Table 2 Accuracy and percentage correct for calling genotypes of sequenced animals and for imputation for 250 young animals with simulated bovine data
From: Fast imputation using medium or low-coverage sequence data
Sequenced population | Software | Genotype calling (1 % error rate) | Imputation from HD to sequence | |||
|---|---|---|---|---|---|---|
Size | Coverage | Percentage correct | Correlation | Percentage correct | Correlation | |
250 | 8× | Findhap | 98.7 | 0.981 | 95.0 | 0.926 |
Beagle | 99.0 | 0.984 | 97.1 | 0.956 | ||
500 | 8× | Findhap | 99.1 | 0.988 | 98.1 | 0.974 |
Beagle | 99.6 | 0.994 | 99.4 | 0.991 | ||
250 | 4× | Findhap | 95.8 | 0.939 | 93.1 | 0.897 |
Beagle | 95.0 | 0.918 | 78.2 | 0.582 | ||
250 | 2× | Findhap | 91.3 | 0.879 | 89.2 | 0.837 |
Beagle | 79.5 | 0.602 | 63.5 | 0.100 | ||