When viewing the complete classification results table for a sample, you may notice that some species have a star icon (or a "TRUE" value in the exported results). This indicates that we have high confidence in calling this species in your sample. How do we define that confidence?

For any given species, there will be regions (k-mers) in its genome that are unique to that genome. To consider that genome present at high-confidence, we need to see above a specific proportion of those unique k-mers. This would indicate that we're covering a good proportion of that genome. The more of a genome that you cover, the more confident you can be that the species is there.

In addition to this, we also need to see a minimum number of k-mers that match to that species in your sample. The more k-mers you see for a species, the more sure you can be that that species is there.

The "high-confidence" flag for a species allows you to quickly identify which species have good genome coverage and good depth.