TB-Profiler result

Run: SRR13837667
Summary

Run ID: SRR13837667

Sample name:

Date: 2025-03-05T03:19:52.427889

Number of reads: 2936466

Percentage reads mapped: 100.0

Median coverage: 98.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 ethA p.Ser424* Assoc w R
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
ethA 4326203 p.Ser424* stop_gained 1.0 ethionamide 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 1057 p.Val353Leu missense_variant 1.0 isoniazid Uncertain significance
gyrB 5532 c.295dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 5832 p.Ala198Gly missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 6976 c.-326A>G upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
ccsA 619735 c.-156G>C upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620100 c.210G>T synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
rpoB 759609 c.-198C>A upstream_gene_variant 1.0 rifampicin Uncertain significance
rpoC 763050 c.-320C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
mmpL5 776796 p.Val562Ala missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 778642 p.Trp88* stop_gained 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1258c 1407009 p.Ala111Asp missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
inhA 1674891 p.Trp230Cys missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1918625 p.Pro229Leu missense_variant 1.0 capreomycin Uncertain significance
ndh 2103309 c.-267C>T upstream_gene_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
Rv1979c 2222721 c.444G>C synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ahpC 2726345 p.Phe51Leu missense_variant 0.99 isoniazid Uncertain significance
Rv2477c 2783258 c.784delC frameshift_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2784427 c.-385T>C upstream_gene_variant 0.99 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2752c 3066881 c.-690C>A upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3067095 c.-904G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv3083 3448912 p.Ile137Phe missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568676 p.Ser2Ala missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
lpqB 3624303 p.Leu203Arg missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626528 p.Ala29Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3840783 c.637_638insT frameshift_variant 1.0 cycloserine Uncertain significance
clpC1 4038326 p.Glu793Asp missense_variant 1.0 pyrazinamide Uncertain significance
panD 4044544 c.-263G>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
glpK 4138911 p.Gly282Val missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4241026 c.1164C>G synonymous_variant 1.0 ethambutol Uncertain significance
embA 4242250 c.-983C>G upstream_gene_variant 1.0 ethambutol Uncertain significance
embB 4247398 c.885G>T synonymous_variant 1.0 ethambutol Uncertain significance
embB 4249328 p.Met939Leu missense_variant 1.0 ethambutol Uncertain significance
aftB 4267490 c.1347G>C synonymous_variant 1.0 ethambutol Uncertain significance