Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV.

We could not test whether this effect was significant using the GLM framework, but a one-sided two-sample Wilcoxon test showed that the difference in estimated selection coefficients for G→A mutations and non-CpG-forming A→G mutations was highly significant ( p = 5 ⋅ 10 −9 ).

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