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Figure 2 | BMC Genomics

Figure 2

From: Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome

Figure 2

The density of differentiating sites affects relative allelic abundance when simulated reads are mapped to only one genome. Relative allelic abundance was measured using the 36-base (A-D) and 50-base (E-H) reads simulated from the two D. melanogaster genotypes as well as using the 36-base reads simulated from D. melanogaster and D. simulans (I-L) aligned to a single reference genome, allowing either one mismatch (A, E, I), two mismatches (B, F, J), or three mismatches (C, G, K), as well as by aligning reads to both allele-specific genomes allowing no mismatches (D, H, L). The number of neighboring differentiating sites is shown on the x-axis of each panel for each differentiating site and describes the maximum number of other sites that differ between the two alleles in any potential read overlapping the focal differentiating site. The y-axis shows the proportion of reads that were assigned to the reference allele for each differentiating site, summarized in box plots where the width of each box is proportional to the number of sites in that class. A proportion of 0.5 (indicated with a red dotted line in each panel) is expected if all reads overlapping a differentiating site are correctly assigned to alleles. The pie chart inset in each panel shows the total number of differentiating sites with equal (white) and unequal (grey) abundance of reads assigned to each allele.

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