Fig. 1: Statistics of within-host mutations in SARS-CoV-2 samples.

a Distribution of number of iSNV site(s) in each sample, colored by ranges of Ct values. The dashed line shows the mean value of the distribution. b Distribution of number of sample(s) sharing iSNVs (e.g., if the iSNV identified in one sample was not shared with any other sample, then the number of samples sharing that iSNV equals to one (x = 1), and so on), colored by variant types, where UTR stands for untranslated region. c Distribution of the frequency of iSNVs per sample per synonymous and per non-synonymous site (\({d}_{S}\) and \({d}_{N}\)) for different types of mutations, colored by variant types. The dashed lines show the average frequency of synonymous and non-synonymous iSNVs among all types of mutations. The points and error bars show mean and standard deviation values based on 10,000 bootstrap replicates at mutation level. d Distribution of the frequency of iSNVs per sample per Kb for synonymous and non-synonymous site (\({d}_{S}\) per Kb and \({d}_{N}\) per Kb) in different genomic regions of 1Kb length, colored by variant types. The points and error bars show mean and standard deviation values based on 10,000 bootstrap replicates at mutation level. e Distribution of high-frequency mutations shared by multiple samples, colored by variant types. Coding regions of the SARS-CoV-2 genome, based on the reference genome (GenBank: MN908947.3), are shown at the bottom of the figure. Source data are provided as a Source Data file.