Full information on isolate 202202042 (id:1285)

Provenance/primary metadata

id
1285
isolate
202202042
alias
2013-VF52
biosample
SAMN34670627
clade
P1
species
santarosai
serogroup
Sejroe
serovar
Sejroe
isolation year
2013
sequencing year
2022
world region
South America
country
Brazil
host
bovine
sample type
Culture
source lab
Universidade Federal Fluminense
sender
Vallier SORDOILLET, CNR Leptospirose PASTEUR
curator
Jean-Fran├žois Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history
12 updates show details
date entered
2022-10-07
datestamp
2024-04-30

Sequence bin

contigs
115
total length
3,980,734 bp
max length
274,417 bp
mean length
34,616 bp
N50
100,276
L50
14
N90
21,571
L90
41
N95
13,044
L95
53
%GC
41.84
Ns
0
gaps
0
loci tagged
584

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
cgMLST54554499

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira santarosai Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira santarosai 94%

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-linkage40experimental338 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental330 (2 isolates)
Test-30cgMLSTSingle-linkage30experimental349 (2 isolates)
Test-60cgMLSTSingle-linkage60experimental327 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental319 (2 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental338 (2 isolates)
Test-50cgMLSTSingle-linkage50experimental330 (2 isolates)
Test-30cgMLSTSingle-linkage30experimental349 (2 isolates)
Test-60cgMLSTSingle-linkage60experimental327 (2 isolates)
Test-80cgMLSTSingle-linkage80experimental319 (2 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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