TB-Profiler result

Run: ERR4812359
Summary

Run ID: ERR4812359

Sample name:

Date: 2024-03-27T03:28:45.292845

Number of reads: 3474481

Percentage reads mapped: 99.73

Median coverage: 110.0

Strain: lineage4.1.1;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 0.4
lineage4.1 Euro-American None 0.56
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.61
lineage4.3.3 Euro-American (LAM) RD115 0.45
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.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Tyr319Ser Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
streptomycin gid p.Pro84Leu Assoc w R - Interim
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 761110 p.Asp435Val missense_variant 0.56 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.42 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.38 pyrazinamide Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.38 ethambutol Assoc w R
gid 4407952 p.Pro84Leu missense_variant 0.44 streptomycin Assoc w R - Interim
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
gyrB 5858 p.Asn207Asp missense_variant 0.55 levofloxacin Uncertain significance
moxifloxacin 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 8040 p.Gly247Ser missense_variant 0.4 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
Rv0565c 657269 p.Ser68Pro missense_variant 0.6 ethionamide Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.52 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.63 linezolid
sigE 1364638 p.Gly76Arg missense_variant 0.63 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.4 pyrazinamide Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917792 c.-148G>A upstream_gene_variant 0.49 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168998 p.Ile539Val missense_variant 0.44 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290113 c.-872G>A upstream_gene_variant 0.54 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.39 isoniazid
Rv2477c 2783921 p.Gly41Glu missense_variant 0.55 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Not assoc w R
amikacin Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.4 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.44 pyrazinamide Not assoc w R
embC 4239629 c.-234G>A upstream_gene_variant 0.64 ethambutol
embC 4242182 p.Ala774Ser missense_variant 0.42 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 0.56 ethambutol Not assoc w R
embB 4248555 p.Gly681Asp missense_variant 0.58 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.58 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 4408156 p.Leu16Arg missense_variant 0.35 streptomycin Not assoc w R