Genome assembly ASM333693v1

Actions
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

RefSeqGenBank
Genome size4.1 Mb4.1 Mb
Total ungapped length4.1 Mb4.1 Mb
Number of scaffolds548548
Scaffold N5017.5 kb17.5 kb
Scaffold L507272
Number of contigs551551
Contig N5017.2 kb17.2 kb
Contig L507373
GC percent5151
Genome coverage100.0x100.0x
Assembly levelScaffoldScaffold

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

PRJNA314558

Shigella boydii strain:G1227 Genome sequencing and assembly

Pathogen Detection Resource

Annotation details

RefSeqGenBank
ProviderNCBI RefSeqNCBI
NameGCF_003336935.1-RS_2024_05_04NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
DateMay 4, 2024Mar 9, 2016
Genes4,4024,397
Protein-coding3,6703,772
Software version6.73.1

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.

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Quality 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 organismBest match type-strain
Type assemblyGCA_002946735.1GCA_002946735.1
Organism nameShigella boydiiShigella boydii
Type categorytypetype
ANI99.63%99.63%
Assembly coverage90.35%90.35%
Type assembly coverage82.72%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_003336935.1GCF_003336935.1ASM333693v1ScaffoldJul 24, 2018