fitness effects of mutations fixed in at least one clade

Interactive plot of the fitness effects of amino-acid mutations fixed in at least one clade, stratified by non-spike and spike mutations. The point shapes show the overall fitness estimate using data from all clades, the estimates from just forward mutation counts in clades without the mutation, and the estimates (when available) for direct amino-acid reversions in clades with the mutation fixed. Note that we exclude direct nucleotide reversions in counts because they are error-prone due to calling to consensus, and so reversion estimates are often unavailable. Missing points indicate no estimate can be made for a mutation from the available data.

Mouseover points for details.

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.

You can click/shift-click on specific genes in the legend below the plot to only show mutations for that gene.

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

See for full computer code and data.

See for links to all interactive plots.

This plot is for the public_2023-10-01 dataset. Here are all plots for that dataset.