Table 4.
Average (standard deviation) imputation accuracy, for different imputation analyses using FImpute
| Analysis 1 | SNP chip 2 | Nb (%) SNPs to be imputed | CORR 3 | PERC 4 |
|---|---|---|---|---|
| 1 | 7 K | 435509 (99.1) | 0.9257 (0.0346) | 90.56 (4.09) |
| 2 | 50 K | 418581 (95.2) | 0.9783 (0.0136) | 97.14 (1.76) |
| 3 | GGP20Ki | 426145 (96.9) | 0.9771 (0.0143) | 96.96 (1.87) |
| 4 | GGP75Ki | 383426 (87.2) | 0.9922 (0.0056) | 98.93 (0.76) |
| 5 | 15K_e | 424451 (96.6) | 0.9784 (0.0135) | 97.15 (1.75) |
| 6 | 15K_em | 424422 (96.5) | 0.9820 (0.0120) | 97.58 (1.61) |
| 7 | 15K_el | 424422 (96.5) | 0.9763 (0.0138) | 96.87 (1.77) |
| 8 | 15K_eml | 424422 (96.5) | 0.9840 (0.0107) | 97.85 (1.43) |
| 9 | 11a7 K | 424305 (96.5) | 0.9823 (0.0117) | 97.63 (1.54) |
| 10 | 17a7 K | 418025 (95.1) | 0.9864 (0.0093) | 98.17 (1.24) |
| 11 | 27a7 K | 408204 (92.9) | 0.9897 (0.0072) | 98.60 (0.97) |
| 12 | 48a7 K | 387005 (88.0) | 0.9931 (0.0049) | 99.05 (0.67) |
1Imputation analyses using FImpute (considering family information) and 202 young sires as the validation set; the numbers of each analysis refer to those in brackets from Figure 1; 2as described in the section “SNP chips” of “Methods”; 3CORR: Pearson’s correlation between imputed and observed genotypes; 4PERC: percentage of correctly imputed genotypes.