as well as SNPs that had strong evidence of an imputation batch effect. The batch effect test is an F test from an ANOVA of the SNP dosages against a factor representing imputation batch; we removed results with P<10−50. Prior to GWAS, we identified, for each SNP, the largest subset of the data passing these criteria, based on their original genotyping platform – either v2+v3+v4, v3+v4, v3, or v4 only – and computed association test results for whatever was the largest passing set. After quality control, the 23andMe discovery GWAS included results for 13,474,321 imputed variants, and 60,949 genotyped variants that did not have imputed results passing our filters, for a total of 13,535,270 variants. Of these, 15,774 test results could not be computed due to logistic regression fitting problems, leaving 13,519,496 tests. HWE and batch-effect pvalues are presented in Supplementary Table 13.
