Table 5.
Evaluation of imputation accuracy
| Number of animals in reference and validation population |
Beagle |
MaCH |
findhap.f90 |
Minimac |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Correct alleles | Correct genotypesa | rTG,IG | Correct alleles | Correct genotypes | rTG,IG | Correct alleles | Correct genotypes | rTG,IG | Correct alleles | Correct genotypes | rTG,IG | |
| 50 / 747 |
0.914 |
0.840 |
0.858 |
0.966 |
0.933 |
0.945 |
0.925 |
0.858 |
0.865 |
0.971 |
0.942 |
0.953 |
| 100 / 697 |
0.963 |
0.927 |
0.940 |
0.985 |
0.970 |
0.976 |
0.959 |
0.921 |
0.933 |
0.986 |
0.972 |
0.977 |
| 200 / 597 |
0.986 |
0.972 |
0.977 |
0.993 |
0.987 |
0.989 |
0.978 |
0.956 |
0.965 |
0.993 |
0.986 |
0.989 |
| 400 / 397 | 0.993 | 0.987 | 0.989 | 0.996 | 0.993 | 0.994 | 0.986 | 0.973 | 0.978 | 0.996 | 0.992 | 0.993 |
The mean allelic and genotypic accuracies over six chromosomes (BTA1, BTA5, BTA10, BTA15, BTA20, BTA25) were assessed for the imputed genotypes based on an increasing size of the reference population. Additionally, the correlation between true and imputed genotypes (rTG,IG) was calculated.
a a genotype is correctly imputed if both alleles are correctly imputed.