The utility of low-density genotyping for imputation in the Thoroughbred horse

Table 4 The mean proportion of correctly imputed genotypes for ECA1 and ECA26, as calculated in the between-population analysis of the US dataset with the 2K panel

Chr	Imputation method	LDP SNP selection method	UK within-population assessment^a	Between-population assessment 1^b	Between-population assessment 2^c
ECA1	Random^d	bpEQ	0.55	0.55	0.56
		bpMAF	0.55	0.55	0.56
		lduMAF	0.56	0.56	0.57
	Beagle^e	bpEQ	0.90	0.90	0.92
		bpMAF	0.91	0.91	0.93
		lduMAF	0.89	0.89	0.92
ECA26	Random^f	bpEQ	0.51	0.50	0.51
		bpMAF	0.52	0.51	0.51
		lduMAF	0.52	0.51	0.51
	Beagle^g	bpEQ	0.82	0.81	0.86
		bpMAF	0.85	0.84	0.89
		lduMAF	0.88	0.85	0.90

^areference population B and test population C; ^breference population B and test population D + E; ^creference population C and test population D; ^dSE across SNPs and samples was equal to 0.003 and 9×10^-4 to 2×10^-3, respectively; ^eSE across SNPs and samples was equal to 0.001 and 2×10^-3 to 5×10^-3, respectively; ^fSE across SNPs and samples was equal to 0.006 and 1×10^-3 to 3×10^-3, respectively; ^gSE across SNPs and samples was equal to 2×10^-3 to 4×10^-3 and 4×10^-3 to 1×10^-2, respectively.

ISSN: 1297-9686