Mutant alleles are differentially expressed. The mutant allele frequency of each mutation observed in the RNA-seq data (y-axis) was plotted against the mutant allele frequency observed in the exome sequencing data (x-axis). We define the mutational frequency as the number of sequencing reads covering a mutation that contain the mutant allele divided by the total number of covering sequencing reads. The degree of similarity between the exome and RNA-seq data are represented by red squares (more similar) and blue circles (less similar). Plots are shown for 4 representative samples. The size of the point on the plot (circle or square) represents the level of statistical certainty, as measured by a Bayesian hypothesis test assessing the dissimilarity in the mutant allele frequencies, given the coverage of a mutation in the RNA-seq and exome sequencing data. Some genes, such as CCND1 contain multiple mutations, and are therefore represented by more than 1 point on the graph. Gray points on the plot correspond to mutations that have zero RNA-seq read coverage and are placed on the plot to show their mutant allele-frequency in DNA.