TB-Profiler result

Run: ERR4829960
Summary

Run ID: ERR4829960

Sample name:

Date: 2024-10-05T14:04:04.540682

Number of reads: 1826604

Percentage reads mapped: 99.45

Median coverage: 44.0

Strain: lineage3;lineage4.5

Spoligotype:

Drug-resistance: MDR-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 0.7
lineage4.5 Euro-American RD122 0.27
lineage4 Euro-American None 0.28
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser441Leu Assoc w R
p.His445Asn Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198dupG 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
rpoB 761128 p.Ser441Leu missense_variant 0.39 rifampicin Assoc w R
rpoB 761139 p.His445Asn missense_variant 0.52 rifampicin Assoc w R
mmpR5 779181 c.198dupG frameshift_variant 0.56 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
katG 2155168 p.Ser315Thr missense_variant 0.32 isoniazid Assoc w R High-level resistance
embB 4247574 p.Asp354Ala missense_variant 0.36 ethambutol Assoc w R
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 0.16 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 0.7 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.28 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.73 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.88 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.66 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 0.85 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.77 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1304463 c.1533C>T synonymous_variant 0.29 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1258c 1406101 p.Pro414Ser missense_variant 0.24 streptomycin Uncertain significance
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv1258c 1406899 p.Ala148Thr missense_variant 0.29 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407133 p.Gly70Arg missense_variant 0.55 streptomycin Uncertain significance
pyrazinamide
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.33 pyrazinamide Uncertain significance
tsnR 1853597 c.-9G>C upstream_gene_variant 0.22 linezolid Uncertain significance
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
ndh 2102283 p.Arg254Cys missense_variant 0.38 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154372 c.1740C>T synonymous_variant 0.32 isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.78 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.34 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
pncA 2289047 c.195C>T synonymous_variant 0.77 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.72 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.74 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.63 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.59 cycloserine
Rv3236c 3612316 c.801T>C synonymous_variant 0.14 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.2 pyrazinamide Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.79 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.64 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.66 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269024 c.810G>A synonymous_variant 0.6 ethambutol Not assoc w R - Interim
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 0.81 streptomycin Not assoc w R