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Full information on isolate Sri Lanka 30 (id:15)

Provenance/primary metadata

id
15
isolate
Sri Lanka 30
biosample
SAMN01920597
accession number
1291356
clade
P1
species
interrogans
serogroup
Pyrogenes
serovar
Pyrogenes
sequencing year
2013
world region
Southern Asia
country
Sri Lanka
host
other rodent
sample type
Unknown
source lab
Craig Venter Institute
comments
Cricetomys sp.
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
878 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
208
total length
5,032,494 bp
max length
199,454 bp
mean length
24,195 bp
N50
41,720
L50
37
N90
12,500
L90
118
N95
7,819
L95
143
%GC
35.20
Ns
0
gaps
0
loci tagged
1,167

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
cgMLST54553898

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)

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-linkage40experimental9 (2 isolates)
Test-75cgMLSTSingle-linkage75experimental9 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental9 (3 isolates)
Test-110cgMLSTSingle-linkage110experimental9 (22 isolates)
Test-150cgMLSTSingle-linkage150experimental9 (22 isolates)
Test-20cgMLSTSingle-linkage20experimental10 (2 isolates)
Test-200cgMLSTSingle-linkage200experimental9 (22 isolates)
Test-220cgMLSTSingle-linkage220experimental9 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental9 (14 isolates)
Test-30cgMLSTSingle-linkage30experimental9 (2 isolates)
Test-300cgMLSTSingle-linkage300experimental9 (25 isolates)
Test-60cgMLSTSingle-linkage60experimental9 (3 isolates)
Test-80cgMLSTSingle-linkage80experimental9 (25 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental9 (2 isolates)
Test-75cgMLSTSingle-linkage75experimental9 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental9 (3 isolates)
Test-10cgMLSTSingle-linkage10experimental11 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental9 (22 isolates)
Test-150cgMLSTSingle-linkage150experimental9 (22 isolates)
Test-20cgMLSTSingle-linkage20experimental10 (2 isolates)
Test-200cgMLSTSingle-linkage200experimental9 (22 isolates)
Test-220cgMLSTSingle-linkage220experimental9 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental9 (14 isolates)
Test-30cgMLSTSingle-linkage30experimental9 (2 isolates)
Test-300cgMLSTSingle-linkage300experimental9 (25 isolates)
Test-60cgMLSTSingle-linkage60experimental9 (3 isolates)
Test-80cgMLSTSingle-linkage80experimental9 (25 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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