TB-Profiler result

Run: ERR4553749
Summary

Run ID: ERR4553749

Sample name:

Date: 2024-10-04T05:18:45.114261

Number of reads: 1662369

Percentage reads mapped: 99.55

Median coverage: 54.0

Strain:

Spoligotype:

Drug-resistance: RR-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 0.96
lineage1.1.3.1 Indo-Oceanic RD239 0.95
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
isoniazid
ethambutol
pyrazinamide pncA p.Tyr41* Assoc w R
streptomycin gid c.104dupT Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Tyr140* Assoc w R
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 761095 p.Leu430Pro missense_variant 0.98 rifampicin Assoc w R
pncA 2289119 p.Tyr41* stop_gained 1.0 pyrazinamide Assoc w R
ethA 4327054 p.Tyr140* stop_gained 0.96 ethionamide Assoc w R
gid 4408098 c.104dupT frameshift_variant 0.97 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
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 0.97 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.91 ethionamide
rpoB 763031 c.3225T>C synonymous_variant 0.94 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.79 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777572 c.909C>T synonymous_variant 0.96 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpR5 779120 p.Leu44Pro missense_variant 0.98 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302646 c.-285C>T upstream_gene_variant 0.97 pretomanid
delamanid
clofazimine
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1854045 p.Tyr147Cys missense_variant 0.97 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.95 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102054 p.Pro330Leu missense_variant 0.93 isoniazid Uncertain significance
delamanid
ethionamide
katG 2154724 p.Arg463Leu missense_variant 0.94 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169269 p.Gln448His missense_variant 1.0 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2222534 p.Ala211Thr missense_variant 0.98 bedaquiline
clofazimine
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.92 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.96 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.98 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640320 c.-223G>A upstream_gene_variant 0.96 pretomanid
delamanid
clofazimine
alr 3841253 c.168C>T synonymous_variant 0.84 cycloserine
alr 3841277 c.144C>T synonymous_variant 0.85 cycloserine
glpK 4138377 p.Val460Ala missense_variant 0.95 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.96 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.98 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.91 ethambutol Not assoc w R
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 0.96 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.9 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.87 streptomycin Not assoc w R - Interim