Fig. 3: Comparison of within-host mutation profiles between vaccinated and unvaccinated Delta and Omicron samples.

a–c Full-genome incidence of iSNVs (adjusted number of iSNVs per Kb), abundance of iSNVs (minor allele frequencies, MAF) and adjusted nucleotide diversity (π) of different samples. For all box plots, the bold horizontal line inside the box shows the median, the upper and lower edges of the box indicate the first and the third quartiles, and whiskers extend to span a 1.5 interquartile range from the edges. Pairwise comparisons between groups were performed by the two-sided two-sample Wilcoxon test; the pairs with Benjamini-Hochberg (BH) corrected P value \(\le 0.01\) and \(\le 0.05\) are labelled with “**” and “*” respectively. d–e Full-genome and gene-specific within-host nonsynonymous nucleotide diversity (\({\pi }_{N}\)) and synonymous nucleotide diversity (\({\pi }_{S}\)) in samples from different groups. The points and error bars showed the mean and standard deviation values under 10,000 bootstrap replicates at codon level. Significance was evaluated using two-sided Z-tests of the null hypothesis that \({\pi }_{N}-{\pi }_{S}=0\) (10,000 bootstrap replicates, codon unit); P-value \(\le 0.01\), \(\le 0.05\) and \(\le 0.10\,\)were labelled with “**”, “*” and “^”, respectively. The number of biologically independent samples in each group are shown in Supplementary Table 5. Source data are provided as a Source Data file.