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Full information on isolate Hardjoprajitno (id:31)

Provenance/primary metadata

id
31
isolate
Hardjoprajitno
biosample
SAMN04102139
accession number
38347
clade
P1
species
interrogans
serogroup
Sejroe
serovar
Hardjo
sequencing year
2015
world region
South-eastern Asia
country
Indonesia
host
human
sample type
Kidney
source lab
Craig Venter Institute
sender
Julien Guglielmini, Institut Pasteur
curator
Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history
698 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
2
total length
4,692,322 bp
max length
4,339,653 bp
mean length
2,346,161 bp
N50
4,339,653
L50
1
N90
4,339,653
L90
1
N95
352,669
L95
2
%GC
35.00
Ns
29599
gaps
66
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
cgMLST54553598

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-linkage40experimental19 (11 isolates)
Test-75cgMLSTSingle-linkage75experimental19 (5 isolates)
Test-50cgMLSTSingle-linkage50experimental19 (11 isolates)
Test-110cgMLSTSingle-linkage110experimental18 (5 isolates)
Test-150cgMLSTSingle-linkage150experimental17 (5 isolates)
Test-200cgMLSTSingle-linkage200experimental17 (5 isolates)
Test-220cgMLSTSingle-linkage220experimental17 (5 isolates)
Test-250cgMLSTSingle-linkage250experimental17 (5 isolates)
Test-30cgMLSTSingle-linkage30experimental116 (11 isolates)
Test-300cgMLSTSingle-linkage300experimental17 (5 isolates)
Test-60cgMLSTSingle-linkage60experimental19 (11 isolates)
Test-80cgMLSTSingle-linkage80experimental18 (11 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental19 (11 isolates)
Test-75cgMLSTSingle-linkage75experimental19 (5 isolates)
Test-50cgMLSTSingle-linkage50experimental19 (11 isolates)
Test-10cgMLSTSingle-linkage10experimental23 (1 isolate)
Test-110cgMLSTSingle-linkage110experimental18 (5 isolates)
Test-150cgMLSTSingle-linkage150experimental17 (5 isolates)
Test-20cgMLSTSingle-linkage20experimental20 (1 isolate)
Test-200cgMLSTSingle-linkage200experimental17 (5 isolates)
Test-220cgMLSTSingle-linkage220experimental17 (5 isolates)
Test-250cgMLSTSingle-linkage250experimental17 (5 isolates)
Test-30cgMLSTSingle-linkage30experimental116 (11 isolates)
Test-300cgMLSTSingle-linkage300experimental17 (5 isolates)
Test-60cgMLSTSingle-linkage60experimental19 (11 isolates)
Test-80cgMLSTSingle-linkage80experimental18 (11 isolates)

Schemes and loci

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