Fig. 2

Characteristics of iSNVs. a Heatmap showing the alternative allele frequencies (AAFs) of intra-host single nucleotide variants (iSNVs) and consensus variants among samples. The sample (e.g., P01N0129) name indicates patient number P01, sample type (N nasal swab, T throat swab, A anal swab, F feces, S sputum) and collection date (January 29). Common iSNVs were marked by star symbols. Variant type and sample type were marked in different colors, and consensus variants were indicated in red. b The number of detected iSNVs per patient. c Number of iSNV sites among protein-encoding genes. d Box plot showing the distribution of alternative allele frequencies (AAFs) of non-synonymous and synonymous iSNVs. Each dot indicates the median AAF among all the detected iSNVs of samples from the same patient. e Box plot showing the distribution of AAFs of common and rare iSNVs. Each dot indicates the median AAF among all the detected iSNVs of samples from the same patient