TB-Profiler result

Run: ERR9119538
Summary

Run ID: ERR9119538

Sample name:

Date: 2024-04-16T12:55:40.346434

Number of reads: 3855943

Percentage reads mapped: 99.71

Median coverage: 122.0

Strain: lineage4.9

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 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.Asp435Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.His445Asn Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Pro69Arg Uncertain significance Mutation from literature
streptomycin gid c.471delG Assoc w R
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 761111 p.Asp435Glu missense_variant 0.99 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289036 p.Pro69Arg missense_variant 1.0 pyrazinamide Uncertain significance Mutation from literature
gid 4407731 c.471delG frameshift_variant 1.0 streptomycin 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 9061 p.Ala587Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
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
PPE35 2168738 p.Phe625Leu missense_variant 1.0 pyrazinamide
ribD 2986913 p.Asp25Glu missense_variant 1.0 para-aminosalicylic_acid
embB 4248003 p.Gln497Leu missense_variant 1.0 ethambutol Uncertain significance
embB 4248005 p.Thr498Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4248009 p.Leu499Pro missense_variant 0.99 ethambutol 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