Table 3.

Cutoffs for MAF in imputed minor allele genotypes and for genotype probabilities (GP) in all genotypes to ensure a level of mean concordance.

	Cutoff MAF (minor allele genotypes)					Cutoff GP
Concordance levels:	95%	90%	85%	80%	75%	95%	90%
Beagle4.1	0.0262	0.0102	0.0062	0.0042	0.0030	0.990	0.950
Beagle5.1	0.0276	0.0108	0.0070	0.0050	0.0032	0.980	0.938
IMPUTE2	0.0300	0.0128	0.0090	0.0060	0.0046	0.980	0.920
IMPUTE4	0.0250	0.0102	0.0062	0.0040	0.0030	0.980	0.940
minimac3	0.0250	0.0100	0.0060	0.0040	0.0030	0.980	0.930
minimac4	0.0250	0.0102	0.0060	0.0040	0.0030	0.980	0.940

Intervals for the grouping, in which the concordance of SNPs is averaged according to MAF, have the length 0.001, while the intervals for genotype probabilities have the length 0.01.