Accuracy of imputation to whole-genome sequence data in Holstein Friesian cattle

Table 1 Mean accuracy of imputation per SNP

		Mean	SD	Minimum	Maximum	Nb SNPs
S80	BovineHD	0.83	0.27	-0.43	1.00	744 896
	BovineSNP50	0.46	0.37	-0.54	1.00	768 907
S60	BovineHD	0.81	0.27	-0.37	1.00	736 216
	BovineSNP50	0.43	0.36	-0.58	1.00	780 388
S40	BovineHD	0.77	0.29	-0.33	1.00	739 859
	BovineSNP50	0.37	0.36	-0.40	1.00	764 439
2-step	Step 1	0.83	0.15	-0.17	1.00	32 880
	Step 2	0.77	0.29	-0.33	1.00	739 859
	Overall	0.65	0.30	-0.41	1.00	764 912

Mean, standard deviation (SD), minimum and maximum accuracy of imputation per SNP on BTA1 for different combinations of scenarios and lower density marker panels; for scenario S40, accuracy of stepwise imputation is also shown for step 1 (BovineSNP50 to BovineHD), step 2 (BovineHD to sequence), and overall; number of SNPs used for analyses are presented in the last column.

ISSN: 1297-9686