Application of imputation methods to genomic selection in Chinese Holstein cattle

Table 2 Datasets in the reference population generated using five different imputation and quality control strategies

Strategy¹	No. of animals	No. of SNPs
Imputation before quality control
S1: Impute A - QC3%	2, 092	45, 072
S2: Impute B - QC3%	2, 092	45, 614
S3: Impute A - QC5%	2, 092	43, 710
S4: Impute A - QC0	2, 092	53, 973
Imputation after quality control
S5: Impute A - QC3%	2, 021	43, 481
S6: Impute A - QC5%	2, 021	41, 866

¹Impute A, imputation with findhap v1 [9]; Impute B, missing genotypes were directly replaced with heterozygote.
Abbreviations: QC3%, SNP MAF > 3%; QC5%, SNP MAF > 5%; QC0, no requirement for MAF.

ISSN: 2049-1891