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Full information on isolate 201601170 (id:343)

Provenance/primary metadata

id
343
isolate
201601170
biosample
SAMEA5168124
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
432 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
477
total length
3,932,914 bp
max length
44,889 bp
mean length
8,246 bp
N50
13,620
L50
91
N90
4,203
L90
288
N95
2,671
L95
346
%GC
35.68
Ns
0
gaps
0
loci tagged
604

Show sequence bin

Assembly checks

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

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
cgMLST54552997

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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