Table 1 Quality control criteria and number of markers failing each criterion expressed as a percentage of the total 625,995 SNPs
From: Use and optimization of different sources of information for genomic prediction
Category | Quality criterion | Proportion of rejected SNPs |
|---|---|---|
Hardy–Weinberg equilibrium | P ≤ 0.001 | 3.6% |
Completeness among individuals | ≤ 0.95 | 5.0% |
Minor allele frequency | <Â 0.01 | 25.0% |
Remaining SNPs | Â | 431,249 (69% of all SNPs) |