TB-Profiler result

Run: ERR4818394
Summary

Run ID: ERR4818394

Sample name:

Date: 2024-10-04T11:10:22.454986

Number of reads: 253137

Percentage reads mapped: 56.49

Median coverage: 5.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.99
lineage4.9 Euro-American (H37Rv-like) None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
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
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
mshA 575659 c.312A>G synonymous_variant 0.33 isoniazid
ethionamide
mshA 575662 c.315C>G synonymous_variant 0.33 isoniazid
ethionamide
mshA 575674 c.327G>C synonymous_variant 0.38 isoniazid
ethionamide
rpoC 765994 c.2625A>T synonymous_variant 0.7 rifampicin Not assoc w R - Interim
rpsA 1834619 c.1078T>C synonymous_variant 0.58 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.62 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.62 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.73 pyrazinamide
thyX 3067545 p.Glu134Ala missense_variant 0.7 para-aminosalicylic_acid
thyX 3067549 p.Thr133Ala missense_variant 0.7 para-aminosalicylic_acid
thyX 3067556 p.His130Gln missense_variant 0.7 para-aminosalicylic_acid
thyX 3067559 c.387C>G synonymous_variant 0.64 para-aminosalicylic_acid
thyX 3067565 p.Asp127Glu missense_variant 0.7 para-aminosalicylic_acid
mtrB 3626154 c.460C>T synonymous_variant 0.7 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626155 p.Ala153Ser missense_variant 0.7 rifampicin
bedaquiline
mtrB 3626158 c.456C>T synonymous_variant 0.7 rifampicin
bedaquiline
mtrB 3626170 c.444T>C synonymous_variant 0.58 rifampicin
bedaquiline
mtrB 3626179 c.435A>G synonymous_variant 0.58 rifampicin
bedaquiline
mtrB 3626185 c.429T>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626188 p.Ser142Thr missense_variant 0.54 rifampicin
bedaquiline
mtrB 3626194 c.420T>C synonymous_variant 0.54 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626203 c.411G>A synonymous_variant 0.47 rifampicin
bedaquiline
mtrB 3626206 c.408T>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3626209 c.405T>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.6 rifampicin
bedaquiline
rpoA 3879121 c.-614T>G upstream_gene_variant 0.6 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.6 rifampicin
clpC1 4038845 c.1860G>C synonymous_variant 0.55 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.53 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.62 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.67 pyrazinamide
clpC1 4039286 c.1419T>C synonymous_variant 0.55 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.56 pyrazinamide
clpC1 4039831 c.874T>C synonymous_variant 0.55 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.5 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.4 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.62 pyrazinamide
glpK 4139597 c.159C>G synonymous_variant 0.55 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4139601 p.Arg52Gln missense_variant 0.62 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4139615 c.141G>A synonymous_variant 0.62 levofloxacin Not assoc w R - Interim
moxifloxacin
isoniazid Not assoc w R - Interim
streptomycin
rifampicin Not assoc w R - Interim
ethambutol
embB 4247776 c.1263G>T synonymous_variant 0.43 ethambutol
embB 4247797 c.1284C>G synonymous_variant 0.57 ethambutol
embB 4247800 c.1287A>T synonymous_variant 0.54 ethambutol
embB 4247803 c.1290G>C synonymous_variant 0.58 ethambutol
embB 4247815 c.1302C>G synonymous_variant 0.58 ethambutol
embB 4247819 p.Val436Ile missense_variant 0.58 ethambutol Uncertain significance
embB 4247914 c.1401G>C synonymous_variant 0.7 ethambutol Not assoc w R - Interim
embB 4247932 c.1419C>G synonymous_variant 0.7 ethambutol