Full information on isolate 2ACAP (id:1329)

Provenance/primary metadata

id
1329
isolate
2ACAP
alias
2ACAP
biosample
SAMN06212382
accession number
GCF_001981425.1
clade
P1
species
santarosai
serogroup
Grippotyphosa
serovar
Bananal
isolation year
2001
sequencing year
2017
world region
South America
country
Brazil
city
Sao Paulo state
host
capybara
sample type
kidney
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
11 updates show details
date entered
2022-10-12
datestamp
2024-04-25

Sequence bin

contigs
44
total length
4,088,850 bp
max length
421,432 bp
mean length
92,929 bp
N50
203,677
L50
8
N90
52,977
L90
24
N95
38,462
L95
28
%GC
41.73
Ns
9
gaps
9
loci tagged
600

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
cgMLST54552596

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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