Fig. 3

Illustrating the pipeline to compare the allele-specific RPF density (A-site tri-nucleotide density). According to the description in previous parts, the allele in normal tissue is the ancestral allele, and the tumor tissues have both the ancestral and derived allele. The A-site and RNA reads count could be extracted from the sequencing data. The A-site/RNA (A-site density) is calculated for each allele. We also classify the synonymous mutations based on codon optimality. Synonymous mutations from A/T to C/G are optimal and the opposite direction are non-optimal