A method for quantifying ribonucleic acid (RNA) mutation expression. For each read pair of a read pair group, a set of contiguously aligned regions and a splice junction configuration are identified. Each read pair is within a selected range of a location of interest. Each read pair of the read pair group is classified based on the set of contiguously aligned regions and the splice junction configuration that correspond to each read pair, a reference genome, and a selected mutation. A mutation-centric output is generated for the read pair group.