Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle

Table 3 Accuracy of imputation for two causal variants in Fleckvieh cattle

Variant	Effect	Minor allele frequency			Proportion of correctly imputed genotypes/r_IMP,SEQ
		Minor allele frequency			Fimpute		Minimac _BG		Minimac _DOS
		TaqMan	Within-breed	Multi-breed	Within-breed	Multi-breed	Within-breed	Multi-breed	Within-breed	Multi-breed
14:1,802,266^a/rs109326954	p.A232K	0.074	0.062	0.183	0.993/0.976	0.998/0.992	0.999/0.996	0.999/0.996	–/0.979	–/0.995
20:31,909,478/rs385640152	p.F279Y	0.074	0.072	0.121	0.861/0.639	0.931/NA^b	0.868/NA^b	0.994/0.938	–/0.703	–/0.895

The minor allele frequencies were calculated using TaqMan-derived and sequence genotypes in either within- or multi-breed reference populations
^aThe p.A232K-variant in the DGAT1 gene results from two adjacent SNPs in LD located at 1,802,265 and 1,802,266 bp (rs109234250 and rs109326954). In the current study, we considered only the variant at 1,802,266 bp
^bThe imputed variant was not polymorphic in the sample of 902 genotyped animals precluding the calculation of r_IMP,SEQ values

ISSN: 1297-9686