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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Bad call on C00001215 #28

Closed Phelimb closed 9 years ago

Phelimb commented 9 years ago

.

iqbal-lab commented 9 years ago

you mean the gyrA call?

iqbal-lab commented 9 years ago

Did we always make this call?

On 16 December 2014 at 18:19, Phelim Bradley notifications@github.com wrote:

{ "expected_depth": "146", "mean_read_length": "96", "species": { "S. aureus": "166" }, "susceptibility" :{ "Gentamicin": "S", "Penicillin": "R", "Methicillin": "S", "Trimethoprim": "S", "Erythromycin": "S", "FusidicAcid": "S", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "S" }, "called_variants" :{ "gyrA_S84L" :{ "R_per_cov": "100", "S_per_cov": "0", "R_median_cov": "1", "S_median_cov": "0", "conf": "10", "induced_resistance": "Ciprofloxacin" } }, "called_genes" :{ "blaZ" :{ "per_cov": "100", "median_cov": "144", "conf": "429", "induced_resistance": "Penicillin" } }, "virulence_toxins" :{ "PVL": "negative" } }

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/myKrobe-predictor/issues/28.

iqbal-lab commented 9 years ago

I think there is an underlying problem with our gyr backgrounds. Why do we only get covg 0 and 1 at this site?

iqbal-lab commented 9 years ago

I propose we dont fix this til after submission, and maybe not until after the revisions also

Phelimb commented 9 years ago

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iqbal-lab commented 9 years ago

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iqbal-lab commented 9 years ago

kill this bug, handled elsewhere