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.