Fig. 6

QC measures reduce false positives, demonstrated with a binomial test for allelic imbalance. a QQ plot of p values generated from binomial testing after various QC measures. Baseline = STAR aligned testing against a null of 0.5 without any correction for double counting, mapping bias, or genotyping error; No Double Counting = as Baseline but without duplicates and overlapping mate pairs counted once; Site Filter = as No Double Counting but without biased and low mappability het-SNPs; Adjusted Null = As Site Filter but using mean per base reference ratio as the binomial null; WASP Filter = as Site Filter but with WASP filtering of reads; Monoallelic Filter = as Adjusted Null but removing monoallelic sites to account for putative genotyping error. b Histogram showing distribution of coverage for sites with significant (5 % FDR) allelic imbalance according to a binomial test (primary axis), and the percentage of all het-SNPs that show significant allelic imbalance in each coverage bin using increasing allelic effect cutoffs (secondary axis). c, d Multidimensional scaling (MDS) clustering of Geuvadis samples based on proportion of sites with significant AE that differs between sample pairs. Samples are colored by sequencing laboratory and labeled by population. If significant sites are assigned based on a simple binomial test (FDR 5 %), the samples cluster first by sequencing laboratory due to lab-specific differences in coverage (c). This effect is mostly removed in (d) by requiring significant sites to have FDR 5 % and effect size > 0.15