Fig. 3: The mutation rate of the SARS-CoV-2 genome is altered by genetic context.

A–D The mutation rate of the SARS-CoV-2 genome differs depending on the bases that directly flank the focal base. The focal base (the mutated base at the center of a triplet) is listed underneath the graph, while the bases that are on its 5’ or 3’ side are located above and below the focal base. The type of mutation that is analyzed is depicted above the bars. So, for example, the first 4 bars on the left-hand side of (A) correspond to an adenine base that is at the center of the triplet (the focal base), and is flanked on its 5’ base by adenine, and on its 3’ side by one of four possible bases. Each bar then corresponds to the impact of these flanking bases on the mutation of adenine (the focal base) to uracil. For example, the mutation rate of A → C is highest when adenine is flanked by guanine on its 5’ side and 3’ side. In contrast, the mutation rate of A → C substitutions is lowest when adenine is flanked on its 5’ side with uracil, and adenine, cytosine, or guanine on its 3’ side. Note that the y-axes for each panel differ for increased visibility. Average of all passages generated (n = 47), error bars represent standard deviation of the mean.