Systematic quality control (QC) was applied to all genotypes generated at the Estonian Biocentre. Duplicates from the Estonian sample were used to assess genotyping reproducibility, i.e. every 40th individual was duplicated and the mean discordance per SNP between pairs of individuals was found to be less than 1 in 5000 (0.0002%). The per individual call rate had to be at least 95% for individuals to be included into subsequent analyses. The number of individuals before and after QC is shown in detail in Table 1.
