Fig. 5From: AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencingAI consistency for different alignment methods for FN1. Detailed Legend: A comparison of fractions over SNPs between a STAR, b STAR with N-replaced SNP reference genome, and c TopHat2. In the normal STAR and TopHat2 run, the fraction lies around 1:1 for most SNPs, except SNP 5 (rs7596677), which shows strong AI. In c, however, the fractions are approximately 1:1 for all SNPs. d This graph summarizes the total counts for each SNP over all samples for the alignment methods. See Additional file 4 for the total allele count for each SNPBack to article page