TB-Profiler result

Run: ERR4812079
Summary

Run ID: ERR4812079

Sample name:

Date: 2024-04-15T13:59:18.105884

Number of reads: 3929215

Percentage reads mapped: 99.73

Median coverage: 155.0

Strain: lineage2.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.79
lineage2 East-Asian RD105 0.24
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage4 Euro-American None 0.79
lineage4.3.3 Euro-American (LAM) RD115 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
streptomycin gid p.Pro84Leu Assoc w R - Interim
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 761110 p.Asp435Val missense_variant 0.78 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.79 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.76 ethambutol Assoc w R
gid 4407952 p.Pro84Leu missense_variant 0.81 streptomycin Assoc w R - Interim
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 8040 p.Gly247Ser missense_variant 0.78 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 0.18 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.26 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.22 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.14 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.21 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.78 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 0.22 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.21 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23 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 0.24 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.15 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.73 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.28 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.21 pyrazinamide Not assoc w R
PPE35 2168998 p.Ile539Val missense_variant 0.74 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.84 isoniazid
Rv2477c 2783921 p.Gly41Glu missense_variant 0.86 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Not assoc w R
amikacin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.75 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087755 c.936G>T synonymous_variant 0.14 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.99 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.17 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242182 p.Ala774Ser missense_variant 0.76 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.32 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.3 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 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.21 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.78 streptomycin Not assoc w R