Full information on isolate 201601175 (id:347)

Provenance/primary metadata

id: 347
isolate: 201601175
biosample: SAMEA5168127
clade: P1
species: interrogans
serogroup: Icterohaemorrhagiae
serovar: Icterohaemorrhagiae
sequencing year: 2016
world region: Western Europe
country: France
host: dog
sample type: Unknown
source lab: CNR_leptospirose
sender: Olivier Schiettekatte, Institut Pasteur
curator: Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history: 565 updates show details
date entered: 2017-01-31
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: 502
total length: 4,516,102 bp
max length: 65,898 bp
mean length: 8,997 bp
N50: 21,075
L50: 68
N90: 5,150
L90: 224
N95: 3,083
L95: 280
%GC: 35.17
Ns: 0
gaps: 0
loci tagged: 619

Show sequence bin

Assembly checks

Check	Status	Warn/fail reason
Number of contigs		too many contigs (warn threshold: 500)
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	542	99

Analysis

rMLST species identification

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

Analysis performed: 2022-12-05

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	6 (146 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	6 (34 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	6 (146 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	58 (30 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	6 (36 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	6 (38 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	54 (36 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	6 (38 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	6 (34 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	6 (34 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	51 (145 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	6 (38 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	6 (146 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	6 (146 isolates)
Cluster_40_cgMLST	cgMLST	Single-linkage	40	experimental	6 (146 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	6 (34 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	6 (146 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	58 (30 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	6 (36 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	6 (38 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	54 (36 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	6 (38 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	6 (34 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	6 (34 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	51 (145 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	6 (38 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	6 (146 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	6 (146 isolates)

Schemes and loci

All loci
- 16S_typing
- 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

Export:

Analysis: