TB-Profiler result

Run: ERR11081269
Summary

Run ID: ERR11081269

Sample name:

Date: 2024-10-05T03:56:08.095230

Number of reads: 6408907

Percentage reads mapped: 99.71

Median coverage: 186.0

Strain: lineage4.7

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) 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.His445Arg Assoc w R
isoniazid inhA p.Ile21Val Uncertain significance Mutation from literature
katG p.Val1Ala Mutation from literature
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embB p.Gly406Cys Assoc w R
pyrazinamide pncA c.66dupC Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.341delA Assoc w R
clofazimine pepQ c.150dupC Assoc w R - Interim
para-aminosalicylic_acid
delamanid
bedaquiline pepQ c.150dupC Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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 761140 p.His445Arg missense_variant 0.99 rifampicin Assoc w R
inhA 1674262 p.Ile21Val missense_variant 1.0 isoniazid Uncertain significance Mutation from literature
katG 2156110 p.Val1Ala missense_variant 1.0 isoniazid Mutation from literature
pncA 2289175 c.66dupC frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
pepQ 2860268 c.150dupC frameshift_variant 1.0 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
embB 4247729 p.Gly406Cys missense_variant 1.0 ethambutol Assoc w R
ethA 4327132 c.341delA 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
dnaA 1126 c.1126C>T synonymous_variant 1.0 isoniazid Not assoc w R - Interim
gyrA 7270 c.-32C>T upstream_gene_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
Rv0010c 13374 p.Ala62Val missense_variant 1.0 isoniazid Uncertain significance
Rv0565c 656743 p.Arg243Leu missense_variant 1.0 ethionamide Uncertain significance
nusG 733897 c.-357A>G upstream_gene_variant 1.0 rifampicin
rpoB 761265 p.Asn487His missense_variant 1.0 rifampicin Uncertain significance
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
sigE 1364215 c.-198A>G upstream_gene_variant 1.0 pyrazinamide
Rv1258c 1407604 c.-264C>T upstream_gene_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834202 p.Asn221Asp missense_variant 1.0 pyrazinamide Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2170675 c.-63G>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
folC 2746280 p.Ile440Ser missense_variant 1.0 para-aminosalicylic_acid
thyA 3073873 p.Ile200Ser missense_variant 0.99 para-aminosalicylic_acid
thyA 3074356 p.Ser39Gln missense_variant 1.0 para-aminosalicylic_acid
rpoA 3877860 c.648C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878970 c.-463C>T upstream_gene_variant 1.0 rifampicin Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269392 p.Val148Met missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R