TB-Profiler result

Run: SRR28044703
Summary

Run ID: SRR28044703

Sample name:

Date: 2024-05-22T09:52:02.846052

Number of reads: 2439050

Percentage reads mapped: 99.57

Median coverage: 69.0

Strain: lineage3;lineage4.1.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.81
lineage4.1 Euro-American None 0.18
lineage4.1.2 Euro-American None 0.19
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.18
lineage4 Euro-American None 0.19
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin
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
katG 2155168 p.Ser315Thr missense_variant 0.74 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491013 c.231C>A synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fgd1 491591 p.Lys270Met missense_variant 0.2 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.77 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.21 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.28 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.78 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.78 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.16 rifampicin Not assoc w R
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 0.74 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777706 p.Ser259Ala missense_variant 0.65 clofazimine
bedaquiline
rpsL 781276 c.-284A>C upstream_gene_variant 0.16 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.76 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.26 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417416 c.-69G>A upstream_gene_variant 0.14 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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 0.59 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.91 pyrazinamide Not assoc w R
PPE35 2169639 p.Gly325Asp missense_variant 0.76 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.83 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.65 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.79 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
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
fbiA 3641454 c.912G>A synonymous_variant 0.17 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4039667 p.Gln346His missense_variant 0.8 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.65 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.67 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.83 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243829 c.597C>T synonymous_variant 0.89 ethambutol
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 0.8 streptomycin Not assoc w R