Fig. 3.

Predicted equilibrium frequencies from mutation rates versus actual nucleotide frequencies at 4-fold degenerate sites in sarbecoviruses. (A) Predicted equilibrium frequencies of nucleotides at 4-fold degenerate sites as calculated from the mutation rates for all of the SARS-CoV-2 clades analyzed here. (B) Actual frequencies of nucleotides at 4-fold degenerate sites in various sarbecoviruses. (C) Manhattan between predicted equilibrium frequencies (from mutation rates) and actual empirically observed nucleotide frequencies at 4-fold degenerate sites for a variety of viruses. SARS-CoV-2 clades are shown in purple squares. See supplementary figure S2, Supplementary Material online for per-nucleotide frequencies for the viruses shown in C.