Allele-specific bias in transcription is evident from pooling reads across phased SNPs. (A, C) orf19.238 (A) and orf19.3556 (C) have 8 and 11 non-overlapping regions, respectively, where RNA-seq reads include SNPs and can be attributed to either allele A in purple, or allele B in green. The bar graphs at top quantify the number of reads per SNP region, with the line graph at bottom indicating read density in a 20 nucleotide sliding window across each region. The density of reads lacking SNP information is indicated in gray. For visual clarity, the x-axis is nonlinear, such that SNP regions show data at every nucleotide, and non-SNP regions show data every 10 nucleotides. (B, D) Allele-specific biases for orf19.238 (B) and orf19.3556 (D), where histograms reflect the results from 10,000 bootstrap iterations. (D) The gray histogram shows how randomly permuting the phasing masks allele-specific bias, and the ‘max phasing’ line indicates the bias calculated if the maximum and minimum values for each bar in the top of (C) were attributed to allele B and allele A, respectively.