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-1229