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Table 2 Sites potentially under selection according to BEB analysis of PAML M8 results for the most frequent haplotype.

From: Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus

Base position P aA ω value S.E. P(ω > 1) Exon Bases SNP alleles and amino acids
4429–31 3 T 9.983 0.878 0.998 1 ACA V, F: CCA (P); B: GCA (A)
4435–37 5 F 10.002 0.772 1.000 1 TTT Chicken, C: CTT (L); R, V, F: TTC (F); B TTG (F)
4477–79 19 L 9.996 0.807 0.999 1 CTG V, F: CGC (R); B: CCA (P)
7453–56 23 V 9.951 1.029 0.995 2 GTT V, F: TTT (F); B: CTT (L)
7534–36 50 E 10.003 0.77 1.000 2 GAA V, F: CCA (P); B: CGA (R)
7582–84 66 L 10.000 0.786 1.000 2 CTT V, F: TTT (F); B: AAT (N)
7594–5, 8394 70 R 9.984 0.871 0.998 2, 3 AGA V: TCA (S); F: ATA (M)
9583–85 125 T 9.999 0.788 1.000 4 ACT C, B: GCT (A); V, F: TCT (S)
9631–33 141 L 9.771 1.636 0.976 4 TTG C, G, B: CTG (L); V, F: ATG (M)
9646–48 146 S 9.995 0.811 0.999 4 AGC V, F: CGC (R); B: GGC (G)
9715–17 169 Q 9.972 0.933 0.997 4 CAA V, F: CGC (R); B: CCC (P)
9721–23 171 E 9.970 0.942 0.997 4 GAA V, F: GCA (A); B: GGA (G)
12367–69 418 M 9.661 1.904 0.964 9 ATG V: CTG (L); B: GTG (V); F: TTG (L)
12628–30 509 A 9.895 1.253 0.989 9 GCA V, F: GTA (V)
12631–33 510 R 9.966 0.963 0.996 9 AGA V: AGT (S); B: AGG (R); F: AGC (S)
12652–54 517 H 9.995 0.811 0.999 9 CAC Chicken, R: CAT (H); RJF, F, V: CAA (Q); B: AAC (N)
12661–63^ 520 P 9.110 2.54 0.930 9 CCT Chicken, R, RJF: CTT (L)
12742–44 * 547 I 9.619 2.097 0.954 9 ATA R, C: TTA (L)
12823–25 574 H 9.941 1.07 0.994 9 CAT V, F: CAC (H); B, F: CAT (H)
12844–46 581 V 9.976 0.914 0.997 9 GTG V, F: ATG (M); B: CTG (L)
12871–73 590 G 9.580 2.076 0.956 9 GGC Chicken, RJF, B, F, V: AGC (S)
12955–57 * 618 E 9.622 2.092 0.955 9 GAG V, F, B: GCG (A)
12979–81 626 S 9.579 2.078 0.956 9 AGC V: CGC (R); F: GGC (G)
12985–87 628 E 9.934 1.101 0.993 9 GAA Chicken: GAG (E); RJF, R, G, C: GAC (D)
13042–44 647 A 9.661 1.902 0.964 9 GCC V, B, F: GTC (V)
13078–80 659 N 9.727 1.746 0.971 9 AAT V, F: AAA (K); B: AAC (N)
13096–98 665 R 9.981 0.889 0.998 9 CGA Chicken: CAA (Q), TGA (stop); R, G, C: AGA (R): RJF, F: ATA (M); V: ACA (T); B: AAA (K)
13123–25 674 S 9.950 1.033 0.994 9 TCT V: TGT (C); B: TTT (F); F: TAT (Y)
13138–40 679 A 9.994 0.82 0.999 9 GCA V: GGC (G); B: GTG (V); F: GGT (G)
  1. P is the amino acid position. S.E. is the standard error for ω. B stands for bamboo partridge, F for grey francolin, V for green JF, C for Ceylon JF, R for red JF, G for grey JF and RJF for the genome sequence. * Significant in analysis with divergent sample FJ542675 only. ^Almost significant.