Flow diagram describing the process of filtering out low quality and functionally irrelevant variants. From 247 909 variants, 164 011 variants were discarded because they were monoallelic, had more than two alleles, had a call rate of <90%, or because their genotype proportions deviated from the expected ones as defined by the Hardy-–Weinberg (H–W) equilibrium law in both cases (patients with major depression) and controls at a P-value of 2 × 10−7. The remaining 83 898 variants were used for exome-wide association analysis. After additional functional filtering using several tools (SIFT, PolyPhen-2, MutationTaster, Gerp++ and phyloP) to exclude tolerated and conserved variants, and after the exclusion of non-exonic variants and variants in the control subjects with allelic frequency >0.01, the remaining 47 296 variants were used in rare variant analysis. MDD, major depressive disorder.