TB-Profiler result

Run: ERR776661
Summary

Run ID: ERR776661

Sample name:

Date: 2024-10-05T02:05:03.128227

Number of reads: 6327064

Percentage reads mapped: 97.64

Median coverage: 134.0

Strain: lineage4.3.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 1.0
lineage4.3.2 Euro-American (LAM) 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.Ser450Leu Assoc w R
isoniazid katG p.Trp161* Assoc w R High-level resistance
ahpC c.-81C>T Uncertain significance Mutation from literature
ethambutol embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gly406Ser Assoc w R
pyrazinamide pncA p.Met175Val Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Gln Assoc w R - Interim
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
rpsL 781687 p.Lys43Arg missense_variant 0.46 streptomycin Assoc w R
rpsL 781821 p.Lys88Gln missense_variant 0.28 streptomycin Assoc w R - Interim
katG 2155629 p.Trp161* stop_gained 0.98 isoniazid Assoc w R High-level resistance
pncA 2288719 p.Met175Val missense_variant 1.0 pyrazinamide Assoc w R
ahpC 2726112 c.-81C>T upstream_gene_variant 0.99 isoniazid Uncertain significance Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.25 ethambutol Assoc w R
embB 4247729 p.Gly406Ser missense_variant 0.72 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
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 490757 c.-26T>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine Uncertain significance
Rv0565c 656323 p.Asn383Thr missense_variant 1.0 ethionamide Uncertain significance
rpoC 764723 p.Phe452Leu missense_variant 0.18 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
tsnR 1854130 c.525C>G synonymous_variant 1.0 linezolid
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2681 2997870 p.Val378Leu missense_variant 1.0 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.99 pyrazinamide Not assoc w R
embC 4242402 p.Arg847His missense_variant 1.0 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R