TB-Profiler result

Run: SRR13838014
Summary

Run ID: SRR13838014

Sample name:

Date: 2025-03-04T18:38:03.934003

Number of reads: 2936638

Percentage reads mapped: 100.0

Median coverage: 99.0

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 ethA p.Trp45* 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
ethA 4327340 p.Trp45* stop_gained 1.0 ethionamide 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
gyrA 8646 p.Gln449Lys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9138 p.Gln613Lys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9604 p.Val768Ala missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13326 c.232delC frameshift_variant 1.0 isoniazid Uncertain significance
ccsA 619641 c.-250T>C upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620748 c.858T>G synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
Rv0565c 656228 p.Ala415Ser missense_variant 1.0 ethionamide Uncertain significance
mmaA3 738274 c.-125A>T upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 761853 p.Ile683Val missense_variant 1.0 rifampicin Uncertain significance
mmpL5 777509 c.972G>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779508 c.-603G>C upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406904 c.436dupT frameshift_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
Rv1258c 1407127 p.Arg72Ser missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
inhA 1674552 c.351C>G synonymous_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834079 p.Arg180Cys missense_variant 1.0 pyrazinamide Uncertain significance
bacA 2063798 p.Thr311Ser missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2168448 p.Gln722Pro missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2221876 p.Val430Glu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2518036 c.-78delG upstream_gene_variant 1.0 isoniazid Uncertain significance
kasA 2518088 c.-27T>A upstream_gene_variant 1.0 isoniazid Uncertain significance
eis 2714449 p.Trp295Ser missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2714773 p.Pro187Gln missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2715525 c.-193G>T upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726611 c.419_420insA frameshift_variant 1.0 isoniazid Uncertain significance
folC 2747455 c.144C>A synonymous_variant 1.0 para-aminosalicylic_acid Uncertain significance
pepQ 2859723 c.696T>C synonymous_variant 0.99 bedaquiline Uncertain significance
clofazimine Not assoc w R - Interim
ribD 2987540 c.702G>T synonymous_variant 1.0 para-aminosalicylic_acid Uncertain significance
fbiD 3339321 c.204G>A synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
clpC1 4038436 p.Ala757Ser missense_variant 1.0 pyrazinamide Uncertain significance
embC 4239186 c.-677A>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4242635 p.Ala925Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4249145 c.2634delC frameshift_variant 1.0 ethambutol Uncertain significance
ubiA 4269803 p.Ala11Pro missense_variant 1.0 ethambutol Uncertain significance
ethA 4326689 p.Lys262Thr missense_variant 1.0 ethionamide Uncertain significance
ethA 4326849 p.Pro209Thr missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338822 c.-301A>C upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance