TB-Profiler result

Run: SRR12199442

Summary

Run ID: SRR12199442

Sample name:

Date: 2025-02-11T16:07:28.133835

Number of reads: 607536

Percentage reads mapped: 98.45

Median coverage: 10.0

Strain: lineage1.2.2

Spoligotype:

Drug-resistance: Sensitive


Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.51
lineage1.2.2 Indo-Oceanic RD239 0.05
lineage1 Indo-Oceanic RD239 0.89
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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.62 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.82 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.92 rifampicin Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364463 c.52_53delGT frameshift_variant 0.75 pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.9 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.8 isoniazid
ribD 2986898 c.60G>A synonymous_variant 0.8 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.83 ethionamide Uncertain significance
whiB7 3568488 c.191delG frameshift_variant 0.83 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
panD 4044878 c.-597C>T upstream_gene_variant 0.75 pyrazinamide
ubiA 4269387 p.Glu149Asp missense_variant 0.83 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.97 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 0.64 ethambutol Not assoc w R