VQSLOD and mapping and variant quality scores (MQ, GQ). For the methylation data, we applied both probe-level (detection P≥0.01 across all samples; not cross-hybridize with the sex chromosomes; not overlapped with known SNPs with MAF≥0.01 within 10 bp region) and subject-level QC (within 3 s.d. from the mean of a principal component (PC) for PC1, PC2 and PC3, and those with poor bisulfite conversion efficiency). The top hits were also successfully replicated in an independent sample34. Experimental replicates and controls were designed to calibrate data.
