TB-Profiler result

Run: ERR2515528
Summary

Run ID: ERR2515528

Sample name:

Date: 2024-03-26T20:24:59.306553

Number of reads: 922841

Percentage reads mapped: 99.79

Median coverage: 37.0

Strain: lineage4.9.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.9.1 Euro-American (H37Rv-like) None 1.0
lineage4 Euro-American None 1.0
lineage4.9 Euro-American (H37Rv-like) 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.Glu405Asp Uncertain significance Mutation from literature
pyrazinamide pncA c.464_465dupTG Assoc w R
p.Gln141Pro Assoc w R
streptomycin
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288776 c.464_465dupTG frameshift_variant 0.17 pyrazinamide Assoc w R
pncA 2288820 p.Gln141Pro missense_variant 0.77 pyrazinamide Assoc w R
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol Uncertain significance Mutation from literature
ethA 4326721 c.752dupG frameshift_variant 0.76 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 7567 p.Asp89Gly missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8978 c.1677C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491310 c.528C>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
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
pncA 2289138 p.Leu35Arg missense_variant 1.0 pyrazinamide Not assoc w R - Interim
fbiD 3339385 p.Asp90Asn missense_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv3083 3449820 c.1317G>C synonymous_variant 1.0 ethionamide
embA 4243200 c.-32delG upstream_gene_variant 1.0 ethambutol Uncertain significance
ethA 4326925 p.Ser183Arg missense_variant 0.11 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R