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Full information on isolate Hond-utrecht (id:143)

Provenance/primary metadata

id
143
isolate
Hond-utrecht
biosample
SAMEA5168039
clade
P1
species
interrogans
serogroup
Canicola
serovar
Canicola
world region
Western Europe
country
The Netherlands
host
dog
sample type
Unknown
source lab
CNR_leptospirose
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
770 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
204
total length
4,620,756 bp
max length
232,573 bp
mean length
22,651 bp
N50
59,553
L50
25
N90
16,118
L90
81
N95
8,765
L95
101
%GC
35.01
Ns
0
gaps
0
loci tagged
1,164

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
cgMLST54554299

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-linkage10experimental87 (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

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