TB-Profiler result

Run: SRR28044357
Summary

Run ID: SRR28044357

Sample name:

Date: 2024-05-22T10:50:57.836923

Number of reads: 9332703

Percentage reads mapped: 99.71

Median coverage: 262.0

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.Thr400Ala Uncertain significance Mutation from literature
p.Gln432Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rrs n.517C>T 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 761004 p.Thr400Ala missense_variant 1.0 rifampicin Uncertain significance Mutation from literature
rpoB 761101 p.Gln432Pro missense_variant 0.99 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.98 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 810 c.810C>A synonymous_variant 1.0 isoniazid
gyrB 5078 c.-162_-161insG upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 5317 c.78C>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6852 p.Gln538Arg 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 8197 p.Ile299Thr missense_variant 0.34 levofloxacin
moxifloxacin
gyrA 9746 p.Ile815Met missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
ccsA 619567 c.-324C>A upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
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
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.13 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R