TB-Profiler result

Run: SRR10380209
Summary

Run ID: SRR10380209

Sample name:

Date: 2024-03-26T14:19:44.785210

Number of reads: 3161573

Percentage reads mapped: 99.75

Median coverage: 100.0

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 0.87
lineage2 East-Asian RD105 0.1
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.09
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4 Euro-American None 0.89
lineage4.3.3 Euro-American (LAM) RD115 0.88
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.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Asn379Asp Assoc w R - Interim
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Arg222Gly Mutation from literature
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 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
thyX 3067961 c.-16C>T upstream_gene_variant 0.13 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.14 para-aminosalicylic_acid Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 0.88 ethambutol Uncertain significance Mutation from literature
ethA 4326339 p.Asn379Asp missense_variant 0.15 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 6579 p.Ser447Tyr missense_variant 0.13 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 8040 p.Gly247Ser missense_variant 0.89 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
Rv0010c 13669 c.-111A>G upstream_gene_variant 0.88 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.15 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.17 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.11 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.15 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 764841 p.Ile491Ser missense_variant 0.86 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.81 rifampicin Not assoc w R
rpoC 765612 p.His748Pro missense_variant 0.21 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 0.12 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254056 p.Asp160Ala missense_variant 0.7 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.13 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.88 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 2156196 c.-85C>T upstream_gene_variant 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.1 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 2518919 p.Gly269Ser missense_variant 0.86 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.87 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.89 para-aminosalicylic_acid
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
mtrB 3626562 p.Pro18Ser missense_variant 0.13 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641810 c.276G>C synonymous_variant 0.14 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.86 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.92 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.15 ethambutol Not assoc w R
embA 4246287 p.Asn1019Asp missense_variant 0.16 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.1 ethambutol Not assoc w R
ubiA 4269089 p.Ala249Thr missense_variant 0.18 ethambutol Uncertain significance
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 0.12 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.11 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.86 streptomycin Not assoc w R