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Full information on isolate 2006006968 (id:8)

Provenance/primary metadata

id
8
isolate
2006006968
biosample
SAMN01920609
accession number
1291360
clade
P1
species
interrogans
serogroup
Pomona
serovar
Pomona
sequencing year
2013
world region
Northern Africa
country
Egypt
host
human
sample type
Unknown
source lab
Craig Venter Institute
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
948 updates show details
date entered
2016-12-01
datestamp
2023-02-03

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
224
total length
4,555,706 bp
max length
117,002 bp
mean length
20,338 bp
N50
33,291
L50
42
N90
11,035
L90
131
N95
7,229
L95
156
%GC
34.97
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
cgMLST54553898

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 (31 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (24 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (40 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (40 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (40 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (43 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (31 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (45 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (77 isolates)
Test-60cgMLSTSingle-linkage60experimental5 (74 isolates)
Test-80cgMLSTSingle-linkage80experimental5 (74 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental5 (74 isolates)
Test-75cgMLSTSingle-linkage75experimental5 (31 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (24 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (40 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (40 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (40 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (43 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (31 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (45 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (77 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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