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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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Rv0678 and mmpR5 on report file #292

Open cimendes opened 1 year ago

cimendes commented 1 year ago

Hi @jodyphelan!

I've been using the JSON output and parsing it out for downstream validation of the results and I came across something that I found a bit odd.

I'm under the impression that mmpR5 is always referred to as Rv0678 but I came across this example where mmpR5 is referred to instead. Dassie_bacillus02.results.zip

Am I under the wrong impression?

Thank you!

jodyphelan commented 1 year ago

You are not wrong. Rv0678 is the gene id and mmpR5 is the gene name. I think when the bedaquiline resistance mechanisms was first discovered this gene hadn't been annotated properly yet so it only had a gene id (Rv0678). Since then the name kind of stuck and most papers still refer to it by the id. Both are presented in the output:

      ...
      "locus_tag": "Rv0678",
      "gene": "mmpR5",
      ...