Fig. 8

Heat map of allelic fractions in positive clinical samples. a Rows and columns indicate samples and the mutations, respectively. Result from a hierarchical clustering is shown as dendrogram. To best represent evolutionary relationship among samples, the clustering was based on the genotype itself (i.e., mutation or no mutation) instead of the allelic fraction values. The mutations are sorted by the genomic position. b Top 20 most frequent co-occurring sets of mutations (“fingerprints”) among 75,681 GISAID genomes, with variants restricted to lie inside the regions of the SARS-CoV-2 genome that we sequenced. Each gray rectangle corresponds to one fingerprint, with vertical line segments located at the positions of the mutation in that fingerprint, and with line segment colors indicating the mutation alleles. The height of each rectangle is equal to the number of GISAID genomes with the associated fingerprint, so the single most frequent fingerprint is the bottommost rectangle. The 3rd most frequent fingerprint (3rd rectangle from the bottom) has no variants relative to the SARS-CoV-2 reference genome within the sequenced regions