TB-Profiler result

Run: SRR13837594
Summary

Run ID: SRR13837594

Sample name:

Date: 2024-04-15T07:52:37.202582

Number of reads: 587644

Percentage reads mapped: 100.0

Median coverage: 20.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
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 fbiC c.1301delC Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fbiC 1304229 c.1301delC frameshift_variant 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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 8880 p.Lys527Gln missense_variant 1.0 levofloxacin
moxifloxacin
rpoB 760972 p.Arg389Leu missense_variant 1.0 rifampicin
rpoC 765111 p.Met581Lys missense_variant 1.0 rifampicin
rpoC 765161 p.Glu598Lys missense_variant 1.0 rifampicin
rpoC 765540 p.Ala724Val missense_variant 1.0 rifampicin
rpoC 767068 c.3699G>T synonymous_variant 1.0 rifampicin
mmpR5 778439 c.-551C>A upstream_gene_variant 1.0 clofazimine
bedaquiline
rplC 801357 p.His183Gln missense_variant 1.0 linezolid
rrs 1472288 n.444delT non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853872 c.267G>T synonymous_variant 1.0 linezolid
tlyA 1917989 p.Ala17Gly missense_variant 1.0 capreomycin
bacA 2063805 c.924G>A synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
bacA 2064585 c.144C>A synonymous_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
ndh 2102525 p.Phe173Tyr missense_variant 1.0 ethionamide
delamanid
isoniazid
ndh 2102538 c.504_505insT frameshift_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Uncertain significance
Rv1979c 2222978 p.Ile63Phe missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223052 p.Glu38Val missense_variant 1.0 clofazimine
bedaquiline
pncA 2289415 c.-174C>G upstream_gene_variant 1.0 pyrazinamide
kasA 2518057 c.-58A>C upstream_gene_variant 1.0 isoniazid
kasA 2518799 p.Pro229Ser missense_variant 1.0 isoniazid
eis 2714983 p.Ala117Glu missense_variant 1.0 amikacin
kanamycin
Rv2477c 2784409 c.-367T>A upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784611 c.-569A>T upstream_gene_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
fbiA 3640404 c.-139C>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3642056 c.522C>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3877967 p.Thr181Ser missense_variant 1.0 rifampicin Uncertain significance
rpoA 3877972 c.535delG frameshift_variant 1.0 rifampicin
clpC1 4039777 c.927_928insG frameshift_variant 1.0 pyrazinamide
glpK 4138934 c.822A>C synonymous_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embB 4247545 p.Ser344Arg missense_variant 1.0 ethambutol Uncertain significance
aftB 4268812 p.Ser9Pro missense_variant 1.0 ethambutol