Table 1 Classification of markers by IamHWE and hiQ
From: Iam hiQ—a novel pair of accuracy indices for imputed genotypes
hiQ | IamHWE | ||||
|---|---|---|---|---|---|
< 0.47 | ≥ 0.47 | ||||
N | %a | N | %a | ||
All markers | |||||
< 0.97 | 59,077 | 0.6% | 59,130 | 0.6% | |
≥ 0.97 | 1,214,620 | 11.7% | 9,094,772 | 87.2% | |
Quality defined by info | |||||
Low quality: info < 0.8 | < 0.97 | 59,077 | 1.2% | 58,592 | 1.1% |
≥ 0.97 | 1,214,612 | 23.8% | 3,777,566 | 73.9% | |
High quality: info ≥ 0.8 | < 0.97 | – | 538 | < 0.1% | |
≥ 0.97 | 8 | < 0.1% | 5,317,206 | 99.9% | |
Minor allele frequency (MAF) | |||||
< 1% | < 0.97 | 15,366 | 0.3% | 136 | < 0.1% |
≥ 0.97 | 1,210,505 | 23.2% | 4,000,616 | 76.5% | |
1% to < 5% | < 0.97 | 13,448 | 0.9% | 12,742 | 0.8% |
≥ 0.97 | 2,317 | 0.2% | 1,472,328 | 98.1% | |
5% to < 10% | < 0.97 | 4,007 | 0.6% | 12,117 | 1.8% |
≥ 0.97 | 7 | < 0.1% | 638,931 | 97.5% | |
10% to < 30% | < 0.97 | 8,441 | 0.6% | 18,576 | 1.4% |
≥ 0.97 | 10 | < 0.1% | 1,288,714 | 97.9% | |
30% to 50% | < 0.97 | 9,283 | 1.3% | 4,188 | 0.6% |
≥ 0.97 | 261 | < 0.1% | 721,679 | 98.1% | |
> 50% | < 0.97 | 8,532 | 0.9% | 11,371 | 1.1% |
≥ 0.97 | 1,520 | 0.2% | 972,504 | 97.8% | |