TB-Profiler result

Run: SRR29385283
Summary

Run ID: SRR29385283

Sample name:

Date: 2025-02-11T11:32:57.573450

Number of reads: 4383553

Percentage reads mapped: 99.71

Median coverage: 93.0

Strain: lineage2.2.1;lineage2.2.2;lineage4

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 0.92
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.32
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.56
lineage2.2 East-Asian (Beijing) RD105;RD207 0.94
lineage4 Euro-American None 0.08
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
rpoB 761139 p.His445Asp missense_variant 0.5 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.37 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid Assoc w R High-level resistance
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 8396 c.1095C>T synonymous_variant 0.65 levofloxacin
moxifloxacin
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 0.97 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.26 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576298 p.Asp317Glu missense_variant 0.65 isoniazid
ethionamide
ccsA 620625 p.Ile245Met missense_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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
rpoB 763031 c.3225T>C synonymous_variant 0.97 rifampicin Not assoc w R
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 0.96 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.95 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 0.82 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254582 c.-48A>G upstream_gene_variant 0.52 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471647 n.-199G>C upstream_gene_variant 0.33 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_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 2154724 p.Arg463Leu missense_variant 0.95 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167928 c.2685G>T synonymous_variant 0.87 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2747589 p.Thr4Ser missense_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88 pyrazinamide Not assoc w R - Interim
Rv3236c 3613709 c.-593C>T upstream_gene_variant 0.74 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.26 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641935 p.Ala134Val missense_variant 0.22 pretomanid
delamanid
clofazimine
clpC1 4040976 c.-272T>G upstream_gene_variant 0.76 pyrazinamide
glpK 4138219 p.Trp513Arg missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.93 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.95 ethambutol 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 4338631 c.-110T>G upstream_gene_variant 0.31 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.82 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R
gid 4407995 p.Ser70Gly missense_variant 0.64 streptomycin Uncertain significance