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!