Table 3.
Imputation accuracy comparison by genetic analysis group and region from empirical masking.
| Region/ group | Number of samples | Imputation setting 1: Phase 1, khap=max mean (SD) | Imputation setting 2: Phase 3, khap=half max mean (SD) | Imputation setting 3: Phase 3, khap=max mean (SD) |
|---|---|---|---|---|
| Mainland | 772 | 0.99005 (0.00197) | 0.99056 (0.00184) | 0.99066 (0.00174) |
| Central American | 184 | 0.98995 (0.00173) | 0.99047 (0.00165) | 0.99063 (0.00154) |
| Mexican | 475 | 0.99011 (0.00203) | 0.99057 (0.00186) | 0.99067 (0.00176) |
| South American | 113 | 0.98994 (0.00207) | 0.99066 (0.00205) | 0.9907 (0.00192) |
| Caribbean | 616 | 0.98822 (0.00182) | 0.98967 (0.00196) | 0.98986 (0.00192) |
| Cuban | 253 | 0.98754 (0.00144) | 0.98875 (0.00171) | 0.98892 (0.00166) |
| Dominican | 132 | 0.98736 (0.00171) | 0.98889 (0.00159) | 0.98913 (0.00151) |
| Puerto Rican | 231 | 0.98946 (0.00156) | 0.99111 (0.00150) | 0.99131 (0.00147) |
Summaries of by-sample dosage r2 metrics from the empirical masking of supplemental array variants on chromosome 22. Mean dosage r2 values and SD are given for samples grouped both by region (Caribbean and Mainland) and by genetic analysis group. These summaries are restricted to the set of mutually unrelated samples from supplemental array genotyping with non-missing genetic analysis group (n = 1388).