Mercurial > repos > jpayne > refchooser
diff test-data/test/resistance/UCLA_1626_resfinder/pheno_table.txt @ 0:91bc7378c1c5 draft
planemo upload commit c5b9a5678302366ab392fc9b24104509beb07c38-dirty
| author | jpayne |
|---|---|
| date | Mon, 11 Aug 2025 15:37:26 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test/resistance/UCLA_1626_resfinder/pheno_table.txt Mon Aug 11 15:37:26 2025 +0000 @@ -0,0 +1,109 @@ +# ResFinder phenotype results. +# Sample: UCLA_1626.fa +# +# The phenotype 'No resistance' should be interpreted with +# caution, as it only means that nothing in the used +# database indicate resistance, but resistance could exist +# from 'unknown' or not yet implemented sources. +# +# The 'Match' column stores one of the integers 0, 1, 2, 3. +# 0: No match found +# 1: Match < 100% ID AND match length < ref length +# 2: Match = 100% ID AND match length < ref length +# 3: Match = 100% ID AND match length = ref length +# If several hits causing the same resistance are found, +# the highest number will be stored in the 'Match' column. + +# Antimicrobial Class WGS-predicted phenotype Match Genetic background +gentamicin aminoglycoside No resistance 0 +tobramycin aminoglycoside No resistance 0 +streptomycin aminoglycoside No resistance 0 +amikacin aminoglycoside No resistance 0 +isepamicin aminoglycoside No resistance 0 +dibekacin aminoglycoside No resistance 0 +kanamycin aminoglycoside No resistance 0 +neomycin aminoglycoside No resistance 0 +lividomycin aminoglycoside No resistance 0 +paromomycin aminoglycoside No resistance 0 +ribostamycin aminoglycoside No resistance 0 +unknown aminoglycoside aminoglycoside No resistance 0 +butiromycin aminoglycoside No resistance 0 +butirosin aminoglycoside No resistance 0 +hygromycin aminoglycoside No resistance 0 +netilmicin aminoglycoside No resistance 0 +apramycin aminoglycoside No resistance 0 +sisomicin aminoglycoside No resistance 0 +arbekacin aminoglycoside No resistance 0 +kasugamycin aminoglycoside No resistance 0 +astromicin aminoglycoside No resistance 0 +fortimicin aminoglycoside No resistance 0 +spectinomycin aminocyclitol No resistance 0 +fluoroquinolone quinolone No resistance 0 +ciprofloxacin quinolone No resistance 0 +unknown quinolone quinolone No resistance 0 +nalidixic acid quinolone No resistance 0 +amoxicillin beta-lactam Resistant 2 blaOXA-61 (blaOXA-61_AY587956) +amoxicillin+clavulanic acid beta-lactam Resistant 2 blaOXA-61 (blaOXA-61_AY587956) +ampicillin beta-lactam Resistant 2 blaOXA-61 (blaOXA-61_AY587956) +ampicillin+clavulanic acid beta-lactam Resistant 2 blaOXA-61 (blaOXA-61_AY587956) +cefepime beta-lactam No resistance 0 +cefixime beta-lactam No resistance 0 +cefotaxime beta-lactam No resistance 0 +cefoxitin beta-lactam No resistance 0 +ceftazidime beta-lactam No resistance 0 +ertapenem beta-lactam No resistance 0 +imipenem beta-lactam No resistance 0 +meropenem beta-lactam No resistance 0 +piperacillin beta-lactam No resistance 0 +piperacillin+tazobactam beta-lactam No resistance 0 +unknown beta-lactam beta-lactam Resistant 2 blaOXA-193 (blaOXA-193_CP013032), blaOXA-489 (blaOXA-489_CP013733), blaOXA-453 (blaOXA-453_KR061507), blaOXA-452 (blaOXA-452_KR061505), blaOXA-451 (blaOXA-451_KR061504), blaOXA-450 (blaOXA-450_KR061502) +aztreonam beta-lactam No resistance 0 +cefotaxime+clavulanic acid beta-lactam No resistance 0 +temocillin beta-lactam No resistance 0 +ticarcillin beta-lactam No resistance 0 +ceftazidime+avibactam beta-lactam No resistance 0 +penicillin beta-lactam No resistance 0 +ceftriaxone beta-lactam No resistance 0 +ticarcillin+clavulanic acid beta-lactam No resistance 0 +cephalothin beta-lactam No resistance 0 +cephalotin beta-lactam No resistance 0 +piperacillin+clavulanic acid beta-lactam No resistance 0 +ceftiofur under_development No resistance 0 +sulfamethoxazole folate pathway antagonist No resistance 0 +trimethoprim folate pathway antagonist No resistance 0 +fosfomycin fosfomycin No resistance 0 +vancomycin glycopeptide No resistance 0 +teicoplanin glycopeptide No resistance 0 +bleomycin glycopeptide No resistance 0 +lincomycin lincosamide No resistance 0 +clindamycin lincosamide No resistance 0 +dalfopristin streptogramin a No resistance 0 +pristinamycin iia streptogramin a No resistance 0 +virginiamycin m streptogramin a No resistance 0 +quinupristin+dalfopristin streptogramin a No resistance 0 +tiamulin pleuromutilin No resistance 0 +carbomycin macrolide No resistance 0 +erythromycin macrolide No resistance 0 +azithromycin macrolide No resistance 0 +oleandomycin macrolide No resistance 0 +spiramycin macrolide No resistance 0 +tylosin macrolide No resistance 0 +telithromycin macrolide No resistance 0 +tetracycline tetracycline Resistant 3 tet(O) (tet(O)_M18896) +doxycycline tetracycline Resistant 3 tet(O) (tet(O)_M18896) +minocycline tetracycline Resistant 3 tet(O) (tet(O)_M18896) +tigecycline tetracycline No resistance 0 +quinupristin streptogramin b No resistance 0 +pristinamycin ia streptogramin b No resistance 0 +virginiamycin s streptogramin b No resistance 0 +linezolid oxazolidinone No resistance 0 +chloramphenicol amphenicol No resistance 0 +florfenicol amphenicol No resistance 0 +colistin polymyxin No resistance 0 +fusidic acid steroid antibacterial No resistance 0 +mupirocin pseudomonic acid No resistance 0 +rifampicin rifamycin No resistance 0 +metronidazole nitroimidazole No resistance 0 +narasin ionophores No resistance 0 +salinomycin ionophores No resistance 0 +maduramicin ionophores No resistance 0