List of sites found to be selected differentially along internal branches between BA.5 and background sequences (FDR ≤ 0.2) using the Contrast-FEL method.

Coordinate (SARS-CoV-2): the starting coordinate of the codon in the NCBI reference SARS-CoV-2 genome. Gene/ORF: which gene or ORF does this site belong to. Codon (in gene/ORF): the location of the codon in the corresponding Gene/ORF. Ratio of omega (BA.1: background): the ratio of site-level omega estimates for the two sets of branches. If this ratio is > 1, then selection on BA.1 is stronger. These values are highly imprecise and should be viewed as qualitative measures. p-value: the p-value for the likelihood ratio test that omega ratios between the internal branches of the two clades are different. This is not corrected for multiple testing. q-value: multiple-test corrected q-value (Benjamini-Hochberg). (CSV)