Fig. 4: Fitness analysis of SARS-CoV-2 mutations.

A Fitness distribution of the 3603 C → U mutations which we calculated fitness values. B Mutations with similar fitness values tend to cluster together. Blue bases indicate locations where C → U mutations are positively selected for, and orange bases indicate locations where C → U mutations are selected against. The intensity of the color indicates the intensity of selection. Five clusters are highlighted. C, D Fitness distribution of all synonymous C → U mutations for which we calculated fitness values, split up into paired or unpaired bases. E, F Fitness distribution of all non-synonymous C → U mutations for which we calculated fitness values, split up into paired or unpaired bases. G, H Fitness distribution of all non-sense C → U mutations that we calculated fitness values for, split up into paired or unpaired bases I. Mutation rate of all mutations, split up into paired or unpaired bases (P = 0.0006 for C-to-U, Mann–Whitney U-test, n = 7). J Presence of paired and unpaired bases in hot spots or cold spots of mutation. K Mutation rate of cytosine in CpG vs non-CpG islands (P = 0.002, Mann–Whitney U-test, n = 7). All analyses were done by the Mann–Whitney U-test. ^**P < 0.01; ^***P < 0.001. All error bars represent the standard deviation of the mean across the seven passages of the Delta (replicate B) virus.