U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



ASM180194v1

Organism name:
Gammaproteobacteria bacterium RIFCSPLOWO2_12_FULL_52_10 (g-proteobacteria)
Taxonomy check:
Inconclusive
BioSample:
SAMN04315884
BioProject:
PRJNA288027
Submitter:
Banfield Lab, University of California, Berkeley
Date:
2016/10/20
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Excluded from RefSeq:
  • derived from metagenome
  • genus undefined
GenBank assembly accession:
GCA_001801945.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
MGYY01
Assembly method:
IDBA_UD v. 06.01.2014s
Genome coverage:
10x
Sequencing technology:
Illumina HiSeq2000

IDs: 833881 [UID] 3558438 [GenBank]

See Genome Information for Gammaproteobacteria bacterium RIFCSPLOWO2_12_FULL_52_10

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::09/08/2016 13:38:53
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::3.3
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::1,413
CDS (total)::1,387
Genes (coding)::1,144
CDS (coding)::1,144
Genes (RNA)::26
rRNAs::1 (16S)
complete rRNAs::
partial rRNAs::1 (16S)
tRNAs::21
ncRNAs::4
Pseudo Genes (total)::243
Pseudo Genes (ambiguous residues)::93 of 243
Pseudo Genes (frameshifted)::10 of 243
Pseudo Genes (incomplete)::152 of 243
Pseudo Genes (internal stop)::12 of 243
Pseudo Genes (multiple problems)::22 of 243
##Genome-Annotation-Data-END##

Global statistics

Total sequence length1,403,244
Total ungapped length1,392,110
Gaps between scaffolds0
Number of scaffolds146
Scaffold N5010,186
Scaffold L5046
Number of contigs320
Contig N507,173
Contig L5066
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)146

Supplemental Content

PubMed articles for this assembly

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
unplaced1,403,2441461,392,11010,1861740

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Gammaproteobacteria bacterium RIFCSPLOWO2_12_FULL_52_10Gammaproteobacteria bacterium RIFCSPLOWO2_12_FULL_52_10

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000021985.1Thioalkalivibrio sulfidiphilustype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type92.620.070.03

ANI result

Taxonomy check statusBest match statusComment
Inconclusivelow-coveragena