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Full information on isolate HAI1594 (id:288)

Provenance/primary metadata

id
288
isolate
HAI1594
biosample
SAMN02436413
accession number
1193060
clade
P1
species
interrogans
serogroup
Unknown
serovar
Unknown
sequencing year
2012
world region
South America
country
Peru
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
1059 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
41
total length
4,608,233 bp
max length
870,200 bp
mean length
112,396 bp
N50
263,356
L50
6
N90
66,429
L90
19
N95
41,312
L95
23
%GC
35.01
Ns
0
gaps
0
loci tagged
621

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
cgMLST54554499

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

Tools

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