Table 2. Summary of imputation scenarios using different reference population size and validation data set
Scenario set | Reference SNP data | Reference set | Test set | Total animal |
Validation 1 | Validation 2 | Validation 3 | Validation 4 |
N | % | N | % | N | % | N | % | N | % |
Ref 500 | 50k | 500 | 0.69 | 222 | 0.31 | 223 | 0.31 | 223 | 0.31 | 221 | 0.31 | 721–723 |
Ref 1,000 | 50k | 1,000 | 0.82 | 222 | 0.18 | 223 | 0.18 | 223 | 0.18 | 221 | 0.18 | 1,221–1,223 |
Ref 1,500 | 50k | 1,500 | 0.87 | 222 | 0.13 | 223 | 0.13 | 223 | 0.13 | 221 | 0.13 | 1,721–1,723 |
Ref 2,000 | 50k | 2,000 | 0.90 | 222 | 0.10 | 223 | 0.10 | 223 | 0.10 | 221 | 0.10 | 2,221–2,223 |
Ref 2,000+ | 50k | 3,600 | 0.94 | 222 | 0.06 | 223 | 0.06 | 223 | 0.06 | 221 | 0.06 | 3,821 |
Total animal, The total number of the reference population and validation animals; Ref, reference population; SNP, single nucleotide polymorphism.