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Table 2 Annotation of each SNV and INDEL across the chIFITM1,2,3 genes

From: Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

  aGenomic location Reference/Variant
3′-5′ (5′-3′)
European Commercial Pirbright Indigenous Amino acid change (5′-3′) Codon Exon
IFITM1 SNVs
13,141 G/A (C/T) x x CGG to TGG Arg to Trp 77 2
14,105 C/T (G/A) x x x TCG to TCA Ser to Ser 56 1
IFITM2 SNVs
14,960 G/T (C/A) CGG to AGG Arg to Arg 111 2
15,078 G/A (C/T) x x x GGC to GGT Gly to Gly 72 2
15,080 C/T (G/A) x x GGC to AGC Gly to Ser 72 2
15,081 T/C (A/G) GTA to GTG Val to Val 71 2
15,083 C/T (G/A) x x x GTA to ATA Val to Ile 71 2
15,084 G/A (C/T) x x x TTC to TTT Phe to Phe 70 2
16,175 A/C (T/G) GCT to GCG Ala to Ala 54 1
16,193 G/A (C/T) x x x TTC to TTT Phe to Phe 48 1
16,242 T/C (A/G) x x AAG to AGG Lys to Arg 32 1
16,292 G/A (C/T) x x x TAC to TAT Tyr to Tyr 15 1
16,295 G/A (C/T) TCC to TCT Ser to Ser 14 1
16,303 T/C (A/G) x x x ATG to GTG Met to Val 12 1
INDELs
16,243–16,244 TG/T (CA/A) x x x Frameshift 31 1
16,269 A/ACC (T/GGT) x x x Frameshift 23 1
IFITM3 SNVs
18,814 T/C (A/G) x x x ATG to GAG Met to Glu 119 2
18,862 C/T (G/A) GTC to ATC Val to Ile 103 2
19,572 G/A (C/T) x x x TGC to TGA Cys to STOP 59 1
INDELs
19,576–19,577 AC/A (GT/T) x x x Frameshift 58 1
  1. a These locations refer to the position on the PacBio consensus reference sequence already published and submitted [5]