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Percent of high-quality reads aligning to SARS-CoV-2 in each metagenomic sample

For each metagenomic sample, this plot shows the percent of all high-quality reads (reads that passed pre-processing) that align with high mapping quality to SARS-CoV-2. Points are colored according to the date that sample was collected.

Click on points in the Collection date legend to subset only to samples collected on specific dates, and use the dropdown to select samples isolated from particular sources. Mouseover points on the plot for details about individual samples.

Note that the y-axis uses a symlog scale.

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.