How do we flag to users when there is a resistance mechanism potentially present in their data, that AMRFP (or CARD) is not able to accurately detect?
Example is in gono, where a mutation in one copy of the 23S gene will be an S phenotype, but mutations in multiple copies of 23S will give an R phenotype. AMRFP will be able to detect the mutation, but won't know if the gene is in multiple copies (unless the genome is closed). Therefore we need to flag this type of situation to users, so they can do downstream investigation if required.
How do we flag to users when there is a resistance mechanism potentially present in their data, that AMRFP (or CARD) is not able to accurately detect?
Example is in gono, where a mutation in one copy of the 23S gene will be an S phenotype, but mutations in multiple copies of 23S will give an R phenotype. AMRFP will be able to detect the mutation, but won't know if the gene is in multiple copies (unless the genome is closed). Therefore we need to flag this type of situation to users, so they can do downstream investigation if required.