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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
  1. In bold are the total number of SNPs and animals retained for analyses