Genome assembly ASM333693v1
- NCBI RefSeq assembly
- GCF_003336935.1
- Submitted GenBank assembly
- GCA_003336935.1
- Taxon
- Shigella boydii
- Strain
- G1227
- WGS project
- LUFZ01
- Submitter
- Nankai University
- Date
- Jul 24, 2018
Assembly statistics
RefSeq | GenBank | |
---|---|---|
Genome size | 4.1 Mb | 4.1 Mb |
Total ungapped length | 4.1 Mb | 4.1 Mb |
Number of scaffolds | 548 | 548 |
Scaffold N50 | 17.5 kb | 17.5 kb |
Scaffold L50 | 72 | 72 |
Number of contigs | 551 | 551 |
Contig N50 | 17.2 kb | 17.2 kb |
Contig L50 | 73 | 73 |
GC percent | 51 | 51 |
Genome coverage | 100.0x | 100.0x |
Assembly level | Scaffold | Scaffold |
Sample details
- BioSample ID
- SAMN04534920
- Description
- Shigella boydii G1227
- Submitter
- Nankai University
- Strain
- G1227
- Host
- Homo sapiens
- Sample name
- wls645
- Models
- Microbe, viral or environmental
- Package
- Microbe.1.0
- Submission date
- 2016-03-07T02:36:03.462
- Publication date
- 2016-03-07T02:36:02.901
- Last updated
- 2016-03-07T02:36:03.462
Assembly methods
- Sequencing technology
- Illumina GAIIx
- 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
- Velvet v. 1.2.03
Additional genomes
Browse all Shigella boydii genomes (863)BioProject
PRJNA314558Shigella boydii strain:G1227 Genome sequencing and assembly
Pathogen Detection Resource
Annotation details
RefSeq | GenBank | |
---|---|---|
Provider | NCBI RefSeq | NCBI |
Name | GCF_003336935.1-RS_2024_05_04 | NCBI Prokaryotic Genome Annotation Pipeline (PGAP) |
Date | May 4, 2024 | Mar 9, 2016 |
Genes | 4,402 | 4,397 |
Protein-coding | 3,670 | 3,772 |
Software version | 6.7 | 3.1 |
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 (v1.2.2)
Completeness: 96.43% (72nd Percentile)
Contamination: 0.62%
Calculated on the Prokaryotic Genome Annotation Pipeline (PGAP) gene set with the Shigella boydii 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
- Shigella boydii
- Submitted species name
- Shigella boydii
Average Nucleotide Identity (ANI) match details
Best match type-strain for submitted organism | Best match type-strain | |
---|---|---|
Type assembly | GCA_002946735.1 | GCA_002946735.1 |
Organism name | Shigella boydii | Shigella boydii |
Type category | type | type |
ANI | 99.63% | 99.63% |
Assembly coverage | 90.35% | 90.35% |
Type assembly coverage | 82.72% | 82.72% |
Chromosomes
Note: This scaffold-level genome assembly includes 548 scaffolds and no assembled chromosomes.
Revision history
This record has not been revised
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_003336935.1 | GCF_003336935.1 | ASM333693v1 | Scaffold | Jul 24, 2018 |