If you want to see how well a specific organism is represented in your sample, you can perform whole-genome alignment against any organism in the One Codex Database.

In addition to the coverage plot showing where the reads align across the genome, we calculate a set of summary statistics:

  • Sequencing depth: The average number of reads piled up at every position in the genome

  • Genome coverage: The percentage of the genome that is covered by the reads or contigs

  • Nucleotide identity: The similarity of the sample to the reference genome (including SNPs and insertion/deletions)

Take a look through an example alignment!

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