E (envelope) amino-acid fitnesses

Interactive plot of fitnesses amino acids at each site estimated from the observed versus expected counts of the amino acids among natural sequences.

The black area plot at top shows the mean fitness for all non-stop amino acids at each site, with more negative values indicating mutations at a site tend to be deleterious. The plot is zoomable, and you can click and drag with the mouse to highlight specific regions to show in the heat map. You can use the site fitness statistic click box at bottom to change whether the black area plot at top shows the mean, maximum, or minimum fitness of amino acids at that site. You can use the show stop option at bottom to overlay the effect of stop codon mutations on this plot.

The heat map shows the estimated fitness values for specific amino acids. Red indicates low fitness (deleterious) amino acids, and blue indicates high fitness amino acids. Gray indicates amino acids with insufficient natural evolutionary data to make estimates (typically only single-nucleotide accessible amino acids will be shown). You can mouse over points in the heat map for details, and zoom using the area plot at top. The x at each site indicates the wildtype amino acid in the SARS-CoV-2 clade indicated by the dropdown box below the plot.

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 gisaid_2024-04-24 dataset. Here are all plots for that dataset.