TB-Profiler result

Run: SRR9613542
Summary

Run ID: SRR9613542

Sample name:

Date: 2024-10-03T20:58:42.433744

Number of reads: 3203169

Percentage reads mapped: 99.99

Median coverage: 53.0

Strain: lineage4.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 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.His445Tyr Assoc w R
isoniazid ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
streptomycin gid c.586_595dupTTGCGTCCGC Assoc w R
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 761139 p.His445Tyr missense_variant 1.0 rifampicin Assoc w R
pncA 2288850 c.390_391dupGG frameshift_variant 0.98 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.96 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.98 ethambutol Assoc w R
gid 4407607 c.586_595dupTTGCGTCCGC frameshift_variant 0.89 streptomycin 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 968 p.Glu323Gly 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9757 p.Ala819Gly missense_variant 0.97 levofloxacin
moxifloxacin
fgd1 491194 c.412C>T synonymous_variant 0.89 pretomanid
delamanid
clofazimine
mshA 575662 c.315C>A synonymous_variant 0.93 isoniazid
ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
hadA 732173 p.Ala82Thr missense_variant 0.92 isoniazid
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254056 p.Asp160Ala missense_variant 0.99 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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 2154644 p.Gly490Cys missense_variant 1.0 isoniazid
katG 2155727 p.Phe129Leu missense_variant 0.94 isoniazid
PPE35 2168077 p.Thr846Ala missense_variant 0.98 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747022 p.Val193Ile missense_variant 0.93 para-aminosalicylic_acid
Rv2752c 3065405 p.Gly263Ser missense_variant 0.94 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449815 p.Gln438* stop_gained 0.98 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641164 p.Ile208Val missense_variant 0.97 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4038413 c.2292C>T synonymous_variant 0.98 pyrazinamide
embC 4241111 p.Val417Met missense_variant 0.96 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin