The calculated effective sample sizes in MVP and reported effective sample sizes in PGC were used in meta-analyses and all downstream analyses. AUDIT-P in UKB is a continuous trait, so we used actual sample sizes for that trait. For the AUD meta-analysis, variants present in only one sample (except MVP phase1 which is much larger than the others) or with heterogeneity test p-value < 5 × 10−8 were removed, leaving 7,003,540 variants. For the PAU meta-analysis, variants present in only one sample (except MVP phase1 or UKB) or with heterogeneity test pvalue < 5 × 10−8 and variants with effective sample size < 45,118 (15% of the total effective sample size) were removed, leaving 14,069,427 variants.
