TB-Profiler result

Run: SRR15368753
Summary

Run ID: SRR15368753

Sample name:

Date: 2024-04-15T07:55:39.622724

Number of reads: 5541886

Percentage reads mapped: 99.48

Median coverage: 171.0

Strain: lineage2.2.2;lineage4.5

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.18
lineage2 East-Asian RD105 0.84
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.84
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
lineage4 Euro-American None 0.18
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.42dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.42dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
mmpR5 779028 c.42dupC frameshift_variant 0.11 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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 7892 c.591G>A synonymous_variant 0.2 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 0.83 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620029 c.139C>T synonymous_variant 0.2 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.83 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.83 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 763835 p.Ala156Thr missense_variant 0.2 rifampicin
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 0.83 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781406 c.-154_-153insC upstream_gene_variant 0.83 streptomycin Uncertain significance
rplC 801126 c.318C>T synonymous_variant 0.2 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.79 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364671 c.259C>T synonymous_variant 0.77 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1833909 p.Asp123Ala missense_variant 0.83 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.82 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 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.17 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
folC 2746579 c.1020G>A synonymous_variant 0.21 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.86 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.89 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627655 c.-306G>T upstream_gene_variant 0.83 bedaquiline
rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 0.21 pyrazinamide Not assoc w R
clpC1 4040857 c.-153C>T upstream_gene_variant 0.78 pyrazinamide
panD 4044920 c.-639C>T upstream_gene_variant 0.83 pyrazinamide
embC 4239859 c.-4C>T upstream_gene_variant 0.19 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.87 ethambutol Not assoc w R
embA 4244365 p.Gly378Ala missense_variant 0.85 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.84 ethambutol Not assoc w R
aftB 4268596 p.Tyr81His missense_variant 0.19 ethambutol Uncertain significance
ethA 4327531 c.-58T>C upstream_gene_variant 0.76 ethionamide
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
whiB6 4338733 c.-212T>C upstream_gene_variant 0.8 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.88 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.86 streptomycin Not assoc w R