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Full information on isolate 201502613 (id:295)

Provenance/primary metadata

id
295
isolate
201502613
biosample
SAMEA5168085
clade
P1
species
interrogans
serogroup
Canicola
serovar
Unknown
sequencing year
2015
world region
South America
country
Venezuela
host
human
sample type
Blood
source lab
Venezuelan Institute for Scientific
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
767 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
166
total length
4,672,978 bp
max length
181,057 bp
mean length
28,151 bp
N50
64,942
L50
23
N90
21,101
L90
70
N95
10,884
L95
84
%GC
34.95
Ns
0
gaps
0
loci tagged
615

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
cgMLST54553998

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)

Some groups only contain this isolate. Show single groups

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

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental28 (53 isolates)
Test-75cgMLSTSingle-linkage75experimental27 (14 isolates)
Test-50cgMLSTSingle-linkage50experimental27 (53 isolates)
Test-110cgMLSTSingle-linkage110experimental26 (25 isolates)
Test-150cgMLSTSingle-linkage150experimental25 (27 isolates)
Test-20cgMLSTSingle-linkage20experimental29 (27 isolates)
Test-200cgMLSTSingle-linkage200experimental25 (27 isolates)
Test-220cgMLSTSingle-linkage220experimental25 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental28 (53 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 isolates)
Test-60cgMLSTSingle-linkage60experimental27 (53 isolates)
Test-80cgMLSTSingle-linkage80experimental26 (53 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental28 (53 isolates)
Test-75cgMLSTSingle-linkage75experimental27 (14 isolates)
Test-50cgMLSTSingle-linkage50experimental27 (53 isolates)
Test-10cgMLSTSingle-linkage10experimental165 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental26 (25 isolates)
Test-150cgMLSTSingle-linkage150experimental25 (27 isolates)
Test-20cgMLSTSingle-linkage20experimental29 (27 isolates)
Test-200cgMLSTSingle-linkage200experimental25 (27 isolates)
Test-220cgMLSTSingle-linkage220experimental25 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental28 (53 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 isolates)
Test-60cgMLSTSingle-linkage60experimental27 (53 isolates)
Test-80cgMLSTSingle-linkage80experimental26 (53 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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