TB-Profiler result

Run: SRR29385325
Summary

Run ID: SRR29385325

Sample name:

Date: 2025-02-11T14:35:27.609729

Number of reads: 6597293

Percentage reads mapped: 99.62

Median coverage: 146.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: Pre-XDR-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 0.45
lineage2 East-Asian RD105 0.55
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.62
lineage2.2 East-Asian (Beijing) RD105;RD207 0.53
lineage4 Euro-American None 0.48
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Tyr Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
c.371delG Assoc w R High-level resistance
ahpC c.-57C>T Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA c.266delC Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Asn Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.22 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7581 p.Asp94Asn missense_variant 0.24 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761139 p.His445Tyr missense_variant 0.47 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.61 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid Assoc w R High-level resistance
katG 2155740 c.371delG frameshift_variant 0.15 isoniazid Assoc w R High-level resistance
pncA 2288975 c.266delC frameshift_variant 0.34 pyrazinamide Assoc w R
ahpC 2726136 c.-57C>T upstream_gene_variant 0.13 isoniazid Uncertain significance Mutation from literature
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 0.51 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
Rv0010c 13145 c.414C>A synonymous_variant 0.42 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.61 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.58 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.43 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.56 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.6 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.61 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.6 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 0.54 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.58 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.54 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 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.39 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407401 c.-61G>A upstream_gene_variant 0.48 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471679 n.-167C>T upstream_gene_variant 0.55 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.62 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 0.53 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.57 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.57 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
ald 3086788 c.-32T>C upstream_gene_variant 0.48 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54 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 0.54 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640243 c.-300T>C upstream_gene_variant 0.25 pretomanid
delamanid
clofazimine
rpoA 3878575 c.-68C>T upstream_gene_variant 0.6 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.37 pyrazinamide Not assoc w R
clpC1 4038659 c.2046C>T synonymous_variant 0.45 pyrazinamide
embC 4239700 c.-163A>G upstream_gene_variant 0.56 ethambutol Uncertain significance
embC 4241497 c.1635G>C synonymous_variant 0.42 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.48 ethambutol Not assoc w R
embA 4244429 c.1197G>C synonymous_variant 0.54 ethambutol Not assoc w R - Interim
embA 4245131 c.1899G>C synonymous_variant 0.34 ethambutol Not assoc w R - Interim
embA 4245482 c.2250G>A synonymous_variant 0.63 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.62 ethambutol Not assoc w R
aftB 4268033 c.804G>A synonymous_variant 0.43 ethambutol
ethA 4328340 c.-867A>G upstream_gene_variant 0.51 ethionamide
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 0.62 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.47 streptomycin Not assoc w R