TB-Profiler result

Run: ERR4817562
Summary

Run ID: ERR4817562

Sample name:

Date: 2024-04-15T18:55:06.907984

Number of reads: 4591317

Percentage reads mapped: 99.54

Median coverage: 102.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American 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 ahpC c.-57C>T Uncertain significance Mutation from literature
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
ahpC 2726136 c.-57C>T upstream_gene_variant 0.45 isoniazid 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
dnaA 1495 p.Thr499Ala missense_variant 0.56 isoniazid Uncertain significance
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 7892 c.591G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
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
Rv1258c 1407380 c.-40C>T upstream_gene_variant 0.38 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide
embR 1416611 p.Thr246Lys missense_variant 0.5 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833734 p.Ala65Thr missense_variant 0.54 pyrazinamide
rpsA 1834112 p.Leu191Val missense_variant 0.16 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
katG 2154144 c.1968C>T synonymous_variant 0.5 isoniazid Not assoc w R - Interim
katG 2155844 p.Trp90Arg missense_variant 0.47 isoniazid Uncertain significance
katG 2155847 p.Pro89Ser missense_variant 0.46 isoniazid
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide 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
eis 2714211 c.1122G>A synonymous_variant 0.51 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
fbiD 3339480 p.Gln121His missense_variant 0.53 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626807 c.-194G>A upstream_gene_variant 0.47 bedaquiline
rifampicin
fbiA 3640325 c.-218C>T upstream_gene_variant 0.46 clofazimine
pretomanid
delamanid
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
glpK 4138498 c.1258C>T synonymous_variant 0.43 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243482 p.Ala84Ser missense_variant 0.51 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin