TB-Profiler result

Run: ERR4796669
Summary

Run ID: ERR4796669

Sample name:

Date: 2024-04-14T07:23:36.950592

Number of reads: 4240285

Percentage reads mapped: 99.56

Median coverage: 115.0

Strain: lineage3.1;lineage4.8

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 0.82
lineage4 Euro-American None 0.19
lineage4.8 Euro-American (mainly T) RD219 0.17
lineage3.1 East-African-Indian RD750 0.82
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Gly97Val Assoc w R - Interim
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94His Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94His Assoc w R
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
gyrA 7581 p.Asp94His missense_variant 0.12 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.25 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.22 isoniazid Assoc w R High-level resistance
pncA 2288952 p.Gly97Val missense_variant 0.19 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.15 ethambutol Assoc w R
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 0.89 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.86 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9788 c.2487C>T synonymous_variant 0.87 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.8 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576108 p.Ala254Gly missense_variant 0.35 ethionamide
isoniazid
Rv0565c 657081 c.390G>A synonymous_variant 0.83 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.79 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.88 rifampicin Not assoc w R
rpoB 762888 p.His1028Tyr missense_variant 0.16 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.82 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 0.88 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
Rv1129c 1253627 p.Ile303Thr missense_variant 0.28 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.71 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303428 c.498C>A synonymous_variant 0.92 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1304265 c.1335C>T synonymous_variant 0.87 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 0.91 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 0.73 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.77 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
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.13 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.81 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.87 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.81 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
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.77 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3642005 c.471C>G synonymous_variant 0.81 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4040396 c.309C>T synonymous_variant 0.14 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.82 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.82 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 0.84 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246811 p.Gly100Ser missense_variant 0.27 ethambutol Uncertain significance
embB 4248399 p.Leu629Pro missense_variant 0.87 ethambutol Uncertain significance
ethA 4326912 p.Val188Ile missense_variant 0.82 ethionamide Uncertain significance
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 0.85 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.71 streptomycin Not assoc w R