Fig. 2

Classifications of transcriptional strand bias. a RNA polymerase uses the template strand to transcribe DNA into RNA. The strand upon which the gene is located is referred to as the coding strand. All regions outside of the footprint of a gene are referred to as non-transcribed regions. b Single point substitutions are oriented based on their pyrimidine base and the strand of the reference genome. When a gene is found on the reference strand an A:T > T:A substitution in the footprint of the gene is classified as transcribed T > A (example indicated by circle) while a C:G > G:C substitution in the footprint of the gene is classified as un-transcribed C > G (example indicated by star). Mutations outside of the footprints of genes are classified as non-transcribed (example indicated by square). Classification of single base substitutions is shown both in regard to SBS-24 and SBS-384