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Full information on isolate UI 09931 (id:40)

Provenance/primary metadata

id
40
isolate
UI 09931
biosample
SAMN02436592
accession number
1049767
clade
P1
species
borgpetersenii
serogroup
Javanica
serovar
Javanica
sequencing year
2012
world region
South-eastern Asia
country
Laos
host
human
sample type
Unknown
source lab
Craig Venter Institute
sender
Julien Guglielmini, Institut Pasteur
curator
Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history
969 updates show details
date entered
2016-12-01
datestamp
2024-04-17

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
31
total length
3,907,928 bp
max length
838,281 bp
mean length
126,063 bp
N50
195,075
L50
6
N90
79,753
L90
17
N95
75,112
L95
20
%GC
40.09
Ns
0
gaps
0
loci tagged
1,166

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
cgMLST54549290

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira borgpetersenii Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira borgpetersenii 100%

Analysis performed: 2022-12-05

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental267 (38 isolates)
Test-75cgMLSTSingle-linkage75experimental24 (4 isolates)
Test-50cgMLSTSingle-linkage50experimental24 (39 isolates)
Test-110cgMLSTSingle-linkage110experimental23 (11 isolates)
Test-150cgMLSTSingle-linkage150experimental22 (11 isolates)
Test-20cgMLSTSingle-linkage20experimental26 (4 isolates)
Test-200cgMLSTSingle-linkage200experimental22 (11 isolates)
Test-220cgMLSTSingle-linkage220experimental22 (4 isolates)
Test-250cgMLSTSingle-linkage250experimental22 (4 isolates)
Test-30cgMLSTSingle-linkage30experimental25 (30 isolates)
Test-300cgMLSTSingle-linkage300experimental8 (146 isolates)
Test-60cgMLSTSingle-linkage60experimental24 (39 isolates)
Test-80cgMLSTSingle-linkage80experimental23 (39 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental267 (38 isolates)
Test-75cgMLSTSingle-linkage75experimental24 (4 isolates)
Test-50cgMLSTSingle-linkage50experimental24 (39 isolates)
Test-10cgMLSTSingle-linkage10experimental29 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental23 (11 isolates)
Test-150cgMLSTSingle-linkage150experimental22 (11 isolates)
Test-20cgMLSTSingle-linkage20experimental26 (4 isolates)
Test-200cgMLSTSingle-linkage200experimental22 (11 isolates)
Test-220cgMLSTSingle-linkage220experimental22 (4 isolates)
Test-250cgMLSTSingle-linkage250experimental22 (4 isolates)
Test-30cgMLSTSingle-linkage30experimental25 (30 isolates)
Test-300cgMLSTSingle-linkage300experimental8 (146 isolates)
Test-60cgMLSTSingle-linkage60experimental24 (39 isolates)
Test-80cgMLSTSingle-linkage80experimental23 (39 isolates)

Schemes and loci

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