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Correlation of mitochondrial composition with SARS-CoV-2 reads for individual species

Correlation across all samples between the percent of all high-quality (preprocessed) reads that align to SARS-CoV-2 versus the percent that align to the mitochondrial genomes for the indicated species. The orange numbers give the Pearson correlation coefficient.

A critical aspect of this plot is the choice of what scale is used to plot the numbers and calculate the correlations. The choices, which are adjustable using the options below the plot, are:

• Quantify the mitochondrial reads is as the percent of all high-quality (preprocessed) reads that map to the mitochondrial genome of that species, or as the percent of reads that align to any chordate mitochondrial genome that align to that species.
• Whether the axis scales show the raw percentages or the log10 of the percentages. When using a log scale, percentages of zero are set to half the lowest observed percentage across all samples and species.

Other at the bottom of the plot enable:

• Selection of samples only from specific collection dates (click on circles next to select).
• Selection of only samples collected from particular sources.
• Selection of samples only with a sufficient number of total aligned mitochondrial reads.
• Which species to show.
• Selection of only samples containing at least one SARS-CoV-2 read.

Mouseover points for details on particular samples.

The correlation coefficients will change accordingly if you select different options for how the percent mitochondrial reads is computed or whether we analyze the direct or log10 percents.

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.