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Full information on isolate Fiocruz L1-130 (id:246)

Provenance/primary metadata

id
246
isolate
Fiocruz L1-130
biosample
SAMN02603847
accession number
267671
clade
P1
species
interrogans
serogroup
Icterohaemorrhagiae
serovar
Copenhageni
isolation year
1996
sequencing year
2004
world region
South America
country
Brazil
city
Salvador de Bahia
host
human
sample type
Blood
source lab
Craig Venter Institute
comments
patient with severe leptospirosis during an epidemic
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
1066 updates show details
date entered
2016-12-01
datestamp
2023-02-02

Publications (2)

  • Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2019). Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 13:e0007374
  • Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M (2020). Correction: Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 14:e0008673

Sequence bin

method
Unknown
contigs
2
total length
4,627,366 bp
max length
4,277,185 bp
mean length
2,313,683 bp
N50
4,277,185
L50
1
N90
4,277,185
L90
1
N95
350,181
L95
2
%GC
35.04
Ns
0
gaps
0
loci tagged
1,167

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
cgMLST545545100

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira interrogans Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira interrogans 100%

Analysis performed: 2022-12-05

Similar isolates (determined by classification schemes)

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental6 (146 isolates)
Test-75cgMLSTSingle-linkage75experimental6 (34 isolates)
Test-50cgMLSTSingle-linkage50experimental6 (146 isolates)
Test-10cgMLSTSingle-linkage10experimental58 (30 isolates)
Test-110cgMLSTSingle-linkage110experimental6 (36 isolates)
Test-150cgMLSTSingle-linkage150experimental6 (38 isolates)
Test-20cgMLSTSingle-linkage20experimental54 (36 isolates)
Test-200cgMLSTSingle-linkage200experimental6 (38 isolates)
Test-220cgMLSTSingle-linkage220experimental6 (34 isolates)
Test-250cgMLSTSingle-linkage250experimental6 (34 isolates)
Test-30cgMLSTSingle-linkage30experimental51 (145 isolates)
Test-300cgMLSTSingle-linkage300experimental6 (38 isolates)
Test-60cgMLSTSingle-linkage60experimental6 (146 isolates)
Test-80cgMLSTSingle-linkage80experimental6 (146 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental6 (146 isolates)
Test-75cgMLSTSingle-linkage75experimental6 (34 isolates)
Test-50cgMLSTSingle-linkage50experimental6 (146 isolates)
Test-10cgMLSTSingle-linkage10experimental58 (30 isolates)
Test-110cgMLSTSingle-linkage110experimental6 (36 isolates)
Test-150cgMLSTSingle-linkage150experimental6 (38 isolates)
Test-20cgMLSTSingle-linkage20experimental54 (36 isolates)
Test-200cgMLSTSingle-linkage200experimental6 (38 isolates)
Test-220cgMLSTSingle-linkage220experimental6 (34 isolates)
Test-250cgMLSTSingle-linkage250experimental6 (34 isolates)
Test-30cgMLSTSingle-linkage30experimental51 (145 isolates)
Test-300cgMLSTSingle-linkage300experimental6 (38 isolates)
Test-60cgMLSTSingle-linkage60experimental6 (146 isolates)
Test-80cgMLSTSingle-linkage80experimental6 (146 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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