Meaning of hyphen in amino acid substitution report

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Antibiotic resistance prediction in minutes

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Closed flashton2003 closed 3 years ago

flashton2003 commented 3 years ago

Hello,

I've noticed that a few of my samples have something like a pncA_T-12C, and I was just wondering what the - between the T and 12 means?

To give an example of the full call, it's pncA_T-12C-A2289253G:0:1013:5961.

It also happens for isoniazid muations e.g. fabG1_C-15X-C1673425T:0:447:3402.

Thanks!

Phil

martinghunt commented 3 years ago

Hi Phil,

Negative numbers mean upstream of the gene. So those are 12bp and 15bp before the start of the pncA/fabG1 genes.

Martin

flashton2003 commented 3 years ago

Awesome, thanks Martin! Sorry if I missed that in the documentation somewhere.

martinghunt commented 3 years ago

I'm sure you didn't miss it! Thanks for pointing it out though, I just added a note in the AMR prediciton output wiki page.