Fig. 2

Accuracy of imputation from medium-density to sequence level for various imputation scenarios for the ECA3 chromosome. Imputation was performed for three reference panels (RP), including 65 (RP1), 175 (RP2) or 317 (RP3) horses. Imputation with RP1 was carried out for three panel sizes, including two (2/5), three (3/5) or four (4/5) fifths of the panel in the reference group. For imputation with RP2 and RP3, always four-fifth of the RP1 animals plus all additional animals of RP2 or RP3 were included. Imputation with RP2 was performed with three computer programs, Beagle 5.1 (B5.1), Impute 5 (I5) and Minimac 4 (M4). Otherwise, the software Beagle 5.1 was used for imputation, which in all cases was carried out for equine chromosome 3 (ECA3), as an example