HIV-AAPcnt

Amino acid prevalence data of HIV-1 pol.

Steps and Criteria for Classifying Unusual Mutations

First we calculate the prevalence of an amino acid at a position:

1. Same amino acid at the same position from a single person is only counted once. (PatientPerMutCount)
2. Multiple Amino acids at the same position from a single sample are not counted. (excludeMixtures)
3. Stop codons are not counted. (excludeStopCodons)

In general, an amino acid at a position with its prevalence < 0.01% is considered unusual, with the following exceptions:

1. It is possessed with drug resistance score in HIVDB algorithm;
2. It is considered as a signature APOBEC-mediated hypermutation.