TB-Profiler result

Run: SRR13837964
Summary

Run ID: SRR13837964

Sample name:

Date: 2025-03-06T06:15:33.993662

Number of reads: 1468210

Percentage reads mapped: 100.0

Median coverage: 50.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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 9502 p.Arg734His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13527 p.Ser11* stop_gained 1.0 isoniazid Uncertain significance
rpoB 759681 c.-126C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoB 761239 p.Cys478Tyr missense_variant 1.0 rifampicin Uncertain significance
mmpL5 776185 p.Lys766Glu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
embR 1417986 c.-639T>A upstream_gene_variant 1.0 ethambutol Uncertain significance
tlyA 1918063 p.Pro42Ala missense_variant 1.0 capreomycin Uncertain significance
ndh 2102985 p.Ile20Val missense_variant 0.98 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155856 p.Thr86Ser missense_variant 0.98 isoniazid Uncertain significance
PPE35 2169233 c.1379delT frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv2752c 3065376 c.815delT frameshift_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066351 c.-160G>T upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyX 3067731 p.Val72Ala missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
thyX 3067825 p.Arg41Gly missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv3083 3448707 c.204G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv3083 3449768 p.Thr422Lys missense_variant 1.0 ethionamide Uncertain significance
lpqB 3623219 c.1692A>G synonymous_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627790 c.-441A>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiB 3641403 c.-132C>T upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3841257 p.His55Leu missense_variant 1.0 cycloserine Uncertain significance
rpoA 3877601 p.Gln303* stop_gained 1.0 rifampicin Uncertain significance
ddn 3986668 c.-176T>C upstream_gene_variant 1.0 delamanid Uncertain significance
pretomanid Uncertain significance
embC 4239401 c.-462A>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4241864 p.Leu668Met missense_variant 1.0 ethambutol Uncertain significance
embB 4245557 c.-957G>A upstream_gene_variant 1.0 ethambutol Uncertain significance
ethA 4327092 p.Ala128Pro missense_variant 1.0 ethionamide Uncertain significance
gid 4408151 p.Leu18Val missense_variant 1.0 streptomycin Uncertain significance