TB-Profiler result

Run: SRR12199432
Summary

Run ID: SRR12199432

Sample name:

Date: 2024-04-15T17:15:16.981905

Number of reads: 329029

Percentage reads mapped: 97.83

Median coverage: 8.0

Strain: lineage1.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.91
lineage1 Indo-Oceanic RD239 0.52
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrB 5075 c.-165C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 5155 c.-85G>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13460 c.99T>C synonymous_variant 0.93 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.9 isoniazid Not assoc w R
fgd1 490639 c.-144C>T upstream_gene_variant 0.73 clofazimine
pretomanid
delamanid
nusG 734116 c.-138T>C upstream_gene_variant 0.83 rifampicin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.91 linezolid Not assoc w R
rplC 800444 c.-365C>G upstream_gene_variant 1.0 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.58 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.54 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726051 c.-142G>A upstream_gene_variant 0.88 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
glpK 4138377 p.Val460Ala missense_variant 0.92 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.85 ethambutol Not assoc w R
aftB 4268468 c.369G>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.61 ethambutol Not assoc w R
whiB6 4338203 p.Arg107Cys missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R