TB-Profiler result

Run: SRR6964676
Summary

Run ID: SRR6964676

Sample name:

Date: 2024-04-16T03:52:40.866080

Number of reads: 3716542

Percentage reads mapped: 99.71

Median coverage: 77.0

Strain: lineage3;lineage4.9

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.15
lineage4 Euro-American None 0.84
lineage4.9 Euro-American (H37Rv-like) None 0.85
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA p.Ser94Ala Assoc w R - Interim
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
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin Assoc w R
inhA 1674481 p.Ser94Ala missense_variant 0.83 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.43 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9163 p.Pro621Leu missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.16 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834856 p.Glu439Lys missense_variant 0.15 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.15 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.2 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288950 p.Ala98Ser missense_variant 0.15 pyrazinamide
pncA 2289047 c.195C>T synonymous_variant 0.2 pyrazinamide Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.18 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.12 cycloserine
ddn 3986818 c.-26G>T upstream_gene_variant 0.16 delamanid Uncertain significance
pretomanid
panD 4044872 c.-591C>T upstream_gene_variant 0.19 pyrazinamide
glpK 4139116 p.Asp214Tyr missense_variant 0.37 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.572dupG frameshift_variant 0.59 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 0.12 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
gid 4407588 c.615A>G synonymous_variant 0.19 streptomycin Not assoc w R