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Full information on isolate 2006006962 (id:7)

Provenance/primary metadata

id
7
isolate
2006006962
biosample
SAMN01920608
accession number
1291359
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
952 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
204
total length
4,563,168 bp
max length
114,058 bp
mean length
22,369 bp
N50
37,213
L50
39
N90
11,623
L90
124
N95
7,572
L95
148
%GC
34.97
Ns
0
gaps
0
loci tagged
622

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)

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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