Genome assembly ASM474511v1
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 5 Mb | 5 Mb |
Total ungapped length | 5 Mb | 5 Mb |
Number of contigs | 78 | 78 |
Contig N50 | 247.8 kb | 247.8 kb |
Contig L50 | 6 | 6 |
GC percent | 50.5 | 50.5 |
Genome coverage | 80.0x | 80.0x |
Assembly level | Contig | Contig |
View sequences | view RefSeq sequences | view 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
PRJNA412557Escherichia sp. Genome sequencing and assembly
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_004745115.1-RS_2024_07_27 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | Jul 27, 2024 | Oct 12, 2017 |
Genes | 4,976 | 5,200 |
Protein-coding | 4,638 | 4,796 |
Software version | 6.7 | 4.2 |
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 readingQuality 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 organism | Best 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_004745115.1 | GCF_004745115.1 | ASM474511v1 | Contig | Apr 8, 2019 |