Table 2.

Mean (and standard deviation) genotype concordance, genotype correlation and allele dosage correlation for validation animals in S1

	Genotype concordance rate	Genotype correlation	Dosage correlation
BEAGLE BSWa	0.964 (0.004)	0.829 (0.019)	0.945 (0.011)
FImpute BSW	0.953 (0.005)	0.766 (0.021)	–
IMPUTE2 BSW	0.971 (0.004)	0.872 (0.021)	0.956 (0.009)
Minimac BSW	0.972 (0.004)	0.872 (0.021)	0.959 (0.008)
BEAGLE Allb	0.967 (0.007)	0.840 (0.035)	0.965(0.010)
FImpute All	0.956 (0.008)	0.775 (0.038)	–
IMPUTE2 All	0.974 (0.007)	0.879 (0.035)	0.972 (0.009)
Minimac All	0.975 (0.007)	0.879 (0.035)	0.974 (0.008)

^aImputation accuracy evaluated for BSW validation animals only

^bImputation accuracy evaluated for all validation animals