Genomic relationships based on X chromosome markers and accuracy of genomic predictions with and without X chromosome markers

Table 3 Allele error rate (ER _A , %), genotype error rate (ER _G , %) and correlation (COR) between imputed and true genotypes for different sets of markers ^a in two datasets ^b

Dataset	Method	ALL			AUTO			PAR			X
Dataset	Method	ER_A	ER_G	COR	ER_A	ER_G	COR	ER_A	ER_G	COR	ER_A	ER_G	COR
IMP_test	Findhap	1.7	3.3	0.972	1.7	3.3	0.974	10.4	19.1	0.829	3.3	4.1	0.940
	Beagle	1.1	2.2	0.982	1.1	2.1	0.983	8.8	15.9	0.858	3.0	3.0	0.941
IMP_0.5ref	Findhap	2.0	3.9	0.967	2.0	3.8	0.968	10.3	18.7	0.833	3.8	4.4	0.930
	Beagle	1.2	2.4	0.981	1.2	2.3	0.982	8.9	16.4	0.854	3.5	3.9	0.933

^aALL: all markers; AUTO: markers on the autosomes; PAR: markers on the pseudo-autosomal region; X: X-specific markers on the X chromosome; ^bIMP_test: for the test animals in genomic prediction, the 54K marker data were imputed from LD marker data; IMP_0.5ref: for half (randomly chosen) of the reference animals, the 54K marker data were imputed from LD marker data.

ISSN: 1297-9686