Meaning of hyphen in amino acid substitution report

Question

flashton2003 opened this issue 4 years ago · 3 comments

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

Answer 1 · 2020-12-07T10:35:48.000Z

Hi Phil,

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

Martin

Answer 2 · 2020-12-07T13:38:57.000Z

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

Answer 3 · 2020-12-07T13:47:21.000Z

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.