TB-Profiler result

Run: SRR13837491
Summary

Run ID: SRR13837491

Sample name:

Date: 2024-10-04T18:09:41.967135

Number of reads: 587726

Percentage reads mapped: 97.01

Median coverage: 20.0

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
dnaA 377 p.Thr126Asn missense_variant 1.0 isoniazid
dnaA 1519 p.Arg507Ser missense_variant 1.0 isoniazid
gyrB 5709 p.Gly157Val missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9028 p.Val576Ala missense_variant 1.0 levofloxacin
moxifloxacin
Rv0565c 657669 c.-199C>A upstream_gene_variant 1.0 ethionamide
mmaA3 737654 p.Ala166Ser missense_variant 1.0 isoniazid
rpoB 762011 c.2205G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762279 c.2474delA frameshift_variant 1.0 rifampicin
mmpS5 778823 p.Ile28Thr missense_variant 1.0 bedaquiline
clofazimine
rplC 800279 c.-530A>C upstream_gene_variant 1.0 linezolid
fbiC 1304640 c.1710A>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1406376 p.Gly322Val missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
PPE35 2169882 p.Ser244Ile missense_variant 1.0 pyrazinamide
eis 2714940 c.392delA frameshift_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
Rv2477c 2782900 c.1143C>G synonymous_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3087311 c.492C>G synonymous_variant 1.0 cycloserine
Rv3236c 3613629 c.-513C>G upstream_gene_variant 1.0 pyrazinamide
fbiB 3642465 p.Asp311His missense_variant 1.0 pretomanid
delamanid
clofazimine
alr 3840300 p.Pro374His missense_variant 1.0 cycloserine
rpoA 3878288 p.Thr74Pro missense_variant 1.0 rifampicin
clpC1 4039415 c.1289dupA frameshift_variant 1.0 pyrazinamide
clpC1 4040792 c.-88A>T upstream_gene_variant 1.0 pyrazinamide
embA 4243235 c.3G>T synonymous_variant 1.0 ethambutol