search

iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
Other
50 stars 19 forks source link

Question about resistance report. R vs r #144

Closed harrismia closed 6 years ago

harrismia commented 6 years ago

Hi, 

    What is the difference between R  vs   r   in the resistance report?

For example see Quinolones in the report below: Thanks.

Probe sets :tb-species-170421.fasta.gz,tb-walker-probe-set-feb-09-2017.fasta.gz

Drug susceptibility: 

Rifampicin  R   rpoB_S450L-S450L    rpoB_S450F-S450F    rpoB_S450I-S450I    
Streptomycin    R   rpsL_K43R-K43R  
Amikacin    S   
Ethambutol  R   embB_M306V-M306V    
Kanamycin   S   
Pyrazinamide    R   pncA_Q141P-Q141P    
Isoniazid   R   katG_S315T-S315T    katG_S315N-S315N    
Capreomycin S   
Quinolones  r   
lineage Beijing_East_Asia
species Mycobacterium_tuberculosis
sub_complex Unknown
phylo_group Mycobacterium_tuberculosis_complex_
iqbal-lab commented 6 years ago

Lower case r means we detect an allele, but at a low/minor within-sample frequency. For example if we had 100x depth, and we saw 20x on a resistance allele, we would report it as r, as it would be more likely to be a low frequency allele than a sequencing error.

Please reopen if this is unclear

harrismia commented 6 years ago

Thanks for the explanation! When there is a r there is no variant reported. Is this expected?