Full information on isolate 5399 (id:102)

Provenance/primary metadata

id
102
isolate
5399
biosample
SAMN02436587
accession number
GCF_000243715.2
clade
P2
species
broomii
serogroup
Unknown
serovar
Unknown
sequencing year
2012
world region
Western Europe
country
Denmark
host
human
sample type
Blood
source lab
Craig Venter Institute
sender
Julien Guglielmini, Institut Pasteur
curator
Jean-Fran├žois Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history
1022 updates show details
date entered
2016-12-01
datestamp
2024-05-24

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

contigs
10
total length
4,485,045 bp
max length
3,575,710 bp
mean length
448,505 bp
N50
3,575,710
L50
1
N90
145,065
L90
3
N95
139,056
L95
4
%GC
42.93
Ns
0
gaps
0
loci tagged
1,118

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
cgMLST54552395

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira broomii Spirochaetota > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira broomii 100%

Analysis performed: 2024-01-11

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-linkage40experimental60 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental59 (2 isolates)
Test-30cgMLSTSingle-linkage30experimental62 (2 isolates)
Test-60cgMLSTSingle-linkage60experimental59 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental56 (2 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental60 (2 isolates)
Test-75cgMLSTSingle-linkage75experimental57 (1 isolate)
Test-50cgMLSTSingle-linkage50experimental59 (2 isolates)
Test-10cgMLSTSingle-linkage10experimental69 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental56 (1 isolate)
Test-150cgMLSTSingle-linkage150experimental55 (1 isolate)
Test-20cgMLSTSingle-linkage20experimental65 (1 isolate)
Test-200cgMLSTSingle-linkage200experimental54 (1 isolate)
Test-220cgMLSTSingle-linkage220experimental53 (1 isolate)
Test-250cgMLSTSingle-linkage250experimental52 (1 isolate)
Test-30cgMLSTSingle-linkage30experimental62 (2 isolates)
Test-300cgMLSTSingle-linkage300experimental49 (1 isolate)
test40_capture_cgMLSTcapture_cgMLSTSingle-linkage40experimental17 (1 isolate)
Test-60cgMLSTSingle-linkage60experimental59 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental56 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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