Table 1 Chromosome X SNPs flagged by three sex-specific QC metrics
From: Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
SNP | Position | Call rate (%) | HWE pin female controls | Abs diff call rate (%) | Proportion male heterozygotes (%) | Missing test by sex |
|---|---|---|---|---|---|---|
rs4893596 | 2.9 × 107 | 95 | 0.144 | 7.36 | 1.95 | 1.69 × 10-11 |
rs7051891 | 2.9 × 107 | 95.49 | 1 | 1.1 | 1.4 | 3.50 × 10-25 |
rs7884174 | 6.4 × 107 | 95.83 | 0.033 | 9.45 | 1.18 | 3.26 × 10-20 |