Table 5. Whole chromosome level comparisons between autoencoder (AE) and HMM-based imputation tools (Minimac4, Beagle5, and Impute5).
Average r-squared per variant was extracted at whole chromosome level. We applied Wilcoxon rank-sum tests to compare the HMM-based tools to the reference tuned autoencoder (AE). * represents p-values ≤0.05, ** indicates p-values ≤0.001, and *** indicates p-values ≤0.0001. Standard errors that are equal or less than 0.001 are not shown.
| MESA | Wellderly | HGDP | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Affymetrix 6.0 | UKB Axiom | Omni 1.5 M | Affymetrix 6.0 | UKB Axiom | Omni 1.5 M | Affymetrix 6.0 | UKB Axiom | Omni 1.5 M | |
| AE (tuned) | 0.410 | 0.395 | 0.452 | 0.537 | 0.605 | 0.586 | 0.363 | 0.364 | 0.392 |
| Minimac4 | 0.390*** | 0.364*** | 0.436*** | 0.500*** | 0.557*** | 0.551*** | 0.350*** | 0.340*** | 0.385*** |
| Beagle5 | 0.383*** | 0.379*** | 0.420*** | 0.484*** | 0.549*** | 0.534*** | 0.326*** | 0.328*** | 0.353*** |
| Impute5 | 0.384*** | 0.356*** | 0.429*** | 0.485*** | 0.547*** | 0.539*** | 0.328*** | 0.314*** | 0.359*** |