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DPV01

Organism name:
Phoenix dactylifera (date palm)
Infraspecific name:
Cultivar: Khalas
Sex:
female
BioSample:
SAMN02981540
BioProject:
PRJNA83433
Submitter:
Joint Center for Genomics Research
Date:
2013/06/24
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000413155.1 (latest)
RefSeq assembly accession:
GCF_000413155.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosomes MT and Pltd (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
ATBV01
Assembly method:
Newbler v. 2.5.3; HAPS v. 0.1.200
Genome coverage:
139.0x
Sequencing technology:
454; SOLiD; ABI3730

IDs: 709858 [UID] 709858 [GenBank] 1183388 [RefSeq]

See Genome Information for Phoenix dactylifera

There are 2 assemblies for this organism

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History (Show revision history)

Comment

Reads were assembled into contigs using Newbler. Mate-pair reads produced by SOLiD sequencer were mapped to the contigs using BioScope (v1.3). The paired reads were used to link the Newbler contigs into super contigs. Gaps inside the super-contigs were ... filled and extended by Newbler contigs. Some other methods were used to merge the adjacent contigs. Finally, BAC-end sequences were aligned to the contigs to construct scaffolds using a Perl script.  more

Global statistics

Total sequence length556,480,649
Total ungapped length507,544,366
Gaps between scaffolds0
Number of scaffolds80,317
Scaffold N50335,289
Scaffold L50325
Number of contigs143,382
Contig N5010,936
Contig L5012,229
Total number of chromosomes and plasmids2
Number of component sequences (WGS or clone)143,382

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
non-nuclear
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
unplaced555,607,18680,315506,670,903334,08363,0650
MoleculeTotal
Length
All873,463
Mitochondrion MT715,001
Chloroplast Pltd158,462
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