average per-site counts of each nucleotide mutation type

Interactive plot of average counts per nucleotide site averaged over all clades and sites. Counts are reported separately for the expected counts (estimated from 4-fold degenerate sites) and the counts for all synonymous mutations (including 4-fold degenerate sites), nonsynonymous mutations, and stop mutations. Counts are stratified by the type of nucleotide change in the mutation.

You can mouseover points for details and click/shift-click the legend to highlight specific types of counts.

See Bloom and Neher (2023) for a paper describing the work.

See https://github.com/jbloomlab/SARS2-mut-fitness for full computer code and data.

See https://jbloomlab.github.io/SARS2-mut-fitness/ for links to all interactive plots.

This plot is for the gisaid_2024-04-24 dataset. Here are all plots for that dataset.