Fig. 8

presents a detailed workflow for the calculation of possible variants and mutation rates for a given sequence, based on the type of variant. The iterative process is represented by a sample sequence composed of three codons: the start codon ATG, the triplet CTG, and the stop codon TAA (1). To further elucidate the process, the calculation of the possible variants and mutation rate for the CTG triplet is emphasized. The first step involves identifying the context triplets for each of the three bases (highlighted in green) of the coding triplet. This is done by considering their direct neighboring bases (shown in purple). Afterwards, both the coding and the context triplet are modified to create all possible single nucleotide variants. This is achieved by replacing the bases of the coding triplet (in green) with all other possible bases, resulting in a total of 9 altered triplets (2). Subsequently, the consequence, and thus the variant type, of each altered triplet is determined by evaluating its impact on amino acid translation (3). The mutation rate for a specific variant type of the whole codon is calculated by summing up the mutation rates of the corresponding context triplets (4). Complementary, the count of possible variants for a given variant type is simply the sum of triplets that align with that variant type (4). Finally, the mutation rate and total count of possible variants for the entire sequence are computed by summing up the mutation rates and possible variant counts, respectively, for each variant type across all codons in the sequence (5)