TB-Profiler result

Run: ERR6866793
Summary

Run ID: ERR6866793

Sample name:

Date: 2024-10-04T17:57:26.869928

Number of reads: 1989621

Percentage reads mapped: 99.78

Median coverage: 52.0

Strain: lineage4.3.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 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.Asp435Val Assoc w R
isoniazid katG p.Ser315Ile Assoc w R - Interim High-level resistance
ethambutol embB p.Glu504Asp Uncertain significance Mutation from literature
pyrazinamide pncA p.Tyr103His Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.752dupG Assoc w R
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 761110 p.Asp435Val missense_variant 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Ile missense_variant 1.0 isoniazid Assoc w R - Interim High-level resistance
pncA 2288935 p.Tyr103His missense_variant 1.0 pyrazinamide Assoc w R
embB 4248025 p.Glu504Asp missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
ethA 4326721 c.752dupG frameshift_variant 1.0 ethionamide 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
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 8040 p.Gly247Ser missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575418 p.Ala24Val missense_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 575820 p.Ser158Leu missense_variant 1.0 isoniazid
ethionamide
mmaA3 738018 p.Phe44Leu missense_variant 1.0 isoniazid
rpoC 764995 c.1626C>G synonymous_variant 1.0 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
rrs 1471777 n.-69C>T upstream_gene_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
inhA 1673787 c.-415G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 1.0 isoniazid
Rv2680 2996026 c.-79A>C upstream_gene_variant 0.87 capreomycin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
thyA 3074591 c.-887_-121del upstream_gene_variant 1.0 para-aminosalicylic_acid
ald 3086772 c.-48A>G upstream_gene_variant 1.0 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641657 c.123C>T synonymous_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249447 c.2934G>A synonymous_variant 0.98 ethambutol Not assoc w R - Interim
whiB6 4338046 c.-984_*124del transcript_ablation 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R