TB-Profiler result

Run: ERR11243568
Summary

Run ID: ERR11243568

Sample name:

Date: 2024-04-15T13:18:08.666145

Number of reads: 6313709

Percentage reads mapped: 99.5

Median coverage: 139.0

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 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.Asp435Tyr Assoc w R
p.Asn437Asp Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
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 761109 p.Asp435Tyr missense_variant 0.99 rifampicin Assoc w R
rpoB 761115 p.Asn437Asp missense_variant 0.99 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4248003 p.Gln497Arg 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
gyrA 7362 p.Glu21Gln missense_variant 0.99 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
Rv0010c 13632 c.-74A>G upstream_gene_variant 0.11 isoniazid
Rv0010c 13824 c.-266A>T upstream_gene_variant 0.3 isoniazid
Rv0010c 13829 c.-271T>A upstream_gene_variant 0.29 isoniazid
Rv0010c 13834 c.-276A>T upstream_gene_variant 0.28 isoniazid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.99 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_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 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254150 p.Ala129Pro missense_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
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
sigE 1364706 c.294G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.22 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.22 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288842 p.Ala134Pro missense_variant 1.0 pyrazinamide Uncertain significance
pncA 2289374 c.-133T>G upstream_gene_variant 0.13 pyrazinamide
pncA 2289379 c.-138T>G upstream_gene_variant 0.13 pyrazinamide
kasA 2518348 c.234A>T synonymous_variant 0.16 isoniazid
Rv2681 2997962 c.1224A>C synonymous_variant 0.13 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641280 p.Ile246Met missense_variant 0.13 clofazimine
pretomanid
delamanid
rpoA 3878567 c.-60C>G upstream_gene_variant 0.23 rifampicin
embC 4239281 c.-582C>G upstream_gene_variant 0.13 ethambutol
embC 4239284 c.-579C>G upstream_gene_variant 0.13 ethambutol
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.18 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.18 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.2 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.2 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.22 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.21 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R