Table 4.
Candidate mutations identified in the evaluated QTL regions.
| Region | SNP (bp)1 | Gene | SNP location2 | No of AA3 reads; depth coverage | Qual4 | AFD5 | PC Score6 | EC Score7 | PE Score8 |
|---|---|---|---|---|---|---|---|---|---|
| C1G1 | 174634021 | Asparagine-linked glycosylation 11 homolog (ALG11) | CpG island, upstream | 7; 10 | 72 | 0.97 | N/A | N/A | N/A |
| C2G2 | 63823523 | Endothelin 1(EDN1) | CpG island, upstream | 3; 13 | 53 | 0.95 | N/A | N/A | N/A |
| C3G4 | 33678270 | Cysteine rich transmembrane BMP regulator 1 (CRIM1) | Protein code, NS K/I | 10; 19 | 182 | 0.97 | 0.67 | 0.63 | 0.42 |
| C4G6 | 12044024 | Similar to receptor tyrosine kinase (VEGFR-2) | CpG island, upstream | 4; 8 | 82 | 0.97 | N/A | N/A | N/A |
| C4G6 | 12902414 | Fibroblast growth factor 16 (FGF16) | CpG island, downstream | 8; 16 | 175 | 0.95 | N/A | N/A | N/A |
| C5G8 | 38316301 | Sorting nexin 6 (SNX6) | CpG island, upstream | 8; 14 | 142 | 0.97 | N/A | N/A | N/A |
| C7G9 | 21686625 | Growth factor receptor-bound protein 14 (GRB14) | CpG island, downstream | 3; 12 | 52 | 0.97 | N/A | N/A | N/A |
| C7G9 | 22711910 | Glucagon (GCG) | CpG island, downstream | 3; 9 | 46 | 0.87 | N/A | N/A | N/A |
| C7G9 | 24802616 | Insulin-like growth factor binding protein 2 (IGFBP2) | Protein code, synonymous, CpG island | 4; 8 | 69 | 0.95 | N/A | N/A | N/A |
| C20G12 | 8715398 | Baculoviral IAP repeat-containing 7 (BIRC7) | Protein code, NS I/V | 5; 8 | 65 | 0.97 | 0.29 | 0.14 | 0.04 |
Coordinates based on the Chicken (Gallus gallus) assembly v 2.1/galGal3;
Location of the SNP in gene and also amino acid substitution in case of non-synonymous (NS) SNP;
Total number of reads in both lines representing the alternate allele (AA) versus the total depth coverage across the SNP position;
The Phred scaled probability that a REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is -10 * log(1 - p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in 1010 chance;
Allele frequency difference between the chicken lines as estimated using the GigaBayes software given that a total of 19 individuals from each line were included in the pools;
Physico-chemical score of amino acid substitution calculated using PASE (Li et al., 2013).
Evolutionary conservation score of amino acid substitution calculated using PASE (Li et al., 2013);
Combined score of PC and EC of amino acid substitution calculated using PASE (Li et al., 2013).