TB-Profiler result

Run: ERR4796732
Summary

Run ID: ERR4796732

Sample name:

Date: 2025-03-07T12:39:23.432934

Number of reads: 2410849

Percentage reads mapped: 99.82

Median coverage: 73.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.99
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 rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.97 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.97 pyrazinamide Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.94 ethambutol Assoc w R
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
dnaA 468 c.468C>T synonymous_variant 0.96 isoniazid Uncertain significance
dnaA 1139 p.Thr380Ile missense_variant 0.96 isoniazid Uncertain significance
gyrB 6902 p.Leu555Val missense_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764833 p.Glu488Asp missense_variant 0.97 rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102072 c.969_970dupGG frameshift_variant 0.99 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
Rv3083 3449713 p.Ala404Thr missense_variant 0.99 ethionamide Uncertain significance
rpoA 3878418 p.Phe30Leu missense_variant 0.99 rifampicin Uncertain significance
embC 4239933 p.Ala24Glu missense_variant 0.98 ethambutol Uncertain significance
embC 4239939 p.Tyr26Cys missense_variant 0.98 ethambutol Uncertain significance
embA 4243616 c.384C>G synonymous_variant 0.97 ethambutol Uncertain significance
ethA 4327269 p.Trp69Arg missense_variant 0.97 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
gid 4408126 p.Leu26Trp missense_variant 0.96 streptomycin Uncertain significance