TB-Profiler result

Run: ERR4810804
Summary

Run ID: ERR4810804

Sample name:

Date: 2025-06-06T16:45:35.250329

Number of reads: 7794500

Percentage reads mapped: 99.59

Median coverage: 229.0

Strain: lineage4.4.2;lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.84
lineage4 Euro-American None 1.0
lineage4.4 Euro-American None 0.16
lineage4.4.2 Euro-American None 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
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 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.81 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
ccsA 620029 c.139C>T synonymous_variant 0.84 amikacin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620566 p.Asp226Asn missense_variant 0.87 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
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 2170568 p.Ile15Met missense_variant 0.88 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
Rv2477c 2783026 p.Asp339Glu missense_variant 0.14 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.16 ethambutol Not assoc w R
isoniazid Not assoc w R - Interim
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine Uncertain significance
Rv3083 3448727 p.Leu75Arg missense_variant 0.14 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640329 c.-214T>C upstream_gene_variant 0.88 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
alr 3840576 p.Ala258Glu missense_variant 0.12 cycloserine Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.91 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.83 pyrazinamide Not assoc w R
clpC1 4039058 p.Phe549Leu missense_variant 0.16 pyrazinamide Uncertain significance
embC 4238963 c.-900C>T upstream_gene_variant 0.19 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243991 c.759T>G synonymous_variant 0.23 ethambutol Not assoc w R - Interim
embA 4246508 c.3276G>A synonymous_variant 0.14 ethambutol Not assoc w R
embB 4248548 p.Ala679Thr missense_variant 0.82 ethambutol Uncertain significance
aftB 4267494 p.Gly448Ala missense_variant 0.13 ethambutol Uncertain significance
ubiA 4268928 c.906C>T synonymous_variant 0.19 ethambutol Not assoc w R
ubiA 4269375 c.459G>A synonymous_variant 0.18 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance