Genome assembly ASM1764142v1

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NCBI RefSeq assembly
GCF_017641425.1
Submitted GenBank assembly
GCA_017641425.1
Taxon
Enterococcus casseliflavus
Strain
3UPD1
WGS project
SIZF01
Submitter
University of KwaZulu-Natal (UKZN), South Africa
Date
Mar 30, 2021

Assembly statistics

RefSeqGenBank
Genome size3.6 Mb3.6 Mb
Total ungapped length3.6 Mb3.6 Mb
Number of contigs8686
Contig N50118.6 kb118.6 kb
Contig L5099
GC percent42.542.5
Genome coverage99.0x99.0x
Assembly levelContigContig
View sequencesview RefSeq sequences

Sample details

BioSample ID
SAMN10984517
Description
Pathogen: environmental/food/other sample from Enterococcus casseliflavus
Submitter
University of KwaZulu-Natal (UKZN), South Africa
Bar Code No
BRU
Strain
3UPD1
Collected by
Christiana Shobo
Collection date
Nov 24, 2017
Geographic location
South Africa: Ethekwini district, KwaZulu-Natal
Host
Hospital environment
Host disease
not applicable
Type of hospital
Tertiary hospital
Isolation source
Peadiatric - patient file
Latitude and longitude
29.4843 S 30.5038 E
Sample name
3UPD1
Models
Pathogen.env
Package
Pathogen.env.1.0
Submission date
2019-02-21T14:22:05.773
Publication date
2019-12-31T00:00:00.000
Last updated
2021-02-24T12:20:41.473

Assembly methods

Sequencing technology
Illumina MiSeq
Comment
Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
Assembly method
CLC NGS Cell v. 2018-09-01T00:00:00

BioProject

PRJNA523601

Bacteria dissemination in different level of health care in South Africa: the effectiveness of infections prevention and control

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_017641425.1-RS_2024_04_23NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateApr 23, 2024Feb 22, 2019
Genes3,4153,483
Protein-coding3,2863,287
Software version6.74.7

About PGAP

The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) uses multiple approaches to predict protein-coding and RNA genes and other functional elements directly from sequence.

Continue reading

Quality analysis

CheckM analysis (v1.2.2)

Completeness: 96.71% (31st Percentile, dark blue bar)

Contamination: 2.91%

Completeness of Enterococcus casseliflavus RefSeq assemblies

Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Enterococcus casseliflavus CheckM marker set. For more information on CheckM, see Parks, et al. Genome Res (2015).

Taxonomy check

Taxonomy check status
OK
Best match status
species_match
Submitted organism name
Enterococcus casseliflavus
Submitted species name
Enterococcus casseliflavus

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assemblyGCA_001544095.1GCA_001544095.1
Organism nameEnterococcus casseliflavus NBRC 100478Enterococcus casseliflavus
Type categorytypetype
ANI99.11%99.11%
Assembly coverage85.33%85.33%
Type assembly coverage86.66%86.66%

Chromosomes

Note: This contig-level genome assembly includes 86 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_017641425.1GCF_017641425.1ASM1764142v1ContigMar 30, 2021