TB-Profiler result

Run: ERR4830184
Summary

Run ID: ERR4830184

Sample name:

Date: 2024-10-05T12:44:30.278557

Number of reads: 3349782

Percentage reads mapped: 99.57

Median coverage: 102.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.21
lineage2 East-Asian RD105 0.82
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.81
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
lineage4 Euro-American None 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.Ser450Leu Assoc w R
rpoC p.Asp485Asn Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Trp119Ser Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide ethA p.Leu35Arg Assoc w R - Interim
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 761155 p.Ser450Leu missense_variant 0.78 rifampicin Assoc w R
rpoC 764822 p.Asp485Asn missense_variant 0.84 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid Assoc w R High-level resistance
pncA 2288886 p.Trp119Ser missense_variant 0.77 pyrazinamide Mutation from literature
eis 2715346 c.-14C>T upstream_gene_variant 0.78 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embA 4243217 c.-16C>T upstream_gene_variant 0.73 ethambutol Uncertain significance Mutation from literature
ethA 4327370 p.Leu35Arg missense_variant 0.83 ethionamide 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
gyrB 5452 p.Glu71Asp missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin
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 7892 c.591G>A synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.8 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.19 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.85 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.79 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.82 ethionamide Uncertain significance
rpoB 760707 p.Asp301Asn missense_variant 0.79 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 767296 c.3927C>T synonymous_variant 0.81 rifampicin Not assoc w R - Interim
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 0.79 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.78 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406101 p.Pro414Ser missense_variant 0.19 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.78 pyrazinamide Not assoc w R - Interim
tsnR 1853597 c.-9G>C upstream_gene_variant 0.18 linezolid Uncertain significance
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 0.79 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.81 pyrazinamide Not assoc w R
PPE35 2170521 p.Trp31* stop_gained 0.29 pyrazinamide Uncertain significance
PPE35 2170568 p.Ile15Met missense_variant 0.27 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
eis 2715323 p.Thr4Pro missense_variant 0.76 kanamycin Uncertain significance
amikacin Uncertain significance
ald 3086731 c.-89A>G upstream_gene_variant 0.73 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.76 cycloserine
Rv3236c 3612666 p.Val151Met missense_variant 0.21 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.84 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.13 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.79 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.86 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.83 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.87 streptomycin Not assoc w R