Full information on isolate LO-9 (id:1328)

Provenance/primary metadata

id
1328
isolate
LO-9
alias
LO-9
biosample
SAMN06212381
accession number
GCA_001952675.1
clade
P1
species
santarosai
serogroup
Grippotyphosa
serovar
Grippotyphosa
isolation year
2001
sequencing year
2017
world region
South America
country
Brazil
city
Parana
host
bovine
sample type
Urine
source lab
GenBank
sender
Vallier SORDOILLET, CNR Leptospirose PASTEUR
curator
Jean-Fran├žois Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history
10 updates show details
date entered
2022-10-12
datestamp
2024-04-25

Sequence bin

contigs
60
total length
4,083,187 bp
max length
461,168 bp
mean length
68,054 bp
N50
115,432
L50
11
N90
37,946
L90
36
N95
25,644
L95
42
%GC
41.74
Ns
0
gaps
0
loci tagged
599

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
cgMLST54552395

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira santarosai Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira santarosai 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 schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental415 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental405 (2 isolates)
Test-30cgMLSTSingle-linkage30experimental426 (2 isolates)
Test-60cgMLSTSingle-linkage60experimental402 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental391 (2 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental415 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental405 (2 isolates)
Test-30cgMLSTSingle-linkage30experimental426 (2 isolates)
Test-60cgMLSTSingle-linkage60experimental402 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental391 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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