TB-Profiler result

Run: ERR5865968
Summary

Run ID: ERR5865968

Sample name:

Date: 2025-09-15T15:10:18.135437

Number of reads: 4650315

Percentage reads mapped: 89.77

Median coverage: 73.0

Strain: lineage4.8

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 Euro-American None 100.0
lineage4.8 Euro-American (mainly T) RD219 100.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Trp68Gly Assoc w R
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Gly missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.97 ethambutol Assoc w R
gid 4408087 c.115delC frameshift_variant 0.99 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
gyrB 5499 p.Ala87Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7724 p.Met141Ile missense_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13262 c.297G>A synonymous_variant 0.99 isoniazid Uncertain significance
fgd1 490829 p.Ala16Val missense_variant 0.99 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mmaA3 737324 p.Ala276Thr missense_variant 0.99 isoniazid Uncertain significance
rpoC 767123 p.Val1252Met missense_variant 0.96 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775677 p.Lys935Thr missense_variant 0.99 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.28 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 0.99 capreomycin Not assoc w R
ndh 2103202 c.-160C>T upstream_gene_variant 0.15 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
PPE35 2168149 p.Pro822Ser missense_variant 1.0 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
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv3083 3448444 c.-59_*1407del transcript_ablation 0.96 ethionamide Uncertain significance
Rv3083 3448507 c.5_*1407del frameshift_variant&stop_lost&splice_region_variant 0.99 ethionamide Uncertain significance
glpK 4138698 p.Val353Gly missense_variant 0.19 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
glpK 4138930 p.Glu276Lys missense_variant 0.36 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4269546 c.-710G>C upstream_gene_variant 0.96 ethambutol Uncertain significance
ubiA 4269864 c.-31C>T upstream_gene_variant 0.95 ethambutol Uncertain significance
ethA 4327006 p.Asp156Glu missense_variant 0.99 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R