Spatiotemporal structure of SARS-CoV-2 mutational frequencies in wastewater samples from Ontario

These data are provided in support of a manuscript in progress. The files are generally derived from the frequencies of SARS-CoV-2 mutations observed in next-generation sequence data derived from wastewater samples collected from the province of Ontario, Canada, along with metadata. A brief description of each file follows: sample_metadata.json - a JSON file associating each sample name to sample collection date and location of sampling (siteID) site_metadata.json - a JSON file associating each site ID to the full site name, latitude and longitude, public health region, municipality, and estimated sewershed population size coverage_all.csv.gz - a gzip-compressed CSV file with read depths for every genome coordinate, by sample (integer index) coverage_meta.csv - a CSV file associating integer indices to sample metadata count_mutations.csv - a CSV file with numbers of each type of mutation (insertion, deletion, non-synonymous and synonymous nucleotide substitutions) per sample count_reads.csv: a CSV file with the total number of reads mapped to the reference genome per sample heatmap.csv: a CSV file with the data required to generate a heatmap visualization of mutation frequencies over time, limited to mutations with an overall mean frequency between 5% and 95% over the study period. all-mutation-counts.csv: a CSV file listing the frequencies that mutations were observed in any sample, given a minimum read depth of 100 reads and a minimum relative frequency of 1%. Note a "~" prefix indicates a substitution, followed by its reference nucleotide coordinate and derived nucleotide. The "+" and "-" prefixes indicate insertions and deletions, respectively, with a ".N" suffix giving the length of the indel. dot-product.csv: a CSV file of the matrix of normalized dot products between every sample, excluding one outlier (n=1,587). dot-prod.meta.csv: a CSV file of metadata for the n=1,857 samples represented by the dot product matrix