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ASM352867v1

Organism name:
Hyphomonas atlantica (a-proteobacteria)
Taxonomy check:
OK
Isolate:
UBA10378
BioSample:
SAMN08019102
BioProject:
PRJNA417962
Submitter:
University of Queensland
Date:
2018/09/07
Assembly type:
na
Assembly level:
Scaffold
Genome representation:
full
Excluded from RefSeq:
  • derived from metagenome
  • fragmented assembly
GenBank assembly accession:
GCA_003528675.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
DOGS01
Assembly method:
CLC de novo assembler v. 4.4.1
Expected final version:
yes
Genome coverage:
12.98x
Sequencing technology:
Illumina HiSeq 2000

IDs: 1955351 [UID] 7383808 [GenBank]

See Genome Information for Hyphomonas atlantica

There are 11 assemblies for this organism

See more

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::04/30/2018 12:55:29
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline
Annotation Method::Best-placed reference protein set; GeneMarkS+
Annotation Software revision::4.5
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::3,198
CDS (total)::3,168
Genes (coding)::3,083
CDS (coding)::3,083
Genes (RNA)::30
tRNAs::28
ncRNAs::2
Pseudo Genes (total)::85
Pseudo Genes (ambiguous residues)::44 of 85
Pseudo Genes (frameshifted)::33 of 85
Pseudo Genes (incomplete)::32 of 85
Pseudo Genes (internal stop)::3 of 85
Pseudo Genes (multiple problems)::26 of 85
##Genome-Annotation-Data-END##

Global statistics

Total sequence length2,707,000
Total ungapped length2,569,635
Gaps between scaffolds0
Number of scaffolds320
Scaffold N5010,453
Scaffold L5075
Number of contigs1,123
Contig N503,796
Contig L50198
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)320

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
unplaced2,707,0003202,569,63510,4538030

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Hyphomonas atlanticaHyphomonas atlantica

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
GCA_000682715.1Hyphomonas atlanticasuspected-type

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_000682715.1Hyphomonas atlanticasuspected-type

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared type98.9485.9561.28
Best-match type98.9485.9561.28

ANI result

Taxonomy check statusBest match statusComment
OKspecies-matchna