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Genome assembly ASM474511v1

FTP
Actions
NCBI RefSeq assembly
GCF_004745115.1
Submitted GenBank assembly
GCA_004745115.1
Taxon
Escherichia sp. E4930
Strain
E4930
WGS project
PDHZ01
Submitter
The Hong Kong University of Science and Technology
Date
Apr 8, 2019

Assembly statistics

RefSeqGenBank
Genome size5 Mb5 Mb
Total ungapped length5 Mb5 Mb
Number of contigs7878
Contig N50247.8 kb247.8 kb
Contig L5066
GC percent50.550.5
Genome coverage80.0x80.0x
Assembly levelContigContig
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN07759788
Description
Environmental sample from Escherichia sp. E4930
Comment
Keywords: GSC:MIxS;MIGS:6.0
Submitter
The Hong Kong University of Science and Technology
Strain
E4930
Collection date
Sep 30, 2009
Depth
not collected
Elevation
not collected
Broad-scale environmental context
Marine
Local-scale environmental context
Intertidal mudflat
Environmental medium
sediment
Geographic location
Hong Kong
Latitude and longitude
22.4117 N 114.2750 E
Reference for biomaterial
Not yet available
Isolation and growth condition
not collected
Number of replicons
NA
Isolation source
marine sediment
Sample name
E4930
SRA
SRS2573686
Models
MIGS.ba, MIGS/MIMS/MIMARKS.sediment
Package
MIGS.ba.sediment.6.0
Submission date
2017-10-09T02:19:05.986
Publication date
2018-11-01T00:00:00.000
Last updated
2021-02-28T04:55:29.293

Assembly methods

Sequencing technology
Ion Torrent
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/

Bacteria available from Prof.Lau lab at Hong Kong University of Science and Technology.

Assembly method
Mira v. 3.9

Additional genomes

Browse all Escherichia sp. E4930 genomes (2)

BioProject

PRJNA412557

Escherichia sp. Genome sequencing and assembly

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_004745115.1-RS_2024_07_27NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateJul 27, 2024Oct 12, 2017
Genes4,9765,200
Protein-coding4,6384,796
Software version6.74.2

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 (v1.2.3)

Completeness: 98.27% (100th Percentile)

Contamination: 1.06%

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

Taxonomy check

Taxonomy check status
OK
Best match status
genus_match
Submitted organism name
Escherichia sp. E4930
Submitted species name
Escherichia sp. E4930

Average Nucleotide Identity (ANI) match details

Best match type-strain for submitted organismBest match type-strain
Type assembly

n/a

GCA_014836715.1
Organism name

n/a

Escherichia whittamii
Type category

n/a

type
ANI

n/a

94.73%
Assembly coverage

n/a

80.43%
Type assembly coverage

n/a

89.01%

Chromosomes

Note: This contig-level genome assembly includes 78 contigs and no assembled chromosomes.

Revision history

This record has not been revised

GenBank
RefSeq
Name
Level
Date
Action
GCA_004745115.1GCF_004745115.1ASM474511v1ContigApr 8, 2019