TB-Profiler result

Run: ERR4819068
Summary

Run ID: ERR4819068

Sample name:

Date: 2024-04-16T09:56:48.433656

Number of reads: 674576

Percentage reads mapped: 78.41

Median coverage: 15.0

Strain: lineage1.1;lineage4.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.37
lineage4.1 Euro-American None 0.43
lineage1.1 Indo-Oceanic RD239 0.37
lineage1 Indo-Oceanic RD239 0.43
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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.4 isoniazid Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.47 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.53 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.47 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.54 streptomycin Uncertain significance
rplC 800357 c.-452C>A upstream_gene_variant 0.62 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.48 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417793 c.-446C>T upstream_gene_variant 0.58 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834021 c.480C>T synonymous_variant 0.33 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.33 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.43 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726051 c.-142G>A upstream_gene_variant 0.43 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.43 ethionamide Uncertain significance
lpqB 3624236 c.675C>A synonymous_variant 0.46 bedaquiline
rifampicin Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.57 pyrazinamide Not assoc w R - Interim
panD 4044788 c.-507G>C upstream_gene_variant 0.29 pyrazinamide
panD 4044791 c.-510G>C upstream_gene_variant 0.29 pyrazinamide
panD 4044800 c.-519C>G upstream_gene_variant 0.3 pyrazinamide
embC 4240671 p.Thr270Ile missense_variant 0.87 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.82 ethambutol Not assoc w R
embB 4247356 c.843C>T synonymous_variant 0.57 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.6 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.56 ethambutol Not assoc w R
whiB6 4338441 p.Tyr27* stop_gained 0.62 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338449 p.Ala25Pro missense_variant 0.67 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.68 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.68 streptomycin Not assoc w R