TB-Profiler result

Run: SRR13837456
Summary

Run ID: SRR13837456

Sample name:

Date: 2025-03-08T01:31:50.231131

Number of reads: 2936472

Percentage reads mapped: 100.0

Median coverage: 98.0

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 c.905delT 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 4326568 c.905delT frameshift_variant 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 8820 p.Asp507His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575967 p.Val207Asp missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 759961 p.Thr52Asn missense_variant 1.0 rifampicin Uncertain significance
rpoB 763050 p.Leu1082Met missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775701 p.Pro927Gln missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778828 c.-348G>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800500 c.-309A>C upstream_gene_variant 1.0 linezolid Uncertain significance
rplC 801353 p.Val182Ala missense_variant 1.0 linezolid Uncertain significance
Rv1129c 1253966 p.Leu190Trp missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1304512 p.Val528Ile missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embR 1417704 c.-357T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
rpsA 1834175 p.Arg212* stop_gained 1.0 pyrazinamide Uncertain significance
katG 2156840 c.-729C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222085 c.1080G>C synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ald 3087218 p.Met133Ile missense_variant 0.99 cycloserine Uncertain significance
whiB7 3568679 p.Val1Leu missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
whiB7 3568989 c.-310A>C upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
mtrB 3625440 p.Gly392Arg missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
clpC1 4040066 c.639G>T synonymous_variant 1.0 pyrazinamide Uncertain significance
embC 4241259 c.1397_1398insT frameshift_variant 1.0 ethambutol Uncertain significance
embA 4243358 c.126C>T synonymous_variant 1.0 ethambutol Uncertain significance
embA 4243469 c.237C>T synonymous_variant 1.0 ethambutol Uncertain significance
embB 4248436 c.1923C>T synonymous_variant 1.0 ethambutol Uncertain significance
ubiA 4269557 p.Ala93Pro missense_variant 1.0 ethambutol Uncertain significance