TB-Profiler result

Run: ERR10680183
Summary

Run ID: ERR10680183

Sample name:

Date: 2024-10-04T03:21:08.776954

Number of reads: 5803358

Percentage reads mapped: 99.76

Median coverage: 182.0

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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Leu172Pro Assoc w R
c.454delG Assoc w R
p.Val139Ala Assoc w R
p.Ser67Pro Assoc w R
streptomycin
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288727 p.Leu172Pro missense_variant 0.16 pyrazinamide Assoc w R
pncA 2288787 c.454delG frameshift_variant 0.12 pyrazinamide Assoc w R
pncA 2288826 p.Val139Ala missense_variant 0.12 pyrazinamide Assoc w R
pncA 2289043 p.Ser67Pro missense_variant 0.15 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 759395 c.-412G>A upstream_gene_variant 1.0 rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv2752c 3066008 p.Pro62Ser missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086739 c.-81G>A upstream_gene_variant 1.0 cycloserine
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4408054 p.Leu50Pro missense_variant 1.0 streptomycin Uncertain significance