TB-Profiler result

Run: SRR12634633
Summary

Run ID: SRR12634633

Sample name:

Date: 2024-04-16T08:14:35.839350

Number of reads: 2487125

Percentage reads mapped: 99.46

Median coverage: 106.0

Strain: lineage3.1.1;lineage4.6.1.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.16
lineage4.6 Euro-American None 0.84
lineage3.1.1 East-African-Indian RD750 0.14
lineage4.6.1.2 Euro-American RD724 0.85
lineage4 Euro-American None 0.87
lineage4.6.1 Euro-American (Uganda) RD724 0.84
lineage3.1 East-African-Indian RD750 0.2
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
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
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 7539 p.Thr80Ala missense_variant 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
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 491742 c.960T>C synonymous_variant 0.22 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.18 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.22 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.17 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.15 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 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777062 c.1418dupT frameshift_variant 0.8 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.11 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1416410 p.Leu313Arg missense_variant 0.84 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674465 c.264C>T synonymous_variant 0.86 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.99 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 0.14 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.17 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.11 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
pncA 2289047 c.195C>T synonymous_variant 0.15 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.16 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.12 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.12 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
Rv2681 2996876 c.138A>C synonymous_variant 0.82 capreomycin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.17 cycloserine
whiB7 3569029 c.-350A>G upstream_gene_variant 0.82 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.19 pyrazinamide
glpK 4139670 p.Cys29Tyr missense_variant 0.89 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4241562 p.Arg567His missense_variant 0.22 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.86 ethambutol Uncertain significance
embA 4245131 c.1899G>A synonymous_variant 0.86 ethambutol Not assoc w R - Interim
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 4338635 c.-114A>C upstream_gene_variant 0.86 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.13 streptomycin Not assoc w R