Table 1 Summary of the different steps of quality control
Genotypes filtration | RI Line |
|---|---|
Individual Call Rate (< 95%) | 8 |
MAF (= 0) | 204,122 |
MAF (< 0.05) | 54,650 |
SNP Call Rate (< 95%) | 7,541 |
Hardy-Weinberg equilibrium (P < 10− 4) | 12,538 |
SNP with unknown location | 1,748 |
SNP located on chromosome 16, 33, W or on linkage group LGE64 | 334 |
Pedigree Incompatibility problem | 0 |
SNP retained for analyses | 300,028 |
Animals retained for analyses | 2,362 |