TB-Profiler result

Run: SRR13837819
Summary

Run ID: SRR13837819

Sample name:

Date: 2024-04-16T05:49:39.881637

Number of reads: 2938385

Percentage reads mapped: 97.01

Median coverage: 99.0

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 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
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
gyrB 5540 p.Thr101Ser missense_variant 1.0 levofloxacin
moxifloxacin
nusG 734249 c.-5A>G upstream_gene_variant 1.0 rifampicin
nusG 734917 p.Phe222Leu missense_variant 1.0 rifampicin
rpoB 760558 c.753delC frameshift_variant 1.0 rifampicin
rpoB 760611 p.Leu269Val missense_variant 1.0 rifampicin
rpoB 762490 p.Val895Gly missense_variant 1.0 rifampicin
rpoC 765707 c.2340delA frameshift_variant 1.0 rifampicin
Rv1129c 1253076 c.1459T>G stop_lost&splice_region_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
tsnR 1854059 p.Leu152Val missense_variant 1.0 linezolid
ndh 2101690 p.Glu451Asp missense_variant 1.0 ethionamide
delamanid
isoniazid
PPE35 2168961 p.Gly551Val missense_variant 1.0 pyrazinamide
PPE35 2170927 c.-315A>G upstream_gene_variant 1.0 pyrazinamide
Rv1979c 2222084 p.Leu361Ile missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2222431 p.Met245Arg missense_variant 1.0 clofazimine
bedaquiline
Rv1979c 2223625 c.-461C>A upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3087020 c.201C>T synonymous_variant 1.0 cycloserine
mtrB 3625191 p.Val475Leu missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625358 p.Asn419Thr missense_variant 1.0 bedaquiline
rifampicin
mtrB 3625682 p.Leu311Gln missense_variant 1.0 bedaquiline
rifampicin
alr 3841157 c.264A>G synonymous_variant 1.0 cycloserine
rpoA 3878047 p.Ala154Asp missense_variant 1.0 rifampicin
embB 4247452 c.939C>T synonymous_variant 1.0 ethambutol
ethR 4326799 c.-750G>A upstream_gene_variant 1.0 ethionamide