TB-Profiler result

Run: SRR13837689
Summary

Run ID: SRR13837689

Sample name:

Date: 2024-10-03T20:34:32.966023

Number of reads: 2966217

Percentage reads mapped: 97.93

Median coverage: 100.0

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
gyrA 9502 p.Arg734His missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13527 p.Ser11* stop_gained 1.0 isoniazid Uncertain significance
rpoB 759681 c.-126C>T upstream_gene_variant 1.0 rifampicin
rpoB 761239 p.Cys478Tyr missense_variant 0.99 rifampicin
mmpL5 776185 p.Lys766Glu missense_variant 1.0 bedaquiline
clofazimine
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0 bedaquiline
clofazimine
embR 1417986 c.-639T>A upstream_gene_variant 1.0 ethambutol
rrs 1472865 n.1020C>G non_coding_transcript_exon_variant 0.98 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1918063 p.Pro42Ala missense_variant 1.0 capreomycin
ndh 2102985 p.Ile20Val missense_variant 1.0 isoniazid
delamanid
ethionamide
katG 2155856 p.Thr86Ser missense_variant 0.98 isoniazid
PPE35 2169233 c.1379delT frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv2752c 3065376 c.815delT frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066351 c.-160G>T upstream_gene_variant 0.98 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyX 3067731 p.Val72Ala missense_variant 1.0 para-aminosalicylic_acid
thyX 3067825 p.Arg41Gly missense_variant 0.98 para-aminosalicylic_acid
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
Rv3083 3448707 c.204G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv3083 3449768 p.Thr422Lys missense_variant 1.0 ethionamide
lpqB 3623219 c.1692A>G synonymous_variant 1.0 rifampicin
bedaquiline
mtrA 3627790 c.-441A>G upstream_gene_variant 1.0 rifampicin
bedaquiline
fbiB 3641403 c.-132C>T upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
alr 3841257 p.His55Leu missense_variant 1.0 cycloserine
rpoA 3877601 p.Gln303* stop_gained 0.98 rifampicin
ddn 3986668 c.-176T>C upstream_gene_variant 1.0 pretomanid
delamanid
embC 4239401 c.-462A>C upstream_gene_variant 1.0 ethambutol
embC 4241864 p.Leu668Met missense_variant 1.0 ethambutol
embB 4245557 c.-957G>A upstream_gene_variant 1.0 ethambutol
ethA 4327092 p.Ala128Pro missense_variant 1.0 ethionamide
gid 4408151 p.Leu18Val missense_variant 1.0 streptomycin