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Full information on isolate 201601168 (id:341)

Provenance/primary metadata

id
341
isolate
201601168
biosample
SAMEA5168122
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
397 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
470
total length
3,450,639 bp
max length
45,486 bp
mean length
7,342 bp
N50
11,478
L50
95
N90
3,672
L90
290
N95
2,370
L95
347
%GC
35.97
Ns
0
gaps
0
loci tagged
560

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly sizeassembly size too small (fail threshold: 3,500,000)
Minimum N50N50 too low (warn threshold: 20,000)
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
cgMLST54548889

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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