A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle

Table 3 Per-variant mean imputation accuracy measures by MAF for Gelbvieh individuals imputed using the breed reference (BR) and composite reference (CR) panels

MAF	BR GC^a	CR GC^a	BR r	CR r	BR IQS	CR IQS
> 0.00–0.05	0.999	0.999	0.984	0.982	0.910	0.926
> 0.05–0.10	0.997	0.998	0.985	0.99	0.959	0.979
> 0.10–0.15	0.996	0.998	0.986	0.992	0.974	0.989
> 0.15–0.20	0.995	0.997	0.988	0.993	0.982	0.991
> 0.20–0.25	0.994	0.997	0.990	0.995	0.986	0.993
> 0.25–0.30	0.994	0.997	0.990	0.995	0.987	0.993
> 0.30–0.35	0.994	0.997	0.991	0.996	0.988	0.994
> 0.35–0.40	0.993	0.997	0.992	0.996	0.988	0.994
> 0.40–0.45	0.993	0.996	0.992	0.996	0.988	0.994
> 0.45–0.50	0.993	0.996	0.992	0.996	0.988	0.994

ISSN: 1297-9686