TB-Profiler result

Run: ERR4831519
Summary

Run ID: ERR4831519

Sample name:

Date: 2024-06-18T07:59:16.706888

Number of reads: 3853697

Percentage reads mapped: 99.52

Median coverage: 116.0

Strain: lineage2.2.1.1;lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.83
lineage2 East-Asian RD105 0.21
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.16
lineage2.2 East-Asian (Beijing) RD105;RD207 0.19
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.17
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide pncA p.Arg154Met Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
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
gyrA 7582 p.Asp94Gly missense_variant 0.85 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.9 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.82 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid Assoc w R High-level resistance
pncA 2288781 p.Arg154Met missense_variant 0.8 pyrazinamide Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.86 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 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
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.12 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.18 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 0.17 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.83 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764820 p.Trp484Ser missense_variant 0.82 rifampicin Uncertain significance
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 0.2 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21 clofazimine
bedaquiline
rpsL 781301 c.-259C>T upstream_gene_variant 0.2 streptomycin
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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.12 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471826 n.-20_-19insTCCAAAGGGA upstream_gene_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.24 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
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.15 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.8 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.85 pyrazinamide
eis 2714846 p.Val163Ile missense_variant 0.17 amikacin Not assoc w R
kanamycin Not assoc w R
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77 isoniazid Not assoc w R
ahpC 2726116 c.-77T>A upstream_gene_variant 0.76 isoniazid Uncertain significance
Rv2477c 2782498 c.1545C>T synonymous_variant 0.78 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.14 pyrazinamide Not assoc w R - Interim
Rv3236c 3613004 p.Leu38Ser missense_variant 0.83 pyrazinamide Uncertain significance
lpqB 3624323 c.588G>A synonymous_variant 0.89 bedaquiline Not assoc w R - Interim
rifampicin 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 0.16 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.87 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.83 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.8 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248115 c.1602C>T synonymous_variant 0.14 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269302 p.Leu178Val missense_variant 0.84 ethambutol Uncertain significance
whiB6 4338596 c.-76_-75delAGinsT upstream_gene_variant 0.78 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338596 c.-75delG upstream_gene_variant 0.22 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338596 c.-76_-75delAGinsT upstream_gene_variant 0.78 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338596 c.-75delG upstream_gene_variant 0.22 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 0.14 streptomycin Not assoc w R