TB-Profiler result

Run: ERR13260390
Summary

Run ID: ERR13260390

Sample name:

Date: 2025-02-11T12:23:03.385687

Number of reads: 4848191

Percentage reads mapped: 99.6

Median coverage: 136.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.84
lineage4.1.2 Euro-American None 0.85
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.85
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
p.Arg448Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile 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 761140 p.His445Arg missense_variant 0.14 rifampicin Assoc w R
rpoB 761149 p.Arg448Gln missense_variant 0.13 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
mmpR5 779181 c.198dupG frameshift_variant 0.13 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 0.2 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.13 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13634 c.-76G>T upstream_gene_variant 0.79 isoniazid Uncertain significance
fgd1 491591 p.Lys270Met missense_variant 0.86 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.87 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 575837 c.490C>T synonymous_variant 0.11 isoniazid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv0565c 656980 c.484_490delTTTGGCG frameshift_variant 0.82 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.87 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.81 rifampicin Not assoc w R
rpoB 761889 p.Val695Leu missense_variant 0.17 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.83 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 777875 c.605delG frameshift_variant 0.13 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781276 c.-284A>C upstream_gene_variant 0.91 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.18 linezolid Not assoc w R - Interim
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
katG 2156173 c.-62C>A upstream_gene_variant 0.13 isoniazid Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.1 bedaquiline Uncertain significance
clofazimine 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 0.86 isoniazid
ahpC 2726141 c.-52C>A upstream_gene_variant 0.2 isoniazid Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
thyA 3074495 c.-24C>T upstream_gene_variant 0.18 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
Rv3236c 3612219 p.Val300Ile missense_variant 0.16 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.9 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.86 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 0.74 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.32 ethambutol
ethA 4328317 c.-844C>T upstream_gene_variant 0.12 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 4407967 p.Leu79Trp missense_variant 0.17 streptomycin Uncertain significance