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Full information on isolate GCA_900504475.1 (id:49550)

Projects

This isolate is a member of the following project:

Hennart_et_al_2022_full_collection
Collection of genomes from the paper "A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains" | PMID: 35700230

Provenance/primary metadata

id
49550
isolate
GCA_900504475.1
alias
EuSCAPE_RO097
sender
Mélanie Hennart, Institut Pasteur, France
curator
Auto Tagger
update history
6 updates show details
date entered
2023-03-23
datestamp
2025-05-30
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
isolation year
0
city
Unknown
country
Romania
continent
Europe
source type
Unknown
host
Unknown
source details
Unknown
accession number
SAMEA3721010

Sequence bin

method
Unknown
contigs
65
total length
5,463,666 bp
max length
1,010,617 bp
mean length
84,057 bp
N50
375,531
L50
5
N90
76,386
L90
16
N95
34,581
L95
21
%GC
57.17
Ns
0
gaps
0
loci tagged
3,415

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
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962499
Kpn_cgMLST2752273199

Analysis

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
2
resistance_score
0
num_resistance_classes
0
num_resistance_genes
0
Yersiniabactin
ybt 17; ICEKp10
YbST
234-6LV
Colibactin
clb 3
CbST
17-1LV
AbST
0
SmST
0
RmST
0
wzi
wzi59
K_locus
KL3
K_type
K3
K_locus_confidence
High
K_locus_identity
99.59%
K_locus_missing_genes
KL3_14
O_locus
O1/O2v2
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.41%
Bla_chr
SHV-1^
ybtS
98
ybtX
15
ybtQ
5
ybtP
4
ybtA
11
irp2
342
irp1
420
ybtU
107
ybtT
14
ybtE
124
fyuA
2
clbA
2
clbB
10
clbC
2
clbD
2
clbE
2
clbF
2
clbG
2
clbH
8
clbI
18
clbL
2
clbM
2
clbN
2
clbO
2
clbP
2
clbQ
2

Analysis performed: 2024-04-16; Kleborate v2.3.2

Similar isolates (determined by LIN codes)

Scheme
scgMLST629_S
LIN code
0_0_47_0_0_0_0_0_0_0
Phylogroup
Kp1
Sublineage
SL8
Clonal group
CG8

Show all thresholds

PrefixThresholdMatching isolates
0_0_47_0_0_071
0_0_47_0_0_0_041
0_0_47_0_0_0_0_021
0_0_47_0_0_0_0_0_011
0_0_47_0_0_0_0_0_0_001
061041312
0_058541312
0_0_4719017
0_0_47_04316
0_0_47_0_0101
0_0_47_0_0_071
0_0_47_0_0_0_041
0_0_47_0_0_0_0_021
0_0_47_0_0_0_0_0_011
0_0_47_0_0_0_0_0_0_001

Similar isolates (determined by classification schemes)

Some groups only contain this isolate. Show single groups

Experimental schemes are subject to change and are not a stable part of the nomenclature.

Classification schemeUnderlying schemeClustering methodMismatch thresholdStatusGroup
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental124 (11 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental154 (10 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (16003 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (15951 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental124 (11 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental154 (10 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental941 (1 isolate)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental1066 (1 isolate)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental1292 (1 isolate)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental1600 (1 isolate)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental1870 (1 isolate)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental2280 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

Tools

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