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Full information on isolate 201700041 (id:411)

Provenance/primary metadata

id
411
isolate
201700041
biosample
SAMEA5168187
clade
P1
species
interrogans
serogroup
Pomona
serovar
Kennewicki
isolation year
1992
sequencing year
2017
world region
Northern America
country
USA
host
bovine
sample type
Unknown
source lab
CNR_leptospirose
sender
Olivier Schiettekatte, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
449 updates show details
date entered
2017-02-13
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
Illumina
contigs
314
total length
4,400,579 bp
max length
81,015 bp
mean length
14,015 bp
N50
28,299
L50
47
N90
7,521
L90
164
N95
4,316
L95
202
%GC
35.09
Ns
0
gaps
0
loci tagged
617

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-linkage40experimental5 (74 isolates)
Test-75cgMLSTSingle-linkage75experimental5 (30 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (23 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (39 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (39 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (39 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (41 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (30 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 isolates)
Test-60cgMLSTSingle-linkage60experimental5 (74 isolates)
Test-80cgMLSTSingle-linkage80experimental5 (74 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental5 (74 isolates)
Test-75cgMLSTSingle-linkage75experimental5 (30 isolates)
Test-50cgMLSTSingle-linkage50experimental5 (74 isolates)
Test-10cgMLSTSingle-linkage10experimental118 (23 isolates)
Test-110cgMLSTSingle-linkage110experimental5 (39 isolates)
Test-150cgMLSTSingle-linkage150experimental5 (39 isolates)
Test-20cgMLSTSingle-linkage20experimental5 (39 isolates)
Test-200cgMLSTSingle-linkage200experimental5 (41 isolates)
Test-220cgMLSTSingle-linkage220experimental5 (30 isolates)
Test-250cgMLSTSingle-linkage250experimental5 (44 isolates)
Test-30cgMLSTSingle-linkage30experimental5 (73 isolates)
Test-300cgMLSTSingle-linkage300experimental5 (75 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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