TB-Profiler result

Run: ERR369667
Summary

Run ID: ERR369667

Sample name:

Date: 2024-04-15T18:43:38.866028

Number of reads: 3997803

Percentage reads mapped: 99.45

Median coverage: 87.0

Strain: lineage3;lineage4.6.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.87
lineage4.6 Euro-American None 0.13
lineage4.6.2 Euro-American RD726 0.17
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.14
lineage4 Euro-American None 0.15
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 0.23 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 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
fgd1 491742 c.960T>C synonymous_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.84 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.88 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 766582 c.3213C>A synonymous_variant 0.81 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.86 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 778298 c.183G>A synonymous_variant 0.17 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.84 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302709 c.-222G>C upstream_gene_variant 0.84 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1833979 c.438T>C synonymous_variant 0.81 pyrazinamide
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
katG 2154724 p.Arg463Leu missense_variant 0.83 isoniazid Not assoc w R
katG 2155389 c.723C>G synonymous_variant 0.22 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.8 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
pncA 2289047 c.195C>T synonymous_variant 0.85 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.8 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.89 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 0.17 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.92 cycloserine
Rv3083 3448567 p.His22Asp missense_variant 0.17 ethionamide Uncertain significance
whiB7 3568951 c.-272G>A upstream_gene_variant 0.89 streptomycin
amikacin
kanamycin
Rv3236c 3612571 c.546C>T synonymous_variant 0.15 pyrazinamide Not assoc w R
Rv3236c 3612910 p.Leu69Phe missense_variant 0.18 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.79 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841473 c.-53G>A upstream_gene_variant 0.78 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.76 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.89 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.83 ethambutol Not assoc w R
embC 4242550 c.2688C>G synonymous_variant 0.13 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.19 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.18 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.21 ethionamide Not assoc w R - Interim
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
gid 4407588 c.615A>G synonymous_variant 0.85 streptomycin Not assoc w R