Extended Data Table 2 Genotype distribution and P values for violation of the Hardy–Weinberg equilibrium in CONVERGE and replication cohorts

From: Sparse whole-genome sequencing identifies two loci for major depressive disorder

  1. This table shows the number of samples with the homozygous reference genotype (HomRef), heterozygous genotypes (Het), and homozygous alternative genotype (HomAlt), as well as P values for violation of the Hardy–Weinberg equilibrium (HWE) for both CONVERGE study samples and the replication cohort from northern China at the top SNPs rs12415800 in the SIRT1 locus and rs35936514 in the LHPP locus from the GWAS on MDD. The top two rows show these measures for all samples in both the CONVERGE and replication study, the next two rows show these measures for just cases in CONVERGE and the replication cohort, and the last two rows show these measures for just the controls. The genotype distributions for CONVERGE are obtained from hard-called genotypes from maximum imputed genotype probabilities for each sample at each of the two sites. As a genotype will not be called if the maximum genotype probability at a site is lower than 0.9 for any single sample, the total number of CONVERGE samples showing called HomRef/Het/HomAlt genotypes does not equal 10,640 for either SNP. For rs12415800, 19 samples (9 cases, 10 controls) have no genotype calls owing to a maximum genotype probability smaller than 0.9, giving a total of 10,621 CONVERGE (5,294 cases, 5,327 controls) samples with genotype calls. For rs35936514, 87 (39 cases, 48 controls) samples have no genotype calls owing to a maximum genotype probability smaller than 0.9, giving a total of 10,553 (5,264 cases, 5,289 controls) CONVERGE samples with genotype calls.