TB-Profiler result

Run: ERR4829940

Summary

Run ID: ERR4829940

Sample name:

Date: 2024-04-14T23:57:30.753280

Number of reads: 2288611

Percentage reads mapped: 99.66

Median coverage: 68.0

Strain: lineage3;lineage4

Spoligotype:

Drug-resistance: Pre-XDR-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 0.22
lineage4 Euro-American None 0.79
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Arg Assoc w R - Interim
p.Asp435Tyr Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.391dupG Assoc w R
p.Leu4Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.193delG Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Thr500Ile Uncertain significance Mutation from literature
ofloxacin
levofloxacin gyrB p.Thr500Ile Uncertain significance Mutation from literature
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.145dupC Assoc w R
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
gyrB 6738 p.Thr500Ile missense_variant 0.32 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
rpoB 761095 p.Leu430Arg missense_variant 0.25 rifampicin Assoc w R - Interim
rpoB 761109 p.Asp435Tyr missense_variant 0.24 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.79 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.391dupG frameshift_variant 0.24 pyrazinamide Assoc w R
pncA 2289231 p.Leu4Ser missense_variant 0.75 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4327328 c.145dupC frameshift_variant 0.33 ethionamide Assoc w R
gid 4408009 c.193delG frameshift_variant 0.24 streptomycin 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
dnaA 94 p.Ser32Gly missense_variant 0.4 isoniazid Uncertain significance
gyrB 6061 p.Ser274Arg missense_variant 0.76 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6735 p.Asn499Ser missense_variant 0.68 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7210 p.Asp657Glu missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Ser missense_variant 0.6 levofloxacin
moxifloxacin
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 0.28 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.19 ethionamide Not assoc w R - Interim
hadA 732110 p.Cys61Gly missense_variant 0.73 isoniazid Uncertain significance
rpoB 759628 c.-179C>T upstream_gene_variant 0.73 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.19 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.25 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 0.24 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 1254562 c.-28T>C upstream_gene_variant 0.11 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1407255 p.Ala29Glu missense_variant 0.8 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471653 n.-193C>T upstream_gene_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673393 c.-809G>A upstream_gene_variant 0.86 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1673431 c.-771G>A upstream_gene_variant 0.12 ethionamide Uncertain significance
isoniazid 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
katG 2154724 p.Arg463Leu missense_variant 0.21 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2169779 c.834A>C synonymous_variant 0.83 pyrazinamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289256 c.-15A>C upstream_gene_variant 0.83 pyrazinamide Uncertain significance
pncA 2289365 c.-125delC upstream_gene_variant 0.22 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28 isoniazid Not assoc w R
Rv2752c 3065855 p.Ala113Pro missense_variant 0.21 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 0.24 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.28 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4043957 p.Asp109Asn missense_variant 0.72 pyrazinamide Uncertain significance
panD 4044399 c.-118C>T upstream_gene_variant 0.28 pyrazinamide
glpK 4138683 p.Gly358Val missense_variant 0.51 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.572dupG frameshift_variant 0.17 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
aftB 4268003 c.834G>A synonymous_variant 0.29 ethambutol Not assoc w R - Interim
ethA 4328317 c.-844C>T upstream_gene_variant 0.78 ethionamide
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 0.24 streptomycin Not assoc w R