Table 4.

Accuracy comparisons between the two-step piecemeal and the classic one-step imputation on the Holstein datasets

		5-Fold cross validation					Independent testing
BaseProgram	Imputation	a c c 1	a c c π	+	#Clusters	#TClusters	a c c 1	a c c π	+
	6 K →50 K	86.98 %	89.81 %	2.87 %	95	189	74.97 %	76.90 %	1.94 %
Beagle	6 K →777 K	82.35 %	85.27 %	2.92 %	1,000	1963	71.29 %	73.25 %	1.96 %
	50 K →777 K	93.09 %	95.16 %	2.07 %	1,000	1956	82.27 %	84.25 %	1.97 %
	6 K →50 K	91.11 %	91.64 %	0.53 %	95	288	81.15 %	81.40 %	0.25 %
FImpute	6 K →777 K	89.22 %	90.14 %	0.92 %	1,000	2942	82.80 %	82.81 %	0.02 %
	50 K →777 K	95.25 %	95.61 %	0.36 %	800	2765	87.72 %	87.83 %	0.11 %

Results are on the Holstein datasets for markers on chromosome 27. Columns 3–7 contain the 5-fold cross validation results on 114 animals, with the selected markers and their associated target marker clusters. Independent testing results on the 8 animals are in columns 8–10, using the selected markers and their associated target marker clusters from the cross validation. In the independent testing, for ¹Beagle 6, 37, and 44 target marker clusters are empty; for ²FImpute 7, 58, and 35 target marker clusters are empty. The columns labelled with + show the improvements, in bold, of the piecemeal imputation over the one-step imputation