TB-Profiler result

Run: SRR13837709
Summary

Run ID: SRR13837709

Sample name:

Date: 2024-04-15T10:14:31.946820

Number of reads: 297239

Percentage reads mapped: 97.11

Median coverage: 10.0

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 497 p.Thr166Ser missense_variant 1.0 isoniazid
dnaA 558 c.558G>T synonymous_variant 1.0 isoniazid
gyrB 5333 p.Met32Val missense_variant 1.0 levofloxacin
moxifloxacin
rpoC 766954 c.3586delG frameshift_variant 1.0 rifampicin
rplC 801220 p.Ser138Gly missense_variant 0.94 linezolid
fbiC 1303494 p.Leu188Phe missense_variant 1.0 clofazimine
pretomanid
delamanid
fabG1 1673622 p.Asp61Glu missense_variant 1.0 ethionamide
isoniazid
fabG1 1673718 c.279_280insT frameshift_variant&stop_gained 1.0 ethionamide
isoniazid
katG 2155998 p.Trp38Cys missense_variant 1.0 isoniazid
katG 2156285 c.-174T>G upstream_gene_variant 1.0 isoniazid
ahpC 2726085 c.-108G>A upstream_gene_variant 1.0 isoniazid
ribD 2987458 p.Val207Ala missense_variant 1.0 para-aminosalicylic_acid
Rv2681 2997953 c.1215C>G synonymous_variant 1.0 capreomycin
lpqB 3623213 p.Trp566Cys missense_variant 1.0 bedaquiline
rifampicin
mtrA 3627307 p.Ala15Ser missense_variant 1.0 bedaquiline
rifampicin
alr 3840445 p.Leu326Met missense_variant 1.0 cycloserine
panD 4044216 c.65_66insT frameshift_variant 1.0 pyrazinamide Uncertain significance
embB 4247289 p.Ala259Gly missense_variant 1.0 ethambutol
ubiA 4270024 c.-191T>G upstream_gene_variant 1.0 ethambutol