a bug maybe? only the first one could be correctly annotated when multiple copies of amr exist

[fengyuchengdu]

Dear all,

The amplification of amr genes seems common and I found that for a sequence containing 3 copies of blaOXA genes, however, only the first one could be correctly labelled as OXA-1041, the rest two could not.

Given that the nucleotide sequences of these 3 blaOXA were identical, this result seemed weird.

I've attached a simple fasta example and the amrfinderplus result to this example in the zip files.
test.zip
test_result.zip

[fengyuchengdu]

3 blaOXA genes are literally identical and why they weren't all labelled "ALLELE" blaOXA-1041?

[evolarjun]

Hi @fengyuchengdu ,

I took a look at the sequences you uploaded and I can reproduce the issue you're reporting. I'm not yet sure what is going on. We'll take a closer look and get back to you.

Thanks for reporting!
Arjun

[vbrover]

Thank you for posting the bug!
It will be fixed in software version 3.10.35.

[fengyuchengdu]

Great ! many thanks to you all.

[evolarjun]

Fixed in version 3.10.36.

Thanks again!