Correlation between RT-qPCR values reported by Chinese CDC in Supplementary Table 2 from Liu et al (2023) and the log10 percent of all high-quality reads that map to SARS-CoV-2. The plot shows only metagenomic samples that were deep sequenced. Ct values for samples not listed as positive in the Chinese CDC table are assumed to be 40 (the cutoff, since all samples are reported tested), and samples with no SARS-CoV-2 reads in the sequencing are assigned a value half the lowest value for samples with reads to avoid having to plot zero values on a log scale.
Mouseover points for details on specific samples.
See Bloom et al, bioRxiv, DOI 10.1101/2023.04.25.538336 for a paper describing this analysis.
See https://github.com/jbloom/Huanan_market_samples for results files and a fully reproducible computational pipeline.
See https://jbloom.github.io/Huanan_market_samples for links to all interactive plots.