Tbdb.bed vs genome.gff coordinates question

[taranewman]

Hi Jody,

I just wanted to clarify the positions in the https://github.com/jodyphelan/TBProfiler/blob/master/db/tbdb.bed file vs the https://github.com/jodyphelan/TBProfiler/blob/master/db/tbdb.gff file

As an example:

Rv2752c is listed as having an end position 3066191 in the tbdb.gff

Chromosome ena gene 3064515 3066191 . - . ID=gene:Rv2752c;

In the tbdb.bed it is listed as having an end position of 3067372 (but the same start position)

Chromosome 3064515 3067372 Rv2752c Rv2752c levofloxacin,moxifloxacin,isoniazid,rifampicin,ethambutol

Is the difference in end position related to upstream variants that may impact gene resistance?

Another example is Rv0010c

Thank you for your time,
Tara

[jodyphelan]

Hi Tara,

Sorry for the delay in getting back to you. Yes the start position in the bed file contains the upstream region where potential promoter mutations may be.

[taranewman]

Thanks Jody!