Point mutations for multiple nucleotides are not reported if a reference base matches a mutated base

[guillaume-bugseq]

We ran into this issue when trying to add a tri-nucleotide mutation to our AMR database in a 16S rRNA. 16S_AGA1928TTC works, but 16S_AGA1928GGC does not. I suspect this is caused by the unaffected G nucleotide in the middle.

[vbrover]

AMRFinderPlus considers this mutation as two point mutations: 16S_A1928G and 16S_A1930C.
This is an interesting case which needs our investigation.

[evolarjun]

@guillaume-bugseq Thanks for reporting this. I hadn't considered wanting to do that before. Could you elaborate as to why you're calling the allele 16S_AGA1928GGC instead of 16S_A1928G and 16S_A1930C?