TB-Profiler result

Run: ERR11043121
Summary

Run ID: ERR11043121

Sample name:

Date: 2024-04-15T06:04:19.393450

Number of reads: 1961741

Percentage reads mapped: 99.58

Median coverage: 34.0

Strain: lineage4.6.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6.5 Euro-American None 1.0
lineage4.6 Euro-American None 1.0
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 embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Trp68Cys Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Asn236Lys Assoc w R
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 1.0 rifampicin Assoc w R
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289038 p.Trp68Cys missense_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 1.0 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 1186 p.Glu396Lys missense_variant 1.0 isoniazid Uncertain significance
dnaA 1326 p.Gln442His missense_variant 1.0 isoniazid Uncertain significance
gyrB 5489 p.Ile84Val missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490756 c.-27T>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
nusG 734156 c.-98C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777974 c.507C>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
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 1475803 n.2146T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
fabG1 1673346 c.-94C>G upstream_gene_variant 0.18 ethionamide
isoniazid
fabG1 1673349 c.-91G>C upstream_gene_variant 0.18 ethionamide
isoniazid
fabG1 1673357 c.-83G>A upstream_gene_variant 0.22 ethionamide
isoniazid
fabG1 1673359 c.-81T>C upstream_gene_variant 0.22 ethionamide
isoniazid
fabG1 1673361 c.-79C>G upstream_gene_variant 0.23 ethionamide
isoniazid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.31 ethionamide
isoniazid
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
folC 2746995 p.Val202Ile missense_variant 1.0 para-aminosalicylic_acid
fbiA 3640346 c.-196delA upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
alr 3841546 c.-126C>A upstream_gene_variant 0.18 cycloserine
clpC1 4038332 c.2373C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
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