Table 1 Summary of the different steps of quality control
From: Design of low density SNP chips for genotype imputation in layer chicken
Genotypes filtration | RI Line | L Line |
|---|---|---|
Individual Call Rate (> 95%) | 8 | 3 |
MAF (= 0) | 204,122 | 228,452 |
MAF (0 < X < 0.05) | 54,650 | 99,000 |
SNP Call Rate (> 95%) | 7541 | 2530 |
Hardy-Weinberg equilibrium (P < 10−4) | 12,538 | 3857 |
SNP with unknown location or on W | 1759 | 1453 |
Pedigree Incompatibility issues | 0 | 6 |
SNP retained for analyses | 300,351 | 245,669 |
Animals retained for analyses | 2362 | 1474 |