TB-Profiler result

Run: ERR017798
Summary

Run ID: ERR017798

Sample name:

Date: 2025-02-11T17:02:52.435115

Number of reads: 2834823

Percentage reads mapped: 99.6

Median coverage: 37.0

Strain: lineage4.6.2.2;lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.93
lineage4.6.2 Euro-American RD726 0.94
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.93
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) None 0.06
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 0.93 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.85 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.94 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.93 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.86 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 0.95 capreomycin Not assoc w R
bacA 2063187 c.1542C>T synonymous_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2155389 c.723C>G synonymous_variant 1.0 isoniazid Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.79 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.75 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyX 3067474 p.Pro158Ala missense_variant 1.0 para-aminosalicylic_acid
Rv3083 3448567 p.His22Asp missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 0.89 pyrazinamide Not assoc w R
Rv3236c 3612910 p.Leu69Phe missense_variant 0.85 pyrazinamide Uncertain significance
embC 4242550 c.2688C>G synonymous_variant 0.92 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 1.0 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.96 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 0.97 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