Accuracy of imputation to whole-genome sequence in sheep

Table 3 Minimac3 imputation accuracy (R²) for variants before (thr0) or after (thr4) filtering based on R² threshold (numbers of variants imputed in millions in brackets) in Merino target set animals using three reference sets

R² threshold^a	Reference set
R² threshold^a	ALL	EUR	MER
Considering all variants tested in each reference set ^b
thr0	0.935 (10.8)	0.938 (10.2)	0.918 (7.9)
thr4	0.965 (7.1)	0.962 (7.5)	0.963 (5.8)
Considering only the variants tested in MER reference set ^c
thr0	0.924 (7.9)	0.929 (7.9)	0.918 (7.9)
thr4	0.962 (6.3)	0.959 (6.7)	0.963 (5.8)

ALL = all 935 animals representing breeds from Europe, Africa, Asia, America and the Middle East; EUR = 726 animals representing breeds from Europe; and MER = 117 Merino animals
^athr0 and thr4 refer to Minimac3 R² thresholds 0 and > 0.4, respectively
^bTotal number of imputed variants in each reference set for OAR1, 5, 10, 15, 20 and 25 in brackets
^cAll scenarios evaluated only on the same variants (30,660,937) in MER reference set

ISSN: 1297-9686