Fig. 2

Schematic representation of the workflow of creating and re-imputing the in silico arrays. The starting point was a 0/1/2 coded marker matrix with SNPs in rows and individuals in columns (different populations separated by vertical lines). In a first step, an array (light blue rows) was constructed in silico from known data by setting all SNPs to missing which were invariable (MAF < 0.05, red rows) in the discovery population (first three columns). In a second step, a reference set (dark blue columns) was set up from animals for which complete knowledge of all SNPs was assumed. This Reference set was then used in a third step to impute the missing SNPs in the study set using Beagle 5.0 and resulting in a certain amount of imputation errors (red numbers)