DGRP SNPs were additionally filtered according to the following criteria: ε ≤ 0.02 (per SNP); p × ε ≤ 0.01 (per allele); coverage ≥ 3 (per allele); median coverage ≤20 (across strains); number of strains with detected homozygous alleles ≥100; number of strains with calls scored as 'heterozygous' ≤5%. The combination of these filters removed 31.3% low-confidence SNPs and increased the overlap with the SNPs detected by the Drosophila Population Genomics Project [69] based on a subset of the same Drosophila lines (not shown).
