The histograms show the effects of all mutations (to the reference genome) with fitness estimates, and just those mutations that have fixed in a clade.
The minimum expected count slider below the plot indicates how many expected counts of an an amino acid we require before making a fitness estimate. Larger values yield more accurate estimates but for fewer amino acids. So move the slider to the left to show estimates for more amino acids at lower confidence, and move it to the right to show estimates for fewer amino acids at higher confidence.
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 public_2023-10-01 dataset. Here are all plots for that dataset.