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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Format of Variants Column #123

Open Owen-haha opened 7 years ago

Owen-haha commented 7 years ago

It is difficult to guess the exact meaning of variants column of Mykrobe results. For some examples below fabG1_C-15T-C1673425T:44:83:93 fabG1_T-8C-T1673432C:83:0:99999994 katG_W191G-CCA2155539CCC:172:6:251 Could anyone kindly explain what is the meaning of these results? Thanks!

possible interpretation as below: 1) fabG1/katG is the gene name 2) W191G means the change of amino acid from W->G at locus 191, but not sure of "C-15T" and "T-8C" 3) CCA2155539CCC indicates the codon change from CCA -> CCC at locus 2155539, but not sure of "C1673425T" and "T1673432C" 4) have no idea about the numbers next to colons

Phelimb commented 7 years ago

@Owen-haha is this after the conversion with json_to_tsv?

Do you know which version of Mykrobe your on?

fabG1/katG is the gene name

Yup

W191G means the change of amino acid from W->G at locus 191,

Also correct

but not sure of "C-15T" and "T-8C"

These are DNA mutation upstream of the gene. We used the naming convention of the original paper https://www.ncbi.nlm.nih.gov/pubmed/26116186.

CCA2155539CCC indicates the codon change from CCA -> CCC at locus 2155539

That's correct, so CCA->CCC in DNA space. This is equivalent to A2155541C.

but not sure of "C1673425T" and "T1673432C"

These are also the SNPs in DNA space - there's no codon change here so we only report a single base.

172:6:251

ref-depth:alt-depth:confidence

The depth are measured in number of kmers so not exactly equivalent to read depth (but comparable). The details should be clearer in in the .json format for depth, confidence numbers - I would recommend going back to the original output if you're interested in these.

Owen-haha commented 7 years ago

@Phelimb Thanks very much for the reply! Yep, I looked at the TSV results. The version of Mykrobe is v0.3.6-0-g9d196c7. Another question: What's the meaning of "R/S/D/T" in the column 'alt' of Supplementary Table 15 (Mykrobe predictor resistance panel for M. tuberculosis)? Could you kindly share this table with me? As it is not easy to copy the table directly from the pdf file. It will be very appreciative if you can add one column of genome location.

Owen-haha commented 7 years ago

I have identified some new drug resistant loci of MTB. I want to check whether the loci identified are in the panel or not. It will be really helpful if you can share the latest panel!