Table 2 Autosomal SNPs flagged by at least two sex-specific QC metrics
From: Application of sex-specific single-nucleotide polymorphism filters in genome-wide association data
SNP | Chr | Position | Call rate (%) | HWE pin controls | Abs diff call rate (%) | Abs diff in Het (%) | Missing test by sex | Sex association in controls |
|---|---|---|---|---|---|---|---|---|
rs12734338 | 1 | 199201380 | 98.3 | 2.76 × 10-12 | 5.91 | 98.87 | 1.22 × 10-18 | 4.86 × 10-212 |
rs12743401 | 1 | 199208305 | 98.4 | 1.32 × 10-11 | 5.8 | 98.98 | 1.77 × 10-19 | 7.36 × 10-212 |
rs3881953 | 1 | 199259678 | 97.48 | 2.29 × 10-11 | 8.17 | 97.5 | 2.74 × 10-23 | 1.16 × 10-207 |
rs6697552 | 1 | 239452393 | 96.41 | 0.097 | 8.39 | 9.28 | 2.09 × 10-17 | 0.009 |
rs7584345 | 2 | 67629941 | 91.22 | 0.389 | 8.24 | 3.88 | 1.57 × 10-10 | 0.007 |
rs689662 | 3 | 16389202 | 96.8 | 0.668 | 10.63 | 2.14 | 3.93 × 10-31 | 0.005 |
rs17042252 | 3 | 16435774 | 95.15 | 0.192 | 5.48 | 5.08 | 6.40 × 10-09 | 0.18 |
rs12508842 | 4 | 92374678 | 90.25 | 0.068 | 13.97 | 11.58 | 2.69 × 10-19 | 0.005 |
rs11739167 | 5 | 25945521 | 71.82 | 1.89 × 10-6 | 31.39 | 21.74 | 4.16 × 10-55 | 0.157 |
rs11155996 | 6 | 155056263 | 85.79 | 5.30 × 10-11 | 13.87 | 10.42 | 1.58 × 10-14 | 0.003 |
rs10277011 | 7 | 64350823 | 94.81 | 0.051 | 5.47 | 6.75 | 4.26 × 10-08 | 0.249 |
rs6989593 | 8 | 47670421 | 83.61 | 1.53 × 10-7 | 16.44 | 13.83 | 7.38 × 10-18 | 0.599 |
rs2309966 | 9 | 71344898 | 90.93 | 0.052 | 12.96 | 6.61 | 5.89 × 10-18 | 0.873 |
rs7046290 | 9 | 87432131 | 93.94 | 1 | 7.64 | 1.08 | 3.50 × 10-14 | 0.785 |
rs11034170 | 11 | 4819429 | 82.59 | 4.96 × 10-10 | 13.61 | 4.64 | 1.32 × 10-14 | 0.63 |
rs7124728 | 11 | 70554083 | 93.06 | 0.855 | 17.85 | 8.24 | 2.16 × 10-40 | 0.02 |
rs703842 | 12 | 56449006 | 94.71 | 0.143 | 6.57 | 1.81 | 4.93 × 10-12 | 0.211 |
rs17768343 | 14 | 37070932 | 87.34 | 1.40 × 10-4 | 22.33 | 16.5 | 1.30 × 10-37 | 0.176 |
rs2236225 | 14 | 63978598 | 90.35 | 4.81 × 10-4 | 11.63 | 8.9 | 3.12 × 10-20 | 0.142 |
rs7294 | 16 | 31009822 | 94.13 | 0.02 | 11.56 | 5.25 | 1.38 × 10-20 | 0.132 |
rs6503096 | 17 | 8122992 | 92.34 | 0.851 | 7.91 | 3.78 | 2.82 × 10-11 | 0.029 |