Full information on isolate UT234 (id:73)

Provenance/primary metadata

id: 73
isolate: UT234
biosample: SAMN00739391
accession number: 1049807
clade: P1
species: interrogans
serogroup: Bataviae
serovar: Bataviae
sequencing year: 2012
world region: South-eastern Asia
country: Thailand
host: human
sample type: Unknown
source lab: Craig Venter Institute
sender: Julien Guglielmini, Institut Pasteur
curator: Vallier SORDOILLET, CNR Leptospirose PASTEUR (E-mail: vallier.sordoillet@pasteur.fr)
update history: 1043 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

method: Unknown
contigs: 408
total length: 4,770,171 bp
max length: 93,314 bp
mean length: 11,692 bp
N50: 24,908
L50: 59
N90: 7,144
L90: 197
N95: 3,998
L95: 241
%GC: 35.00
Ns: 373
gaps: 80
loci tagged: 1,154

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	537	98

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
- 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: