A method can determine the likelihood that targeted somatic mutagenesis of a nucleic acid molecule by a mutagenic agent has occurred. The method includes analyzing the sequence of the nucleic acid molecule to determine, for a number of mutations of a mutation type at one or more motifs recognized or targeted by the mutagenic agent, the codon context of those mutations to thereby identify the location of a mutation and mutation type for each of the mutated codons in the nucleic acid molecule. The codon context of an individual mutation can be determined by determining at which of the three positions of a corresponding mutated codon the individual mutation occurs. The mutagenic agent can be one of aflatoxin, activation-induced cytidine deaminase (AID), or an apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) cytidine deaminase.
