TB-Profiler result

Run: SRR23402847
Summary

Run ID: SRR23402847

Sample name:

Date: 2024-10-04T17:37:16.439000

Number of reads: 18157735

Percentage reads mapped: 99.65

Median coverage: 494.0

Strain: lineage4.1.2.1;lineage4.8

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.45
lineage4.1.2 Euro-American None 0.46
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.45
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.51
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
dnaA 902 p.Val301Ala missense_variant 0.55 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.46 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.44 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.45 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 760838 c.1032G>A synonymous_variant 0.51 rifampicin
rpoC 764861 p.Leu498Val missense_variant 0.57 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.45 rifampicin Not assoc w R
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 0.52 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834770 p.Gln410Arg missense_variant 0.56 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.48 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1917999 c.60T>C synonymous_variant 0.47 capreomycin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2290014 c.-773T>C upstream_gene_variant 0.56 pyrazinamide
kasA 2518076 c.-39C>T upstream_gene_variant 0.51 isoniazid
eis 2715491 c.-159G>T upstream_gene_variant 0.59 kanamycin
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 0.49 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.49 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626567 p.Ser16Phe missense_variant 0.51 rifampicin
bedaquiline
alr 3841546 c.-126C>A upstream_gene_variant 0.56 cycloserine
alr 3841612 c.-193_-192insC upstream_gene_variant 0.52 cycloserine
embC 4239298 c.-565C>T upstream_gene_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.48 ethambutol Not assoc w R
aftB 4269087 c.-251G>A upstream_gene_variant 0.52 ethambutol
ethA 4326395 p.Gln360Arg missense_variant 0.53 ethionamide Uncertain significance
ethA 4326582 p.Asn298His missense_variant 0.61 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.48 kanamycin
capreomycin
amikacin