TB-Profiler result

Run: SRR16088594
Summary

Run ID: SRR16088594

Sample name:

Date: 2024-04-15T06:12:39.404872

Number of reads: 4715372

Percentage reads mapped: 99.58

Median coverage: 158.0

Strain: lineage2.2.1;lineage4.1.2.1

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 0.09
lineage4.1 Euro-American None 0.87
lineage4.1.2 Euro-American None 0.88
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.87
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.06
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage4 Euro-American None 0.94
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.Gly406Ala Assoc w R
pyrazinamide
streptomycin
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 alr p.Leu113Arg Mutation from literature
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 761155 p.Ser450Leu missense_variant 0.2 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
eis 2715346 c.-14C>T upstream_gene_variant 0.18 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
alr 3841083 p.Leu113Arg missense_variant 0.16 cycloserine Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.14 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
gyrB 6000 p.Pro254Leu missense_variant 0.91 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 491591 p.Lys270Met missense_variant 0.88 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.88 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657142 p.Arg110His missense_variant 0.15 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.89 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.9 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.86 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14 clofazimine
bedaquiline
rpsL 781276 c.-284A>C upstream_gene_variant 0.91 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.87 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.13 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 0.15 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.14 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.86 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.2 capreomycin
Rv2752c 3065110 c.1081delA frameshift_variant 0.61 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.86 ethambutol Not assoc w R
embC 4240413 p.Leu184Arg missense_variant 0.14 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.88 ethambutol Not assoc w R
whiB6 4338513 c.9C>T synonymous_variant 0.93 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
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 0.13 streptomycin Not assoc w R