TB-Profiler result

Run: ERR4553822
Summary

Run ID: ERR4553822

Sample name:

Date: 2024-04-15T01:57:52.941918

Number of reads: 1077888

Percentage reads mapped: 99.46

Median coverage: 30.0

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.2 Indo-Oceanic RD239 0.17
lineage1.1 Indo-Oceanic RD239 0.19
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Arg Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Gln432Arg Mutation from literature
isoniazid inhA p.Ile21Val 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
rpoB 761101 p.Gln432Arg missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rifampicin Mutation from literature
inhA 1674262 p.Ile21Val missense_variant 1.0 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
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
fgd1 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575837 c.490C>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
nusG 734555 p.Asn101Ser missense_variant 1.0 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 779061 c.-581G>C upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290018 c.-777C>T upstream_gene_variant 0.94 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
kasA 2519116 c.1002C>A synonymous_variant 1.0 isoniazid
ribD 2987319 p.Glu161Lys missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 0.93 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625806 c.808A>C synonymous_variant 1.0 bedaquiline
rifampicin Not assoc w R - Interim
rpoA 3877964 p.Arg182Trp missense_variant 1.0 rifampicin Uncertain significance
ddn 3987092 c.249G>A synonymous_variant 1.0 delamanid
pretomanid
glpK 4138377 p.Val460Ala missense_variant 0.94 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
glpK 4138627 p.Ala377Pro missense_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
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
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407600 c.603C>T synonymous_variant 1.0 streptomycin Not assoc w R - Interim
gid 4408144 p.Arg20Pro missense_variant 0.95 streptomycin Uncertain significance