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Ppicta_v2.0

Organism name:
Paroedura picta (lizards & snakes)
BioSample:
SAMD00069447
BioProject:
PRJDB5392
Submitter:
Phyloinformatics Unit, Center for Life Science Technologies (CLST), RIKEN
Date:
2021/09/14
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_003118565.2 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
BDOT02
Assembly method:
Platanus v. 1.2.4; P_RNA_scaffolder 7941e0f in github; Tigmint v. 1.1.2; ARKS v. 1.1.0; 3D-DNA 180922
Genome coverage:
77.7X
Sequencing technology:
Illumina HiSeq

IDs: 10899121 [UID] 28844418 [GenBank]

See Genome Information for Paroedura picta

History (Show revision history)

Comment

Please visit our website
http://www2.clst.riken.jp/phylo/reptiliomix.html
Two types of unknown gaps (100 bp and 500 bp in size) are included within the nucleotide sequences.
100 bp: connected by P_RNA_scaffolder (scaffolding based on transcripts)
500 bp: connected by 3d-DNA (scaffolding by Hi-C)

Global statistics

Total sequence length1,562,175,643
Total ungapped length1,420,221,990
Gaps between scaffolds0
Number of scaffolds4,871
Scaffold N50109,004,681
Scaffold L506
Number of contigs115,644
Contig N5021,853
Contig L5016,181
Total number of chromosomes and plasmids18
Number of component sequences (WGS or clone)4,871

Supplemental Content

PubMed articles for this assembly

Recent activity

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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
Assembly Unit: Primary Assembly (GCA_003118575.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1n/an/an/a1
Chromosome 2n/an/an/a1
Chromosome 3n/an/an/a1
Chromosome 4n/an/an/a1
Chromosome 5n/an/an/a1
Chromosome 6n/an/an/a1
Chromosome 7n/an/an/a1
Chromosome 8n/an/an/a1
Chromosome 9n/an/an/a1
Chromosome 10n/an/an/a1
Chromosome 11n/an/an/a1
Chromosome 12n/an/an/a1
Chromosome 13n/an/an/a1
Chromosome 14n/an/an/a1
Chromosome 15n/an/an/a1
Chromosome 16n/an/an/a1
Chromosome 17n/an/an/a1
Chromosome 18n/an/an/a1
unplacedn/an/an/a4,853

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule1,562,175,6434,8711,420,221,990109,004,681110,7730
Chromosome 1AllAssembled moleculeUnlocalized scaffolds184,258,7610184,258,761101165,950,1900165,950,190184,258,7610184,258,76113,860013,860000
Chromosome 2AllAssembled moleculeUnlocalized scaffolds166,775,6600166,775,660101153,845,1960153,845,196166,775,6600166,775,6608,56408,564000
Chromosome 3AllAssembled moleculeUnlocalized scaffolds164,868,6160164,868,616101144,676,0220144,676,022164,868,6160164,868,61614,292014,292000
Chromosome 4AllAssembled moleculeUnlocalized scaffolds123,787,4970123,787,497101111,684,0890111,684,089123,787,4970123,787,4979,70809,708000
Chromosome 5AllAssembled moleculeUnlocalized scaffolds120,918,7340120,918,734101113,057,3170113,057,317120,918,7340120,918,7345,38005,380000
Chromosome 6AllAssembled moleculeUnlocalized scaffolds109,004,6810109,004,68110198,442,177098,442,177109,004,6810109,004,6818,50508,505000
Chromosome 7AllAssembled moleculeUnlocalized scaffolds104,430,2770104,430,27710197,763,839097,763,839104,430,2770104,430,2774,88504,885000
Chromosome 8AllAssembled moleculeUnlocalized scaffolds93,612,396093,612,39610184,901,019084,901,01993,612,396093,612,3967,49907,499000
Chromosome 9AllAssembled moleculeUnlocalized scaffolds81,485,636081,485,63610175,201,811075,201,81181,485,636081,485,6365,33205,332000
Chromosome 10AllAssembled moleculeUnlocalized scaffolds74,280,646074,280,64610169,114,303069,114,30374,280,646074,280,6464,63204,632000
Chromosome 11AllAssembled moleculeUnlocalized scaffolds57,637,647057,637,64710152,318,160052,318,16057,637,647057,637,6474,54704,547000
Chromosome 12AllAssembled moleculeUnlocalized scaffolds50,697,019050,697,01910146,594,275046,594,27550,697,019050,697,0193,29803,298000
Chromosome 13AllAssembled moleculeUnlocalized scaffolds46,434,084046,434,08410140,778,969040,778,96946,434,084046,434,0844,23604,236000
Chromosome 14AllAssembled moleculeUnlocalized scaffolds39,459,723039,459,72310135,097,345035,097,34539,459,723039,459,7233,41203,412000
Chromosome 15AllAssembled moleculeUnlocalized scaffolds29,056,103029,056,10310126,259,288026,259,28829,056,103029,056,1032,39402,394000
Chromosome 16AllAssembled moleculeUnlocalized scaffolds27,502,113027,502,11310123,510,287023,510,28727,502,113027,502,1132,97602,976000
Chromosome 17AllAssembled moleculeUnlocalized scaffolds18,544,606018,544,60610116,223,288016,223,28818,544,606018,544,6061,89501,895000
Chromosome 18AllAssembled moleculeUnlocalized scaffolds14,691,838014,691,83810113,627,110013,627,11014,691,838014,691,8389930993000
unplacedAssembled molecule54,729,6064,85351,177,30525,0004,3650
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