TB-Profiler result

Run: SRR13837600
Summary

Run ID: SRR13837600

Sample name:

Date: 2025-03-09T09:35:02.407386

Number of reads: 2936695

Percentage reads mapped: 100.0

Median coverage: 99.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 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 katG c.926_927insA Assoc w R High-level resistance
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
katG 2155185 c.926_927insA frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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 8396 p.Tyr365* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13610 c.-52A>C upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 490821 p.Glu13Asp missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 575959 p.Gln204His missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoC 766364 p.Ala999Ser missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775945 p.Val846Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778345 p.Leu46Ile missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778992 c.-512C>T upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpR5 779231 p.Glu81Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800526 c.-283G>T upstream_gene_variant 1.0 linezolid Uncertain significance
fbiC 1303186 p.Tyr86His missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
bacA 2063272 c.1456delC frameshift_variant 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2101749 p.Thr432Ser missense_variant 0.99 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155982 p.Asn44His missense_variant 1.0 isoniazid Uncertain significance
PPE35 2168042 c.2571G>C synonymous_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169365 c.1248C>T synonymous_variant 1.0 pyrazinamide Uncertain significance
Rv2477c 2784596 c.-554A>T upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
thyX 3067878 p.Val23Gly missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
fbiD 3339188 p.Thr24Ser missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
whiB7 3568496 p.Pro62Ser missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612323 p.Pro265Gln missense_variant 1.0 pyrazinamide Uncertain significance
fbiA 3641121 c.579C>A synonymous_variant 1.0 clofazimine Not assoc w R - Interim
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4038346 p.Glu787* stop_gained 1.0 pyrazinamide Uncertain significance
glpK 4139375 p.Asp127Glu missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
glpK 4139545 p.Leu71Val missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4238896 c.-967C>A upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4239894 p.Ala11Gly missense_variant 1.0 ethambutol Uncertain significance
ethA 4327073 p.Leu134Pro missense_variant 1.0 ethionamide Uncertain significance