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Full information on isolate RGA (id:97)

Provenance/primary metadata

id
97
isolate
RGA
biosample
SAMN01920605
accession number
1291351
clade
P1
species
interrogans
serogroup
Icterohaemorrhagiae
serovar
Icterohaemorrhagiae
sequencing year
2013
world region
Western Europe
country
Belgium
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
1049 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
143
total length
4,600,016 bp
max length
214,076 bp
mean length
32,168 bp
N50
61,199
L50
23
N90
15,703
L90
79
N95
9,525
L95
97
%GC
35.00
Ns
0
gaps
0
loci tagged
1,159

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
cgMLST54554099

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-linkage40experimental6 (146 isolates)
Test-75cgMLSTSingle-linkage75experimental6 (34 isolates)
Test-50cgMLSTSingle-linkage50experimental6 (146 isolates)
Test-10cgMLSTSingle-linkage10experimental58 (30 isolates)
Test-110cgMLSTSingle-linkage110experimental6 (36 isolates)
Test-150cgMLSTSingle-linkage150experimental6 (38 isolates)
Test-20cgMLSTSingle-linkage20experimental54 (36 isolates)
Test-200cgMLSTSingle-linkage200experimental6 (38 isolates)
Test-220cgMLSTSingle-linkage220experimental6 (34 isolates)
Test-250cgMLSTSingle-linkage250experimental6 (34 isolates)
Test-30cgMLSTSingle-linkage30experimental51 (145 isolates)
Test-300cgMLSTSingle-linkage300experimental6 (38 isolates)
Test-60cgMLSTSingle-linkage60experimental6 (146 isolates)
Test-80cgMLSTSingle-linkage80experimental6 (146 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental6 (146 isolates)
Test-75cgMLSTSingle-linkage75experimental6 (34 isolates)
Test-50cgMLSTSingle-linkage50experimental6 (146 isolates)
Test-10cgMLSTSingle-linkage10experimental58 (30 isolates)
Test-110cgMLSTSingle-linkage110experimental6 (36 isolates)
Test-150cgMLSTSingle-linkage150experimental6 (38 isolates)
Test-20cgMLSTSingle-linkage20experimental54 (36 isolates)
Test-200cgMLSTSingle-linkage200experimental6 (38 isolates)
Test-220cgMLSTSingle-linkage220experimental6 (34 isolates)
Test-250cgMLSTSingle-linkage250experimental6 (34 isolates)
Test-30cgMLSTSingle-linkage30experimental51 (145 isolates)
Test-300cgMLSTSingle-linkage300experimental6 (38 isolates)
Test-60cgMLSTSingle-linkage60experimental6 (146 isolates)
Test-80cgMLSTSingle-linkage80experimental6 (146 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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