TB-Profiler result

Run: ERR4812995
Summary

Run ID: ERR4812995

Sample name:

Date: 2024-04-14T07:27:02.164556

Number of reads: 1482438

Percentage reads mapped: 97.56

Median coverage: 43.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.86
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Leu159Val Assoc w R - Interim
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288767 p.Leu159Val missense_variant 1.0 pyrazinamide Assoc w R - Interim
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
gyrB 6187 c.948C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
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 8040 p.Gly247Ser 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
mshA 574862 c.-486T>C upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
Rv0565c 657730 c.-260A>C upstream_gene_variant 1.0 ethionamide
rpoB 761880 p.Ala692Thr missense_variant 1.0 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765639 p.Glu757Ala missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 1254132 p.Glu135Lys missense_variant 0.28 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254580 c.-46C>G upstream_gene_variant 1.0 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 1.0 pyrazinamide Not assoc w R - Interim
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154459 c.1653C>T synonymous_variant 1.0 isoniazid 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
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.98 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
panD 4044824 c.-543C>G upstream_gene_variant 1.0 pyrazinamide
whiB6 4338474 p.Trp16Cys missense_variant 0.1 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.31 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.69 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338594 c.-75_-73delGCTinsCC upstream_gene_variant 0.31 capreomycin Uncertain significance
amikacin Not assoc w R
kanamycin Uncertain significance
whiB6 4338594 c.-75delG upstream_gene_variant 0.69 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 4407720 c.483C>G synonymous_variant 0.96 streptomycin Not assoc w R - Interim
gid 4408003 p.Asp67Gly missense_variant 0.96 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R