TB-Profiler result

Run: SRR13837490
Summary

Run ID: SRR13837490

Sample name:

Date: 2025-03-08T08:09:04.856132

Number of reads: 2936547

Percentage reads mapped: 100.0

Median coverage: 98.0

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 Uncertain significance
dnaA 558 c.558G>T synonymous_variant 1.0 isoniazid Uncertain significance
gyrB 5333 p.Met32Val missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
ccsA 620509 p.Thr207Ser missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620749 p.Trp287Arg missense_variant 0.99 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
rpoC 766954 c.3586delG frameshift_variant 1.0 rifampicin Uncertain significance
mmpL5 776080 p.Ala801Pro missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801220 p.Ser138Gly missense_variant 1.0 linezolid Uncertain significance
fbiC 1303494 p.Leu188Phe missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrl 1476502 n.2845G>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673622 c.-580C>A upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673718 c.-484_-483insT upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155998 p.Trp38Cys missense_variant 1.0 isoniazid Uncertain significance
katG 2156285 c.-174T>G upstream_gene_variant 1.0 isoniazid Uncertain significance
ahpC 2726085 c.-108G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2477c 2782501 c.1542T>C synonymous_variant 1.0 amikacin Not assoc w R - Interim
ethambutol Uncertain significance
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Uncertain significance
ribD 2987458 p.Val207Ala missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2681 2997953 c.1215C>G synonymous_variant 1.0 capreomycin Uncertain significance
Rv3236c 3612721 c.395delT frameshift_variant 1.0 pyrazinamide Uncertain significance
lpqB 3623213 p.Trp566Cys missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625250 p.Leu455Gln missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627307 p.Ala15Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3840445 p.Leu326Met missense_variant 0.99 cycloserine Uncertain significance
alr 3841156 p.Leu89Val missense_variant 1.0 cycloserine Uncertain significance
rpoA 3877966 p.Thr181Asn missense_variant 1.0 rifampicin Uncertain significance
panD 4044216 c.65_66insT frameshift_variant 1.0 pyrazinamide Uncertain significance
glpK 4138295 p.Trp487Cys missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embB 4247289 p.Ala259Gly missense_variant 1.0 ethambutol Uncertain significance
embB 4249154 p.Gly881Arg missense_variant 1.0 ethambutol Uncertain significance
ubiA 4270024 c.-191T>G upstream_gene_variant 1.0 ethambutol Uncertain significance