122940024 AX-123297809 6 89195250 CACCTTTGTCAACTATGGATCGCTGTGATCAGGCA[C/T]GGAAAGGACACTGGCAGGTGTGGTACATGTAGAAA Y 2 1 2 1 201000 f 74 goat snp41435-scaffold539-1290176 6 92505590 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779366 Affx-122936765 AX-385266470 6 89240731 GAGTAAGTGAAAACAAAACGTGAAATGTCAGCTCA[C/T]GCTGCATTGATTTGTAGCTAATAATGCGCACTTAC Y 2 1 2 1 101000 r 74 goat snp41434-scaffold539-1244695 6 92551747 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399927 Affx-122961314 AX-123270282 6 89270348 ATCTGATTTCACCATGCATGTTTTGTTTTAATGAT[G/T]GGCACACCACTCTAATGAAGAGTCACTATGCAAGC K 2 1 2 1 101000 r 74 goat snp41433-scaffold539-1215078 6 92580787 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777652 Affx-122955671 AX-385264771 6 89302596 CCCGGGGCCTCAACTCTCTATTCCAAAAAAAACTT[A/G]TAATGTTCATCCTCCCAACAAAAACGTCCCTGACG R 2 1 2 1 101000 f 74 goat snp41432-scaffold539-1182830 6 92613115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780245 Affx-122961774 AX-385267340 6 89340232 ATGCTACTTAACTTCACCTTAGAACAGATGGTGTT[A/G]CTAGGCATATTCAGGGATATGGCAGATGCTGGTCT R 2 1 2 1 101000 f 74 goat snp41431-scaffold539-1145194 6 92650356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385291 Affx-122971691 AX-123255649 6 89388222 CTTGGTCACCATTTTCAGCCCCACTGGCCTCTGTC[A/G]GCATTGCTAGCATGTCAAACTCTTCATATTTCACT R 2 1 2 1 201000 r 74 goat snp41430-scaffold539-1097204 6 92698960 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791780 Affx-122941658 AX-385278771 6 89433167 TGACAAATAAGAGAGGATAGGTTTAGAAATAATTC[C/T]GGTGTGTCCTCTCAGTTGGCACAAGTATTACCAGT Y 2 1 2 1 101000 r 74 goat snp41429-scaffold539-1052259 6 92743827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429814 Affx-122938188 AX-123300155 6 89475739 CTTCCTGATCCAGGGATTGAAATTGTGTCTCTTTA[C/T]GTCTCCTGGCATAAGAGATCCTAATTTTACAGGTT Y 2 1 2 1 303000 r 74 goat snp41428-scaffold539-1009687 6 92786528 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448977 Affx-122923118 AX-123319312 6 89505201 TGGTTGAAGTCACACATCTTGACACACTGAAATAT[A/G]TTGACTTTTGCTTTCTCTTCTATATGAGGTTCCTG R 2 1 2 1 201000 f 74 goat snp41427-scaffold539-980225 6 92816467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395785 Affx-122963664 AX-123266140 6 89545291 TTTATTTTAATTTTATTGTGGCATTACTCTGTACT[A/G]TGTCATACATTGGTATGCATGAATGCAAAACATGT R 2 1 2 1 101000 r 74 goat snp41426-scaffold539-940135 6 92856658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408901 Affx-122953969 AX-123279252 6 89598288 ACTTTTTGGCCAACCCAGTAGTATTGTCTGTCACA[A/G]TTGAGTTCTCCAGAAACAAGACTCCCACGTTAGTT R 2 1 2 1 102000 r 74 goat snp41425-scaffold539-887138 6 92909796 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787001 Affx-122963235 AX-385274030 6 89636295 AATGCAAATATTTACGGGAGGCTACTCATCTTACA[A/G]TAAGTAGGCTTTCCATATGTATGTGGAGATTAAAT R 2 1 2 1 101000 r 74 goat snp41424-scaffold539-849131 6 92947776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789018 Affx-122945681 AX-385276031 6 89671853 AAAAGTGGATTAGCTGCATTGTTTAATGCTATCTC[A/G]TTTGGATCAGTGTGAGTCTGCATTGGCCTTGCCTT R 2 1 2 1 101000 r 74 goat snp41423-scaffold539-813573 6 92983706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410156 Affx-122952793 AX-123280506 6 89708041 ATAAACTGATTGCCCCTGAGATAACCATGCTGAGC[A/G]TAGGGAATGGAGTGAAGATCCTCCTTTAGGCAGTT R 2 1 2 1 101000 r 74 goat snp41422-scaffold539-777385 6 93019669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451140 Affx-122921369 AX-123321474 6 89762487 AACCACCTGGACCACCCACCACTTCCAGACATGTA[C/T]GGGAAGTCAGTCGGAAAATCCCAAATAATGGCATG Y 2 1 2 1 201000 r 74 goat snp41421-scaffold539-722939 6 93075400 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797393 Affx-122971475 AX-385284332 6 89806451 CTGAAAAGAAAATTATTCTCATCATCATCAGACAA[G/T]ATTTATTCAACATGCACTTGGGTATGATACAGTAT K 2 1 2 1 101000 r 74 goat snp41420-scaffold539-678975 6 93119275 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785441 Affx-122924067 AX-385272486 6 89856081 CCAAAATATGCTCTTTTAAACGGGCAAAAAGAATG[C/T]ATATTTCTTCACATAACTTTAACAAAAAGGGGGAT Y 2 1 2 1 101000 r 74 goat snp41419-scaffold539-629345 6 93169191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786843 Affx-122977199 AX-385273872 6 89910616 CTCAGTGTCCCTACCTCCCAGGCTGTTAAATATCT[A/G]TGATATCATCCTATGTTAAATGCAATAGCACAGCA R 2 1 2 1 102000 f 74 goat snp41418-scaffold539-574810 6 93223920 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446353 Affx-122925607 AX-123316689 6 90043188 TTTTATTGCTTTAACTGCCCCGTCATTTTTATCCA[C/T]GATGGCTCTCCAATGCAATGTTTTAAGTGAGGAGC Y 2 1 2 1 101000 r 74 goat snp41415-scaffold539-442238 6 93356714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769503 Affx-122923396 AX-385256673 6 90084820 TGGTCATTACACTAAGGGAACACAGACTCTGTACC[G/T]ACATCATAACAGCTGACAGCACAGACTGCATCCAA K 2 1 2 1 101000 r 74 goat snp41414-scaffold539-400606 6 93398426 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417125 Affx-122947369 AX-123287473 6 90121855 TAAAAGCCTCTGTTCTCATTCCTTCAGTTTGTCTC[A/G]TATCTGTCTGTCTCTCTCTGACCTTTTTCTTTGAC R 2 1 2 1 101000 f 74 goat snp41413-scaffold539-363571 6 93435610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278405 Affx-1111836407 AX-519551890 6 90126608 AAAGTCATTGACCTCTGTGTTATGTCTCATAGGAT[A/G]AAAAAGGCAGAAAAAGCTTGTTGTCATCCTTAGTA R 2 1 2 1 101000 f 74 goat Random2.2K-719 6 90126608 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441577 Affx-122928679 AX-123311914 6 90163532 GAGACTGAGAGCAGGTCAAGCAGTCTGGGTGGCAA[C/T]GAACTATGATCAAGGACAAAGAAGAGGAGAACTCA Y 2 1 2 1 101000 r 74 goat snp41412-scaffold539-321894 6 93477032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403421 Affx-122957751 AX-123273774 6 90194421 TCTGACTCTGCTTTGATTTATGTGTTAGCCAGAAC[C/T]AGAAAAGCCCTTCATAACAACACAGGTACTTACAT Y 2 1 2 1 201000 r 74 goat snp41411-scaffold539-291005 6 93508327 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442272 Affx-122928268 AX-123312609 6 90248500 ACAATCCCCTGACAGAAGACCACATAAAACCAATA[C/T]GCTCTCAAATCTTGCTGTGGAGTCAACCTGAAGGT Y 2 1 2 1 201000 f 74 goat snp41410-scaffold539-236926 6 93561024 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278407 Affx-1111836408 AX-519551892 6 90290741 CTTTATCTTGGTACATGTGATTGTTTCAGCTGCCA[A/G]CAGCATTAATGGACTGAAAATCCAAAGATATTAAA R 2 1 2 1 101000 f 74 goat Random2.2K-720 6 90290741 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796544 Affx-122959807 AX-385283490 6 90307076 CATAATTTCTAAAACTCTACCTGCTGTCTTTGTTG[C/T]GATTCAGGGCTGCTATACCACTTTGGAGTGTAATT Y 2 1 2 1 101000 f 74 goat snp41409-scaffold539-178350 6 93619419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767306 Affx-122952924 AX-385254587 6 90346432 TGTTCAGAAAGACACTAAGCATCCTAGGGCTGAGG[C/T]ATATTATGCTATTTTCAAGGGTCATGTGTATGTAA Y 2 1 2 1 101000 f 74 goat snp41408-scaffold539-138994 6 93658836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449322 Affx-122922993 AX-123319657 6 90394947 GAGCTGTTTCTCACATATTTCTTATTAAAAAGAGT[A/G]CGGTAGAGGAAACATTTTAAAGCACTTTGAAATGC R 2 1 2 1 201000 f 74 goat snp41407-scaffold539-90479 6 93706638 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419745 Affx-122945886 AX-123290093 6 90505282 TGCCAAGAGGTTAGCATAATGCCGAGCATGTCGTA[C/T]GTGCCTGACGAATGTTTATTTAAAAAGTACAATTT Y 2 1 2 1 101000 f 74 goat snp4469-scaffold1143-680238 6 93816114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380852 Affx-122975443 AX-123251210 6 90546624 CTCTCTGAGAACACTCCTGATTCTTACTCACCACT[C/T]CCACCATCACCACAATTTTCTAATGACTAAGTATA Y 2 1 2 1 101000 f 74 goat snp4468-scaffold1143-638896 6 93858147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792541 Affx-122937919 AX-385279522 6 90586915 AGGCAAGCACAAAGCCAGCCAGGCTTAGATGAAAT[A/G]CACACTGTTTGCTAAATGGCCGTGGTGTTTTGAGG R 2 1 2 1 101000 f 74 goat snp4467-scaffold1143-598605 6 93899141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420243 Affx-122945070 AX-123290591 6 90630129 ATAAACGGCAGCAGCAGAAGGCCTAGGAGTTCCCA[A/G]TCTGGGAGATCTCTGCTTCCTCAGTCTTCCAGAGA R 2 1 2 1 201000 r 74 goat snp4466-scaffold1143-555391 6 93942330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779740 Affx-122955175 AX-385266840 6 90661713 GTTGTTTTCAGTTTGGGGTATTGTGATTGACAGCA[A/C]CTTCTTCCCTCATGAGCAAATATTGCTTGGGTTGC M 2 1 2 1 101000 r 74 goat snp4465-scaffold1143-523807 6 93973861 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415159 Affx-122949403 AX-123285508 6 90765427 ACAATCACTTCATGAAGGTGGAGAGGGAGCAGTTC[A/C]AGCACGACTACTGTCGAACCCTGTTATCTCATACA M 2 1 2 1 201000 r 74 goat snp4463-scaffold1143-420093 6 94078100 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413378 Affx-122950135 AX-123283727 6 90817084 AGTCCTTACCCTTTGATTATAATCAACTCTTTATA[C/T]GTCCGCCCCCTCATAGCCTGTGAGCTCTCCCACTG Y 2 1 2 1 103000 f 74 goat snp4462-scaffold1143-368436 6 94130124 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774228 Affx-122959127 AX-385261365 6 90856846 ATCTCTGGTTCTCACATACCAACAGGATAAAATTA[G/T]ATACCTTTAATAAAAGTGCTTAGGCTCTACTGCAA K 2 1 2 1 101000 f 74 goat snp4461-scaffold1143-328674 6 94169915 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382399 Affx-122973837 AX-123252757 6 90906599 GATATCTCAGCCTCACCTAGATGACTTCTTCGGGT[A/G]TGTTGACAGCAACTTGTGATCATCTAGGCACTTCT R 2 1 2 1 101000 r 74 goat snp4460-scaffold1143-278921 6 94219862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440877 Affx-122929239 AX-123311214 6 90954350 GCATTCATTCACTTAACAGAATTTTTTAAACATCT[A/G]CTCTATGCCAGACATTTTTCTGAGCACTGAATACC R 2 1 2 1 101000 r 74 goat snp4459-scaffold1143-231170 6 94268080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802369 Affx-122973441 AX-385289273 6 90984012 ACCTTTGCCATCACTCCATCATCCCAATACATACA[A/G]TAGTTTCCCTAAGTGTTTAGAATGCCCACTCACCT R 2 1 2 1 101000 f 74 goat snp4458-scaffold1143-201508 6 94297562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439186 Affx-122931049 AX-123309523 6 91042623 GTACAGAACAAAAGAAATGTTTCTTTCCACTTCCT[A/G]AGAAGCATTTTTGAATTATGAAAACCTCAGTATCT R 2 1 2 1 201000 r 74 goat snp4457-scaffold1143-142897 6 94356420 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776928 Affx-122962769 AX-385264052 6 91071169 CACAAATTGTCTATACTGAACACTTCTACCGTCTA[C/T]ATTTTTGGCCCATAGAAATTGCCTCCCTGTGAGTA Y 2 1 2 1 101000 r 74 goat snp4456-scaffold1143-114351 6 94384925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401340 Affx-122959262 AX-123271693 6 91109382 TATCTAATGTTCAAATCCATCCTACCTTATGCTAC[A/C]GGGATGGCCTAGTCAGGTGTCAATCAAGCGTTCCT M 2 1 2 1 201000 f 74 goat snp4455-scaffold1143-76138 6 94423117 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799491 Affx-122964461 AX-385286421 6 91145301 AATGCTGCTGACCTTGCATAATAATTTTTCCCTTA[C/T]AACATATTAATTATTGTTCTGGCACCTCTGGCCTA Y 2 1 2 1 101000 r 74 goat snp4454-scaffold1143-40219 6 94459436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453926 Affx-122919899 AX-123324259 6 91180953 CTGTAGGAAATGACCCACACCCACTCCTGTACTTG[A/C]TGCTTTAAAGAAACTATCTGGGTGGGCTCAGGTCT M 2 1 2 1 101000 r 74 goat snp4453-scaffold1143-4567 6 94495194 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781950 Affx-122930430 AX-385269031 6 91237016 TGTCCATATCATTGATGTTAATCTAGCTCACAGCT[A/G]CTTTTCACTATTCTTCTAAAAGCATAATGATTTTC R 2 1 2 1 101000 f 74 goat snp19320-scaffold1951-51397 6 94551442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425101 Affx-122941234 AX-123295447 6 91271049 AGAGAAGAGGCCTTTTAAAATCAGTTCCAATGAGG[C/T]GGTTCCCTGGGAATTCTGAATGTTGATGGGAACAT Y 2 1 2 1 201000 r 74 goat snp19321-scaffold1951-85430 6 94585913 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394912 Affx-122964319 AX-123265267 6 91315559 TCCTGAAATGAAAACAGTTGCAAATTATTTTGACA[C/T]GTACTTAGTGTGTTTTGTGTCTCTGAAGGTAGCAT Y 2 1 2 1 101000 r 74 goat snp19322-scaffold1951-129940 6 94630919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390602 Affx-122967179 AX-123260959 6 91346618 GTGTGTAAAGGACTTTGAGCCTAAGGTTTAGTGGA[A/G]TTGAAAGTTACACATCTAAAAGGTGATGCCAAATG R 2 1 2 1 101000 f 74 goat snp19323-scaffold1951-160999 6 94661877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278409 Affx-1111836409 AX-519551894 6 91347477 CCCTTCAGCTAGAGAAGCGACTGCCTACCAATGGC[A/G]CCTTCACACAGCCCTGCAGGAGCTCACCTTGGTGA R 2 1 2 1 102000 f 74 goat Random2.2K-721 6 91347477 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791433 Affx-122925339 AX-385278424 6 91383058 AAGTCTTGTTCTATACAGGAAATATCTGACATGTC[A/G]TGTCCATATTCATCTCATTGTTGGGATTTGAAGGC R 2 1 2 1 101000 r 74 goat snp19324-scaffold1951-197439 6 94698397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401146 Affx-122959376 AX-123271499 6 91416430 CATGAAATTATTTATCATCCCCCTTAGAATCAGAA[G/T]TTCTCTTTCTTCTCTATGATTTTTCTACACGGTAT K 2 1 2 1 303000 r 74 goat snp19325-scaffold1951-230811 6 94731572 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443650 Affx-122927202 AX-123313987 6 91511073 ACTTATGTTAAAATATAATGCTATATAATACTTCC[A/G]ACCATTCAAAACTAGATAGCATGGCTTACTGAATA R 2 1 2 1 101000 r 74 goat snp19327-scaffold1951-325454 6 94827100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404224 Affx-122957653 AX-123274576 6 91551718 CCCTTGGCCTAACTGGGCCCCTACCTGGGACTCTC[A/G]TGCTACCCAAGTTCACCCTCCAGAAATCAGCACTC R 2 1 2 1 101000 r 74 goat snp19328-scaffold1951-366099 6 94868112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278579 Affx-1111836410 AX-519552058 6 91576002 AAAAATGGGACTAATGATGGAGACTATGTTTTTCT[A/G]ACTGGAGAAGACAATTACCTTAACTTTTCCAAGAT R 2 1 2 1 101000 r 74 goat Random2.2K-722 6 91576002 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403911 Affx-122957481 AX-123274263 6 91580420 CATAAAAGTTTCCAATAAAATTTGTTTTAGATACT[C/T]GCAATAAAACATTCTTTGCTTGCCTCTTAGCTCCA Y 2 1 2 1 101000 r 74 goat snp19329-scaffold1951-394801 6 94897010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386267 Affx-122970948 AX-123256625 6 91614825 ATGTGCGAGGACTAATGATGGCCCGGGGCCTGGGA[C/T]TGGCGACGAGCTGTGCTTGGGAAACAGTCAGAGGT Y 2 1 2 1 101000 r 74 goat snp19330-scaffold1951-429206 6 94932402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436244 Affx-122932559 AX-123306583 6 91645351 AGACTCCCTACTCTCGGCTTCCCAGTAAGTTTAGC[A/G]TTGAGAGAAACTCATGGAAGTTTAGGGAGAGGAGA R 2 1 2 1 101000 r 74 goat snp19331-scaffold1951-459732 6 94963107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453504 Affx-122919817 AX-123323837 6 91677741 CTGGTTTCTAAGTGTCTAAAGAAAGACCTTATTCC[A/G]TGAAATACATTTTTTGGACATTCATGTGATCTCTG R 2 1 2 1 101000 f 74 goat snp19332-scaffold1951-492122 6 94995511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387836 Affx-122969661 AX-123258194 6 91711763 TTCATGCTTTAGCAAAATTGTTCTCATCAGTAAAA[G/T]CCTTGTCTGAATTATACGTTTCTTTGAATGTAGTA K 2 1 2 1 101000 r 74 goat snp19333-scaffold1951-526144 6 95029782 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273286 Affx-1111833523 AX-519546930 6 91712964 TTGCAGGGTAACTGTGTAGCTCTTCATCACACAGG[A/C]TGGACAGCATTTTTTGATGATAGGAGCCAAACAAC M 2 1 2 1 101000 r 74 goat 6_91712964_AF-PAKI 6 91712964 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441715 Affx-122929149 AX-123312052 6 91746422 TTATCTTATATTTTCATTTAAAGGTAATCAAATCC[C/T]GTATGCATAGGGTTTGAGGTAGGCTATGTGTGCAC Y 2 1 2 1 101000 r 74 goat snp9903-scaffold1352-2650363 6 95065806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409205 Affx-122953170 AX-123279556 6 91785387 GAGGACAGGACAGATATCTGTTTTTAGATGGTCTT[A/G]TATTTTGATATATTAGTGATACCAAGGTTATATAT R 2 1 2 1 101000 f 74 goat snp9902-scaffold1352-2611398 6 95105044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408782 Affx-122953375 AX-123279133 6 91825476 TTTTTGTTTTCACCATTGTTAACAATGTAGAAAGT[A/G]TACTTGCCAGGATTTCAAAATCAATTTGAATTTAT R 2 1 2 1 101000 r 74 goat snp9901-scaffold1352-2571309 6 95144406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418571 Affx-122946381 AX-123288919 6 91922278 AACCATGAGGAAAACCTGTAAGGGAGTTTGGGAAA[C/T]GTCCATTTTTAGCTTTTTCTAGCACGCAAAAGACA Y 2 1 2 1 101000 f 74 goat snp9899-scaffold1352-2474507 6 95237741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401045 Affx-122959659 AX-123271398 6 91973070 ATTTGAAACTCAATTGACAGAGACTAAAACAAAGA[C/T]AGTCATTATATTACAGTTCTTAAAATGTGCATTGG Y 2 1 2 1 101000 r 74 goat snp9898-scaffold1352-2423715 6 95288815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428793 Affx-122938404 AX-123299135 6 92017807 TCTCAGAGCCCTTTGGCTGCAAGTTCCTACTAGCA[A/C]TGATTTCCAGAGGTCTTGGCAGGCTGTGTAAGCCA M 2 1 2 1 101000 f 74 goat snp9897-scaffold1352-2378978 6 95333419 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417129 Affx-122947366 AX-123287477 6 92054489 GGTTTGTTATTTATTAGTAGTAGCAAAAAGTACAA[C/T]ATTTTCTTAGTCCTGCTTAAAACATCATCTAATAC Y 2 1 2 1 101000 r 74 goat snp9896-scaffold1352-2342296 6 95370112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772228 Affx-122977678 AX-385259383 6 92087376 AAGTTAACAACAGTAGTACACAAGTTTTGTGGGCT[A/G]TGGAATAATGGTCGCTCACATCTTCCCATTACTGG R 2 1 2 1 101000 f 74 goat snp9895-scaffold1352-2309409 6 95403210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786212 Affx-122947297 AX-385273247 6 92138914 ATTTCTGCTAAAAATATGTGTCATTTTTCCTAAAG[C/T]GCCCTTTCCTTTGCCCTCTACTGTATTTTGAAGAC Y 2 1 2 1 101000 r 74 goat snp9894-scaffold1352-2257871 6 95454706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381464 Affx-122974979 AX-123251822 6 92170100 AAGATAAAAATAGCAAAACGACTCACTACTTGTGC[A/G]TTCCCAGAAAGAGAAAGGTGAATCGAGGTTTAAAG R 2 1 2 1 201000 f 74 goat snp9893-scaffold1352-2226685 6 95487331 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400149 Affx-122960698 AX-123270504 6 92222898 ACAACCTGATTTTTTAAATGGACCTAAGACCTTAA[C/T]AGATACCTCACCCCAAATGAAGAATATGTATAATC Y 2 1 2 1 201000 f 74 goat snp9892-scaffold1352-2173887 6 95539069 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445254 Affx-122925479 AX-123315591 6 92304909 TTAGCATTCCAGACAGAGAGATCTCAGTTAGAACC[G/T]AGTTTCAGGCTGATAAGCCAGATCCTCAGGCAGCA K 2 1 2 1 201000 r 74 goat snp9891-scaffold1352-2091876 6 95623196 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801910 Affx-122938955 AX-385288815 6 92353866 TTGTGAAGGTGAGGGTAATCACTATTCTACACTTG[C/T]AAAAGTTATTTTTTGCCAATCAGGGCTGTATAAAG Y 2 1 2 1 201000 f 74 goat snp9890-scaffold1352-2042919 6 95673548 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383437 Affx-122973470 AX-123253795 6 92392023 CCACAGATTTAACAACTGCAGGTCTTATAATACTG[C/T]AGTACATATATTTTTTTTAATCCACATATAAGTGG Y 2 1 2 1 103000 f 74 goat snp9889-scaffold1352-2004762 6 95711661 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789086 Affx-122960667 AX-385276099 6 92456638 CCTTGGAGAGTTCAGACCTCATAAAATTCACATAT[A/G]ATTTCTGCTGACAGCAAATTAATATAGATTCAAAT R 2 1 2 1 101000 f 74 goat snp9888-scaffold1352-1940147 6 95777545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765526 Affx-122946730 AX-385253010 6 92501014 ACCTGCATTTGATAAAACATTAACTTTGTTCTCTG[C/T]GTAAATAAAATGGTGGCTCTCCAGGTGCACCTGCT Y 2 1 2 1 101000 f 74 goat snp9887-scaffold1352-1895771 6 95822843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453807 Affx-122919568 AX-123324140 6 92540250 GAAACTGGGAATAAGGGTCCTTTGGGAATAAATTA[C/T]AGCACTGGTACTCTAGACAGTAGATCTGTTATAAT Y 2 1 2 1 101000 r 74 goat snp9886-scaffold1352-1856535 6 95862319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773148 Affx-122925155 AX-385260291 6 92611018 AACTACTTTAGTCTACCATTAGTGAGTAATATAGT[C/T]AGCCCCCACAATGTTTAAGTTAGTGAAGAAATGGA Y 2 1 2 1 101000 r 74 goat snp9885-scaffold1352-1785767 6 95932409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789812 Affx-122948640 AX-385276819 6 92642913 AGTTGGAGAACTATTACAATTGATTCACAATAGGC[A/G]TAGTATTTTCTGTGTTAAAACTACCTAAACTGCAA R 2 1 2 1 101000 r 74 goat snp9884-scaffold1352-1753872 6 95964303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772225 Affx-122921893 AX-385259380 6 92690096 ATTATTGTTATGTCATCATTATCCAAAAGAAGTGT[A/G]TTTATATAAGATTCCATAATTTCATATTTTCATTT R 2 1 2 1 202000 r 74 goat snp9883-scaffold1352-1706689 6 96013396 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401469 Affx-122958965 AX-123271822 6 92751924 CTGACTTACATTATGGTTGAAGAAATGGTGATAAG[A/C]TTGGATTTAGTAAGAATACTCCAGACCCTCAAATC M 2 1 2 1 101000 r 74 goat snp9882-scaffold1352-1644861 6 96076212 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789241 Affx-122962993 AX-385276252 6 92826883 CAGGACATTATGAGATACTTATACATTAGCACAGA[A/C]GAATTGTGTCTTCTTTCATTTGCTGGTGTCATGGA M 2 1 2 1 101000 r 74 goat snp9881-scaffold1352-1569902 6 96151594 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406203 Affx-122956133 AX-123276555 6 92907534 AAAGAAAACAGCCCCATAATTGGGTACTGAGCTAA[C/T]AGTTGGGAAGTAGCTCAAGAAGATGAAAGGAAGGT Y 2 1 2 1 202000 f 74 goat snp9879-scaffold1352-1489251 6 96234686 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392757 Affx-122966002 AX-123263114 6 92947590 TACATTCAGAATAAATGAAATGACGAGATGTTAAG[C/T]GGGTAGAATGATCCCTAGCTGGACTCTCACCTGTA Y 2 1 2 1 101000 r 74 goat snp9878-scaffold1352-1449195 6 96274732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429381 Affx-122938548 AX-123299723 6 92979177 GATCTGGGTTTTTAAAAACTGGGTTGCTGGTTGCC[A/C]TTCTTGTGAGGGCTATGCAATGAAAACATCAGTAT M 2 1 2 1 201000 r 74 goat snp9877-scaffold1352-1417608 6 96306278 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788660 Affx-122966435 AX-385275676 6 93013459 CTGGAAACCAAGTAGACCAAACAGGGTAAGAAGAG[C/T]GAAAATATTAAGGTGTAACTAGAAATACTTAAAAA Y 2 1 2 1 101000 f 74 goat snp9876-scaffold1352-1383326 6 96339593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402106 Affx-122958687 AX-123272459 6 93067225 GCCCTTCTCTGAATTCTCCAGCCTAGTCACAGCGA[C/T]GATACATAAAATATTGGAAGTTTGAGAACTGAAGT Y 2 1 2 1 201000 r 74 goat snp9875-scaffold1352-1329560 6 96393473 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792872 Affx-122941950 AX-385279850 6 93098222 AAGGATTTCCACATAATGAATGGTAGTTATAAGGG[G/T]CAAGTGTTGGTGGAGCTAGAAAAGACTTTTTGTCT K 2 1 2 1 101000 r 74 goat snp9874-scaffold1352-1298563 6 96424327 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408132 Affx-122954239 AX-123278483 6 93143445 CAGGGTTCTTTCTCAAGTCTCTGCGTGCATGTGTT[A/C]GTTGCTCAGTTGTGCCCGGCTCTTTGCAACCCCAT M 2 1 2 1 101000 f 74 goat snp9873-scaffold1352-1253340 6 96470025 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414938 Affx-122949092 AX-123285287 6 93174494 CTTACCGACTTGAAAACTGCAAAGGAAAGATATTT[A/G]CAAAAGATGAAGCGTGTCATTGTGTTCCTTTTTTC R 2 1 2 1 101000 r 74 goat snp9872-scaffold1352-1222291 6 96501544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415638 Affx-122948579 AX-123285987 6 93230491 TGAGAGAGTCTTTCTGAATCATCATAAACCTGAAT[G/T]AGAAAAGGGCTGAGTTTTATACAGCTTAACTTAGG K 2 1 2 1 101000 f 74 goat snp9871-scaffold1352-1166294 6 96557544 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382053 Affx-122974933 AX-123252411 6 93271146 AAACAGAAGAGACAGAATAACCATACAGAACCCCC[A/G]TCTGATGTTTTGATTAAGCCTTGGTGAGGATGTGA R 2 1 2 1 101000 r 74 goat snp9870-scaffold1352-1125639 6 96598371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421007 Affx-122944556 AX-123291354 6 93322577 GGGAAACGTCTGCACACCCCCACATGCTCACCAAC[A/G]CCAGGGACCAGTGCCCGAGGCATTTCCTCTTTTCC R 2 1 2 1 101000 r 74 goat snp9869-scaffold1352-1074208 6 96649422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464470989 Affx-1110499642 AX-515943445 6 93349772 TCATTGTAGTAGGGGGACAGCCATTGATCTTGGTG[A/T]CAGTTGACTGATACTTTTAAAGCATTTTCTATTAG W 4 1 2 1 202000 r 74 goat Random2.2K-726 6 93349772 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417851 Affx-122946779 AX-123288199 6 93360140 AAGTCAGAAAGAAAATACGAGAGGATGCTCTGCTC[A/G]TGATTCAACAGTAGCAGGGGCGGTAAAGACAGGAT R 2 1 2 1 101000 f 74 goat snp9868-scaffold1352-1036645 6 96687011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454274 Affx-122919637 AX-123324607 6 93400720 CTTACTTTAAGGAGATGTATGTTGAAGTATTTAAG[C/T]GTGTCAGCAACTTTCAAATTGTTCTTCAGCAGCCC Y 2 1 2 1 201000 f 74 goat snp9867-scaffold1352-996065 6 96727903 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426149 Affx-122940607 AX-123296495 6 93429960 TAATTCAATCCAGTAGCATTATTGCTTCAACCACA[C/T]GTATCTAGTGGGTAACATATGACTCACCAAAGCGT Y 2 1 2 1 101000 r 74 goat snp9866-scaffold1352-966825 6 96757224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802658 Affx-122955461 AX-385289557 6 93476928 TCAGAGGTCAATTGGAATTTTTGGTTCTTAAGTGC[C/T]TCTAAATGTACCATTAAATAAACTTGGGCACCATC Y 2 1 2 1 101000 f 74 goat snp9865-scaffold1352-919857 6 96804893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376811 Affx-122977933 AX-123247170 6 93531203 GAGACAGTCAGGAAGAATAAACTTTCCTTTCAGAA[G/T]ATTGAGGATCAGAAAGAAAGTGTTCCTTGAGTGCG K 2 1 2 1 101000 r 74 goat snp9864-scaffold1352-865582 6 96858925 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406355 Affx-122955429 AX-123276707 6 93567095 CTTGGGACTGTGTGAAGATTGGATCAGTTTATGTA[C/T]GTATCAATACAAATCTTTATTGTGGTATCTGGAAC Y 2 1 2 1 101000 f 74 goat snp9863-scaffold1352-829690 6 96895191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448393 Affx-122923686 AX-123318729 6 93619286 CTGATGAGATGAGATTCTGCTCCTCTACCTTATTC[A/G]TTTTCAGCGCTAACTAAAGCAATTGACAAGTGTGT R 2 1 2 1 201000 r 74 goat snp9862-scaffold1352-777499 6 96947441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445769 Affx-122926068 AX-123316106 6 93668905 CCCCAAAGGGGAGCGTCTGTAAGTAGTGGGGAGGC[A/G]TTGAGGAGTGTTGGCAGTGGAGTAACCATATCAGA R 2 1 2 1 101000 r 74 goat snp9861-scaffold1352-727880 6 96996890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393847 Affx-122965153 AX-123264202 6 93698947 CATTTTTTTCACTCACTTCAATTTAAAAACAAATA[A/G]CAATCTCTTTTTGTCCTAGCACATGCTATGGTATA R 2 1 2 1 303000 r 74 goat snp9860-scaffold1352-697838 6 97026363 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427600 Affx-122939367 AX-123297943 6 93738088 CTGGCCGAATCAGAGCTTGCCATCTTGTATCAACT[C/T]TGGAAATCCCAAGGTTCTCTAAGTAGGATGACGTT Y 2 1 2 1 101000 r 74 goat snp9859-scaffold1352-658697 6 97063867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381908 Affx-122974149 AX-123252266 6 93778498 GTTTAACCTTCCATCTCTTAAAGGAGGAAATGACT[A/C]TTTTGGGCTTCCCTGGTAGCTGAGATGGTAAAGAA M 2 1 2 1 201000 f 74 goat snp9858-scaffold1352-618287 6 97104282 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413585 Affx-122950578 AX-123283934 6 93820402 ACTAAAACTGAAAAAAAAAAAATGACTTAGGTGGT[A/G]CCCTTCCTAGTGACAAGTCTGAGTATTTAATGCTA R 2 1 2 1 101000 r 74 goat snp9857-scaffold1352-576383 6 97144011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452890 Affx-122920220 AX-123323223 6 93858116 TACATATGTGGCGGGCATTGACAAAATGTGGGTGC[A/G]TCTTTGCCATCTCAGCTCCAGGACTTAAACAGCCT R 2 1 2 1 101000 r 74 goat snp9856-scaffold1352-538669 6 97189243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802302 Affx-122972191 AX-385289206 6 93909892 AGAAGTGCTGGTTTTAAGGAGCTCAGATTCACGCC[A/G]TTCATTCAGTTTACTGCATAGTAATCACTTACTTG R 2 1 2 1 101000 f 74 goat snp9855-scaffold1352-486893 6 97241865 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38393752 Affx-122965217 AX-123264107 6 93950010 AATCATTTTTGATTGATTTCTTTCACTCTGCATCC[A/G]TCTCCTTTACAAACAAACTGGAAACTCTGACAAGA R 2 1 2 1 101000 r 74 goat snp9854-scaffold1352-446775 6 97282038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396341 Affx-122963061 AX-123266696 6 93988222 TAATTTTTGAAAGTGAGGTGGACATTGAATGGACA[C/T]GTGATGGGAACGGGAAATGTCCAAGAGAAGGTACC Y 2 1 2 1 201000 f 74 goat snp9853-scaffold1352-408563 6 97320058 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772591 Affx-122928626 AX-385259740 6 94038060 TGGTGAGAAAGGGTTAATTTGGCAACAAAGCCACG[A/C]TGAGGTTATATTCATCTCAGAACCGAGTTGCTGGA M 2 1 2 1 101000 f 74 goat snp9852-scaffold1352-358725 6 97370118 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435718 Affx-122933302 AX-123306057 6 94071400 TCCCTACCATTCTGTTACTTATGTGGTCCACATTC[A/G]TGAATAAATATTAGAGCTTTACTTGCCTGGAATTA R 2 1 2 1 101000 f 74 goat snp9851-scaffold1352-325385 6 97404136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447423 Affx-122924389 AX-123317759 6 94114856 AATTCCACAGTTTTAAAAATTCATTTTCTAGATAT[A/G]CATAGTTATCAGAATATGTTCTTTGCATGATTTCT R 2 1 2 1 101000 r 74 goat snp9850-scaffold1352-281929 6 97447254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434394 Affx-122934690 AX-123304735 6 94163806 AGTGAACTCCCCATTTTATTTCCAGAGACTTCACC[A/G]TCTTTCTCTGTTCCCACTTTGGCTTTTATACATTT R 2 1 2 1 201000 r 74 goat snp9849-scaffold1352-232979 6 97496389 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378505 Affx-122976649 AX-123248864 6 94202912 TAGCATCGTCATTATTATTTTTAATTTAGAAAAGT[C/T]ATTGTGTAAAGTAACACTCCTCATGGTTTAAAGTC Y 2 1 2 1 101000 r 74 goat snp9848-scaffold1352-193873 6 97536858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453983 Affx-122919449 AX-123324316 6 94269622 TTATTTTTTAAGGTTTTAAATGTCAGTCAATTTCT[A/G]AGGCCACCCCTTCCGACCTGTTATTCCATGGGTTA R 2 1 2 1 201000 f 74 goat snp9847-scaffold1352-127163 6 97604470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378527 Affx-122976629 AX-123248886 6 94303804 CTTTCAGGACCACGTGGCCTCTGGTTCTTTCTATA[C/T]GTCTGCTCATTTTTTCTCTCTCTCTTCCTTCACAC Y 2 1 2 1 201000 f 74 goat snp9846-scaffold1352-92981 6 97638837 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438182 Affx-122931832 AX-123308520 6 94337697 ATCACCAAAACAATTACCAGCCGTATTAAAGGGGA[C/T]ACTGCAGAAAACAGGTGTGTATCAGAGTTCAAGAA Y 2 1 2 1 101000 r 74 goat snp9845-scaffold1352-59088 6 97672694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425082 Affx-122941247 AX-123295428 6 94373747 TCGACAGAAAAAAGAAATATAAGCAGCTAGTAACC[A/G]TCTTGGATCGTAGGCTTTACATCAGGCAATGCCCT R 2 1 2 1 101000 r 74 goat snp9844-scaffold1352-23038 6 97704927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396871 Affx-122963242 AX-123267226 6 94409070 CTGCAGGGGAAGCATGGAGTTCTAAATACTGGACT[A/G]CCAGGAAATTCCCTTTTCTCCCCCATTATAATAAG R 2 1 2 1 103000 r 74 goat snp913-scaffold1025-12186 6 97740256 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273288 Affx-1111833524 AX-519546932 6 94412502 AAAGGAATGATATTCCACTGATCAAGAATGGTGAG[A/G]CTTGTGGTCCCTCAATTCAGCCATGTAAACGTGCC R 2 1 2 1 101000 r 74 goat 6_94412502_AF-PAKI 6 94412502 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426421 Affx-122940829 AX-123296767 6 94439813 AGAGTCCAGGGAAATCCTCAGGATGAACGAGGTCC[A/G]CGAATGAAGAAAGACAGAGAAAGCGATAAGGAAAG R 2 1 2 1 101000 r 74 goat snp914-scaffold1025-42929 6 97771372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403888 Affx-122957496 AX-123274240 6 94469753 AAGACCAGAAACAAGATGAGATCATTGGATCTGAC[A/G]GTTCAGAAATCATTGATGACGCTGGCATGAATGGT R 2 1 2 1 201000 r 74 goat snp915-scaffold1025-72869 6 97801339 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774200 Affx-122951869 AX-385261337 6 94513109 ACTAGTGAAAGGCATTTGATGAGAAATACATGAGT[G/T]AAGCAACTGCTATAAAGACACTTTAAGGTCAATTT K 2 1 2 1 101000 f 74 goat snp916-scaffold1025-116225 6 97844840 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397284 Affx-122962335 AX-123267639 6 94592948 TGTTTGAATGACATGTTGTAGCTATAGCGATTAAA[C/T]CACATGTCCGCGTTCTAGTGTTAAAGCATAGTTAC Y 2 1 2 1 101000 f 74 goat snp918-scaffold1025-196064 6 97923699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419027 Affx-122946035 AX-123289375 6 94643585 AAGTGAGGAAGTGAAAGCTGAGGGCTGATAAGAGA[C/T]GGCAGCCTTCCATCAATGAACTGTCCATCAAGTCT Y 2 1 2 1 201000 r 74 goat snp919-scaffold1025-246701 6 97975207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396246 Affx-122963329 AX-123266601 6 94678132 TAAAATTCATAAACCATAACTATAGTTCAGCTTGC[A/G]TATTACCCAGAGATCATATTACTTTCCCCTGGTCC R 2 1 2 1 101000 r 74 goat snp920-scaffold1025-281248 6 98009447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402040 Affx-122958733 AX-123272393 6 94723323 CTGTCAGACACCAGATCCCACTGTGGACAGAGATG[C/T]GAGGCTGAAACAGAAGGGGACAGAAAAGCTGGGTA Y 2 1 2 1 201000 f 74 goat snp921-scaffold1025-326439 6 98054724 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388570 Affx-122969170 AX-123258928 6 94790824 AAGTTTTACCAGCTGAGCTGCTGGGATCACTATGT[A/G]GCCCTGGATTCACAAACTCGTTATCAAACCCTCTG R 2 1 2 1 201000 r 74 goat snp922-scaffold1025-393940 6 98122325 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417435 Affx-122947209 AX-123287783 6 94819532 CTCAAACTGTACAGAAAAGTCTCCCTGCCCCTCAA[C/T]ACACACTATTTGAGACACAGACTCTATCTAGTTGA Y 2 1 2 1 201000 r 74 goat snp923-scaffold1025-422648 6 98150451 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772879 Affx-122967692 AX-385260024 6 94927840 CCTTCTTCCACCCTTTCCTATTGTCCACTCCCTAA[C/T]AGCTTCAATCCAATTAAACTTAAGACAATGCTGAG Y 2 1 2 1 101000 f 74 goat snp925-scaffold1025-530956 6 98258349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419736 Affx-122945892 AX-123290084 6 94957295 TCTTGCTAAGTGGCCAAAAAAGTGGAAGAGAGAAC[G/T]CAAAACAAAACAAAAATATAAGGAGAGAAATTACA K 2 1 2 1 101000 f 74 goat snp926-scaffold1025-560411 6 98287229 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417438 Affx-122947207 AX-123287786 6 94998169 GATGGTTTCCATCTCTCTCTCTAGTTCTTCCACTT[A/G]GGATCCCTTCTCCGAACTCTGCCACTCCCTACCCC R 2 1 2 1 102000 f 74 goat snp927-scaffold1025-601285 6 98328030 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780792 Affx-122930658 AX-385267881 6 95109542 CCCAGTTATACCAATTGAACACTTTAAAAAGGGAC[C/T]TACCAGGTCATCTGTGATTGGAGTTAAATCAGGAC Y 2 1 2 1 101000 r 74 goat snp930-scaffold1025-712658 6 98436619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779895 Affx-122950588 AX-385266994 6 95169513 TTTTTATTGCTAAAGTGCTAAAAATCATGTAATTC[C/T]TGTGACTCTAGATGAGGATTACAACAGGAAGAAAG Y 2 1 2 1 101000 r 74 goat snp931-scaffold1025-772629 6 98497277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453960 Affx-122919465 AX-123324293 6 95302469 CAAGGATGGGTGATTCTCCCAAATAAGATGTGATC[A/G]TTATTGCTCTCATCAGCTTCTAGCAACTGCTGGAC R 2 1 2 1 101000 r 74 goat snp934-scaffold1025-905585 6 98631918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791959 Affx-122935620 AX-385278948 6 95343924 GCTTCAAGGTGACTCACTGTGGAGCCAAGCTGTTG[C/T]ATTAGTCAGCATTCTCTTACACGTAGCCTTAGAAT Y 2 1 2 1 101000 f 74 goat snp935-scaffold1025-947040 6 98673636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771354 Affx-122935337 AX-385258512 6 95375413 AGTTATGATTACATTAATGATCACTTGAACAACAT[A/G]TATCAAGCATTTCATGCCAGGATTTACATTACTGT R 2 1 2 1 101000 r 74 goat snp936-scaffold1025-978529 6 98704551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797177 Affx-122969536 AX-385284117 6 95429832 TACTCTTTTTATTGCCGGATACCCTCTCTGATAGC[A/G]ACTAAACGGCACTAAACGACCTACTAACTTTTTTT R 2 1 2 1 101000 r 74 goat snp937-scaffold1025-1032948 6 98757845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401696 Affx-122959548 AX-123272049 6 95501133 TAATGCTTTCACTGGATCAGGGATGGGCTTCCAAA[C/T]GCCCAGAGCCTCATTCACTGGGCCTCCCTTTGCCT Y 2 1 2 1 102000 f 74 goat snp939-scaffold1025-1104249 6 98829880 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420907 Affx-122944604 AX-123291254 6 95603714 GTGATGAGGCAGGCAGCCTCATACAGTGTTAGCCC[A/G]TCTTCTCTCTCTGGGCCACCTGCAGCTCCAGAGAT R 2 1 2 1 101000 f 74 goat snp941-scaffold1025-1206830 6 98932429 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388775 Affx-122968934 AX-123259133 6 95634077 CACAGTGCCTATCTTATAATAAGCACTCAATAAGT[A/G]TTAGCTGACATTATTATGAATCCAAAAAAGGTACT R 2 1 2 1 201000 r 74 goat snp942-scaffold1025-1237193 6 98961621 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379590 Affx-122976030 AX-123249948 6 95663380 TTAAAGAGGAAGTTTTGATTAGGTTTGTGAAGAAC[A/G]TGCTTTCTGCATATGTCACCCTTTCACCTCTTGCT R 2 1 2 1 101000 r 74 goat snp943-scaffold1025-1266496 6 98990988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789512 Affx-122978475 AX-385276521 6 95694032 AATCATCCCAATCCATTCCCATGGTAACAAATCAC[A/C]TTTAAGACTAATGTTGCACTATGTGATTCTGGTAG M 2 1 2 1 202000 f 74 goat snp944-scaffold1025-1297148 6 99021532 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450288 Affx-122922162 AX-123320623 6 95725920 GAGATGGAAGTTGGAGTTTAGGGCTTATAAGATAT[C/T]GTGGCTCTGGTGAATACCCCAGGCTTTCATTTGAG Y 2 1 2 1 101000 f 74 goat snp945-scaffold1025-1329036 6 99053758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782281 Affx-122978470 AX-385269359 6 95770631 TCAAAGAATAAATTAAGATGAGACATATTAACAAA[A/C]GAAAATCAAACAAAAATTTGGTGAGATCTATACAT M 2 1 2 1 103000 r 74 goat snp946-scaffold1025-1373747 6 99099108 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420717 Affx-122944778 AX-123291064 6 95805495 TAACTTTACAGAACTCTCTCTTTCTGCTTTATTGT[C/T]TGCTTATTTTCATGTAGCATTAAAAAGCATGAGAG Y 2 1 2 1 201000 r 74 goat snp947-scaffold1025-1408611 6 99134404 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431692 Affx-122936778 AX-123302033 6 95840225 AAATCCAAAACAGTTGCATATTTTAAGGAAGAAAA[C/T]GATGATTATTAATATTTTCCCCAACAAATAGGAAA Y 2 1 2 1 103000 f 74 goat snp948-scaffold1025-1443341 6 99169858 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441032 Affx-122928940 AX-123311369 6 95891648 CAGCCATCTGGGCATTTCCCTTCAGTCATTACCAG[C/T]ACTCAAAAGGCCTTTGGTTCAGAACTGGACTCTGC Y 2 1 2 1 101000 f 74 goat snp949-scaffold1025-1494764 6 99221084 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446991 Affx-122924640 AX-123317327 6 95934828 GTATAAATGGAATCATACAATTGGTGACTTTTCCT[A/G]TGTAACTATTTTAACTTCTTTTTGAGCTTCAGTTT R 2 1 2 1 101000 r 74 goat snp950-scaffold1025-1537944 6 99265658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386019 Affx-122971496 AX-123256377 6 95976714 CAGTTGGGAGCTCAACAGAAAGGACTGGCTGGATG[C/T]GGAAGAACTGTAAGTTGGATCACCCAACATCCAAC Y 2 1 2 1 101000 r 74 goat snp951-scaffold1025-1579830 6 99307290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801100 Affx-122946485 AX-385288014 6 96027196 ACCCTTTAACATCTGTTCACGATGGAGACTCGCAG[A/C]ACATTTTCTATGAAATGAAGCCATTCTAAAAACAT M 2 1 2 1 101000 f 74 goat snp952-scaffold1025-1630312 6 99358113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408399 Affx-122954481 AX-123278750 6 96067380 AACAAAACTTTCCTGTTTATCTCCCCTATGCACTA[C/T]ATACACATATGAAATATTTATTTGGATGTTATATC Y 2 1 2 1 101000 f 74 goat snp953-scaffold1025-1670496 6 99398397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424163 Affx-122942533 AX-123294509 6 96105553 TGTGGGCTGGTCACTTACCTGCACTGAAGCTCAGC[A/G]TCCTCATCTGTAAAATAAGCAGAAACATGGTGCTC R 2 1 2 1 201000 f 74 goat snp954-scaffold1025-1708669 6 99436540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416725 Affx-122947547 AX-123287073 6 96144838 CCTTTTTTCAATATTAAGAAGGATAAGCCATGCAC[A/G]TTATTTCAAGTGTACAGTCCTCTGGCATTAAGGGA R 2 1 2 1 101000 f 74 goat snp955-scaffold1025-1747954 6 99476254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802333 Affx-122976987 AX-385289237 6 96178085 GGAATATCAGTCAGGGTCTCAGCAGGAAATAGAAG[A/C]TGTTTTTATAAACTGAAGAGAGTTTAAGAGAAGGG M 2 1 2 1 101000 f 74 goat snp956-scaffold1025-1781201 6 99509885 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445456 Affx-122925344 AX-123315793 6 96215626 TATCTCTGTGCATAAAGCCTTTGTTCAGCCATAAA[C/T]TGCAAAAATCTAAGTTGTTGTTATTATGCAGTATC Y 2 1 2 1 101000 r 74 goat snp957-scaffold1025-1818742 6 99547912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409369 Affx-122954162 AX-123279720 6 96274663 ACCACTTCCAGTTTGTTCATTTTCTAGCATAGCAG[C/T]AGGATGAGTTGTTTTAATATTTCAAAGGTCCTTGT Y 2 1 2 1 101000 f 74 goat snp958-scaffold1025-1877779 6 99605076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425866 Affx-122940651 AX-123296212 6 96310768 CCATGCAAGGAAGATGGAATTTTTATAGAAGCTGT[A/C]GACATTTAAAAGCACATAGTCACGTGGAGTGATAA M 2 1 2 1 101000 f 74 goat snp959-scaffold1025-1913884 6 99641465 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419293 Affx-122946238 AX-123289641 6 96344638 AGGCAACCAAACTGAGGGTCTAAGAAAGTGATATC[A/G]CAAACAAAGGGAGACAATGACTAAGGAGGCAATGG R 2 1 2 1 201000 f 74 goat snp960-scaffold1025-1947754 6 99675698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793246 Affx-122958901 AX-385280224 6 96377547 CTCTTCAAATACTTTTGTACACATAATCTCAAGTA[C/T]GTCATCCATCCATCAGTACGAGGCTAGATATCTAC Y 2 1 2 1 101000 r 74 goat snp961-scaffold1025-1980663 6 99708724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423685 Affx-122942321 AX-123294031 6 96429633 TAACAACAGGCTCAGGCCAAGGATGGAACGAAAAC[A/G]CCTCACCCAGCCCCATGGAAGAGTTAACACACATG R 2 1 2 1 101000 f 74 goat snp962-scaffold1025-2032749 6 99761404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405940 Affx-122955560 AX-123276292 6 96482462 TGCACTGGCAGGCCGATTCTCAGCCACTGGACCAC[A/C]GCGAAAATCCTCTCTGCTTTTGTTTTTGTGTTTCA M 2 1 2 1 101000 r 74 goat snp963-scaffold1025-2085578 6 99813876 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391279 Affx-122967353 AX-123261636 6 96519478 TGCTCTTAGCGAAGAGGGCATAGCTGGACACTATA[C/T]GGAGACAACAGGAAAGGCTTTGAAAGAGGAGATTA Y 2 1 2 1 101000 f 74 goat snp964-scaffold1025-2122594 6 99851245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385874 Affx-122971603 AX-123256232 6 96575411 TAAGCGTCAATTTCTAGTGAATTACCAGGCTGAAT[G/T]ACTTGTATAATGCAGCCAGGTGTAATTAAGCAAGT K 2 1 2 1 101000 f 74 goat snp965-scaffold1025-2178527 6 99907267 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418741 Affx-122946217 AX-123289089 6 96607853 CCTGTCACCAGGGCCTAAGGATGAAAAATTGGGAA[C/T]GCCAAAGCCGCTGTCCTTCGTATGATACTCCGAGA Y 2 1 2 1 101000 f 74 goat snp966-scaffold1025-2210969 6 99939712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771501 Affx-122942289 AX-385258659 6 96645465 TTTCAAACTATGGAGGACAACCTACTGGTGGGTCA[C/T]GAAATCGGTTCAGTGGATTGTGGTCAGCATTTTGA Y 2 1 2 1 101000 f 74 goat snp967-scaffold1025-2248581 6 99977370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448476 Affx-122923624 AX-123318812 6 96686954 AATGAAATAAAACAACAACAAAACTAGTACCAATT[G/T]TGAGTCGACAGAAAAAGAAAGGTCAAGAAGACAGA K 2 1 2 1 101000 r 74 goat snp968-scaffold1025-2290070 6 100018914 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278413 Affx-1111836411 AX-519551898 6 96697678 GCAAACAATGAGGGAAAGGCAAACTCCAGAGCTTG[A/G]ACTGACAGGCCCAGGGTGTTTGAAGGCTGCAGGAG R 2 1 2 1 102000 f 74 goat Random2.2K-727 6 96697678 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787949 Affx-122939756 AX-385274970 6 96716125 ATCCTACCTAGTTTATATTTCAAAGGTCTTTTCCA[C/T]GAGTTCTCCATTTCATTCTAAGGGAATGAATTCCA Y 2 1 2 1 101000 r 74 goat snp969-scaffold1025-2319241 6 100048079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779955 Affx-122943702 AX-385267054 6 96851584 TTGGATATTGTACGAGAAATAGCAGGTTAACAACT[C/T]AGCAAAGCGTACAGACAGGTACCCCTTGAATTCTA Y 2 1 2 1 101000 r 74 goat snp971-scaffold1025-2454700 6 100183383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390309 Affx-122967715 AX-123260666 6 96912199 TCACCTAAACGTGAGTTGTTTTTCTAATTGGGCTG[C/T]GGATTTCTTGGGGGTCGAAGAGTAGACATTTATGG Y 2 1 2 1 101000 f 74 goat snp972-scaffold1025-2515315 6 100244918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778509 Affx-122923659 AX-385265623 6 96953090 GTTTTGAACATCAATAATTTCCCTTCATAGAGAGA[C/T]ATTTTATGATGTTATTCAATTTAATGAGATCTGCA Y 2 1 2 1 101000 f 74 goat snp973-scaffold1025-2556206 6 100284206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453850 Affx-122919537 AX-123324183 6 96982070 TTAGAGAACAAAATTTTCCTTAAGAACTGTCAGGA[G/T]CTGGCTTTTAGCAGACTAACTGGGGCAACCACAGC K 2 1 2 1 201000 f 74 goat snp974-scaffold1025-2585186 6 100313004 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795115 Affx-122922615 AX-385282073 6 97021068 TAAAGACTATATGGGAACTTTTCTGCTAATCCCAA[C/T]ATATGAATCATCTCTGGGTCTGATTGTGTTTTTTA Y 2 1 2 1 101000 f 74 goat snp975-scaffold1025-2624184 6 100351778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391456 Affx-122966735 AX-123261813 6 97056129 ACACAATTCTGTTTGAACTTCTTTTATTTAAAAAA[C/T]AGCCTCAATTCTCTTGGATAAGTTAGATATGTGGT Y 2 1 2 1 103000 r 74 goat snp976-scaffold1025-2659245 6 100384143 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762489 Affx-986697019 AX-385250610 6 97058118 CCTGTAAGAATTCACACTGAATGGCTTCTTGACAT[A/C]AAAAATGGTGTTTCTAGATCTTTGTAAGTAACTAC M 2 1 2 1 600010 f 74 goat 6_97058118 6 97058118 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 320764770 Affx-986697021 AX-385252383 6 97058119 CTGTAAGAATTCACACTGAATGGCTTCTTGACATC[A/G]AAAATGGTGTTTCTAGATCTTTGTAAGTAACTACA R 2 1 2 1 600010 r 74 goat 6_97058119 6 97058119 Ancestral_priority_1043 ancestry 0.75 neutral IMAGE 10K 10K ancestral 320762493 Affx-986697023 AX-385250614 6 97058141 GCTTCTTGACATCAAAAATGGTGTTTCTAGATCTT[C/T]GTAAGTAACTACAGTTTTTCCAGGTACCTGACAGA Y 2 1 2 1 600010 f 74 goat 6_97058141 6 97058141 Ancestral_priority_1043 ancestry 0.658 neutral IMAGE 10K 10K ancestral 320764780 Affx-986697027 AX-385252394 6 97058156 AAATGGTGTTTCTAGATCTTTGTAAGTAACTACAG[C/T]TTTTCCAGGTACCTGACAGACACTGGGGTTGTGAT Y 2 1 2 1 600010 r 74 goat 6_97058156 6 97058156 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 320762499 Affx-986697029 AX-385250619 6 97058217 GGGTTGTGATCATATTCGGGGTGCAGAAAAAAGAA[G/T]AAGATAAACTGTAGGGTGTTCTGTATGGCAGAACT K 2 1 2 1 600010 f 74 goat 6_97058217 6 97058217 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320769729 Affx-122920214 AX-385256899 6 97145813 AAAAAATGTAATAGCTGCAAATCTCAATAAAGTGA[C/T]GAACATTAAACAAGGTGTGCTTGTATTATAGTCCT Y 2 1 2 1 101000 r 74 goat snp978-scaffold1025-2748929 6 100474517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380369 Affx-122975345 AX-123250727 6 97194004 AGCCTCTTGACTGATGTGGTGGGGCTCCTTACCCA[C/T]GTAAGTGTTATTTTCCCTGTGTGCACTAGATTGTA Y 2 1 2 1 101000 r 74 goat snp979-scaffold1025-2797120 6 100522887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793250 Affx-122963922 AX-385280228 6 97227426 TCTGAGGGTCTCAAGCAAGAAAATTGCTTAAAGAT[C/T]AAGAAAATTATGCTTATTTGGGCATCTACAATGTA Y 2 1 2 1 101000 f 74 goat snp980-scaffold1025-2830542 6 100556772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398203 Affx-122962227 AX-123268558 6 97279271 TTTGCATGCACCTGGCATAAAGTTCAATTTCAACC[A/G]CAGGCAATGGGTATACATCCAGGGTTTTAAGCTGG R 2 1 2 1 101000 r 74 goat snp981-scaffold1025-2882387 6 100609135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414701 Affx-122949278 AX-123285050 6 97308631 GGATTTCCAGAATTGTTATAACTGGATTATCATTG[C/T]ATAGCAAAGTAACTGAGGAAGCAGTTATTTAAATT Y 2 1 2 1 101000 f 74 goat snp982-scaffold1025-2911747 6 100638524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273246 Affx-1111833525 AX-519546899 6 97344063 GCTTGGAGATGGTGTGGGCAATGCTCTTCCCATCA[A/C]GGCAGAGTCAGTGGGTGCCTGCCCTTCAGGAATGT M 2 1 2 1 101000 f 74 goat 6_97344063_AF-PAKI 6 97344063 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421027 Affx-122944541 AX-123291374 6 97344742 TATTTTTAGGGGTGATTTTTCATCCCAACTCTCAA[G/T]ATTGAGTTGGAAAGTTTTTCAGTGTAATTAGTTTC K 2 1 2 1 101000 f 74 goat snp983-scaffold1025-2947858 6 100674671 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397592 Affx-122961993 AX-123267947 6 97396726 AGTAATTTCAAAGCTAGTCTTTCTCAAGATAGGAG[C/T]GTTTATCCCAGAAACTGTTGGAGGGCATGTCACTC Y 2 1 2 1 101000 f 74 goat snp984-scaffold1025-2999842 6 100727119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380746 Affx-122975131 AX-123251104 6 97443273 GTGCTGATGTTTAACTTTTAGGATTATTACACATC[A/G]TTTGTACATTTATTTTGTAACTTATTTCTGAGGCG R 2 1 2 1 201000 f 74 goat snp985-scaffold1025-3046389 6 100773606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387772 Affx-122969716 AX-123258130 6 97479817 TCTGTTTGTTTGTTTGTTTTCTCATAGCAATGGAA[C/T]AGATCCCTATTTTTTTGAACAACAGTGGGGAGTTT Y 2 1 2 1 101000 r 74 goat snp986-scaffold1025-3082933 6 100810429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278583 Affx-1111836412 AX-519552062 6 97488308 ATTACTGGATTACATTGTTTTACAAACAAAGACTT[A/G]CAAAATTCTAGGAGCAGAGAGTGTGTTGTAGTAAA R 2 1 2 1 101000 r 74 goat Random2.2K-729 6 97488308 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415530 Affx-122948669 AX-123285879 6 97568213 ACCTGTGTCTCCTGCATTGGCAGACATTCTTTACC[A/G]CTGATACACCAGAGAAGCCCATGTAAGCACTAGCT R 2 1 2 1 303000 r 74 goat snp987-scaffold1025-3171329 6 100899078 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425974 Affx-122941162 AX-123296320 6 97604781 GAAGTAAATACAGATTTGGAATTTTATTACTAAAT[C/T]GAAACCAATTAATACTGAGAGCTAAAATGTACCAC Y 2 1 2 1 101000 r 74 goat snp988-scaffold1025-3207897 6 100936057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432503 Affx-122935579 AX-123302844 6 97610419 ACTGTACCATCGATAAGGTATAAAAATATATATAC[A/G]TAATGAACTGGTCAACTTCACTAAGATATTCAGGC R 2 1 2 1 101000 r 74 goat snp8746-scaffold1313-240208 6 100941940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771048 Affx-122919911 AX-385258208 6 97640124 CCCAGATGAACAATGATCATGAGCATCACAAGAAA[C/T]AAGGTGAAGTCTCAGCTTGACAATATATATGAATT Y 2 1 2 1 101000 f 74 goat snp8745-scaffold1313-210503 6 100971740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376033 Affx-122978944 AX-123246392 6 97690788 AACACCCTGAAGTTGGACTTCTCCTCAAGAAACTT[C/T]CACCCACTGAGTTTAAAGGCTCGTAGCATGTAAGC Y 2 1 2 1 101000 r 74 goat snp8744-scaffold1313-159839 6 101022226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417540 Affx-122946927 AX-123287888 6 97748659 GACGTAGGGGGTAGGGCAGTTGTATGCTGCAACAC[C/T]TAATGACCTCCAGCTAGGACAAAATTTCATTCTTT Y 2 1 2 1 201000 r 74 goat snp8743-scaffold1313-101968 6 101080210 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385455 Affx-122971306 AX-123255813 6 97779140 TCCCTCTCCAGGTCTCAATTTCCTTACCTGTCTAA[C/T]GACACTCCAATCAGACAATGGATGCTGAGATGTCA Y 2 1 2 1 101000 r 74 goat snp8742-scaffold1313-71487 6 101110540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774994 Affx-122962472 AX-385262126 6 97812225 TACTGCCTGGCAAGCTTTACATTTATTTTACTAAG[C/T]ACTATCCATACATAATGCAATATTATTATATATCT Y 2 1 2 1 101000 f 74 goat snp8741-scaffold1313-38402 6 101143576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429072 Affx-122938287 AX-123299414 6 97843846 TTTCAATTGCTGTGTAAACTCTGGGAGATTGAATG[C/T]GCATTACCTTAACCAGATACTGAGTGTTTTCTCTT Y 2 1 2 1 201000 r 74 goat snp8740-scaffold1313-6781 6 101175737 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441192 Affx-122929537 AX-123311529 6 97883679 GCACACACAGGGAGGCCACCAGGACATCATGGCTG[A/C]GAACAAGAGTCCCAGGAGGGGGAAAGAGCCACATG M 2 1 2 1 201000 f 74 goat snp31697-scaffold352-347477 6 101215199 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793672 Affx-122975027 AX-385280644 6 97918420 TATGCCTTCTAAGATGTATTTAAGAATGGCTCATA[C/T]GCATATAAAATGATGCACAGAATCAGTGTCATCAA Y 2 1 2 1 101000 r 74 goat snp31696-scaffold352-312736 6 101250006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769306 Affx-122937650 AX-385256477 6 97979673 TTGAGAGGATCATTCAGTAAAGCCAGAGATGGATA[C/T]AGTTGAGAAGGCATATAGTATAGTGCAATAGAAAA Y 2 1 2 1 101000 f 74 goat snp31695-scaffold352-251483 6 101311551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773755 Affx-122927038 AX-385260895 6 98022117 TAATTGACTATTAGATTTGGCTATCAGTCATAGCT[A/G]TAACCAAAAGAGTTAATGCCCTTCTTAAAAAAATC R 2 1 2 1 101000 r 74 goat snp31694-scaffold352-209039 6 101354265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381034 Affx-122974643 AX-123251392 6 98073350 TTGGATACATACTGTTCTGTAAGTAATAGTTAAGG[C/T]AGTAATTACCTGGTAAGCTTTTATAAATTCTGAAA Y 2 1 2 1 101000 f 74 goat snp31693-scaffold352-157806 6 101405174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403996 Affx-122957201 AX-123274348 6 98104481 AAGAATACATAAATAAATCTCTTTTCTATTTTGGT[G/T]CTTTATGAGTGTTGGGTGTCTTGGGTTCCTAAATT K 2 1 2 1 101000 r 74 goat snp31692-scaffold352-126675 6 101436404 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788806 Affx-122975224 AX-385275821 6 98203668 AAGAAAAAATACGGTTTCATGCTCTTTACTAACCC[A/G]TGTGCCCAATAAAGAAGTTTCAAAATATCTTTACA R 2 1 2 1 101000 r 74 goat snp31690-scaffold352-27488 6 101536585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438568 Affx-122931165 AX-123308906 6 98260962 ATCCCCAGAAAACTGGCTTTCAACCTTAATATTTG[C/T]GAAGTCTTAAAAATTAAAAAATAACAGTTTACTTC Y 2 1 2 1 101000 f 74 goat snp9293-scaffold1338-444199 6 101592607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377510 Affx-122977483 AX-123247869 6 98295991 ATAATTTGACTCCAAGATCCCAGTTCCAGTGTCGG[C/T]CTTTTCCTCATGGCTCAGATGGTAAAGAATCTGCC Y 2 1 2 1 102000 f 74 goat snp9292-scaffold1338-409170 6 101627469 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398904 Affx-122961017 AX-123269259 6 98346882 CTGCTAGTTGTCAGACCCCGGAAGATCTCACAGAA[C/T]GCTGATGCATGTGTTAAAATGGTTGCAGGAAGGCC Y 2 1 2 1 101000 r 74 goat snp9291-scaffold1338-358279 6 101678738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784406 Affx-122946839 AX-385271455 6 98384529 CTGTTTAATATAGGGCATACAGCCACAGTAGTATT[A/G]TTAATAAACATGTAGATGTTTCTTGTTAAGGACTA R 2 1 2 1 201000 r 74 goat snp9290-scaffold1338-320632 6 101716228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778269 Affx-122952306 AX-385265384 6 98493166 AAAGTTGAACTAGAGCATATTGCATAGATATACCA[C/T]TGCAATGGACTTTCTAATAATCTGTCGTTGGGATT Y 2 1 2 1 101000 r 74 goat snp9288-scaffold1338-211995 6 101825349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404763 Affx-122957217 AX-123275115 6 98523138 AGGTGAGTGTGGTACATGGCTACCAGATTCAGCAA[A/G]TAAAAACACAGGATGCCCTGCATTTTACCTGACGT R 2 1 2 1 101000 f 74 goat snp9287-scaffold1338-182023 6 101855285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278418 Affx-1111836414 AX-519551903 6 98540183 AACTGAACTGAAACAAGTTGGTTTTCAAGCAATCG[A/G]GTTTGTGGAGGTTGGACAAGATGGTGATTTAGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-731 6 98540183 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786776 Affx-122961620 AX-385273807 6 98557102 CTTAAATGCAATCCTTGAAAGGTACTGATAATAAT[A/G]CATAATAACTTATAGATTACTTCTGAGACTTATTT R 2 1 2 1 101000 f 74 goat snp9286-scaffold1338-148059 6 101890074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799756 Affx-122975336 AX-385286683 6 98587446 AATTATACATATATAATTTAAGCGCTTTACTTTTA[C/T]GAAAAAAATCTGTCATTATACGTTCATTAGCAAAT Y 2 1 2 1 101000 r 74 goat snp9285-scaffold1338-117715 6 101920346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399249 Affx-122960574 AX-123269604 6 98648947 GGAGGACACCAGTTTGCCATCTTTTCAGACACTTG[G/T]CTTCCGGAATAAAGTTGCTATTTCTCCTCTCCTGA K 2 1 2 1 101000 f 74 goat snp9283-scaffold1338-56214 6 101981643 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791920 Affx-122956057 AX-385278910 6 98692861 TAGCATTAAAATTACGAAATCAACAAGTAACAACC[A/G]AGCATACAAACTTCAATTTTATAACATGGCCACTT R 2 1 2 1 101000 r 74 goat snp9282-scaffold1338-12300 6 102025381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440211 Affx-122930691 AX-123310548 6 98705925 CCATTTGCTGCCCCCTTCTGCAGGTAGTAGTTTGG[A/C]TATGTGAAGTCTGAGAGAAGTGTTTTTACATTTGA M 2 1 2 1 101000 r 74 goat snp2775-scaffold1080-665 6 102038298 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781615 Affx-122941058 AX-385268699 6 98739775 ACATTAGTCTTAGATCCCTGATGTGATGAATGCTC[A/G]TCTTTACGGCATCTTTTAAGGCATATGGATCACTG R 2 1 2 1 101000 f 74 goat snp2776-scaffold1080-34515 6 102072349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384847 Affx-122971959 AX-123255205 6 98775438 TGCCGTGTTTCTCTGCTAAGAATTCAGGGAAAAGA[C/T]AAGACTCGGGTACACGTCCTGACTCTCCCAGTGAC Y 2 1 2 1 101000 f 74 goat snp2777-scaffold1080-70178 6 102107644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389816 Affx-122968193 AX-123260173 6 98815960 AATGACATGAGAAGAACAGCCTTCTGGATGTCTGT[C/T]CATTTCTTTGCTCTCTACTTAAAGGTCACAGGACA Y 2 1 2 1 101000 r 74 goat snp2778-scaffold1080-110700 6 102148311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448169 Affx-122924262 AX-123318505 6 98868783 CTTAGTCCAATGCACACAGAAACTGAAGACCCTAG[C/T]AAGTTTGTTGAAGGGTTTCATGTCCTAAGGCTGGT Y 2 1 2 1 201000 r 74 goat snp2779-scaffold1080-163523 6 102202032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429894 Affx-122938121 AX-123300235 6 98913221 AAACTTTTTGCCTGGCTATGTGGTATAAATCTCTC[A/G]CCTGTATTCCAGGAAAACTGTAAATAAAGATCTAT R 2 1 2 1 103000 f 74 goat snp2780-scaffold1080-207961 6 102246995 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450158 Affx-122922736 AX-123320493 6 99039745 CGTGGTTGATTGCAGCAGCGTTTTGAATTAGTTCA[C/T]GGGGGAAAAATATACAGAAAGGGAGATAGGTAGGT Y 2 1 2 1 101000 f 74 goat snp2782-scaffold1080-334485 6 102373063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794423 Affx-122928902 AX-385281386 6 99080875 ATAAACTGCTAAGTGTGTACTTTAGACACTTGTTC[A/G]TATTTTAGTTGAAGAAAAACTTCCACAAGTTAGCC R 2 1 2 1 201000 r 74 goat snp2783-scaffold1080-375615 6 102413903 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400405 Affx-122959994 AX-123270760 6 99111260 TACGATAAATATCTCGAGAGTGACTCTAAAAGCAT[A/G]TACAATTACCCAGGAATTGTAAAAAAACAAATTGG R 2 1 2 1 101000 f 74 goat snp2784-scaffold1080-406000 6 102444191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440738 Affx-122929878 AX-123311075 6 99149286 CAGAGAGCATATGTTGAACTTTGTACCACAACAGC[A/G]TCAGTTGCTTTGATTCTGCCATGTGCAGACATAAC R 2 1 2 1 101000 f 74 goat snp2785-scaffold1080-444026 6 102482193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427789 Affx-122939771 AX-123298132 6 99233101 AACTCACAAGAATCAACTAAATTATTCACAGACAA[C/T]GAATTCTCTTGTACAGCCTTTAAAAAAAGTTTCAT Y 2 1 2 1 101000 f 74 goat snp2786-scaffold1080-527841 6 102567515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422002 Affx-122943781 AX-123292349 6 99279871 TTCTAGATCGTACGTCTCTTTCGGTTCACTTTCCA[C/T]TGTGTGAAGAACCTCCTCTAGTAGCTTTCCAAGAA Y 2 1 2 1 101000 f 74 goat snp2787-scaffold1080-574611 6 102614137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395059 Affx-122964193 AX-123265414 6 99327030 ATCATCTCGGGTTTACTGGCCTGTTGTGGGGCAAG[C/T]AGAGCCAGCTTAGACTTGGTCACAGTACTGTTAGA Y 2 1 2 1 101000 r 74 goat snp2788-scaffold1080-621770 6 102661464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776411 Affx-122971500 AX-385263538 6 99368122 GTAATTAAATATTCATTTGGATGAACTTTTTAAAC[A/G]TCTGGCCCCATAACATCACTATAATAATCGCTATG R 2 1 2 1 101000 r 74 goat snp2789-scaffold1080-662862 6 102698879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779489 Affx-122969935 AX-385266592 6 99418738 TGGTAACTTGTTACAGCATCCTGGAGAAACAAATA[C/T]ATCTGCACTTACAAATTATTAGATATACTGTGTGA Y 2 1 2 1 101000 f 74 goat snp2790-scaffold1080-713478 6 102748730 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801060 Affx-122950601 AX-385287974 6 99450940 CTTTTGATAAATATGATGGTAGAGTTGTAAAATGT[A/G]CTGACTACAAGCTAGGCACTGTATACTAAATGTTT R 2 1 2 1 101000 r 74 goat snp2791-scaffold1080-745680 6 102781195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378033 Affx-122977575 AX-123248392 6 99485471 ATAAGCATTGGATTTATATGGATTTTTATTAGGAT[A/G]TTAAGATATTGACAATAACACACACCAGTAACAAA R 2 1 2 1 101000 r 74 goat snp2792-scaffold1080-780211 6 102815687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784051 Affx-122957176 AX-385271104 6 99520378 ACAGTTTGTAAGCAGCAATGAAGAATTGGCATGGG[C/T]ATTAAATATCTTGAGTGAAATATTCTTTAGAAGTA Y 2 1 2 1 101000 f 74 goat snp2793-scaffold1080-815118 6 102850454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420775 Affx-122944705 AX-123291122 6 99576412 TTACTATGATTATATTAGCAATTCACTGACTTCTT[G/T]TTGCATGAAGGGATAAATAAATAAAGGACAAAAAC K 2 1 2 1 101000 f 74 goat snp2794-scaffold1080-871152 6 102906365 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440989 Affx-122928973 AX-123311326 6 99609624 TGGACATCAAGTAGCTGAAAGCAGTAATAGTACAG[A/G]TCAGGAGGCGGAAATCAATGGGAATTCCTGTAGAA R 2 1 2 1 101000 f 74 goat snp2795-scaffold1080-904364 6 102939561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415433 Affx-122948718 AX-123285782 6 99672176 TCTGTGAACCTTGGTCTTCAGGAGCTGATCCAAGC[A/G]AGCAATGAGGCTTTGGCAATAGTCACTGGGAAGGT R 2 1 2 1 201000 r 74 goat snp2796-scaffold1080-966916 6 103003834 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392167 Affx-122966309 AX-123262524 6 99722725 GCTTAAGCCTGGAGCAGGGTGACATACAACTCCTG[C/T]AGCCTAACTCAGAGCCTCAGGCTTCTGACCTGTGC Y 2 1 2 1 101000 f 74 goat snp2797-scaffold1080-1017465 NW_017189523.1 83776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779425 Affx-122941407 AX-385266528 6 99760803 ACACTATTCAACCCAAAACAGGTAGTGCTAAAATT[A/G]TCCTAGATGGAGAAATTAAGGCCAAAAATGTAAGG R 2 1 2 1 101000 r 74 goat snp2798-scaffold1080-1055543 NW_017189523.1 45688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390509 Affx-122967248 AX-123260866 6 99789653 TCCTATGCTGCAGTAACAAAGAACCCAAATTCTCA[C/T]GGTCCAAACACAACACAGGGTTATTTTGCCCTTAC Y 2 1 2 1 101000 f 74 goat snp2799-scaffold1080-1084393 NW_017189523.1 19225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791330 Affx-122960968 AX-385278323 6 99831538 TTATCTTGAAAGGCCTAGGAATAAGACACTCCAAA[C/T]GGTTTCTGGTACAATGAATTCAAGATCATCCCTGG Y 2 1 2 1 101000 r 74 goat snp2800-scaffold1080-1126278 6 103085595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411896 Affx-122951187 AX-123282246 6 99889357 TCAGCTTAGAAAAGAAAATTAAAATGGGGTGTGTA[A/G]GTTAGAAAAAGGCAGTGATGTGGTCAGAAATTTAA R 2 1 2 1 101000 r 74 goat snp2801-scaffold1080-1184097 6 103144243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445905 Affx-122925942 AX-123316242 6 99921445 TCCATTCTTCTCATGATGGGTTCCTCGCCTGGCAC[C/T]GGACAACACATTGCAGTTTGTAGAGCCTTGCAGCA Y 2 1 2 1 101000 r 74 goat snp25682-scaffold2643-1656 6 103178690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393750 Affx-122965218 AX-123264105 6 99976735 GGCCTTCAGCTCATCGCTGCCCCAGGGCCTTTGCA[C/T]ATGATATGACTTCTGCCTGGAGTCCTCCTCCCTGG Y 2 1 2 1 101000 r 74 goat snp25683-scaffold2643-56946 6 103233689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444304 Affx-122926751 AX-123314641 6 100044623 TTATTTGTCCAGAGTCACACAGAATTCTTACCCCC[A/G]TACAATATACTAATTACAGAAAACTTGGAGGATTA R 2 1 2 1 201000 r 74 goat snp25684-scaffold2643-124834 6 103301267 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431215 Affx-122937155 AX-123301556 6 100085511 TAAAACCACACTCCCCCAGTACTTACATCAACTGC[C/T]GAGAAGTCAAGGTCCTTGCCCTCAAATTCATGTCC Y 2 1 2 1 201000 r 74 goat snp25685-scaffold2643-165722 6 103341166 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439157 Affx-122931071 AX-123309494 6 100161365 ACGGGCCTGGCCTGGGTCTCGTTATCTTGCCCTGT[G/T]TCGGCTCCGTCCTCATTAGAGGCACTGCTTTCTGC K 2 1 2 1 201000 f 74 goat snp25687-scaffold2643-241576 6 103417295 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272327 Affx-1111833486 AX-519546062 6 100201228 AGCCCGTGCTCAGAGATTTCATGAAAATAATCACA[A/G]CCAGGTGGCAGGAGAAGCAGTTACGCAAGGGACCA R 2 1 2 1 101000 f 74 goat 6_100201228_AF-PAKI 6 100201228 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38383772 Affx-122973209 AX-123254130 6 100221994 AGCATCCATGGCCCCTCTGTTACTGTTAGTGTCAG[C/T]GGCCCCCTCTGTCTCTCCCAGGGACAGGCCCAGCC Y 2 1 2 1 103000 f 74 goat snp25688-scaffold2643-302205 6 103477997 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409508 Affx-122953633 AX-123279859 6 100266992 TGGGGTTCAGAAGTTAGGTCATCCTGACAGCGTGT[A/G]AGTAATGAGGGTTAAAAAGGCCTAAAAGTAAATGC R 2 1 2 1 101000 r 74 goat snp25689-scaffold2643-347203 6 103522407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425723 Affx-122940760 AX-123296069 6 100299154 CCTACAGCCTAAAAAAAAAATCCTAGGGCCTCATC[A/G]TGGTAGAAGGGTGTATTAAATCGTTTCTATGGCTG R 2 1 2 1 101000 r 74 goat snp25690-scaffold2643-379365 6 103554400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454090 Affx-122919370 AX-123324423 6 100409110 AGAGTACATTTCTGTGGTTGATAAGCGACCCAGTC[A/G]ATGGTACTTTTTATCCCAGCAGGCATGGACTAAGA R 2 1 2 1 101000 r 74 goat snp25693-scaffold2643-489321 6 103663955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439107 Affx-122931108 AX-123309444 6 100448754 CCCTTTCACGTGTGGCTTTTTAAAAAATTAATGGC[A/G]CAGCCGGGATTAATTTAAAGCGGGTTTTTGGTGCC R 2 1 2 1 101000 r 74 goat snp25694-scaffold2643-528965 6 103703455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404801 Affx-122956662 AX-123275153 6 100478595 CTTTCTCAGTTTCCTCATCTGTACAGCATGATCAC[C/T]GCTGGCCCTGTCAACCTCAAACAATTGTTATGTGG Y 2 1 2 1 201000 r 74 goat snp25695-scaffold2643-558806 6 103733282 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802362 Affx-122969767 AX-385289266 6 100525126 TTCCCACCAAGTTCTCCGGGGCCAAGAAAAAGAGA[C/T]GGTGAGCTTGTCCCTCACTCGTAGGTCAAAAAAAC Y 2 1 2 1 101000 r 74 goat snp25696-scaffold2643-605337 6 103779833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447671 Affx-122923955 AX-123318007 6 100576471 TAAATCAGATCTTAGAAGGGAAAGGAGAACCCTAT[A/G]TATGGAGCCCTTCAAACCCCCACATAGAGTGTGGG R 2 1 2 1 101000 r 74 goat snp25697-scaffold2643-656682 6 103831565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425098 Affx-122941235 AX-123295444 6 100617084 AGTGGCCTTAAGATTTGAGACCAGTGAGTCTTTGT[C/T]CCTTAGCCCGAAGGACTGGACTGGGGTCTGGAGGT Y 2 1 2 1 101000 f 74 goat snp25698-scaffold2643-697295 6 103872003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381624 Affx-122974772 AX-123251982 6 100672269 AGGGGGCTTCCAGAAAATAAATGGGATGACAGACC[A/G]TGTCTAGTATTGCCTGGAGTTCAGTCAAGTGTCTT R 2 1 2 1 201000 r 74 goat snp25699-scaffold2643-752480 6 103927848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387145 Affx-122970643 AX-123257503 6 100709651 CCCATTGGTGGGGGAGGGATTCCACCTGCTGGTTA[C/T]GGGCATAGCCAGACACATGACACCTGATCCTGAGA Y 2 1 2 1 101000 r 74 goat snp25700-scaffold2643-789862 6 103964963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273532 Affx-1111833674 AX-519547147 6 100755325 ACAGGGATAAAGAAAGAGTTCCTCAAAGCAAAAGT[A/G]TTCTGCAGGTACTGCTTCAACTTTCTGTGCTAAAG R 2 1 2 1 101000 f 74 goat GoatD01.001140 6 100755325 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447127 Affx-122924463 AX-123317463 6 100773013 TGAGTTGAGCAAAAATGAAAATACAACTTGAAAAA[C/T]GTATGGATGCAGCACAAACAGTATGTAAGGGAAAA Y 2 1 2 1 101000 r 74 goat snp25701-scaffold2643-853224 6 104025861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782652 Affx-122943965 AX-385269725 6 100799919 ACTTGGGGAGTTAGTTTCGATTGCTTAGTGATCGC[A/G]TTCCTTTACTTAGGTTTTTAAGGTTAGAGAAGACA R 2 1 2 1 101000 f 74 goat snp26884-scaffold2836-1687 6 104052587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453185 Affx-122920459 AX-123323518 6 100851774 CATTCCAGATGAGGAGGTAGAGACATGAAGGGGTG[C/T]ATTTGGGTGAATGAAAGTGAAAATGTTAGTTGCTC Y 2 1 2 1 101000 f 74 goat snp26885-scaffold2836-53542 6 104104780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762468 Affx-986696998 AX-385250594 6 100868099 CTATTTGTCCTCTTTGTAAACATTTTCAACATCTT[C/T]ATTGAGATATAATTCATCTAAGGTGTACTGTTTAG Y 2 1 2 1 600010 f 74 goat 6_100868099 6 100868099 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 320764738 Affx-986697001 AX-385252354 6 100868101 ATTTGTCCTCTTTGTAAACATTTTCAACATCTTCA[A/T]TGAGATATAATTCATCTAAGGTGTACTGTTTAGTG W 4 1 2 1 600010 r 74 goat 6_100868101 6 100868101 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38431501 Affx-122936242 AX-123301842 6 100921543 TCAATTGGCTATGTTACACTACAAAATAAAAAGTT[C/T]AGTAAAAGAAATCAAAAGGTGCATAATCCTATTAA Y 2 1 2 1 101000 r 74 goat snp26886-scaffold2836-123311 6 104174904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278588 Affx-1111836415 AX-519552067 6 100928424 ATATGAACATCAACTAATTTTTTCTGATTTTCAAT[A/C]AATGCAGATTTCTTGTGATATTATTATTTTCATGG M 2 1 2 1 101000 r 74 goat Random2.2K-732 6 100928424 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419358 Affx-122945635 AX-123289706 6 100952843 AAGAGAACAATAATTTAGGCAATAACTCTGGTTAC[C/T]GCTTTTTCTCACTGCGGATCCTTTGTCACCTGGGC Y 2 1 2 1 201000 f 74 goat snp26887-scaffold2836-154611 6 104206641 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393754 Affx-122965215 AX-123264109 6 101008970 GTTCCAAGATGTTCATGTCAATAGGGAACTCATAC[A/G]TTACAAGGTATATTGTAACTTGGAGACACAATATG R 2 1 2 1 101000 f 74 goat snp37608-scaffold4601-7753 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453067 Affx-122920059 AX-123323400 6 101017473 TCCCCTTCAGCGTCCACCCACCAGAGGTTGTCACT[A/G]TCTTGACCTAGAACAGCATGAATTCGCTTTGCCTG R 2 1 2 1 101000 r 74 goat snp48638-scaffold690-4047171 6 104242178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420377 Affx-122944943 AX-123290724 6 101046702 TCCAATGCCTGGTTATTGAGGTGGGACAGGAGGGA[A/C]GATCCATTTAAAAATTCATTGATCACCTCATGGTG M 2 1 2 1 101000 r 74 goat snp48637-scaffold690-4017942 6 104271646 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437148 Affx-122932144 AX-123307486 6 101088510 TAGCAACCACGGAAGCTAGTATCCTATTTTGTTTA[C/T]GCAAGATCATGTTGCTGTTGTTCAGTTGCTCAGTC Y 2 1 2 1 201000 f 74 goat snp48636-scaffold690-3976134 6 104313510 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396230 Affx-122963342 AX-123266585 6 101133528 CAGCTTGAGGTGGTCTTCATAATGTGATACCTGTA[C/T]GACCACTGCTTATATCAAGAAATTCAAAATGGGAA Y 2 1 2 1 101000 r 74 goat snp48635-scaffold690-3931116 6 104358496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778163 Affx-122935617 AX-385265278 6 101179466 ATCCACATGTGGCTCACAGCTACCCTATAGGACAG[C/T]ACACTTTTTCCTCCTTGCCATTATTTGCTGTTATG Y 2 1 2 1 101000 f 74 goat snp48634-scaffold690-3885178 6 104404490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413355 Affx-122950151 AX-123283704 6 101212746 CGATTCCAGTATTCAATGTCGATCCAGTTGCTAAT[A/G]TAAAGAATCTGTAAGACTTCCCTGTTGGTCCAGTG R 2 1 2 1 201000 f 74 goat snp48633-scaffold690-3851898 6 104438042 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389119 Affx-122968560 AX-123259477 6 101269923 ATTATTGTGTGTTCATTCCTAGTATCAGGCTAGCC[A/G]TTCCAGGCTCCTCCTTATACACCCAGCACCATGAA R 2 1 2 1 201000 f 74 goat snp48632-scaffold690-3794721 6 104495474 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416216 Affx-122948229 AX-123286565 6 101306511 TAGGGAAGGAGGGTAAGGAGCAAACTCTAGCTGGA[C/T]GGTAGCTTGCATTACTCTAGCCTGAGACTCTTTGT Y 2 1 2 1 101000 r 74 goat snp48631-scaffold690-3758133 6 104531980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377620 Affx-122977885 AX-123247979 6 101335969 TGTTATTTTACCCCACACCCCCCAACATCTTCCCC[C/T]ACAAAGATTCCTGTTTTGTAATCCTTCAGCTTCTA Y 2 1 2 1 201000 r 74 goat snp48630-scaffold690-3728675 6 104561434 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385313 Affx-122971674 AX-123255671 6 101369505 AGAGACTTCCTGATAGAAACCGAAGGACCCAGAGA[C/T]AGCAGAGGGGTGAAGAGATCGAGGTTCCCAGATCT Y 2 1 2 1 201000 f 74 goat snp48629-scaffold690-3695139 6 104593721 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412641 Affx-122950795 AX-123282990 6 101402801 ACGCTCAGACATTCTCCAACTGGACAAGTTATAAG[C/T]ATCACAGATCACAAAAGAGTTCTACTTGTTTGATA Y 2 1 2 1 101000 f 74 goat snp48628-scaffold690-3661843 6 104627336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799863 Affx-122941140 AX-385286789 6 101461595 ACTTTTGAATTAAGCAGTCTACAGCAATTTAGTGC[A/G]CACTGGCTTTGAAGTGCCAACATCAGTCAGGCCAG R 2 1 2 1 101000 r 74 goat snp48627-scaffold690-3603049 6 104685697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427158 Affx-122939627 AX-123297501 6 101515155 CTAAGCAAAAGGAAGCTAAATGTGCTTATACTAAC[A/G]TCTGACAAGGTAGACTTTAGGATGAGAAGCATTAT R 2 1 2 1 101000 f 74 goat snp48626-scaffold690-3549489 6 104739577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420996 Affx-122944561 AX-123291343 6 101550835 CTTTTGTGCCCTCTGAGCCCCAAAATGAAAACATG[A/C]TTTTGTTGATTTGAATTTTCTCTTTTCAAGTAACA M 2 1 2 1 103000 f 74 goat snp48625-scaffold690-3513809 6 104775254 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416259 Affx-122947962 AX-123286608 6 101583505 ATCCGGAACCTGCTCAAGTGGCAGAATATTAGTGC[A/G]GTCATCAGCCTGGGGTCCCACATGAGCTCTGCTTG R 2 1 2 1 101000 f 74 goat snp48624-scaffold690-3481139 6 104807887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800448 Affx-122954785 AX-385287369 6 101624121 TAGCGAATGGCATGCAATAGGTGTTTAAGAAATGT[C/T]AGCATATTAAGATGACTCCCCTAATATTGAGCATT Y 2 1 2 1 101000 f 74 goat snp48623-scaffold690-3440523 6 104848845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447516 Affx-122924066 AX-123317852 6 101653868 CAGCTCATTCATACACAAGCGTATTTATGCTACAA[C/T]ATTTATTCAACATCCCCTAATAAAACTTTTCTTTG Y 2 1 2 1 101000 f 74 goat snp48622-scaffold690-3410776 6 104878675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402420 Affx-122958638 AX-123272773 6 101693550 TGACAGATCCTTCTCAATCTAGCACTTATACAAGC[A/G]TTTACAGAATTTTCCTCCATTTCCTAAGTGGCTTG R 2 1 2 1 101000 f 74 goat snp48621-scaffold690-3371094 6 104918551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425840 Affx-122940671 AX-123296186 6 101740963 GCATAGGGTCAGTCAGTACTTGCAGACCGAGTAAA[C/T]GTCTAAATACAAAAACAGTATTTACCACTAAAGAA Y 2 1 2 1 101000 f 74 goat snp48620-scaffold690-3323681 6 104966276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409668 Affx-122953509 AX-123280019 6 101772206 ACAGGAACCTGGTAACAGACTGCTGACTGGTGGTG[C/T]AGGAACATTTTAACCTAGAGAAAGTTTTCATCATG Y 2 1 2 1 201000 r 74 goat snp48619-scaffold690-3292438 6 104997835 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441737 Affx-122929133 AX-123312074 6 101848664 TTCCTCTCAGGAGGGTCAGAGGGTCAGATGAACTC[A/G]TCTTAAATTAGGGGTGGCATGAGCTAAGTTTTGTA R 2 1 2 1 102000 r 74 goat snp48618-scaffold690-3215980 6 105072961 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441394 Affx-122928846 AX-123311731 6 101899240 AGCCGACACGTCAGGCACTACGTTAGGCACTGGGG[A/G]GACTGGGGGTGCTGTGTGTATAAGTCCCAGGTAGG R 2 1 2 1 101000 r 74 goat snp48617-scaffold690-3165404 6 105126097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446203 Affx-122925718 AX-123316539 6 101928598 CCTTGTTAACAGGAAGCGAATTCCTCATCAAATAC[A/G]GTCTTCTGTTGATTGTCTCCTTGTGAAAAGGTCAG R 2 1 2 1 101000 f 74 goat snp48616-scaffold690-3136046 6 105155598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406828 Affx-122955677 AX-123277179 6 101972747 GGTATGGTTGCACAACCCTATGAATATACCAAGCC[A/G]CCAAACTGTACAATTTAAATCAGTGTGTTGTGTGG R 2 1 2 1 101000 f 74 goat snp48615-scaffold690-3091897 6 105200118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390412 Affx-122967651 AX-123260769 6 102031783 TGGAACTAAACACCTCCCCTCTGCAGTGCAGGTGG[A/C]AGAGAGGAAAAACTAAAAGACTGGAATTCATTGGG M 2 1 2 1 103000 r 74 goat snp48614-scaffold690-3032861 6 105259694 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394029 Affx-122965002 AX-123264384 6 102153111 ATCTGCACTCCCTCCTAGTTTATCTTCTAGGAGAG[C/T]TGAAGATGCAGACTAGTTCATTGGAAGCAGTCCTA Y 2 1 2 1 101000 r 74 goat snp48612-scaffold690-2911533 6 105381841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453490 Affx-122919829 AX-123323823 6 102187731 CCCTCTTCAATATTTTATGAGCCACAGAGCTCCAC[A/G]TCGGAAGCAGTGGAATGGAGACTTTTCAGTCCCAA R 2 1 2 1 101000 f 74 goat snp48611-scaffold690-2876913 6 105416710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408548 Affx-122953683 AX-123278899 6 102236776 CTGGGGGGCTTAAAAGAAGAGTTCTAGGGGCCAGG[A/G]GTCCAAAATCAAGGTATCTGCAGACTTGGTCCCTT R 2 1 2 1 201000 f 74 goat snp48610-scaffold690-2827868 6 105465502 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388386 Affx-122969306 AX-123258744 6 102278141 GCCTCCCTGCATGACTGATACGCAGAATGAATATT[A/G]GACTGAATGATTCATGCACTCGGTAGATACCCAAC R 2 1 2 1 101000 r 74 goat snp48609-scaffold690-2786503 6 105506640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776959 Affx-122921644 AX-385264083 6 102309689 GGCATAAAAGAAAATGGCCTGTCGCTAATGATTTT[C/T]ATTCGAATTATTCAGACAAATGAAAACGCTATGGT Y 2 1 2 1 101000 f 74 goat snp48608-scaffold690-2754955 6 105537591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384116 Affx-122972827 AX-123254474 6 102351335 TAACCCATGCCTGTCAGTGTTTACTGCGCTGCCTC[C/T]AGGCCTTCGGATCCTTTGTTAACGGGACGGGAGGC Y 2 1 2 1 101000 f 74 goat snp48607-scaffold690-2713309 6 105579813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779487 Affx-122936227 AX-385266590 6 102398428 GTTGTTTTTTTCAGGAACTTGCCCAGATCGCTTGA[A/G]ACCACTGACTATTCAATGGGACCTGCCTGAGTGTG R 2 1 2 1 101000 f 74 goat snp48606-scaffold690-2666216 6 105626466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275366 Affx-1111834857 AX-519548940 6 102409835 GACTGCTTCTTTCTTGTTCGCTTCGCAGCTCAAGC[A/G]CTGGAGACAGAAGTAGGTAAACGCATGCTTGCTCT R 2 1 2 1 201000 f 74 goat GoatD01.056729 6 102409835 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436529 Affx-122932935 AX-123306867 6 102443735 GGGTCAGTCATAACTTTTTGCAAAACAAATTAATC[A/G]TCTTGTAGGCCCCATCACTTTCCTTTCCCCCTTGA R 2 1 2 1 201000 f 74 goat snp48605-scaffold690-2620909 6 105671357 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406589 Affx-122956262 AX-123276941 6 102483316 AAATGTTCAAGGACTCTGGCCACAACCTCGCTGTG[C/T]TCAATCTGCACTTCCAATGTACACTTTCCAGCAGG Y 2 1 2 1 101000 r 74 goat snp48604-scaffold690-2581328 6 105710818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418342 Affx-122946596 AX-123288690 6 102521591 TATCATCTCCTGCATTGGCAGGCAGATTCTTTACC[A/G]CTGGGGACCCTCTTCTTTATTTATCCTAGGCCTTA R 2 1 2 1 101000 r 74 goat snp48603-scaffold690-2543053 6 105749187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423045 Affx-122942966 AX-123293391 6 102552284 CATTGTCTTGTATTCTTTAGCGCTTTAGTCCTCAT[A/G]CAGCTCTGTGGAGGAAGCTGACTAAGTCTGTAATT R 2 1 2 1 101000 f 74 goat snp48602-scaffold690-2512360 6 105780499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802419 Affx-122923559 AX-385289323 6 102594396 GACACTTCTCACCTAGGTAGCCTGGTCATTGTTTC[A/G]TCTTCAGATCAGTGGATCCAGTGCTTCTATCATTT R 2 1 2 1 101000 r 74 goat snp48601-scaffold690-2470248 6 105823076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378636 Affx-122977107 AX-123248995 6 102636828 TACCCTATTTTAAAGGTGATAAAACTAAAGCAAAA[C/T]AAGGTAAGCCTGAGATTTTAAAATGAAATTCTTAT Y 2 1 2 1 201000 f 74 goat snp48600-scaffold690-2427816 6 105865707 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410809 Affx-122952648 AX-123281159 6 102668410 GTGACACAAGATACAAAGAGCAGGGAGCTGCATCA[C/T]TTAGGCCAACCAGAGGCTTCTGAGAAGCCTTCTGC Y 2 1 2 1 101000 f 74 goat snp48599-scaffold690-2396234 6 105896865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420506 Affx-122944849 AX-123290853 6 102701287 CTTTGGAGCTGGAGTAAGAGGCCTCTGGGCTCAGC[A/G]CTCTCAACTAGGTAAATGAGATGGAAAGAAGAAGA R 2 1 2 1 101000 r 74 goat snp48598-scaffold690-2363357 6 105929769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272328 Affx-1111833487 AX-519546063 6 102703096 CTCCGTCCATGGGATTTTCCAGGCAAAAGTACTGG[A/G]GTGGGGTGCCATTGCCTTCTCCGAATGTAGCCATA R 2 1 2 1 303000 f 74 goat 6_102703096_AF-PAKI 6 102703096 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421870 Affx-122944278 AX-123292217 6 102781603 AAAGATAGCAGGCCTTCAAAGTGTAAGAAATATTT[A/C]TGATGAAAAACAAAAGTCCTTTAAATTGGGGTATT M 2 1 2 1 101000 r 74 goat snp48596-scaffold690-2283041 6 106010154 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793735 Affx-122974115 AX-385280707 6 102840879 GGGTAGACGCAAAGTCAAATGCTTGGTCTAAGGAC[A/C]CAGGGTCTCACCTACCATAAAGCAAGTAATTGACT M 2 1 2 1 201000 f 74 goat snp48595-scaffold690-2223765 6 106069097 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278590 Affx-1111836416 AX-519552069 6 102883861 GATAAATTAAAAGTCATTATTCCCGTACTTGCATT[A/G]CATTACCAACTGCCTCCATCAGACATTACATGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-734 6 102883861 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421659 Affx-122944447 AX-123292006 6 102892446 CAGAAATCACTTCCATACCCCAGAAGTCATTTCTG[C/T]ACCCCCAGAAGGCTGTGGAAGGCAATGGACAAAGC Y 2 1 2 1 102000 r 74 goat snp48594-scaffold690-2172198 6 106120592 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399966 Affx-122960831 AX-123270321 6 102928229 TTGACCTAGATAATTGAGTGAGAATCTGAAATTAA[C/T]GGGAGAGGGGATCTATCATGAGGCAGAAACAATAG Y 2 1 2 1 201000 f 74 goat snp48593-scaffold690-2136415 6 106157001 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784550 Affx-122938353 AX-385271599 6 102974349 AAAGCCCTTGAATCAGATTTCTGAAGAGCCAAAAT[A/G]TTTTCCTGTACTTCCTTAAACGAAAGGAAAAATTC R 2 1 2 1 101000 f 74 goat snp48592-scaffold690-2090295 6 106203503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442796 Affx-122927723 AX-123313133 6 103017766 TAGTCTGAAACCATCTATTATTTGATTATTTGTTC[A/G]TGTCCTTGCCCCACCCTCAACTAATCCATCATCTT R 2 1 2 1 101000 r 74 goat snp48591-scaffold690-2046878 6 106246954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393010 Affx-122966182 AX-123263367 6 103066388 CATGTCGTAGTGACTAAACAACAATGCAAAATCAG[C/T]GAGTTTAGCAATAAAAATTTATCTGGGCTTTAGCT Y 2 1 2 1 101000 f 74 goat snp48590-scaffold690-1998256 6 106295249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780430 Affx-122921294 AX-385267522 6 103107038 ATATAAAGCATGATAAGTGATGGGAAAAACAAGTT[C/T]TCTGAGTCCTATACCTACTGAGGGTTGCTGAAGCC Y 2 1 2 1 201000 f 74 goat snp48589-scaffold690-1957606 6 106335906 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384296 Affx-122972289 AX-123254654 6 103137750 GCTGACATTCTAGTGTCTAAAATAGTGTCCCGTAT[A/G]TAAAAGGAACTCAGTAAACACATGCTGAGTAAATG R 2 1 2 1 101000 f 74 goat snp48588-scaffold690-1926894 6 106366612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800195 Affx-122970802 AX-385287118 6 103188775 CTCTATTCACACAGCAAAGTGTGTGATAATAAGAT[A/C]CAGGTTTCAAAAGTAACTAGGAGAAGTTTTACTTG M 2 1 2 1 101000 r 74 goat snp48587-scaffold690-1875869 6 106417480 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768227 Affx-122927908 AX-385255409 6 103226788 TCTTGGTCAAGACTGAATCCTGCTGCTGTGGGTAT[A/G]TTACAGGAATCTTACTTTGTCTCAACTTCCATAGT R 2 1 2 1 102000 f 74 goat snp48586-scaffold690-1837856 6 106456012 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765021 Affx-122974837 AX-385252592 6 103255472 TGAAAACTAAATGAGAGAATGTTTAAAAATTCCCA[A/G]CACTATTTCTGACACACGTGAATCATGCAATAAAT R 2 1 2 1 101000 f 74 goat snp48585-scaffold690-1809172 6 106486451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380049 Affx-122975572 AX-123250407 6 103294155 TCCAGATACTCCTCATTTGCTGCTGAGAGATAGGA[C/T]GCATCACCTAGACACGGAAGCACCCTCTATGATTT Y 2 1 2 1 101000 f 74 goat snp48584-scaffold690-1770489 6 106525496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422062 Affx-122943603 AX-123292409 6 103344149 ATCAGAAGAATAGACGATGGATTCAGACTGTTAGA[C/T]GGACCAGTGATTTCATAATATATCATTCTGTTTGA Y 2 1 2 1 101000 f 74 goat snp48583-scaffold690-1720495 6 106575810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780321 Affx-122933691 AX-385267416 6 103399444 TACACTGGAAAGAAAAGACCTTTATTTTTGTATCA[G/T]CTCTGCTTGTCAGTTTGATGTGACCATGGGCAAGT K 2 1 2 1 101000 r 74 goat snp48582-scaffold690-1665200 6 106631905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781153 Affx-122976950 AX-385268238 6 103437612 TTTCATACTTAAGAAAGCAAACCAGGGGCTAAAAG[C/T]AGATGAGGAATTAAAAATCAAGGTGGCAGATGAGA Y 2 1 2 1 101000 r 74 goat snp48581-scaffold690-1627032 6 106665727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387135 Affx-122970650 AX-123257493 6 103482245 TGGAGAGAGTGGGGATTATTCCTATACTACTGACT[C/T]TCTCTCCAGCACAATTTCTAATTTATCATATTATG Y 2 1 2 1 101000 f 74 goat snp48580-scaffold690-1582399 6 106710174 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432687 Affx-122936038 AX-123303028 6 103530176 TGTCATTGGATTTCAACCTTATAAACACCCATGAC[A/G]TTGTTACTATGTCCCATTTAAAGAATTAAGAGAAT R 2 1 2 1 101000 f 74 goat snp48579-scaffold690-1534468 6 106759462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405730 Affx-122956519 AX-123276082 6 103574194 TCCAACACCATGAGAGTAGGGATTTTGCATCTTCC[A/G]TTCCTTCCTGAACCCTCAGAGCCAGCAGAGCGTCT R 2 1 2 1 101000 f 74 goat snp48578-scaffold690-1490450 6 106781738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437546 Affx-122931902 AX-123307884 6 103610874 TTTCTCAGCCCTAACCTTAGTGCAGTTATCACGTA[C/T]GTTGCCTCCTCTCTCTCATCTGCCCCCCAAAACAC Y 2 1 2 1 101000 f 74 goat snp48577-scaffold690-1453770 6 106818314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278593 Affx-1111836417 AX-519552071 6 103640826 GACTTGGAGGACATCCATCCCAAGGAGCTGTGGGT[A/G]GAAAAAGGTCTCAGGGGTGAATTGGGGAAAGCCTA R 2 1 2 1 202000 r 74 goat Random2.2K-736 6 103640826 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425015 Affx-122941885 AX-123295361 6 103646801 TGAACCACCAGGGAAGCCTTATTTCACAATTATCT[A/G]CCACCTTTAAGTGCCCGTTTTAGCCACCTTCTGTG R 2 1 2 1 201000 r 74 goat snp48576-scaffold690-1417843 6 106854209 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385970 Affx-122971531 AX-123256328 6 103701600 CTAGACTGTAAGGAAGAGGAGCAGACTCATTTCCA[C/T]GTATCCCCCTTGAGCAATTTGGTGGCTGGTGGTAT Y 2 1 2 1 201000 r 74 goat snp48575-scaffold690-1363044 6 106910041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408455 Affx-122954440 AX-123278806 6 103776669 TGAACTTGACCACTTTCCAACAGCTCCACCATTAC[A/G]CCATCAGCTGAAGCTCTCACTGGACACAGCAACGT R 2 1 2 1 101000 f 74 goat snp48574-scaffold690-1287975 6 106985761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774841 Affx-122972758 AX-385261975 6 103810683 AACATTGCCAGGAAAATGTCTTAATCCATGGAAGG[C/T]GAGATTTAGGGACGAATGTCCCAGTGCCATCACAG Y 2 1 2 1 101000 f 74 goat snp48573-scaffold690-1253961 6 107020050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382593 Affx-122973720 AX-123252951 6 103841088 AATGAACATTTGTTGAATGCGCTGGACAGACCAAA[A/G]GTCTAGTTAATTGATGGAGCAAATGAGACCATTCT R 2 1 2 1 101000 f 74 goat snp48572-scaffold690-1223556 6 107050142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446738 Affx-122925342 AX-123317074 6 103870631 ATGCATTGACTGGTCTTTAGTCCTACCTAGAAACT[A/G]TAATTCTGAGAAGTCTGTTTCTATTGCTCACGATG R 2 1 2 1 101000 f 74 goat snp48571-scaffold690-1194013 6 107080847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797414 Affx-122943863 AX-385284353 6 103932759 AAAAATTTCAAACTTGAAAAAGGCTATATAATATT[A/G]TTCTACCAGTAAGACTTCATAGATAACTACTATGA R 2 1 2 1 202000 f 74 goat snp48570-scaffold690-1131885 6 107143729 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441047 Affx-122928929 AX-123311384 6 103973544 GCCTTGAGACAAAGGAACATGGATTCTGGCATCGT[G/T]TCTGACACCTTCCTACCAAGAGGGTAAAATAAGTC K 2 1 2 1 101000 r 74 goat snp48569-scaffold690-1091100 6 107183678 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404861 Affx-122956615 AX-123275213 6 104024885 TCTATATTAATTTCTGTGGTACAATGATTATATCA[C/T]ATTTTTAGATTTATCATATAAAATATTTAGTATTA Y 2 1 2 1 103000 f 74 goat snp48568-scaffold690-1039759 6 107234920 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451069 Affx-122921422 AX-123321403 6 104056957 ATCATTAACCTCATTTTATTCATTAGGACTCTGAG[A/G]CAGAGAGTGGTTAATTAATCACTCCAAAGTCCCAT R 2 1 2 1 101000 f 74 goat snp48567-scaffold690-1007687 6 107266984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427475 Affx-122940017 AX-123297818 6 104086795 TCCATATGCTCTCTAATTCACTTATATTTTTATTT[A/G]CTTTTTTTCAAGACTACTTTATTAGGATATAGAGA R 2 1 2 1 101000 r 74 goat snp48566-scaffold690-977849 6 107296634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417341 Affx-122947732 AX-123287689 6 104134157 TGTCTGAGGGGCCCTTGCCGAGCTCCCTGCAACAG[C/T]AGTGTCATAAAAGGCACATCTGTAGACTTAGGAAA Y 2 1 2 1 101000 r 74 goat snp48565-scaffold690-930487 6 107344449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275279 Affx-1111834811 AX-519548855 6 104153760 TTTGTTCTTCTCTGCTACACCCTTGCAGCATCCTC[A/G]CACTGCAGGGAGACTGGACCAAGGCCCTCGCCCTA R 2 1 2 1 202000 f 74 goat GoatD01.054430 6 104153760 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434673 Affx-122933968 AX-123305014 6 104180504 TATAAACACTGATTCAAAAACTCTAGTAGTCTTGC[A/G]CTATTTTTTCTTTATTATTTCACAATTATTATTCC R 2 1 2 1 101000 f 74 goat snp48564-scaffold690-884140 6 107391888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783064 Affx-122947650 AX-385270131 6 104225398 ATTGAGAACACTGCAGTGTTAAGAGTGGCCATCAA[C/T]AGCAAATATTCCTATAGAGAGTTTCCCACTCACCA Y 2 1 2 1 101000 r 74 goat snp48563-scaffold690-839246 6 107436950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445608 Affx-122925110 AX-123315945 6 104293150 TCCTTTGATGTGCACCTCATTATCTAGGGCCAGTA[G/T]CCTGTTCCTTCCTATCTTCTGCCCCCTCAGGATGC K 2 1 2 1 101000 f 74 goat snp48562-scaffold690-771494 6 107503161 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428238 Affx-122939427 AX-123298581 6 104342124 ATTACTTTTTAATATGTATATACACAAAGAACAGA[C/T]ATGTAACTATCTCTTTAGTTTTGGTCTCAGCACAA Y 2 1 2 1 101000 r 74 goat snp48561-scaffold690-722520 6 107552045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432979 Affx-122935268 AX-123303320 6 104402846 GACATTCCCGGGGTCACTCTTGTGGCAGCACTCAC[A/G]TAGGAGCTTGAATTCCAGTGACTGCTTCAGGGTGG R 2 1 2 1 101000 r 74 goat snp48560-scaffold690-661798 6 107614358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411561 Affx-122951637 AX-123281911 6 104448968 ATTAAATTTTAGTTTAGAGTTAAGTTGTCCAGTAA[C/T]AGACATTTGCCTGTTTTCTATTTCAGGAATTCCCG Y 2 1 2 1 201000 f 74 goat snp48559-scaffold690-615676 6 107660476 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775338 Affx-122935281 AX-385262469 6 104504109 TGAATCACTGAAGGACTGAATGGACCATTTAAGAG[C/T]AAATCTTGCCAAACTCCAGTGCCTTGTTTCGATAG Y 2 1 2 1 101000 r 74 goat snp48558-scaffold690-560535 6 107715087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278595 Affx-1111836418 AX-519552074 6 104523250 TGGATTAAGTGAGATGGGTTGCATATACAGTACGC[A/G]TAGAAGAGTGTCTGTCCTACCCTAAGCTCTCTACC R 2 1 2 1 101000 r 74 goat Random2.2K-737 6 104523250 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398076 Affx-122961732 AX-123268431 6 104541817 AGACAGCTGACAGACAAATAATACAGTTGAGCCTA[C/T]ATGAGACCTCATCTTTGTTGGGTCCAATGTGTGTT Y 2 1 2 1 101000 f 74 goat snp48557-scaffold690-522827 6 107752270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278428 Affx-1111836419 AX-519551913 6 104546106 TCTGCCAGAATCTGGGCTCCGTTTCCGTGTGTTTA[A/G]CAATGAAGATCCCTTTCTTTGCTCCTGGTGTCCCT R 2 1 2 1 201000 f 74 goat Random2.2K-738 6 104546106 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416055 Affx-122948347 AX-123286404 6 104601372 AAAATTATCTAAAAGACTGACCCTATGTCTGAAGA[C/T]GGGGAACTTCTGAAGGGCCATATCAATGTTTGAGT Y 2 1 2 1 201000 f 74 goat snp48556-scaffold690-463272 6 107810588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791887 Affx-122935526 AX-385278877 6 104631767 CATCTCATCAAGTTGAGATGCAGATCTGATATTCT[A/G]CCAGATCAGTAGGGAGCTCCAGACAAAATTGCCAG R 2 1 2 1 101000 r 74 goat snp48555-scaffold690-432877 6 107841440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444469 Affx-122926538 AX-123314806 6 104681989 GGAGACAGACAAAGAAAATACATAGATATATGGGC[A/G]TGGATAAGCCCGAATGCAGCTTTATTTACAAAGCA R 2 1 2 1 101000 r 74 goat snp48554-scaffold690-382655 6 107893685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435404 Affx-122933558 AX-123305744 6 104734673 GACCAGGGAAGTCCCAAGACAGGTCTCACCTACTA[C/T]AAGTCGCTTCATTTATAAGTGGTATTGCATGGAAG Y 2 1 2 1 101000 r 74 goat snp48553-scaffold690-329971 6 107946915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789459 Affx-122949433 AX-385276469 6 104806588 TTTAAAGACTAATTGTCATATAATGAATGTGTATG[C/T]GTATGCACACAAATACACGCACACATACCCCTGCA Y 2 1 2 1 102000 r 74 goat snp48552-scaffold690-258056 6 108020076 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445967 Affx-122925893 AX-123316304 6 104844112 TGACCCTATACTAGAAAGACTTTGGCCTTAGCACA[G/T]AGCAGGATGCTTTGGAAGCCCCAGTCACACACGCG K 2 1 2 1 101000 f 74 goat snp48551-scaffold690-220532 6 108057657 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388584 Affx-122969161 AX-123258942 6 104875528 ACTGTTTAACACATCCCTAATATAAACCAATGCCA[G/T]AACAGTGAACATTAGCACATTTCTACCCATGTTAA K 2 1 2 1 101000 f 74 goat snp48550-scaffold690-189116 6 108090550 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378165 Affx-122976964 AX-123248524 6 104924291 AGGGTTTCTGGCCTCACAGAATCTACAGTTTATGG[C/T]GGAGAGAGACATAGAAAAAACATAAGCTATATGGA Y 2 1 2 1 101000 f 74 goat snp48549-scaffold690-140353 6 108139280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430035 Affx-122937575 AX-123300376 6 104957870 AAGGGGTCCTTGAGTTAAGAGACAGGGAAGCCTGG[C/T]ATGCTGTAGTCCATAGACTCGCAAAGAGTAAGACA Y 2 1 2 1 103000 r 74 goat snp48548-scaffold690-106774 6 108172833 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782197 Affx-122940058 AX-385269275 6 105001524 AATAAGGCACTGATGGAATTATTAGGGATAACAAA[C/T]GGACAAGGTTTTATTGCTAATAATGAAGGTCCTGA Y 2 1 2 1 101000 f 74 goat snp48547-scaffold690-63120 6 108216012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388331 Affx-122969360 AX-123258689 6 105030608 TACTCACCACCTTCATCTAACAAATGCTATCATTC[C/T]ATCATATTATTTCAGCCTTTAAAAAATATACAGAT Y 2 1 2 1 101000 f 74 goat snp48546-scaffold690-34036 6 108245012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385211 Affx-122971710 AX-123255569 6 105077529 AAATGCATTATGACTCTTGTCAATGGCCCAAATTA[C/T]ATTTTCAGTTCAGTGCAGTCACTGAGGCATATCCA Y 2 1 2 1 201000 f 74 goat snp4376-scaffold1139-12786 6 108294194 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766629 Affx-122926247 AX-385253980 6 105106989 CTTGATTGTATGACACTGAATAATTTCACTCTATC[A/G]TTTACTTCACCGATCTTCAAAAATCTTATTTTTAT R 2 1 2 1 101000 f 74 goat snp4377-scaffold1139-42246 6 108323330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775927 Affx-122935647 AX-385263058 6 105151959 AGAACTGATATTTTTAACAGAGTATTTATTCCATT[A/C]TTTCTGCTTATTAAGAAGTTAGTTTTCATATACCT M 2 1 2 1 101000 f 74 goat snp4378-scaffold1139-87216 6 108368547 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274281 Affx-1111834159 AX-519547878 6 105173487 CAGCCTCAGTCCAAAACTATCCTGTTCTAATCATC[A/G]CTTTGGACAGAGATGTCTCTGCAGAAGCTAGAATG R 2 1 2 1 201000 f 74 goat GoatD01.022462 6 105173487 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395063 Affx-122964190 AX-123265418 6 105189071 TCTGTGTTGACTGGGGCTTTAGCTAGGATGGTTCA[A/G]ATGGCTTGGGACTTGCCTGGGAAATCTGAGTTCTC R 2 1 2 1 303000 f 74 goat snp4379-scaffold1139-124328 6 108405188 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447750 Affx-122924580 AX-123318086 6 105284222 AATTATTCTCTTAAGACAACCCACAGCAAGGTTGA[C/T]GGAAGCCTGGGGCTGTCATGAGCGATCACATGAAA Y 2 1 2 1 201000 f 74 goat snp4381-scaffold1139-219479 6 108500560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408685 Affx-122953445 AX-123279036 6 105344328 TTCCCCGCTCATACCTCCCACCTTTCTAAAATTGC[A/G]CTCTCCCCATGGCCATCGATTCCACCGGGAATGCC R 2 1 2 1 103000 f 74 goat snp4382-scaffold1139-279585 6 108560682 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784434 Affx-122965392 AX-385271483 6 105382931 AGTGATTTGTCCAAATCACATAGCCAGTTATTCTT[A/G]TAGCTGGAATTTGAACTCAGATTTCTTTGATTATT R 2 1 2 1 303000 r 74 goat snp4383-scaffold1139-318188 6 108599248 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272237 Affx-1111833489 AX-185187933 6 105400668 GTCCGACTCTGTGCGACCCCATAGACGGCAGCCCA[A/C]CAGGCTCCCCTGTCCCTGGGATTCTCCAGGCAAGA M 2 1 2 1 303000 r 74 goat 6_105400668_AF-PAKI 6 105400668 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781260 Affx-122958544 AX-385268345 6 105436619 AGCTTATTTTTTTATGGCACTCATAGTTATCTGAT[A/G]CATTATTATTATACTTAGGTCTATGTTTATTAATG R 2 1 2 1 101000 f 74 goat snp4384-scaffold1139-371876 6 108653699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376083 Affx-122978907 AX-123246442 6 105475528 CCCATAATAATAATAGAAATAAAATCCACAATGTA[C/T]GTAATGTGCTTGAAGTATCTGCAAACCACTTCCCC Y 2 1 2 1 101000 r 74 goat snp4385-scaffold1139-410785 6 108692607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433450 Affx-122935063 AX-123303791 6 105571648 TTTTTGCTCTGGTGAATGATATGAAGATAACAGGA[C/T]GGCCTGGAAGAAAGAGGAACTGAGGGCAAGGAGAA Y 2 1 2 1 201000 f 74 goat snp4387-scaffold1139-506905 6 108788010 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404944 Affx-122956426 AX-123275296 6 105613611 TGGTGGATGAATCAAAAGGAGGAAGACCCTGGGGT[A/G]CACTTTGAAAAGCACAGCCTGAAGCTGCCCTCACG R 2 1 2 1 101000 f 74 goat snp4388-scaffold1139-548868 6 108829907 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424578 Affx-122942218 AX-123294924 6 105705178 GTTCAACTGTTCTTTCTTTTTTTTTTTTTTAACAC[A/G]TGCACACGGAGTTCTGTGGCAAGAAAGACAGTAGA R 2 1 2 1 101000 r 74 goat snp4390-scaffold1139-640435 6 108922321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764747 Affx-986697007 AX-385252362 6 105705589 TCTGCCACACACCTACCCATTTCTGAGGAAAGCCA[A/C]ACCTCCTGGGTTTTCCTTTCAGAAGAAAAGGGACA M 2 1 2 1 600010 r 74 goat 6_105705589 6 105705589 Ancestral_priority_1043 ancestry 0.598 neutral IMAGE 10K 10K ancestral 320764750 Affx-986697009 AX-385252366 6 105705612 TGAGGAAAGCCAAACCTCCTGGGTTTTCCTTTCAG[A/T]AGAAAAGGGACACATTAGTCTCCACGAGCAAGGCT W 4 1 2 1 600010 r 74 goat 6_105705612 6 105705612 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320764754 Affx-986697011 AX-385252368 6 105708448 CTTGAGCTTCTCAAAACCTTCATTCAAACTTGAAT[A/T]TGGGTGAACGATGCTCATCTGTGGAGGGAAGTGTT W 4 1 2 1 600010 r 74 goat 6_105708448 6 105708448 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 38400033 Affx-122960784 AX-123270388 6 105748992 ACATAATTTCAAGACTTAAAATCATTTATTCAACT[A/G]TCTCCCACCTGAGAGGTTTATATTCCAATATTGAG R 2 1 2 1 101000 r 74 goat snp4391-scaffold1139-684249 6 108966512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776958 Affx-122944650 AX-385264082 6 105785940 AATTTAAAAGAGGTAGGTATATCTATGTGTACAAA[C/T]GTGGAAAGCTCCTTAGATAACATTACAAGGTGAAA Y 2 1 2 1 201000 r 74 goat snp4392-scaffold1139-721197 6 109003824 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440387 Affx-122929629 AX-123310724 6 105843233 GCCTGGAAAACCTTACCTTTAGCCCTGTGAGCTCC[G/T]AACATCTTTTGGCTCTAAAAATCTGACCAGGGCAC K 2 1 2 1 101000 r 74 goat snp4393-scaffold1139-778490 6 109061607 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419349 Affx-122945642 AX-123289697 6 105877105 TCAGCAATTAACATCAACATCAAGTGGCAAAAGCT[A/G]TATCAAAGTAGTTTAAGGGTATTTGTAGGTCCAAC R 2 1 2 1 101000 r 74 goat snp4394-scaffold1139-812362 6 109095718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449548 Affx-122923248 AX-123319883 6 105913244 AGTGAGGAGGGTTCAGAAGGGCCGAGACCCTGTTA[C/T]GAAACCTCTCTAAGCCTCAGCGGCCTCATATGCTC Y 2 1 2 1 303000 f 74 goat snp4395-scaffold1139-848501 6 109131996 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765590 Affx-122942469 AX-385253069 6 105941839 GTTTAAACCTATAATTCTCTATTAACTGTATATTA[C/T]GAGGTATATTACTATGAATTTTAATGTGAACTGGC Y 2 1 2 1 201000 f 74 goat snp4396-scaffold1139-877096 6 109157234 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411852 Affx-122951221 AX-123282202 6 105979872 CTCAAGGTGCGAAGAGGATGCAAAAACAACATAAA[G/T]GGAAAGCCCAGGAAATGGGCCCAGACCCAGCTGGG K 2 1 2 1 101000 f 74 goat snp4397-scaffold1139-915129 6 109195358 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38438994 Affx-122930373 AX-123309331 6 106029098 CTGAGACAGGTTAAATGACTTGCCCACAGTCAGCA[A/G]TCTCTGAAGAGCCTCCTTATCTTCCTGCTCCACAT R 2 1 2 1 201000 r 74 goat snp4398-scaffold1139-964355 6 109244442 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435302 Affx-122934025 AX-123305642 6 106066465 AATCTACTGCCCTTTAGGGACAGACTCCCGAACAC[A/C]CCAATCAGTGCCCTGCACTCTTCCAGCCTCTTGGG M 2 1 2 1 101000 f 74 goat snp4399-scaffold1139-1001722 6 109283218 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278430 Affx-1111836420 AX-519551915 6 106128421 TTGTTTTCATTCCTGGTAACTTCCTATCAAACTGC[A/G]CAGGCCCCCCTCTCTTAGAACTGTCTCAAATATCT R 2 1 2 1 101000 f 74 goat Random2.2K-739 6 106128421 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453446 Affx-122919863 AX-123323779 6 106151351 ATGCTCCAACCAAACTGAGCTACCAGCTGTCTTCC[A/G]CATCTCCTGATTTCCTTCTTTTGTAATTTGCTGCT R 2 1 2 1 201000 f 74 goat snp4401-scaffold1139-1086608 6 109367865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397293 Affx-122962328 AX-123267648 6 106202907 TTTGTGGCAGATTTGTGATGTTCAATAGTAAGAAA[C/T]GGGCTTCCGTGGTGGCTCAGACGGTAAAGAATCTG Y 2 1 2 1 101000 f 74 goat snp4402-scaffold1139-1138164 6 109419324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380728 Affx-122975142 AX-123251086 6 106240879 ATACAACAAAGACTATGAGCTTAAGGGATAAACAA[C/T]GAATGTATTTTAAAGGCAAATAAATGTTATAAGGG Y 2 1 2 1 101000 f 74 goat snp4403-scaffold1139-1176136 6 109456269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797213 Affx-122977809 AX-385284152 6 106270978 ATGATATGTGAAACTGTGATAATAATGGTTCTGAC[C/T]TCTGGCTTATGCAAGGATTAAGAGAGTTGATACTT Y 2 1 2 1 101000 r 74 goat snp4404-scaffold1139-1206235 6 109486697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791670 Affx-122937291 AX-385278661 6 106312647 TGAAAGATATTATCCCAGTGTGAATTCTTCATATA[C/T]GGAACAACCTCAGATTGTGGATTTAGAGTAACAAT Y 2 1 2 1 101000 r 74 goat snp4405-scaffold1139-1247904 6 109528830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395431 Affx-122963937 AX-123265786 6 106352919 TGCACTAGCTCAATGGCCTGAGAAGAGGTTACTTT[C/T]ATTTTGTGTGATGGAGGAAAATAGGATATGTCTCA Y 2 1 2 1 101000 f 74 goat snp4406-scaffold1139-1288176 6 109569665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777867 Affx-122953227 AX-385264984 6 106392132 GATCATCAGCTTTAACAGGAGCCCAAACTGATCAA[C/T]GTTTCGGTACCACTGACCCAGTAGCTGATAATACA Y 2 1 2 1 101000 r 74 goat snp4407-scaffold1139-1327389 6 109608340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452110 Affx-122920838 AX-123322443 6 106426116 AGGAGACCTTGATTTCATGCATTTGGACAGAGCAG[C/T]AGCTCTGGTTATCTGTGTTGTGCTCATGGAGTCGC Y 2 1 2 1 101000 f 74 goat snp4408-scaffold1139-1361373 6 109642257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391810 Affx-122967026 AX-123262167 6 106481850 ACCGTGCACAGGTCACAGTAGGGCTCGTGTTCTTA[C/T]GAGAATCTAATGTCTCTGCTGACCTGACGGGAAGC Y 2 1 2 1 101000 f 74 goat snp4409-scaffold1139-1417107 6 109700548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452102 Affx-122920846 AX-123322435 6 106526428 TCTGCATTATATATAGGATTATTGGAAGCATTACT[A/G]CTTCTTTACAAAATTTTTTGTTTGTGTATTTCAGA R 2 1 2 1 103000 f 74 goat snp4410-scaffold1139-1461685 6 109745122 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400682 Affx-122959946 AX-123271037 6 106555164 TTCAAATATAGAAAACAATTTTGTAAACTCCCTGC[C/T]GTTTCTGTTTTGCTTGGGCTCTGCAGAGGCTCAAA Y 2 1 2 1 201000 f 74 goat snp4411-scaffold1139-1490421 6 109773851 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394141 Affx-122965319 AX-123264496 6 106588034 CACATAATTCAAAACAAAGCTATAGGGAAGTCAGG[C/T]GTTTCTCCTCTACAATGTCAAGATTTATTAGGAAT Y 2 1 2 1 101000 f 74 goat snp4412-scaffold1139-1523291 6 109806743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278432 Affx-1111836421 AX-519551917 6 106606246 AGTACATTCTTGGCAGAGCTCTGCCTAGAACCCAA[C/G]AGGGGCTGATGGTTCCAAGCACATTAATTGCATTT S 4 1 2 1 202000 f 74 goat Random2.2K-740 6 106606246 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382856 Affx-122973530 AX-123253214 6 106621580 TCTGATTTAGTCTTATCAACCTTGGAACATGTTCC[A/G]TGGTCAGCACAAATGGCCAGGCTTTGGAACGACTG R 2 1 2 1 102000 r 74 goat snp4413-scaffold1139-1556837 6 109839838 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782530 Affx-122968086 AX-385269605 6 106654587 TCATGTTCTTAGTCTACATGTTAACATGTTGGAGA[C/T]GCTGGATTCAGTTTTTAAACACCTGCTATAGCATC Y 2 1 2 1 201000 r 74 goat snp4414-scaffold1139-1589844 6 109872807 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784188 Affx-122935135 AX-385271239 6 106689326 ATGACATTCATATTACTTTGGTAGAGCAAGTGTTG[C/T]GTTTTCTGTGCTGTCCTCTTCATGGCTGAACTCAC Y 2 1 2 1 201000 f 74 goat snp4415-scaffold1139-1624583 6 109907902 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437298 Affx-122931980 AX-123307636 6 106734402 TGAACAACTTCCATAGGGAAATAACATAATCAAGC[A/G]TCTGTTTTGGAAATAGTATTCTGATTACACTGCAT R 2 1 2 1 101000 f 74 goat snp4416-scaffold1139-1669659 6 109953548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434308 Affx-122934755 AX-123304649 6 106783020 AGCATTGGGGAACTATTCCACTGGTCCAGATAAGA[C/T]ACAATGATGGCTCAGAATAGGGTAAGAATGTAGTA Y 2 1 2 1 101000 f 74 goat snp4417-scaffold1139-1718277 6 109999715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784296 Affx-122930718 AX-385271347 6 106825474 CAGGTACCAGAAATGTATAAAAGGACTATTTATAA[C/T]ACCACTTAATATTTTGTTATTGACACAAAGGAAGA Y 2 1 2 1 101000 r 74 goat snp4418-scaffold1139-1760731 6 110042226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393417 Affx-122965879 AX-123263773 6 106860475 GGTCCTGGGTGGTGCATCTCTATGTCAGCTGAAGC[A/G]CCTACTCCATGAGAGTCTGATGGAAACAGATGGAA R 2 1 2 1 101000 f 74 goat snp4419-scaffold1139-1795732 6 110077035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411547 Affx-122951649 AX-123281897 6 106898468 AATCTTAGTCTTGAGTGTTAAGAACAATCTGGATG[A/G]TTGCAAACAAGAGCAAGAGAACAATGGTAAGACTT R 2 1 2 1 101000 f 74 goat snp4420-scaffold1139-1833725 6 110115172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794346 Affx-122945961 AX-385281310 6 106928162 TTCAGCCTGAGACAAATTCATAAACATGTTATTTT[A/C]TAATCTGCTTGGTGGGTCATTAAAGAATGAGGCTG M 2 1 2 1 101000 r 74 goat snp4421-scaffold1139-1863419 6 110144401 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399047 Affx-122960912 AX-123269402 6 106958322 TTCCCTTTAACACTTTTCTGATTAAAAGCTTTCCC[G/T]CCAAGCTTCTGAAACCAACTGTTTCCAAGATCATT K 2 1 2 1 101000 r 74 goat snp4422-scaffold1139-1893579 6 110174649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430271 Affx-122937297 AX-123300612 6 106987657 GTCCAGAGTCTACCTACTTTCATCTTCTGGCTATA[C/T]GAGACCTATGAAAATGGGTACCATATATCTCACCT Y 2 1 2 1 101000 r 74 goat snp4423-scaffold1139-1922914 6 110203969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443280 Affx-122927478 AX-123313617 6 107004855 AGCGTCGTTAGATTGTTGTGCTAAAGGTAAGGTTT[A/G]CATGTGACACTGTATATAAATTTCCTAGTGTGATT R 2 1 2 1 101000 f 74 goat snp8115-scaffold1296-951242 6 110220732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382790 Affx-122973577 AX-123253148 6 107049253 TCTATTTTGGGGGAAAGGGGTGATGAGCTGGGGAC[C/T]GGGCTCTTAATCTAGCCTCAAGCGCTACAGCTGTG Y 2 1 2 1 201000 r 74 goat snp8114-scaffold1296-906844 6 110264941 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405609 Affx-122956610 AX-123275961 6 107082036 CAGATCTGAATTTGAATCCCCTCTTCAACTAGCAG[G/T]TCTGAAGCTTTGGGCAAATTACTGGAGTTTGTTGA K 2 1 2 1 103000 f 74 goat snp8113-scaffold1296-874061 6 110297805 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780869 Affx-122921473 AX-385267957 6 107121598 TCTTCCTGTCTCCTCTCTTACTTTTCCTCTGTGCT[A/G]CTTCTAATTGTTGACTAAGCTTGTTGTTCAGAGTG R 2 1 2 1 101000 f 74 goat snp8112-scaffold1296-834499 6 110338290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790636 Affx-122949191 AX-385277638 6 107174494 GCAATCCTTAGGACTTTTGGACTTGGGGAGTTTGA[G/T]ACTTGAATCAGTCATTTTCTATTGATTGAAGCTGT K 2 1 2 1 101000 f 74 goat snp8111-scaffold1296-781603 6 110392085 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435175 Affx-122933653 AX-123305515 6 107252140 TTTACTCTTTCAAAGTCATTTTGTCACTGTTCATC[A/G]CCCATTACCACAACTGACTTTTACTGTCAGGAACT R 2 1 2 1 101000 r 74 goat snp8110-scaffold1296-703957 6 110470931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444713 Affx-122926420 AX-123315050 6 107317932 CAATAGCCAAAGTTCATAGAAGTTGTACACTGTCC[A/G]TGGGTACCCAGTCCATCCCAGCAGTGGGAGAGGCT R 2 1 2 1 101000 f 74 goat snp8108-scaffold1296-638165 6 110536839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398670 Affx-122961880 AX-123269025 6 107396881 TGCAGGGAAGGAGAGACAAGACAAAGTATGCATTT[A/G]TTTTAGAAACAGCAGAGAGCAGGGAAGTAGGAAGA R 2 1 2 1 102000 r 74 goat snp8107-scaffold1296-559216 6 110615922 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418097 Affx-122947138 AX-123288445 6 107507640 AGGCTCTAGCTTTTGGGGGCCAGAAGGAGCTGGCT[A/G]TGTACAGGATGCTGGAGAGTCAAGGCTACTCTGGA R 2 1 2 1 101000 f 74 goat snp8105-scaffold1296-448457 6 110727512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387738 Affx-122969742 AX-123258096 6 107539639 CAGACTGAGAAATGCATGTGGGACTTTGAGCTCCC[A/G]TCTAATCCTTTGGCCGTGGACAGGTCACTTTACCT R 2 1 2 1 101000 r 74 goat snp8104-scaffold1296-416458 6 110759803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411090 Affx-122951926 AX-123281440 6 107579794 TCAAATCAAGGGGTAACAAGTCTAAACTAGGACCA[C/T]ATGGGTGGTGAGGGGATGGAATGGAACCAAAGGAC Y 2 1 2 1 101000 f 74 goat snp8103-scaffold1296-376303 6 110799782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449094 Affx-122923595 AX-123319429 6 107621029 ACAGACAAATGCCAATCACTAAGATTAGAGATTCA[A/G]AGATAACTAAGTCAGGGGTCTGTCATGAATAAGGT R 2 1 2 1 201000 f 74 goat snp8102-scaffold1296-335068 6 110840573 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385848 Affx-122971000 AX-123256206 6 107655325 TGGATACAGCAGCAACAGCACAGTCAGCATTGTTA[G/T]TGATCATAGGGCTGTTCTCCAGCTCTGGATGACCT K 2 1 2 1 201000 r 74 goat snp8101-scaffold1296-300772 6 110874949 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427536 Affx-122939507 AX-123297879 6 107692736 CAGGGTGAGCAGAAGCGCACAGCTTACAGGGGAAG[A/C]GCACAGAGAATGAGCCTGGGGCGCTGGGCAGACAG M 2 1 2 1 101000 f 74 goat snp8100-scaffold1296-263361 6 110913416 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438497 Affx-122931220 AX-123308835 6 107743192 AGAAGGAAAGAAAATAGTTTACAAAAATAAACAGC[A/G]CTTGTGGGGAAACTCTCTGTCACCACGTATTATGT R 2 1 2 1 101000 f 74 goat snp8099-scaffold1296-212905 6 110963666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784885 Affx-122975321 AX-385271932 6 107782061 AAGTAACCAAAGACATCTCTCCAAGAATAATTTCT[A/G]CATGAAAAATCATACTGCTTTTGATCAAAGACCTA R 2 1 2 1 101000 r 74 goat snp8098-scaffold1296-174036 6 111002469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417260 Affx-122947264 AX-123287608 6 107833625 TGGTTTGGTACTTCAAAAAACAAAATGAAACTAAT[G/T]TAGCATATTTTTCTGAGTTAAAGTCTTGGTATCAT K 2 1 2 1 102000 r 74 goat snp8097-scaffold1296-122472 6 111053959 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275346 Affx-1111834742 AX-519548921 6 107852633 TTAAACAAATGGGTAAATTCCTTTTATCCTCAAGT[A/G]TATTTGGATCTTGTCTGCTAGACTGCAGTGGGAAA R 2 1 2 1 201000 r 74 goat GoatD01.051143 6 107852633 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386155 Affx-122971394 AX-123256513 6 107892440 GAAAAAGACATGGTCGTATGGATGAAAGTAAAATG[C/T]AACACACTCAATATTGTTACTGAGGAACTATACCA Y 2 1 2 1 101000 f 74 goat snp8096-scaffold1296-63657 6 111112916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379397 Affx-122976131 AX-123249755 6 107922768 CCACAACAATAATGTCTTTCGGAATCCTTGGATCC[A/G]TTCCATCTGTTGCAATACATCATTGTTTTTCCCCT R 2 1 2 1 101000 r 74 goat snp8095-scaffold1296-33329 6 111142905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377723 Affx-122977392 AX-123248082 6 107952550 AGCATCTCTCTGTAAGTATCTCAAACTCCCCTTAA[C/T]ACAAATCACGGGTAGTGTGGCATCCAGAGAAGCAA Y 2 1 2 1 201000 r 74 goat snp8094-scaffold1296-3547 6 111173230 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272331 Affx-1111833490 AX-519546065 6 107986988 CCACAGCAAGTCATTTTCCAATCTTTCTAGTTAGA[A/G]TAACTTGCTGTCCCTTCTGTAGTCACAGAGCAATT R 2 1 2 1 101000 f 74 goat 6_107986988_AF-PAKI 6 107986988 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797234 Affx-122958423 AX-385284173 6 108030960 ACAGCAGGACAGGCTGAAAGCTGAAGTGCTCCCAC[A/G]TCACTCCTGATTCATAACCAGAAATTGAGACAAGG R 2 1 2 1 102000 f 74 goat snp6947-scaffold1255-69991 6 111257699 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791495 Affx-122946355 AX-385278486 6 108060000 CCTCTTCATGAGGCAATGAAACTTAATTTTCCCAT[A/G]TGTTAACTACACAGGATGTTTTCAAACTTTCTGAT R 2 1 2 1 101000 f 74 goat snp6948-scaffold1255-99031 6 111287859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395311 Affx-122964058 AX-123265666 6 108093725 AAACTCATTTGGAAATCCTTCAGGGAGCCCAGTAG[A/G]TTTGTTGAAAACAGCATACATTTTGAAGTCGGACG R 2 1 2 1 201000 r 74 goat snp6949-scaffold1255-132756 6 111320639 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440542 Affx-122929325 AX-123310879 6 108126710 GACCAGAACAGGGGCAGCAAAACAGAGCAAGGAGT[A/C]GGAGCTATTAGAAATTAGAGATGAGACCAGAGAGA M 2 1 2 1 101000 r 74 goat snp6950-scaffold1255-165741 6 111353653 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785022 Affx-122945114 AX-385272069 6 108176232 TTGGCTCATCCTGAGATCCATCTCCATTGCTATGA[C/T]CATCACCTCATTGAATCATGACTTGCTCAAACAGG Y 2 1 2 1 101000 f 74 goat snp6951-scaffold1255-215263 6 111403063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417764 Affx-122947403 AX-123288112 6 108206352 ACGGGCGCTATGGCCAAGAAAAAGAGAGAGACAAA[C/T]AGATTGGAGTTGGAAAGACAAATAGATTTCTAGCT Y 2 1 2 1 201000 r 74 goat snp6952-scaffold1255-245383 6 111429008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422747 Affx-122943245 AX-123293093 6 108237574 TTTTTGCAGATTTATTTATCGGCTGCTGCAGCCCA[C/T]GGACTCTCGAGGTGTGGCTCGTGGGCTCATCACAA Y 2 1 2 1 101000 f 74 goat snp6953-scaffold1255-276605 6 111460300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429933 Affx-122938091 AX-123300274 6 108268179 GTAACTATGTTTCTAAAAGTTTTGCAAATAATATG[C/T]AAACTTTGAGGGAAAATATGATTCAGAATATGAAG Y 2 1 2 1 303000 f 74 goat snp6954-scaffold1255-307210 6 111490725 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797563 Affx-122960384 AX-385284502 6 108297837 AGCTAAAATCTGCAAAATTTCAGATGTTTCCCAAT[A/G]CATAATCATTGAAAAGGTCATAATCAAATGTTCAA R 2 1 2 1 101000 f 74 goat snp6955-scaffold1255-336868 6 111519460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423535 Affx-122942439 AX-123293881 6 108375129 CCACACTGTTATGACCCCAGGTAAGGTGGTGGGCC[A/G]CTCTTCATCTAAGGAAGTTACTGTTAGTGGACAGC R 2 1 2 1 101000 r 74 goat snp28932-scaffold3114-9539 6 111596981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403068 Affx-122958520 AX-123273421 6 108440735 AGTGCTCGCGCTGGTGCCTTGGCATGTTCGAACAG[C/T]GATTTGAACATGAAGTAGGCACGGATTACCGTGGT Y 2 1 2 1 101000 r 74 goat snp11988-scaffold1440-817770 6 111661862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422357 Affx-122943436 AX-123292703 6 108509968 TTTTCAGAGAAGACAAAGACCAGCCAGATTCCCCC[A/G]ATATATGTTTAGATAAGGTTTACAGGATCTCTTTT R 2 1 2 1 201000 r 74 goat snp11987-scaffold1440-748537 6 111731768 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800453 Affx-122952403 AX-385287374 6 108563347 TCCGTTAAGCAAACTTGTTCCCTCTAGCTGTGAAG[C/T]ATTCTTGTGGCCCAAAGTGAGTCAATCCCAACTTT Y 2 1 2 1 101000 r 74 goat snp11986-scaffold1440-695158 6 111785161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777218 Affx-122933449 AX-385264341 6 108649440 GGTCCAGTCACTGAACCATGGCCCATGGCCTCTAA[C/T]GAGTCCAAACCATATAGATATCATTCAAGTTTGGT Y 2 1 2 1 101000 f 74 goat snp11984-scaffold1440-609065 6 111871771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440955 Affx-122928999 AX-123311292 6 108682146 ACTGGCAAAGAAGTCTCCTCTCCCTCACGTCTCAA[C/T]ATCCCATGGATTCTACACAATCTGTGAGGCCATCA Y 2 1 2 1 101000 r 74 goat snp11983-scaffold1440-576359 6 111904181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433574 Affx-122934971 AX-123303915 6 108714830 TTCAGTCGCTGTCATGTTTGACTCTTTGTGACCCC[A/G]TGGACTGCAGCTTCCCACCCCAAGGAAGTCAGGCT R 2 1 2 1 103000 f 74 goat snp11982-scaffold1440-543675 6 111929464 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448493 Affx-122923467 AX-123318829 6 108748139 TCAACCACTGGGCCACCAGGGAACTCCTGGAACTT[C/T]TATTCTAAATAAGACCAAGATAAGTGCCATATGTA Y 2 1 2 1 101000 r 74 goat snp11981-scaffold1440-510366 6 111963122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421032 Affx-122944536 AX-123291379 6 108825731 CCAGAGTGATTACAACTTCACACTTTCAGTGCAAA[C/T]GGTACAGGCTCAATCCCTGGTCAGAGAACTAGACT Y 2 1 2 1 101000 f 74 goat snp11979-scaffold1440-432774 6 112041070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443601 Affx-122927313 AX-123313938 6 108855574 TGCCTAATTAAAAGCACTAATGCACAGTATGGTAG[C/T]ATGATTTCCTTTTCCAATGAGGTAGAAAATCACTA Y 2 1 2 1 101000 f 74 goat snp11978-scaffold1440-402931 6 112069202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430756 Affx-122937496 AX-123301097 6 108888931 CCCTTACCTGTGTTGAGCATCAAATGATGGACTTG[A/C]GTGCAGAAAGTAGAACATGCCTGCCTCTGTGCGCT M 2 1 2 1 101000 f 74 goat snp11977-scaffold1440-369574 6 112102568 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788741 Affx-122946558 AX-385275757 6 108928743 CAGATACTTCCATTTATCTTTTAGGGGATAATGAG[A/C]AGAAGTCTAGACTGCAAGAACTTGCTTAAGAATCA M 2 1 2 1 101000 r 74 goat snp11976-scaffold1440-329762 6 112141861 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451262 Affx-122921930 AX-123321595 6 108959206 TGTAACAGTTATTATAGCTACAGAGTAAAATGCTC[A/G]TCTGTGCTTTTTTAAGAAAATGGAATAAAAGGAAA R 2 1 2 1 101000 f 74 goat snp11975-scaffold1440-299299 6 112173392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404456 Affx-122956742 AX-123274808 6 109007223 GCTGATTTGGATTATCTGTCCATTTACTCTATCTA[G/T]CAATGTGGATAATTGAGAACTGACTCTGGTTTAAT K 2 1 2 1 101000 f 74 goat snp11974-scaffold1440-251282 6 112221282 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396885 Affx-122963231 AX-123267240 6 109051593 CTCATCAGCTGCTTTGCTGACAGTCGGGTGATGTG[C/T]GCACGCTTGCTGATGTGCGGGCTAGTGACAGCTGA Y 2 1 2 1 101000 f 74 goat snp11973-scaffold1440-206912 6 112264887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787032 Affx-122930458 AX-385274060 6 109087772 TTCTGGACTTGAGAACTGTGGAAGAACAAGTTTCC[A/G]CTGTCTTAAGCTACCAGCGTGTGGACATTGGTTAC R 2 1 2 1 202000 r 74 goat snp11972-scaffold1440-170733 6 112296759 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796501 Affx-122948679 AX-385283450 6 109150145 TGGACCAACCATGGCATGTCACATGGACAGGGTTA[C/T]ACCCCAGATGCTGATAAATCTGGGCTTTTCCCTGA Y 2 1 2 1 101000 r 74 goat snp11971-scaffold1440-108360 6 112359265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778301 Affx-122963996 AX-385265416 6 109184185 TTCATAATGAAATAAGCAGTAATTGCTATTAATAA[C/T]AGTCCTGTAAGGGACAGTAGTATCTCCATTTTAGA Y 2 1 2 1 201000 f 74 goat snp11970-scaffold1440-74320 6 112393301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401882 Affx-122958852 AX-123272235 6 109227668 TCAACAGAGCCATAGAGAACTCCTGATCTTTAATG[C/T]ATTTAATGTAGCTATCAAGATGTGACCCGCTTTCT Y 2 1 2 1 101000 r 74 goat snp11969-scaffold1440-30837 6 112436822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414956 Affx-122949076 AX-123285305 6 109296963 ATAAGGGTGGGGCTCCCGTAATGGGATTAGTGTCC[A/G]TATAGGAAAAGAAGGGAGGAGAGACAGAATCCTCT R 2 1 2 1 103000 f 74 goat snp16074-scaffold1692-38359 6 112507634 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376173 Affx-122978834 AX-123246532 6 109440131 GGCACACCTTGGTATTTTAAGATCACTTACTAAAT[A/G]TATGATTCAAATACTCCATGCTTCTTGCCCTGGCT R 2 1 2 1 101000 f 74 goat snp16077-scaffold1692-181527 6 112651995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393516 Affx-122965803 AX-123263872 6 109477575 TAGGGTCACCTAGAAAGCTTTTAAAAACTACCCAC[A/G]TCTGGGACTTCTCTGGTGGTCCAATGGTTAAGACC R 2 1 2 1 101000 f 74 goat snp16078-scaffold1692-218971 6 112689477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448531 Affx-122923440 AX-123318867 6 109508284 ACAGCCTTCAGAGCAGTTCTGGAAGCTCAGAGAAA[C/T]GACCAGCAGCCTCTGAAGGGGCCCTGCTCAGCTAG Y 2 1 2 1 101000 f 74 goat snp16079-scaffold1692-249680 6 112720697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382807 Affx-122973565 AX-123253165 6 109543757 GGAAAGCAACATAGATGATTAAAGTAAATCTGACC[A/G]CTTTCACTGAGAAATCTTTTTTTTAAATTTTTTTC R 2 1 2 1 101000 f 74 goat snp16080-scaffold1692-285153 6 112755828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452165 Affx-122921650 AX-123322498 6 109574269 AGACGGCTTGTCACCATGGCTGTATTTCATCCAAT[A/G]GGAAGGGAGAAAAGGGGATGGAAAGGCATCTTTCT R 2 1 2 1 102000 f 74 goat snp16081-scaffold1692-315665 6 112787413 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396519 Affx-122962960 AX-123266874 6 109619430 CAGCTAATTAAGAGTCGTCATCTCTGCAGCTCGGC[A/G]TGGGCTTCTGACTTTCTTTACCTGTAAACTTAGTT R 2 1 2 1 101000 f 74 goat snp16082-scaffold1692-360826 6 112832134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405193 Affx-122956919 AX-123275545 6 109658048 GATTTCTGCCTCTACAGGAAAAAGCACACGCCAAG[C/T]GACCAGCAGAATCCATGAGACAGTGTTCCAGGCTC Y 2 1 2 1 201000 r 74 goat snp16083-scaffold1692-399444 6 112870846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799590 Affx-122926972 AX-385286520 6 109706111 TGTGGAGAATTCCTATCTGTTAGGCTTGTGTATAA[C/T]GACAAAGGTGATTCTCACCCAAAATATGTTTGTTA Y 2 1 2 1 101000 f 74 goat snp16084-scaffold1692-447507 6 112918873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801032 Affx-122937629 AX-385287946 6 109744288 CCAAATAAATATATTGTACAGACATTATACAAACA[C/T]GCACCACTTTGGCCAAAACTTAATTACAAGCAGAA Y 2 1 2 1 101000 r 74 goat snp16085-scaffold1692-485684 6 112955297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770582 Affx-122936760 AX-385257746 6 109778960 GCAGACACCGCTGCACATCTGTAAGATGTTTATAG[C/T]GTTATTTAAGATACTCAGTTCTGCTAAGTAGAAAT Y 2 1 2 1 101000 f 74 goat snp16086-scaffold1692-520356 6 112990107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397381 Affx-122962273 AX-123267736 6 109818704 AAGGCAGATGAATTCGAGGCTATGAACACTACAGC[C/T]GTGATACAGGCACAACATTCAGAAACAAGTCAGGC Y 2 1 2 1 101000 f 74 goat snp16087-scaffold1692-560100 6 113029913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392949 Affx-122965693 AX-123263306 6 109852107 ATCTAAACTTTGAAAGAAGAGGAGACTTTTTCCAG[C/T]GGTAAAGGAAGCAAGGTTGAAGGATTCCAGGTCAA Y 2 1 2 1 101000 f 74 goat snp16088-scaffold1692-593503 6 113063405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424460 Affx-122941776 AX-123294806 6 109883131 CCTTGTAACCCTGAAGATGAGGCACCATCACAAAT[A/G]TGACTGTACACAGTCACTGCGGTGTTATTTCTGCC R 2 1 2 1 101000 f 74 goat snp16089-scaffold1692-624527 6 113103536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452094 Affx-122920853 AX-123322427 6 109953970 GGATCTGGGAGTCACTGGACATGCTCTCATCCTGC[A/G]GCACATCTGGTGGAGGACAGAGCAGAAAGAGAATC R 2 1 2 1 201000 f 74 goat snp23630-scaffold2388-62059 6 113307084 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398477 Affx-122961580 AX-123268832 6 110058292 TGGGGAGAGTCTAGAGAAATGCAAGAGATACATCA[A/G]TGTTAACAGTAACTGTTTCTGGGAGATGGAATTAA R 2 1 2 1 101000 f 74 goat snp23632-scaffold2388-166381 6 113408179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444700 Affx-122926430 AX-123315037 6 110097742 GATGGCATTTGGGCCCCCAACTTTAAACCTGGTTC[C/T]GCAAGCCCATACTGAGCACAGACTGTGCCAGCCAA Y 2 1 2 1 201000 r 74 goat snp23633-scaffold2388-205831 6 113447672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405861 Affx-122955853 AX-123276213 6 110246178 GGGCCACCACTGTTCGGACTTCTGTCACCATAGAC[A/G]TGTTCCGCTCATTTTGAACTTTAGGTGTATGGCGT R 2 1 2 1 101000 r 74 goat snp31682-scaffold3510-2471 6 113595989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410069 Affx-122953216 AX-123280419 6 110315998 GGACCAGAGTCTTTAGCTTCGACGTTATCTGCTTA[G/T]GCCACCGAGTTAGATTCTTAGGATTCCAGGCTCAC K 2 1 2 1 101000 f 74 goat snp31684-scaffold3510-72291 6 113662634 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389847 Affx-122968162 AX-123260204 6 110396800 TTAGAGCTCTCCACTTAACAAATACTGAAAGCTCC[A/G]CTCTGTCCTAGGCCCTGATCCGGGCACTGGTGCTT R 2 1 2 1 101000 f 74 goat snp17700-scaffold1835-179311 6 113745536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395373 Affx-122963979 AX-123265728 6 110429585 GGGAGGAGAGAAGCTTTCAGTTCTAACGCCCTCAC[A/G]CCAGGAGTGAGCTGAGAATAGCAGAACAGGACATG R 2 1 2 1 101000 r 74 goat snp17699-scaffold1835-146526 6 113777113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430984 Affx-122936694 AX-123301325 6 110471654 CGACTTCCTGGCAGAAGGAATCTCAGCCCTGCCCA[C/T]ATTTCACTCCCCATGGGGAACTCTGTAGCTCAGGG Y 2 1 2 1 201000 r 74 goat snp17698-scaffold1835-104457 6 113819857 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405218 Affx-122956899 AX-123275570 6 110502512 AGATGAGGTGGAAAGCCTTTGTAAACCTTTGGATC[A/G]GGTCCAGGGTAGATTCTCCCCGGGGGTGGCCAAGG R 2 1 2 1 101000 f 74 goat snp17697-scaffold1835-73599 6 113850554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416116 Affx-122948304 AX-123286465 6 110531528 TCCAGGTCTATGAGAACTGGTTGGCATGAAACGAA[C/T]GTGCCCAGCACAGGTCTGTGAGAATGGGAGGAAGG Y 2 1 2 1 101000 f 74 goat snp17696-scaffold1835-44583 6 113879530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425534 Affx-122941455 AX-123295880 6 110569016 TGGTGAGTGGATGGATGAGTGGACAGATGGATGGA[C/T]GGTAGGCTGGGTGGACGGGGGAAAGTGGATGGGAG Y 2 1 2 1 103000 f 74 goat snp17695-scaffold1835-7095 6 113916509 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272332 Affx-1111833491 AX-186966361 6 110592768 AAGACTCTTGAGGGTCCCTTGGACTGCAAGGAGAT[A/C]TAACCAGTCCATCCTAAAGGAGATCAGTCCAGTCC M 2 1 2 1 103000 f 74 goat 6_110592768_AF-PAKI 6 110592768 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422490 Affx-122943312 AX-123292836 6 110602800 TGTTATTTATGGTGTCACGAAGCAGGAGATGACAG[C/T]AGTGCCCTACTGTTGGACTGTCTTGAAGTAAGCTG Y 2 1 2 1 101000 f 74 goat snp23729-scaffold2398-26590 6 113949728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437459 Affx-122932387 AX-123307797 6 110638581 AAAGACTATGACCAGATATGAGGGTTCATCAGAGG[C/T]GAGGTGCCCTGCAGTGGCCCTGCAGCCCGAGCTCA Y 2 1 2 1 101000 f 74 goat snp23730-scaffold2398-62371 6 113984656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788125 Affx-122943672 AX-385275145 6 110676063 ACATGTAAACACATGTGTACTTGCAACCGTCATCC[A/G]TTCACCATATGTCTTCATCAGACAATGAGTTCACT R 2 1 2 1 101000 f 74 goat snp23731-scaffold2398-99853 6 114020201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447437 Affx-122924379 AX-123317773 6 110719434 CTGGTGGGTTCAAGCCCTTCCCCTGTATGGTCTGA[C/T]GCTATCTACAGGTAGACAGTGTTGGAACTGAGCTG Y 2 1 2 1 201000 r 74 goat snp16468-scaffold1734-501206 6 114064855 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381435 Affx-122974348 AX-123251793 6 110771088 AATAGTGTCACCAAAACTGCTCCCAGGATTGCCAG[C/T]GGGATCAGTGCCCCACTCCATGCCCAGCACCCCAG Y 2 1 2 1 101000 f 74 goat snp16467-scaffold1734-449552 6 114116677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781386 Affx-122942605 AX-385268471 6 110814419 GCCACAGAAGGGTTCACCTGAAAGGGCTAATTGTA[C/T]GTTATGTGAATTGCGTCTCAATTTTAAAAAATATT Y 2 1 2 1 101000 f 74 goat snp16466-scaffold1734-406221 6 114160070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425525 Affx-122941461 AX-123295871 6 110848916 CTAAAGGGGCTGACGCTGAGGCTCTGGAGTGAGTA[G/T]GATGTAATTGTTCTGTTTGGCTGTCTGAGGATGTT K 2 1 2 1 101000 r 74 goat snp16465-scaffold1734-371724 6 114194423 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399905 Affx-122960201 AX-123270260 6 110882587 AACAAGGCACGGTTTCCTGAGTTGAAAGTTTTGCC[A/G]TCATTTACAAGGGGCTCTCATGTATCATTTGGGAA R 2 1 2 1 101000 r 74 goat snp16464-scaffold1734-338053 6 114228059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413260 Affx-122950225 AX-123283609 6 110930970 TGTAAATTATGTTCATTCACCTTTCTTCACAAATA[C/T]GGTGTGAAAGGTTGGATCATCTCTCCCCCATCCAC Y 2 1 2 1 101000 f 74 goat snp16463-scaffold1734-289670 6 114275573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797223 Affx-122930725 AX-385284162 6 110961310 CATCATCAATTTTACGATGCTCTTAAAAATGACTA[C/T]CTTTTCAGCGACCAGTTAGCCAGAAATCAGAGCAG Y 2 1 2 1 101000 r 74 goat snp16462-scaffold1734-259330 6 114296686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442039 Affx-122928399 AX-123312376 6 111013516 ATAAAATATAATTTAAATATAAAATAAAATTCTAC[A/G]TGCAAATGAGAGACTCATTGTGAGCAGCTGGCTCA R 2 1 2 1 103000 r 74 goat snp16461-scaffold1734-207124 6 114349047 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423109 Affx-122942916 AX-123293455 6 111044781 CTCTGTCTCTCCCTGCATCTGTGCTTTAACAGGCC[A/G]TCACCTCTGCCCGCGTCTGTAACCCCTGAGGCAGA R 2 1 2 1 201000 r 74 goat snp16460-scaffold1734-175859 6 114380279 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781767 Affx-122944620 AX-385268849 6 111078594 CTCACATCTCGCTTGTGAATTTGCCTCGAAAGGGT[A/G]TAGCGTTACATGGCTGTGTTTGTGCTTGTAGAGTA R 2 1 2 1 101000 r 74 goat snp16459-scaffold1734-142046 6 114414154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420410 Affx-122944919 AX-123290757 6 111136161 TGTGTCCTCGGGGTGGGTTGCCTCCCATCACATCT[A/G]CATGGAAGGCGCATTCTACAGCTAGGTCCCCTGGG R 2 1 2 1 201000 r 74 goat snp16458-scaffold1734-84479 6 114468243 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381023 Affx-122974652 AX-123251381 6 111180335 TGGGAGGGCCCGGGTCGGGCAATGAAAGTGAAATC[A/G]CATTCTAAACTGTCGTGATGCGGGATTGTTATTGC R 2 1 2 1 101000 r 74 goat snp16457-scaffold1734-40305 6 114512168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394161 Affx-122964938 AX-123264516 6 111218990 CTTCCGCGGACAGATCTGTGAGTGGTCTTCCGTCG[C/T]GTTTGTCCCACTCGCCCGGTGACGACCCTGTGATC Y 2 1 2 1 101000 f 74 goat snp16456-scaffold1734-1650 6 114549341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411631 Affx-122951581 AX-123281981 6 111237824 AGTGCTGTTCCTGAAGCCGTTTTCTGTAGTTACAG[A/C]CTCTGCTCCAGACAGAAATGGGAGCTTTGTCAAGG M 2 1 2 1 201000 f 74 goat snp38111-scaffold4753-105874 6 114567302 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453610 Affx-122920132 AX-123323943 6 111266875 GATGTTGTCACTCAGACTATTAATTCTCACCCCTG[C/T]GGGGCGCCGTTCTGTGCTCTGAGTCACCAAACGCA Y 2 1 2 1 101000 f 74 goat snp38110-scaffold4753-76823 6 114594989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384858 Affx-122971950 AX-123255216 6 111378869 TTTTCTCAGTGAAGAAGAAAGGTCTTTCTTTAGCC[A/G]TGAAGGACGCTTTTCTGAGGAGGAGGCCAGGCAGC R 2 1 2 1 101000 f 74 goat snp18927-scaffold1907-35072 6 114701418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436745 Affx-122932292 AX-123307083 6 111420199 GGCTCCCGGCGTTCCTGGGCTTGTGGCCCATCATG[C/T]GCTCCAGTCTCCATCTCCATCGTCACGTGGACATT Y 2 1 2 1 201000 f 74 goat snp18928-scaffold1907-76402 6 114737082 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437419 Affx-122932415 AX-123307757 6 111487234 TGAGACTGTTCAAAATTACTTTATTTTCTAAAAAC[A/G]ACTTTATTTTCATTTCTGAATAGATAATACAAGAG R 2 1 2 1 103000 f 74 goat snp18929-scaffold1907-143437 6 114800424 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379085 Affx-122976319 AX-123249444 6 111540304 AGAGGCTTTACAAGTGGGAACCAGCACTATCATGA[C/T]GATTTCCTGCACTGCAAGACATACACTTGCTCGCA Y 2 1 2 1 101000 r 74 goat snp18930-scaffold1907-196507 6 114855956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764762 Affx-986697016 AX-385252375 6 111555289 CCTTAGTACCGCCTCATACGTCCCACTCCAGTCCC[A/G]TCCGCACAGACCTGCCAATGGAAGGACCCTCGACT R 2 1 2 1 600010 r 74 goat 6_111555289 6 111555289 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 38400389 Affx-122960007 AX-123270744 6 111581297 TTTAGAAGTAATAAGGCCTCTCAAAGTATACAAAA[C/T]CAGAAGAACTTAGAGAAAACTGGAAGGAACTAACA Y 2 1 2 1 201000 f 74 goat snp18931-scaffold1907-237500 6 114896829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762488 Affx-986697018 AX-385250609 6 111590903 ACGCCTCAAGCCCTGAAGCTCGGAAGCCGCCTCAG[G/T]CCTGAGCTCTCAGCACCACCCGCTCAGCGTGCTCA K 2 1 2 1 600010 f 74 goat 6_111590903 6 111590903 Ancestral_priority_1043 ancestry 0.482 neutral IMAGE 10K 10K ancestral 38403281 Affx-122957856 AX-123273634 6 111648664 GCTAAGCAAAATCCTAATTGGTGTCTTGACTTTCA[C/T]TATCAAGTAAAAAACTGAGACACAATTGCCTTGTC Y 2 1 2 1 101000 f 74 goat snp18932-scaffold1907-304867 6 114943099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390907 Affx-122967096 AX-123261264 6 111782844 ACTTTCACTCCCATCTCCCATTATTCGGTGTTTGC[C/T]GTTTTCAAAGAACTTTCACATCCAAGATTTCATTT Y 2 1 2 1 101000 f 74 goat snp18934-scaffold1907-439047 6 115075158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398691 Affx-122961862 AX-123269046 6 111796313 GCTGACGCACTCTTTTATACTCTAAGCCCCATCCC[A/G]AAATGACATCAGCTGCAAGCCCTCCGTAGCCTGAG R 2 1 2 1 201000 r 74 goat snp24779-scaffold2535-231601 6 115087407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452818 Affx-122920746 AX-123323151 6 111864571 GCCACTGACATGGGCTGTGAGTGAGAAATTGATGC[A/G]TTTTGGATGGAGGGATGCTTGTTATCAGGCAAAGC R 2 1 2 1 101000 r 74 goat snp24778-scaffold2535-163343 6 115153661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439413 Affx-122930242 AX-123309750 6 111946411 GTTCATGGGGTCGCAAAGAGTCGGGCATGACTGAG[C/T]GACTGAACTGAAGTGGAACCAGGGTTCATGCCCTC Y 2 1 2 1 103000 r 74 goat snp24777-scaffold2535-81503 6 115230601 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443193 Affx-122927596 AX-123313530 6 112002932 TAAAGAAAAGAAGAAGAAGATGACCTCTTCTTCCA[C/T]TAAACACGGCTGCACCTACTGTGACCTCTGGAGCG Y 2 1 2 1 201000 r 74 goat snp24776-scaffold2535-24982 NW_017216320.1 7631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278603 Affx-1111836422 AX-519552082 6 112034217 GACTCATGGAGCACGTGGTCACAAGTCAAGGGCAC[A/G]TGACCCACAGTTGGACAAGCACTGACTAGAGCGTC R 2 1 2 1 101000 r 74 goat Random2.2K-744 6 112034217 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417011 Affx-122947977 AX-123287359 6 112035963 CACATTGACAAGTAATCAGTCCCTGGTGGCTCAGA[C/T]GGTAAACAATCCGCCTGCAATGCAGAAGAACCAGG Y 2 1 2 1 103000 f 74 goat snp27710-scaffold2951-473946 6 115318731 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791463 Affx-122966768 AX-385278454 6 112068334 ATAACGAGGCTCTTCTCTTATTACTGTGCAATTCC[A/G]TTAGAGATCGAAATCAAAAGATCTTTGAAATAACC R 2 1 2 1 101000 f 74 goat snp27709-scaffold2951-441575 6 115351393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381310 Affx-122974445 AX-123251668 6 112104044 CTTTTTCCGTTTGAGCCTGCATTTCTGTCTTTCTT[A/G]TTGGATGCCTTCTCGATGTTGGTGATCCAGGGTCA R 2 1 2 1 201000 r 74 goat snp27708-scaffold2951-405865 6 115384409 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430003 Affx-122938035 AX-123300344 6 112133690 GAAAATCAGCCGTATTTGTCTGATCGGAGAGACCA[C/T]GGCAGATTCACCAGGGACTGGGCTGCTTTAATTCC Y 2 1 2 1 101000 f 74 goat snp27707-scaffold2951-376219 6 115413517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376583 Affx-122979071 AX-123246942 6 112193973 CTTTCTCTTCAGCAGGAAGTCTCAGGGTCTGTCAA[A/G]GGCTGCTGGCCAAACAGCCTTTCAGATCAGGAGCA R 2 1 2 1 101000 f 74 goat snp27706-scaffold2951-315936 6 115473655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404531 Affx-122957401 AX-123274883 6 112242129 ACGACCTTAAACAGACGTTCACCCCTCAGTCTCCC[A/G]GAGGGACTGCAGGGTCAGGCTCGGTTCTGGGGAGG R 2 1 2 1 201000 r 74 goat snp27705-scaffold2951-267780 6 115521563 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391206 Affx-122967412 AX-123261563 6 112373202 TCATCTGCGTACCTGAGGTTGCTGATATTTCTTGC[A/G]TCTGGGCTGCGGCTTCTGCTTCATCCAGCTGATGT R 2 1 2 1 101000 f 74 goat snp27703-scaffold2951-136707 6 115648298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443659 Affx-122927195 AX-123313996 6 112406194 TTGTCAGGGAAGCGAACGGCAGTCCGTGAGGTCCA[C/T]ACTGCAGAGTGTCCGACATGGAAAGACCCGTGGCC Y 2 1 2 1 201000 r 74 goat snp27702-scaffold2951-103715 6 115615131 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379097 Affx-122976763 AX-123249456 6 112447547 AATGTAAACTTTATATAGCATCAGAATCAGAAAGG[C/T]GTAACACTAATACATCTGAGCGAGTAACATGGACC Y 2 1 2 1 101000 r 74 goat snp27701-scaffold2951-62362 6 115573662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380375 Affx-122975341 AX-123250733 6 112482304 TTTGTGCCCGCTTTCTTTTCGTCTCAGGGTTTCCG[C/T]GGTTCCTGATAAGGACGCACTCATTTTTGTTGTGG Y 2 1 2 1 101000 r 74 goat snp27700-scaffold2951-27605 NW_017218119.1 8072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439753 Affx-122930527 AX-123310090 6 112531139 CACCTGGGCCTGACTTTGCACCGTGACTTGTGTGA[A/G]TGTTGGTGAGAAACAGCTCTGCGCAGTTTCAGGCT R 2 1 2 1 101000 r 74 goat snp16120-scaffold1698-458655 6 116929335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788722 Affx-122956786 AX-385275738 6 112604012 TGAAATTATGCAGTTTTTATGTTACAGGGTGGTGG[C/T]TAAGCACCACCTGTGGAAATAACGTTTACGTGTTT Y 2 1 2 1 101000 f 74 goat snp16119-scaffold1698-385782 6 116866391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447387 Affx-122924417 AX-123317723 6 112652804 AATAACTTATAACCGTGACCCATTCCAGACTTAGC[A/G]TAGTTCTTCTCGGTGGAGGTAGGAGTCAGAGAAGT R 2 1 2 1 101000 f 74 goat snp16118-scaffold1698-336990 6 116827997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425030 Affx-122941873 AX-123295376 6 112692374 GCTATTTCTGTAAAATGTGCATTTTTGAGACAAGC[A/G]TTGGAATTTAATGGCTATGTCTGCTGGGAGTTCTG R 2 1 2 1 201000 f 74 goat snp16117-scaffold1698-297420 6 116787989 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793352 Affx-122968873 AX-385280330 6 112723527 ATGGTTCATTTTTAAAGGTACAGTAAATATATTTT[C/T]AGAAGTTAACAGGATTTTCTTGTATAAGTTACTTA Y 2 1 2 1 202000 f 74 goat snp16116-scaffold1698-266267 6 116756704 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790237 Affx-122924048 AX-385277241 6 112827501 ATTCAGGCTTGGTTTATTTTTGGCAAGAAGACTTC[A/G]TAGGTTAGTAGCAGATAAGGATTAGTAGTCTTTTT R 2 1 2 1 101000 f 74 goat snp16114-scaffold1698-162293 6 116652595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379420 Affx-122976112 AX-123249778 6 112873642 GTTGGGGCGCACCCTGGCCAGAGGAGTAGATGGCC[C/T]GTACTGACCCCTGTTAGCCATCTGGAAAAAGGGTC Y 2 1 2 1 101000 r 74 goat snp16113-scaffold1698-116152 6 116608885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426099 Affx-122940642 AX-123296445 6 112912092 AAAGAAAGCGACGCAGAGCCCGGAAATCGACCCCC[A/G]CCTGGCGGACGGGTTGAGAAGGGCGCTAGGACCTT R 2 1 2 1 201000 r 74 goat snp16112-scaffold1698-77702 6 116572235 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449928 Affx-122922916 AX-123320263 6 112943808 GAATAAACTGGAAGAAAGTGAAACAAAGGAGATAA[C/T]ACATAAGAGAAATAGTGGAACAGGAACCAGAGATC Y 2 1 2 1 101000 r 74 goat snp16111-scaffold1698-45986 6 116541002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450482 Affx-122922932 AX-123320816 6 112984266 TCCCCCAGGTTCTTACTTGTGGTCGAGTCTTCCTC[C/T]TCAGACCTGGCCACCCTCGCGGCGTCCGAGTCTGC Y 2 1 2 1 101000 f 74 goat snp16110-scaffold1698-5528 6 116501794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446572 Affx-122924832 AX-123316908 6 113090803 CTGGAATCAATCCAAGAACACAAATAGGGTAGTTG[C/T]GGAAAACTTAGTGAAACCCAGATAGTCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp31937-scaffold3576-100910 6 116407319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272333 Affx-1111833492 AX-519546066 6 113107191 CTACCAGATGCAGCGCAGGCCCTACAGGAACTACA[A/G]GAGCAACACCATCGCTCGGGTACGTCCTGAGCTGT R 2 1 2 1 102000 f 74 goat 6_113107191_AF-PAKI 6 113107191 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452511 Affx-122920971 AX-123322844 6 113162795 TCAGTCTCCTCCAAGCTCTGGGATGCCCAAGACAC[A/G]ACTATGACTCTAGTATCACCAGAGTGCTGGCTCAC R 2 1 2 1 101000 r 74 goat snp43773-scaffold588-1729470 6 116345452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448851 Affx-122923289 AX-123319187 6 113193210 CGAGGCCTTGGTGATCTGCAGGAACCTCTGACATC[A/G]ATGTAGGCGGAATCATGGGTGGCCTCTGAATCACA R 2 1 2 1 101000 r 74 goat snp43772-scaffold588-1699055 6 116373942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764769 Affx-986697020 AX-385252382 6 113263394 GGCAGAAAGGCCAGGTAACGCTACCCTCAGGGCGT[C/G]CTCACCAGGCAGATGAGAGTGGATGCCCTGGGGAT S 4 1 2 1 600010 r 74 goat 6_113263394 6 113263394 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 38441014 Affx-122928951 AX-123311351 6 113300715 TAATTCTCCCTTCTGTCAGCTACTTCCTGGAGGGG[A/G]TAGAAGCCTTATGGTGTGAAAGTGGGGCTAATTTT R 2 1 2 1 102000 f 74 goat snp12813-scaffold1495-99146 6 116117057 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405548 Affx-122955967 AX-123275900 6 113345217 GTTAGTCCAGCTGTCACTTACTTAGCACGAGCTTA[A/G]TTTGGGGGGACTCGGTGGGGGATCGGACTCGTAAC R 2 1 2 1 101000 f 74 goat snp12814-scaffold1495-143648 6 116072762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789730 Affx-122932659 AX-385276738 6 113377581 CAAGTGTTTCTCCAGTCCCATAGACTTCAGGAAGC[G/T]GATATCAGCCTTTCAACTATCACTTGAAAAATATC K 2 1 2 1 101000 f 74 goat snp12815-scaffold1495-176012 6 116039961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438798 Affx-122930804 AX-123309135 6 113409526 TTCTCCTGGGGGACTCACAGGCCCCTTCCCTACCC[A/G]CTGCAAGGGGCACCTGCAGAATGCCCAGGCTGGTC R 2 1 2 1 303000 r 74 goat snp12816-scaffold1495-207957 6 116007013 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397059 Affx-122962733 AX-123267414 6 113459182 CAGGGACTTTCCACTCTAAGCGCAATCAACATAAA[C/T]GTGGTTTTGATCTGGCTTTCACTCGGCAGCAGCAT Y 2 1 2 1 101000 f 74 goat snp12817-scaffold1495-257613 6 115958780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408894 Affx-122953974 AX-123279245 6 113498207 GTGGTCTTCATGGAAGTCCATGCAAAACCTAGGAA[C/T]GTTCCAGGCAGAGTGCTTCAGGTCCAGGATGGGGG Y 2 1 2 1 101000 f 74 goat snp11461-scaffold14176-10263 6 115929420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391454 Affx-122966737 AX-123261811 6 113563723 AGGCTCCCCAGCACGCTGCAAGGGGGCAGCACACA[G/T]TAGGACCTCACCACACCGCTCTTGGACAGAAGGTT K 2 1 2 1 101000 r 74 goat snp27406-scaffold2914-70136 6 115867377 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448193 Affx-122924242 AX-123318529 6 113605312 GCTGTAGTCCTGGACGTCCCCCTTTAGCAGCTCCA[A/G]CTCCTCCTTCTCCTTTGTCAGGGACTTCTTCTGCT R 2 1 2 1 101000 r 74 goat snp27405-scaffold2914-28547 6 115831560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278605 Affx-1111836423 AX-519552084 6 113615673 TAAACTGTTTTGGAATGCACTGCACTGGTTCATTC[A/G]TTGAAAATGAAAGGTTTCTAGGTCTCACTGGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-745 6 113615673 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432792 Affx-122935416 AX-123303133 6 113637732 TGCTTCAGACAGAAGAGACGTTAGGGCCGTGTGAC[C/T]GCTGTTCTTAGGCCGGAGGGCTGCCTGACTGTACA Y 2 1 2 1 101000 f 74 goat snp29346-scaffold3166-62970 6 117131301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432871 Affx-122935351 AX-123303212 6 113672597 CGCTTTGCGATGCTCCGTAGCCCTGCACCAGGCGG[C/T]GTGAGCCAGCGCGTGCCCCTGAGCCAGTGCTGCGG Y 2 1 2 1 101000 f 74 goat snp29345-scaffold3166-28105 6 117121073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783692 Affx-122930408 AX-385270750 6 113735935 CACCAAAATGTGAAAGTATGTTTTATAAGGTTGAC[A/G]CCTCCTCATCTTTGGCTAAAAACACACCTTAACTT R 2 1 2 1 101000 r 74 goat snp38583-scaffold4894-81000 6 117210693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380638 Affx-122975229 AX-123250996 6 113807848 CAAAAAGGAGGTGCACTTTCCAATCACGCTGAGAT[C/T]AACTTTCCAAATCCTTAGAGGAAAAAACGATAATC Y 2 1 2 1 101000 f 74 goat snp38582-scaffold4894-9087 6 117144237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412250 Affx-122950902 AX-123282599 6 113836628 TCCATGGGCTGAAACCCTGATGGCTCACGCCCCCA[A/G]TCCAGCGCTCCTCTGCCCTGGGGATGCTGCCCTGT R 2 1 2 1 103000 r 74 goat snp56632-scaffold8959-19594 NW_017189684.1 10786 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430769 Affx-122937487 AX-123301110 6 113873325 AGGTGTGCATAAGGGGGCTGGTTTCCTGGGGGTCA[A/G]AAGGCATGGAGTAGGGGGACCGACTCCCTGGAGGT R 2 1 2 1 102000 f 74 goat snp56633-scaffold8959-56291 6 117234337 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380057 Affx-122975567 AX-123250415 6 113883161 CTCGGGGTCGGGCCTTGTTGCTCTGCAGATGGGGC[A/G]CTGACCTCTGCTGTGGCCAGGTGGTCCAGAGCCCC R 2 1 2 1 103000 f 74 goat snp1272-scaffold1033-245117 6 117255452 G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386285 Affx-122970935 AX-123256643 6 113928208 CGGTCCAGCATGGGCTCCTCGTTCGCCAGCACCGT[A/G]CGCTGGACTGCGGGGTTGAGACGCCACCGTTAGCC R 2 1 2 1 101000 f 74 goat snp1271-scaffold1033-200070 6 117277230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439432 Affx-122930193 AX-123309769 6 114047623 TTTGTGTCTTTATATTTCAGGTGCGTTTCTTACAG[G/T]TGTGATAAAGTTGGGTCTTGATTTTCTACCAAATC K 2 1 2 1 101000 r 74 goat snp1269-scaffold1033-80655 6 117376330 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413147 Affx-122950357 AX-123283496 6 114114152 TGTTGCCTGCTCCCAGTTAGTGTGATAGTAGGTAG[C/T]GGTTAGGGCAGTGGAGGCCCAGAGCCCATGAACGT Y 2 1 2 1 101000 f 74 goat snp1268-scaffold1033-14126 6 117434575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430743 Affx-122937504 AX-123301084 6 114174001 TATGAGAGGTCAGACGCCCCCTCCCACCATATAGA[C/T]AAAAAATGAGAACAGTTACATATCCATCTCAGAAC Y 2 1 2 1 103000 r 74 goat snp8925-scaffold1321-38657 6 117491214 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377146 Affx-122978225 AX-123247505 6 114221133 TTCGTCTGAATGGATTCACGCAGTGCCTGTCCCTC[A/G]CCTGCCTCCCTCTGCCTGTCCCACCTCTGTCTGGG R 2 1 2 1 101000 f 74 goat snp8926-scaffold1321-85789 6 117528233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392913 Affx-122965718 AX-123263270 6 114263833 TCAGCTCCATTCCTGATAAAACTTTCTTCTAAAAC[A/G]TGTCAGATTGTGCTGTCCTTCCCAGGAACTTTCAA R 2 1 2 1 101000 r 74 goat snp8927-scaffold1321-128489 6 117571285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454294 Affx-122919266 AX-123324627 6 114319123 GCTCAGCTGTGAGCGCACAAGGCTGTGCTGAGACA[C/T]GTGAGCCTCCCAGCAAGTCCCCGAAGATGAGAGTG Y 2 1 2 1 201000 r 74 goat snp8928-scaffold1321-183779 6 117627235 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272334 Affx-1111833493 AX-431558663 6 115650573 AGGATTAACTGGTTTGATCTCCTTGCTGTCCAAGG[A/G]ACTCTCAAGGATCTTCTCCAACATAATTCGAAAGC R 2 1 2 1 303000 f 74 goat 6_115650573_AF-PAKI 6 115650573 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275168 Affx-1111834634 AX-519548747 6 116266182 TGGGGACCTCGGGTTCTGCTTCCCTGGCAGCCAGA[A/G]TTCGGGCCATTCCTGCCACGGGCACCGTGCCCTTC R 2 1 2 1 102000 r 74 goat GoatD01.044110 6 116266182 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278607 Affx-1111836424 AX-519552086 6 117535649 AAAAAAAGATCATTTTAAGCCTAAAGCAAGCAGAA[A/G]GAAATGACTAATAAGTAACAAATATTAAAAACCAC R 2 1 2 1 101000 r 74 goat Random2.2K-749 6 117535649 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790186 Affx-122922739 AX-385277190 7 19596 TTGAATACAATCAGAAAATTCAAGGATGATGCTCA[A/G]AACAAAGATGGTACTCAGAACATGATTTAGACACT R 2 1 2 1 101000 r 74 goat snp2565-scaffold1075-600374 7 108322088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273301 Affx-1111833531 AX-519546945 7 20666 CGAAAAAAAGAAATAAAATAATGAAAGGACCTACC[A/G]TTCAATCTGTTGCTTTCCAGATATAAAGAGAAAAC R 2 1 2 1 201000 r 74 goat 7_20666_AF-PAKI 7 20666 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375514 Affx-122979121 AX-123245873 7 64914 ATCGAGGATGAAAAAATTGCAGATGGCCACTTAAG[A/G]AAGAAACAAAACTTAAATTGGTCACAGTCATCAGA R 2 1 2 1 201000 f 74 goat snp2564-scaffold1075-555056 7 108274700 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413845 Affx-122949873 AX-123284194 7 164091 TCCTGTCTGTGTGGCCATGGTCCCAAGGACCTTGA[C/T]GGTCCCCTCTCAGGGGGCAGTCCCCAGACAGCTCT Y 2 1 2 1 303000 r 74 goat snp2562-scaffold1075-455879 7 108175941 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423131 Affx-122942901 AX-123293477 7 205057 CCCACTCATCCCCTCTGACCACTTCTCACTTTTTG[C/T]ACAACTGGAGCTCTTACTGCCTTTCCTGCCCCAGG Y 2 1 2 1 102000 r 74 goat snp2561-scaffold1075-414913 7 108134786 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417722 Affx-122947439 AX-123288070 7 235391 GCCAACAAAAGTGCACATAACGTATCCTCATGCAC[A/G]TATCACACAGACAAGCACTTTTGTCAACGTCAGTA R 2 1 2 1 101000 r 74 goat snp2560-scaffold1075-384579 7 108104319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422458 Affx-122943339 AX-123292804 7 265919 ATGTGTAAAACATTTTTCCAGGTGCTGTACTAGGC[A/G]TATGTAAGATATATAGATGGGGGAAAAAAAAGGTC R 2 1 2 1 101000 f 74 goat snp2559-scaffold1075-354051 7 108072676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422586 Affx-122943744 AX-123292932 7 311743 GAACCTTAACTCTGTGAAGACTCCCTGGTCTTCCC[G/T]AGCACTCTCCTCAGGGCTTCTGGTCCTATCAGCAA K 2 1 2 1 202000 r 74 goat snp2558-scaffold1075-308227 7 108026576 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429996 Affx-122938041 AX-123300337 7 342984 TCCGTGACCCAGTCTGCACTGCAAGGAGGAGCCTT[A/G]CAGAAGGCAAGAAACCTGGGTCACATCCTACCCTG R 2 1 2 1 102000 r 74 goat snp2557-scaffold1075-276986 7 107995112 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415469 Affx-122949160 AX-123285818 7 395229 TGGTGACAATTCAGTAAGCCTTGCATAAAAGGCAC[A/G]TGCTTCAGGCTTGCCCTCCAGCCAAGCTAGAGTCT R 2 1 2 1 101000 f 74 goat snp2556-scaffold1075-224741 7 107942625 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785712 Affx-122939643 AX-385272753 7 451339 CCTCTTTGTGCCTCATGGTGAATGGCTATCTTGTA[C/T]GGTTTCTGTGAGACAAAGCATTTTAAGTGCCTAGA Y 2 1 2 1 101000 r 74 goat snp2555-scaffold1075-168631 7 107886639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394026 Affx-122965005 AX-123264381 7 503066 AGCTGGACTTAGAACTCGATTCTCCTGAATCACAG[C/T]GTTCCTATGCCTTATATCATATATCTACTTTATCA Y 2 1 2 1 101000 f 74 goat snp2554-scaffold1075-116904 7 107834923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441163 Affx-122929559 AX-123311500 7 535861 ATATTTAAATTTACATCAGTCAAAACTATGTTTCA[C/T]TACTGCTAAGGGCTTTCTTTCTGAAAATTCGGAAT Y 2 1 2 1 101000 r 74 goat snp2553-scaffold1075-84109 7 107802996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278611 Affx-1111836426 AX-519552090 7 550696 TCAGATTAGAGGAAGATGTAGCTTTAATATGCTTT[C/G]ACCTCAGTAGAGCATTTTAGAAATTTCCCCTGCTC S 4 1 2 1 101000 r 74 goat Random2.2K-750 7 550696 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779719 Affx-122920627 AX-385266819 7 565145 CCCTTGTGCTCAGCCTGAGGATGGAGTAGGGAACT[A/G]CTCTAGCATGCGCCAAAGGCTATTTGTAGAAGACC R 2 1 2 1 202000 f 74 goat snp2552-scaffold1075-54825 7 107773803 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403058 Affx-122958527 AX-123273411 7 595952 TCGTTGTTGTCTTTTCTGGGAAGAATGAAGTCATC[C/T]GTGTTATAATAAAACAAAGAAACATACTGTTTTTC Y 2 1 2 1 101000 f 74 goat snp2551-scaffold1075-24018 7 107742699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392999 Affx-122965656 AX-123263356 7 622912 TCTGTTGTATCTGACAAGTGATCAGATGGAAATGC[G/T]AACCTATTTAAGGGGACAGATATTAACAGTGCTTG K 2 1 2 1 201000 f 74 goat snp4723-scaffold1154-240097 7 107678357 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427050 Affx-122939817 AX-123297395 7 657975 TAGAAGGCGCTCAGATTTGGTCTCCTGACTGAAGG[C/T]GCTCACCTGTGAGAAGGAAGAAGGAGTGAGGACTT Y 2 1 2 1 101000 f 74 goat snp4722-scaffold1154-205034 7 107643836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770605 Affx-122953044 AX-385257769 7 694651 GTATCCTGAATGAAGAATGATCCCATAAATGTAAA[A/G]TGGATGCATAACTCCCTCACACACGTTTTTTCAGT R 2 1 2 1 101000 r 74 goat snp4721-scaffold1154-168358 7 107606457 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381489 Affx-122974878 AX-123251847 7 735144 GAGAGCCCCAATTCCTTATGAAAAGGAGAAAAACA[C/T]TGTCATTTATAACACAAAAGTTGGTACTTGCTGGC Y 2 1 2 1 201000 r 74 goat snp4720-scaffold1154-127865 7 107565751 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405517 Affx-122955993 AX-123275869 7 771646 CACAAGCCCCTTCGCCATGACAAGGCTGTGATCCA[C/T]GAAGGGGCCCATTTGTCTAGAGTTTACTGTTTATT Y 2 1 2 1 303000 r 74 goat snp4719-scaffold1154-91363 7 107528186 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453159 Affx-122920478 AX-123323492 7 815192 ACTCTCTGCTAGAACTTGAAATAATGTGAAAAGGG[C/T]GAAAGCACAGTAATAAAACAGTAACACTGGCATTG Y 2 1 2 1 201000 f 74 goat snp4718-scaffold1154-47817 7 107484364 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778096 Affx-122920736 AX-173924733 7 845105 AGACCTCTTAAGAGAGTCCCAAGTAAGAGATGGGA[C/T]GCTTGATCTCTGATTGCTGAGTCTCAGCGCTCAGA Y 2 1 2 1 102000 r 74 goat snp4717-scaffold1154-17904 7 107453803 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774106 Affx-122926930 AX-385261244 7 877998 TGTATGTGCTATTATCAATCTAGATTTGTGAAAAC[A/G]CTAGAAGAGTCCATATGAAAATCCACCTGTCTGGC R 2 1 2 1 101000 r 74 goat snp19383-scaffold196-14890 7 107420885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782474 Affx-122972874 AX-385269551 7 981965 CTAAAAGCCTCTTCTTGTTCCACAGTCCAAAGTAA[C/T]GGTTCTGTATCTGGGCATTTAGTGGCTTCATATAG Y 2 1 2 1 101000 r 74 goat snp19386-scaffold196-118857 NW_017192263.1 16212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800891 Affx-122935708 AX-385287806 7 1041681 ATACGGGAGTCATGAGGACACTTGGCATCCCCAGG[C/T]GTCACTGTCAGTCAGACCTCGTATCCAAGTGACCT Y 2 1 2 1 102000 f 74 goat snp19387-scaffold196-178573 7 107267597 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400438 Affx-122959964 AX-123270793 7 1117133 ATAACGAGAAATCAAAGATTGAATTACGAAGTATA[C/T]GAACAGAAACAGGTATGCCAGCAGGAAAAGCTAGT Y 2 1 2 1 201000 f 74 goat snp19388-scaffold196-254025 7 107193425 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403660 Affx-122957515 AX-123274012 7 1148060 GCATAGGGCAAGTTATGGGTGTATATGTTTGTGAA[C/T]GTGTACAGCTTCTATACCCACTGCAGGCATGCCAA Y 2 1 2 1 201000 r 74 goat snp19389-scaffold196-284952 7 107162748 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800438 Affx-122956638 AX-385287359 7 1200430 TAGACTTAAAAGTTGAGAAGCTTAGGTATTTAAAT[A/G]GGTTGTGAGTATATGCAGATGTTTTCTTCCTGGAG R 2 1 2 1 101000 r 74 goat snp19390-scaffold196-337322 7 107110289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278444 Affx-1111836427 AX-519551929 7 1217432 TAACATAGTACTGAAATCCCTAGTGATAGCAAGTA[A/G]TAGAAATAATTTAATAGTTTTGCAAATGATGTGAT R 2 1 2 1 101000 f 74 goat Random2.2K-751 7 1217432 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380536 Affx-122975675 AX-123250894 7 1249622 CTCTTTGCCGCCGTCTAGATCCTGCACGTCTTTAA[C/T]GTAGAGAGAAAAATCGATCACTCCAACCTGATTGA Y 2 1 2 1 101000 r 74 goat snp19391-scaffold196-386514 7 107060768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407078 Affx-122954907 AX-123277429 7 1305632 TTCTTCTCAGTCTGTTGGCTAGAACTAGTCACATG[C/T]GGTCTTCTGGTTGCTGGGAAGGAGTGGGAGGAGAT Y 2 1 2 1 101000 f 74 goat snp19392-scaffold196-442524 7 107003510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384314 Affx-122972275 AX-123254672 7 1350291 ATTAATTATAAACTGTGAAACTATACAGCTCTCAC[A/C]ACATAACATCTAGAAAAATCTCAAAGGCCTAGTTC M 2 1 2 1 101000 f 74 goat snp19393-scaffold196-487183 7 106958687 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379955 Affx-122975640 AX-123250313 7 1388185 GTAGATTTGCCCTGAGCTGCTAGCCTTGGCTTCAC[A/G]GTCCTCTTTCTTCCTATTTCCCTTTCATCTGGGGC R 2 1 2 1 101000 f 74 goat snp19394-scaffold196-525077 7 106921229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395710 Affx-122963720 AX-123266065 7 1416912 TTTTCAAGGTAGCTTTCTTTCTTGTCCCTCTTTAC[A/G]TCCCTATCCTTGTTTTTCTTTCTTTTTTGTCTCCC R 2 1 2 1 101000 f 74 goat snp19395-scaffold196-553804 7 106892402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425392 Affx-122941556 AX-123295738 7 1462967 TGTCTGATATGAGTATTGATATCCTTACTTTCTTG[A/C]TATTTCTATTTGCATTTTCCATCCATTCACTTTAA M 2 1 2 1 201000 f 74 goat snp19396-scaffold196-599859 7 106846903 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432438 Affx-122935815 AX-123302779 7 1498319 TCACAGGGTTAAACACTCCACCCTGGGTGCACCCC[A/G]CTGCCATACTGCTTCTGAGCGCATGTCACATGGAG R 2 1 2 1 101000 r 74 goat snp19397-scaffold196-635211 7 106811270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403826 Affx-122957953 AX-123274178 7 1537347 TTACTAACTCACCCTTCCTCCTGACTTTGGGGTGC[A/G]TATTTCGTATCTCTGAAGTTCATGAAGGTGATCTG R 2 1 2 1 101000 r 74 goat snp19398-scaffold196-674239 7 106772037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443439 Affx-122927358 AX-123313776 7 1574920 GACTCTGTGGGGACAAAGTAACATGACGGCCGTTG[C/T]GCCCCCTTTTTGGGAGCGCAGGGGGATGAGGGGCC Y 2 1 2 1 101000 f 74 goat snp19399-scaffold196-711812 7 106734513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376624 Affx-122979037 AX-123246983 7 1614195 AGCTACTTACATTCTTGGCAAACTCACCAGTAGGA[C/T]GAACAGGGCCTGTCCTTGTCCTGGGACCTTGGACT Y 2 1 2 1 101000 f 74 goat snp19400-scaffold196-751087 7 106695496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413889 Affx-122949842 AX-123284238 7 1655014 CCCTGTGAGGCTGTGTCACAGATTGAATTTACAGC[A/G]TTCAGCACTTGCTCTGATTTCTCATTTCTGCCCTT R 2 1 2 1 101000 r 74 goat snp19401-scaffold196-791906 7 106654198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449516 Affx-122922612 AX-123319851 7 1687626 CCTGGCGCAGGTCTGGGAAGGCCAGAGCTGACCAG[C/T]GAGGTGCAGCCATCGTTTCTTCATCTATGATGCCT Y 2 1 2 1 101000 r 74 goat snp19402-scaffold196-824518 7 106624333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451660 Affx-122921594 AX-123321993 7 1723537 CAGCAGCCGGGGGCTGCCCACCCATTATGCCATCG[A/G]AGCACTTGGGCAGGAGGGTCTTCTCACCCAGTTCT R 2 1 2 1 101000 r 74 goat snp19403-scaffold196-860429 7 106583314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411668 Affx-122951556 AX-123282018 7 1814701 CAAAGAGCAGCAGGAAGGGCATCAAAACAGACAGG[C/T]ACACTTTTAATTCTACAGAGATTTGTCCTTTCCCA Y 2 1 2 1 101000 r 74 goat snp19405-scaffold196-951593 7 106494659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447045 Affx-122924526 AX-123317381 7 1848980 AGAAGTTATGAGAAGTGTCTGGAAATACTAAAATT[C/T]AAAATATGGAAAAGATGAGAATGTTAACATTGGAA Y 2 1 2 1 101000 f 74 goat snp19406-scaffold196-985872 7 106460237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445098 Affx-122926199 AX-123315435 7 1885917 AGATGGTTTCTCTTGTTGGATTTTATGTCTCACTG[A/C]TTTTCACCCTCCATATCCTTCAGTGCTTCTTTGTT M 2 1 2 1 202000 r 74 goat snp19407-scaffold196-1022809 7 106422527 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391225 Affx-122967399 AX-123261582 7 1966454 ACAAGCTGTCAGTGGTAGGAAAGATGGTAACAGGT[A/C]GGTTTTGAGTTACAAGAAGTCCTTACCCAGTGAAA M 2 1 2 1 101000 f 74 goat snp19409-scaffold196-1103346 7 106343223 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395329 Affx-122922435 AX-123265684 7 2043010 CTGCTGCCCCAGGAAAAATTCCTGGGTCAGTGAGG[A/G]GCAGACAAGGCAGATAGAGGGTGATGCTAAGACAG R 2 1 2 1 101000 r 74 goat snp19411-scaffold196-1179902 7 106265859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428281 Affx-122939394 AX-123298624 7 2079958 GTCCTACAGGGATTGTCATGGAAGCCTCATTACAC[A/G]GGCACGGTTGATTGAATCATTGGATGTCAGTGATT R 2 1 2 1 101000 f 74 goat snp19412-scaffold196-1216850 7 106228892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400933 Affx-122959716 AX-123271286 7 2111676 TCCTATGGCTAAGTGAATACAACTTATTACTTTCA[C/T]GTCTTCATGATAATGTTGCTAATTTTCTCCTGCAA Y 2 1 2 1 101000 f 74 goat snp19413-scaffold196-1248568 7 106197624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768644 Affx-122956867 AX-385255823 7 2148716 AAAGCAGAAATGATACAGGCCATATTTTCTGGTCA[C/T]TGTAAAATGACATTGCTGACTGTTGGTGAAAGGAT Y 2 1 2 1 101000 f 74 goat snp58165-scaffold941-229990 7 106160944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427331 Affx-122940125 AX-123297674 7 2199528 TCACAGGTGCCCAGAAACTGCTCCCCAGAGAGCAT[A/G]TGCCCCTAAGGGGTGAAGTGTGTGTGTGAAAATGC R 2 1 2 1 303000 f 74 goat snp58164-scaffold941-179178 7 106110283 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447133 Affx-122924458 AX-123317469 7 2296987 GAGGTATGCAAAATATTTGAAAAATTGTTATTCCA[C/T]GCTTATGGAGATGGTCCTAGAGAGAGAAGAATGAG Y 2 1 2 1 101000 r 74 goat snp58162-scaffold941-81719 7 106015314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376459 Affx-122978051 AX-123246818 7 2359777 CTGAGATCCTCTCTGTATTTACTTAAGTTTGATGG[A/C]GTATACACAGTTATTACAATTGGTGATATAAGCTG M 2 1 2 1 101000 f 74 goat snp58161-scaffold941-18929 7 105956464 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274800 Affx-1111834427 AX-515961991 7 2396254 AGAGG[A/G]GTGAGCTAGAAGGCCATCTGGAGGCCTCAAGGTCA R 2 1 2 1 102000 r 74 goat GoatD01.035377 7 2396254 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423497 Affx-122942563 AX-123293843 7 2415670 TGCTAAGCCTTGGCTCTGGCCATTGAAGATCCAAC[A/G]GTGACCACATGGAGGCCCTGGAGTAGCTTCGTGGT R 2 1 2 1 101000 f 74 goat snp24183-scaffold2463-10708 7 105903754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777973 Affx-122971929 AX-385265089 7 2431310 CAAAAATGTGCCAGGAACAAAACCTCACTTCAAAG[C/T]GCAGGACCATCGATTGCACTGACAATGGGAAGGTT Y 2 1 2 1 101000 f 74 goat snp12675-scaffold1488-4833 7 105871510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380563 Affx-122975280 AX-123250921 7 2497711 TTCTAGCCCTAAGGGAAGGTAGAGGGAGTGTGAGC[A/G]GGAAAGGGGTCCAGGACATACAAACCATGGAGCAG R 2 1 2 1 201000 r 74 goat snp12676-scaffold1488-71234 7 105828175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448876 Affx-122923268 AX-123319211 7 2530584 AAACCCTAGTGGCTTAAAATAACAGTCCTCATATA[C/T]GCAATCTCCTTGGGGGTTAGGACCTAGGAGCATCT Y 2 1 2 1 101000 f 74 goat snp12677-scaffold1488-104107 7 105795691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429568 Affx-122937813 AX-123299910 7 2561660 GGGTGTCTCTGACACTCCCTTCCCTTGGAGGGACA[C/T]GGAAAGGGCTAATATGGAGGGTGTCACCTACCCCC Y 2 1 2 1 101000 r 74 goat snp12678-scaffold1488-135183 7 105764673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418753 Affx-122946207 AX-123289101 7 2593169 ACTGCAGTAGTTAATCCTGTCCCCGTGAAACTGTG[C/T]AACTGTTTTTCAGAAAAGGGGAAGCAGGAGGAATC Y 2 1 2 1 202000 r 74 goat snp12679-scaffold1488-166692 7 105733773 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436755 Affx-122932285 AX-123307093 7 2625416 CTTGATCCCAAAACCACTTGAGGCATGGGGCAACT[A/C]TCCTCAGGATGTGAGTCAGAACTGAGGCCCAGAGG M 2 1 2 1 101000 f 74 goat snp12680-scaffold1488-198939 7 105701840 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378476 Affx-122976670 AX-123248835 7 2723209 GCTTACGTGATGCCTTTTCCATCCATACGGGTCCT[C/T]TCTGCTATGAGTTCTCTCGGAGTCAGATATTCCAT Y 2 1 2 1 101000 r 74 goat snp12682-scaffold1488-296732 7 105608819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273265 Affx-1111833534 AX-519546915 7 2734229 AGGATAGACTGACGTGGAATCTGTTACGATGTATT[A/G]CAGCTGATGGTGTTAAGAATAAATGTGGATCAAAA R 2 1 2 1 101000 f 74 goat 7_2734229_AF-PAKI 7 2734229 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453288 Affx-122920378 AX-123323621 7 2766487 TGAGGGCACATCCTTCTACTCCACCATCTTGCTGG[G/T]AGTATGGAGCTCCCTAAAACCATTTTTAACATTGG K 2 1 2 1 201000 r 74 goat snp12683-scaffold1488-340010 7 105564223 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405813 Affx-122955892 AX-123276165 7 2818236 TAAAACAGCTTTCCCTCCGATATTCTTTCCTTCCT[A/C]GTCAGATCTAGACACACTGTTTCTTTTTGAAAATT M 2 1 2 1 201000 r 74 goat snp12684-scaffold1488-391759 7 105509430 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417350 Affx-122947724 AX-123287698 7 2885782 TCAACCATTGCTGTGTCTGCCCTCAATGACAAGCA[C/T]ATGAATTAGCTAATGTAAGTCAGAGAAACCAGGCT Y 2 1 2 1 101000 f 74 goat snp12685-scaffold1488-459305 7 105437902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414737 Affx-122949726 AX-123285086 7 2925761 GAAGGCAACGGGGTCTGCGCTGAGCAGGCCACGCC[A/G]GAGAGGCAGGCTCAGGACTGAACGCGATTCTGGAG R 2 1 2 1 101000 r 74 goat snp12686-scaffold1488-499284 7 105398029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403502 Affx-122957636 AX-123273855 7 2988452 ACACTGAGATTATGCACAAATCCCCCAAAGAACTA[C/T]TGAGTCTGGCACTGCAGCATCCAAGGAACCATGCT Y 2 1 2 1 101000 f 74 goat snp12687-scaffold1488-561975 7 105335477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784220 Affx-122940526 AX-385271271 7 3067764 AATTTTTTTCCCTTAAATGCATATTATGGGATACT[A/G]TGGTAAGTGGTATAATAAGGGGAATAGATTGTTTG R 2 1 2 1 201000 f 74 goat snp12688-scaffold1488-641287 7 105254447 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414994 Affx-122949045 AX-123285343 7 3100768 GTAATGTGTTAATCAAAATCTGTATTTCAGAACAC[A/G]CTCTCATAGTCTGTCTCTCCATGGCCTGCATTAAT R 2 1 2 1 201000 f 74 goat snp12689-scaffold1488-674291 7 105220342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776507 Affx-122931815 AX-385263634 7 3136353 AAATCAATGGAGAACTACAAAGAACCCATCCAGGC[A/G]ATACTACTAATGACCTACTAATGACTCTTCGGGAA R 2 1 2 1 101000 f 74 goat snp12690-scaffold1488-709876 7 105182048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438004 Affx-122931578 AX-123308342 7 3170397 AAATGAATGCTCCCCTTCTGTCAAGGATGTGCAAA[C/T]ACATTACATGTATCTCATTTAATCCTAACACCTTT Y 2 1 2 1 103000 f 74 goat snp12691-scaffold1488-743920 7 105147871 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450589 Affx-122922025 AX-123320923 7 3200842 CAGAGGGAAAGGCCCCAGCACTGCCTTACGACCAA[C/T]GTCATCCAGAAAAGTTTTCAGTCCAAAAGTGAAGT Y 2 1 2 1 101000 r 74 goat snp12692-scaffold1488-774365 7 105116655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410621 Affx-122952096 AX-123280971 7 3237770 GGCCCCAGCGTCCCGGGAGATGAGGGCTGTTCCCC[C/T]GTTCCACCCCATCTTAGGGGAAAGTTGAGACTGGC Y 2 1 2 1 101000 r 74 goat snp12693-scaffold1488-811293 7 105079660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791676 Affx-122921557 AX-385278667 7 3272099 TTGGCATGCACCGTCTTAGTTGAAATTCAGCCCTC[A/G]TCAGCTGGAGACTTCCTGTGTAAGGGATAACCAGT R 2 1 2 1 101000 r 74 goat snp12694-scaffold1488-845622 7 105044835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429540 Affx-122937832 AX-123299882 7 3334072 TTAATCAGGCGGTTGAGTCATGTAGTGGAATAGTA[G/T]ACAACCATTAAAAAGCTGAAGACGTTTTTCTCCAC K 2 1 2 1 101000 f 74 goat snp12696-scaffold1488-907595 7 104981541 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426132 Affx-122940619 AX-123296478 7 3386489 CAGCCTGCAAAAGCTTTGCTGAGAAGCAACGCTGG[A/G]GCACTTTAGAAAGCTGCAGGCTCGGCATCCTCGAC R 2 1 2 1 102000 r 74 goat snp12697-scaffold1488-960012 7 104929356 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431801 Affx-122936119 AX-123302142 7 3420304 AAAAATGGATCCCAATGGCCAGCCCCCACCAGATA[C/T]AGCAGAGAACAAGGACGAACCTTAGGAAGCAACTG Y 2 1 2 1 201000 r 74 goat snp12698-scaffold1488-993827 7 104895355 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394265 Affx-122964721 AX-123264620 7 3533097 CACGTTAAAAAAAAGTCTTAAAAAAAATAAAGCAT[A/G]CCCTTTGTAAAATTGAAAGAGAGAGAAAGTAATGA R 2 1 2 1 101000 f 74 goat snp12700-scaffold1488-1106620 7 104783934 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275023 Affx-1111834640 AX-519548605 7 3581936 AGAAGGGAGGTCAAACGAAAATGCCTGCAGGTTGA[A/G]AGTACCAAAGAACAGCCAGCCAGTTTCCCTCCCAG R 2 1 2 1 201000 f 74 goat GoatD01.044192 7 3581936 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786738 Affx-122932506 AX-385273769 7 3603410 TAAGCTCACTTGACCAAAAAAATAGCTCAATATGA[C/T]AGGACCTAAAAACTAAAGGGCTGGAATTTGCAGGC Y 2 1 2 1 101000 r 74 goat snp12701-scaffold1488-1176933 7 104712755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413689 Affx-122950095 AX-123284038 7 3638010 TGGTGAATATTTCCTGGAGTGCTGTTGGAAACAAC[G/T]TTTTTATTAGACATGCATCAATGTGGCGGCAACAT K 2 1 2 1 102000 f 74 goat snp12702-scaffold1488-1211533 7 104679094 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450912 Affx-122922190 AX-123321246 7 3678926 TCACCATCTGCCTTTAGGTGGCGCCCAACAGTGCC[C/T]TCTGGATTCCGAAGTCCCCATGTCAAGTTTCAAAA Y 2 1 2 1 101000 r 74 goat snp12703-scaffold1488-1252449 7 104648946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441340 Affx-122929424 AX-123311677 7 3715480 CCATGGGACACAAAGGCAAATCAAAGCACTCCCAG[C/T]GGCCAGAGCAGGAACACCCCGAGCAACACGAGCAG Y 2 1 2 1 101000 f 74 goat snp12704-scaffold1488-1289003 7 104612861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401087 Affx-122959627 AX-123271440 7 3766955 TCACACCTCAGCCTAGTTAATTAAGTCAGGATGCC[C/T]CAGGACTGCAGTGTGCAGCAGAATCTAGGTGCTGC Y 2 1 2 1 101000 f 74 goat snp12705-scaffold1488-1340478 7 104561294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432365 Affx-122935868 AX-123302706 7 3808398 GACACATGTTGGGACTTCGCTAGTGGTGGAGCAGA[G/T]AAGAACCCACTTGCCAGTGCAGGGAACATGGGTTT K 2 1 2 1 101000 f 74 goat snp12706-scaffold1488-1381921 7 104520257 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399464 Affx-122961200 AX-123269819 7 3853454 TCCATAAAGTTGCAAAGAGTCGGACAGGACTAAAG[C/T]GAGTTAGCACAGAAGGGCTAATAGAAGGCGATTTT Y 2 1 2 1 101000 r 74 goat snp12707-scaffold1488-1426977 7 104475448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407490 Affx-122954756 AX-123277841 7 3891867 TGGATTATAAGAAACTTCTTCTGGCTCCCAGGAGA[C/T]GAATCCTGGGTAAGAAGGGGAGCCGGGCCCAGAGG Y 2 1 2 1 101000 f 74 goat snp12708-scaffold1488-1465390 7 104437319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453127 Affx-122920010 AX-123323460 7 3968014 TAAAATTTATTTCAGACCATGCCAAAGTCCTGACA[A/G]GCCTCCACCACAGCTCAGGCTGGATTCCAGGTAGA R 2 1 2 1 101000 f 74 goat snp12710-scaffold1488-1541537 7 104360761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603189 Affx-1002479442 AX-413837375 7 4002714 GGCCTGAGAAAATCTGTATTGGCATTTATGTTAGT[C/T]ATTTTGCAGGTGAAAGGTATTCTGATTTACATTTC Y 2 1 2 1 101000 f 74 goat 7_4002714_RH-map 7 4002714 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38389983 Affx-122968060 AX-123260340 7 4007720 TTGAGTCTCTGAGGGGAGGCTGGCCTAGAGACCCC[A/G]AACTTAGGCAGTGGTGATGGGGACTGCCATTGACT R 2 1 2 1 102000 r 74 goat snp12711-scaffold1488-1581243 7 104321849 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415269 Affx-122948842 AX-123285618 7 4046979 TAGCCAGGCGGGGGGTTAGGGGAGCACAGTGAAAA[C/T]GGAAGAGACCCCTGGAGCATACAGCCTGGGATGCG Y 2 1 2 1 103000 f 74 goat snp25492-scaffold2621-416911 7 104291183 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603276 Affx-1002479443 AX-413837456 7 4056409 AATTAAATAAGCAGGGTGACAATATACAGTCTTGA[C/T]GTATTCCTTACCAATTTGGAATCAGCCTATTGTTC Y 2 1 2 1 101000 r 74 goat 7_4056409_RH-map 7 4056409 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429794 Affx-122938203 AX-123300135 7 4085344 GTTGACTGTGCTTTTGGTGTGATAGCCAAGAAGTC[A/G]TTGCCAAATCTAACGTTATGAGACTTTTCCTCTGC R 2 1 2 1 101000 r 74 goat snp25491-scaffold2621-378546 7 104253434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395991 Affx-122963504 AX-123266346 7 4145509 CTTCACACACAAATGATTGAGTACCCACTGTGTAC[A/G]GACCCTCTGCTAGAGATAGATCAGTTGCGTCTGGT R 2 1 2 1 201000 r 74 goat snp25490-scaffold2621-318381 7 104193334 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771285 Affx-122935943 AX-385258443 7 4192615 GGTGTTAGGTAAATGCTGATAAATAAATGCTGGAG[G/T]AAAGACCTGTACCTCAGCAACTCTAAGGCTGAGGA K 2 1 2 1 101000 f 74 goat snp25489-scaffold2621-271275 7 104150954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603278 Affx-1002479444 AX-413837458 7 4222118 GACTAAGTATGAATAGAATGCTAGATTCCTAATTT[A/C]TATTCACCAAATACTTTGATAAGTTTCATTTATTC M 2 1 2 1 201000 r 74 goat 7_4222118_RH-map 7 4222118 C A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38405825 Affx-122955883 AX-123276177 7 4224218 ATATGGGTTCTCCTAGTTTCTCTCTTCCAGGACTT[C/T]TCTCAACACTGAGCACACTAATGAAGACTATGAAT Y 2 1 2 1 101000 r 74 goat snp25488-scaffold2621-239672 7 104116063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430672 Affx-122936931 AX-123301013 7 4265512 GGACCACCCTTGCAGGACCAAATGATGGGGAAATC[A/G]CAGCTCCCTTCAGGGAAGCAGTGCTGTGTCGGGCT R 2 1 2 1 101000 f 74 goat snp25487-scaffold2621-198378 7 104075829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603196 Affx-1002479445 AX-413837381 7 4321559 ATATGTGAAACATTTTATAAGCATATAGTTACATA[A/T]AAATACTGTTGTCCCTTGAACAACATGGGTTTGAA W 4 1 2 1 202000 f 74 goat 7_4321559_RH-map 7 4321559 A T 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38449106 Affx-122923585 AX-123319441 7 4361720 TGTGCAAAACCATGATTTGCGGGAAATCCAACACG[G/T]CAATGTGCCCCAGATGGTTGGAGGGCCTCTCTGAG K 2 1 2 1 101000 f 74 goat snp25485-scaffold2621-102170 7 103992457 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413273 Affx-122950214 AX-123283622 7 4395878 CTGATGCTTGGAACTACGATTAAGAAATGTCATAG[C/T]GGAACTTCCCTAGTGATACCGTGGATAAGAATCTG Y 2 1 2 1 101000 f 74 goat snp25484-scaffold2621-68012 7 103958251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410228 Affx-122952553 AX-123280578 7 4426483 CTGTACCAGAGTCACGGCCGCTCAGCCTTTGTTCA[C/T]GTGCCCCCTCTGGGCAAGCCGTACAATGCAGACCA Y 2 1 2 1 101000 f 74 goat snp25483-scaffold2621-37407 7 103929268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784709 Affx-122921214 AX-385271757 7 4455825 ACTTCATGATGTTTGACGCCTGTGTACCTCTGTGG[C/T]GCCTGAGCCCAGTTGAAATCTAGAACATTCTCAGC Y 2 1 2 1 101000 r 74 goat snp25482-scaffold2621-8065 7 103900144 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385565 Affx-122971218 AX-123255923 7 4470037 TTTTCTAGACTTCAGTGCTAACCTGGGAGGCGGAT[A/G]TGTGGCCTGGGGTTGGGGAGAGTTCAGAGGCTGTG R 2 1 2 1 101000 f 74 goat snp44962-scaffold6120-6048 7 103877735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603198 Affx-1002479446 AX-413837383 7 4488613 TCCCACATGAAATATATTTCATAGCAGTTTTTTTA[C/T]AATCAACAAAATGAAAAAGACATGTGTTAAACATA Y 2 1 2 1 101000 f 74 goat 7_4488613_RH-map 7 4488613 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38431770 Affx-122936716 AX-123302111 7 4526767 CTATCTCTTCAAGCACATTTTTTACTTTCACTTTC[A/G]TTTTTCTCTTTCTTTTCTTTTGAATATGTTTGTCT R 2 1 2 1 303000 r 74 goat snp40026-scaffold510-2843752 7 103820194 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603200 Affx-1002479447 AX-413837385 7 4539528 ATGTAACTTGATACAGCCACTGTGCAGGACAGTGT[G/T]GAGATTCCTTAAAAATCTAGGAATAAAGCTACCAG K 2 1 2 1 303000 f 74 goat 7_4539528_RH-map 7 4539528 G T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445797 Affx-122926044 AX-123316134 7 4565365 ACCCTTCCCAGATCCCCAACCCCCAGAGAAGAATT[A/C]TCCCTCTTGAACAAATGCAAACATTTTCTCAAAAT M 2 1 2 1 202000 r 74 goat snp40025-scaffold510-2805154 7 103782945 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603202 Affx-1002479448 AX-413837387 7 4591935 GTGTAACATTGTAATAGGCAGGTGATTTAATTTGT[A/G]TTATTTAAAAAATGTAATTATTAAATATTCATGAC R 2 1 2 1 101000 f 74 goat 7_4591935_RH-map 7 4591935 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429141 Affx-122937995 AX-123299483 7 4604088 GTATGTGGTTAGAATGCTTAAAATATACTTGCTTC[A/G]CAACTTTCTCATGTAGCAATACAACACTCTAACTA R 2 1 2 1 101000 r 74 goat snp40024-scaffold510-2766431 7 103743420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409196 Affx-122953178 AX-123279547 7 4643072 GCAGGGACATGGCTTGGAAGGGTTCATCCGTGATC[C/T]TGGTCCTTACTCGCCCCGAGCATAGGGTTCTAGGA Y 2 1 2 1 101000 f 74 goat snp40023-scaffold510-2727447 7 103704042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603204 Affx-1002479449 AX-413837389 7 4643574 TGTACCTTTGCCCAAATGTATGGCTACTTCACGCA[A/G]AACCCTATTTCTAACCTGAATTGTCTGGGTGTCTT R 2 1 2 1 101000 f 74 goat 7_4643574_RH-map 7 4643574 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603206 Affx-1002479450 AX-188570479 7 4664639 TGGAATGTGAAGTCAAGTGGGCCTTAGGAAGCATC[A/G]CTATGAAGAAAGCTAGTGGAGGTGATGGAATTCCA R 2 1 2 1 303000 f 74 goat 7_4664639_RH-map 7 4664639 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320801616 Affx-122927496 AX-385288524 7 4680516 TTTTCCCTAATTTCTCCTGCCACCTTGTTTCTAAC[A/G]CCCATCACCTAATTGCTAACACTCACCACCTTACT R 2 1 2 1 101000 f 74 goat snp40022-scaffold510-2690003 7 103666849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427083 Affx-122939795 AX-123297426 7 4724483 GCAGGTGGGAGGGAGGCCAGAGGCAGGAGGATCCT[A/G]CCTGTCTGTGGAGTCTGGGCGGTTGTTGCTTTTCT R 2 1 2 1 101000 r 74 goat snp40021-scaffold510-2646036 7 103623130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603291 Affx-1002479451 AX-413837471 7 4729190 GTGGGCCTCATCCAGTCCGCTGAGGCCTGAACAGA[A/G]CACAAAGGCTGATATGCCTTTGAGTGTGGGGGAAT R 2 1 2 1 202000 r 74 goat 7_4729190_RH-map 7 4729190 G A 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429957 Affx-122938073 AX-123300298 7 4761793 CACCCAAAGGTCCCTCTGTAATCAACCCATCATTT[A/G]TAAAAGAGCTCACTCGAGGGCCTTTGCTGTCTGGT R 2 1 2 1 101000 r 74 goat snp40020-scaffold510-2608726 7 103585941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436999 Affx-122933138 AX-123307337 7 4801805 TAAGAAAAGAATCTAGAGTTTTCAAGGGTCAGATT[C/T]CTAGAATTGGGGGATTTTAGGGGTAAAAACCTTTT Y 2 1 2 1 201000 f 74 goat snp40019-scaffold510-2568714 7 103546180 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418207 Affx-122947058 AX-123288555 7 4830799 GTCTTGTTTTCTTTACACACCCTGCAGAACTCAAG[A/G]GGGTGCAGCCAAGCTGTGAGTGCGCTGGGAGGGGT R 2 1 2 1 101000 f 74 goat snp40018-scaffold510-2539720 7 103517635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603210 Affx-1002479452 AX-413837394 7 4833970 AATTCTAGAAACTATAGGGAAGGAGAGCAGGCAAG[C/T]AACGATTCTCTAGTTCACTTTGCTTTCTCTTCATT Y 2 1 2 1 101000 f 74 goat 7_4833970_RH-map 7 4833970 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425411 Affx-122941542 AX-123295757 7 4880812 CCCTAGATGTGGGGTTTCATGGTGCTGTGTGGCAT[C/T]AGGAGTTTACCAGACTGGACTCCTGTGGGTCTCAG Y 2 1 2 1 101000 f 74 goat snp40017-scaffold510-2489707 7 103468743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603660 Affx-1002479453 AX-413837798 7 4917489 CAGAGCTGCCAAGCAGACGACCCACAAATAGCAAA[A/C]CAATTATACTGAACAATGCAATCTGATATCACAGT M 2 1 2 1 101000 r 74 goat 7_4917489_RH-map 7 4917489 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790468 Affx-122955129 AX-385277471 7 4941609 AGAGGCTGAACTGAGATTTGATGGAGGTGAGGATG[A/G]AGCCATGTGGACTCCAGGAATGGAATTCTCAGCAG R 2 1 2 1 101000 r 74 goat snp40016-scaffold510-2428910 7 103407682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603295 Affx-1002479454 AX-413837475 7 4954369 TCAGCATAATGTAAGCTCTTTACCACCTGTTTTGG[A/G]TTTTGCTGATTTTCTGGGTACATGGAAACCTACTC R 2 1 2 1 101000 r 74 goat 7_4954369_RH-map 7 4954369 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38420799 Affx-122944687 AX-123291146 7 4996496 TCACTTTGCCTTCCCAGCAGCATCTGCCTTTGCCC[A/G]TGTACCAAATGTTATTAAGGATAGAGGTGGTAGCA R 2 1 2 1 101000 r 74 goat snp40015-scaffold510-2374023 7 103353268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448545 Affx-122923432 AX-123318881 7 5042197 GACCTGGGTTCAAACCCTGGCTCTGCCTCCTGCCA[C/T]GTGTGTGACCTTGGCAAGTCAACCCTCCTCTCAGA Y 2 1 2 1 101000 r 74 goat snp40014-scaffold510-2328322 7 103307821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795038 Affx-122939264 AX-385281997 7 5132537 TTGCTCCAAATCTTAACTTAGATTCAAGTTTCCCA[A/G]CTGACAGTAGAGGTTTTACTGGTTTCCCCCTGCCT R 2 1 2 1 101000 r 74 goat snp40012-scaffold510-2237982 7 103218154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426436 Affx-122940816 AX-123296782 7 5171479 GTGTTTGGTGCATCTCTTCCTTTTCGGCATTTTTC[C/T]GAGGACTAGGAAGTTTGAGCGAATCATCTCACACC Y 2 1 2 1 101000 r 74 goat snp40011-scaffold510-2199040 7 103178942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435181 Affx-122933649 AX-123305521 7 5202152 TTGTCATAATACCAGTGTTCTAGTGTCCTCACAAT[A/C]TTGTAAGGAAGGAATGCTTACTAATCCCATTGGAT M 2 1 2 1 101000 f 74 goat snp40010-scaffold510-2168367 7 103148278 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780438 Affx-122976398 AX-385267529 7 5238471 GGAAGATTTAACACTGAGTCTCCAGAATCAGCAAC[A/G]TATTTTTCAAGATTGTAACAAAATATAAGATGTCA R 2 1 2 1 202000 r 74 goat snp40009-scaffold510-2132048 7 103111562 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420765 Affx-122944713 AX-123291112 7 5267661 CATCCTTTAGAGCCACTTTAAAATAAAAAGAGGGC[A/G]TATGGGGATTGAATTAGAGCAACAAGCTGCCTTTG R 2 1 2 1 103000 r 74 goat snp40008-scaffold510-2102858 7 103082087 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413746 Affx-122950051 AX-123284095 7 5322614 GGAGGCTGCTCGAAACAACTGAGGTCGACCTAGCT[A/C]GGGCGGCCGCACTTCTTTGTGACTAGCTGTGCGGC M 2 1 2 1 101000 f 74 goat snp40007-scaffold510-2047905 7 103029797 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273328 Affx-1111833545 AX-519546969 7 5343861 AAATACAAAGTTTTCTCAAAATCCAATTAGGAAAA[A/G]AAGGTTAGTAATGTACCGTAAAATTGGAAGGAATT R 2 1 2 1 101000 r 74 goat 7_5343861_AF-PAKI 7 5343861 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437901 Affx-122931660 AX-123308239 7 5386668 ACGCGAGAGCACCAAGCAAAGGAGGGAGGGTGTGT[A/G]TGTATGTCGAAGGCAGGCTTCAAATGCCTGTCAAA R 2 1 2 1 201000 r 74 goat snp40006-scaffold510-1983851 7 102965994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396460 Affx-122962972 AX-123266815 7 5416007 TTTAATGGCCCCATGTGGGTGGCTCATAGCATCTT[A/G]AGCTGATTAAGGCCTAAGAGCTCTGGTCTCCCTTC R 2 1 2 1 201000 r 74 goat snp40005-scaffold510-1954512 7 102936661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403026 Affx-122958554 AX-123273379 7 5453766 CCCAGTCCAGAGTGAGGGACAGATGGTGAACCCCA[C/T]ATTCCCAGCCTCTGGGAGCAGTGGGAACTGGCAGC Y 2 1 2 1 202000 f 74 goat snp40004-scaffold510-1916753 7 102898707 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443014 Affx-122928172 AX-123313351 7 5508582 ACAGGAAGGAGCCCCAGACAACCTGCTCCTACAAA[C/T]ACCTTTTACCTTCATCTGTGCTTCTCAATCCCCAG Y 2 1 2 1 101000 r 74 goat snp40003-scaffold510-1861937 7 102843517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426552 Affx-122940180 AX-123296898 7 5545484 GACATCCCCCGAAGCTGTGGTCATCACAGCACCGC[A/G]ACAGGCAGGTATCAACAGCCCAGAGGCAGACCCAC R 2 1 2 1 101000 r 74 goat snp40002-scaffold510-1825035 7 102806626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799519 Affx-122924166 AX-385286449 7 5585772 AATGAATAGCTGTTCTTTGAAGAGTTTTCAGTTTC[A/G]TTCTTAACACGACACAGAGTTTTACATTCCATCCG R 2 1 2 1 101000 f 74 goat snp40001-scaffold510-1784747 7 102766349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376239 Affx-122978784 AX-123246598 7 5626727 TTGAAAAACACCATGCTGAGAGGAGGAAGCCAGAC[A/G]CAAAACAGACAGACGGTGTATGATTCTATTTATGC R 2 1 2 1 201000 r 74 goat snp40000-scaffold510-1743792 7 102725137 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383233 Affx-122972759 AX-123253591 7 5682737 AGAACAAAGAAGGTGGGAAGGAAGACAGTGAGAGA[C/T]GGAGGAACGTAAGAGGGGTACAAAGGGGGAGACGG Y 2 1 2 1 101000 f 74 goat snp39999-scaffold510-1687782 7 102668694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439182 Affx-122931051 AX-123309519 7 5715219 CTTGCCCTAAGGACTTGATTCATGGCAATGGAAGA[C/T]GTCCAGTGCTGTGTTATTTATCTATGAAGATGTTC Y 2 1 2 1 101000 f 74 goat snp39998-scaffold510-1655300 7 102638042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433590 Affx-122934961 AX-123303931 7 5745404 GATGTTACCATTGGGAAAGTTGGGTGAAAGGGTGC[A/G]TGAGACCTCTGCTCTGTTGCTATGCTGCTGCTGTT R 2 1 2 1 201000 f 74 goat snp39997-scaffold510-1625115 7 102607758 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786502 Affx-122947578 AX-385273536 7 5774581 GTTTGCCTCTGTTTTGTTTGAAGGCAGCACGATTT[A/G]TCCACCCAGCCCACCCTTCGTGTGGTGTCTCTGCA R 2 1 2 1 303000 r 74 goat snp39996-scaffold510-1595938 7 102578259 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408552 Affx-122953681 AX-123278903 7 5813705 TTCATTGCCCCCTCCAGACACGGCTATCTCATCCG[C/T]GAGCGTTTCCAGTGCCCTTCGTCAAGACTCTCACA Y 2 1 2 1 101000 r 74 goat snp39995-scaffold510-1556814 7 102540300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428827 Affx-122938375 AX-123299169 7 5844733 GGGATTTCTTAGTCAAATCGTATGCACATTTTTCA[C/T]GTTTTCTATCTTTTTCTTAGCTTCTTATACTAAAA Y 2 1 2 1 101000 f 74 goat snp39994-scaffold510-1525786 7 102510173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444806 Affx-122926334 AX-123315143 7 5881940 ACATGCATATCCTTTCAAGATTAACTAGGAGTCTG[C/T]TTTATCTCTGTGTTACAAGAAGGGGAACACTTTCC Y 2 1 2 1 102000 r 74 goat snp39993-scaffold510-1488579 7 102472791 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451475 Affx-122921138 AX-123321808 7 5939457 GGCCCCCAGGGTCTATCTCCCCCCTGATGCTTGGC[A/G]TTCTCTCCCCAAAGGTACTTGATTTTCTTCTGCCC R 2 1 2 1 101000 r 74 goat snp39992-scaffold510-1431062 7 102404233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397799 Affx-122962497 AX-123268154 7 5972982 AAGTCCTGGGGCAACCTTAGTGGCACCGTGTGGCC[A/G]AGCACAGTCCATTGTGATGGGGAAGGAATCTGGAC R 2 1 2 1 103000 r 74 goat snp39991-scaffold510-1397537 7 102370856 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450155 Affx-122922738 AX-123320490 7 6020372 TCTGATGAACTTTACACGTTCCCCAAACGGGTGCC[A/G]TTCTGTGACTCAAACTGCCTCTACCACAAGTCAGT R 2 1 2 1 101000 r 74 goat snp39990-scaffold510-1350147 7 102323428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438065 Affx-122931533 AX-123308403 7 6073589 GGTTTCTGAGGCTCAGGCTGAGGGGAGAGTGAGAC[A/G]GCTGTGTCTTCAGACGGTGGGAGTTTTTATCCAGG R 2 1 2 1 101000 r 74 goat snp39989-scaffold510-1296930 7 102270440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414021 Affx-122949801 AX-123284370 7 6125886 TTTAAAAGGTGGGCAGTGTTTCAGTCCCACCCCTG[C/T]GCTTCCAGGGAGTGAGTCTTTAGCTTCTGAGACTG Y 2 1 2 1 101000 r 74 goat snp39988-scaffold510-1244633 7 102218371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396956 Affx-122963173 AX-123267311 7 6162669 CTTTCTAGAAGCAGTAACACAGCTCTGTGGCCTTA[C/T]CATCCTGTCTTTAAAGGAACACTGTAAGTGGTGAG Y 2 1 2 1 101000 f 74 goat snp39987-scaffold510-1207850 7 102181429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383274 Affx-122972728 AX-123253632 7 6196793 TGTCTCCTGCACACTGGTGGCCTCACCGCTGTTTC[C/T]TCTTCTCCAAAATGGAACTGATGAGTAAGAGCCCT Y 2 1 2 1 101000 r 74 goat snp39986-scaffold510-1173726 7 102147421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395983 Affx-122963510 AX-123266338 7 6237778 CAAATAGATCTCTGAGTCTCCAACGTGTACAGGGG[A/C]CTTGAGGCCAAACGAGACGACAGGGTCCAGAGATG M 2 1 2 1 101000 f 74 goat snp39985-scaffold510-1132741 7 102105906 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375403 Affx-122979205 AX-123245762 7 6285794 TATGAATTCAGTCATCACTGAAAAGTCGTACCTCT[A/G]CAACCAGGTGTTGCGATATCCCTGATGCCGAATGT R 2 1 2 1 101000 f 74 goat snp39984-scaffold510-1084725 7 102063117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389076 Affx-122968594 AX-123259434 7 6322008 TTATAAAGAGATCCCAGAGGGCTCCCTTGCGCTTT[A/C]TGCCATGTAAAAACCCAGTGAAAAGGCAACAGTTA M 2 1 2 1 101000 r 74 goat snp39983-scaffold510-1048511 7 102027467 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381330 Affx-122974429 AX-123251688 7 6358818 TCTGTCCTTCCACGACCAGCTTCTTCCACTCAGTG[C/T]AACAGCCTCCCGGTTCATTCCACCTGCAGCAGGTG Y 2 1 2 1 201000 r 74 goat snp39982-scaffold510-1011701 7 101990608 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448025 Affx-122923719 AX-123318361 7 6388866 TTCTGAAAATCTGGTTCTACGGGTCTAATTAGCAG[C/T]CGTATTGCTGACACTCATCTCCACGCCTGCCCTGG Y 2 1 2 1 101000 f 74 goat snp39981-scaffold510-981653 7 101960803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433758 Affx-122934495 AX-123304099 7 6460819 GAATCTTTCTTAACACAGTGCCCCCCAGGCAGCTG[C/T]TCTCAGTCCATTAGGGTTTAGCCAGAATGCACTTT Y 2 1 2 1 101000 r 74 goat snp39980-scaffold510-909700 7 101898530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776847 Affx-122956900 AX-385263971 7 6505315 ACTATGGGCAGATTGTGTAATTCACAGAAGTGGCC[A/G]TTTCTGTGTGATGGTCAGTGGGTTCCTTGTGTGGT R 2 1 2 1 101000 f 74 goat snp39979-scaffold510-865204 7 101854121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422709 Affx-122943646 AX-123293055 7 6541230 TTCAGGATGGCTGAAACTGGGGCTAATCTCACCCT[A/G]GTCTCTGAGTTCCTGCTCCTGGGCCTCTCAGAGGA R 2 1 2 1 101000 f 74 goat snp39978-scaffold510-829289 7 101817987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784276 Affx-122925846 AX-385271327 7 6604970 TGTGACTGTCCCAGGAGTTTGTTGCATCTTCATGG[C/T]ATTTATCTTGCAATATCCTGAATGACGTATGCACT Y 2 1 2 1 101000 f 74 goat snp39977-scaffold510-765549 7 101746363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411863 Affx-122951213 AX-123282213 7 6658775 ACAATAGCCATGAGGTGGAAGCACCCCAAATGTTC[A/G]TCCTTGGATGAATGGTAAGCAAAACGTGGTCTATC R 2 1 2 1 201000 r 74 goat snp39976-scaffold510-711744 7 101692807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416506 Affx-122947780 AX-123286854 7 6688694 CGTTTTCTAATTTGGGGAACTGAATAGTTATACGG[C/T]GAAATTCCATCACCCTTCCCTCTCTTCCTACCTTC Y 2 1 2 1 101000 f 74 goat snp39975-scaffold510-681825 7 101662766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383057 Affx-122973285 AX-123253415 7 6732080 TATAAGCAGACAGGGAGCATCAGATGGGTGTGGGG[A/G]CACTGATGCAGGTGGATTGTCTTGAATGGGCAAGC R 2 1 2 1 201000 r 74 goat snp39974-scaffold510-638439 7 101618442 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394915 Affx-122964317 AX-123265270 7 6767625 TTGACCCCCTTTTTCTCTCTTTTTCCTTCTGGGAA[C/T]GTCTATAGCCTGTAAAAGGAATGTTGGTATGCTTG Y 2 1 2 1 201000 r 74 goat snp39973-scaffold510-602894 7 101582635 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439925 Affx-122930010 AX-123310262 7 6809788 CAGACAACACAAAGGTGAGAGCCACATGTGGAGAA[C/T]GCTTTCCATCTGCCCTGGGCAGAAGGCACCTTCCA Y 2 1 2 1 101000 f 74 goat snp39972-scaffold510-560731 7 101540701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438657 Affx-122930893 AX-123308994 7 6868888 AGCATCTAAGCTACTACCCTATATTGCATATGATT[A/G]TTATGTCCCTTGAATTTCATGACCCTGGCTTATTG R 2 1 2 1 101000 r 74 goat snp39971-scaffold510-501631 7 101480470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440343 Affx-122929665 AX-123310680 7 6912911 GTTGGCATGATCAGGGTGGCAGGCTCCTTGCATTG[C/T]AGCCCTCACCTGTAAGGTCCTCATCTACAGGGAAA Y 2 1 2 1 101000 r 74 goat snp39970-scaffold510-457608 7 101434796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404981 Affx-122956403 AX-123275333 7 6942553 GCTTGGAACCAGGTTGGACACACAGCAGAACTTAG[C/T]GTTGGTCAGTGGAATCCAAGTGATGGCCAGAACCA Y 2 1 2 1 101000 r 74 goat snp39969-scaffold510-427966 7 101404986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774882 Affx-122949772 AX-385262015 7 6972097 CATACAGAATCCTGGATCAGAGCAGCCCATTTATT[A/G]CTCATGGCAAAAACAGTAACCAGAGTAGAACTGTA R 2 1 2 1 101000 r 74 goat snp39968-scaffold510-398422 7 101375323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407780 Affx-122954961 AX-123278131 7 7002675 TGATTCATGAGGTCGCAGAGTTGGACACGACTGAG[C/T]GACTAAACTGAACTGAGAACCCTAAACGAATGAGA Y 2 1 2 1 103000 r 74 goat snp39967-scaffold510-367844 7 101344715 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436288 Affx-122932527 AX-123306627 7 7064302 CCAGGGAGCCGATGTCCTGCCACGGCCAGCACAAG[C/T]GAGGAGTCGCACCTGCACAGGGAGAGAACGGAGCG Y 2 1 2 1 303000 f 74 goat snp39966-scaffold510-306217 7 101280287 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390077 Affx-122968034 AX-123260434 7 7099454 CCATTTTATCATCCTGGGTCAGTGTCAGGTCCACA[C/T]GCCCTTGCAGACAGGAGTTTACTCACCCGCTGTAT Y 2 1 2 1 101000 f 74 goat snp39965-scaffold510-271065 7 101243842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380136 Affx-122975987 AX-123250494 7 7153615 TCCTTCCCTCTGGCAGCCTAGAAGAGTGTGAATTG[G/T]GTCCTATTTGTTCCTCTCCAGATTCAGAGTTCAGA K 2 1 2 1 101000 r 74 goat snp22603-scaffold224-33971 7 101185252 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403989 Affx-122957207 AX-123274341 7 7184278 TTTCAAGTTACTATTAATAGAAGAAAACAGCCTGA[C/T]ATTTTTAGAAGAATTTCTGAGCAAAGCACAACACT Y 2 1 2 1 101000 r 74 goat snp22604-scaffold224-64634 7 101154667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431547 Affx-122936207 AX-123301888 7 7230291 TAAACAACGCCTGCGAATGCATGTGTATGTGTGCA[C/T]GTGTTTGTATATGCGATGAAAAAGTCCAGAAGAAT Y 2 1 2 1 201000 r 74 goat snp22605-scaffold224-110647 7 101108729 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399630 Affx-122961076 AX-123269985 7 7261702 AGAAGTGAGACTGGAAGAGTTCAGAGGAAAGAGCT[A/G]TGGTCTGTGTGGGGAATCAAGGGAGGTTTCCAGGA R 2 1 2 1 202000 r 74 goat snp22606-scaffold224-142058 7 101077400 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430359 Affx-122937793 AX-123300700 7 7311165 AAATAAATAAAACCTTCTCTCAGAGACCCGTACAC[A/G]AGTTTATCAGGGTCTTCACTCTTATTATCGTTACT R 2 1 2 1 101000 r 74 goat snp22607-scaffold224-191521 7 101027845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278446 Affx-1111836428 AX-519551931 7 7316400 GAGAAATGGCACTGTGTCAGGCTGAAACTAAAAGC[A/G]TGAGACAGAGAATGAAGGCAAAGGATGAGAGCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-754 7 7316400 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421467 Affx-122943929 AX-123291814 7 7402318 ACCCACCGCTCAGAGTTGAGGCCGTGCCCTCCTGC[C/T]GCCTGTTGGCAGGTGACGTGTGCAGTGCTGGGGCA Y 2 1 2 1 201000 r 74 goat snp22608-scaffold224-282674 7 100936748 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379297 Affx-122976206 AX-123249656 7 7547311 CTGGGGGCTGGGGTGGGGGGAATCTTGTGGGTGAC[G/T]CTAAGGACTGAGTCAGCTACTTAAGCTTAGCCCCA K 2 1 2 1 101000 r 74 goat snp22611-scaffold224-427667 7 100792887 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385456 Affx-122971305 AX-123255814 7 7667603 AGTGACTAGTTCTAGTTTATCTGTCTCCTTGTTCA[G/T]ACTGGGGCTGCATGAGGTAACACTTGTCTGTCTTA K 2 1 2 1 201000 f 74 goat snp22613-scaffold224-547959 7 100671811 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410461 Affx-122952216 AX-123280811 7 7698784 TTCAGGGCCAGTGTCCTCCCACTGTGGTCTCTGTG[C/T]TGCCTGCTTCAGGACCACCTGGAGAGCCTGTTAAG Y 2 1 2 1 103000 f 74 goat snp22614-scaffold224-579140 7 100640708 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386504 Affx-122970753 AX-123256862 7 7758943 CCTCTGGGCTCCCACAGCTCTGCCAGTCTACACTT[A/G]CGTTCCAGCTTTTGATTCTTATTCTAGTGACTGAA R 2 1 2 1 101000 r 74 goat snp22615-scaffold224-639299 7 100591581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434454 Affx-122934647 AX-123304795 7 7796749 TGGAAACTTTCAAAGGGGAAAAAACTCATTAAAAA[G/T]CAATATAAGCAAAATTGAATTAAATCTGTCAAATA K 2 1 2 1 303000 r 74 goat snp22616-scaffold224-677105 7 100558698 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411948 Affx-122951145 AX-123282298 7 7878339 CAAAAAGCTGGAGCATTACAAAAATTACTCTTGTA[C/T]GTAATGGGAGCTGAAATTTATTTAGGACTTGCCAC Y 2 1 2 1 101000 r 74 goat snp22618-scaffold224-758695 7 100477563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393529 Affx-122965427 AX-123263885 7 7976080 TGCATTTCTAATGGCTGTGTAGGGTTATGAAGCTG[C/T]AGATTCTGCTCTTGAGGGTCACTCTTTGAGTAACA Y 2 1 2 1 101000 f 74 goat snp22620-scaffold224-856436 7 100376975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273752 Affx-1111833819 AX-519547363 7 7996958 TCACCCTCTCTATCCACGTCTCTGCCTGCAGACTT[A/G]AGGCAACAGAGGACCATTGCTTTTTT R 2 1 2 1 102000 f 74 goat GoatD01.005893 7 7996958 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440553 Affx-122929316 AX-123310890 7 8006436 AGACAACAGGAAGGTGTCTCCTGTTGATCCTTTAG[C/T]CAGATATAGGATTCCAAAACCACAGCTGTGTCTCA Y 2 1 2 1 201000 r 74 goat snp22621-scaffold224-886792 7 100346549 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435179 Affx-122933650 AX-123305519 7 8048850 AAGCGTAAAGACCTGTCACATTGCCTGGAGTTTGA[A/G]CTTTTAAACCAGTAGCAAAAGCAATGTTGTTAATT R 2 1 2 1 101000 f 74 goat snp22622-scaffold224-929206 7 100303196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426104 Affx-122940638 AX-123296450 7 8085665 CTAATTTAGTGCAGTACATGGTGTGTACCGAGCTT[C/T]CATGGTGGCTCAGGTGGTAAAGAATCTGCCTGCAG Y 2 1 2 1 103000 f 74 goat snp15572-scaffold1647-534096 7 99117466 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464488362 Affx-1110511173 AX-515960676 7 8094475 AAAATGGAGGGGGGTAATAATATACACCACAATTA[A/G]TAGGTCAACTGCAATTTTTAAAATGCACAAAATTG R 2 1 2 1 201000 f 74 goat 7_8094475_AF-PAKI 7 8094475 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791718 Affx-122948298 AX-385278709 7 8143104 TTCTTTAATTGAGACGTAACTTATATAAAAGTCCG[C/T]AAGTCTCAGTGTTCACCTCAGTGAATTTTATGTGT Y 2 1 2 1 101000 r 74 goat snp15571-scaffold1647-476657 7 96459974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796587 Affx-122933382 AX-385283533 7 8184879 TATATGTAATCTAGATCACAAAATGGAGGGTTTCC[C/T]CCTTCCACTCCTGGCCAATAGATGGTAATTATAAC Y 2 1 2 1 101000 r 74 goat snp15570-scaffold1647-434882 7 96502184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419588 Affx-122945387 AX-123289936 7 8215010 CCAAAGAAGTTCTCCTGACCTTATTAGCACTTTAG[C/T]GAGTAGATGAGGAGAGAGGCCCTCTCTTCACTCTC Y 2 1 2 1 101000 f 74 goat snp15569-scaffold1647-404751 7 96532513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379404 Affx-122976125 AX-123249762 7 8247303 CTCCTGCATTGCAGCTCCTCTTCTTTTTAGAGTTA[G/T]ATCTCTTTCCTTTCTGAGATTCATCAAGGACACAT K 2 1 2 1 201000 r 74 goat snp15568-scaffold1647-372458 7 96565059 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416884 Affx-122948079 AX-123287232 7 8290463 CAGCCTGCTCACGCTGGGCACCGTAATGGTGGGAG[C/T]ATCCATGCCTCCATCTTGAGGGTCTCTCAGTCTGA Y 2 1 2 1 101000 r 74 goat snp15567-scaffold1647-329298 7 96608644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418652 Affx-122946330 AX-123289000 7 8330946 TGTACTTAACAGGGAAGGAACCTGAGGCCCAGAGA[A/C]GTCAGTTAAGTTGCTCAAGGTCATAGAACCAGCAA M 2 1 2 1 201000 r 74 goat snp15566-scaffold1647-288815 7 96649115 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769767 Affx-122933780 AX-385256937 7 8362484 AGATTCTACCATGCCACTCCCTCATATTTTATTCA[C/T]AGCATTTATCAACCTCTTCCAAGTGTTTTCTTTAT Y 2 1 2 1 101000 f 74 goat snp15565-scaffold1647-257277 7 96680311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781860 Affx-122940531 AX-385268942 7 8397245 TTCCTGTGTATCTCAGTGTCTGAATACCTGAGGGC[A/G]TCTCAACCCAACTGTCGTCCTGAATTTGAGACAGG R 2 1 2 1 101000 f 74 goat snp15564-scaffold1647-222516 7 96715280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424858 Affx-122941342 AX-123295204 7 8436689 AACCAAACAGAATGAATGCTGGAGGTGTCCTGCTA[C/T]GCGAGGCATTTATTCTTGTTAATTAAATGTGATTA Y 2 1 2 1 201000 r 74 goat snp15563-scaffold1647-183072 7 96754736 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426255 Affx-122940332 AX-123296601 7 8509377 TCTCAAGTCTGTTAGCAAAGGGCCAGGAAGAATCC[A/G]TGTGGGGAAACAGCCCCACACAGACCCTGGCCCAG R 2 1 2 1 101000 f 74 goat snp15561-scaffold1647-110384 7 96826816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395834 Affx-122964027 AX-123266189 7 8556968 ACTGGCCCTGGAGAGTAAGTGGTCCAGTCTCAGAG[C/T]AAAAGAAAGCTCTTAAAGTTTCTTTTCTACCCCTC Y 2 1 2 1 202000 r 74 goat snp15560-scaffold1647-62793 7 96874657 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433701 Affx-122934536 AX-123304042 7 8587310 GAGCAAAAACTCGGTATGGATTTCCGCAGCCGAGC[A/G]ACTATACTGCAGCTGGTGGACTTGAAGTAGGACGA R 2 1 2 1 101000 f 74 goat snp15559-scaffold1647-32451 7 96904129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389358 Affx-122968465 AX-123259716 7 8617316 GCCAGGCCTCAGAGGGGGACCTGCTTCTCTATGGG[C/T]ATAATGTTCAGCTTCCAGGATTGGGAAGGGGCAGG Y 2 1 2 1 101000 r 74 goat snp15558-scaffold1647-2445 7 96934197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446824 Affx-122925279 AX-123317160 7 8694649 TGAGTCCCCTTATCAGAATCCAAGTCCTCCCCCTC[A/G]CTATGGGAGAATGCCAGTTTGGGCCACTGAACCGC R 2 1 2 1 201000 r 74 goat snp36377-scaffold437-74789 7 97007886 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416303 Affx-122947929 AX-123286652 7 8735725 CATCTTAGTAACTGAACAACAACAAAAACAACTAT[G/T]CAGTCAGCTAATACATACTGTGTGCCAGCCCCTGC K 2 1 2 1 101000 r 74 goat snp36378-scaffold437-115865 7 97048774 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403992 Affx-122957204 AX-123274344 7 8786564 CCACTCCAGTATGCTTGCCTGGAGAATCCCATGCA[C/T]ACCTGAGTTGTTTGCGTTTTGAGAAGTTTCATGAC Y 2 1 2 1 101000 r 74 goat snp36379-scaffold437-166704 7 97099681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278447 Affx-1111836429 AX-519551932 7 8795111 GAAGGCCTACAACGGAGGCAAATTCAACATGCTGC[A/G]TGGTTGCTAGGGGGATCGAGCAAGGGGCTAGTGGA R 2 1 2 1 101000 f 74 goat Random2.2K-755 7 8795111 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770692 Affx-122948912 AX-385257856 7 8821306 TGATGTGAAATTGCTAGCTTTGTGGGATGGAGGGC[A/G]ACAGAGAGTTTTTGCTCTGTTTAATGACTCTGCAG R 2 1 2 1 101000 f 74 goat snp36380-scaffold437-201446 7 97134845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278620 Affx-1111836430 AX-519552099 7 8835808 TTTGACATTGATTCTTTTGGTAGTAGAGAGGTAAA[A/G]TAAACTTAGGATTCTACATGAAAGCGAAATCTGAT R 2 1 2 1 101000 r 74 goat Random2.2K-756 7 8835808 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391093 Affx-122966825 AX-123261450 7 8853120 TGTGCAAAGAAACCTGCTTCACATCATCAAATAGA[C/T]GGGAGGAGACAGAGTCTTACAGATGTCACGTGATT Y 2 1 2 1 101000 f 74 goat snp36381-scaffold437-233260 7 97166371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388785 Affx-122968926 AX-123259143 7 8895212 CAAAAGCCCAAGTCCTCCCCACAGCCCTGCACACT[A/C]TATCTTTCTTGTCCCCTCCCTGCCTCACCTCCTCT M 2 1 2 1 201000 r 74 goat snp36382-scaffold437-275352 7 97208706 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439737 Affx-122930540 AX-123310074 7 8955865 AGGGCCCTTATGGATGAATTTTAGGCACCTGGCCA[C/T]AGTCAGGAAGTGTGGGGAAGCTGAGAAATATCTGT Y 2 1 2 1 102000 r 74 goat snp36383-scaffold437-336005 7 97269673 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382227 Affx-122973968 AX-123252585 7 8995749 GAACTCTGCCTCTAGTGGGTTTGACAGTAAAGTTC[C/T]GTGGTGCAGGGTGTGGGTTGGGGAGGAGTGAATAA Y 2 1 2 1 101000 f 74 goat snp36384-scaffold437-375889 7 97309857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770011 Affx-122946743 AX-385257178 7 9088760 GTGAGCAAGAACAATGTAGGGAGGCTCAGTCTTCA[A/G]ATATTTTTTCAGGACTGGAAACCCAGACGACTCAC R 2 1 2 1 201000 r 74 goat snp36386-scaffold437-468900 7 97404023 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413815 Affx-122949895 AX-123284164 7 9121848 CCCCTCCCAGGGATCATATCACTCTGTTCATTACC[A/G]TTAGGTATTTTCTCTTCCATTATTAGACTGCCAGC R 2 1 2 1 101000 r 74 goat snp36387-scaffold437-501988 7 97436729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392659 Affx-122966437 AX-123263016 7 9173836 TCTCATACTATTATTGTAATGGCTCTATAAGTTTC[G/T]TTTCCTTAGAACCTACCTAACAATTCTGCTATTTG K 2 1 2 1 101000 r 74 goat snp36388-scaffold437-553976 7 97488676 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410708 Affx-122952726 AX-123281058 7 9203040 AGGCAACCTGTAAAGGCTTACCCACAGGCACAGAA[C/T]GGAGAATTTATGTAAAGATGTATCACCTTGTCTAG Y 2 1 2 1 101000 f 74 goat snp36389-scaffold437-583180 7 97518222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799351 Affx-122963847 AX-385286281 7 9259315 TGTGTGAGTTGGGCTCTTTTGGTAGAGGCTTTCAG[A/G]TTTGAGTGGTCTGTTATGAGGGCCAGCCCTAGTGC R 2 1 2 1 101000 f 74 goat snp36390-scaffold437-639455 7 97574499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445461 Affx-122925219 AX-123315798 7 9300871 CCAACCTCAGGGGGTTGTAAAATATATAGAGCATC[A/G]TTATAACAGTGAGGAGGAGGAGACTATGTTACCAG R 2 1 2 1 101000 f 74 goat snp36391-scaffold437-681011 7 97616042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395890 Affx-122963619 AX-123266245 7 9331929 AGACAAAAGTCTCCACCCTCGTCGGGGAGACAGAC[A/G]TGACCAGTAAACGCTGATAAATAATAAACTGCTCA R 2 1 2 1 101000 r 74 goat snp36392-scaffold437-712069 7 97647083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403434 Affx-122957740 AX-123273787 7 9368872 TTTTACAGAGCTGGGAAAGGGAAGGCTAGGATTCA[A/G]ACCCAGACTTGGCAAGTTCCAGAGCCTGAGTTCTT R 2 1 2 1 101000 f 74 goat snp36393-scaffold437-749012 7 97683946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411532 Affx-122951660 AX-123281882 7 9440969 CAAGTAAAGAGAGCAGGAGGTGCCCCCAAATCGAG[C/T]GAAAGAATCAGGGGTGAGGCTGAGACTCGGAACAG Y 2 1 2 1 201000 f 74 goat snp36395-scaffold437-821109 7 97755919 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403672 Affx-122957506 AX-123274024 7 9492895 ATCAGCCCTCTACCTCCGGAGGCGTAGGGGCTTCG[A/G]GCAATAACCCGCAGGAAGGCGCAGTGACTCAGGCC R 2 1 2 1 102000 f 74 goat snp36396-scaffold437-873035 7 97808091 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430446 Affx-122937729 AX-123300787 7 9562781 CTTTGTCGTGGTGGCACTCTGCTTTGGAGAGAGCC[C/T]GTGGGACTTCCTCCCACACCCTGGGGAAGGGCAGC Y 2 1 2 1 101000 f 74 goat snp36397-scaffold437-942921 7 97878054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389948 Affx-122968085 AX-123260305 7 9636804 ATTCCCCAGCCTGGGCACACTTGGCACACAGCTGG[C/T]AAGGCTCAGGTCGGCAGAGGGGACAATTAGGACCC Y 2 1 2 1 201000 f 74 goat snp36398-scaffold437-1016944 7 97949501 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386361 Affx-122970856 AX-123256719 7 9682106 GCAGCATCTTCTTCCTCCTCCTCTTCCTTCTCATC[G/T]TCATCCTCCTCATCCTCATCCTTGTCCTCGTCATC K 2 1 2 1 103000 r 74 goat snp36399-scaffold437-1062246 7 97992918 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764797 Affx-986697037 AX-385252405 7 9728133 TGGAGCTGGGAGATCAATGAATGCGTTGTTTACTA[A/T]TTTTATTAGTGGGTGAGTTTTTCGGATGTTGGTCA W 4 1 2 1 600010 r 74 goat 7_9728133 7 9728133 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320762509 Affx-986697039 AX-385250626 7 9728287 TACATTGTATTTATTTTAAGTGTTATTTTTGTGAT[A/G]GGTTTTGTGGGGTTTTCTTCAAAACCTTCACCTAT R 2 1 2 1 600010 f 74 goat 7_9728287 7 9728287 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 38440909 Affx-122929216 AX-123311246 7 9729962 CCCCACCCTTTCGCCTCGCCTTCCAGAGCCAAACA[C/T]GCCTGTTAGTCCTTATCCTAAATCAAGGAGATATC Y 2 1 2 1 101000 r 74 goat snp36400-scaffold437-1110102 7 98040330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414255 Affx-122949620 AX-123284604 7 9777784 ATTGGTGCGATCATGGAAGTGAGGGCTGGTCTATA[C/T]CCTAGAGCATCTCACAACTTGGAATATTCGGATGC Y 2 1 2 1 101000 f 74 goat snp36401-scaffold437-1157924 7 98086659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377169 Affx-122978210 AX-123247528 7 9825665 GGGTGTAGCCTTTAGCCCCGTTCTGGTCACCCACC[A/G]CCCCTTCTATTAGACACAGCCCGCAGTCAGAGGAT R 2 1 2 1 101000 r 74 goat snp36402-scaffold437-1205805 7 98133949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391511 Affx-122966668 AX-123261868 7 9867368 CAACGAAGTTTCAGCTTCTCAACCTTTTCCCCCTG[C/T]CCAGGGCTGCAGACCCTGACTGGCCTCGATCTGCA Y 2 1 2 1 201000 r 74 goat snp36403-scaffold437-1247508 7 98175840 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407908 Affx-122954389 AX-123278259 7 9916386 CTGCAGCCCACATAGAGACCAGTGTTTGGATGCTT[A/C]GGCCCCTGATTGTCAGATGTGCCTCCAGAAGGTAT M 2 1 2 1 101000 f 74 goat snp36404-scaffold437-1296526 7 98224644 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418539 Affx-122946407 AX-123288887 7 9946879 TAAATTTAAATCTAAAATAACCAAACTCACAAACA[A/G]TGTAAAGCTGCTTCATTTAAGTATGCAGGTGATGT R 2 1 2 1 101000 r 74 goat snp36405-scaffold437-1327019 7 98255427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425249 Affx-122940992 AX-123295595 7 9982011 ACTCAGAACTCCGACTGTCACAAACTTTCTCAATG[C/T]AGACAAATTACATTCTCGGCACAGCTACACTGTGA Y 2 1 2 1 101000 r 74 goat snp36406-scaffold437-1362151 7 98290793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443633 Affx-122927290 AX-123313970 7 10068020 AACGGTACGATTCCAAGTATATGAGTGCCTTCAAG[C/T]ACTTCCCCTTGAAGGCGCCACGGGGGCCTTAGCCT Y 2 1 2 1 103000 f 74 goat snp36408-scaffold437-1448160 7 98379218 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443825 Affx-122927065 AX-123314162 7 10104102 GGCTTCGGGGAAGGGGATGCAGAACAGGGAGGAAG[A/G]GAGATGGGGTGATGGCTGCCCAGGAGTCAAGGAGA R 2 1 2 1 101000 f 74 goat snp36409-scaffold437-1484242 7 98416415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446557 Affx-122924844 AX-123316893 7 10152989 AAAATATCTCAGTGGATCAGTGGAATCAGTGGAAA[C/T]GGGAAGACCTAGAATCATGTCTGGAGGGCAAAGGT Y 2 1 2 1 101000 f 74 goat snp36410-scaffold437-1533129 7 98465370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446392 Affx-122925580 AX-123316728 7 10191342 CTCAGGGACCAGCAGGAATCTTCTGGGGATCCAGT[A/G]CCTGGGAAAGTGTTGATTTTCTGAGACTGAATGTT R 2 1 2 1 101000 r 74 goat snp36411-scaffold437-1571482 7 98505186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376847 Affx-122977905 AX-123247206 7 10220115 CTGTGCCAGGGTGATCCTCTGTAGGTACGTGATCC[A/G]CAGTGGCCCGCATGCGCCTGCCTCATCCAGGGGCT R 2 1 2 1 101000 f 74 goat snp36412-scaffold437-1600255 7 98533846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386057 Affx-122971466 AX-123256415 7 10261617 GCACCAGATTTCAACTTGGTTCAGCTCAGTTCTGA[C/T]ACTATCTCTGCAGAGGTAGCATCAGGTTACCTGGG Y 2 1 2 1 201000 r 74 goat snp24505-scaffold2480-37460 7 98574280 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423357 Affx-122943150 AX-123293703 7 10293357 TGGGGGCAAAAGGGGGCCAATGAGGGGCTGCTGGC[A/G]TGACTCAGGGAAGCATAATTTGATTCATAGTGATG R 2 1 2 1 101000 r 74 goat snp24506-scaffold2480-69200 7 98606198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427904 Affx-122939681 AX-123298247 7 10329359 GGGTCAACAAATGATGGAAGTTGATATCAGAATGA[C/T]GAACAAGACAAATCTCTCCCAGAGCTCTGATTTTT Y 2 1 2 1 101000 f 74 goat snp24507-scaffold2480-105202 7 98643074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433033 Affx-122935769 AX-123303374 7 10392722 ATAATTGTTGCCATCACTCCCCCAGATGGTCTCCA[C/T]GTCTCTTCATTGGTCTCCCTAATTCCAGTCCAGCC Y 2 1 2 1 201000 r 74 goat snp52408-scaffold780-1254936 7 98862720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429452 Affx-122938493 AX-123299794 7 10454373 CACAATCCAGTGAGTGCCAAGTGCAGTGGGAGACA[C/T]GAATGCAGGAGGGATTGAGTTGAGTCGGGGGGGAG Y 2 1 2 1 201000 r 74 goat snp52407-scaffold780-1193285 7 98924279 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406192 Affx-122956143 AX-123276544 7 10513687 TTGGAAACATCTGTTTGATTTCTGGTTTCCATATT[A/G]TTGATGAATCTGAAGGAAAAATGGAGTGAAAATAA R 2 1 2 1 101000 f 74 goat snp52406-scaffold780-1133971 7 98983676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435960 Affx-122933527 AX-123306299 7 10552134 CATTTAGAGAGGGAGCTGTGTCCTCTCTAATTGAG[C/T]AGAAATCAAAGGTTTGTTGAACTCAGACACTGAAT Y 2 1 2 1 101000 r 74 goat snp52405-scaffold780-1095524 7 99023056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437812 Affx-122932116 AX-123308150 7 10582935 CTCCAAGGAAGGATGTAGCAGCCTCAGTGGTTTAC[A/G]CTGTGGTCACCCCCATGCTAAACCCCTTCATCTAT R 2 1 2 1 201000 f 74 goat snp52404-scaffold780-1064723 7 99055983 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273250 Affx-1111833527 AX-519546902 7 10600022 TTAGAGTAAATGTTTGACTGGTAGGGCTGAAATGT[A/G]ACTTCCAGTTCTTTGATATCCCGCTTGTTAATTCA R 2 1 2 1 101000 f 74 goat 7_10600022_AF-PAKI 7 10600022 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407670 Affx-122954597 AX-123278021 7 10621827 AAGAGTTTTAAAAAATGTGGTTTTGGTTCACTTGT[A/G]TGTGTGTAGTGGATAAAGTGGGATGATTGTGAATA R 2 1 2 1 101000 r 74 goat snp52403-scaffold780-1025831 NW_017189632.1 15427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395795 Affx-122963655 AX-123266150 7 10653866 TAGATCAATGATTGAGTTCTGGGTCTTTCACCCTC[G/T]ATTAATGAAATGTCTGTAAATCTCCCCACCTCTCT K 2 1 2 1 101000 f 74 goat snp52402-scaffold780-993792 7 94010427 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452429 Affx-122920581 AX-123322762 7 10706079 TAATTTTAATGAATCTTCACTTGGGGTCACAAGAA[G/T]CAGACATGATTTAGCAACTAAACCACCGCCAAACC K 2 1 2 1 303000 f 74 goat snp52401-scaffold780-941579 7 94067051 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789807 Affx-122959073 AX-385276814 7 10747951 GCAAGAGATGTAAGTGGATAGATGAGGGAGCCCTG[C/T]ACTGAGGATTAAGTGGGCTATAATTTTATTGTCAA Y 2 1 2 1 101000 f 74 goat snp52400-scaffold780-899707 7 94109059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800198 Affx-122936427 AX-385287121 7 10805142 GTCTTAGGTCCTCTTCTTTCTAGCCACACTCACTC[A/G]TGATTGATATGGAACCAATAACACAATCCTAAGCA R 2 1 2 1 102000 f 74 goat snp52399-scaffold780-842516 7 94167054 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396129 Affx-122963403 AX-123266484 7 10988091 CAGAGGTGGCCAAACCTGCTCCTGTGGGAGGAAGC[C/T]TCCCTCCCTGTCTCCCCATCTCTAATTAATGGCCT Y 2 1 2 1 101000 r 74 goat snp52395-scaffold780-659567 7 94350712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388147 Affx-122969463 AX-123258505 7 11032593 TGGGTGCCTGGGAACATGTGGTTTGGAGGTCTTCC[A/G]CTCAGTTGGGATTTACAAGTAGGAGTTTTCTCTTG R 2 1 2 1 101000 r 74 goat snp52394-scaffold780-615065 7 94393288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449514 Affx-122922613 AX-123319849 7 11078259 CACTGTCACACACAGAAGTACCACATCCTGGCAGA[C/T]GCTAGATACACAGATGGACACGCAACCCCACACAC Y 2 1 2 1 101000 r 74 goat snp52393-scaffold780-569399 7 94439034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392631 Affx-122966458 AX-123262988 7 11108368 CTCGAGTTCCATACTTTTGGCATCTTGTTCTGGCA[C/T]AGTTACCTTGCGTTTGTGTGTGCTAAGTCTCTTCA Y 2 1 2 1 101000 f 74 goat snp52392-scaffold780-539290 7 94469295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382843 Affx-122973539 AX-123253201 7 11161278 AGCAGCAGCGTCCTGGATTTTAGCTCATCTGCCCA[C/T]GTGCCTAACCACTGGACAGCACTTTCCCTGCCTCT Y 2 1 2 1 101000 f 74 goat snp52391-scaffold780-486380 7 94521926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381964 Affx-122974106 AX-123252322 7 11210950 AACATGGTGGCCATGAGCTTCACATGCATGCCATG[A/C]GGGCCAAAGCTGTTGAGCACCAGGAGGGGCGGGTG M 2 1 2 1 101000 f 74 goat snp52390-scaffold780-436708 7 94571118 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396104 Affx-122963419 AX-123266459 7 11248048 TTGTTCCTAACTCTTACTTCCCTGAGTTCTAATGA[A/G]GTTAAACTTACATATTTTAAAATTCACCAAAAACT R 2 1 2 1 101000 f 74 goat snp52389-scaffold780-399610 7 94608030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447184 Affx-122925003 AX-123317520 7 11290911 CGGCGGCATTTTGGGTGTTACTTTTAAAAGTGCAT[A/G]CTCTATCTAAAGTGAAAAAAAGAAAAAAGAAAAAC R 2 1 2 1 101000 f 74 goat snp52388-scaffold780-356747 7 94651324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425192 Affx-122941039 AX-123295538 7 11322477 TCCCACTCCCTCCATGCCAGCCCCACTGCCCCCTC[G/T]ACCTACTTAGCTCCTACCTATCACACAGCTGAGGT K 2 1 2 1 101000 r 74 goat snp52387-scaffold780-325181 7 94682718 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390648 Affx-122967143 AX-123261005 7 11359628 TTCAGTGAGGACTAATAGAATGTCAAATAGTGATC[A/G]TGCTACAGAGAAAAATAAAGTGGAACTTCCTGGTG R 2 1 2 1 201000 f 74 goat snp52386-scaffold780-288030 7 94719906 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414844 Affx-122949187 AX-123285193 7 11413741 GTGGCGATACAAGTAGGAGGTAGGAAGTCAGGAAA[C/T]ACCTGGAGTAACAGGCAAATTTGGCCTTGGAATAT Y 2 1 2 1 201000 f 74 goat snp52385-scaffold780-233917 7 94773358 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445959 Affx-122925900 AX-123316296 7 11514736 ATCTACCATGCTTTTGTGGCTCCCCGATAACAAAT[A/G]CTGGCTATTTTTTTCCTCTGATTATGAAATAACTT R 2 1 2 1 201000 r 74 goat snp52383-scaffold780-132922 7 94874347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413173 Affx-122950340 AX-123283522 7 11553563 AGGATTCCTATTTACTGATAAGGAAACTGAGGCTC[A/G]AATGAATCCATCTGCTGATCACTAGAGGCAGAATT R 2 1 2 1 101000 r 74 goat snp52382-scaffold780-94095 7 94913469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444232 Affx-122927232 AX-123314569 7 11582875 TGGGTCTCATCTGTATTAGCAAAGCTGGTCATTGG[C/T]ATGGAGACCCCTCCCCTGGCTTGAGTCTGCTGGGA Y 2 1 2 1 101000 f 74 goat snp52381-scaffold780-64783 7 94942349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434554 Affx-122934134 AX-123304895 7 11625619 GTACCATTTGACAGAGGAGGCAAACAGAGGTCACA[C/T]GCTCAGACCGCATAGCTGATGAGGGAAGGAGCTCT Y 2 1 2 1 201000 r 74 goat snp52380-scaffold780-22039 7 94984417 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449434 Affx-122922678 AX-123319769 7 11689087 TTTCACAGGCACCTTATCAGCAAAATTGAACAGTT[A/C]TATAAACATAGTTGGCGATTTGATCTCTGGTTCCT M 2 1 2 1 101000 f 74 goat snp19195-scaffold1931-41330 7 95048654 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395407 Affx-122963954 AX-123265762 7 11735494 CCAGTGAGGGTGTCCACAACCTGTCCCATTGTCCC[A/G]TTGCCATCTGAACTCAGCCTCCTTACCTGTACGAT R 2 1 2 1 101000 r 74 goat snp19196-scaffold1931-87737 7 95095503 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399811 Affx-122960276 AX-123270166 7 11768363 CGGCCTCCCTCCTGCCTGCTTATCCCGCGTGCCCC[A/G]CCTCCTCTCTTTTCCTGTTCTATGCTTTCCATCTT R 2 1 2 1 101000 r 74 goat snp19197-scaffold1931-120606 7 95128429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791655 Affx-122939116 AX-385278646 7 11873897 AAAGGTTCACCCAGCTTCCCGCAACTGATAACATT[G/T]CATACTGTCCTTATTGTTCCATTGCTAACTGGAGT K 2 1 2 1 201000 r 74 goat snp19199-scaffold1931-226140 7 95233498 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392248 Affx-122967566 AX-123262605 7 11973151 CTAAATGTTGTCCTGCTGCCAAGAGCTTTTGGGAA[C/T]GAAGCAACTTATACTCTAGTTTAAAAAAAAATTTT Y 2 1 2 1 101000 f 74 goat snp19201-scaffold1931-325394 7 95332783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423901 Affx-122942284 AX-123294247 7 12007804 GAGCAAGGCTGGAAGGCTCGCAGCCCTGGTGCGTA[G/T]CGGGTGGGGGTGAGGTACTCTCCAGGGGATTTCTG K 2 1 2 1 201000 f 74 goat snp19202-scaffold1931-360047 7 95367504 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425475 Affx-122941496 AX-123295821 7 12049404 ACTGGGGAGCATTTTAAAATAAAAGGGATCGGGCC[C/T]CTTTTCCAAGTGTTTTATTTTTTCTTCCAGCTTTA Y 2 1 2 1 201000 r 74 goat snp19203-scaffold1931-401647 7 95409137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401357 Affx-122959247 AX-123271710 7 12207159 ACAGCCTGCGTATGTATGTGCGTTAGTTGATCAGT[C/T]GTGTCCGACTCTTTGGGATCCCACGGACTGTGGCT Y 2 1 2 1 103000 f 74 goat snp19206-scaffold1931-559402 7 95567946 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438072 Affx-122931529 AX-123308410 7 12242012 GCCCAGAGCAGCCCCCAGTTTCCAGAATTCTATTC[C/T]GGATCGGGAATGCAGTGGGTCAGCTGTAACAGTGG Y 2 1 2 1 201000 r 74 goat snp19207-scaffold1931-594255 7 95600491 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278624 Affx-1111836432 AX-519552102 7 12284593 ACATTAGACCTTCTGAATCGAATGAAATGGTTCTA[A/T]AAGATGGCTGAATGTACTCTAACATTTAATTTGTA W 4 1 2 1 101000 r 74 goat Random2.2K-761 7 12284593 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381259 Affx-122974487 AX-123251617 7 12314961 TCTGAGGAGTGGGGACATGGTCTGTGTTTTTCACC[A/G]TATGGCAACCAATACCTAAAGCCATGCCAGGCACA R 2 1 2 1 101000 r 74 goat snp19208-scaffold1931-667204 7 95670649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440717 Affx-122929894 AX-123311054 7 12403781 ACACTTAGAGGTGCCAGAACACATGGAAAGGATTC[A/G]GGAGTTCCACACCCCTCCCACGCCTTGCTCTGTAT R 2 1 2 1 101000 f 74 goat snp23249-scaffold2321-637241 7 95757426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794364 Affx-122926831 AX-385281328 7 12453735 GAGGACTACCATACACTGGTAAATAAACTAAGCAT[A/G]TTACAGCTCATTGTGGACTTATAATCTAATATTGT R 2 1 2 1 101000 f 74 goat snp23248-scaffold2321-587287 7 95807407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410661 Affx-122952764 AX-123281011 7 12516044 GATGTGTCCCCCTTGCTCCCCTCTGTGACTTCCAC[C/T]TACTTCTCATGGCCAGCAGAGCATGGGTTTTGGGG Y 2 1 2 1 101000 r 74 goat snp23247-scaffold2321-524978 7 95870624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442895 Affx-122927648 AX-123313232 7 12609984 TTGCGTTCTGGAATCTTCTCCTCTTCCCCTTCCTC[A/G]TCCACCTCCCCCTGGTGGGGATGTAGCTGTGTTAA R 2 1 2 1 103000 f 74 goat snp23245-scaffold2321-431038 7 95965426 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405532 Affx-122955982 AX-123275884 7 12654744 GATGAACACATTGTTTAATTACCATGAGAAAACAC[G/T]TTCACCAGGTTGCTATTCTTGAAAGGAGCTGATAC K 2 1 2 1 201000 f 74 goat snp23244-scaffold2321-386278 7 96010310 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430785 Affx-122937476 AX-123301126 7 12699429 CTGTAGCTTGCTGTCACTCTTGACCTTCCAATGAC[A/G]TAGGCAGAACAGAATAATTCCTATTGCTGTTTGTA R 2 1 2 1 201000 r 74 goat snp23243-scaffold2321-341593 7 96054851 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403997 Affx-122957200 AX-123274349 7 12789506 CCGAGTTTCTGGCTGGTCATCTTATGAAACAGGCC[A/G]CGTAAATTCTGTCCTCTGTCCTCTGTCTGCCGGCT R 2 1 2 1 201000 f 74 goat snp23241-scaffold2321-251516 7 96144539 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376207 Affx-122978810 AX-123246566 7 12839648 CGACATTTTTTTTAACATGAGGTTTTCTACTTGAA[C/T]GCTGCTGAACGCAACACTTCGAGAACCACCTCGAA Y 2 1 2 1 101000 f 74 goat snp23240-scaffold2321-201374 7 96194598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428822 Affx-122938380 AX-123299164 7 12935219 CAGCAACAGAGACAGGTGGGAGAAAGAGACAGAGA[C/T]GAGTGGCCAAAGATATGGAAGGAAAGAGAATCCAG Y 2 1 2 1 101000 r 74 goat snp23238-scaffold2321-105803 7 96287405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438032 Affx-122931558 AX-123308370 7 13032718 AGTTAGTTTCCCCCACCCAGGGGATTTGGTAACTG[C/T]GAACCAGCTCCAAGCATATGACACAGTATTATCTG Y 2 1 2 1 101000 r 74 goat snp23237-scaffold2321-8304 NW_017189666.1 6645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419107 Affx-122945773 AX-123289455 7 13051998 GTGAGCTGAGCTTGGGGTCTGAGGAGGATGGATGA[A/G]CATGTGAACACAGGGCTCCAGCCCTCCATGAGTTG R 2 1 2 1 201000 f 74 goat snp514-scaffold1013-1040227 7 93896860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376359 Affx-122978323 AX-123246718 7 13084506 AGGGTTGTTGAGAGGATGTGAGAAGGTGGAGTGTG[C/T]AAATGCATCTATGCTGCTGCTGCTGCTGCCAAGTC Y 2 1 2 1 101000 f 74 goat snp513-scaffold1013-1007719 7 93864466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273255 Affx-1111833529 AX-519546906 7 13104625 ACATCCATCACGCAAGGGCTCTAGAAATATGAATG[A/G]CAGTTCTTTCACTTTTCCATATGGTAGAGACATTT R 2 1 2 1 101000 f 74 goat 7_13104625_AF-PAKI 7 13104625 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781853 Affx-122966881 AX-385268935 7 13117051 ATCCCCCTATTGGAAAATAACTTTGCAATGACCCA[C/T]CCACTTTTTTTCAGGTACAACTTCCTTGACCCTGC Y 2 1 2 1 101000 f 74 goat snp512-scaffold1013-975174 7 93832098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420115 Affx-122945084 AX-123290463 7 13172444 ACCCCCTGAGTCCTGTCCGTCTGATCACAGGCACT[A/C]TGTTCCAGGTTGAGCAAGAACCTCTCACTGAGATG M 2 1 2 1 101000 r 74 goat snp511-scaffold1013-919781 7 93776704 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412275 Affx-122950885 AX-123282624 7 13211587 TACATTCTTTCTAGTCCAAATCCTATTCCTCTGGA[A/G]GCAGAAAAGGCTTTCTCTCCGGTTTGCTCGATAAC R 2 1 2 1 201000 f 74 goat snp510-scaffold1013-880638 7 93739114 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453248 Affx-122920411 AX-123323581 7 13306120 ATAATCTGGAGAGCTTAGCGGAGAGTCTGAGATGC[A/G]CCTATGATCACTGAGAGTGTGCTGGGATTGATTAG R 2 1 2 1 201000 r 74 goat snp509-scaffold1013-786105 7 93643989 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408423 Affx-122954463 AX-123278774 7 13351088 CTAATATGTGCAGATACTACATACCCACACAGTTG[C/T]GCATTCACACACTTATATATACTCACACACAGGAA Y 2 1 2 1 101000 f 74 goat snp508-scaffold1013-741137 7 93599611 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437827 Affx-122932104 AX-123308165 7 13412217 TCTGTGAAGCAAGTGCATTGAAAATCCCCATTTTG[C/T]TGCAGCAAGGGGGAACCCTTCCAGGTCCCAAAAGA Y 2 1 2 1 101000 f 74 goat snp507-scaffold1013-680008 7 93538452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404347 Affx-122956826 AX-123274699 7 13445528 AGCAATACCCACCTCGCAGCCCAGCTTCATAAGGC[A/G]CACAAAGTGCTTAGCCTGGTGACTACGGACCCTTA R 2 1 2 1 101000 r 74 goat snp506-scaffold1013-646697 7 93507251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403248 Affx-122957882 AX-123273601 7 13487007 GGTTCTAGGTGGTATCTTTTTGCCATGTCCTCACA[C/T]GGGGGAAGGAGTCAGGGGTCTGAAGGGTCTCTTAT Y 2 1 2 1 101000 f 74 goat snp505-scaffold1013-605218 7 93465818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404710 Affx-122957257 AX-123275062 7 13548707 TGGCCAAGAAAGATCCTTCAGTAGGCTGGAGGAGG[A/G]GGTGTGACAACCCCACTCAGATCTGACAACCCCAG R 2 1 2 1 101000 r 74 goat snp504-scaffold1013-543518 7 93403689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275503 Affx-1111834843 AX-519549075 7 13574411 GTCCTGATGACTGAAGAAAATGTCTAGGCTTACAT[A/G]AGAGACGTGAAAACCATTGGCAGATAAGTAGGTGT R 2 1 2 1 101000 r 74 goat GoatD01.056206 7 13574411 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399902 Affx-122960204 AX-123270257 7 13588780 ACAAAATAGATCTAAGTGTTCCTAACTGCCTAAAA[C/T]ATTCTCTATTTAAACAGTCTCAGACTGAGGTTCTT Y 2 1 2 1 101000 f 74 goat snp503-scaffold1013-503445 7 93363803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476230 Affx-1251763736 AX-586011654 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 4 1 4 1 20000 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 539476484 Affx-1251763736 AX-586011883 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 4 1 4 1 20000 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165447 Affx-1251763736 AX-606940858 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165501 Affx-1251763736 AX-606940912 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165709 Affx-1251763736 AX-606941118 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165971 Affx-1251763736 AX-606941380 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562166047 Affx-1251763736 AX-606941456 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 320803174 Affx-122968779 AX-385290036 7 13657749 AATAAAAACAGTGTAGAATCACATTCAAAATAGAT[A/G]TTGTTAGTGATAGAAACTTGGGCTGCTCTGGTGGC R 2 1 2 1 101000 r 74 goat snp502-scaffold1013-434476 7 93294681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390072 Affx-122968404 AX-123260429 7 13762230 GGGAACGATTTTGAGGAATTTAATGCATTCACCAC[A/C]ACCTCTATCTCAGTCCAAAACATTTTCATCACCTC M 2 1 2 1 201000 f 74 goat snp500-scaffold1013-329995 7 93190250 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424671 Affx-122942147 AX-123295017 7 13809868 CATTTTAAGTTTTTCAGACATCTTTATTTGGGACC[A/G]TTTTGATGCTGGGTATAGAATTTTGTCTTGACATG R 2 1 2 1 101000 f 74 goat snp499-scaffold1013-282357 7 93142056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385383 Affx-122971623 AX-123255741 7 13847191 CACCACAAAATATCATTCCAATTATAAATATTCAT[A/G]TTAGAGGAAAACACCATGGAATGAACTCATGTTCA R 2 1 2 1 101000 f 74 goat snp498-scaffold1013-245034 7 93106618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795070 Affx-122949989 AX-385282029 7 13917706 TTTTATACAATGAAAATAACATTTGATGGATACAG[C/T]GACTCCCTTTGACTCTCCAACCCTAGATTCTATTT Y 2 1 2 1 201000 f 74 goat snp497-scaffold1013-174519 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795945 Affx-122955319 AX-385282897 7 13978739 TAGGAATCTATCCAGGGGATATTGCAATCAGTGTA[A/G]TTTATAAATACAGGGACATAGGATATATAAATTTA R 2 1 2 1 101000 f 74 goat snp496-scaffold1013-113486 7 93051758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421383 Affx-122944036 AX-123291730 7 14012766 GTTAGAGTGTGTTATTCCCCATATTTCATTTGACT[A/G]TTACTTTTCTTTCTCAGAGGATGCCAATAATGAGA R 2 1 2 1 101000 r 74 goat snp495-scaffold1013-79459 7 93017205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389475 Affx-122968328 AX-123259833 7 14058559 TCTTTTCCCAGCACCTATTAATATTTGAAACCATA[C/T]TGATTTTTTGTTGTTGTTGTTTTACTTATCGTGTA Y 2 1 2 1 102000 f 74 goat snp494-scaffold1013-33666 7 92962595 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783608 Affx-122958395 AX-385270667 7 14089168 CTGATTTTTATGGAGATATGTGATGTCATCTCTGA[C/T]GTTTCTGGTGTATTTGTAGCAGTTAGCTATTGCTG Y 2 1 2 1 201000 f 74 goat snp493-scaffold1013-3057 7 92931457 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381359 Affx-122974407 AX-123251717 7 14093792 ATGAGGATTATATTTCCTCCCCTTGAATCTGAGCA[C/T]GCATGTGACTGTGGTGGTGGTGACACTAGGTCATA Y 2 1 2 1 303000 r 74 goat snp4921-scaffold1166-1468 7 92918718 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407338 Affx-122955292 AX-123277689 7 14122726 CAACTCGGAGTTTCCTATTGCTTTCCTCTAGCTCT[A/G]CCTCTCATAACTCAAATCCATCCCAAACCAGAGTA R 2 1 2 1 101000 r 74 goat snp4922-scaffold1166-30402 7 92889387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398458 Affx-122961593 AX-123268813 7 14178357 ACACAGAGATTAAACCCAGGTCTCCTGCACTGCAC[A/G]TGGATTTTTTTTACCATGTGAGCTAGGTAAACCAA R 2 1 2 1 303000 f 74 goat snp4923-scaffold1166-86033 7 92832827 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416223 Affx-122948224 AX-123286572 7 14207548 AGCTCCTGTCACATCTGCTTAGTGGACTTCTGCTC[A/G]TCCTTCAAGGCTCATCTCCAATAGCTCTTCTTCCA R 2 1 2 1 101000 f 74 goat snp4924-scaffold1166-115224 7 92803503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790082 Affx-122953455 AX-385277088 7 14276898 TTGTAGTTTCAGGTTTTAAGGGTCTAGAGACTTCG[C/T]GTGGGTGTATGTGGCTGAGGGAGTGGATCTGGGTC Y 2 1 2 1 202000 r 74 goat snp4925-scaffold1166-184574 7 92735452 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389483 Affx-122968321 AX-123259841 7 14308922 TCATGCATAGAGGTCCTAGACACTCTCATCCAACC[A/G]CCCCCAAACCATTTTGCTACTCCACTACAAAACCC R 2 1 2 1 101000 r 74 goat snp2708-scaffold1079-3652 7 92644109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274453 Affx-1111834206 AX-519548043 7 14324360 TTTAGGGGAGAAAAATGAGGCTGCAGCTACCTGAA[A/G]GCTGGTTACCATGAAGTGTTGCTCACTTCTGAATC R 2 1 2 1 201000 r 74 goat GoatD01.025369 7 14324360 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409726 Affx-122953029 AX-123280077 7 14341084 CTGGTTTGATCTTGTTGATTGGCTCTGACCAAAAG[A/G]ACACAATGGAAGTGACATAGTGCCTATCCCAGTTC R 2 1 2 1 101000 f 74 goat snp2709-scaffold1079-35814 7 92612874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411555 Affx-122951642 AX-123281905 7 14383974 GATGTGGCTGGGGTTTCATTGCTCTAACTAACTCA[A/G]CCATTATCAGTTTTCAAATTCTGTTGACTGTAAAG R 2 1 2 1 101000 f 74 goat snp2710-scaffold1079-78704 7 92569832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392011 Affx-122966488 AX-123262368 7 14422892 TCACGAGAATAACAAAAATCCCATGCCTAAGGCAC[A/G]GGGCAGTTTGAAGCCTCAAGATAACTCACATTGTC R 2 1 2 1 101000 r 74 goat snp2711-scaffold1079-117622 7 92530701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389652 Affx-122968729 AX-123260010 7 14464313 TAAGCCCACCCACCCTGAAAATGCAATGCTCTCTG[C/T]TCTCTTCTCTGCAGGGACACTCCGATCCTACCAGC Y 2 1 2 1 101000 r 74 goat snp2712-scaffold1079-159043 7 92491142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404482 Affx-122956723 AX-123274834 7 14532193 GGTGGAAAACCTCCCCACCCAGTTCTACAGGCCCT[G/T]GGCTGCCAAGTCAGAATGCCTGAGATGTCCGGCTA K 2 1 2 1 101000 r 74 goat snp2713-scaffold1079-226923 7 92423447 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278626 Affx-1111836433 AX-519552105 7 14647547 TGTTTTGGTTCAGATTCTAGTTCCACCATCTTTAC[A/G]GTGCAATGTAACATGCGCATCTTTTCTAAGTGCTA R 2 1 2 1 101000 r 74 goat Random2.2K-764 7 14647547 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412599 Affx-122951290 AX-123282948 7 14652710 CCTGTTCTACCAAGCTGAATGCTTTCTTTTTCATC[A/G]TCTTGTGCACTTTATTCTGTTCTGGCTCATTGCTG R 2 1 2 1 101000 f 74 goat snp2715-scaffold1079-347440 7 92303457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771611 Affx-122945766 AX-385258769 7 14733257 CACACATACGAATAGCTCCTTCCATAAACCCATTC[A/G]CATAATTTATGCTGTTCCATACTCTTTTTTCCAAT R 2 1 2 1 101000 f 74 goat snp2716-scaffold1079-427987 7 92222272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394708 Affx-122964343 AX-123265063 7 14789228 GTCTCTGCTGGAGAAGGAGGGATGGCTTGGCTCCC[A/G]TCACGAAAACAGCAACAGAAGCCCAATTCTGACCA R 2 1 2 1 202000 f 74 goat snp2717-scaffold1079-483958 7 92165686 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382759 Affx-122973589 AX-123253117 7 14848028 GAATGGAAAGGGCCAGGGTGGCCAGTCTCTCAGGG[A/C]TTTGCCTTTTGGTCTCTTTTTAGTGTGTTTGGCTA M 2 1 2 1 101000 r 74 goat snp2718-scaffold1079-542758 7 92106887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782915 Affx-122976536 AX-385269985 7 14886211 CAAGCCTCAGTAGACGGAATACTAGTAATTGCCGT[C/T]GATTCAGCCTTTACACAAAGGACGGGCGCTTCTCA Y 2 1 2 1 201000 r 74 goat snp2719-scaffold1079-580941 7 92068680 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439706 Affx-122930563 AX-123310043 7 14960350 CTCACTAACGATGCCTACAATTCCACCAGTGTGCC[A/C]ACCCCAAAGATGTGTGTCTAGAGTTAATTCATGGG M 2 1 2 1 101000 r 74 goat snp2720-scaffold1079-655080 NW_017189930.1 20183 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393358 Affx-122965924 AX-123263714 7 15016023 AAAGTTTAAAAAGTTGCCCCAAGTCCCATCATACG[A/G]ACCAGGGGTCAGCAAGTTTCTTCTGTAAAGGACCA R 2 1 2 1 102000 r 74 goat snp2721-scaffold1079-710753 7 91950772 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428638 Affx-122938668 AX-123298980 7 15057327 TGGTCCAGGTCATCATCCAGCTCACCTGAGCCACT[A/G]CAGCAATCTTCTTACCTGCTGAAAACCCTGCCTGT R 2 1 2 1 101000 r 74 goat snp2722-scaffold1079-752057 7 91909338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385252 Affx-122972086 AX-123255610 7 15090789 TGAAAATTCTTGTTAGTCACATAAAGCAAGCACTC[A/G]CCAGACATTTGACTTATTTTTAATATTATCACCAC R 2 1 2 1 101000 f 74 goat snp2723-scaffold1079-785519 7 91876658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278628 Affx-1111836434 AX-519552107 7 15118359 GTGAGCTACTTCATAGACAGAGAATAATATCTGAC[A/C]TTTACTGAGTGCTAATTGAGCACTTTAAGCTAAGT M 2 1 2 1 101000 r 74 goat Random2.2K-765 7 15118359 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443852 Affx-122927524 AX-123314189 7 15136184 TGCTATGGTTGTGCTCTTAAATTGTTAAGTGTTAT[C/T]GTCAGCTAAATAGAATTGATTTTTAAGAATCTGAC Y 2 1 2 1 101000 f 74 goat snp2724-scaffold1079-830914 7 91831328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406820 Affx-122955683 AX-123277171 7 15178022 AGTCAAAGCCTAGCAGCTGAATGATGCACAAATGC[C/T]CACACAAGCAATGTTCAATATACAGTAAGCATTCA Y 2 1 2 1 101000 f 74 goat snp2725-scaffold1079-872752 7 91789243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396700 Affx-122962823 AX-123267055 7 15221110 CCTTGTGTTGCCTTACTTTCCCTGCTACCACAGCC[C/T]GTGAGTCTGTAGGTCTTGCCTCTTCTCCCCGCAAA Y 2 1 2 1 101000 f 74 goat snp2726-scaffold1079-915840 7 91747232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428884 Affx-122938935 AX-123299226 7 15273779 TCCCTAGTAATTCAGTCATTAAGACTTTGTGCTTG[C/T]GATGCAGAGGGACTCAAGTTCAATTCCTGGTTGGA Y 2 1 2 1 101000 f 74 goat snp2727-scaffold1079-968509 7 91716567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415829 Affx-122948881 AX-123286178 7 15316037 TTTCCATCTATATCTCCTCTGACTCAAAACCCCTC[A/G]CTGGTTTCTTAAGGTCCCCAGGATATACAAAACCC R 2 1 2 1 201000 r 74 goat snp2728-scaffold1079-1010767 7 91674193 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386157 Affx-122971392 AX-123256515 7 15358012 GGACAATTGGGTTGTTTCCGCCTTTTGGCTTACCG[C/T]GAATCATACTGCTTTGAATACACACGTACGGGTTT Y 2 1 2 1 101000 r 74 goat snp2729-scaffold1079-1052742 7 91631947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414032 Affx-122949792 AX-123284381 7 15387445 AGGTTGGGCCCTGCCTTCCGGACGACCCCTGAAAC[A/C]CGGAGCCTGAACTTGAGCTGCAGCTGCAGTTTGCA M 2 1 2 1 101000 r 74 goat snp2730-scaffold1079-1082175 7 91602336 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406112 Affx-122956209 AX-123276464 7 15422080 GTCATAAATCTGACAATTACCAGCCTCAGGCAGAA[C/T]GGAGCTGAGATTGTTCCCATTAATAGATGAGGAAA Y 2 1 2 1 101000 f 74 goat snp2731-scaffold1079-1116810 7 91567868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377969 Affx-122977622 AX-123248328 7 15470575 CACAGAGGCTAAGAGTCCCACGTAGGAAGAGGAGT[A/G]CTCTGAGAAGCAGGGGGACATGGGGAGTTACAAGA R 2 1 2 1 101000 f 74 goat snp2732-scaffold1079-1165305 7 91520721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381899 Affx-122974156 AX-123252257 7 15499689 TGTTCAGCTCCAGGCGAAAAGATTTGGTTGCGTGT[C/T]ATTTATCAGCCACCACCCACCCCTTGTTAACTTCC Y 2 1 2 1 101000 f 74 goat snp2733-scaffold1079-1194419 7 91492027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797053 Affx-122976806 AX-385283993 7 15529555 AAAACTGTCAAGCTGTACTCTGAAGGTTGGAGCAT[C/T]GCTTTGTAGTTAAGTTCTAACTTGATTTGTAAGAG Y 2 1 2 1 101000 f 74 goat snp2734-scaffold1079-1224285 7 91463507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422740 Affx-122943250 AX-123293086 7 15600048 ATTATTATCAAGAACAATGAAAATAAATAAGCAAA[C/T]GCCTTGTGAGTTAAAAATTAAATGAGTGTGTCAGG Y 2 1 2 1 102000 r 74 goat snp2735-scaffold1079-1294778 7 91392163 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393890 Affx-122965118 AX-123264245 7 15633834 GGCATGCCTGCCTCTGTTCAGACGTTCCCAGGGAC[A/G]TGAAAATCCACAACCATGAGCACCTTTCCCCCAAA R 2 1 2 1 101000 r 74 goat snp2736-scaffold1079-1328564 7 91361123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464493079 Affx-1110513525 AX-515965360 7 15657036 AACCAAATATCCAGATTTTAAGCAGTACGTTCAGA[C/T]AAATCTTTATGGAAAAGTGAGTCTTAAAGACCCTA Y 2 1 2 1 101000 f 74 goat 7_15657036_AF-PAKI 7 15657036 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433560 Affx-122934982 AX-123303901 7 15670011 GTGAGGGTTTCAACTGGCCCCAGCGGGACTTCTCC[A/G]CTTTTCCTTGGAACAGTTTCCTGCTGGTGATGCGG R 2 1 2 1 101000 r 74 goat snp2737-scaffold1079-1364741 7 91325083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424300 Affx-122941972 AX-123294646 7 15710024 TACAACAACCATGCCAGGTACCAGGAAAGCAGCAG[C/T]AAAGAAAACAGGAAAGGTCCCTGGCATCCCTGGGG Y 2 1 2 1 201000 r 74 goat snp2738-scaffold1079-1404754 7 91285677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440810 Affx-122929825 AX-123311147 7 15748410 CAGTGGGGTTCTCATGTCTTGTCACTGCCTGGCAC[A/G]CTGTGGGTGTCAAGGTCATGTTCAAACAAGTGAGC R 2 1 2 1 101000 r 74 goat snp2739-scaffold1079-1443140 7 91247199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419964 Affx-122945199 AX-123290312 7 15793303 TTTTTCATCATGACTGTATTTGTCACGATGAGCTG[C/T]GATCAGTCTCTTTGACTATTGTAATTTTGGGGATG Y 2 1 2 1 101000 r 74 goat snp2740-scaffold1079-1488033 7 91201927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406680 Affx-122955784 AX-123277032 7 15823253 GGTGCATCTGAGGGACATGGCCAACAGCATATATC[A/G]CCATATGTTCTTGGGGTGGATGCCCCCTATATTGT R 2 1 2 1 101000 f 74 goat snp2741-scaffold1079-1517983 7 91173821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391586 Affx-122966609 AX-123261943 7 15884863 TTGAAAGCCAATTCCTCCTACAAGGGAATATGTAC[A/G]TGTGTCCACAGAAGCACTAATCCCAGAGGATGAGG R 2 1 2 1 101000 f 74 goat snp2742-scaffold1079-1579593 7 91112137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412942 Affx-122951465 AX-123283291 7 15916719 CTGAGAGACGAGACTGGAGACCCTGCCCGAGCTGA[C/T]GGCACTCCTGGTACTTGAGTTTCTAATGGCACAAT Y 2 1 2 1 101000 r 74 goat snp2743-scaffold1079-1611449 7 91080155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391478 Affx-122966716 AX-123261835 7 15948105 CCACCAGGGAAGCCCAGTTGTAAAACGGGTACCAG[C/T]AGCCAATCTATGGTTGCTGTGGATAAATGAAAGCA Y 2 1 2 1 202000 f 74 goat snp2744-scaffold1079-1642835 7 91048671 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383195 Affx-122972790 AX-123253553 7 15992536 AGCGCACCACTCCATCGTGGATTAAAAAAATGAAT[C/T]AACAAAAGGCCTCTCAGAGAGTAGGACGTTGACCA Y 2 1 2 1 101000 f 74 goat snp2745-scaffold1079-1687266 7 90999531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394700 Affx-122964349 AX-123265055 7 16043582 ATCTAGACCTGTCTGAGAACAATCTCCACTCCCTG[A/C]CCCCTGGGCTCCTGGAGAATTTCCCCGACCTGCTC M 2 1 2 1 101000 f 74 goat snp2746-scaffold1079-1738312 7 90949468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405868 Affx-122955848 AX-123276220 7 16080988 TCCTCCAAAAACAGACCACCCCTAACAGAGGGCCA[C/T]GGCTGACCATGGAGAGATGCGCAAGGAATTTTCCC Y 2 1 2 1 102000 r 74 goat snp2747-scaffold1079-1775718 7 90911962 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764731 Affx-122920857 AX-385252348 7 16141807 CTTAGGCCAAATCTCAAGAAGATAAAGTTATAGCC[A/G]TTCAGTAAGGTTTATCCAAATGTATGGTAAAGCAG R 2 1 2 1 101000 f 74 goat snp32989-scaffold3846-61867 7 90851828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384165 Affx-122972426 AX-123254523 7 16192526 CAAAGATTAGCCTTGGGAATTCACTGAAGAACTGT[A/G]TAACTCTTCCTCTCCTGAACTGTCTGGTAATGTTG R 2 1 2 1 101000 r 74 goat snp32988-scaffold3846-11148 7 90801069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404465 Affx-122956734 AX-123274817 7 16291240 GGATATGGATATGTATGGATATAGATATGGATATG[A/C]GGATATGGACCAGTATGGGCAAAGGTTTGGAGGCT M 2 1 2 1 101000 f 74 goat snp55237-scaffold85-2363783 7 90700993 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408533 Affx-122953693 AX-123278884 7 16437203 CTCTGTTTTGAGAAATTGAGAGTTGCCCTAGAGAT[A/G]CAGGGGTCCGAACCCTGCCAGCCCAAGGTGGCATC R 2 1 2 1 101000 f 74 goat snp55235-scaffold85-2217820 7 90555022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425643 Affx-122940889 AX-123295989 7 16490418 CTGCAGACCTACTGGGAGGCCCATGCTCCTTGTAG[C/T]ACTCAGCACTAACTTGCACCACCGCCCCCCCAATC Y 2 1 2 1 202000 f 74 goat snp55234-scaffold85-2164605 7 90502756 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425957 Affx-122941175 AX-123296303 7 16539778 GGAGGGCAGATCTGATTCAAGAAAAGACTGAAATC[G/T]AGAGTTTTTGTGTCTCATCTCTGATTTGACAGCGA K 2 1 2 1 101000 f 74 goat snp55233-scaffold85-2115245 7 90454437 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414774 Affx-122949241 AX-123285123 7 16571640 TTCATCCAGGTCAATGGTCTTGGTCCTTACTTCCA[C/T]AGCCACATAGAAGAACACCAATTACACTCAATGTG Y 2 1 2 1 101000 f 74 goat snp55232-scaffold85-2083383 7 90422629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389127 Affx-122968556 AX-123259485 7 16604814 TCCGCTGCTTAAAGCCCTCCAGTCTCCCCATTGCC[C/T]TGAGGAGGCAGTCACACCTCCGCACACGGCCTTCC Y 2 1 2 1 201000 r 74 goat snp55231-scaffold85-2050209 7 90389722 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383673 Affx-122972505 AX-123254031 7 16673383 GGCAGCTCATGAGATAGTGTTGCTTATTAATGTTA[A/C]ACAGAGGAGAAAGGTCATTATTATTCTCACTACAA M 2 1 2 1 101000 f 74 goat snp55230-scaffold85-1981640 7 90322724 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393787 Affx-122965190 AX-123264142 7 16702787 GGGGTCCTGCAGACCTGGGGACTGTCTCACCTTGA[A/G]TCAGCCAACTCCCAGATCACAAACAACATGTCCAT R 2 1 2 1 101000 r 74 goat snp55229-scaffold85-1952236 7 90294761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382136 Affx-122974052 AX-123252494 7 16764414 CAGGGACATAGACCCTGAGTCTGTTTCACACTTCC[C/T]ATATGTGGGAATAAAAACTGCAACCCCAGGGCCCC Y 2 1 2 1 101000 f 74 goat snp55228-scaffold85-1890609 7 90233482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413225 Affx-122950250 AX-123283574 7 16806084 CACTTGGCCCCAACCCTGAGCTCAAGTCCTTGGGA[A/G]CACCCCTCCCAGCCCCCCCAGCTCACCCGGAACAC R 2 1 2 1 303000 r 74 goat snp55227-scaffold85-1848939 7 90191819 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376634 Affx-122979029 AX-123246993 7 16878963 ACTGAACTTCCTGAGTTTTATCCAGCAGCCCTGCT[C/T]AGGGGCCCAATCACTCGCCCAGGGTCACCTAGCAG Y 2 1 2 1 101000 f 74 goat snp55226-scaffold85-1776060 7 90119800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433468 Affx-122935051 AX-123303809 7 16915150 TATGTGTAAGCACTGTTTAAGCACCAATTGCATGC[C/T]AGGCTCCATGAAGAGAGGCCACAGGAGGACCAGGG Y 2 1 2 1 201000 f 74 goat snp55225-scaffold85-1739873 7 90084856 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278630 Affx-1111836435 AX-519552109 7 16923739 TGTTCATTTACATCTAGGTATTCAAAGACATGGCA[A/C]TATGTTTATCCCTGGGCTTCAAATTGTGAGCCAGA M 2 1 2 1 101000 r 74 goat Random2.2K-767 7 16923739 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432031 Affx-122935911 AX-123302372 7 16974423 ATGTGAGGCTAATGCTGGGATCCCAGCTTCAGGGA[C/T]GGAAAGCAAGGGTGGGATTGTTCCTGAGATGGGAG Y 2 1 2 1 201000 f 74 goat snp55224-scaffold85-1680600 7 90025440 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414108 Affx-122949737 AX-123284457 7 17028582 GAGCTAGATCCTGGGGACAGAGGGGCTTGGCTTAC[A/G]TTTTTTCTTAAAATTTGAAAAATACTGCACATTTA R 2 1 2 1 202000 r 74 goat snp55223-scaffold85-1626441 7 89971016 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405625 Affx-122956599 AX-123275977 7 17102206 TGCCTGAGTAATGGTCGCATCCCCGGGTAAATGAC[A/G]CAGGGTTTGTTATCAGCGACCCATATTTCTTAGAA R 2 1 2 1 101000 r 74 goat snp55222-scaffold85-1552817 7 89898201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405622 Affx-122956601 AX-123275974 7 17184388 ATATCCTGTGTGGGGAGACTGATGTTCTCTTGACT[A/G]AAGTGCCAGGTGCCCTAGGGAACCACCTTTCCTCC R 2 1 2 1 101000 f 74 goat snp55220-scaffold85-1470635 7 89824932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413494 Affx-122950645 AX-123283843 7 17255866 CTGCCTGGGATGGAGGAGCCAAGTAGGGCACATAG[A/G]TGTGGGGGGAACACTTGGGCTGAGGGCCAGATGAC R 2 1 2 1 201000 f 74 goat snp55219-scaffold85-1399157 7 89753336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762517 Affx-986697047 AX-385250632 7 17257039 AGGAATTAATTAGGTAGATGTTTCTGACCCATTCT[C/G]ATAACTGTAATATTTGAATTTTCATTGAGTGCACT S 4 1 2 1 600010 f 74 goat 7_17257039 7 17257039 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320803636 Affx-986696152 AX-385290415 7 17257094 TTTCATTGAGTGCACTGGTATTTATTCTTGATGCT[A/G]AAATGGTTTTGCCACTGCTTTTAGCTCAAATGAAG R 2 1 2 1 600010 r 74 goat 7_17257094 7 17257094 Ancestral_priority_1043 ancestry 0.75 recommended IMAGE 10K 10K ancestral 320762519 Affx-986697049 AX-385250634 7 17257189 TCAAAACTGCCAGAAGCATTTAATGTCCCTTAACT[A/C]ATCTTTTTTTCTCTTGCCTTCCCTCCCTCCACCAA M 2 1 2 1 600010 f 74 goat 7_17257189 7 17257189 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320762521 Affx-986697051 AX-385250635 7 17257263 GTCTGTAGTATATTTACTTTATATCTGTCGTATAT[C/T]CATTCATTATTTCAGAGGAATAATGCAGTTCAATA Y 2 1 2 1 600010 f 74 goat 7_17257263 7 17257263 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 320764826 Affx-986697053 AX-385252430 7 17257265 CTGTAGTATATTTACTTTATATCTGTCGTATATTC[A/G]TTCATTATTTCAGAGGAATAATGCAGTTCAATAAT R 2 1 2 1 600010 r 74 goat 7_17257265 7 17257265 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38382668 Affx-122973660 AX-123253026 7 17304333 TGTGTCACTTACTAAGCTACTGTCTCTCCTTCAGA[C/T]CCATGCTATGAGTTACCTGTTGCTGCTGTAACAAA Y 2 1 2 1 101000 f 74 goat snp55218-scaffold85-1350690 7 89704514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394812 Affx-122964804 AX-123265167 7 17349263 AATGACCGTCATTAGGGTTAAAGTTGCCAGAAATG[C/T]TCTCCCAATTCATTTTTATCCTACTTAAAACGCAC Y 2 1 2 1 101000 f 74 goat snp55217-scaffold85-1305760 7 89659342 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401346 Affx-122959257 AX-123271699 7 17381410 GTCACTCTACCCTCCTGGGTGAAGGTGCTGAGAAC[A/C]AATAGGAGGCTTGCCAGCACATCTGGCTGTCCTCA M 2 1 2 1 101000 r 74 goat snp55216-scaffold85-1273613 7 89627079 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434236 Affx-122934834 AX-123304577 7 17410952 GACATGTGGGATGCTAGTGGTGGTACCAGAATGGC[A/G]GGTATGGGTACTGGCTCATCCTACACCCATTTCAC R 2 1 2 1 201000 r 74 goat snp55215-scaffold85-1244071 7 89597572 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785374 Affx-122928904 AX-385272419 7 17470374 ACTTATGACTGCTTTAAGGGCCCTCCAGGATAATC[G/T]CTTCATCTCAGAAGGCTTAATTGAATCACACCTGC K 2 1 2 1 101000 r 74 goat snp55214-scaffold85-1184649 7 89538233 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464499404 Affx-1110514094 AX-515971627 7 17640028 ACAAAGCTGCAGTTTTGTTCTTTCCTTCTAAATGA[A/G]TAAATACTTTTCTCAGGTTTAAAGAAGGAAGAGTA R 2 1 2 1 101000 r 74 goat GoatD01.060175 7 17640028 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407286 Affx-122955331 AX-123277637 7 17642717 CGGAACAGGGGTGGGGGTAGGTAATGAGATCCACC[A/G]CTGCAAAGCCATAAAGGTGACTCATCCCTCCTAGA R 2 1 2 1 101000 r 74 goat snp55211-scaffold85-1012306 7 89367303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411427 Affx-122951832 AX-123281777 7 17679986 CTCACTAAGCACCCTGGCATGGATGCTGTCAGTGT[A/C]ATCTTGAAGTTCCTGAACCTGCTTTGTGGTTGTAA M 2 1 2 1 101000 r 74 goat snp55210-scaffold85-975037 7 89329920 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421852 Affx-122944289 AX-123292199 7 17716371 TTACCCAGAGCAGGGTTCCCAATGCCAGATGCTCC[C/T]GAATTTTCCATGACTTGGCATTTCTGAGAAAAATG Y 2 1 2 1 101000 r 74 goat snp55209-scaffold85-938652 7 89293291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383105 Affx-122973274 AX-123253463 7 17751071 TTTAAATATAGCAGTGAGAACATTAACAGCAGAAG[C/T]AGAGGTGTTTCTGGCTGTGAGTCAGATGGCTGGTG Y 2 1 2 1 101000 f 74 goat snp55208-scaffold85-903952 7 89258650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400699 Affx-122959936 AX-123271054 7 17970340 AATGAATGTCTACCCATAACTGAATCGTGTATCTG[C/T]ACAACTGAAACAAACACACCAGAAATCAACAATAT Y 2 1 2 1 101000 f 74 goat snp55205-scaffold85-684683 7 89043742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393693 Affx-122965256 AX-123264048 7 18027048 GACCCCAGAAAATGTAACAAGGACAGGTCTCCCCC[A/G]AGATTCCTGGGGCCTGCAGGCAGATAACCAGCCAC R 2 1 2 1 101000 r 74 goat snp55204-scaffold85-627975 7 88987749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386906 Affx-122970033 AX-123257264 7 18062527 GTTTCTCAATCAGAAAGTCTGGTTTTTCCTTCAGG[C/T]AGAAGATTAAAAACACAAATATTTGTGACAACATT Y 2 1 2 1 101000 f 74 goat snp55203-scaffold85-592496 7 88952209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278632 Affx-1111836436 AX-519552111 7 18201824 CCTTCCATTCTCATCTACCCACACTTCCCCACTCT[A/G]TCTTGGTAGAGTAAACTGGTTCACATCCTTTAGAA R 2 1 2 1 201000 r 74 goat Random2.2K-768 7 18201824 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433537 Affx-122935000 AX-123303878 7 18203718 TGTTAGATTTTGACAGGCTACTTTTGTTTTTACAG[A/C]TATTTCTTTTCTTTTTCGTATTTCAAAACTACTAG M 2 1 2 1 101000 f 74 goat snp55200-scaffold85-451305 7 88810263 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380533 Affx-122975678 AX-123250891 7 18234280 AAGTTCATACAGTTAGTAGGAGACAGAGTTAATTT[A/G]CTGGTATATATCTTATGATATGTAAGACATCTGAC R 2 1 2 1 101000 f 74 goat snp55199-scaffold85-420743 7 88779673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273256 Affx-1111833530 AX-519546907 7 18240107 GAAACATTAAACTGTATGGAGAAAAACAAAAGTAA[A/C]ATGAGCAAAGAAATAGAATCGACAAGAAGAATATA M 2 1 2 1 101000 f 74 goat 7_18240107_AF-PAKI 7 18240107 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784300 Affx-122928092 AX-385271351 7 18328598 CCTAAAATATTTACTTTGCTTCTGAAGTTTAATTA[C/T]ACTGAATATAAAGACTCCACCATTGGCTGGCCCTC Y 2 1 2 1 101000 r 74 goat snp55198-scaffold85-326425 7 88684270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414150 Affx-122949694 AX-123284499 7 18397702 ACCCTCATCTGCCCGCCCCTCTGGTCTCCCACACC[A/G]CACACACCTGAGTTTGTGCTCAGCCAGGCACAAAC R 2 1 2 1 101000 r 74 goat snp55197-scaffold85-257321 7 88614936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444799 Affx-122926339 AX-123315136 7 18446344 TGGAAGCTCTGTGAGAGCAGGGACTTGTCTTTTGC[A/G]TTCATGCCGTTGTTCCCAGGTCCTAGAGCAGCATC R 2 1 2 1 201000 r 74 goat snp55196-scaffold85-208679 7 88566427 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405096 Affx-122956987 AX-123275448 7 18480801 AGGGAGGCAGGCTACATCTCAGAGTCCTTATTGCT[A/G]GAGTCAACAAGCCTTGGCAACCAGCTGGGTTGCTC R 2 1 2 1 101000 f 74 goat snp55195-scaffold85-174222 7 88531454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444153 Affx-122926790 AX-123314490 7 18556482 AGGTTTTAGAAGTCTCTCCATCTGGAGGAGGTTGA[A/G]CAGGGAGGGAGGTGCCTCTCTTCCTGTCCTGCTGG R 2 1 2 1 202000 r 74 goat snp55193-scaffold85-98541 7 88455754 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412516 Affx-122951357 AX-123282865 7 18590142 ACTGGTCTGTGATGGATCCAGAACTTGGGACCTAG[C/T]ATGTGGGACTGTCTGTCTCTCCGTGGCGGCTTTGC Y 2 1 2 1 101000 f 74 goat snp55192-scaffold85-64881 7 88422191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398280 Affx-122962168 AX-123268635 7 18643964 AGAAAGATCACTGTGCATACATCATAGAGGGTTGA[C/T]GAAGGAGGGGTCAGAGCAGGAACAAGGAGGCCAGT Y 2 1 2 1 101000 f 74 goat snp55191-scaffold85-11059 7 88369781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388327 Affx-122969364 AX-123258685 7 18659829 GCAGACTGTTTACTGCTGAGCTATCTGGGAAGCCC[A/G]TCTAAAATACATTAAACACAAATACTAATCCTGAG R 2 1 2 1 201000 r 74 goat snp29284-scaffold316-4707 7 88353797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476231 Affx-1251763737 AX-586011655 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 4 1 4 1 20000 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 539476485 Affx-1251763737 AX-586011884 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 4 1 4 1 20000 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165104 Affx-1251763737 AX-606940516 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165418 Affx-1251763737 AX-606940829 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165599 Affx-1251763737 AX-606941010 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165785 Affx-1251763737 AX-606941194 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562166113 Affx-1251763737 AX-606941521 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562166231 Affx-1251763737 AX-606941639 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 38434936 Affx-122933866 AX-123305276 7 18693174 TCTGTGAGCTTTTCCTCATGTTTCTGAATCTCTTT[A/C]TGAGCTTGTGAGAGTACTTGAGAGTGTGTTCCTTG M 2 1 2 1 101000 r 74 goat snp29285-scaffold316-38052 7 88320099 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400178 Affx-122960674 AX-123270533 7 18738047 TTTCCTTCATCTTTTGGTTGTGTGGATAACTCTTT[A/G]TTTCTTATTAAAATTTGAAAAACAACCTTTCTGGG R 2 1 2 1 103000 f 74 goat snp29286-scaffold316-82925 7 88275396 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406767 Affx-122955721 AX-123277118 7 18816632 AAGGCCCTGGCCTGTGTGTACAAGGCACAGGGAGG[C/T]ATGTACATGTGTGCTTGGCTGCACATGTCTGCTCA Y 2 1 2 1 102000 f 74 goat snp29287-scaffold316-161510 7 88196269 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428496 Affx-122938773 AX-123298839 7 18859436 ACTCCGCAGCCTCTGATCTCTCTGCACGGAGTCTG[C/T]GTTGTCTGCCCACTTCCTGCAGTGACTGGCTACTG Y 2 1 2 1 101000 f 74 goat snp29288-scaffold316-204314 7 88153480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402579 Affx-122958439 AX-123272932 7 18948318 TAGTGACAGAGTGGGCAGCTCAGCTCTGGGCTCCA[C/T]GTTCTGTTCCCAAGCCTAAACCCAGACTTTTGGGG Y 2 1 2 1 101000 r 74 goat snp29290-scaffold316-293196 7 88064278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403708 Affx-122958037 AX-123274060 7 18978510 GAAAGTATTTGAGCATACTTAACCATGATTTAACC[A/G]TTTTCTTGACATTTATATGGCTTATTAGTTTTTAT R 2 1 2 1 101000 f 74 goat snp29291-scaffold316-323388 7 88034036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420081 Affx-122945110 AX-123290429 7 19011106 TTTAAGAGTGATGCTCTCCTTTCATCTGTTATCCC[A/G]CACTCCACCAGTTTCTGTTAGTGTTGACCTCTGTT R 2 1 2 1 201000 r 74 goat snp29292-scaffold316-355984 7 88000331 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382089 Affx-122974904 AX-123252447 7 19053395 TGCATGACAATTCCTAGGGTAGAATAATCCCTGTT[A/G]TTCAGATGAACATATTAAAAGATTATATAGCTAAT R 2 1 2 1 101000 f 74 goat snp29293-scaffold316-398273 7 87956771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801368 Affx-122957403 AX-385288279 7 19102522 GGAAATTGTTTAAAAAGTTTCATTGTTAAGCTTAA[A/C]GCTTGTACAAACTTATTTTATAGACAACTTGTATT M 2 1 2 1 201000 f 74 goat snp29294-scaffold316-447400 7 87907525 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788849 Affx-122926886 AX-385275864 7 19144804 GAAAGACAGTGCTTTCTAGGGGAAGATACTCTTTA[G/T]ATTTTCTCCACCAGGATACTTTTCAGTGGAAGTAA K 2 1 2 1 101000 r 74 goat snp29295-scaffold316-489682 7 87864773 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375568 Affx-122978748 AX-123245927 7 19199815 ATGCTTTTTTGTAGTCCCAGTTTAAATGTCACTTC[A/G]TTCATCTGCCTAGATTAACTTAAGTTCTTTCTTGG R 2 1 2 1 201000 r 74 goat snp29296-scaffold316-544693 7 87809023 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394307 Affx-122964689 AX-123264662 7 19261607 CCTGAAGTTGGTGTGCCTGCAGGCAGTTTGGCCCC[C/T]GTATCCTATCAGCTGTTTTAGTGCCTGAGTCTCCC Y 2 1 2 1 201000 r 74 goat snp29297-scaffold316-606485 7 87746885 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406455 Affx-122955184 AX-123276807 7 19302359 TGGGTGCGCAAGTTGCAAATGTCTTCTTCCATTGT[A/G]TGGCTTGCTTTTTTTATTCCATTAACGGCGTCTTT R 2 1 2 1 101000 f 74 goat snp29298-scaffold316-647237 7 87706042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798807 Affx-122923971 AX-385285738 7 19333733 CCAAAAAGATGTCATCTCACGGATTTTAAAACTCT[A/G]CAGGATGAACATAAACTCTAACAGGATAAATACAA R 2 1 2 1 101000 r 74 goat snp29299-scaffold316-678611 7 87674586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793434 Affx-122923087 AX-385280411 7 19473547 AAGGCCTACACTCATGATTTTTAACAGGAGAATTT[A/G]AACAAAGAATTGAAAAAGTGAGACGTCAAGAGGCC R 2 1 2 1 101000 r 74 goat snp29301-scaffold316-818425 7 87533099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420639 Affx-122945220 AX-123290986 7 19504658 TGTGTAGGGTAACTTGGAAGAACTGGGGGAAGAAA[C/T]CCTGCCATGTTTCACCTCTATAAACCCAGTATTTA Y 2 1 2 1 101000 f 74 goat snp29302-scaffold316-849536 7 87501398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793780 Affx-122947611 AX-385280752 7 19584929 CTCAGTGGTGAACACTGCAGACGTTCCAATTAATG[C/T]AATGTTTTGTGAAACATCAGAGGCATTAAATTAAT Y 2 1 2 1 201000 r 74 goat snp29303-scaffold316-929807 7 87420316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416614 Affx-122947628 AX-123286962 7 19615271 CTAAGGGACTGGAGCTGAAGAATACCACAGGAATC[A/G]TAGCTGGAGGTTCCCACACATGGAATCCCCAAGAA R 2 1 2 1 201000 f 74 goat snp29304-scaffold316-960149 7 87389932 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404232 Affx-122957647 AX-123274584 7 19670982 TTTTAGGAACACAGAGATACACTCTGTCTCTAAAA[C/T]GAAACTGTATTGTTATTTCTTAGCTACTGAAATAA Y 2 1 2 1 202000 f 74 goat snp29305-scaffold316-1015860 7 87333993 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412712 Affx-122950743 AX-123283061 7 19718859 CCCTGCTCTGTCAAGTCCATGTTAATTTGATCCTT[A/G]CCCTCACATTTGTTAATATGTGGCTGTCACTGTAA R 2 1 2 1 101000 f 74 goat snp29306-scaffold316-1063737 7 87286544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429039 Affx-122938311 AX-123299381 7 19754441 ATTATACACTCAAGAAAGTACAATTTACACACAGC[A/G]TTGTGCAAATTATACGTGGTATGTTCACCCTCTAG R 2 1 2 1 101000 r 74 goat snp29307-scaffold316-1099319 7 87250516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780498 Affx-122968157 AX-385267589 7 19784426 TGACAGTGAAGGGAACATTGAGTGGGTGAAAGAAT[A/G]CAATAAAAACATGGCAAAAGTTGAGAATTTTTTAA R 2 1 2 1 201000 r 74 goat snp29308-scaffold316-1129304 7 87219544 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378766 Affx-122977011 AX-123249125 7 19828734 TAAGCAAATGATCTCCATAACTGGAACTTCAAAAA[C/T]AGAACAAAGAGAATGACCGTATTAAAAAACCTGAA Y 2 1 2 1 101000 f 74 goat snp29309-scaffold316-1173612 7 87174978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376036 Affx-122978942 AX-123246395 7 19895403 ACTCAAAGACTGTTATTAAATAAAATGCATCTGGG[A/G]AAAGCTAGGAAAAAGGTGATAGAATCTCTAGAAGG R 2 1 2 1 101000 r 74 goat snp29310-scaffold316-1240281 7 87108423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417002 Affx-122947984 AX-123287350 7 19930419 CCTGCCAGGATGCAATGACAAAATAGGGATTATTC[G/T]CAGATGGAAAAGAATCTGCCTACAATGCAGGAGAC K 2 1 2 1 101000 f 74 goat snp29311-scaffold316-1275297 7 87072459 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443758 Affx-122927117 AX-123314095 7 19973203 TACTGTCTAATACCGCTTAGTACAACTCACTTAAT[A/G]TAAGACTTGTGGTTTCACTGATCTTTTAAGAAATA R 2 1 2 1 101000 f 74 goat snp29312-scaffold316-1318081 7 87029996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774080 Affx-122958627 AX-385261218 7 20020121 AGGAATGTCAGACAAGGACATAAAGTGATACAGGC[A/C]TTCCGTACTAAATAATAGAGAACATCCTGCAATTG M 2 1 2 1 101000 f 74 goat snp29313-scaffold316-1364999 7 86982771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404175 Affx-122957690 AX-123274527 7 20065201 CTCCAGGGAAAGAGGAAGATGTCTCCTCTAAGTGA[C/T]GTTTCAACACACAGTGGTAAATAAAATAACGCTGT Y 2 1 2 1 101000 f 74 goat snp29314-scaffold316-1410079 7 86936870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767535 Affx-122921316 AX-385254791 7 20094048 TTACTACCGTGTTACCTTATACATCTAGGTTAATG[C/T]AAATGATGTTCTTAATTATCCTGCCCTACCTTCTG Y 2 1 2 1 101000 f 74 goat snp29315-scaffold316-1438926 7 86907999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409110 Affx-122953315 AX-123279461 7 20150375 AATTTCCACAAATCTCATTAAGGCTACAGTAGTGA[C/T]GGGCCTTTAAAACACTGTCACTTTTTCTAGGAAGT Y 2 1 2 1 101000 f 74 goat snp29316-scaffold316-1495253 7 86851263 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437612 Affx-122931852 AX-123307950 7 20180565 TTATCAATTAAAGAAATATTTTATTGAGACCTGGG[A/G]CAGGTATTGGGGACATAAAAATTAGAGGAAATCTT R 2 1 2 1 103000 r 74 goat snp29317-scaffold316-1525443 7 86820971 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420092 Affx-122945101 AX-123290440 7 20209196 AGTAAAAAGTTAAATACTCTAAAAGAAATAGCTAT[A/G]TGGTCACTAAAAATAAAAGAAACATTTCCCTAGAT R 2 1 2 1 303000 f 74 goat snp29318-scaffold316-1554074 7 86792156 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414675 Affx-122949299 AX-123285024 7 20289969 CCACTGGGATACAAAAAGTCTGCACACATACACAC[A/G]CATACACATATGTGCATACCTACAAGTTATGGAGT R 2 1 2 1 102000 f 74 goat snp29320-scaffold316-1634847 7 86710593 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434004 Affx-122934237 AX-123304345 7 20379667 TGAGATCCCTGAGCCAGTGCATGAATTCAGTTCCA[C/T]GCTTTTCCAGAGCCTAAGCGCCCGGCACTGAGCAA Y 2 1 2 1 101000 f 74 goat snp29322-scaffold316-1724545 7 86620504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408885 Affx-122953981 AX-123279236 7 20469000 GAGCATGATGCTTACAGATAACTTCAAATATATCA[C/T]GAACACATTTAAATATACAAGCATCTATGTGACTT Y 2 1 2 1 101000 f 74 goat snp29325-scaffold316-1813878 7 86530950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436249 Affx-122932555 AX-123306588 7 20525776 ACATGGCTTGTATTTTTCTGTTTGTTTTTTATTAG[C/T]ATTAGATACAGGCTAAGAGCTACTATGAATTCTTC Y 2 1 2 1 201000 r 74 goat snp29326-scaffold316-1870654 7 86474575 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765679 Affx-122973482 AX-385253143 7 20583084 TTTTATGCACAGTCCTAACTCGACAACTTAACCCA[G/T]ATTTCCACTGTTTGGAAAATGTTCCTCCTTGTTTT K 2 1 2 1 101000 f 74 goat snp29327-scaffold316-1927962 7 86417341 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420394 Affx-122944930 AX-123290741 7 20620797 AATACATTATAAAGAATTGGGGGTTTGAAAGCAGA[C/T]AAACTTGACTCAGCAATTTTTTAGTGATCTGGCTT Y 2 1 2 1 101000 f 74 goat snp29328-scaffold316-1965675 7 86379760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410517 Affx-122952175 AX-123280867 7 20696549 GTCTGTATATTTTAACTCTTTTCGGTGTTTTCTTG[G/T]CATTGCACCACTGAGAGCTGTGCTGAGGAGCAGGC K 2 1 2 1 201000 f 74 goat snp29330-scaffold316-2041427 7 86303527 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389824 Affx-122968187 AX-123260181 7 20737623 AAGTCAGTTTCTGTCAGATTTCCTTACCATCTTCA[C/T]GCAAAACAGAGTCAACATTTTCCCATTTGTATTCG Y 2 1 2 1 202000 r 74 goat snp29331-scaffold316-2082501 7 86261716 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380184 Affx-122975509 AX-123250542 7 20787152 TTAAAGGAGAATGATGAGTTACAAACTTAAATAAG[C/T]GTATAATTTTTCATCATTAGAGAATGACTTTCATA Y 2 1 2 1 101000 f 74 goat snp29332-scaffold316-2132030 7 86213764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406295 Affx-122956071 AX-123276647 7 20845615 TCTCAATAGGTAGGTTAAGATCAGCATATAGAAAG[C/T]GTTGAACATCAGAGTGAGTACATGAAAGTGAAAGT Y 2 1 2 1 101000 r 74 goat snp29333-scaffold316-2190493 7 86155917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273261 Affx-1111833532 AX-519546911 7 20863367 GGCCTTCTTTTATTTCCTGGAGAAATAAATAAGTT[A/G]TAAAAAAGGTAAGGCTTTCAAGCTGTAATAATAAA R 2 1 2 1 101000 f 74 goat 7_20863367_AF-PAKI 7 20863367 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424819 Affx-122941372 AX-123295165 7 20876860 GTTATCCCATAGTACACAATATCAAGCTTAGAACT[A/G]TACCATCGTGTATGGTACAACCATACATATTTTAA R 2 1 2 1 101000 f 74 goat snp29334-scaffold316-2221738 7 86124692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794021 Affx-122923796 AX-385280990 7 20935279 CATCATTCAGTTGATTCCTTTATTGCTTTAACAAA[C/T]ACTTATTGAACACTCTTTTAGGAGACAGAGGTACC Y 2 1 2 1 101000 r 74 goat snp29335-scaffold316-2280157 7 86065982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446363 Affx-122925598 AX-123316699 7 20976522 AAGAAAGGGTACACTGTGAGAGAGAAGTCACTTCC[A/G]TATGAAAATTAAAGAATAAATGGTGATGAAATAAA R 2 1 2 1 103000 f 74 goat snp29336-scaffold316-2321400 7 86024585 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402199 Affx-122959168 AX-123272552 7 21006349 TGATTCTAAGAAAATGTGAGAATAATTAAATTACT[A/G]TACCTTTTACCTGATATAATCCTGAAACACTGTGT R 2 1 2 1 101000 r 74 goat snp29337-scaffold316-2351227 7 85993922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425222 Affx-122941015 AX-123295568 7 21037235 TAACAAATAAGTATTCTTTTATCGTATTAAAGCTA[C/T]GCCTAGTCATTTCTTCCCTTTCTATTTCAGGATAT Y 2 1 2 1 303000 f 74 goat snp29338-scaffold316-2382113 7 85962683 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415414 Affx-122948731 AX-123285763 7 21072124 ATTTGCTCTAAGAAAGTGATACTAAATTAGGGTTC[A/G]TTTTTTTATTTATTTGTTTTTGGCTGTGCTGGGTC R 2 1 2 1 303000 f 74 goat snp29339-scaffold316-2417002 7 85927913 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422366 Affx-122943429 AX-123292712 7 21109041 AAGTGGAAGTTCAAGAACTTTCCAGAGCAGAAGGC[A/G]TTTGTGTCCCAGGTGATTGCTCCTCAAAACCCTCC R 2 1 2 1 201000 r 74 goat snp29340-scaffold316-2453919 7 85891153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786982 Affx-122928924 AX-385274010 7 21151757 GAATCATATTCACAACCAAATCTCAGAAAAACTTT[A/G]CCATAGTGGTCTGCAAGTTATCTATAGTTGTAATT R 2 1 2 1 101000 r 74 goat snp29341-scaffold316-2496635 7 85846558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433050 Affx-122935757 AX-123303391 7 21181931 TCACCTACGGACCCAAAGCTTCCTGTCACTTTTCT[A/G]CCAGATACCTGGGGGCAGTCTGAGTCTAACTTAGC R 2 1 2 1 101000 f 74 goat snp29342-scaffold316-2526809 7 85816479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782362 Affx-122922898 AX-385269438 7 21213523 GTACTCTCTAATAAGCCATCTGAGAATCTCATGTG[C/T]GTATTAAATTATATACCACACATACTGTAAAATCG Y 2 1 2 1 101000 f 74 goat snp29343-scaffold316-2558401 7 85783881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411310 Affx-122952286 AX-123281660 7 21247665 CAGTTAAACAGAGGAGGAGAAAACACATAGCTGAA[C/T]GAAAGATGGGTCAACTCTATATGTTGGTGCTGCTC Y 2 1 2 1 101000 f 74 goat snp29344-scaffold316-2592543 7 85749755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386426 Affx-122970807 AX-123256784 7 21285995 AAATGATATACTTCATTTATTTTAGAAGTTTCAAG[C/T]AGAAAAATGTTCTTAGTTCCTGAGCACATGAAAGA Y 2 1 2 1 101000 r 74 goat snp1218-scaffold1031-37241 7 85721173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449765 Affx-122922445 AX-123320100 7 21346333 GCTGAGATATGTATTTCAAGTAGGTATTGTAATGA[C/T]ACTCTATACTTCCTTTCCATAGAAATTCTCTCATT Y 2 1 2 1 101000 f 74 goat snp1219-scaffold1031-97579 7 85661515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801735 Affx-122960622 AX-385288643 7 21383942 TGGGAGATTCCTTTCTTTGTGACAGTACAGGAAAA[C/T]TTCACAAGAGTGTGCACTTTTGAAAATATGATCAG Y 2 1 2 1 202000 r 74 goat snp1220-scaffold1031-135188 7 85623652 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785018 Affx-122959297 AX-385272065 7 21425896 TAATTCTCAGCATTTCTGTCTTCTCAGCCACTAAT[C/T]GTTTTACTGTCTTGTTAGGATAGTGATCTTTTCAA Y 2 1 2 1 101000 f 74 goat snp1221-scaffold1031-177142 7 85581755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774777 Affx-122967732 AX-385261911 7 21567638 TGAGAATTTGTTTGGTCAAAAAGATAGAACTGCTT[A/G]TAATACAAACAATGGAACATTGCTTGGAATTATTT R 2 1 2 1 201000 r 74 goat snp1223-scaffold1031-318884 7 85438479 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439807 Affx-122930485 AX-123310144 7 21599258 GCTCAGGGTCAAAGTCTATATCCTGAACAAAGAGG[C/T]AGATGTGATCCAAAGCAAAAGAAACGTCACATTCT Y 2 1 2 1 101000 f 74 goat snp1224-scaffold1031-350504 7 85407538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436983 Affx-122933150 AX-123307321 7 21631203 AAAGCCCTGGATTTTTCAGCTTGAGTGATAAGGAG[A/C]CTACTCTTGGATATACAGAGGGAAATTAGGATGGA M 2 1 2 1 101000 f 74 goat snp1225-scaffold1031-382449 7 85375826 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792131 Affx-122943866 AX-385279116 7 21660427 TAAATAATTTACAAAAATTGATTACACTTGAATAC[A/G]TAGAAACAGTAGGTGTTATTATAATTGGGCTCTGA R 2 1 2 1 101000 r 74 goat snp1226-scaffold1031-411673 7 85346585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378289 Affx-122976864 AX-123248648 7 21693961 CACACCTTACAATATATCTGAAGAAAATGACTGCC[C/T]ATCTCAGAGTAGAACTGCTAGGTCAAGTGTGTGTT Y 2 1 2 1 201000 r 74 goat snp1227-scaffold1031-445207 7 85312880 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402957 Affx-122958165 AX-123273310 7 21730961 ATGTGTGTTTGAGGAATTTACCAAAAAGGTAAGGA[A/G]AGCCAGGAAGATGTGTAAAAGGTAAACCTGCAAGT R 2 1 2 1 201000 f 74 goat snp1228-scaffold1031-482207 7 85275951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770598 Affx-122964500 AX-385257762 7 21769882 TCTTTACAGATTTTGATCTACCATTGGACATTTCA[G/T]ATCTACTGTTTAAATGCAAGATATTTAATACCACA K 2 1 2 1 101000 r 74 goat snp1229-scaffold1031-521128 7 85236624 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436457 Affx-122932988 AX-123306795 7 21835594 AGGCAATACGGTAAAGCAGAAGGAGCAAAGACCTC[A/G]TGGTACTTTGGCTTCAATTCCAGTCAAGATTATCA R 2 1 2 1 101000 r 74 goat snp1230-scaffold1031-586840 7 85170802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794986 Affx-122927740 AX-385281946 7 21877769 ATTTCATCCTTAGGTTATATCTTACTGAAGATGTA[C/T]AGTTCAAACACTGTGTTTAAATGTAACTTTAAATA Y 2 1 2 1 101000 f 74 goat snp1231-scaffold1031-629015 7 85127912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400008 Affx-122960802 AX-123270363 7 21923095 TATATTATATACCAAAAAAAGATAACATGAAAAAT[A/G]TGAGTATATTTAAAGGTACTGGAGGAAGATGTTTC R 2 1 2 1 101000 r 74 goat snp1232-scaffold1031-674341 7 85082457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440665 Affx-122929932 AX-123311002 7 21954458 ACCTTCAATACCTGGTATATATAAGTAAGTCTTTC[A/G]TTTTTTTCCCCTTTCCAAAAGGCAGTATTGGGATT R 2 1 2 1 103000 r 74 goat snp1233-scaffold1031-705704 7 85050785 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441348 Affx-122928879 AX-123311685 7 21988297 TGTTTGCTTGAGCTTTACAGAAGTTTCAGTGTGCA[A/G]TATTGCCATGGAGTATTCTCAAGAAAACATAATGT R 2 1 2 1 101000 f 74 goat snp1234-scaffold1031-739543 7 85016897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380713 Affx-122975152 AX-123251071 7 22056110 GAAATTGGTGCCCACAACTGTGACATGCATGCCTC[A/G]TGTCTGAACGTCCCAGGAAGCTTCAAATGTAGCTG R 2 1 2 1 201000 r 74 goat snp1235-scaffold1031-807356 7 84954574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769149 Affx-122958447 AX-385256325 7 22110942 ATTCAAGAGATGTTTCCTTTGGTTTTCTGCCAGTC[A/G]TCCAACTGGTACACATCTGATTATTTTAAAGGAAG R 2 1 2 1 202000 f 74 goat snp1236-scaffold1031-862188 7 84899729 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377532 Affx-122977467 AX-123247891 7 22144303 TGTAGAGTTGTGCTCACTAAGATCCTATTGGTAGA[C/T]GTTGACTAATATTGTCATGTAGTTTTCCAAGACAG Y 2 1 2 1 101000 f 74 goat snp1237-scaffold1031-895549 7 84866240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779469 Affx-122978593 AX-385266572 7 22190668 AGCAAAGCAAAACAAGGGGCTTTTGCTTGAAGTTT[C/T]CTTTTGAAGAAACAGGTTCCTATAAAAATAAGTTG Y 2 1 2 1 101000 f 74 goat snp1238-scaffold1031-941914 7 84819536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394674 Affx-122964366 AX-123265029 7 22223501 CTCCATCAGCTAGCTGGCAGTGCTAGTTCTACTCC[A/G]TGGAAATAGAGGACTGAGGCAATGGTTCTCTAACT R 2 1 2 1 101000 r 74 goat snp1239-scaffold1031-974747 7 84786485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278636 Affx-1111836438 AX-519552115 7 22250487 AGGGTTTACATAGAAGATTCCCTCAGGGAGTCTCT[A/C]ATAACCCACTGTACAAATTTAAATGCATATGTGCC M 2 1 2 1 101000 r 74 goat Random2.2K-770 7 22250487 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779577 Affx-122966878 AX-385266680 7 22266343 TAAACATATGTGTAAGTTTTGATAAAAGTTACAAA[G/T]CAAATATCTGTATAAATCACAGTCTAGGTCACATA K 2 1 2 1 101000 r 74 goat snp1240-scaffold1031-1017589 7 84743523 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797576 Affx-122972407 AX-385284515 7 22357432 TCAGAAGTGACCTGAGGTAAAACTGAAACTGCTAG[A/C]GAGTATCTCATCTTTGTTGAGGTTTTTCTTTATAA M 2 1 2 1 101000 f 74 goat snp1242-scaffold1031-1108678 7 84651695 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444254 Affx-122927216 AX-123314591 7 22388818 CGGACACGACTGAAGCGACTTAGCAGCAGCAGCAA[C/T]AGCAGCAGCAATGATACTGTGCAAGTTTCCAAAGC Y 2 1 2 1 103000 r 74 goat snp1243-scaffold1031-1140064 7 84619931 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402578 Affx-122958440 AX-123272931 7 22452314 AAGAACAGAGATAGAGAATGTCTACCAGATATTTT[A/G]TCAGGTGCTGAAGAGAGGGAAAATGAATAGATAAA R 2 1 2 1 101000 f 74 goat snp1245-scaffold1031-1203560 7 84555318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380403 Affx-122975320 AX-123250761 7 22503903 TGTTTCCCAAATTTCTTTTCTCCCTACAAGCAACT[A/G]CTATTTTGAATTTTTGAGTGATTCTTTCAGGTTAA R 2 1 2 1 201000 r 74 goat snp1246-scaffold1031-1255149 7 84503823 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419671 Affx-122945942 AX-123290019 7 22549945 AGCTAGATGTTTTGAATATCATCATTAAATAGATC[A/G]TCGCTCCCATCTCTCTCTTCCACTCCATGGAAGAA R 2 1 2 1 201000 f 74 goat snp1247-scaffold1031-1301191 7 84458127 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772100 Affx-122954117 AX-385259255 7 22578694 TTCCATTTTATACAATTAATCTGCTAAACACTGAA[C/T]GGAAGTATCTGAGTGTTATATGTTACATAAAGGGA Y 2 1 2 1 101000 r 74 goat snp1248-scaffold1031-1329940 7 84429319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403968 Affx-122957437 AX-123274320 7 22620492 CAATCTACCAGATGCTCCTCAGCCAGTGAATTATT[A/G]TTTGTCCCAATAAGCCTTTATTATTATTTTATGAA R 2 1 2 1 101000 f 74 goat snp1249-scaffold1031-1371738 7 84387859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452332 Affx-122920657 AX-123322665 7 22657858 TGAAAAGTGAGGGGGTTGAAACAGATGATAGCAGT[A/G]TTTCTTTCCAGCTTTGCAAACTCCAGAGAATCCAG R 2 1 2 1 101000 f 74 goat snp1250-scaffold1031-1409104 7 84350492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793973 Affx-122923174 AX-385280942 7 22731467 GGTCCTGGACATGTAGCAAAACTTAAGCAAATATG[C/T]GCTATAATGATTTAAGAGGGAAAACTTTTTACAGT Y 2 1 2 1 101000 f 74 goat snp1251-scaffold1031-1482713 7 84276534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274011 Affx-1111833984 AX-519547616 7 22765442 AGATTTGTGAACTAAAGGTCTGCAGATTGAATGCT[A/G]TACTTGTTTGCTATAGGAAATAGACAACTGCAACA R 2 1 2 1 201000 f 74 goat GoatD01.012797 7 22765442 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278466 Affx-1111836439 AX-519551949 7 22853476 ATCTGGGATTATTGGAATGGTAGCTTTCTCCCTCC[A/G]CTTGTGCTTCAGATTTATACCTCTCCAAGGTAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-771 7 22853476 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382140 Affx-122974049 AX-123252498 7 22864179 TCAGGCCGGCCAGTTTCATCAATGAGGGGTCTTTG[C/T]ATCATCTACCTGAGACTCTCAGCCTGGGTATCAGT Y 2 1 2 1 101000 f 74 goat snp36505-scaffold44-17777 7 84142027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435663 Affx-122933341 AX-123306002 7 22912307 GGAGTTTCCAGGCAAGAGTACTGGAGTGGGGTGCC[A/G]TTGCCTTCTCCAAAGAAACCCTATGATGCCACAAA R 2 1 2 1 103000 r 74 goat snp36506-scaffold44-65905 7 84097003 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401629 Affx-122959596 AX-123271982 7 22950451 AACAGATATTACTTAAAAAGTTTCTAATAAAAACA[C/T]AGATTTTTAAAAAACTACTCAAAGATGAAAAAGAC Y 2 1 2 1 303000 f 74 goat snp36507-scaffold44-104049 7 84058969 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380800 Affx-122975092 AX-123251158 7 23001802 CAAATATGCCTTCCCACAGCATGCTTTGCACCCCC[A/G]TGACATCTCTCTGTCTGCCCTACTTCATTGCGCTG R 2 1 2 1 101000 r 74 goat snp36508-scaffold44-155400 7 84007453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768681 Affx-122921441 AX-385255859 7 23042254 GAAGGCAGGCTTTGCCCATTCTGATACAAAAACCA[C/T]AGTAAACAATCAGGTTGAATAAAATCATCACAATG Y 2 1 2 1 101000 f 74 goat snp36509-scaffold44-195852 7 83971314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774676 Affx-122945736 AX-385261810 7 23075229 AATTTTCTAATGCATTTAACAGTATTTGAATCTCA[C/T]AAGATTCTCAGCTTCTAAACTAACATCTGAATCTA Y 2 1 2 1 101000 r 74 goat snp36510-scaffold44-228827 7 83938345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408081 Affx-122954726 AX-123278432 7 23138263 TGTTTCCCAACTACCTAGCATAGTACCATATTACC[A/G]GCAAATACTTTGTGAGGGCCTGCTATGCCCCAGCC R 2 1 2 1 101000 f 74 goat snp36511-scaffold44-291861 7 83875376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775766 Affx-122945345 AX-385262897 7 23166834 TATATAAAACACCATATCAGTGTCTCTCCTTCAAG[C/T]AGACACATAAATTTAAAACTCTGGGAAACACATGG Y 2 1 2 1 101000 r 74 goat snp36512-scaffold44-320432 7 83846861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405149 Affx-122956952 AX-123275501 7 23208970 TTATGATAATTATATGTACTTCTGAACATTTATAC[A/G]CCTAATTAGAAGATTGAAAGTTTTAAGGCAAGTAA R 2 1 2 1 101000 r 74 goat snp36513-scaffold44-362568 7 83804722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768624 Affx-122938263 AX-385255804 7 23255568 TTCTCTTTAAATGGGCCTAGCATTTTAGACTGCTA[C/T]AGCTAACTACTTCCAAGGCTTTCTTTGGAGCCTTT Y 2 1 2 1 101000 r 74 goat snp36514-scaffold44-409166 7 83757463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383319 Affx-122972694 AX-123253677 7 23290308 CTGTACAGGAAGTCTGTTGGTTAGGGAAATTAGTA[C/T]TATGCATAGTTATTGTTTTTTAAATAAGGTTAATT Y 2 1 2 1 101000 f 74 goat snp36515-scaffold44-443906 7 83722712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391078 Affx-122966836 AX-123261435 7 23348687 CAAGTAAATATTGCACACTTGTGTGTGTCTGAAGG[A/C]TGAATTTCTGGAATAGGTATTTCTGTTTCATGAAT M 2 1 2 1 201000 r 74 goat snp36516-scaffold44-502285 7 83664157 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442213 Affx-122928783 AX-123312550 7 23392442 TTCCCCTCTTGAGGGTTCTAAAATGTTATTCACTC[A/G]TCCTTTTTTTCTAAATACAATAAAATTATTTTTTA R 2 1 2 1 101000 f 74 goat snp36517-scaffold44-546040 7 83620854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376979 Affx-122977748 AX-123247338 7 23421525 AACAATGTCAAGATTAAAATGAAACAGCCAGGAAA[C/T]GGTGGAAATCTGCAGGAAAGGCTTCCTAGGATCTG Y 2 1 2 1 101000 r 74 goat snp36518-scaffold44-575123 7 83591980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273304 Affx-1111833533 AX-519546948 7 23430743 GGACGGTTGCTGCCAGAGATCAGCTTCCCAGAAGT[A/G]ACATATGGCACACTTGAGAAGGTGTGCCCGTTGTA R 2 1 2 1 102000 r 74 goat 7_23430743_AF-PAKI 7 23430743 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425811 Affx-122940693 AX-123296157 7 23466807 TAGGCAATGCCCAGCAAAGCTAAATCGCCAGTGAA[C/T]GGTTATTGAAGGAATGAATGAATAAATGACTTAAC Y 2 1 2 1 101000 f 74 goat snp36519-scaffold44-620405 7 83546555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400601 Affx-122960391 AX-123270956 7 23502136 CAGACACAATGACTGAGAGGTGAGGGTGCTTTACA[C/T]ACCAGCTAGCTCAGGTCTATCCTTGCAGGTGTAAC Y 2 1 2 1 101000 f 74 goat snp36520-scaffold44-655734 7 83511376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447582 Affx-122924019 AX-123317918 7 23535096 CAATACCCAACTGGGAGTGGAGCAATATACAACAG[C/T]GGATAATCTAAATCCCCTTGTGTCAGAAAGCATTT Y 2 1 2 1 101000 f 74 goat snp36521-scaffold44-688694 7 83477829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400017 Affx-122960797 AX-123270372 7 23574719 ATCCTCAGTGTTCTTCGTTTTTAATTGTTACGTTT[A/C]TCCCAGGTTGTATTTCATGTATTCAATAAATATTT M 2 1 2 1 101000 f 74 goat snp36522-scaffold44-728317 7 83437621 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801716 Affx-122948879 AX-385288624 7 23628697 ACGTGTACAAAGAATCTTACTGGCAGCCAGAAAGC[A/G]AGGAGAATTAAATTCTCTATTGAAATGTCTGAGAA R 2 1 2 1 101000 f 74 goat snp36523-scaffold44-782295 7 83379163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781230 Affx-122925945 AX-385268315 7 23665155 GGAAACTGGTTAGCCTGTAAATTTCCAGATGCTAG[C/T]GGCACTGTAAACAGATCTGCTGTGTATTTTCTGCA Y 2 1 2 1 101000 f 74 goat snp36524-scaffold44-818753 7 83342754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395290 Affx-122964074 AX-123265645 7 23738266 CTTGGTCCTGAGTGAGGAATAGATTAGCAAGAAGA[C/T]GTGCGCTGGGGTAGCCAGGAAGGAAGGGAAAAGTA Y 2 1 2 1 101000 f 74 goat snp36525-scaffold44-891864 7 83270065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377063 Affx-122978290 AX-123247422 7 23816162 TTGGACATGACTGAGCATACAAGTTCACATGTAGC[A/G]CTTATATATGGCAGGCAGATTTCTAAGCACCTAAA R 2 1 2 1 101000 f 74 goat snp36527-scaffold44-969760 7 83192061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796219 Affx-122974981 AX-385283169 7 23862238 GGAGGGGCCCTGTATGAATCCATTTACGTAAAATT[C/T]GAAAACAGGCTAAGTTCATGTATAATTTGACCAGA Y 2 1 2 1 201000 r 74 goat snp36528-scaffold44-1015836 7 83146068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438773 Affx-122931383 AX-123309110 7 23890782 AAACTGCTGAGCTCTTCTGTTAACAATGCTTTATA[C/T]GAGAATTTGGGAAAAGGTCCTCATTTTTCCCTTTT Y 2 1 2 1 101000 f 74 goat snp36529-scaffold44-1044380 7 83117252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789198 Affx-122970389 AX-385276210 7 23928994 TGTTATTAGGATCAGTGTTATGTGATCTTCCAAAA[C/T]GAATAGCTCTGATTACTGTGCATGTCCTATGTCTT Y 2 1 2 1 101000 r 74 goat snp36530-scaffold44-1082592 7 83077358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445950 Affx-122925906 AX-123316287 7 23958101 TTGAGTTTAGCTAACTCAATAAGGCAACAAAAGCT[A/G]CTGACATTCAAAACCTGAAGAAGGCAGAGGAGGAC R 2 1 2 1 101000 f 74 goat snp36531-scaffold44-1111699 7 83048159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778939 Affx-122977955 AX-385266046 7 23994033 CAAGCAGAAGTACATGTTGACTCTCAGGAAATAAG[C/T]TGTTATCTAAATTCAACTATTTGGACCAGATACAA Y 2 1 2 1 201000 r 74 goat snp36532-scaffold44-1147631 7 83012086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411579 Affx-122951623 AX-123281929 7 24022742 AGTCTGAACCACCAGGGCTGGCCCCTAGATAGCTG[C/T]ATTTTAAACAAGTTTGTCAAGTGATTGCGATGTAC Y 2 1 2 1 101000 r 74 goat snp36533-scaffold44-1176340 7 82983221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795061 Affx-122946198 AX-385282020 7 24076279 ACACCTTTCAAGTCTCCAGAACTTTTAGTTAGCTT[A/G]AATTGTCTTTGGATATCACAGAGCTAGTTGCCAGG R 2 1 2 1 101000 f 74 goat snp36534-scaffold44-1229877 7 82929419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274704 Affx-1111834450 AX-519548290 7 24077404 TCGCTTTTTTCTTCCTGGTTCCCTGTCACTCCAGT[A/C]GCACTCCACCCTGGCAGCAGCAATTCGTTTCTGTT M 2 1 2 1 201000 f 74 goat GoatD01.036487 7 24077404 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793087 Affx-122921700 AX-385280065 7 24115534 ATTGCGATGGGCCAGTGGATGAGATATAGTGGTAA[C/T]AGAAGGAGTTGTCCTTTTCTAGAGCTTTTACAGTT Y 2 1 2 1 101000 f 74 goat snp36535-scaffold44-1269132 7 82889887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416397 Affx-122947858 AX-123286746 7 24155186 AGTAGAGACACAAAAGTATACACACTATATCAAGC[A/G]TGATAGTTTAACTCTGTTCTCACTTTATTCATGTG R 2 1 2 1 101000 f 74 goat snp36536-scaffold44-1308784 7 82848918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452570 Affx-122920515 AX-123322903 7 24200420 GAAGGCTACACTCTAATACACAGTGGATATAGGGA[C/T]GGGATTGAGGATAAAAGAAATGCATTCCAAAAAAT Y 2 1 2 1 201000 r 74 goat snp36537-scaffold44-1354018 7 82803172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398844 Affx-122961064 AX-123269199 7 24242398 TGATCTTTTTCTTCCAGGATGTTGTAATGATTAAC[A/G]TGGTCATCTCTACAGGATTTGAGTTTCAGTAGAAA R 2 1 2 1 101000 f 74 goat snp36538-scaffold44-1395996 7 82760502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787918 Affx-122954364 AX-385274940 7 24298328 GACAACTTATGTTAAGTATGTTTGACTGAACTGCC[A/G]TTTGAAAGACTTCTATATATTTCAAATAGTGGAAT R 2 1 2 1 202000 r 74 goat snp36539-scaffold44-1451926 7 82704934 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419862 Affx-122945370 AX-123290210 7 24331167 TACTGTTTGACTCTTGCCCTCAAATCTTTAGTGTC[C/T]TATAGTCTTATATATTAAAGACTGTAATAATTTAT Y 2 1 2 1 101000 f 74 goat snp36540-scaffold44-1484765 7 82671785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389495 Affx-122968312 AX-123259853 7 24342888 CTGCTTCTTTGGGCTATTTTTTAAATGACTAGATA[C/T]ATAAAATTTTGAGTTTGGTTCTAGCAGGCTTCTGA Y 2 1 2 1 103000 r 74 goat snp50484-scaffold724-910315 NW_017196265.1 16457 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775042 Affx-122943593 AX-385262174 7 24373800 CAGAGAAACAGAAGTTTTTAATAAGCGATGACCAA[C/T]ATTCTATTGCAAGTTGTGCCAGGAATTTTGTATTG Y 2 1 2 1 101000 f 74 goat snp50483-scaffold724-879403 7 82615208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419074 Affx-122945800 AX-123289422 7 24403133 CATAACACAAGTGCTATTCATGGGTCCCACACTCC[A/G]CAGCTGTAAAACGAGATGTGTAGGAGCAGCCCCTA R 2 1 2 1 101000 f 74 goat snp50482-scaffold724-850070 7 82585912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401544 Affx-122958908 AX-123271897 7 24451268 GGTCACAAAGAGTCCGACACAACTGAGCGACTTTC[A/G]CTTTCACCCATTGGTCAGCCAATATGTTTATGCAA R 2 1 2 1 101000 r 74 goat snp50481-scaffold724-801935 7 82539014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377701 Affx-122977409 AX-123248060 7 24504551 GCTTTAATGAGGGAAAAAAGTCAGGGTATTGACAA[C/T]GAGGAATAAGATGGAAATGACTACTGGTTAGATGA Y 2 1 2 1 201000 f 74 goat snp50480-scaffold724-748652 7 82485241 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414382 Affx-122949997 AX-123284731 7 24551032 GATATCTTGTCATGCAAGAAAAGTAAATATCCCAA[C/T]GTTAAAGTTATTTTTTTGTTAACTTATTATTGATT Y 2 1 2 1 101000 f 74 goat snp50479-scaffold724-702171 7 82438580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432204 Affx-122936383 AX-123302545 7 24595884 ATATGTTTCCTTGTTCAGAAAATGAGGATATCAAA[A/C]TTCACCTTAGAGCAGATATTAAAATAAAGTAATAT M 2 1 2 1 201000 r 74 goat snp50478-scaffold724-657319 7 82393442 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401924 Affx-122958821 AX-123272277 7 24634939 ATAAAAAGTTGTCTAACAACCAATTGTTGGTAAAG[C/T]AGGCTAGACTGAAGTCAGGAGACAGCTCTTAGCCT Y 2 1 2 1 101000 f 74 goat snp50477-scaffold724-618264 7 82352355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382873 Affx-122973515 AX-123253231 7 24668667 GAAGCTTCAATAAAAGCCCCATCTCTAAGCTATTG[C/T]TCCAGGACTGATGAGCCAGTGTTTGCCCTGTCCAG Y 2 1 2 1 201000 f 74 goat snp50476-scaffold724-584536 7 82317994 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414230 Affx-122949638 AX-123284579 7 24749370 ATCCCTGACCCACCTCCTTGCCATCACAGGCAACC[A/G]CTCTTCTGAGTTTTATTCCTATAGATTAGTTTTCC R 2 1 2 1 201000 r 74 goat snp50474-scaffold724-503833 7 82237350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384326 Affx-122972264 AX-123254684 7 24805807 TGTTAACTGGTCAGGAGAGTCACTGTCACAAAAAG[C/T]ACTTGGCAAAAATCTTGAAAAATTTGAATACTATT Y 2 1 2 1 101000 f 74 goat snp50473-scaffold724-447396 7 82182575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376680 Affx-122978996 AX-123247039 7 24851364 TCCCTCGGCTTCCCTTAAAGATAATTGGTAGTTGA[C/T]GCAGGAAGAGCAAAGAATGTGATAAATCTATAATA Y 2 1 2 1 101000 f 74 goat snp50472-scaffold724-401839 7 82137124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799569 Affx-122977732 AX-385286499 7 24927572 AGTGAGACTAAGGAAATTTTCAGAGTGTGAATAGC[A/G]TGAAAAGAATGTAGTTGAGAATTCACTCCTGCATG R 2 1 2 1 101000 f 74 goat snp50470-scaffold724-325631 7 82060667 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800548 Affx-122964764 AX-385287467 7 24973149 GTAGCTTCAGGTAAGCTGGTTTAGTTGTTTAACAC[A/G]TTTGTGCTCAGTTATTGGTTCTTGGGGATATGGTG R 2 1 2 1 202000 r 74 goat snp50469-scaffold724-280054 7 82014640 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427041 Affx-122939824 AX-123297386 7 25002159 TTCAAGCCTCACATCAGTTGGTGGGAGTGTAGATT[C/T]AATGACATTTATTTTGGAAAACATGTTCTGCTAAA Y 2 1 2 1 101000 f 74 goat snp50468-scaffold724-251044 7 81984325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781812 Affx-122956938 AX-385268894 7 25101359 ACTTTAGGAAAATCCCATGTTCATCCTATTTTACC[A/G]TTGCAGAAGTCTGTGGGATAACCTTAATATTAAAA R 2 1 2 1 101000 f 74 goat snp50466-scaffold724-151844 7 81884915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273600 Affx-1111833693 AX-519547214 7 25138280 ATTTTATGCTGCCACGTGGCCTGCAGAAGACTTGA[A/G]CTGACACTAACCCCTCTTGCCAGTGTCAACCCTAG R 2 1 2 1 101000 r 74 goat GoatD01.001728 7 25138280 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38450792 Affx-122921819 AX-123321126 7 25139385 GCTCTTCTTGCCAAGTCCTGCTACGTTCTGTGCTG[C/T]ATCATTGCCAGAAAGTTTTCTTCCTCCCCTTAGGT Y 2 1 2 1 101000 r 74 goat snp50465-scaffold724-113818 7 81846883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429681 Affx-122937645 AX-123300022 7 25172890 CTATCATCTGTCTTTTCTCATTTTGTTCAAATCTA[C/T]GTTTCTAATGCATGTGATTCTCCTTAGAATCAGAT Y 2 1 2 1 101000 r 74 goat snp50464-scaffold724-80313 7 81812994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413120 Affx-122950379 AX-123283469 7 25212695 TAAAGTTTAAATCAGTATCTTTATGCATAGGGCTA[C/T]ATGAGGGTTATAGATTACTAGATGAAACTAAATGT Y 2 1 2 1 201000 r 74 goat snp50463-scaffold724-40508 7 81772446 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766895 Affx-122939032 AX-385254213 7 25242540 GCACTGGAGCCAAAAGCAACAAGCAGAATCTAATC[A/G]TGAGGAATTGCATAAGTAAGTGGTTCTCTTCAGCC R 2 1 2 1 101000 f 74 goat snp50462-scaffold724-10663 7 81741491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772134 Affx-122962659 AX-385259289 7 25303837 GCCTCGTGCTAGGTTCGGGCAAAGCCATCAGTATA[C/T]GTTAGTTTCCAAGTTTAAAGGAAGGAGTTTCCCAA Y 2 1 2 1 101000 r 74 goat snp52632-scaffold786-1309169 7 81680273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451359 Affx-122921250 AX-123321692 7 25360919 TGCTTGAACATACGGAGACTATTTCAAGAAAGACA[G/T]ACAAAACTGTTCCAAGTAGTTGACTCTGGGGAGTA K 2 1 2 1 101000 r 74 goat snp52631-scaffold786-1252087 7 81623183 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401456 Affx-122958975 AX-123271809 7 25395571 TGACGCTATTCAAACTTAAACAGGTATCAAGACCA[A/G]ATCATTTCGTTCTGTGAATTTATTCAACATTCAAC R 2 1 2 1 201000 r 74 goat snp52630-scaffold786-1217435 7 81588962 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435061 Affx-122933738 AX-123305401 7 25437693 TTGTTAAGACCCTTCTTTTTGCCAGAATTCTTCCC[A/C]GCCTTCGCTCCAATAACAGAACCTGGGCCGTTGCT M 2 1 2 1 101000 f 74 goat snp52629-scaffold786-1175313 7 81546833 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453793 Affx-122919579 AX-123324126 7 25497964 AGGAAAGATATAACTTGAACCCCATATCTGGCACC[G/T]CTCCCACTTCACCTCAAATGTTGTTTGTGCCTCTA K 2 1 2 1 201000 r 74 goat snp52628-scaffold786-1115042 7 81486343 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414299 Affx-122949589 AX-123284648 7 25546614 CATTAAAATAGCACTGATGTTGGAAAAAACAGTAA[G/T]ATTTGTCTGATGCCATACATACCAAGCAATGATTC K 2 1 2 1 101000 r 74 goat snp52627-scaffold786-1066392 7 81438161 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786892 Affx-122927900 AX-385273921 7 25625508 TCATTCTGAAATTTAAAAACCAACAAAGGCATACC[A/G]CTGCAGTTAGACAAAAAATCTAATGTTCTCACGGT R 2 1 2 1 101000 f 74 goat snp52625-scaffold786-987498 7 81359142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448516 Affx-122923451 AX-123318852 7 25674658 CCCACCACTTTATGCTCTCATTCTAATGGCTATTT[A/G]TTTTCTTCTGGTTAATTTCCCTTTCCTTTTCATAG R 2 1 2 1 101000 r 74 goat snp52624-scaffold786-938348 7 81309760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408634 Affx-122953484 AX-123278985 7 25705672 AAACACAACTACTATCCAGAAGATCCTCTCTTCCC[C/T]CTATCTGTTCGTATTTTCGGTTACAATAGCCACAT Y 2 1 2 1 201000 r 74 goat snp52623-scaffold786-907334 7 81278831 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798875 Affx-122967564 AX-385285805 7 25744593 ACCCTGGCTGATACCAATAAAGGTTGGGCAATGGA[C/T]GTCAAAGAGAGTCTTATTGAAAGAGAAAGAAAATG Y 2 1 2 1 101000 f 74 goat snp52622-scaffold786-868413 7 81240097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391925 Affx-122966936 AX-123262282 7 25798007 CCCAATTGTAAATGACTGGGGAATTTCAGTACCTA[C/T]GAGCTCAGCTTTATCTTTCTTTTCAGTATAAAGAT Y 2 1 2 1 101000 f 74 goat snp52621-scaffold786-814999 7 81186029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783972 Affx-122939778 AX-385271026 7 25832473 GGACAGACTTGGAATTTTATCAAAACATATTCCAC[A/G]TTCAACCCATTGTGGACTCTCAGCTTATTGCAAGT R 2 1 2 1 101000 r 74 goat snp52620-scaffold786-780533 7 81151173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399845 Affx-122960250 AX-123270200 7 25870071 TTTAACCAGAGTGATCGTGACAAAATGTGTAAGTC[G/T]CTTCTTAGAAGCTGCTCAGTGGATGTTCAATACGA K 2 1 2 1 201000 f 74 goat snp52619-scaffold786-742935 7 81113251 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381692 Affx-122974721 AX-123252050 7 25899986 GTATAGCCACACACTCAACGCTTTCACATGCGCTC[A/G]TTGACTCTCTTCACAATACAGTGATGTGGGGCTCG R 2 1 2 1 101000 r 74 goat snp52618-scaffold786-713020 7 81083633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781288 Affx-122944606 AX-385268373 7 25983257 AAATTCTTTTTCTTTTAGTACACTATAAAACATGA[A/G]GCAGAAGCACAATGACTTAATGAGTTTCTGTCTCT R 2 1 2 1 101000 r 74 goat snp52616-scaffold786-629749 7 80999001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464498600 Affx-1110516330 AX-515970828 7 26001149 TGTTGAATTCAACTGTGCTCTCACTGACTTTATGT[C/T]GACTAGACAGGTTAGTTTCTGACAGACAGATATTG Y 2 1 2 1 101000 f 74 goat 7_26001149_AF-PAKI 7 26001149 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401406 Affx-122959209 AX-123271759 7 26012099 ATCTTTGCACTTGTCCTTCTCTTTGTTTGGAAATG[C/T]ATTACCTTAAACCCTCTCATAGCTTTTCTTTCTCA Y 2 1 2 1 101000 f 74 goat snp52615-scaffold786-600907 7 80969711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418357 Affx-122946585 AX-123288705 7 26056006 AAGCACCACAGTGGCTGCGAAGATTAAAGGGCAAA[C/T]GGAGTGCAACTCACCAGGTGACCTGAGCCATGCGA Y 2 1 2 1 101000 f 74 goat snp52614-scaffold786-557000 7 80925789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405048 Affx-122956352 AX-123275400 7 26098137 GTGAACCGCCACAGAGCAGTCATCTCATTCCTTTC[C/T]GCAGTCAACTGCCCAGGGAACTCATGGAACAGACT Y 2 1 2 1 101000 f 74 goat snp52613-scaffold786-514869 7 80883685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802408 Affx-122928506 AX-385289312 7 26135571 ACCTTCACTGATCTATGGAGAGTGATTTTACAATT[A/G]TGTTTTTTGGTATTCACTGTTAACAGAAAGACCCC R 2 1 2 1 101000 r 74 goat snp52612-scaffold786-477435 7 80846515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388730 Affx-122968967 AX-123259088 7 26170671 TGAAACCCTGTCTTAGTCACTGGCAGTGTTTTCCC[A/G]TGGACACAGCACTGCAGTCTTTAGGGAAGTGGGGA R 2 1 2 1 201000 r 74 goat snp52611-scaffold786-442335 7 80810413 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423668 Affx-122942335 AX-123294014 7 26227934 AATATCTCAGAGCATTTCAGAGGCTAATGTGCTCC[A/G]TGAGATACCATGAACACATGTACCGTAAGGGGCTC R 2 1 2 1 101000 f 74 goat snp52610-scaffold786-385072 7 80751585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402196 Affx-122959171 AX-123272549 7 26282682 GCTAAGATCCCATTGTTTCCAGAAGCAGCTTCCTC[A/G]TGGAGCTCAATTCAGGGATGAAGAAGCTAGGAGGG R 2 1 2 1 101000 r 74 goat snp52609-scaffold786-330324 7 80696992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383335 Affx-122972683 AX-123253693 7 26319244 AATGGCAAAAGCCCATTGATTAAGGTAAGGAATGA[C/T]AAAAGCTTGGATGATAAGGCCAGAGAAGAGGAGAG Y 2 1 2 1 101000 f 74 goat snp52608-scaffold786-293762 7 80660521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382974 Affx-122973353 AX-123253332 7 26353181 GAGGCATCAGCTGTCTCTTTTTTGCTTACCTTGCT[A/G]CACTTTCACTTTTAATACTCCGGTCACTCTTTCAA R 2 1 2 1 101000 r 74 goat snp52607-scaffold786-259825 7 80625938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426588 Affx-122939987 AX-123296934 7 26387084 AGAGAGATACCAGTCCTCAGGCAGCCCACAGAAAA[G/T]ATAGAATGCTGGATGTATGTTCCAACTCTCTCTCC K 2 1 2 1 101000 r 74 goat snp52606-scaffold786-225922 7 80591513 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793637 Affx-122966781 AX-385280610 7 26418342 TTACAAGGATAGTAAATTAAACCGAAAGTCCAGTT[A/C]GGAAATGACAGGTTGTTTACTTGTAAGAGGTTTTT M 2 1 2 1 101000 r 74 goat snp52605-scaffold786-194664 7 80560320 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391185 Affx-122967427 AX-123261542 7 26559403 GGGGAATCTTGGAAAATGATTTTCTTTTTAACTGA[C/T]GATTTAGTGTGCTCATTGGCCAAGAGGTCGTTAAC Y 2 1 2 1 101000 r 74 goat snp52601-scaffold786-53603 7 80420370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446989 Affx-122924641 AX-123317325 7 26601706 ATAGGATTTATTGACCACACCAGGACAGTCTGGAG[C/T]GGGAAAGGAGATGACATGCTAATGAAAAGTATCCT Y 2 1 2 1 201000 r 74 goat snp52600-scaffold786-11300 7 80377740 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781832 Affx-122932170 AX-385268914 7 26628682 GTTCTAAAACCAAGTTGTTACTAGTGGTTCAAGAC[A/G]CTGGCATTTTCTGTTAAAGCTGACTCAGAGACAAA R 2 1 2 1 101000 r 74 goat snp56907-scaffold902-15577 7 80351081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450712 Affx-122921884 AX-123321046 7 26712206 TCTCTTCCCCTCAATGGCTCAGCACAACAGTAGCT[A/G]TTATTTCCTGCCCTTTTCAGGATCAAATGCAGTTG R 2 1 2 1 201000 r 74 goat snp56908-scaffold902-99101 7 80267867 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794665 Affx-122943604 AX-385281626 7 26758554 GGTTTTGGCAAAAAACAATGCCAGTAACTAGTAAC[A/G]TTTTGAAAAACTTTGCCTGAGACTCCGGGTCTAAA R 2 1 2 1 201000 r 74 goat snp56909-scaffold902-145449 7 80221744 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446498 Affx-122925044 AX-123316834 7 26798697 CTATTCATGGGTTGACAGAATTAGTATTGTTAAAA[C/T]GGTAATACTATCCAAATCAATCTTCAGGTTTAATC Y 2 1 2 1 303000 f 74 goat snp56910-scaffold902-185592 7 80182034 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767471 Affx-122930041 AX-385254737 7 26843268 ATAGTCCCCTAAATTATAGCTAAATCACTGATAAC[G/T]CTTTGTATACACCATGAACTTCCATTCAGTTGGGT K 2 1 2 1 201000 f 74 goat snp56911-scaffold902-230163 7 80136724 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779844 Affx-122929514 AX-385266943 7 26871900 AAATAAATGTGGTGACCACACAGCCTGGGAATAAT[A/G]CTCTGTTTTTGGCAGGATGACAGTCCTCCTGTTGG R 2 1 2 1 201000 r 74 goat snp56912-scaffold902-258795 7 80108020 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396549 Affx-122962938 AX-123266904 7 26906731 CTTAATGCAGTGTCTTGAGGCATCGTGTTCCTGGT[C/T]GAGAAAGAAAACTATGGACGTGTTCATATATACTG Y 2 1 2 1 101000 r 74 goat snp56913-scaffold902-293626 7 80073300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399153 Affx-122960648 AX-123269508 7 26969064 CTGGCTGAAGAGACAGATATTTGGCCCCGGAGAGA[G/T]CAGAAAGGAAGAGTTCATTTAAAGAAAAAATTTCA K 2 1 2 1 101000 f 74 goat snp56914-scaffold902-355959 7 80010488 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421507 Affx-122943898 AX-123291854 7 27008311 TCTGTGTGTTAGGGCTGCTCAGTATCCTTCAGACC[A/G]CAGAACTCTTCAATGAGAACACTTTGGGAAACTGC R 2 1 2 1 101000 r 74 goat snp56915-scaffold902-395206 7 79971354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390413 Affx-122967650 AX-123260770 7 27049556 ATTTGTTCCAGAGGAATAAATAAGGAGCGTGAGTG[C/T]ATTAAATGCAAACGGGGGACACGGTGGTGTTTTTC Y 2 1 2 1 101000 f 74 goat snp56916-scaffold902-436451 7 79930153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777872 Affx-122920209 AX-385264988 7 27080700 CTTACTTATAAAGTAACACTTGGGATGGAAAAATT[G/T]TTTAATGATATATTGGCTGACTGAAACAAATTACC K 2 1 2 1 101000 f 74 goat snp56917-scaffold902-467595 7 79898860 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798651 Affx-122971358 AX-385285583 7 27160287 AAAATAGAAGCGATACAATCATAGCTTTAAAATAA[C/T]TGCTCATTACTTTGCTGCATGTGTTTGAAGGATTT Y 2 1 2 1 101000 r 74 goat snp56919-scaffold902-547182 7 79817948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448421 Affx-122923666 AX-123318757 7 27190988 CTACATATTTTTCACAGAAAAAGGCAAAACAAAAT[A/G]CAACTGCTGATAATCATCATTCCTGGAATGCCATA R 2 1 2 1 101000 r 74 goat snp56920-scaffold902-577883 7 79787284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417803 Affx-122947371 AX-123288151 7 27231201 GAAGCAATGCATTCCACTCACAACTGGGATTCCAC[A/G]TTACAGAGATCAGCTCTGGGTTCTGTCAAAACTGT R 2 1 2 1 101000 f 74 goat snp56921-scaffold902-618096 7 79747578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429537 Affx-122937834 AX-123299879 7 27286941 GAAATTGCTGAAAGTGATGGCATCCCTGGTACCCC[A/G]TGCAACACAGGGTGTACTGTGGGCCTTCAAGAACC R 2 1 2 1 102000 f 74 goat snp56922-scaffold902-673836 7 79691267 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392899 Affx-122965729 AX-123263256 7 27325112 ACCATCATTTTTGCTTCAGTTTCACGTTTTTTGAG[C/T]AAAGTAATTTGGGCATCTTCCCATTTCTGCCAGCA Y 2 1 2 1 101000 r 74 goat snp56923-scaffold902-712007 7 79653040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414525 Affx-122949518 AX-123284874 7 27376463 TATACCTTGTCATAAATCTCTTTCTAGTGTTTCCC[A/G]TGCAGTTGTCTTTAAATACCTGGTCAGAAAATGTC R 2 1 2 1 101000 r 74 goat snp56924-scaffold902-763358 7 79601396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451533 Affx-122921094 AX-123321866 7 27425741 GTGGCCACCCACGAGTGCAGGATTTTCCTTCCTTT[C/T]TGGTCTTACTGTCACTCCCCTAGAACTAATGGTTA Y 2 1 2 1 101000 r 74 goat snp56925-scaffold902-812636 7 79551979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379832 Affx-122975818 AX-123250190 7 27456545 TCTTATTTTCTAATTCATGGTAAGAAGCTGGAATT[A/G]CATACTTTCTCTCAGAGAAGAACTCTACAAGAAGG R 2 1 2 1 202000 f 74 goat snp56926-scaffold902-843440 7 79520395 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379255 Affx-122976256 AX-123249614 7 27487257 ATATTTTCCCACCAGACAGCATTTAGATTCTCCTT[A/G]TTCAAGGAACTCATGTGAACATGCATTTAACAAAT R 2 1 2 1 101000 r 74 goat snp56927-scaffold902-874152 7 79489728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411054 Affx-122951952 AX-123281404 7 27534450 TTGGTTGAGGTAAAGAACATTGAGAAAGCTTTTGC[A/G]CATCATCCATGCATCCATCCATTCACTCTTTCATC R 2 1 2 1 101000 f 74 goat snp56928-scaffold902-921345 7 79442837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400946 Affx-122959705 AX-123271299 7 27576087 ATTAATTACAAATAGAAAAAGTATATAACTTTTGG[C/T]GAAAAAGAAGTGACCATTTTGATGTGACTTAATGG Y 2 1 2 1 101000 r 74 goat snp56929-scaffold902-962982 7 79400980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770127 Affx-122967870 AX-385257294 7 27608432 AAGTAACCACTGTTGCTCATTTATTTATGACCATT[A/G]CTATTTTTTGATTTTAATGTGCCCACAAATATTTA R 2 1 2 1 101000 f 74 goat snp56930-scaffold902-995327 7 79369738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427326 Affx-122940129 AX-123297669 7 27659176 CTTTATTCTTAGAAAAAGTCAAATAAGCCAAATGA[C/T]AAACCATGAATTGGGTCTAGAGTATGGATCTGAAA Y 2 1 2 1 101000 r 74 goat snp56931-scaffold902-1046071 7 79318483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411357 Affx-122952253 AX-123281707 7 27759665 TAATACCACAGAACTGCCTTATCAAAATGAAAAGC[A/G]TCCCCTAAACATGTGATTCACTTTTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp56934-scaffold902-1146560 7 79221325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769504 Affx-122927332 AX-385256674 7 27953823 AGAGATAGGAAAACGGATCAACAGAACACTAATCT[A/G]TTTGATATGTGAAAACTTAAGCAAAGAAAAAAAAG R 2 1 2 1 101000 f 74 goat snp56938-scaffold902-1340718 7 79026257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450788 Affx-122921822 AX-123321122 7 27993254 CAACCACAACAGAAAACTACGTTCCCCAGGAGAGG[A/C]TTTCTGCTGAAAGCGCAACGCAGTGGCAAATGTCT M 2 1 2 1 201000 r 74 goat snp56939-scaffold902-1380149 7 78986494 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419930 Affx-122945319 AX-123290278 7 28028176 GCTCACATGTGCTAAGTGGGCAACCAGAAACCAGT[A/G]CAAGCTTAAAGACAATGGTGTTGTCCTTCTCCTGC R 2 1 2 1 201000 f 74 goat snp56940-scaffold902-1415071 7 78951515 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389504 Affx-122968304 AX-123259862 7 28080645 GCCCAGAATAGTGGTCAAACTATTCACTGCCATTA[C/T]GTGACCTATGGGGGACAGAGTTCCCACAAACAGTA Y 2 1 2 1 101000 f 74 goat snp56941-scaffold902-1467540 7 78898667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422280 Affx-122943492 AX-123292626 7 28154356 CAGAACTTCATTATGGATTGTGTGGGTTATAATAA[C/T]GTAACTGAGTTTCCTGCCTCCACAACCAGTAATTC Y 2 1 2 1 201000 f 74 goat snp56943-scaffold902-1541251 7 78824138 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782005 Affx-122971940 AX-385269084 7 28208298 ATGTAATGTACCATACTCTCAACAATGTAATTGTA[G/T]AATTTATTCCTCCTGCTAAGAGAATCAGTAAGCTT K 2 1 2 1 202000 f 74 goat snp56944-scaffold902-1595193 7 78770049 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775120 Affx-122965982 AX-385262252 7 28245317 GTTTTGATCTTTTACCTTTAGATGTACACACCATG[C/T]GGAATTGATTTTGGTCAACAGAGAAAAATAGGGGT Y 2 1 2 1 101000 f 74 goat snp56945-scaffold902-1632212 7 78732275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406158 Affx-122956172 AX-123276510 7 28275898 AGTTTTAATAGAGAAAAATCTTAGAATACTTGAGT[C/T]ATCAGATATCATAGGATAGTGTAAACTTTCTGAAA Y 2 1 2 1 101000 r 74 goat snp56946-scaffold902-1662793 7 78701751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393002 Affx-122965653 AX-123263359 7 28341368 CTGCGTCTGGCCACTTGACCGCCCTTCATCTGGGT[A/G]TGAGTGTCTCCCACCACAGAAGTTTAAAGACCCTT R 2 1 2 1 202000 f 74 goat snp56948-scaffold902-1728263 7 78635594 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435465 Affx-122933457 AX-123305805 7 28494728 ACATCTTGCTGACTTTTTACATTCCATTGATATAA[C/T]GTTGGGGCGTAAAATCAGGAATATTTCAGATCGAA Y 2 1 2 1 201000 f 74 goat snp56951-scaffold902-1881623 7 78483123 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383120 Affx-122973263 AX-123253478 7 28526733 AAGGCTGTCTACTTGATTTACTATTGCATTTGTTT[A/G]TTTATCTTCCAGTCACTCTGCTAGACATTTTCTGA R 2 1 2 1 101000 r 74 goat snp56952-scaffold902-1913628 7 78450343 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440888 Affx-122929230 AX-123311225 7 28567281 TGCACACTGATCTCATGAAAGGAGTGAAAGATTAA[C/T]GACAAATGAATCAAATGAATTAATGACAAATGAAT Y 2 1 2 1 101000 f 74 goat snp56953-scaffold902-1954176 7 78409136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273267 Affx-1111833535 AX-499506897 7 28645612 CCCAGGTCTCCCACATTGTAGGCAAACGCTTTACC[A/G]TCTGAGCTACCAGGAAAGCCCTGAATCATTTTAAG R 2 1 2 1 303000 f 74 goat 7_28645612_AF-PAKI 7 28645612 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802044 Affx-122967681 AX-385288948 7 28649867 TTTTAAGAAGCTGGGTTTTCCTATGGCGAAAATTC[A/G]TTTCTCCAGAATACTGATCAAAACCCCCAAATACA R 2 1 2 1 101000 r 74 goat snp56955-scaffold902-2036762 7 78326691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415881 Affx-122948484 AX-123286230 7 28692563 CTCTGGTAGTGTAGAAACCTAAAGGAGACAGTCCC[A/G]TGGACTGCAGAATGCCCAACTTCCCTGTCTTCCAC R 2 1 2 1 101000 f 74 goat snp56956-scaffold902-2079458 7 78281281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791145 Affx-122976575 AX-385278140 7 28728065 TCAAAGCAATTACTGTTTCTTGTACTGCTTCTTAA[A/C]TTGAATGCTAAAAATGTTTTTCCACTCTTAAGGTT M 2 1 2 1 101000 r 74 goat snp56957-scaffold902-2114960 7 78245848 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780613 Affx-122927196 AX-385267703 7 28758970 TCTGTAAAGCTTCACTCTTGACAGTAAATCAGAAA[C/T]GTACCTTAAGTATTTATGGTCCCCTTGGCACCAAT Y 2 1 2 1 101000 r 74 goat snp56958-scaffold902-2145865 7 78214772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777194 Affx-122950865 AX-385264317 7 28788805 AATATCCAGAGTAAAGTACTCTGTCCTCAGTTTGT[A/G]TGATATCATGGACAAAGTGTCTCATTTGGTTTAAT R 2 1 2 1 101000 f 74 goat snp56959-scaffold902-2175700 7 78184974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418622 Affx-122947151 AX-123288970 7 28827997 ACATGTAGTCCTTTATTTGCCACCCCGAATCTGAC[A/G]CTATTCAGCATCACAATATAGTGCTGATATCTGAT R 2 1 2 1 201000 r 74 goat snp56960-scaffold902-2214892 7 78144994 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453392 Affx-122919920 AX-123323725 7 28857214 CAATGGTATGGTGCAGTCACTGAATGGTCGTTATG[C/T]AAAGCCTGTTAAACAAGTTATTTAAATCTTCTTCT Y 2 1 2 1 101000 f 74 goat snp56961-scaffold902-2244109 7 78115977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410965 Affx-122952023 AX-123281315 7 28923157 GTTGAAAGAAATTTTCCAGTGAAAACAGTGTGATC[C/T]ATGGGTTAGAGGCCTCATTCTCATTCACTCTTCAG Y 2 1 2 1 101000 r 74 goat snp56963-scaffold902-2310052 7 78048948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399349 Affx-122961354 AX-123269704 7 28957336 AACTTAGGCTGGTGTTTTTCCTTTGGAAAGGTTTG[C/T]GATTTAAATTAGCTTTTACCAATAAGAGAATAATA Y 2 1 2 1 201000 r 74 goat snp56964-scaffold902-2344231 7 78014662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791112 Affx-122945316 AX-385278107 7 28999071 TTCTAAATAGGGTACAGAGACTAACAGCTGAAAGG[C/T]GCTTAACTTCTCAGAACATATCTGCGTTTTGACAG Y 2 1 2 1 101000 r 74 goat snp56965-scaffold902-2385966 7 77973011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429521 Affx-122937846 AX-123299863 7 29036757 TCCCAATTTTAGCTAAGAATCACTGTAAAATCCTA[G/T]AGTCTCTCACACATCAATATTTACTCTGTGAAAAT K 2 1 2 1 101000 r 74 goat snp56966-scaffold902-2423652 7 77935935 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785337 Affx-122936254 AX-385272382 7 29069955 TATGAGGACTATCAATACCTGTCTCTGAGATAACT[A/G]CAGGAATATCTTAAAGAATTTAGAGGTATTGAGAT R 2 1 2 1 101000 f 74 goat snp56967-scaffold902-2456850 7 77903551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408880 Affx-122953984 AX-123279231 7 29145851 CTGTGCTAAAGAACTGATGGCAAAAAAAGGAAGCC[A/G]CAAAATTCTTGAACTAAAACTAGACAAAATCAATG R 2 1 2 1 101000 f 74 goat snp56969-scaffold902-2532746 7 77825853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785860 Affx-122952882 AX-385272897 7 29250629 CCGTTTCCTCTAGAATATATCAAATTCCTTCTTTG[A/C]CCATAAAATTCTTCTGTTGTGTCTTAGATCATTCC M 2 1 2 1 101000 f 74 goat snp56971-scaffold902-2637524 7 77719794 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378070 Affx-122977177 AX-123248429 7 29312139 GTGCAGATCAGAGAGACACTGGCAGGTAAGCACTC[A/G]TAGGACTAGTACCTCCCTCACATTTGACAGAGGGG R 2 1 2 1 201000 r 74 goat snp56972-scaffold902-2699034 7 77656805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452151 Affx-122921662 AX-123322484 7 29378297 TTTAGTGACTAGTTAAGGGACAGTTATCAGGTTAT[A/G]TTTAAGGCTTATTTTCTGACTTTGATAAATCTGTC R 2 1 2 1 201000 r 74 goat snp56973-scaffold902-2765192 7 77587693 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774347 Affx-122978076 AX-385261483 7 29411071 AGCAAATTATTAGAAATCTCAAAGACACAGAGTAA[C/T]GGTTTTAAGTGTATTTTTAATCCCTTAAATCCATC Y 2 1 2 1 101000 r 74 goat snp56974-scaffold902-2797966 7 77553825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774696 Affx-122933450 AX-385261830 7 29457232 CCAACCACACTGGTATTCTTAGTAAATGCTATAGC[C/T]TGCATCCTCAAACACAAAAAAATAATCACCTAGAA Y 2 1 2 1 101000 r 74 goat snp56975-scaffold902-2844127 7 77507546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426139 Affx-122940614 AX-123296485 7 29488734 TTACATATCCATCCACAACTAGGTATTCAGCCTTA[C/T]ATTCATCCCAGGAATTAAGCCAGCACCGCTGATAC Y 2 1 2 1 201000 r 74 goat snp56976-scaffold902-2875629 7 77475916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434218 Affx-122934848 AX-123304559 7 29552796 TGAATAGTCCCTTTTCTTTTTGAGCAAATCTGAAT[A/G]TATGTTTTAGAGAAGTTTCAGGTTTTCCAGTCCAT R 2 1 2 1 101000 f 74 goat snp59880-scaffold995-2759707 7 77403347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449412 Affx-122922694 AX-123319747 7 29581607 AATAAATCTCATTGTCAAATATTCTGTTACCTGAG[C/T]AAGCCCTCATGTCCCAGCCTCTCCCCACCTGGATC Y 2 1 2 1 201000 f 74 goat snp59879-scaffold995-2730896 7 77373959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439475 Affx-122930163 AX-123309812 7 29621439 TGTGTATGTGAAACTAAAATGAAAAAATAGAATGA[C/T]GATCATAATACAATTATATTTTCAATTTTATTCAA Y 2 1 2 1 101000 f 74 goat snp59878-scaffold995-2691064 7 77334295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425406 Affx-122941546 AX-123295752 7 29652892 ATGCTTGCTTTTGACCATTCTTCCCAGATGTATGG[G/T]ACAGATGGATGAATTTCATCTTGCAGGGGGTTGGT K 2 1 2 1 101000 f 74 goat snp59877-scaffold995-2659611 7 77303374 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772788 Affx-122935283 AX-385259933 7 29687684 ATCTTTTTCCATAGAAAAGCTGTTAATCTGTGTAG[G/T]GTGGCAACTGGCCAAGTTTTTAGAACACCTCTTTG K 2 1 2 1 101000 r 74 goat snp59876-scaffold995-2624819 7 77268586 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399134 Affx-122960662 AX-123269489 7 29775684 CTCAAACTAACAGCTTAACAACGCTCATGAGTACA[A/G]TACTTGCACTATATATTTGCCTATTTTTCTGAAAG R 2 1 2 1 101000 f 74 goat snp59875-scaffold995-2536819 7 77178132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278641 Affx-1111836440 AX-519552120 7 29784609 GTCACATTCTGCCTCCTTTCCGCCTACTTATTGCT[A/G]TGGAGAGAGACAGAACTTAGCCGCTCAACAGAGTT R 2 1 2 1 102000 r 74 goat Random2.2K-777 7 29784609 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794880 Affx-122924572 AX-385281840 7 29804508 CTTAACAACTTCTGTTTGATTAAATTGTGGTTAAT[C/T]AGCTCTGAGTATTTTGTGGGCATGTTTAGATTTCC Y 2 1 2 1 101000 r 74 goat snp59874-scaffold995-2507995 7 77148449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780894 Affx-122959793 AX-385267981 7 29834199 TTTTAAAACTCTGCCATGACTATGTACCTGGATTA[C/T]ATTATTTTATAGATAGCTGGGAGTTATTTTAGCCT Y 2 1 2 1 101000 f 74 goat snp59873-scaffold995-2478304 7 77118408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381663 Affx-122974744 AX-123252021 7 29878092 TAATGTGTAACTACCATATATCTAGAAAAAGACAA[C/T]GGAAACTTTTCCTACCAAAGGCCGCTAAGTGATCA Y 2 1 2 1 201000 f 74 goat snp59872-scaffold995-2434411 7 77074656 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376051 Affx-122978931 AX-123246410 7 29963833 AATGAATAAAAGAAATGAGAATCCAGGAAGCTACA[C/T]GCCCTGCATCAGTTCAGTTCAATTCAGTTGCTCAG Y 2 1 2 1 201000 f 74 goat snp59870-scaffold995-2348670 7 76980132 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384241 Affx-122972364 AX-123254599 7 30016042 CTCCTTCATTCTTAGGTTTAAATTTGCTGTGGATG[A/C]TAAACTAAGACCATTCATTCATTCATTATTAACTC M 2 1 2 1 101000 f 74 goat snp59869-scaffold995-2296461 7 76927017 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453971 Affx-122919457 AX-123324304 7 30098464 TGACCTTGGGACAAATGCATGGTTCTTGGAGCTCT[A/G]TCTTAGTGAATTCTATTGTAGCATAAAGATGATGA R 2 1 2 1 201000 r 74 goat snp59868-scaffold995-2214039 7 76843313 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415315 Affx-122948808 AX-123285664 7 30128867 TGCATAAACCTTAAGTTCTTAGAAGTGAAATTGCT[A/G]TTTGAAAGTTGAAAATTTTTATTTGTTTCCTTCCA R 2 1 2 1 103000 f 74 goat snp59867-scaffold995-2183636 7 76812535 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377360 Affx-122977651 AX-123247719 7 30185365 TTGTGGTAAGTAATGGTAGTAGTGATACTGCTATA[C/T]GATGAAGATAATATGAGCTAGATGCTGCCACAGTG Y 2 1 2 1 201000 f 74 goat snp59866-scaffold995-2127138 7 76757958 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427754 Affx-122939248 AX-123298097 7 30265456 TTTATACTTTTGATTCTTTTTAAATTGCTCATACC[A/G]TAATGTTACTTGAAAGGAGTAGAATTTAGAACACA R 2 1 2 1 101000 r 74 goat snp59865-scaffold995-2047047 7 76677203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375954 Affx-122978447 AX-123246313 7 30306286 TATTTGAGGACTTGTATTTAAATATTTTAGTGTTA[C/T]AGAATATACAGTGGGTCTTGAAAGTCTTGTCATCC Y 2 1 2 1 101000 r 74 goat snp59864-scaffold995-2006217 7 76635824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398909 Affx-122961013 AX-123269264 7 30338105 TCATAATCAGATAGTTTTTCTAATGAAATCTTTCA[C/T]AGTTGTGTGTACAGTTACTGGTATGTAGAATCCTC Y 2 1 2 1 101000 r 74 goat snp59863-scaffold995-1974398 7 76604165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444465 Affx-122926540 AX-123314802 7 30392306 TTGATTTTCAACAGCATATTTTTTAAAGTAAAAAT[A/G]CCATGTTTATGAAACTCATTTACAGCCTACATGCT R 2 1 2 1 101000 r 74 goat snp59862-scaffold995-1920197 7 76549450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382341 Affx-122973883 AX-123252699 7 30542945 GCCCAAAGGTTCCATGGTAAGAATAGGTATTGTGC[A/G]TGCCCAGGATGGACTGGTTTAGCCTGTAGGCCTTG R 2 1 2 1 101000 f 74 goat snp59859-scaffold995-1769558 7 76391448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403009 Affx-122958565 AX-123273362 7 30573904 AGCAACTGAGGCACAGGTGGCAGCCTTGATTTGCT[A/G]CTGGCATCTGAGTGTGTGTGTGCTCTCGTAGGACT R 2 1 2 1 303000 f 74 goat snp59858-scaffold995-1738599 7 76358830 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408013 Affx-122954309 AX-123278364 7 30611720 GGCTCAGATGGCGTCCCCTCCAGCCCTCCATCCCC[A/G]CTCCAGAATCTATCAAGTAACTTCTGCTGCCAGCA R 2 1 2 1 101000 r 74 goat snp59857-scaffold995-1700783 7 76320655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777852 Affx-122926781 AX-385264969 7 30668891 TGTTAGTGAACAATAGAAATTGAACAGAGTAGAAC[A/G]GGAGAAATTGCACAGATTTCTTTTGTCAGGTCAGA R 2 1 2 1 101000 r 74 goat snp59856-scaffold995-1643612 7 76262764 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273641 Affx-1111833717 AX-519547255 7 30695349 CGTGCCCCAGTGCCTCCCTGAGCTCACCATACCTC[A/G]AGTGAGCTGTCCCCTCAACAGCCTTCTGCAGGTTC R 2 1 2 1 202000 r 74 goat GoatD01.002314 7 30695349 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278469 Affx-1111836441 AX-519551952 7 30720207 AGCCTGCCTTCCAGGGCTGCTCTGAAAACAAAAAT[C/G]AGCTAACAAGGGAGTATTTTGGAAAAGGTTAAGGG S 4 1 2 1 101000 f 74 goat Random2.2K-779 7 30720207 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278472 Affx-1111836443 AX-519551956 7 30724499 TATTCGGATATGGGCTGAAGATTAGATTATCTTCT[A/G]TCAATGTTAATTTTGTTGTTATTGTTGTTGTTTGG R 2 1 2 1 101000 f 74 goat Random2.2K-780 7 30724499 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401449 Affx-122958981 AX-123271802 7 30732978 TTTTATTTTATTGACTTATTTTGTTACCCTCTCCC[A/G]TTTTCTCTGTGATATTTCAAAGCAAATCTCAGGCA R 2 1 2 1 101000 r 74 goat snp59855-scaffold995-1579525 7 76198961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398705 Affx-122961852 AX-123269060 7 30795564 TATACATGGTTAATATAGAAATCAGATGTAGGTAA[A/C]ATGTACCTACTCTTTTTCTTTAATGCCGAAAAGGG M 2 1 2 1 101000 r 74 goat snp59854-scaffold995-1516939 7 76132878 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781981 Affx-122965035 AX-385269061 7 30838551 TCTGTTTTCAAGAGTGAGGCAGGAAAGAGTAAGGT[A/C]GTCCCTGCTATGGCTTGGATTAGAACTTGATAAAA M 2 1 2 1 101000 f 74 goat snp59853-scaffold995-1473952 7 76089778 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417939 Affx-122946712 AX-123288287 7 30872532 ACCTGGAACTGTTCCTCCTTCTCTCTCCTAACCTC[A/C]CTTTCTTTGGCTAATTCTTCGACCTTCAGATCTTA M 2 1 2 1 201000 r 74 goat snp59852-scaffold995-1439971 7 76055097 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409900 Affx-122952895 AX-123280251 7 30904605 CTTCAATATTAAAAGGGGTTAAATACATTGAAAGG[A/C]TATTATATAAGGTAAAAAATGGTTGACAGTACTCA M 2 1 2 1 101000 f 74 goat snp59851-scaffold995-1407898 7 76022845 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407721 Affx-122955005 AX-123278072 7 30941708 CATGTCTGTGTGTCCCAGTCTCTTCTTCTTGTAAG[C/T]ACAGCAGTCAGATTGCATTAGGGCCACCCGAGAAG Y 2 1 2 1 101000 f 74 goat snp59850-scaffold995-1370795 7 75985758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423334 Affx-122943169 AX-123293680 7 30971104 TCAAAAAATAATATCTCCATTAATACTGTCATTGG[A/G]ACTTTAGTGATAAATGAGTCAAATGGCTCCTTACG R 2 1 2 1 101000 f 74 goat snp59849-scaffold995-1341399 7 75955969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376294 Affx-122978374 AX-123246653 7 31005794 TACCTCCCCCTGAATGTCAAAACACAGAATTTTCT[A/G]TCTTCCCCTAATTCCAGCCTAAACCCACTCTTTCC R 2 1 2 1 101000 r 74 goat snp59848-scaffold995-1306709 7 75920817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427633 Affx-122939341 AX-123297976 7 31037195 TTAAGGCTTTTTATAAAAGATTTAAACATCATCCT[A/G]TGCTTAGTGATTGTTACGTAGCCAAGTTTGTATTG R 2 1 2 1 101000 r 74 goat snp59847-scaffold995-1275308 7 75888842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795830 Affx-122932593 AX-385282783 7 31153065 CTTATAAATCTTTAATAACACCTTCACTGACATAA[C/T]CTCACCCTGTTCAAGCAAAGCATAACTATTGAAAG Y 2 1 2 1 101000 r 74 goat snp59845-scaffold995-1159438 7 75771708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451172 Affx-122921345 AX-123321506 7 31192114 ACCGTGAAAACTCGTAAGATCATCTGTGGGAAGTG[C/T]ATGGGATTAAACAAGAGAATATAGAAAAGAGACCT Y 2 1 2 1 101000 f 74 goat snp59844-scaffold995-1120389 7 75731614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792169 Affx-122944124 AX-385279154 7 31246454 GACAGGAAATTAGACTTATATAAATTTAACTCTGC[A/G]TAACAGTATGACCTCAAACAAGACTTATACTCTGA R 2 1 2 1 101000 r 74 goat snp59843-scaffold995-1066049 7 75678116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273269 Affx-1111833536 AX-519546917 7 31252448 GGCTGAAAGAAGCCTTGTTTCCAGAGTTCCACCTG[A/G]AGGGAAGGAACCTAGGCCTCAGCATTACTGATTTC R 2 1 2 1 201000 f 74 goat 7_31252448_AF-PAKI 7 31252448 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320787622 Affx-122959779 AX-385274645 7 31292916 AACATTATACAAAAACAGTCTACAGAAAACAGATT[A/C]GAGATTCACCAAGCTGACCTACCTGTGATGGTCAC M 2 1 2 1 101000 r 74 goat snp59842-scaffold995-1019587 7 75631115 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428917 Affx-122938911 AX-123299259 7 31332418 TGCAATGGACCAAATGTTCATGTCCCCTCAAACTT[A/C]ATGTGTTGAAATTCTAACCAATGTTATGGTATTAG M 2 1 2 1 201000 f 74 goat snp59841-scaffold995-980085 7 75591473 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421588 Affx-122944498 AX-123291935 7 31382640 CTTGAATACAATTGTCAATTATCAGGGTCTCTTTG[C/T]AGACTAGACAAGTAACAATGAATGTAAGGTCTAAA Y 2 1 2 1 101000 f 74 goat snp59840-scaffold995-929863 7 75540090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390149 Affx-122967985 AX-123260506 7 31415496 CTTTCCAGGCACTGCTTGTCAGCACTCTCCTTAAA[C/T]GCCCTTTTGTCTTCTCTAGCCTAATTCTAAAAGCC Y 2 1 2 1 101000 f 74 goat snp59839-scaffold995-897007 7 75506989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391383 Affx-122967272 AX-123261740 7 31489379 CCACTTGTTCAACTATAAAGGTTACAAAACTAAAC[A/G]CTCACTATGCCAGCTCCCTCTGTAGCTAGAGAAAG R 2 1 2 1 101000 f 74 goat snp59838-scaffold995-823124 7 75431931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785061 Affx-122920710 AX-385272108 7 31534666 ATCTCACAAAGGCCTTGTGTGGAAATCAGATGAGA[C/T]AGGTGAGGATCCAACACAGAAGTTGCTAAGAAAAT Y 2 1 2 1 101000 r 74 goat snp59837-scaffold995-777837 7 75386921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789883 Affx-122924564 AX-385276890 7 31566664 CTTAAAATGGTCCAAAGGCTCCTAGGCTTTAAATA[G/T]ATGATTGATTTAAGATACAGTGAGAGAATCAAAAT K 2 1 2 1 101000 f 74 goat snp59836-scaffold995-745839 7 75354713 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398787 Affx-122961423 AX-123269142 7 31613771 TGTGAGTTGCTGCCTTCTTAGCTCAAATTGCATTT[A/G]ATCTCAGGAAGGGCTCTTCAGAGGAAAAGCATATA R 2 1 2 1 101000 f 74 goat snp59835-scaffold995-698732 7 75308214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780917 Affx-122935492 AX-385268004 7 31657055 GTGCTAAAAGCAGGCTTGCTGCTTGTTGATGACAA[C/T]GTTTCTTTTGTGATATGTTTCCTTTCTTATTCAGA Y 2 1 2 1 101000 f 74 goat snp59834-scaffold995-655448 7 75265252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770167 Affx-122948223 AX-385257334 7 31716395 CACTGTTAGTTCATGCACTTGGTAACCACTTTAAC[A/G]TATGTTGGCCAAACTCAAGCCACTCCAGCTTTCTG R 2 1 2 1 101000 r 74 goat snp59833-scaffold995-596108 7 75205642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776825 Affx-122961553 AX-385263949 7 31774797 GAGAAAGCGAATTCTTCGAAAGTCATCCTCCAAAC[A/G]TGATCTCCATCTTAGGTAGTCCCCTGTGTCCTCCA R 2 1 2 1 101000 f 74 goat snp59832-scaffold995-537706 7 75146491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391230 Affx-122967394 AX-123261587 7 31845797 GTCTGATGGACGGAAAGTGTGAGATAGTGAGAGCA[C/T]GCGTGGGAGGGTGGGGGGACTGTGGGGGACTGGTC Y 2 1 2 1 101000 f 74 goat snp59831-scaffold995-466706 7 75075126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390831 Affx-122967840 AX-123261188 7 31898006 ATGTAGTATTCAGTTCACGTGATTCATGAATTCAT[A/G]CTAAGCCTCTCAGTTTCTCCTTAAGGCCTCAGCGA R 2 1 2 1 101000 r 74 goat snp59830-scaffold995-414497 7 75022478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413859 Affx-122949862 AX-123284208 7 31969000 CATTATGCAACTCTCAATGATAAGAAATTTTCTTC[A/G]TGAGCAGAACGCCTCATGTCATTTGACTCAATTTC R 2 1 2 1 101000 r 74 goat snp59829-scaffold995-343503 7 74952611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792187 Affx-122947786 AX-385279172 7 32010688 TCTGCTATTACATGTTTAATAAATAGTGGTTCCCT[A/G]CAATAGTAATTTGAAAGCCAAAAAATACTGCAAGA R 2 1 2 1 101000 f 74 goat snp59828-scaffold995-301815 7 74910187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799767 Affx-122924051 AX-385286694 7 32054049 TTGCCAACCACTCAATACATTAAACAAGATAGTGC[A/G]TGGATAGAGATAAAACAGGTGATAAAGATTCCAAT R 2 1 2 1 101000 f 74 goat snp59827-scaffold995-258454 7 74866993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448086 Affx-122924327 AX-123318422 7 32096832 CCTCAGGCTGGAGCTCAGGAAGCTACCGAACTCAA[A/G]GGCTCAGCCCCAGAGGACCCACGACATGGTAAGGA R 2 1 2 1 101000 f 74 goat snp59826-scaffold995-215671 7 74823907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770193 Affx-122970729 AX-385257360 7 32165418 CTGACCTGAGATTATCTATTTTATGATCTTGAAAA[C/T]GTATATGAGCAATCTTCAAAGGAGGTTGTCTTTTG Y 2 1 2 1 201000 f 74 goat snp59825-scaffold995-147085 7 74754986 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38436788 Affx-122932258 AX-123307126 7 32208730 GTTAATTTTAGTGATACTGCCCATAGAGCTGAGGT[A/C]TATTAAGGCCAGCCAATTACATTAGCTTGCTAATT M 2 1 2 1 101000 f 74 goat snp59824-scaffold995-103773 7 74711456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791683 Affx-122972104 AX-385278674 7 32244753 GTTTTTTCCAACATGATTTCCAACTTCTCTTCAAA[C/T]GTTAAGTATAATGGCAGAATAACATTGTTATAGGT Y 2 1 2 1 101000 f 74 goat snp59823-scaffold995-67750 7 74675493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800600 Affx-122953992 AX-385287519 7 32301275 AATTTATTATATTCCCTGGGGCTTGACATCTTATT[A/G]TGATTCATTTTCCATGTAAATGGACTTTAAAAAGA R 2 1 2 1 101000 f 74 goat snp59822-scaffold995-11228 7 74619931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274064 Affx-1111834017 AX-519547668 7 32302837 CCCTATACTGCTGCAACTGGTTGACCTTCAACTCC[A/G]TGAAGGGAATTCAGGATGAGGCACTCTGTGCTGCA R 2 1 2 1 201000 f 74 goat GoatD01.014109 7 32302837 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434576 Affx-122934116 AX-123304917 7 32337542 TTTCTGTCTCTCTGTACACTTAGTTAAATGCTCTC[A/G]TGGGCTTTTCTTCTCTTTATTTATCACTGGAAGCT R 2 1 2 1 101000 f 74 goat snp8842-scaffold1317-953886 7 74577020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422408 Affx-122943378 AX-123292754 7 32367413 TAGACACTGCTCCCCCTGGGCCTCTAGAGTACTTC[A/G]TTTACTCATTCAACAAAATTTTGGGAGCATCTATT R 2 1 2 1 101000 r 74 goat snp8841-scaffold1317-924015 7 74546819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776856 Affx-122922379 AX-385263980 7 32402393 TTAAGCTTAATAGATGTCCTCACGTGTCACCACCC[A/G]TGCATATGTACTTGTAAGCATACATATACACACAC R 2 1 2 1 201000 r 74 goat snp8840-scaffold1317-889035 7 74510498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378483 Affx-122976666 AX-123248842 7 32433807 GAATGTGAACTGAAAGAGAGACACAAAGAGACGAC[A/G]AGAGAGCAGAGGCCTGGCTGTGTATGATTTCATGT R 2 1 2 1 201000 r 74 goat snp8839-scaffold1317-857621 7 74479085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802632 Affx-122927745 AX-385289533 7 32463717 TTTAAATCATTTATCAGCTCAGTAATTGCATAAAA[C/T]GTGAAATGCTCTAACACTTTGTGGTTCTATGTAAC Y 2 1 2 1 101000 r 74 goat snp8838-scaffold1317-827711 7 74449176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439283 Affx-122930976 AX-123309620 7 32509737 CACACAAGTAATCAAAATTTAAATCCAGATTTTTC[C/T]GAAAGAGGGAAAGCATGATATTAAATCAGAATTTT Y 2 1 2 1 201000 f 74 goat snp8837-scaffold1317-781691 7 74403155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769841 Affx-122931154 AX-385257011 7 32548906 AAAAATGATTGGAAAAACTTAAATATGCCCAAATT[A/G]TGGCTACTAATTGAGATATTCCTTCAGGTATCTCC R 2 1 2 1 101000 r 74 goat snp8836-scaffold1317-742522 7 74363725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786363 Affx-122932658 AX-385273397 7 32585452 ATCACACTGAATAGGTTAAAAAGCGTCACCCAGCA[C/T]ATCCACCAACAACACATTATGGACATTATTGCCAT Y 2 1 2 1 101000 f 74 goat snp8835-scaffold1317-705976 7 74326102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791786 Affx-122945708 AX-385278776 7 32613960 TATTATATGTTTGATAGAATCCATTCCTTTTTGCC[A/G]CATATTCTGCAGCCATTCTTTACAGTGAACCTCGC R 2 1 2 1 101000 f 74 goat snp8834-scaffold1317-677468 7 74297017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434365 Affx-122934711 AX-123304706 7 32657269 TGGCAAGTCAGGATTCCATGGGTAGCTTCAAGGTT[A/G]CAGTTAAAAAACCTCCTCCATTCACTGTCTCTAAT R 2 1 2 1 101000 r 74 goat snp8833-scaffold1317-634159 7 74251917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778501 Affx-122941439 AX-385265615 7 32694953 CCCTGAGTGAAATTGTTGCATGATACTGAAACTCT[A/G]TTTTTAGTTTATTGAGGAATCCCCACACTGTTTTC R 2 1 2 1 303000 r 74 goat snp8832-scaffold1317-596475 7 74214524 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793945 Affx-122963475 AX-385280914 7 32742289 AGCTTATGTCCTAATAGAAGAGACATCTATCATTC[A/G]TATCTAATTCACTTAAATTCTAAGGGAGAATCCTA R 2 1 2 1 101000 f 74 goat snp8831-scaffold1317-549139 7 74166895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793630 Affx-122960078 AX-385280604 7 32795078 TCAACCATAATATTATAATTCTCTTAGATATTTTC[A/G]TGGCAACCATAGCACAGGATAGCCTACCCTCTGTA R 2 1 2 1 101000 r 74 goat snp8830-scaffold1317-496350 7 74114434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442849 Affx-122927684 AX-123313186 7 32854041 TGGGAATGACTGCTAATGTATCAGTTAGATGCCTT[A/G]TCTTCCATTCTCTTTGTACTAAATAGTATCGAACA R 2 1 2 1 101000 f 74 goat snp8829-scaffold1317-437387 7 74054934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425740 Affx-122940748 AX-123296086 7 32889111 CACTGACTTCCATTTTTCCAATATTTAAAAATGTT[A/G]CCTTTAAAACTAACACTTATTTCTGAGACTAGTCA R 2 1 2 1 101000 r 74 goat snp8828-scaffold1317-402317 7 74019888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772961 Affx-122971914 AX-385260105 7 32970531 ATTTAAAAAGATACATATCACCAAGTCTCATATGA[C/T]AGAGAATCTGATTTAATTTGTCTAGGATGGGGTCC Y 2 1 2 1 101000 r 74 goat snp8826-scaffold1317-320897 7 73938212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439520 Affx-122930126 AX-123309857 7 33008909 GGCACCTGACTTTGTAGTGAGGGACTTGCCAGCTT[A/G]CAAATTCATTCTTCTCTGAAGTTATGCTACTTTAC R 2 1 2 1 101000 f 74 goat snp8825-scaffold1317-282519 7 73900870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786378 Affx-122948760 AX-385273412 7 33038639 GGTGCTTGAGCTCGGAGTCCACAAATGACTTTTCA[C/T]GTTCTAAAAAGAAATTACTGGCAGTGTCCAAACAA Y 2 1 2 1 101000 f 74 goat snp8824-scaffold1317-252789 7 73871148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772430 Affx-122963602 AX-385259582 7 33072824 TATACTTCATCATGCTTAAATGACTGAGGACAGCC[A/G]CCTTTTGTCCTTCCCTGGGACATAAATTCCACTCT R 2 1 2 1 101000 f 74 goat snp8823-scaffold1317-218604 7 73837418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418285 Affx-122946999 AX-123288633 7 33102014 AAGAATTAAATGAGTTAAGCTACCGGGAAAGTTCT[G/T]TATAACCTGTAATGCTTTATTACATATTCACCCCT K 2 1 2 1 101000 f 74 goat snp8822-scaffold1317-189414 7 73808687 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784027 Affx-122940652 AX-385271080 7 33136510 TGAGTCTAAAAGACCTGAAGCGAGGAGTAAGGTTG[A/G]ATTATTTCAGGAAGAAAAAGGCCAGTATGAATGAG R 2 1 2 1 201000 r 74 goat snp8821-scaffold1317-154918 7 73774138 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446187 Affx-122925731 AX-123316523 7 33186811 AAGCTGTTAAAATACTGAAAAAGTAAAAATTTCTT[A/G]TGCACAAAAATTCTCATTTCTATGAGCTAGATCTT R 2 1 2 1 101000 r 74 goat snp8820-scaffold1317-104617 7 73723780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431589 Affx-122936176 AX-123301930 7 33218942 ATGACATCTCATAGGGACTCTCTAATCCCTTCCTT[C/T]TAAATAACTTTTTGTGAATTTGGGGTTTTGACCTA Y 2 1 2 1 202000 r 74 goat snp8819-scaffold1317-72486 7 73691517 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802272 Affx-122943155 AX-385289176 7 33276321 CAGAACATCTGTTTTAGCTTGCGATTCAATATTTG[C/T]ATGCTTGCTTATTGCCTGTGACCCCCATTAGATTG Y 2 1 2 1 101000 r 74 goat snp8818-scaffold1317-15107 7 73633921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440112 Affx-122929706 AX-123310449 7 33304204 GAGAGCTGGGAACACCACACTGCAGGAGCCAGGAA[C/T]GAGAGAAGCCTGGCCTCCTTCCGGAGCTTGCTGCA Y 2 1 2 1 101000 f 74 goat snp33081-scaffold386-12677 7 73605832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379648 Affx-122975945 AX-123250006 7 33333240 CCTCTGGTTTGTAATTTTTAAAGGACTATAAGCCA[A/G]CCTTTATCCTGACACAGAGGCATCTTGAACTCTTA R 2 1 2 1 101000 r 74 goat snp33082-scaffold386-41713 7 73576052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389082 Affx-122968590 AX-123259440 7 33363973 CTGTGTGGATAAGGTTTTCTCTCCCTTCTGTCTGG[C/T]GCAGGGAGGACAATGCACAAACCGAACCATTGCTT Y 2 1 2 1 201000 r 74 goat snp33083-scaffold386-72446 7 73545040 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791562 Affx-122939713 AX-385278553 7 33401484 AGAACAGTGAGGCTGGCTTAACACCATTTAAAATC[A/G]TGGAAGAACACTCATGGAAAAAGTTACACTTGCCG R 2 1 2 1 101000 f 74 goat snp33084-scaffold386-109957 7 73507326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418502 Affx-122946434 AX-123288850 7 33447581 AAGGTCAACTCAGCTGTTCACAAATCACTAGTGCT[A/G]CATATTTGTCCTTGACTTCATATTTTCCTTTTTGT R 2 1 2 1 101000 f 74 goat snp33085-scaffold386-156054 7 73461190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411034 Affx-122951967 AX-123281384 7 33495107 TGTGGTTGGTTTGAACCTTTTTCAACATTCTGTAC[A/G]TTGCTTGTCTCTTTAATTAATCTTGACCTTGAATT R 2 1 2 1 101000 f 74 goat snp33086-scaffold386-203580 7 73413020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407508 Affx-122954741 AX-123277859 7 33589260 GCTCCCTTCTTTTTCCAGCTTAAAGAGACATACAG[A/G]GCAGAAAACAGATTGTCCATGGTAAGTAAAATTCA R 2 1 2 1 101000 f 74 goat snp33088-scaffold386-297733 7 73318930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393194 Affx-122965510 AX-123263551 7 33624308 GGTTCGACACACATTACTGAAGGGCTAGGGACCAT[C/T]TGACTGCGTTTTGCAACCCTGGCCCAGAGGTCTAC Y 2 1 2 1 101000 f 74 goat snp33089-scaffold386-332781 7 73285086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400998 Affx-122959694 AX-123271351 7 33653847 CCTCTGCACAGTCTGCATGAACAGTCAGGGATTCC[A/G]ATGGCCAAAAGGTTACTAAGTAGGTGTGACACAGG R 2 1 2 1 101000 f 74 goat snp33090-scaffold386-362320 7 73255657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802904 Affx-122959780 AX-385289801 7 33688374 ATCAAGTGAAAGGAAAGGGCAAGGACATGTATTTT[A/G]TCAAAATGAGCATAATTTAGCAAGTTAATGTGGAT R 2 1 2 1 201000 r 74 goat snp33091-scaffold386-396847 7 73221243 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441712 Affx-122929151 AX-123312049 7 33729741 CATATCACTGGCACTTTCTACAGCTGTTTCATGCC[A/G]AACTAAGACCTCTGTGCTGGTAAAGCTGAGCCCCA R 2 1 2 1 201000 r 74 goat snp33092-scaffold386-438214 7 73179984 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273271 Affx-1111833537 AX-519546919 7 33759264 TGTTCCATGGTATTAGGCCACAGGTAAAAGTTATG[A/G]ATAAGTAACTATCAATAATCATTTCTCAAGGGTAT R 2 1 2 1 101000 f 74 goat 7_33759264_AF-PAKI 7 33759264 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789620 Affx-122975964 AX-385276629 7 33787812 ACAGGAGGACTAGAGATTTCAGGCTGCAGATTTCC[G/T]CAATCACAGGATGACAGGCAAAAACAGGTACAGAA K 2 1 2 1 101000 f 74 goat snp33093-scaffold386-496285 7 73122843 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787985 Affx-122968225 AX-385275006 7 33825395 TTAATACATTGTCCCCTCAACAAACTCTTTAAGAA[C/T]CCATTAACAGCCTGGATTGTTCAGAAGGGTGATTC Y 2 1 2 1 202000 f 74 goat snp33094-scaffold386-533868 7 73085374 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392753 Affx-122966006 AX-123263110 7 33859881 CTCTGGCCAGCAGCAAAATGGTCAGAGCAAGAATC[C/T]TTTTCTGCAAGAAACTGAACAGGGTAGTATAAAGG Y 2 1 2 1 201000 r 74 goat snp33095-scaffold386-568354 7 73050633 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278474 Affx-1111836444 AX-519551957 7 33869749 AAATACCTTAACGTGTTCCTCCTCTTCCTTGCCTC[A/C]TGTAATTAGAGCATATTTTAAAATTAAGGAAGAGA M 2 1 2 1 103000 f 74 goat Random2.2K-781 7 33869749 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400623 Affx-122960375 AX-123270978 7 33909315 TAAAAGTTCTGGGGAAATAAGGATGGAGATGGGGC[A/G]TGTAGGATAAAAAGGAAAGGGGGATGGGGCTGGCC R 2 1 2 1 101000 f 74 goat snp33096-scaffold386-617788 7 73001821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418087 Affx-122946600 AX-123288435 7 33962188 TGAAATAGGTGTCAGGAGATACAAAAAGATGAGAG[C/T]AGATTCAAGACAAAATTTGAAGAAAGAAGCAATAA Y 2 1 2 1 101000 f 74 goat snp33097-scaffold386-670661 7 72949179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769494 Affx-122942601 AX-385256664 7 34007238 GAACAAAAGAGTAAAAATGCCACACCTTCCTAGAA[C/T]GCACTTCCTTGTTGGAGTCATTATGAATCATTAGG Y 2 1 2 1 201000 r 74 goat snp33098-scaffold386-715711 7 72903849 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447881 Affx-122923825 AX-123318217 7 34039809 AATCCCACAGGGAGTTCAAGTAGACTATAACGTAA[C/T]ACTAGTAATTAAGGAAGTGGCATTCTTCCTCTATA Y 2 1 2 1 101000 f 74 goat snp33099-scaffold386-748282 7 72871376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440345 Affx-122929663 AX-123310682 7 34076296 ATATACGACCTTACCCAGCATTAAGCCCCTGTCAG[C/T]ATTTATAAGTGGCAGGATTAAAGAGATAAAATCCA Y 2 1 2 1 202000 r 74 goat snp33100-scaffold386-784769 7 72834876 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386027 Affx-122971488 AX-123256385 7 34104967 ACTCTCTAGGAAATCCAGAGGACCTTTCCTAACCA[C/T]GCCAACTTTGCTTTCATATTCCCCTTAATACATAA Y 2 1 2 1 201000 r 74 goat snp33101-scaffold386-813440 7 72804089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476232 Affx-1251763738 AX-586011656 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20000 f 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 560378500 Affx-1251763738 AX-605230915 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20000 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562165098 Affx-1251763738 AX-606940510 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 f 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562165891 Affx-1251763738 AX-606941300 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562166128 Affx-1251763738 AX-606941536 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 38452721 Affx-122920290 AX-123323054 7 34152044 TCTTTCCTCTTTGTTTCCACTCAATCTCAAGAAAT[A/C]GGCACTAGCCAAGCAGATCAGACCCCAAATGGTCC M 2 1 2 1 101000 f 74 goat snp33102-scaffold386-860517 7 72757000 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441693 Affx-122929167 AX-123312030 7 34186905 AACACTATGCTTCCATTTCTTCCTCTCAGTTTTTG[C/T]GCAGTTGTTATTCTACATCTTATTTCTGTGTATGG Y 2 1 2 1 103000 f 74 goat snp33103-scaffold386-895378 7 72722273 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771076 Affx-122959875 AX-385258236 7 34224281 ATAATAAACATAGTGGTATAAACGAAGGAAATTTA[A/G]GGAATAATAGTATTGATGAAGGTGGGAGGGATAAA R 2 1 2 1 101000 r 74 goat snp33104-scaffold386-932754 7 72684183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393661 Affx-122965281 AX-123264016 7 34256850 TGAAGTTAAGACAAGAAATTTTTTGTTTGTTTTAA[C/T]ATACATGATAACCATTTGAGTGAATTCTGAATAGT Y 2 1 2 1 103000 r 74 goat snp33105-scaffold386-965323 7 72651680 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376400 Affx-122978093 AX-123246759 7 34287976 CATCAAACAGCTACTGCAGCATCTCCTGAGGACTC[A/G]CTTCTCCCACCTCCAGAGAAGAGAGGAGAGAAGGC R 2 1 2 1 202000 r 74 goat snp33106-scaffold386-996449 7 72620090 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410138 Affx-122952805 AX-123280488 7 34343047 AGACAGAGAGCAGACTTGAGGCTCAGCGCCTTTCA[C/T]GGACACATCTCATCAGAAGTCGACACTTTTGCTTT Y 2 1 2 1 201000 r 74 goat snp33107-scaffold386-1051520 7 72564980 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399287 Affx-122960543 AX-123269642 7 34375434 TGCCAAAGAAACCGAACCCACTTCGCCTGAAGACA[C/T]GGGGTCCATATTTTTCAAAGACATGGGCTCCACCT Y 2 1 2 1 101000 f 74 goat snp33108-scaffold386-1083907 7 72532436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427793 Affx-122939767 AX-123298136 7 34414583 ACAGGCCTGGCAGCACCACCTGGAGCCTAGAGATG[C/T]GGGTTGAACGGATATTAACTGTCACCCATGGCTCT Y 2 1 2 1 101000 r 74 goat snp33109-scaffold386-1123056 7 72493234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399488 Affx-122961179 AX-123269843 7 34456968 AGAAGTGAACTCCACTGTGAACCTCAACCCAGCCC[A/G]CAGTCGCTGGTGCTCCTAGACCTGATGCCCATCAC R 2 1 2 1 201000 f 74 goat snp33110-scaffold386-1165441 7 72450724 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447193 Affx-122924997 AX-123317529 7 34513382 GTGGGACTTGGGAAGGGGCGGGGTGGAGGGAGGGC[G/T]AGGATCTGCAGTGACAGAGCTGCACAAATACCAGG K 2 1 2 1 101000 r 74 goat snp33111-scaffold386-1221855 7 72394605 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448618 Affx-122923378 AX-123318954 7 34550029 GGTAACATGTCTTCCGGCTTGAAGTGTTTGCCAAG[C/T]TCATGTTCAGGAGCCGCCAGGAACAGGAGGGCTGC Y 2 1 2 1 101000 f 74 goat snp33112-scaffold386-1258502 7 72357643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451232 Affx-122921954 AX-123321566 7 34585799 TAACTGAAAGGCCAGGGGTAGCTCTGGCTTCAGGC[A/G]TGGTTGGATCCAGGGAAAACGTGTGACCAGGATTC R 2 1 2 1 201000 r 74 goat snp33113-scaffold386-1294272 7 72321966 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414170 Affx-122949679 AX-123284519 7 34636152 AGCAGGGCTCATGGTTTCCCCTCAGCATCTGCATT[A/C]GCTGACTAAGTACCTGACTGAGCATACCCCGCCCC M 2 1 2 1 201000 r 74 goat snp33114-scaffold386-1344625 7 72271678 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404733 Affx-122957241 AX-123275085 7 34666781 CTTAAATTTTCTTTTTAACTATACTTGAATTCAAA[C/T]AGATTGTTATAAAACAAAACACTACACACAGTTGT Y 2 1 2 1 101000 r 74 goat snp33115-scaffold386-1375254 7 72241537 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400358 Affx-122960032 AX-123270713 7 34715611 TTTTTCCAAGATTGTTCATCTCTGTTACATCATTA[C/T]GTTAACAGAAAATGCTCCAGGACTTTGGAGACAAA Y 2 1 2 1 201000 r 74 goat snp33116-scaffold386-1424084 7 72192738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407594 Affx-122954654 AX-123277945 7 34766743 AATACCACCTATGACCAATGCCTTCAACATTATTA[A/G]GAGACAAATCATACCGCAGAATTCAAATAACCAGT R 2 1 2 1 101000 r 74 goat snp33117-scaffold386-1475216 7 72140639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425511 Affx-122941470 AX-123295857 7 34800413 AGCCTGGCCAAAAATAAACACCCAAAACTTGTTGA[C/T]TGAATTGAATTGGGAAATGGGGAGATCAGAAAAGC Y 2 1 2 1 201000 f 74 goat snp33118-scaffold386-1508886 7 72106966 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796569 Affx-122949186 AX-385283515 7 34855446 GAAAGCCCAAAAGGATAGATACGTATGAAAAAATT[A/G]CAGTGACTGACACATGATAGAAGCTATGTGAATGA R 2 1 2 1 201000 r 74 goat snp33119-scaffold386-1563919 7 72051288 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393053 Affx-122965621 AX-123263410 7 34896868 AATGTAGAAGCCTTCAGAGGACATGTTTCTGCTGC[A/G]GAGACACTCCAAGCAGCGATGGTATCTGCATTCCT R 2 1 2 1 101000 r 74 goat snp33120-scaffold386-1605341 7 72009894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435563 Affx-122933379 AX-123305903 7 34913707 AAAATAACTACAAAAACAAATTTTTTAAATCTGCA[A/G]CTGCCAAACTAAGAAATCAAGGAGTAGTACTAAAG R 2 1 2 1 101000 r 74 goat snp27549-scaffold2948-216447 7 71991795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403804 Affx-122957967 AX-123274156 7 34966737 CAAGTAGCCCAACGGTAAATAATTCATCTACTGAG[C/T]AGCAGTCATGGGTTTGATCCCTGGGTCGGGAAGAT Y 2 1 2 1 101000 f 74 goat snp27548-scaffold2948-163417 7 71938715 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784330 Affx-122946711 AX-385271381 7 35017975 ACAATCTTAGTGTTACTATTAAGTAGAAATTTTAA[C/T]ACATGCTTGCTGATGTGATATAATAGGAAGTATAC Y 2 1 2 1 101000 r 74 goat snp27547-scaffold2948-112179 7 71887465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388054 Affx-122969534 AX-123258412 7 35055085 AGTTCTCTAGCTACTTGTGGAAGCTATGGGTTCCT[C/T]CTCAGAAAGGCTTCCTGGGGAACCAGCTTAGAGGC Y 2 1 2 1 101000 f 74 goat snp27546-scaffold2948-75069 7 71850364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273611 Affx-1111833700 AX-519547224 7 35081217 CTTCACTGCTGAGAACAGGGCAGGAGTG[A/G]CAGTGGGGACTCTGACTCCGTTCCTCTAGCTGCAA R 2 1 2 1 102000 r 74 goat GoatD01.001901 7 35081217 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375847 Affx-122978526 AX-123246206 7 35112508 GAAGTTCATCAGAGCACTGGGTGCCAAAGTCCAGG[C/T]CTTTGAGGACCGTAAGTGTGCTCCCCTTTCCCGTC Y 2 1 2 1 201000 r 74 goat snp27545-scaffold2948-17646 7 71793591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424428 Affx-122941801 AX-123294774 7 35157754 GAGGCTCCCTAAGGGTCAGAGGGAAGGGCTGATGG[G/T]CGGGTGTGCCATAGAGATGCGGACAGAGTAAGAGA K 2 1 2 1 101000 r 74 goat snp1811-scaffold105-1450869 7 71748671 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425415 Affx-122941539 AX-123295761 7 35214385 ATGGCAAGGCCTACATGGTTGGAAACTGGCCAACC[A/G]TCAAGAAGAATGAAGTCAATAGCTTTATGAATGAA R 2 1 2 1 101000 r 74 goat snp1810-scaffold105-1394238 7 71696659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383873 Affx-122973134 AX-123254231 7 35244572 TGGGGTGTTAAGAGCGCTGCCTCCTGAGCTATTTT[A/G]TGGGTCTCTTTGGACTCCCCGCCCCCCATCCTCAG R 2 1 2 1 101000 f 74 goat snp1809-scaffold105-1364051 7 71666162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446033 Affx-122925849 AX-123316370 7 35274588 TAAGTTCAGTTCAGTTGTGTCCAACTCTTTGTCAC[C/T]CCATAGACTACAGCATGTCAGGGAAGGACAGGGAA Y 2 1 2 1 303000 r 74 goat snp1808-scaffold105-1334035 7 71635780 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407386 Affx-122955259 AX-123277737 7 35319094 TGTCTCACACTTCCCAGGATAGTCCCGCTTACCCA[A/G]TGCTCAGCGAGATATTGCCTCCTCTGGGAAGCACC R 2 1 2 1 201000 r 74 goat snp1807-scaffold105-1289529 7 71592091 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772783 Affx-122937449 AX-385259928 7 35350320 TTCTCACAGCCTATAACATAGGTTCTACTGCTCTT[A/G]CCCAGTTATTTAATGATCAGGAGCCATTACTGGTT R 2 1 2 1 101000 f 74 goat snp1806-scaffold105-1258303 7 71560817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420556 Affx-122945284 AX-123290903 7 35396650 CAGCACCAAGGCCTCTGCTTGGCCTGATCCCAGTT[C/T]CTTTAGTCCCCAAAAGAACAACCACATAAAGAACC Y 2 1 2 1 102000 r 74 goat snp1805-scaffold105-1211973 7 71513509 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387633 Affx-122969857 AX-123257991 7 35439923 CCTTGAGAGCTAAAACGGAGGGGTGCCATCCCATA[A/G]TAGGTGATGTCAACCTACCCATAGGCCTCTTCACT R 2 1 2 1 101000 f 74 goat snp1804-scaffold105-1168700 7 71469597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416447 Affx-122947824 AX-123286796 7 35504800 GTCCCAAGGCTACCTGTCTAGTGCCCTAGTTCCGA[C/T]GAGGGGCCAGTGTGTGACTGGGGTCACAGGGGGAC Y 2 1 2 1 101000 f 74 goat snp1802-scaffold105-1103823 7 71404946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278476 Affx-1111836445 AX-519551959 7 35523627 CCTCCAGGAATCAGGATCTGATATACCTTTATTGT[A/G]TTACATGGTACATTTTGGTCACTCAGGAGTTCAAT R 2 1 2 1 101000 f 74 goat Random2.2K-783 7 35523627 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429513 Affx-122937852 AX-123299855 7 35564393 TGGCTACAGCATGCAGAGGGGCCCAGCCTGGCTTC[A/G]TGTCACAGATCTCCTGTGTAGCTTCTAAGACTACT R 2 1 2 1 101000 r 74 goat snp1801-scaffold105-1044230 7 71346599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394071 Affx-122964970 AX-123264426 7 35643467 TGAAAGAGGAGACCAAGGAGACTATCTTGGGACGC[A/G]TGTTGAACTTGTCATTTGAGAAAAAGGCATTAAAA R 2 1 2 1 201000 r 74 goat snp1799-scaffold105-965156 7 71268245 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790905 Affx-122955480 AX-385277902 7 35683446 TGCCAAAGTGTTTAGTGAACAGAGGAAGGAGGTAG[A/G]TGGAGAGGATAGAGCCTGTTATCACTGAGTTTAAG R 2 1 2 1 101000 r 74 goat snp1798-scaffold105-925177 7 71227864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449697 Affx-122922546 AX-123320032 7 35719076 CTTCCCACCAGCCAAGTCCCCTTGCCTTAGGGCCC[A/G]CCATCTCATCTATTGAGGGAACAATTTTTGCCTTG R 2 1 2 1 101000 r 74 goat snp1797-scaffold105-889547 7 71192032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414941 Affx-122949090 AX-123285290 7 35763380 GTCCTTGAGCCATCCCCCCTGGAGTGACCCCCATC[C/T]GAGGACTGATTAGTCAGGTTACTGCAACCCTTGGC Y 2 1 2 1 102000 r 74 goat snp1796-scaffold105-845243 7 71147654 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410735 Affx-122952706 AX-123281085 7 35798740 AGCTCCCTGGACTCAGGGTCTTCAGCCCCCCACTG[A/C]TGGCACAAACCACATCACTCACCCTGCAAGGCAAG M 2 1 2 1 201000 r 74 goat snp1795-scaffold105-809883 7 71111905 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278653 Affx-1111836446 AX-519552132 7 35887342 TCTTTTGGTAAAAAAAAAAAAAAAACAAAGAAAAA[A/G]AAGGTCATTCCAGCCCTCATTATTTTCAAAGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-784 7 35887342 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437117 Affx-122932169 AX-123307455 7 35948200 CTTGATAATAATTTAGAAAGAAATGACATCTTCAC[A/G]ATACCAAGGTCTTCAATTTATGAACATGATGTATT R 2 1 2 1 101000 r 74 goat snp1792-scaffold105-660423 7 70963497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412624 Affx-122951271 AX-123282973 7 35990831 GGCTGTTCCTTCTAGCCATTCTGCTCACAGATGTC[A/G]CTGGATGGGAAGTGTACACAGCCTGGACAGTGACC R 2 1 2 1 101000 f 74 goat snp1791-scaffold105-617792 7 70920986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386975 Affx-122969963 AX-123257333 7 36030590 AATGTCTTCCTGTAACATAGAGTTGACGTTGTTTA[A/G]TCGCTAAATCATGTCTGCACTCTTCTGACTGCAGC R 2 1 2 1 101000 f 74 goat snp1790-scaffold105-578033 7 70881307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390629 Affx-122967158 AX-123260986 7 36075076 ATGTCAAATAGTCTAGTAGATTTAGAGTTCCATCC[A/G]TCATAATATACACTGAGCATTAAATGTGAAGACTC R 2 1 2 1 101000 f 74 goat snp1789-scaffold105-533547 7 70836818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801701 Affx-122950405 AX-385288609 7 36135770 ATGGTATTATATGCAAATTTGGGGCGTCAGAAAAC[C/T]GAGCTTTTGAATCCTGGATCTATCACATGCTAATT Y 2 1 2 1 101000 r 74 goat snp1788-scaffold105-472853 7 70775969