TB-Profiler result

Run: SRR21798489
Summary

Run ID: SRR21798489

Sample name:

Date: 2024-10-05T02:41:48.473904

Number of reads: 896089

Percentage reads mapped: 99.83

Median coverage: 28.0

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) RD219 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 657500 c.-30G>A upstream_gene_variant 0.95 ethionamide
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
inhA 1673380 c.-822C>G upstream_gene_variant 0.33 isoniazid
ethionamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156357 c.-246C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv2680 2996031 c.-74G>A upstream_gene_variant 0.13 capreomycin
Rv2680 2996054 c.-51delTinsCAG upstream_gene_variant 0.16 capreomycin
Rv2680 2996060 c.-45T>C upstream_gene_variant 0.17 capreomycin
Rv2680 2996061 c.-44C>G upstream_gene_variant 0.17 capreomycin
Rv2680 2996082 c.-23G>A upstream_gene_variant 0.21 capreomycin
Rv2680 2996083 c.-22C>A upstream_gene_variant 0.21 capreomycin
Rv2680 2996133 p.Arg10Gln missense_variant 0.22 capreomycin
Rv2680 2996142 p.Glu13Gly missense_variant 0.21 capreomycin
Rv2752c 3064944 c.1248G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
fbiA 3640260 c.-283T>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R