Fig. 1

Classifications of single base substitutions, doublet base substitutions, and indels. a Classification of single base substitutions (SBSs). The complete classification of an SBS includes both bases in the Watson-Crick base-pairing. To simplify this notation, one can use either the purine or the pyrimidine base. SigProfilerMatrixGenerator uses as a standard the pyrimidine classification. b Classification of doublet base substitutions (DBSs). The complete classification of a DBS includes bases on both strands. To simplify this notation, in most cases, SigProfilerMatrixGenerator uses the maximum number of pyrimidines. c Classification of small insertions and deletions. The complete classification includes the length of the indel and the number of repeated units surrounding the sequence. For deletions at microhomologies, the length of the homology, rather than the number of repeat units surrounding the indel, is used in the classification