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jodyphelan / tbdb

Standard database for the TBProfiler tool
GNU Lesser General Public License v3.0
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get_genome_positions.py output #26

Closed arturotorreso closed 3 years ago

arturotorreso commented 4 years ago

Hi @jodyphelan ,

I'm getting a bit confused with the output of get_genome_positions.py.

For example, a line like the following:

katG p.Ser315Ile isoniazid 2155168 G T

would mean that the nucleotide change G -> T is associated to isoniazid resistance. Are the G and the T as they will appear in the genome, or are they translated from C and A? I'm saying that because when I look at the position 2155168 in the reference genome H37Rv I get a C.

Thanks, Arturo

jodyphelan commented 4 years ago

Hi @arturotorreso

The second last column is the reference the last one is the alternate. In this case because katG is in the reverse direction it uses the reverse complement base.

Jody