Fig. 1

Read counts are simulated for different scenarios in two conditions. A scenario is defined as a specific number of simulations, number of allele specific reads, number of biological replicates (bioreps), level of allelic imbalance (AI) θ, and the probability of mapping an allele g1 (g2) specific read. Without loss of generality, let allele g1 be allele A and g2 be allele C (blue boxes). The number of allele specific reads (yellow reads) is the sum of unambiguously mapped reads in the experiment. Grey reads are reads that map equally well, i.e. ambiguously, to both alleles. Biological replicates in an experiment are samples from the same genotype and condition. In this example, there are k biological replicates, \(12\times k\) allele specific reads, and the probability of an allele specific read is \({r}_{i,g1}={r}_{i,g2}=0.8\). The null H1 and H2 hypotheses are allelic balance θ₁ = 0.5 in condition 1 (ex. liver) and θ₂ = 0.5 in condition 2 (ex. kidney), respectively. These cases are used to estimate the Type I error in rejecting allelic balance in conditions 1 (H1) and 2 (H2). In this example, θ₁ = 0.55 under the alternative (alt) H1 hypothesis and θ₂ = 0.55 under the alternative (alt) H2 hypothesis. These cases are used to estimate the power in rejecting allelic balance in conditions 1 (H1) and 2 (H2). θ₁ = 0.5 and θ₂ = 0.55 under the alternative (alt) H3 hypothesis, which allows estimation of the power rejecting equal levels of AI between the two conditions (H3). The null H3 hypothesis is simulated in both the complete null case: θ₁ = θ₂ = 0.5 and in the scenario where there is allelic imbalance in both conditions θ₁ = θ₂ = 0.55. These cases can be used to estimate the Type I error in rejecting equal levels of AI between the two conditions (H3)