TB-Profiler result

Run: ERR4810804
Summary

Run ID: ERR4810804

Sample name:

Date: 2024-04-16T12:31:10.408860

Number of reads: 7800117

Percentage reads mapped: 99.42

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 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620566 p.Asp226Asn missense_variant 0.87 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 streptomycin
kanamycin
capreomycin
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 2170568 p.Ile15Met missense_variant 0.88 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2477c 2783026 p.Asp339Glu missense_variant 0.14 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2752c 3066099 p.Met31Ile missense_variant 0.16 ethambutol Not assoc w R
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.15 cycloserine
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
pretomanid
delamanid
alr 3840576 p.Ala282Glu missense_variant 0.12 cycloserine
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
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
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 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin