Figure 3
From: Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies
Comparison of allelic ratios with different read types. Reference allele ratio obtained from simulated reads over SNPs (A, C) and indels (B, D) comparing genome versus transcriptome-based reads (A, B) in single-end 50 bp reads mapped with the GEM mapper, and comparing single- versus paired-end reads (C, D) in genome-based 50 bp reads mapped with BWA. The dotted lines denote 5% difference of the ratio for reference/non-reference allele. The color scale from dark blue to light blue denote the density of the points.