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Table 3 Verification of 14 SNPs using PCR and Sanger sequencing in larger numbers of non-vitiliginous parental BL (20) vs. vitiliginous SL (70) chickens

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

Ch Ref Pos Ref base Called base Impact SNP% Feature name Protein change Results of larger population
BL (20 birds) SL (70 birds)
2 7746258 CT - FS 1 LOC100859401 Y129fs All_CT All_Del
5 21158570 - A FS 0.9 LOC770458 A35fs Ins_A_30% Ins_A_100%
9 21419266 C A N-Syn 0.82 SPTSSB [1] P15Q C:A = 3:1 C:A = 1:4
1 54936701 G T N-Syn 0.8 STAB2 A2052D All_G G:T = 1:1
3 48575253 C T N-Syn 0.9 SYNE1 A3892T C:T = 10:1 C:T = 1:10
3 18177438 T C N-Syn 1 EPRS C315R T:C = 4:1 T:C = 1:7
1 105941417 T C N-Syn 0.9 SETD4 I396V T:C = 10:1 All_C
19 5858876 T C N-Syn 1 ERAL1 M396V All_T T:C = 1:10
1 177772554 C A N-Syn 0.86 EFHA1 A220D C:A = 4:1 C:A = 1:10
1 177772568 G A N-Syn 0.86 EFHA1 V225I All_G G:A = 1:10
13 11337736 C G N-Syn 0.9 GEMIN5 H283Q All_C All_G
5 44443744 G G|C N-Syn 0.75 KIAA1409 Q692H All_G G:C = 1:10
5 44443754 G A N-Syn 0.8 KIAA1409 E696K All_G G:A = 1:4
5 44443755 A T N-Syn 0.8 KIAA1409 E696V All_A A:T = 1:4
  1. Ratios between reference base and SNP (Called base) in large chicken populations were bolded. FS; frameshift mutation.
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