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NHGRI_mPonPyg2-v1.1-hic.freeze_pri

Organism name:
Pongo pygmaeus (Bornean orangutan)
Isolate:
AG05252
Sex:
male
BioSample:
SAMN10521809
BioProject:
PRJNA916742
Submitter:
National Human Genome Research Institute, National Institutes of Health
Date:
2023/02/28
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_028885625.1 (replaced)
RefSeq assembly accession:
GCF_028885625.1 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAQQLS01
Assembly method:
Verkko v. 1.1
Expected final version:
no
Genome coverage:
62.0x
Sequencing technology:
PacBio Sequel; Oxford Nanopore PromethION
Linked assembly:
GCA_028885525.1 (alternate pseudohaplotype of diploid)

IDs: 16017321 [UID] 41102998 [GenBank] 41494988 [RefSeq]

See Genome Information for Pongo pygmaeus

Pathogen Detection Resources

There are 5 assemblies for this organism

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History (Show revision history)

Comment

The unspecified linkage evidence came from assembly graph analysis

Global statistics

Number of regions with alternate loci or patches2
Total sequence length3,249,335,160
Total ungapped length3,244,861,008
Gaps between scaffolds0
Number of scaffolds1,554
Scaffold N50140,977,933
Scaffold L5010
Number of contigs1,593
Contig N5090,555,683
Contig L5013
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)1,593

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Assembly Information

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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

Regions

NameLocation
PARX:48679-2356735
PARY:49817-2337056
Assembly Unit: Primary Assembly (GCF_028885635.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM054630.1=NC_072373.10
Chromosome 2ACM054631.1=NC_072374.10
Chromosome 2BCM054632.1=NC_072375.10
Chromosome 3CM054633.1=NC_072376.10
Chromosome 4CM054634.1=NC_072377.10
Chromosome 5CM054635.1=NC_072378.10
Chromosome 6CM054636.1=NC_072379.10
Chromosome 7CM054637.1=NC_072380.10
Chromosome 8CM054638.1=NC_072381.10
Chromosome 9CM054639.1=NC_072382.10
Chromosome 10CM054640.1=NC_072383.10
Chromosome 11CM054641.1=NC_072384.10
Chromosome 12CM054642.1=NC_072385.10
Chromosome 13CM054643.1=NC_072386.10
Chromosome 14CM054644.1=NC_072387.10
Chromosome 15CM054645.1=NC_072388.10
Chromosome 16CM054646.1=NC_072389.10
Chromosome 17CM054647.1=NC_072390.10
Chromosome 18CM054648.1=NC_072391.10
Chromosome 19CM054649.1=NC_072392.10
Chromosome 20CM054650.1=NC_072393.10
Chromosome 21CM054651.1=NC_072394.10
Chromosome 22CM054652.1=NC_072395.10
Chromosome XCM054653.1=NC_072396.10
Chromosome YCM054654.1=NC_072397.10
unplacedn/an/an/a1,529

Assembly statistics

MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
All3,249,335,1601,5543,244,861,008140,977,933390
Chromosome 1229,755,8511228,833,323229,755,85160
Chromosome 2A131,528,9271131,523,927131,528,92710
Chromosome 2B140,977,9331140,677,120140,977,93310
Chromosome 3209,315,5641208,856,852209,315,56440
Chromosome 4188,985,0661188,608,345188,985,06660
Chromosome 5186,347,3791186,347,379186,347,37900
Chromosome 6172,451,6101172,104,141172,451,61030
Chromosome 7158,535,5411158,535,541158,535,54100
Chromosome 8158,848,2131158,827,646158,848,21320
Chromosome 9113,107,9831113,107,983113,107,98300
Chromosome 10139,153,1171138,965,601139,153,11720
Chromosome 11140,978,1981140,567,456140,978,19820
Chromosome 12132,184,6591132,184,659132,184,65900
Chromosome 13119,493,6421119,493,642119,493,64200
Chromosome 14104,345,3141104,345,314104,345,31400
Chromosome 1583,708,911183,593,81683,708,91110
Chromosome 1687,866,749187,866,64987,866,74910
Chromosome 1797,833,983197,610,93097,833,98320
Chromosome 1879,883,193179,806,97579,883,19310
Chromosome 1962,157,734162,157,63462,157,73410
Chromosome 2067,020,140167,020,14067,020,14000
Chromosome 2135,039,558134,965,79135,039,55810
Chromosome 2242,224,227142,224,22742,224,22700
Chromosome X161,100,5311161,100,531161,100,53100
Chromosome Y49,349,692149,349,69249,349,69200
unplaced157,141,4451,529156,185,694265,45450
Region
Name		LocationScaffold
Count		Total
Length		Ungapped
Length		Scaffold
N50		Spanned
Gaps