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Clint_PTRv2

Organism name:
Pan troglodytes (chimpanzee)
Isolate:
Yerkes chimp pedigree #C0471 (Clint)
Sex:
male
BioSample:
SAMN06272697
BioProject:
PRJNA369439
Submitter:
University of Washington
Date:
2018/01/19
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_002880755.3 (latest)
RefSeq assembly accession:
GCF_002880755.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosomes MT and Y.
  • Data displayed for RefSeq version
WGS Project:
NBAG03
Expected final version:
yes
Genome coverage:
124x

IDs: 1642151 [UID] 5907448 [GenBank] 6084388 [RefSeq]

See Genome Information for Pan troglodytes

There are 6 assemblies for this organism

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History (Show revision history)

Comment

This is the whole-genome assembly of a male chimpanzee, Clint (Yerkes pedigree number C0471). Genome assembly was done in stages, incorporating data from multiple genomic platforms including PacBio, Illumina, and BioNano optical maps, resulting in three progressive versions:
V0 (GCA_002880755.1): ... The backbone of the assembly is made up of contigs obtained by assembling the PacBio (P6-C4 chemistry) reads using the Falcon assembler. These contigs are error-corrected using the tool Quiver and then further error-corrected using Pilon with 37-fold Illumina paired-end reads.
V1 (GCA_002880755.2): BioNano optical maps are used to place the contigs into scaffolds, followed by chromosome-level scaffolding using bicolor FISH.
V2 (GCA_002880755.3): The assembly is further error-corrected, particularly in regions that have clustered 1-2 bp indels. This is done by applying an Eichler-lab-created Freebayes-based indel correction method.  more

Global statistics

Total sequence length3,050,398,082
Total assembly gap length31,805,092
Gaps between scaffolds86
Number of scaffolds4,432
Scaffold N5053,103,722
Scaffold L5019
Number of contigs5,061
Contig N5012,268,567
Contig L5067
Total number of chromosomes and plasmids26
Number of component sequences (WGS or clone)5,254

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
Assembly Unit: Primary Assembly (GCF_002880765.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM009238.2=NC_036879.10
Chromosome 2ACM009239.2=NC_036880.10
Chromosome 2BCM009240.2=NC_036881.10
Chromosome 3CM009241.2=NC_036882.10
Chromosome 4CM009242.2=NC_036883.10
Chromosome 5CM009243.2=NC_036884.13
Chromosome 6CM009244.2=NC_036885.10
Chromosome 7CM009245.2=NC_036886.10
Chromosome 8CM009246.2=NC_036887.10
Chromosome 9CM009247.2=NC_036888.10
Chromosome 10CM009248.2=NC_036889.10
Chromosome 11CM009249.2=NC_036890.10
Chromosome 12CM009250.2=NC_036891.10
Chromosome 13CM009251.2=NC_036892.10
Chromosome 14CM009252.2=NC_036893.10
Chromosome 15CM009253.2=NC_036894.10
Chromosome 16CM009254.2=NC_036895.11
Chromosome 17CM009255.2=NC_036896.10
Chromosome 18CM009256.2=NC_036897.10
Chromosome 19CM009257.2=NC_036898.10
Chromosome 20CM009258.2=NC_036899.10
Chromosome 21CM009259.2=NC_036900.10
Chromosome 22CM009260.2=NC_036901.10
Chromosome XCM009261.2=NC_036902.10
Chromosome YDP000054.3=NC_006492.40
unplacedn/an/an/a4,316

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule3,050,381,5284,4313,018,576,43653,103,72262986
Chromosome 1Assembled molecule224,244,39910221,240,46962,558,157549
Chromosome 2AAssembled molecule108,022,9532106,965,52988,356,612331
Chromosome 2BAssembled molecule128,755,4052128,244,484110,049,840131
Chromosome 3Assembled molecule196,562,5562195,744,141104,859,889201
Chromosome 4Assembled molecule189,151,5975187,617,635111,823,338194
Chromosome 5AllAssembled moleculeUnlocalized scaffolds176,324,783159,319,37817,005,405853175,394,503158,389,09817,005,405112,733,944112,733,9445,402,38924240440
Chromosome 6Assembled molecule168,369,3914167,945,328109,974,799163
Chromosome 7Assembled molecule156,046,5439153,540,66857,194,980468
Chromosome 8Assembled molecule143,338,8104142,278,35039,995,652213
Chromosome 9Assembled molecule110,513,6714109,916,04440,094,278233
Chromosome 10Assembled molecule129,809,6135128,403,66536,696,116284
Chromosome 11Assembled molecule130,782,6062130,236,00080,809,026161
Chromosome 12Assembled molecule130,995,9164130,402,86238,095,789213
Chromosome 13Assembled molecule95,599,650495,196,88868,162,86143
Chromosome 14Assembled molecule87,716,528187,240,79587,716,528100
Chromosome 15Assembled molecule80,519,282378,595,37247,345,541192
Chromosome 16AllAssembled moleculeUnlocalized scaffolds77,728,73575,912,3621,816,37365175,851,60974,035,3361,816,27346,068,11346,068,1131,816,37333321440
Chromosome 17Assembled molecule76,554,115775,701,02218,350,852226
Chromosome 18Assembled molecule74,774,469174,228,10474,774,469100
Chromosome 19Assembled molecule56,733,099355,520,08931,678,890242
Chromosome 20Assembled molecule64,035,432562,899,87633,519,817184
Chromosome 21Assembled molecule33,232,379233,051,61718,868,34441
Chromosome 22Assembled molecule33,698,415433,420,34929,467,495103
Chromosome XAssembled molecule151,576,1765147,390,11553,103,7221004
Chromosome YAssembled molecule26,350,5151325,417,2853,655,2081012
unplacedAssembled molecule198,944,4904,316196,133,63774,005310
MoleculeTotal
Length
Mitochondrion MT16,554
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