Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes

Table 1 Accuracy of imputation (±SD) in the validation animals, number of SNP that were imputed per chromosome, and number of high-density genotyped animals in the training population for genotyping scenarios SC1 to SC4

Scenario	Chromosome Z		Chromosome 2		Chromosome 4		Nb HD
Nb SNP	1137		3913		2211
Nb SNP	Acc.	Nb SNP edited	Acc.	Nb SNP edited	Acc.	Nb SNP edited
SC1	0.96 ± 0.06	1083	0.98 ± 0.01	3669	0.98 ± 0.01	2061	1091
SC2	0.93 ± 0.08	1072	0.95 ± 0.02	3638	0.96 ± 0.02	2044	776
SC3	0.89 ± 0.10	1072	0.92 ± 0.08	3649	0.93 ± 0.08	2054	763
SC4	0.91 ± 0.22	749	0. 96 ± 0.02	3774	0. 96 ± 0.02	2192	1438

Nb SNP = number of SNP that were imputed per chromosome; Nb HD = number of high-density genotyped animals in the training population; Acc. = mean accuracy of imputation; Nb SNP edited = number of SNP that survive the internal editing criteria of AlphaImpute; SD = standard deviation of accuracy of imputation.

ISSN: 1297-9686