Table 3 Accuracies of imputations on whole-genome sequences in Holstein (HOL) and Montbéliarde (MON) breeds
Breed | HOL | MON |
|---|---|---|
Number of cows | 168 | 2142 |
EuroG10k chip version | V1 | V4 |
Number of markers in the custom part | 721 | 3082 |
Number of markers after quality control and MAF ≥ 0.02 | 221 | 1108 |
R2 (%) | 83.7 | 76.1 |
Genotypic concordance rate (%) | 93.7 | 89.7 |
Allelic concordance rate (%) | 96.5 | 94.0 |