TABLE 5.
Imputation reliability for different levels of imputation reference population size and SNP density.
| Software | Reference population size | Proportion of target markers or SNP density/% | |||||
|---|---|---|---|---|---|---|---|
| 1 | 5 | 10 | 30 | 50 | 90 | ||
| Beagle5.1 | 100 | 0.21 | 0.56 | 0.80 | 0.97 | 0.99 | 1.00 |
| 1,000 | 0.25 | 0.78 | 0.94 | 0.99 | 1.00 | 1.00 | |
| 3,000 | 0.26 | 0.90 | 0.97 | 0.99 | 1.00 | 1.00 | |
| 5,000 | 0.26 | 0.94 | 0.98 | 1.00 | 1.00 | 1.00 | |
| 10,000 | 0.27 | 0.96 | 0.99 | 1.00 | 1.00 | 1.00 | |
| Minimac4 | 100 | 0.14 | 0.47 | 0.63 | 0.82 | 0.88 | 0.94 |
| 1,000 | 0.20 | 0.58 | 0.72 | 0.86 | 0.90 | 0.95 | |
| 3,000 | 0.25 | 0.63 | 0.74 | 0.87 | 0.91 | 0.95 | |
| 5,000 | 0.28 a | 0.64 | 0.75 | 0.87 | 0.91 | 0.95 | |
| 10,000 | 0.33 a | 0.67 | 0.77 | 0.87 | 0.91 | 0.95 | |
a
The imputation reliability of Minimac4 is higher than Beagle5.1 only for these two scenarios.