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NHGRI_mPanTro3-v1.1-hic.freeze_pri

Organism name:
Pan troglodytes (chimpanzee)
Isolate:
AG18354
Sex:
male
BioSample:
SAMN30216104
BioProject:
PRJNA916736
Submitter:
National Human Genome Research Institute, National Institutes of Health
Date:
2023/02/27
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_028858775.1 (replaced)
RefSeq assembly accession:
GCF_028858775.1 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAQQLN01
Assembly method:
Verkko v. 1.1
Expected final version:
no
Genome coverage:
70.0x
Sequencing technology:
PacBio Sequel; Oxford Nanopore PromethION
Linked assembly:
GCA_028858805.1 (alternate pseudohaplotype of diploid)

IDs: 16014001 [UID] 41093778 [GenBank] 41498728 [RefSeq]

See Genome Information for Pan troglodytes

Pathogen Detection Resources

There are 10 assemblies for this organism

See more

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 length3,225,356,997
Total ungapped length3,222,180,001
Gaps between scaffolds0
Number of scaffolds1,471
Scaffold N50144,388,002
Scaffold L509
Number of contigs1,500
Contig N5094,528,342
Contig L5012
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)1,500

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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:799433-3166326
PARY:597421-2969625
Assembly Unit: Primary Assembly (GCF_028858785.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM054434.1=NC_072398.10
Chromosome 2ACM054435.1=NC_072399.10
Chromosome 2BCM054436.1=NC_072400.10
Chromosome 3CM054437.1=NC_072401.10
Chromosome 4CM054438.1=NC_072402.10
Chromosome 5CM054439.1=NC_072403.10
Chromosome 6CM054440.1=NC_072404.10
Chromosome 7CM054441.1=NC_072405.10
Chromosome 8CM054442.1=NC_072406.10
Chromosome 9CM054443.1=NC_072407.10
Chromosome 10CM054444.1=NC_072408.10
Chromosome 11CM054445.1=NC_072409.10
Chromosome 12CM054446.1=NC_072410.10
Chromosome 13CM054447.1=NC_072411.10
Chromosome 14CM054448.1=NC_072412.10
Chromosome 15CM054449.1=NC_072413.10
Chromosome 16CM054450.1=NC_072414.10
Chromosome 17CM054451.1=NC_072415.10
Chromosome 18CM054452.1=NC_072416.10
Chromosome 19CM054453.1=NC_072417.10
Chromosome 20CM054454.1=NC_072418.10
Chromosome 21CM054455.1=NC_072419.10
Chromosome 22CM054456.1=NC_072420.10
Chromosome XCM054457.1=NC_072421.10
Chromosome YCM054458.1=NC_072422.10
unplacedn/an/an/a1,446

Assembly statistics

MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
All3,225,356,9971,4713,222,180,001144,388,002290
Chromosome 1231,323,2371231,215,894231,323,23710
Chromosome 2A122,662,9531122,429,329122,662,95310
Chromosome 2B144,388,0021144,141,630144,388,00210
Chromosome 3201,486,9431201,429,640201,486,94310
Chromosome 4191,629,5401191,421,453191,629,54020
Chromosome 5179,213,9891178,796,461179,213,98920
Chromosome 6183,319,1901183,319,190183,319,19000
Chromosome 7168,706,2921168,271,236168,706,29220
Chromosome 8160,286,8641160,286,864160,286,86400
Chromosome 9118,877,7161118,877,516118,877,71620
Chromosome 10136,718,3211136,717,321136,718,32110
Chromosome 11136,206,5711136,008,246136,206,57120
Chromosome 12138,751,7631138,751,763138,751,76300
Chromosome 13115,559,4421114,955,694115,559,44220
Chromosome 1497,839,707197,823,21797,839,70730
Chromosome 1593,821,071193,699,75393,821,07110
Chromosome 1694,528,342194,528,34294,528,34200
Chromosome 1797,779,623197,779,52397,779,62310
Chromosome 1889,634,659189,468,44189,634,65910
Chromosome 1968,087,069168,087,06968,087,06900
Chromosome 2078,170,909178,170,60978,170,90930
Chromosome 2149,003,045149,002,94549,003,04510
Chromosome 2252,552,756152,426,61952,552,75610
Chromosome X153,892,4271153,892,427153,892,42700
Chromosome Y36,445,859136,445,85936,445,85900
unplaced84,470,7071,44684,232,96060,24210
Region
Name		LocationScaffold
Count		Total
Length		Ungapped
Length		Scaffold
N50		Spanned
Gaps