TB-Profiler result

Run: SRR15364434
Summary

Run ID: SRR15364434

Sample name:

Date: 2025-03-07T00:32:28.095729

Number of reads: 2190607

Percentage reads mapped: 99.67

Median coverage: 56.0

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 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 rpoB p.Gln432Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.392_423delTCGGTATTGCCACCGATCATTGTGTGCGCCAG Assoc w R
c.392_423delTCGGTATTGCCACCGATCATTGTGTGCGCCAG Assoc w R
streptomycin gid p.Gln125* Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Asp461His Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Asp461His Assoc w R - Interim
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
gyrB 6620 p.Asp461His missense_variant 0.99 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761101 p.Gln432Pro missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288818 c.392_423delTCGGTATTGCCACCGATCATTGTGTGCGCCAG frameshift_variant 1.0 pyrazinamide Assoc w R
pncA 2288818 c.392_423delTCGGTATTGCCACCGATCATTGTGTGCGCCAG frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 0.98 isoniazid Uncertain significance Mutation from literature
gid 4407830 p.Gln125* stop_gained 1.0 streptomycin 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7381 p.Ser27Thr missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 574906 c.-442G>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
nusG 734471 p.Leu73Arg missense_variant 1.0 rifampicin Uncertain significance
rplC 801355 p.His183Tyr missense_variant 1.0 linezolid Uncertain significance
embR 1417263 p.Pro29Thr missense_variant 0.98 ethambutol 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
ahpC 2726109 c.-84T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
embB 4248465 p.Ser651Asn missense_variant 1.0 ethambutol Uncertain significance
ethA 4326288 p.Asp396Tyr missense_variant 1.0 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