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Full information on isolate Sri Lanka 39 (id:16)

Provenance/primary metadata

id
16
isolate
Sri Lanka 39
biosample
SAMN01920626
accession number
1291355
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
938 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
215
total length
4,852,809 bp
max length
179,397 bp
mean length
22,572 bp
N50
39,737
L50
35
N90
10,587
L90
122
N95
6,730
L95
151
%GC
35.10
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
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-linkage40experimental10 (4 isolates)
Test-75cgMLSTSingle-linkage75experimental10 (12 isolates)
Test-50cgMLSTSingle-linkage50experimental10 (4 isolates)
Test-110cgMLSTSingle-linkage110experimental9 (22 isolates)
Test-150cgMLSTSingle-linkage150experimental9 (22 isolates)
Test-20cgMLSTSingle-linkage20experimental11 (3 isolates)
Test-200cgMLSTSingle-linkage200experimental9 (22 isolates)
Test-220cgMLSTSingle-linkage220experimental9 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental9 (14 isolates)
Test-30cgMLSTSingle-linkage30experimental10 (3 isolates)
Test-300cgMLSTSingle-linkage300experimental9 (25 isolates)
Test-60cgMLSTSingle-linkage60experimental10 (19 isolates)
Test-80cgMLSTSingle-linkage80experimental9 (25 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental10 (4 isolates)
Test-75cgMLSTSingle-linkage75experimental10 (12 isolates)
Test-50cgMLSTSingle-linkage50experimental10 (4 isolates)
Test-10cgMLSTSingle-linkage10experimental12 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental9 (22 isolates)
Test-150cgMLSTSingle-linkage150experimental9 (22 isolates)
Test-20cgMLSTSingle-linkage20experimental11 (3 isolates)
Test-200cgMLSTSingle-linkage200experimental9 (22 isolates)
Test-220cgMLSTSingle-linkage220experimental9 (14 isolates)
Test-250cgMLSTSingle-linkage250experimental9 (14 isolates)
Test-30cgMLSTSingle-linkage30experimental10 (3 isolates)
Test-300cgMLSTSingle-linkage300experimental9 (25 isolates)
Test-60cgMLSTSingle-linkage60experimental10 (19 isolates)
Test-80cgMLSTSingle-linkage80experimental9 (25 isolates)

Schemes and loci

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