Table 2. Imputation quality metric (r 2) for the two-step approach compared with direct imputation.
| Two stepa | Direct | |||
|---|---|---|---|---|
| Minor allele frequency | N | r2, mean (SD) | N | r2, mean (SD) |
| >0–1%b | 684 334 | 0.16 (0.28) | 839 141 | 0.10 (0.20) |
| 1–5%b | 309 759 | 0.87 (0.23) | 303 608 | 0.68 (0.31) |
| 5–10%b | 144 718 | 0.94 (0.17) | 143 065 | 0.85 (0.24) |
| 10–50%b | 538 142 | 0.97 (0.11) | 539 322 | 0.92 (0.17) |
a
First imputation filter on r2 0.3.
b
Comparing two step and direct imputation in each minor allele frequency bin revealed P-values <10−15.