TB-Profiler result

Run: ERR4872174

Summary

Run ID: ERR4872174

Sample name:

Date: 2024-04-14T10:04:59.193071

Number of reads: 4577449

Percentage reads mapped: 99.08

Median coverage: 145.0

Strain: lineage4.6.4

Spoligotype:

Drug-resistance: MDR-TB


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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.99
lineage4.6.4 Euro-American None 0.99
lineage4 Euro-American 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 rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Gly406Ala Assoc w R
pyrazinamide pncA p.Thr160Pro Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288764 p.Thr160Pro missense_variant 0.99 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.98 ethambutol Uncertain significance Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.98 ethambutol 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
dnaA 29 p.Thr10Ser missense_variant 0.99 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761461 p.Arg552Leu missense_variant 0.98 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 775733 c.2748C>T synonymous_variant 1.0 clofazimine
bedaquiline
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 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474750 n.1093C>T non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156724 c.-613C>T upstream_gene_variant 0.99 isoniazid
Rv1979c 2222795 p.Asp124Asn missense_variant 0.98 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714393 p.Val314Leu missense_variant 0.99 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2783928 p.Pro39Ser missense_variant 0.97 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv3083 3449945 p.Gly481Asp missense_variant 0.99 ethionamide Uncertain significance
fbiB 3641526 c.-9A>C upstream_gene_variant 0.99 clofazimine
pretomanid
delamanid
rpoA 3878745 c.-238C>G upstream_gene_variant 0.99 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407847 p.Ala119Asp missense_variant 0.98 streptomycin Uncertain significance