Full information on isolate MM0010CK (id:851)

Provenance/primary metadata

id
851
isolate
MM0010CK
aliases
A1_Mm_MM010; L2; MM0010; MM010
clade
P1
species
borgpetersenii
serogroup
Ballum
serovar
Ballum
isolation year
2016
sequencing year
2018
passage
0
world region
Australia and New Zealand
country
New Zealand
city
Manawatu-Wanganui
host
house mouse
sample type
kidney
source lab
mEpiLab Massey University
living area
rural
clinical conditions
subclinical
comments
Species=Mus musculus
sender
Marie Moinet, Massey University, New Zealand
curator
Jean-François Mariet, Institut Pasteur, Paris (E-mail: jean-francois.mariet@pasteur.fr)
update history
17 updates show details
date entered
2019-03-11
datestamp
2024-04-17

Sequence bin

contigs
148
total length
3,892,974 bp
max length
190,752 bp
mean length
26,304 bp
N50
49,331
L50
24
N90
16,194
L90
76
N95
10,850
L95
90
%GC
40.01
Ns
0
gaps
0
loci tagged
602

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
cgMLST54554399

Analysis

rMLST species identification

RankTaxonTaxonomySupportMatches
SPECIES Leptospira borgpetersenii Spirochaetes > Spirochaetia > Leptospirales > Leptospiraceae > Leptospira > Leptospira borgpetersenii 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-linkage40experimental15 (118 isolates)
Test-50cgMLSTSingle-linkage50experimental15 (118 isolates)
Test-110cgMLSTSingle-linkage110experimental14 (80 isolates)
Test-150cgMLSTSingle-linkage150experimental13 (80 isolates)
Test-20cgMLSTSingle-linkage20experimental16 (80 isolates)
Test-200cgMLSTSingle-linkage200experimental13 (80 isolates)
Test-30cgMLSTSingle-linkage30experimental15 (118 isolates)
Test-300cgMLSTSingle-linkage300experimental8 (146 isolates)
Test-60cgMLSTSingle-linkage60experimental15 (118 isolates)
Test-80cgMLSTSingle-linkage80experimental14 (118 isolates)
Cluster_40_cgMLSTcgMLSTSingle-linkage40experimental15 (118 isolates)
Test-50cgMLSTSingle-linkage50experimental15 (118 isolates)
Test-110cgMLSTSingle-linkage110experimental14 (80 isolates)
Test-150cgMLSTSingle-linkage150experimental13 (80 isolates)
Test-20cgMLSTSingle-linkage20experimental16 (80 isolates)
Test-200cgMLSTSingle-linkage200experimental13 (80 isolates)
Test-30cgMLSTSingle-linkage30experimental15 (118 isolates)
Test-300cgMLSTSingle-linkage300experimental8 (146 isolates)
Test-60cgMLSTSingle-linkage60experimental15 (118 isolates)
Test-80cgMLSTSingle-linkage80experimental14 (118 isolates)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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