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Full information on isolate 201601172 (id:345)

Provenance/primary metadata

id
345
isolate
201601172
biosample
SAMEA5168126
clade
P1
species
interrogans
serogroup
Pomona
serovar
Unknown
sequencing year
2016
world region
Western Europe
country
France
host
dog
sample type
Unknown
source lab
CNR_leptospirose
sender
Olivier Schiettekatte, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
445 updates show details
date entered
2017-01-31
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
4,544,893 bp
max length
198,210 bp
mean length
27,379 bp
N50
57,044
L50
22
N90
17,858
L90
73
N95
12,437
L95
89
%GC
34.92
Ns
0
gaps
0
loci tagged
620

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
cgMLST54554499

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-linkage10experimental179 (7 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-linkage10experimental179 (7 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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