Average imputation sensitivities of heterozygous genotypes obtained using HRC and 1kGP reference panels
| HET sensitivity | Number of HETs | Missing HETs | |||||
|---|---|---|---|---|---|---|---|
| Filter | MAF bin | HRC | 1kGP | HRC | 1kGP | HRC | 1kGP |
| No filter | 0.001–0.01 | 52.7 | 50.9 | 17,188 | 14,039 | 0 | 0 |
| 0.01–0.05 | 78.8 | 74.0 | 83,397 | 77,676 | 0 | 0 | |
| 0.05–0.1 | 88.0 | 84.1 | 127,130 | 120,522 | 0 | 0 | |
| 0.1–0.3 | 91.9 | 88.5 | 677,999 | 647,528 | 0 | 0 | |
| >0.3 | 93.7 | 90.4 | 789,923 | 755,478 | 0 | 0 | |
| max(GP) ≥ 0.99 | 0.001–0.01 | 54.2 | 50.4 | 5046 | 5669 | 71.5 | 59.3 |
| 0.01–0.05 | 93.7 | 88.1 | 48,631 | 46,943 | 50.9 | 49.3 | |
| 0.05–0.1 | 97.7 | 96.1 | 88,139 | 82,656 | 37.6 | 40 | |
| 0.1–0.3 | 98.8 | 98.3 | 479,079 | 452,659 | 34.3 | 37 | |
| >0.3 | 99.3 | 99.1 | 559,099 | 531,081 | 33.2 | 35.9 | |
| GDI | 0.001–0.01 | na | na | na | na | 0 | na |
| 0.01–0.05 | na | na | na | na | 0 | na | |
| 0.05–0.1 | 93.1 | na | 101,500 | na | 0 | na | |
| 0.1–0.3 | 96.0 | na | 432,852 | na | 0 | na | |
| >0.3 | 97.4 | na | 417,039 | na | 0 | na | |
[i] HET sensitivity: heterozygote genotype sensitivities are expressed in percentage.
[ii] Number of HETs: number of correctly imputed heterozygous genotypes in the given MAF bin#.
[iii] Missing HETs: proportion of imputed heterozygous genotypes that were set to missing by the GP ≥ 0.99 filter in the given MAF bin.