Table 5.

Average imputation accuracy of BEAGLE, fastPHASE and findhap with different reference population size in scenario of randomly masking 95% genotypes on chromosome 16

Composition of the reference population	Composition of the test population	BEAGLE 3.3 (20 iterations)	fastPHASE 1.4 (20 haplotype clusters)	findhap 2.0 (20 iterations)
87 bulls	2021 cows	0.687 ± 0.006	0.702 ± 0.005	0.775 ± 0.004
87 bulls and 101 cows	1920 cows	0.831 ± 0.005	0.704 ± 0.010	0.812 ± 0.008
87 bulls and 404 cows	1617 cows	0.878 ± 0.007	0.720 ± 0.033	0.829 ± 0.007
87 bulls and 1011 cows	1010 cows	0.901 ± 0.007	0.709 ± 0.008	0.842 ± 0.009