Genomic selection using low density marker panels with application to a sire line in pigs

Table 2 Genotype imputation error rate and imputation accuracy for different methods

Phasing	Imputation method	Marker selection	Marker position	Number of markers in low-density panel
Phasing	Imputation method	Marker selection	Marker position	384	768	1152	3000
Beagle	This paper	large MAF	known	0.133/0.79	0.079/0.87	0.054/0.91	0.022/0.96
			estimated	0.148/0.76	0.095/0.84	0.066/0.89	0.029/0.95
Beagle	Beagle	large MAF	known	0.263/0.56	0.140/0.76	0.088/0.85	0.027/0.95
			estimated	0.283/0.52	0.165/0.71	0.107/0.82	0.036/0.94
Beagle	This paper	equally spaced	known	0.164/0.74	0.110/0.82	0.085/0.86	0.037/0.94
			estimated	0.183/0.70	0.128/0.79	0.101/0.83	0.050/0.92

Genotype imputation error rate and imputation accuracy (error/accuracy) for different sizes of low-density marker panels using two imputation methods for markers with known and estimated chromosomal positions.

ISSN: 1297-9686