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Fig. 3 | Genome Medicine

Fig. 3

From: Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples

Fig. 3

Sequencing coverage and depth of the cultured isolate and eight clinical samples. a Amplicon sequencing coverage by sample (row) across the SARS-CoV-2 genome. Dark blue, sequencing depth ≥ 100×; heatmap (bottom) sums coverage across all samples. HNA, negative control prepared from human nucleic acids; water, negative control prepared from nuclease-free water. Green horizontal lines on heatmap, amplicon locations. Overlap regions between amplicons range from 59 to 209 bp. bd Normalized coverage across viral genomes of the clinical samples across methods. e SARS-CoV-2-RPM sequence plotted against genome copies per milliliter for the cultured isolate. Three independent experiments were performed for amplicon sequencing. Dark blue, ~ 400 bp amplicon-based sequencing including human and lambda phage nucleic acid background; soft blue, ~ 200 bp amplicon-based sequencing; fluorescent cyan, ~ 400 bp amplicon-based sequencing excluding human and lambda phage nucleic acid background (NAB); red, capture sequencing; grey, meta sequencing. f SARS-CoV-2-RPM (reads per million) sequence plotted against qRT-PCR Ct value for the clinical samples. Dark blue, amplicon; red, capture; grey, meta. g Estimated minimum amount of bases required by each method for high-confidence downstream analyses. Dark blue, amplicon; red, capture

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