TB-Profiler result

Run: ERR4553782
Summary

Run ID: ERR4553782

Sample name:

Date: 2024-03-27T05:59:58.966199

Number of reads: 1987446

Percentage reads mapped: 99.54

Median coverage: 67.0

Strain: lineage1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.97
lineage1.1 Indo-Oceanic RD239 0.3
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser347Thr Uncertain significance Mutation from literature
pyrazinamide pncA p.His82Asp Uncertain significance Mutation from literature
p.Tyr34Asp Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288998 p.His82Asp missense_variant 0.27 pyrazinamide Uncertain significance Mutation from literature
pncA 2289142 p.Tyr34Asp missense_variant 0.41 pyrazinamide Assoc w R
embB 4247553 p.Ser347Thr missense_variant 0.49 ethambutol Uncertain significance Mutation from literature
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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.96 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13640 c.-82T>C upstream_gene_variant 0.97 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576675 p.Arg443His missense_variant 1.0 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.88 ethionamide
rpoB 759886 p.Pro27His missense_variant 1.0 rifampicin Uncertain significance
rpoB 761005 p.Thr400Asn missense_variant 0.95 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.88 rifampicin Not assoc w R
rpoC 766042 c.2673C>T synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoC 767308 c.3939C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778099 p.Asp128Asn missense_variant 0.98 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.98 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407190 c.122_150delNNNNNNNNNNNNNNNNNNNNNNNNNNNNA frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1407190 c.123_150delTGGGCAGGCCTCGATCGTGGCCAGTGCG frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1416574 c.774A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.95 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.93 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518132 c.18C>T synonymous_variant 0.97 isoniazid
ahpC 2726590 p.Arg133His missense_variant 0.98 isoniazid Uncertain significance
ald 3086767 c.-53A>T upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4243056 p.Pro1065Leu missense_variant 1.0 ethambutol Uncertain significance
embA 4243848 p.Val206Met missense_variant 0.98 ethambutol Not assoc w R
embA 4245314 c.2082G>C synonymous_variant 0.99 ethambutol Not assoc w R - Interim
ubiA 4269133 p.Gly234Val missense_variant 0.95 ethambutol Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.92 streptomycin Not assoc w R - Interim
gid 4408252 c.-50A>G upstream_gene_variant 1.0 streptomycin Uncertain significance
gid 4408338 c.-136A>G upstream_gene_variant 1.0 streptomycin