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Full information on isolate GCA_002903005.1 (id:53901)

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
53901
isolate
GCA_002903005.1
alias
KPNIH50
sender
Mélanie Hennart, Institut Pasteur
curator
Auto Tagger
update history
3 updates show details
date entered
2023-04-03
datestamp
2023-04-12
taxonomic designation
K. pneumoniae
phylogroup from ST
Kp1 (7 loci)
isolation year
0
city
Unknown
country
USA
continent
North America
source type
Unknown
host
Unknown
source details
Unknown
accession number
SAMN06040389

Sequence bin

contigs
6
total length
6,209,759 bp
max length
5,616,605 bp
mean length
1,034,960 bp
N50
5,616,605
L50
1
N90
5,616,605
L90
1
N95
172,259
L95
3
%GC
56.35
Ns
0
gaps
0
loci tagged
689

Show sequence bin

Assembly checks

CheckStatusWarn/fail reason
Number of contigs
Assembly sizeassembly size too large (fail threshold: 6,132,847)
Minimum N50
%GC

Annotation quality metrics

Scheme completion

SchemeScheme lociDesignated lociAnnotation
ScoreStatus
MLST77100
Ribosomal MLST5353100
scgMLST629_S62962699

Analysis

Kleborate

species
Klebsiella pneumoniae
species_match
strong
virulence_score
0
resistance_score
3
num_resistance_classes
5
num_resistance_genes
7
YbST
0
CbST
0
AbST
0
SmST
0
RmST
0
wzi
wzi81
K_locus
KL81
K_type
K81
K_locus_problems
none
K_locus_confidence
Very high
K_locus_identity
99.98%
O_locus
O1/O2v2
O_type
O1
O_locus_problems
none
O_locus_confidence
Very high
O_locus_identity
98.45%
AGly_acquired
strA.v1^;strA.v1^;strB.v1;strB.v1
Sul_acquired
sul2;sul2
Bla_Carb_acquired
KPC-2
Bla_chr
SHV-1^
Col_mutations
MgrB-0%
Flq_mutations
GyrA-83F
spurious_resistance_hits
fosA7*?-0%

Analysis performed: 2024-04-26; Kleborate v2.3.2

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 (13437 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13416 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental43 (28 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental227 (8 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental351 (3 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental1502 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental1847 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental2305 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2692 (2 isolates)
klebs_species_v1.0scgMLST629_SSingle-linkage610experimental1 (13437 isolates)
klebs_subspecies_v1.0scgMLST629_SSingle-linkage585experimental1 (13416 isolates)
klebs_sublineage_v1.0scgMLST629_SSingle-linkage190experimental43 (28 isolates)
klebs_clonalgroup_v1.0scgMLST629_SSingle-linkage43experimental227 (8 isolates)
klebs_threshold10_v1.0scgMLST629_SSingle-linkage10experimental351 (3 isolates)
klebs_threshold7_v1.0scgMLST629_SSingle-linkage7experimental1502 (2 isolates)
klebs_threshold4_v1.0scgMLST629_SSingle-linkage4experimental1847 (2 isolates)
klebs_threshold2_v1.0scgMLST629_SSingle-linkage2experimental2305 (2 isolates)
klebs_threshold1_v1.0scgMLST629_SSingle-linkage1experimental2692 (2 isolates)
klebs_threshold0_v1.0scgMLST629_SSingle-linkage0experimental3295 (1 isolate)

Schemes and loci

Navigate and select schemes within tree to display allele designations

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