Table 2 Consensus nonsynonymous SNPs differentiating the QQ and qq genotypes for a QTL affecting pH after slaughter on chicken chromosome 1
Gene IDGenotypeNonsynonymous SNPsPASE Scoresa
CoordinateCodon (Ref/Alt)Amino Acid SubstitutionPhysicochemical Properties ScoresSequence Conservation Scores
PRDX4QQ117796698ACT/CCT (4/5)bT179P0.220.79
EIF2S3QQ117669996GGT/AGTG335S0.260.83
E1BTD2QQ117608741TTT/ATTF129I0.190.83
PCYT1Bqq117503317GCA/GGAA44G0.220.86
  • SNP, single-nucleotide polymorphism; QTL, quantitative trait locus.

  • a PASE score comprises physicochemical properties scores and sequence conservation scores. Each of score ranges from 0 and 1, where 0 is neutral, and the greater ratio indicates the stronger effect on the hosting protein.

  • b The consensus nsSNP located in the gene PRDX4 has been detected in four of a total of five in the QQ genotype samples.