Consequences of splitting whole-genome sequencing effort over multiple breeds on imputation accuracy

BMC Genomic Data

Table 4 Average imputation accuracy for scenarios HOL80 and MIX140 per category of minor allele frequency

MAF range	n alleles¹	n variants	HOL80		MIX140
			MAF	r	MAF	r
> 0.1	> 16	525,647	0.27237	0.92	0.27159	0.93
0.05625-0.1	9-16	143,313	0.07639	0.78	0.08784	0.79
0.03125-0.05	5-8	94,021	0.04073	0.66	0.05596	0.69
0.01875-0.025	3-4	56,235	0.02187	0.56	0.03884	0.62
0.0125	2	25,698	0.01250	0.42	0.03216	0.56
0.00625	1	25,101	0.00625	0.19	0.02385	0.45

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 MIX140 for 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.

ISSN: 2730-6844