TB-Profiler result

Run: SRR6824479
Summary

Run ID: SRR6824479

Sample name:

Date: 2024-04-15T20:15:32.553447

Number of reads: 10445256

Percentage reads mapped: 99.38

Median coverage: 307.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-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 rpoB p.Ser450Leu Assoc w R
isoniazid ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Lys48Glu Assoc w R - Interim
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
pncA 2289100 p.Lys48Glu missense_variant 0.59 pyrazinamide Assoc w R - Interim
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
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 796 p.Asp266His missense_variant 1.0 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
mshA 576612 p.Ala422Val missense_variant 1.0 ethionamide
isoniazid
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
rpoB 762427 p.Ser874Tyr missense_variant 1.0 rifampicin Uncertain significance
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
fbiC 1303436 p.Ser169Phe missense_variant 0.99 clofazimine
pretomanid
delamanid
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 2154181 p.Gly644Asp missense_variant 1.0 isoniazid Uncertain significance
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
folC 2747195 p.Asp135Ala missense_variant 1.0 para-aminosalicylic_acid
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
clpC1 4040498 c.207G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
embC 4241584 p.Ile574Met missense_variant 1.0 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243526 c.294G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embA 4243760 p.Asp176Glu missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.43 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.57 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.43 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.57 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 4408115 p.Gly30Arg missense_variant 1.0 streptomycin Uncertain significance