Performance of MBASED on simulated data in one-sample analysis. Genes were broken into 25 strata, based on number of SNVs in a gene and average number of reads per SNV. Within each strata 25% of genes were randomly chosen to exhibit ASE. For each SNV in a true positive ASE gene, one allele was randomly assigned to major haplotype and the corresponding read counts were simulated as described in Materials and methods. MBASED was run on the simulated data and genes with Benjamini-Hochberg adjusted P-values ≤0.05 (false discovery rate (FDR) control of 5%) were declared ASE. The average (across 100 simulations) true positive rate (TPR) and FDR within each strata and for each level of ASE signal (MAF used for ASE true positive genes) are shown. The overall TPR and FDR levels are obtained by giving each stratum weight proportional to the fraction of genes in that stratum (that is, these values are heavily weighted towards genes with few SNVs and low coverage, common in our data), and the average values are given in panel titles, along with their estimated standard errors (SE). MBASED performs very well at higher coverage levels and higher ASE extent.