Table 5.

Average imputation accuracy of Holstein specific variants for HOL80 and MIX80 per category of MAF

MAF range	n alleles 1	n variants	HOL80		MIX80
			MAF	r	MAF	r
> 0.1	> 16	15,736	0.16529	0.87	0.04369	0.78
0.05625-0.1	9-16	23,057	0.07367	0.79	0.02289	0.63
0.03125-0.05	5-8	14,825	0.04061	0.63	0.01046	0.30
0.01875-0.025	3-4	9,185	0.02152	0.54	0.00855	0.24
0.0125	2	2,616	0.01250	0.38	0.00679	0.13
0.00625	1	1,663	0.00625	0.18	0.00625	0.14

¹number of minor alleles present in the HOL80 reference population at corresponding MAF range in the HOL80 reference population.

Average imputation accuracy (r) and average minor allele frequency (MAF) of the reference population for scenarios HOL80 and MIX80 for Holstein specific variants on chromosome 1 per category of MAF range in the HOL80 reference population. Results are only shown for one cross-validation, but are similar for all cross-validations on chromosome 1.