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Full information on isolate CSL10083 (id:212)

Provenance/primary metadata

id
212
isolate
CSL10083
biosample
SAMN01886735
accession number
1240692
clade
P1
species
interrogans
serogroup
Pomona
serovar
Unknown
sequencing year
2013
world region
Northern America
country
USA
host
other mammal
sample type
Unknown
source lab
Craig Venter Institute
comments
Sea lion
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
942 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
182
total length
4,574,387 bp
max length
155,590 bp
mean length
25,134 bp
N50
44,679
L50
30
N90
12,867
L90
105
N95
8,619
L95
126
%GC
34.99
Ns
0
gaps
0
loci tagged
622

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-linkage40experimental5 (74 isolates)
Test-75cgMLSTSingle-linkage75experimental5 (30 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (23 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (39 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (39 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (39 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (41 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (30 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 isolates)
Test-60cgMLSTSingle-linkage60experimental5 (74 isolates)
Test-80cgMLSTSingle-linkage80experimental5 (74 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental5 (74 isolates)
Test-75cgMLSTSingle-linkage75experimental5 (30 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (23 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (39 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (39 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (39 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (41 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (30 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 isolates)
Test-60cgMLSTSingle-linkage60experimental5 (74 isolates)
Test-80cgMLSTSingle-linkage80experimental5 (74 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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