TB-Profiler result

Run: SRR12199395
Summary

Run ID: SRR12199395

Sample name:

Date: 2024-10-05T03:34:25.190981

Number of reads: 298513

Percentage reads mapped: 94.57

Median coverage: 7.0

Strain: lineage1.2.2.2

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 0.99
lineage1.2.2.2 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 1.0
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 6960 p.Gln574Arg missense_variant 0.9 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13606 c.-48C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv0010c 13699 c.-141A>G upstream_gene_variant 1.0 isoniazid Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2170048 p.Leu189Val missense_variant 0.67 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.59 pyrazinamide
Rv1979c 2223553 c.-389C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3626467 c.147G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim