Full information on isolate UI 08452 (id:41)

Provenance/primary metadata

id: 41
isolate: UI 08452
biosample: SAMN02436590
accession number: 1049935
clade: P1
species: interrogans
serogroup: Unknown
serovar: Unknown
sequencing year: 2012
world region: South-eastern Asia
country: Laos
host: human
sample type: Unknown
source lab: Craig Venter Institute
sender: Julien Guglielmini, Institut Pasteur
curator: Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history: 950 updates show details
date entered: 2016-12-01
datestamp: 2024-04-17

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: 272
total length: 4,853,568 bp
max length: 161,427 bp
mean length: 17,844 bp
N50: 46,973
L50: 30
N90: 10,236
L90: 111
N95: 4,958
L95: 144
%GC: 35.22
Ns: 4
gaps: 4
loci tagged: 614

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	484	88

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	26 (3 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	25 (3 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	25 (3 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	30 (3 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	24 (3 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	23 (4 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	27 (3 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	23 (4 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	23 (3 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	23 (3 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	26 (3 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	5 (75 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	25 (3 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	24 (3 isolates)
Cluster_40_cgMLST	cgMLST	Single-linkage	40	experimental	26 (3 isolates)
Test-75	cgMLST	Single-linkage	75	experimental	25 (3 isolates)
Test-50	cgMLST	Single-linkage	50	experimental	25 (3 isolates)
Test-10	cgMLST	Single-linkage	10	experimental	30 (3 isolates)
Test-110	cgMLST	Single-linkage	110	experimental	24 (3 isolates)
Test-150	cgMLST	Single-linkage	150	experimental	23 (4 isolates)
Test-20	cgMLST	Single-linkage	20	experimental	27 (3 isolates)
Test-200	cgMLST	Single-linkage	200	experimental	23 (4 isolates)
Test-220	cgMLST	Single-linkage	220	experimental	23 (3 isolates)
Test-250	cgMLST	Single-linkage	250	experimental	23 (3 isolates)
Test-30	cgMLST	Single-linkage	30	experimental	26 (3 isolates)
Test-300	cgMLST	Single-linkage	300	experimental	5 (75 isolates)
Test-60	cgMLST	Single-linkage	60	experimental	25 (3 isolates)
Test-80	cgMLST	Single-linkage	80	experimental	24 (3 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

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Analysis: