Figure 4

Fragment mutation rules. As an example of the process each fragment goes through, this fragment from chromosome 4 is mutated based on information from the tables shown in Figure 2. In step 1 the GC content of the fragment is calculated then fit to the pre-determined bins, all observed fragments within that bin are then available to sample. Step 2 samples one of these observed fragments to get the counts of specific variants. In this case the observed fragment had a single deletion and three SNVs. In step 3 these observed variant counts are applied in stages. Sites for each variation are selected randomly (without replacement), and the mutation applied. For a size-dependent variant such as the deletion, a size is determined from a probability table, for SNVs the probability of the point mutation is determined based on the nucleotide present at that site. The resulting fragment will not replicate the sampled fragment (from step 2) in specific mutations, but only in the number of mutations applied.