Fig. 2: Broad overview of the dataset.

A Circos plot depicting the coverage and mutations detected in SARS-CoV-2 sequencing libraries. Black dots represent the mutations detected, with mutations detected at higher frequencies located further away from the center of the plot. The blue surface represents sequencing coverage, with higher coverage extending further away from the center of the plot. The two outer rings depict the genes present in the SARS-CoV-2 genome, while the numbering outside of these rings indicates the position of these genes along the genome in 1 kb steps. B Mutation rate of six variants of the SARS-CoV-2 virus. Each dot represents a single measurement of a variant at 1 out of 7 passages for 2 replicates (n = 14 for USA, Alpha, and Delta, Mann–Whitney U-test, two-sided alternative, no correction for multiple testing). The mutation rates of the Beta, Gamma, Delta, Delta Calu, and Omicron variants were only measured once, for one replicate and one passage, and are depicted here for comparison. All mutations are presented in the context of the sense strand of the SARS-CoV-2 genome. C The mutation spectrum of the USA, Alpha, Delta, and Omicron strains. Of these strains, USA, Alpha, and Delta were monitored in duplicate across seven passages, while Omicron was monitored once across one passage. Error bars represent the standard deviation of the mean across the seven passages.