BMC Genomics

Table 1 Empirical accuracies (R²dose, R²gt, CR) and model-based (Rsq) imputation quality score from Minimac3 using different reference panels

From: Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

		Size of the reference panel
		250	500	1000	2000
Rsq	Low-frequency (MAF < 5%)	0.829	0.856	0.871	0.876
	Common (MAF > 5%)	0.942	0.960	0.971	0.978
	Global	0.909	0.928	0.938	0.944
R²*dose*	Low-frequency (MAF < 5%)	0.688	0.737	0.778	0.818
	Common (MAF > 5%)	0.909	0.936	0.953	0.965
	Global	0.845	0.874	0.897	0.917
R²gt	Low-frequency (MAF < 5%)	0.690	0.746	0.792	0.832
	Common (MAF > 5%)	0.887	0.920	0.941	0.956
	Global	0.832	0.868	0.895	0.917
CR	Low-frequency (MAF < 5%)	0.992	0.995	0.996	0.997
	Common (MAF > 5%)	0.962	0.973	0.98	0.985
	Global	0.971	0.980	0.986	0.989

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com