TB-Profiler result

Run: ERR2679289
Summary

Run ID: ERR2679289

Sample name:

Date: 2024-10-05T07:09:37.079493

Number of reads: 522547

Percentage reads mapped: 99.59

Median coverage: 27.0

Strain: lineage4.1.2.1;lineage6.2.3

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6.2 West-Africa 2 RD702 0.09
lineage4.1 Euro-American None 0.8
lineage4.1.2 Euro-American None 0.7
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.73
lineage4 Euro-American None 0.86
lineage6.2.3 West-Africa 2 RD702 0.21
lineage6 West-Africa 2 RD702 0.16
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 gid c.351delG Assoc w R
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 0.85 isoniazid Assoc w R High-level resistance
gid 4407851 c.351delG frameshift_variant 0.71 streptomycin 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
dnaA 1302 c.1302C>T synonymous_variant 0.75 isoniazid Not assoc w R - Interim
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 8478 p.Gly393Ser missense_variant 0.72 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.85 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.71 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 656298 c.1173G>C synonymous_variant 0.25 ethionamide
Rv0565c 657269 p.Ser68Pro missense_variant 0.73 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.76 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.32 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.86 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 0.35 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 0.22 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406685 p.Val219Ala missense_variant 0.25 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.26 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
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
PPE35 2169269 c.1340_1344delGCCAAinsT frameshift_variant&missense_variant 0.26 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.64 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627756 c.-407A>T upstream_gene_variant 0.85 rifampicin
bedaquiline
alr 3840559 p.Arg288Ser missense_variant 0.23 cycloserine
clpC1 4038408 p.Pro766Leu missense_variant 0.72 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.76 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.23 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.92 ethambutol Not assoc w R
embA 4243541 c.309C>T synonymous_variant 0.36 ethambutol Not assoc w R - Interim
embA 4244220 c.988C>T synonymous_variant 0.26 ethambutol Not assoc w R
ubiA 4269351 c.483C>T synonymous_variant 0.27 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.29 ethambutol Not assoc w R
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