Coverage and Identity cut-off explanation

[lauraflows]

Hello everyone,

I've changed the identity percentage cutoff (-id) to 0, 0.2, 0.3, 0.4 while keeping the coverage fixed at 0.5, but the number of matched counts and AAI remains the same. Is it possible for the number of Matched counts to always stay the same?

I also tried using 0 as coverage and varying the identity percentage (0.2, 0.4), but also in this case, the value of matched counts remains identical.

In detail, for my experiments, I would like to see what difference there is between 0.2 and 0.4 as identity cutoffs, and I would expect at least a slight variation in the AAI.

Is there any explanation for this?

Thank you so much.

Laura