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ASM179919v1

Organism name:
Deltaproteobacteria bacterium RIFOXYA12_FULL_61_11 (d-proteobacteria)
Taxonomy check:
Inconclusive
BioSample:
SAMN04314405
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_001799195.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
MGSU01
Assembly method:
IDBA_UD v. 06.01.2014s
Genome coverage:
10x
Sequencing technology:
Illumina HiSeq2000

IDs: 832511 [UID] 3555688 [GenBank]

See Genome Information for Deltaproteobacteria bacterium RIFOXYA12_FULL_61_11

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 10:32:35
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)::3,899
CDS (total)::3,857
Genes (coding)::3,409
CDS (coding)::3,409
Genes (RNA)::42
rRNAs::1, 1 (5S, 23S)
complete rRNAs::1 (5S)
partial rRNAs::1 (23S)
tRNAs::36
ncRNAs::4
Pseudo Genes (total)::448
Pseudo Genes (ambiguous residues)::83 of 448
Pseudo Genes (frameshifted)::5 of 448
Pseudo Genes (incomplete)::369 of 448
Pseudo Genes (internal stop)::4 of 448
Pseudo Genes (multiple problems)::13 of 448
CRISPR Arrays::3
##Genome-Annotation-Data-END##

Global statistics

Total sequence length4,641,089
Total ungapped length4,634,963
Gaps between scaffolds0
Number of scaffolds342
Scaffold N5017,262
Scaffold L5089
Number of contigs481
Contig N5013,859
Contig L50105
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)342

Supplemental Content

PubMed articles for this assembly

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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
unplaced4,641,0893424,634,96317,2621390

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Deltaproteobacteria bacterium RIFOXYA12_FULL_61_11Deltaproteobacteria bacterium RIFOXYA12_FULL_61_11

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
no-typeno-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_028368995.1Nannocystis bainbridgetype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type85.500.020.01

ANI result

Taxonomy check statusBest match statusComment
Inconclusivelow-coveragena