TB-Profiler result

Run: ERR13191363
Summary

Run ID: ERR13191363

Sample name:

Date: 2025-02-27T15:53:07.535421

Number of reads: 2823956

Percentage reads mapped: 99.59

Median coverage: 131.0

Strain: lineage2.2.1;lineage2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.76
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.21
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.Asp435Val Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ile21Thr Uncertain significance Mutation from literature: doi: 10.1128/AAC.47.12.3799-3805.2003
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
p.Gly406Ala Assoc w R
pyrazinamide
streptomycin gid c.303dupT Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile21Thr Uncertain significance Mutation from literature: doi: 10.1128/AAC.47.12.3799-3805.2003
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 0.27 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.78 rifampicin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.82 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674263 p.Ile21Thr missense_variant 0.69 ethionamide Uncertain significance Mutation from literature: doi: 10.1128/AAC.47.12.3799-3805.2003
isoniazid Uncertain significance Mutation from literature: doi: 10.1128/AAC.47.12.3799-3805.2003
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.81 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.23 ethambutol Assoc w R
gid 4407899 c.303dupT frameshift_variant 0.7 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 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 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
hadA 732277 c.348C>T synonymous_variant 0.77 isoniazid Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764616 p.Asn416Ser missense_variant 0.12 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.67 rifampicin Uncertain significance
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 777597 p.Arg295Pro missense_variant 0.81 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 778656 p.Ala84Thr missense_variant 0.23 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.23 streptomycin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1407255 p.Ala29Gly missense_variant 0.13 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416724 p.Trp208* stop_gained 0.23 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1833909 p.Asp123Ala missense_variant 0.24 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.99 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 2154239 p.Thr625Ala missense_variant 0.8 isoniazid Uncertain significance
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2752c 3064631 p.Ala521Ser missense_variant 0.23 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
fbiD 3339564 c.447G>A synonymous_variant 0.77 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv3083 3449528 p.Ile342Thr missense_variant 0.23 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
lpqB 3623495 c.1416G>A synonymous_variant 0.15 bedaquiline Uncertain significance
rifampicin Not assoc w R - Interim
lpqB 3624444 p.Asp156Ala missense_variant 0.18 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3624456 p.Gly152Glu missense_variant 0.19 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626548 c.66C>T synonymous_variant 0.81 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.81 bedaquiline Uncertain significance
rifampicin Not assoc w R
ddn 3987084 p.Gly81Ser missense_variant 0.17 delamanid Uncertain significance
pretomanid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ethA 4326930 p.Gly182Ser missense_variant 0.31 ethionamide Uncertain significance
whiB6 4338224 p.Glu100* stop_gained 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Ala missense_variant 1.0 streptomycin Uncertain significance