Full information on isolate Prea (id:240)

Provenance/primary metadata

id
240
isolate
Prea
biosample
SAMN04009303
accession number
173
clade
P1
species
interrogans
serogroup
Unknown
serovar
Unknown
sequencing year
2015
world region
South America
country
Brazil
host
other rodent
sample type
Unknown
source lab
Craig Venter Institute
comments
Guinea pig
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
945 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
106
total length
4,441,322 bp
max length
252,051 bp
mean length
41,900 bp
N50
46,508
L50
31
N90
20,937
L90
82
N95
18,902
L95
94
%GC
35.18
Ns
4
gaps
2
loci tagged
550

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
cgMLST54547687

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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