TB-Profiler result

Run: ERR4818394
Summary

Run ID: ERR4818394

Sample name:

Date: 2024-03-26T18:33:38.810729

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 ethionamide
isoniazid
mshA 575662 c.315C>G synonymous_variant 0.33 ethionamide
isoniazid
mshA 575674 c.327G>C synonymous_variant 0.38 ethionamide
isoniazid
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 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626155 c.457_459delGCGinsTC frameshift_variant&missense_variant 0.7 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626158 c.456C>T synonymous_variant 0.7 bedaquiline
rifampicin
mtrB 3626170 c.444T>C synonymous_variant 0.58 bedaquiline
rifampicin
mtrB 3626179 c.435A>G synonymous_variant 0.58 bedaquiline
rifampicin
mtrB 3626185 c.429T>G synonymous_variant 0.54 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626188 c.424_426delTCTinsAC frameshift_variant&missense_variant 0.54 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3626194 c.420T>C synonymous_variant 0.54 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626203 c.411G>A synonymous_variant 0.47 bedaquiline
rifampicin
mtrB 3626206 c.408T>C synonymous_variant 0.47 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626209 c.405T>C synonymous_variant 0.44 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3627209 c.-596G>A upstream_gene_variant 0.6 bedaquiline
rifampicin
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 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139601 p.Arg52Gln missense_variant 0.62 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139615 c.141G>A synonymous_variant 0.62 ethambutol
moxifloxacin
streptomycin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
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 c.1306_1308delGTTinsAC frameshift_variant&missense_variant 0.58 ethambutol
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