Full information on isolate 2006006986 (id:3)

Provenance/primary metadata

id: 3
isolate: 2006006986
biosample: SAMN02436575
accession number: 1193017
clade: P1
species: interrogans
serogroup: Grippotyphosa
serovar: Grippotyphosa
sequencing year: 2012
world region: Northern Africa
country: Egypt
host: human
sample type: Unknown
source lab: Craig Venter Institute
sender: Julien Guglielmini, Institut Pasteur, France
curator: Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history: 718 updates show details
date entered: 2016-12-01
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: Unknown
contigs: 60
total length: 4,935,986 bp
max length: 745,790 bp
mean length: 82,267 bp
N50: 348,371
L50: 5
N90: 63,695
L90: 19
N95: 24,999
L95: 25
%GC: 35.09
Ns: 1
gaps: 1
loci tagged: 1,167

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs
Assembly size
Minimum N50
%GC

Annotation quality metrics

Scheme completion

Scheme	Scheme loci	Designated loci	Annotation
Scheme	Scheme loci	Designated loci	Score	Status
cgMLST	545	528	96

Analysis

rMLST species identification

Rank	Taxon	Taxonomy	Support	Matches
SPECIES	Leptospira interrogans	Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira interrogans	100%

Analysis performed: 2022-12-02

Similar isolates (determined by classification schemes)

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

Classification scheme	Underlying scheme	Clustering method	Mismatch threshold	Status	Group
Cluster_40_cgMLST	cgMLST	Single-linkage	40	experimental	2 (7 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	2 (5 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	2 (7 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	2 (4 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	2 (7 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	2 (7 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	2 (6 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	2 (7 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	2 (5 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	2 (5 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	2 (7 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	2 (12 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	2 (7 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	2 (7 isolates)
Cluster_40_cgMLST	cgMLST	Single-linkage	40	experimental	2 (7 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	2 (5 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	2 (7 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	2 (4 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	2 (7 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	2 (7 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	2 (6 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	2 (7 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	2 (5 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	2 (5 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	2 (7 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	2 (12 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	2 (7 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	2 (7 isolates)

Schemes and loci

All loci
- 16S_typing
- capture_cgMLST
- cgMLST
- Ictero
- lfb1
- MLST_1
- MLST_2
- MLST_3
- Ribosomal MLST
- Loci not in schemes

Navigate and select schemes within tree to display allele designations

Tools

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Analysis: