TB-Profiler result

Run: ERR6865869
Summary

Run ID: ERR6865869

Sample name:

Date: 2024-10-05T12:48:51.944260

Number of reads: 2136254

Percentage reads mapped: 99.62

Median coverage: 59.0

Strain: lineage4.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.42
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.42
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
dnaA 970 p.Trp324Gly missense_variant 0.4 isoniazid Uncertain significance
gyrB 6052 p.Ile271Met missense_variant 0.38 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.38 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 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.29 ethionamide Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.6 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.46 rifampicin Not assoc w R
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
rplC 800219 c.-590T>C upstream_gene_variant 0.4 linezolid
rplC 801009 c.201A>G synonymous_variant 0.51 linezolid Not assoc w R - Interim
embR 1416699 p.Leu217Val missense_variant 0.47 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673865 c.-337C>T upstream_gene_variant 0.3 isoniazid Uncertain significance
ethionamide 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
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.63 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
Rv2752c 3065517 c.675C>T synonymous_variant 0.63 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.48 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086788 c.-32T>C upstream_gene_variant 0.36 cycloserine
Rv3083 3448439 c.-64delA upstream_gene_variant 0.62 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 0.42 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627511 c.-162C>G upstream_gene_variant 0.41 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.45 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.4 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.5 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