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Table 2 The 156 reliable marker SNPs that induced amino acid changes showing ≥10 read depths

From: Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model

Contig ID c Ref Pos Ref base Called base Impact SNP% Gene symbol DNA change AA Change Depth A Cnt C Cnt G Cnt T Cnt Del
NC_006088 1 12587537 C T N-Syn 0.80 FGL2 c.368C > T T123I 10 0 - 0 8 0
NC_006088 1 24296415 G C N-Syn 1.00 CTTNBP2 c.2600G > C R867P 12 0 12 - 0 0
NC_006088 1 33755434 G A N-Syn 0.91 TBC1D30 c.304G > A V102I 11 10 0 - 0 0
NC_006088 1 34386453 G A N-Syn 1.00 HELB c.2342G > A G781E 12 12 0 - 0 0
NC_006088 1 34386455 C T N-Syn 1.00 HELB c.2344C > T R782W 12 0 - 0 12 0
NC_006088 1 45803846 A G N-Syn 1.00 LOC417921 c.1457A > G Q486R 11 - 0 11 0 0
NC_006088 1 45804772 T A N-Syn 0.92 LOC417921 c.1700 T > A I567K 13 12 1 0 - 0
NC_006088 1 54936701 G T N-Syn 0.80 STAB2 c.6155G > T A2052D 10 0 0 - 8 0
NC_006088 1 67320079 C C|A N-Syn 0.77 CASC1 c.[949C > C] + [949C > A] V317V, V317F 13 10 - 0 0 0
NC_006088 1 82856208 G T N-Syn 1.00 CD200R1 c.197G > T R66L 11 0 0 - 11 0
NC_006088 1 88049869 C T N-Syn 0.90 LOC418423 c.229C > T V77I 10 0 - 0 9 0
NC_006088 1 88157238 C T N-Syn 1.00 CGGBP1 c.428C > T R143Q 10 0 - 0 10 0
NC_006088 1 105941417 T C N-Syn 0.90 SETD4 c.1186 T > C I396V 10 0 9 0 - 0
NC_006088 1 107377588 C G N-Syn 0.92 LCA5L c.1331C > G G444A 13 0 - 12 0 0
NC_006088 1 108406755 T T|C N-Syn 0.77 LOC770616 c.[37 T > T] + [37 T > C] M13M, M13V 13 0 10 0 - 0
NC_006088 1 108764081 C T N-Syn 0.91 UBASH3A c.1144C > T L382F 11 0 - 0 10 0
NC_006088 1 109036880 G T N-Syn 1.00 CBS c.1492G > T Q498K 10 0 0 - 10 0
NC_006088 1 112264749 A G N-Syn 1.00 OTC c.5A > G L2P 12 - 0 12 0 0
NC_006088 1 112303781 A G N-Syn 1.00 RPGR c.2359A > G I787V 13 - 0 13 0 0
NC_006088 1 112303950 G A N-Syn 1.00 RPGR c.2528G > A G843E 10 10 0 - 0 0
NC_006088 1 121737171 G A N-Syn 1.00 FANCB c.1988G > A R663K 12 12 0 - 0 0
NC_006088 1 121737188 C A N-Syn 1.00 FANCB c.2005C > A L669M 12 12 - 0 0 0
NC_006088 1 133392696 A G N-Syn 1.00 MFSD9 c.790A > G F264L 11 - 0 11 0 0
NC_006088 1 137555484 C T|C N-Syn 0.79 MYO16 c.[1232C > T] + [1232C > C] T411T, T411I 14 0 - 0 11 0
NC_006088 1 138584430 C T N-Syn 0.90 ANKRD10 c.551C > T R184H 10 0 - 0 9 0
NC_006088 1 152732014 A G N-Syn 1.00 RNF219 c.794A > G Q265R 10 - 0 10 0 0
NC_006088 1 153202063 C T N-Syn 1.00 SLAIN1 c.1486C > T G496S 11 0 - 0 11 0
NC_006088 1 166907615 G C N-Syn 0.90 NUFIP1 c.925G > C Q309E 10 0 9 - 0 0
NC_006088 1 169375045 A G N-Syn 0.91 SERPINE3 c.254A > G H85R 11 - 0 10 0 0
NC_006088 1 173852809 T C N-Syn 1.00 BRCA2 c.355 T > C T119A 10 0 10 0 - 0
NC_006088 1 176891377 A G N-Syn 1.00 SACS c.6235A > G I2079V 11 - 0 11 0 0
NC_006088 1 177772554 C A N-Syn 0.86 EFHA1 c.659C > A A220D 14 12 - 0 0 0
NC_006088 1 177772568 G A N-Syn 0.86 EFHA1 c.673G > A V225I 14 12 0 - 0 0
NC_006088 1 178541726 G T N-Syn 0.92 CENPJ c.2041G > T V681L 12 0 0 - 11 0
NC_006088 1 187399843 G A N-Syn 0.90 GRM5 c.2842G > A A948T 10 9 0 - 0 0
NC_006088 1 194954389 A G N-Syn 1.00 RNF169 c.992A > G V331A 10 - 0 10 0 0
NC_006089 2 2046630 C T N-Syn 1.00 CCDC13 c.860C > T S287N 12 0 - 0 12 0
NC_006089 2 2059597 T C N-Syn 1.00 CCDC13 c.209 T > C D70G 11 0 11 0 - 0
NC_006089 2 2141930 A G N-Syn 0.90 OBSCN c.17225A > G I5742T 10 - 0 9 0 0
NC_006089 2 2155796 T C N-Syn 1.00 OBSCN c.14875 T > C N4959D 11 0 11 0 - 0
NC_006089 2 4669968 C T N-Syn 0.90 DLEC1 c.1592C > T A531V 10 0 - 0 9 0
NC_006089 2 4948035 C T N-Syn 1.00 XIRP1 c.4696C > T A1566T 11 0 - 0 11 0
NC_006089 2 7746258 C - Frameshift 1.00 LOC100859401 c.388C > - Y129fs 10 0 - 0 0 10
NC_006089 2 20725367 C A N-Syn 1.00 DBF4 c.1114C > A P372T 11 11 - 0 0 0
NC_006089 2 21576571 C T N-Syn 0.90 C2H7orf63 c.962C > T T321M 10 0 - 0 9 0
NC_006089 2 23984791 G A N-Syn 0.90 PON2 c.521G > A P174L 10 9 0 - 0 0
NC_006089 2 26789159 T C N-Syn 1.00 VWDE c.2678 T > C N893S 11 0 11 0 - 0
NC_006089 2 42356129 C T N-Syn 1.00 LOC100857506 c.757C > T P253S 12 0 - 0 12 0
NC_006089 2 43749632 C T N-Syn 1.00 TGM4 c.160C > T A54T 10 0 - 0 10 0
NC_006089 2 47501151 C A N-Syn 1.00 SEPT7 c.764C > A G255V 10 10 - 0 0 0
NC_006089 2 48103938 C T N-Syn 1.00 BMPER c.1957C > T V653I 11 0 - 0 11 0
NC_006089 2 67476715 T A N-Syn 1.00 MYLK4 c.2071 T > A I691L 12 12 0 0 - 0
NC_006089 2 79168177 C T N-Syn 1.00 MTRR c.2027C > T R676K 11 0 - 0 11 0
NC_006089 2 96844408 T G N-Syn 1.00 CEP192 c.3655 T > G K1219Q 11 0 0 11 - 0
NC_006089 2 107668292 C G N-Syn 1.00 PRKDC c.3938C > G C1313S 10 0 - 10 0 0
NC_006089 2 107767247 A G N-Syn 0.91 LOC421108 c.77A > G N26S 11 - 0 10 0 0
NC_006089 2 115050472 C A N-Syn 1.00 CSPP1 c.1303C > A H435N 10 10 - 0 0 0
NC_006089 2 120054459 T G N-Syn 1.00 FAM164A c.605 T > G V202G 10 0 0 10 - 0
NC_006089 2 126210593 G A N-Syn 0.80 C2H8orf38 c.730G > A V244I 10 8 0 - 0 0
NC_006089 2 148002272 C T N-Syn 1.00 TOP1MT c.1149C > T M383I 10 0 - 0 10 0
NC_006090 3 18177273 C T N-Syn 1.00 EPRS c.778C > T H260Y 10 0 - 0 10 0
NC_006090 3 18177438 T C N-Syn 1.00 EPRS c.943 T > C C315R 11 0 11 0 - 0
NC_006090 3 19964716 A T N-Syn 0.90 USH2A c.9152A > T E3051V 10 - 0 0 9 0
NC_006090 3 20371026 T C N-Syn 0.92 CENPF c.2726 T > C E909G 13 0 12 0 - 0
NC_006090 3 20377057 T T|A N-Syn 0.75 CENPF c.[1411 T > T] + [1411 T > A] N471N, N471Y 12 9 0 0 - 0
NC_006090 3 28850511 A G N-Syn 1.00 LOC100858112 c.586A > G F196L 10 - 0 10 0 0
NC_006090 3 47388200 G G|A N-Syn 0.77 ZC3H12D c.[998G > G] + [998G > A] T333T, T333M 13 10 0 - 0 0
NC_006090 3 48575253 C T N-Syn 0.90 SYNE1 c.11674C > T A3892T 10 0 - 0 9 0
NC_006090 3 48577869 C T N-Syn 0.93 SYNE1 c.11335C > T D3779N 14 0 - 0 13 0
NC_006090 3 54551285 T C N-Syn 1.00 PDE7B c.868 T > C T290A 11 0 11 0 - 0
NC_006090 3 66462814 C T N-Syn 1.00 LOC421765 c.1076C > T R359Q 12 0 - 0 12 0
NC_006090 3 66468226 G T N-Syn 1.00 LOC421765 c.334G > T Q112K 10 0 0 - 10 0
NC_006090 3 75929093 G A N-Syn 0.93 ZNF292 c.7835G > A T2612I 14 13 0 - 0 0
NC_006090 3 80234352 G A N-Syn 1.00 COL12A1 c.2659G > A A887T 10 10 0 - 0 0
NC_006091 4 4124961 C T Nonsense 1.00 DDX26B c.151C > T Q51. 11 0 - 0 11 0
NC_006091 4 9883806 G A N-Syn 0.91 SLITRK4 c.1715G > A R572K 11 10 0 - 0 0
NC_006091 4 49489771 G T N-Syn 0.91 RUFY3 c.1588G > T A530S 11 0 0 - 10 0
NC_006092 5 3898544 C T N-Syn 0.80 KIF18A c.1567C > T D523N 10 0 - 0 8 0
NC_006092 5 8035275 A G N-Syn 1.00 LOC100859209 c.79A > G C27R 11 - 0 11 0 0
NC_006092 5 20708767 A G N-Syn 1.00 API5 c.506A > G K169R 10 - 0 10 0 0
NC_006092 5 21158570 - A Frameshift 0.90 LOC770458 c.105- > A A35fs 10 9 0 0 0 1
NC_006092 5 22076516 T C N-Syn 1.00 C1QTNF4 c.230 T > C I77T 11 0 11 0 - 0
NC_006092 5 38183079 C T N-Syn 0.83 LOC100859479 c.82C > T P28S 12 0 - 0 10 0
NC_006092 5 44443744 G G|C N-Syn 0.75 KIAA1409 c.[2076G > G] + [2076G > C] Q692H, Q692Q 12 0 9 - 0 0
NC_006092 5 44443754 G A N-Syn 0.80 KIAA1409 c.2086G > A E696K 10 8 0 - 0 0
NC_006092 5 44443755 A T N-Syn 0.80 KIAA1409 c.2087A > T E696V 10 - 0 0 8 0
NC_006092 5 45296293 G G|A N-Syn 0.75 C5H14orf49 c.[596G > G] + [596G > A] A199A, A199V 12 9 0 - 0 0
NC_006092 5 50316949 A G N-Syn 1.00 APOPT1 c.440A > G H147R 12 - 0 12 0 0
NC_006093 6 4563260 G C N-Syn 0.90 BMS1 c.1666G > C L556V 10 0 9 - 0 0
NC_006093 6 15062678 A G N-Syn 0.80 PLAU c.925A > G W309R 10 - 0 8 0 0
NC_006093 6 25651167 G A N-Syn 1.00 RBM20 c.1687G > A D563N 10 10 0 - 0 0
NC_006093 6 30617911 C T N-Syn 0.80 ATE1 c.518C > T G173D 10 0 - 0 8 0
NC_006093 6 32898174 T C N-Syn 1.00 MKI67 c.2414 T > C M805T 10 0 10 0 - 0
NC_006094 7 9605730 T C N-Syn 1.00 ANKRD44 c.584 T > C K195R 15 0 15 0 - 0
NC_006094 7 18282262 G G|A N-Syn 0.75 LRP2 c.[3775G > G] + [3775G > A] A1259T, A1259A 12 9 0 - 0 0
NC_006094 7 21828274 A G|A N-Syn 0.75 CCDC108 c.[2902A > G] + [2902A > A] N968N, N968D 12 - 0 9 0 0
NC_006094 7 25803714 T G N-Syn 0.80 IQCB1 c.952 T > G T318P 10 0 0 8 - 0
NC_006095 8 1373656 G A N-Syn 1.00 CAMSAP1L1 c.1955G > A A652V 12 12 0 - 0 0
NC_006095 8 2290270 A G N-Syn 1.00 LOC100859900 c.65A > G L22P 13 - 0 13 0 0
NC_006095 8 2506276 C T N-Syn 1.00 CRB1 c.1814C > T S605N 12 0 - 0 12 0
NC_006095 8 2612732 T C N-Syn 1.00 ASPM c.6907 T > C C2303R 11 0 11 0 - 0
NC_006095 8 7596287 G T N-Syn 0.91 NCF2 c.1234G > T P412T 11 0 0 - 10 0
NC_006095 8 8053190 G C N-Syn 0.81 LOC768407 c.875G > C G292A 16 0 13 - 0 0
NC_006095 8 8188888 T A N-Syn 0.82 LOC768392 c.512 T > A E171V 11 9 0 0 - 0
NC_006095 8 12666139 G G|A N-Syn 0.75 ABCA4 c.[4678G > G] + [4678G > A] V1560I, V1560V 12 9 0 - 0 0
NC_006095 8 23585119 C G N-Syn 0.93 LRP8 c.583C > G G195R 14 0 - 13 0 0
NC_006096 9 800651 G G|A N-Syn 0.75 LOC424748 c.[5G > G] + [5G > A] R2K, R2R 12 9 0 - 0 0
NC_006096 9 2123518 A G N-Syn 1.00 YEATS2 c.602A > G N201S 11 - 0 11 0 0
NC_006096 9 4127341 G A N-Syn 1.00 GAL3ST4 c.505G > A A169T 10 10 0 - 0 0
NC_006096 9 4217231 A G N-Syn 0.92 RNF168 c.806A > G D269G 13 - 0 12 0 0
NC_006096 9 15175477 T G N-Syn 1.00 CAPN10 c.1660 T > G T554P 11 0 0 11 - 0
NC_006096 9 21419266 C A N-Syn 0.82 SPTSSB c.44C > A P15Q 11 9 - 0 0 0
NC_006097 10 3986458 T C N-Syn 0.82 VPS13C c.3727 T > C Y1243H 11 0 9 0 - 0
NC_006099 12 9103119 G A N-Syn 1.00 COPG c.1771G > A A591T 12 12 0 - 0 0
NC_006099 12 15133837 T C N-Syn 1.00 LOC100858715 c.89 T > C V30A 11 0 11 0 - 0
NC_006099 12 19738746 C T N-Syn 1.00 NR2C2 c.1061C > T S354N 10 0 - 0 10 0
NC_006100 13 2703509 A G|A N-Syn 0.77 LOC769940 c.[2875A > G] + [2875A > A] S959P, S959S 13 - 0 10 0 0
NC_006100 13 2703511 A G|A N-Syn 0.77 LOC769940 c.[2873A > G] + [2873A > A] F958S, F958F 13 - 0 10 0 0
NC_006100 13 11337736 C G N-Syn 0.90 GEMIN5 c.849C > G H283Q 10 0 - 9 0 0
NC_006100 13 11349274 A G N-Syn 0.83 GEMIN5 c.3739A > G S1247G 12 - 0 10 0 0
NC_006101 14 5552664 G A N-Syn 0.82 TEKT4 c.1192G > A V398I 11 9 0 - 0 0
NC_006101 14 5975913 T C N-Syn 0.93 CHTF18 c.1934 T > C E645G 14 0 13 0 - 0
NC_006101 14 6002290 G G|C N-Syn 0.75 MSLN c.[774G > G] + [774G > C] S258S, S258R 12 0 9 - 0 0
NC_006101 14 7697077 C T N-Syn 0.80 ABCC6 c.1213C > T V405M 10 0 - 0 8 0
NC_006101 14 13378210 T C N-Syn 0.93 C14H16orf89 c.68 T > C D23G 14 1 13 0 - 0
NC_006102 15 3706306 T C N-Syn 1.00 GLT1D1 c.968 T > C Q323R 10 0 10 0 - 0
NC_006102 15 4915706 T C N-Syn 0.90 ATP6V0A2 c.1246 T > C I416V 10 0 9 0 - 0
NC_006102 15 4926428 G A N-Syn 1.00 LOC100857705 c.1552G > A R518C 10 10 0 - 0 0
NC_006102 15 5060494 G A N-Syn 1.00 MPHOSPH9 c.755G > A R252K 14 14 0 - 0 0
NC_006102 15 5695994 G A N-Syn 0.90 WDR66 c.1690G > A D564N 10 9 0 - 0 0
NC_006102 15 6317399 C T N-Syn 1.00 C15H12orf51 c.7777C > T D2593N 10 0 - 0 10 0
NC_006102 15 6633596 T C N-Syn 1.00 USP30 c.488 T > C I163T 13 0 13 0 - 0
NC_006102 15 8096384 T C N-Syn 1.00 DDX51 c.1493 T > C M498T 11 0 11 0 - 0
NC_006102 15 8693805 G C N-Syn 1.00 RTDR1 c.118G > C V40L 10 0 10 - 0 0
NC_006104 17 6506143 T C N-Syn 0.87 SETX c.4564 T > C I1522V 15 0 13 0 - 0
NC_006104 17 6581087 G A N-Syn 1.00 C17H9orf171 c.682G > A D228N 12 12 0 - 0 0
NC_006104 17 6922987 A G N-Syn 1.00 ADAMTS13 c.3103A > G I1035V 12 - 0 12 0 0
NC_006104 17 7858127 A T N-Syn 1.00 SEC16A c.4079A > T H1360L 15 - 0 0 15 0
NC_006104 17 7905701 G C N-Syn 1.00 SNAPC4 c.2609G > C G870A 11 0 11 - 0 0
NC_006105 18 1082307 C T N-Syn 0.90 DNAH9 c.6700C > T P2234S 10 0 - 0 9 0
NC_006105 18 1111244 G A N-Syn 0.80 DNAH9 c.8491G > A V2831M 10 8 0 - 0 0
NC_006105 18 6605385 C G N-Syn 1.00 ATAD5 c.3652C > G P1218A 11 0 - 11 0 0
NC_006105 18 6605422 G A N-Syn 1.00 ATAD5 c.3689G > A R1230K 10 10 0 - 0 0
NC_006105 18 6967029 C T N-Syn 1.00 C18H17orf58 c.1018C > T L340F 12 0 - 0 12 0
NC_006106 19 5858876 T C N-Syn 1.00 ERAL1 c.1186 T > C M396V 14 0 14 0 - 0
NC_006106 19 6213750 G C N-Syn 1.00 SLC6A4 c.242G > C A81G 10 0 10 - 0 0
NC_006106 19 7495965 C G N-Syn 0.82 BRIP1 c.1718C > G P573R 11 0 - 9 0 0
NC_006107 20 12338968 T G N-Syn 0.83 CASS4 c.1169 T > G N390T 12 0 0 10 - 0
NC_006107 20 12696859 T A N-Syn 1.00 CYP24A1 c.878 T > A L293Q 12 12 0 0 - 0
NC_006108 21 2336588 G A Nonsense 0.80 TAS1R3 c.1108G > A R370. 10 8 0 - 0 0
NC_006108 21 3215527 C T N-Syn 0.92 ENO1 c.1265C > T R422H 12 0 - 0 11 0
NC_006108 21 4657639 G A N-Syn 1.00 KIAA0090 c.2716G > A R906C 11 11 0 - 0 0
NC_006110 23 5163924 T C N-Syn 1.00 ZBTB8A c.232 T > C F78L 10 0 10 0 - 0
NC_006112 25 1498400 G A N-Syn 1.00 HORMAD1 c.844G > A A282T 11 11 0 - 0 0
NC_006113 26 4679877 G A N-Syn 1.00 LOC768535 c.1097G > A P366L 10 10 0 - 0 0
NC_006127 Z 71529316 G A N-Syn 1.00 DMXL1 c.4394G > A A1465V 11 11 0 - 0 0
  1. Contig ID, chromosome (Chr) numbers, reference position (Ref Pos), reference base (Ref Base), called (SNP) base, impact (kinds of protein mutation), SNP%, feature name (gene name), DNA change, amino acid (AA) change, Depths, and five columns for SNP counts (cnts) are indicated.