U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM167504v1

Organism name:
Paenibacillus oryzae (firmicutes)
Taxonomy check:
OK
Infraspecific name:
Strain: 1DrF-4
BioSample:
SAMN04954875
BioProject:
PRJNA320665
Submitter:
SinoGenoMax Co.,Ltd
Date:
2016/06/21
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_001675045.1 (latest)
RefSeq assembly accession:
GCF_001675045.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
LYPA01
Assembly method:
SOAPdenovo v. 2.04
Expected final version:
yes
Genome coverage:
60.0x
Sequencing technology:
Illumina HiSeq

IDs: 762701 [UID] 3319188 [GenBank] 3407748 [RefSeq]

See Genome Information for Paenibacillus oryzae

History (Show revision history)

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/

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI
Annotation Date::05/25/2016 10:34:30
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::3.2
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::5,182
CDS (total)::5,096
Genes (coding)::5,020
CDS (coding)::5,020
Genes (RNA)::86
rRNAs::7, 4, 4 (5S, 16S, 23S)
complete rRNAs::7 (5S)
partial rRNAs::4, 4 (16S, 23S)
tRNAs::67
ncRNAs::4
Pseudo Genes (total)::76
Pseudo Genes (ambiguous residues)::1 of 76
Pseudo Genes (frameshifted)::13 of 76
Pseudo Genes (incomplete)::58 of 76
Pseudo Genes (internal stop)::11 of 76
Pseudo Genes (multiple problems)::7 of 76
CRISPR Arrays::3
##Genome-Annotation-Data-END##

Global statistics

Total sequence length5,905,968
Total ungapped length5,905,217
Gaps between scaffolds0
Number of scaffolds80
Scaffold N50153,070
Scaffold L5012
Number of contigs89
Contig N50153,070
Contig L5012
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)80

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced5,905,968805,905,217153,07090

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Paenibacillus oryzaePaenibacillus oryzae

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_003388735.1Paenibacillus paeoniaetype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type81.793.593.66

ANI result

Taxonomy check statusBest match statusComment
OKlow-coverageAssembly is the type-strain, no match is expected