Fig. 3

Strategies for reducing mapping bias in AE analysis. a Summary of various strategies to correct for mapping bias (Baseline = STAR aligned only, Filtering = STAR aligned with bias and mappability filters, P. Genome = STAR aligned to a personalized genome generated with Allele-Seq, WASP = STAR aligned with removal of biased reads using WASP, Variant Aware = GSNAP in variant aware alignment mode). The boxplot (axis on the left) shows reference ratios for AE sites covered by eight or more reads. The mean reference ratio for each strategy is shown with a white dash; the solid black line indicates a reference ratio of 0.5, while dotted lines indicate ±0.05. The percentages of sites that are monoallelic reference (grey circle) or alternative (grey diamond) are plotted against the secondary axis. The number of sites with AE data for each strategy is shown as a percentage of the baseline strategy underneath their respective labels. Outliers are hidden for ease of viewing. b Percentage of sites that are removed when bias and mappability filters are applied to resulting data from all strategies, shown for each reference ratio bin