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Pan_troglodytes-2.1

  • Record removed. This version of the assembly has been suppressed.
Organism name:
Pan troglodytes (chimpanzee)
Isolate:
Yerkes chimp pedigree #C0471 (Clint)
Sex:
male
BioProject:
PRJNA13184
Submitter:
Chimpanzee Sequencing and Analysis Consortium
Date:
2006/03/16
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
n/a
RefSeq assembly accession:
GCF_000001515.3 (suppressed)
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
AACZ02
Genome coverage:
6x

IDs: 237668 [UID] 237668 [RefSeq]

See Genome Information for Pan troglodytes

There are 6 assemblies for this organism

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History (Show revision history)

Comment


Sequencing/Assembly: The whole genome shotgun sequence data were assembled and organized by the Washington University Genome Sequencing Center. The underlying whole genome shotgun data were generated at the Washington University School of Medicine and the Broad Institute. A 5 ... megabase region of chromosome 7 was finished at the Washington University Genome Sequencing Center (chr7:84674857-89461887). The chromosome Y sequence was finished at the Washington University Genome Sequencing Center with detailed mapping and extensive collaboration with David Page's group at the Whitehead Institute (The DNA Sequence of Chimpanzee Chromosome Y, unpublished; Hughes et al., Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature, 2005 437:100-3; PMID:16136134). The chromosome 21 sequence data was kindly provided by Todd Taylor and the Riken Genome Sciences Center (Watanabe et al., DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004 May 27;429(6990):382-8. PMID: 15164055).

This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It is composed of 246,375 contigs with an N50 length of 29 kb, and 44,454 supercontigs with an N50 length of 9.7 Mb. The total contig length, not including estimated gap sizes, is 2.97 Gb. Of that total, 2.82 Gb has been ordered and oriented along specific chimpanzee chromomes, 107Mb has been linked to chromosomes but is unplaced, and 50Mb remains unlinked (chrUn).

The whole genome shotgun data from primary donor-derived reads (Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center (Atlanta, USA)) were assembled using PCAP (Huang 2006) using stringent parameters derived by eliminating detectable global mis-assemblies (interchromosomal cross-overs determined by alignment of the chimpanzee genome against the human genome) larger than 50kb.

The assembly data were aligned against the human genome at UCSC (B. Raney) utilizing BLASTZ (Schwartz 2003) to align and score non-repetitive chimpanzee regions against repeat-masked human sequence. Alignment chains differentiated between orthologous and paralogous alignments (Kent 2003) and only "reciprocal best" alignments were retained in the alignment set. The chimpanzee AGP files were generated from these alignments in a manner similar to that already described (The Chimpanzee Genome Sequencing Consortium 2005). Centromeres were introduced into the chimp sequence at the positions of the centromeres in the human chromosomes. Ten documented/known human inversions (Yunis 1982) supported by the assembly were introduced into the ordering as was the separation of alignments to human chromosome 2 into chimpanzee chromosomes 2A and 2B. We removed the contigs from the WGS project that corresponded to the finished chromosome 21 and chromosome Y sequences and a 5 Mb finished region from chimpanzee chromosome 7 because they are represented by the corresponding finished sequences. The chromosome 21 sequence is GenBank Accession Number BA000046 and the chromosome Y sequence is GenBank Accession Numbers DP000054-DP000056 and AC163716.2.  more

Global statistics

Total sequence length3,349,648,539
Total assembly gap length440,224,488
Gaps between scaffolds3,108
Number of scaffolds32,300
Scaffold N508,803,938
Scaffold L5086
Number of contigs246,708
Contig N5030,554
Contig L5025,977
Total number of chromosomes and plasmids26
Number of component sequences (WGS or clone)246,863

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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
chr6_hla_hap1
non-nuclear
Assembly Unit: Primary Assembly (GCF_000000075.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1n/an/aNC_006468.21,554
Chromosome 2An/an/aNC_006469.2693
Chromosome 2Bn/an/aNC_006470.2684
Chromosome 3n/an/aNC_006490.21,156
Chromosome 4n/an/aNC_006471.21,260
Chromosome 5n/an/aNC_006472.21,049
Chromosome 6n/an/aNC_006473.21,321
Chromosome 7n/an/aNC_006474.21,197
Chromosome 8n/an/aNC_006475.21,031
Chromosome 9n/an/aNC_006476.2968
Chromosome 10n/an/aNC_006477.21,485
Chromosome 11n/an/aNC_006478.2825
Chromosome 12n/an/aNC_006479.2785
Chromosome 13n/an/aNC_006480.2539
Chromosome 14n/an/aNC_006481.2537
Chromosome 15n/an/aNC_006482.2552
Chromosome 16n/an/aNC_006483.2811
Chromosome 17n/an/aNC_006484.2572
Chromosome 18n/an/aNC_006485.2495
Chromosome 19n/an/aNC_006486.2428
Chromosome 20n/an/aNC_006487.2381
Chromosome 21n/an/aNC_006488.20
Chromosome 22n/an/aNC_006489.2223
Chromosome Xn/an/aNC_006491.2703
Chromosome Yn/an/aNC_006492.23
unplacedn/an/an/a9,958

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule3,349,625,61732,2952,909,401,1298,803,938214,4093,108
Chromosome 1AllAssembled moleculeUnlocalized scaffolds239,356,275229,974,6919,381,5841,7942401,554225,789,517217,202,6068,586,9116,480,1606,980,33915,62215,84214,8589842412410
Chromosome 2AAllAssembled moleculeUnlocalized scaffolds117,495,023114,460,0643,034,959836143693108,685,523105,878,7742,806,74910,239,66110,239,6618,8896,6406,3882521441440
Chromosome 2BAllAssembled moleculeUnlocalized scaffolds250,773,555248,603,6532,169,90274359684129,840,465127,875,2421,965,22317,248,55417,248,5543,8237,3657,18018560600
Chromosome 3AllAssembled moleculeUnlocalized scaffolds207,450,639203,962,4783,488,1611,215591,156198,172,063194,972,0553,200,00817,759,35317,759,3533,09311,08910,81727260600
Chromosome 4AllAssembled moleculeUnlocalized scaffolds201,576,879194,897,2726,679,6071,334741,260193,003,251186,964,4656,038,78613,974,37213,974,37212,09110,5989,87672275750
Chromosome 5AllAssembled moleculeUnlocalized scaffolds187,128,649183,994,9063,133,7431,138891,049178,092,449175,233,4992,858,9509,986,41910,903,8963,1819,9559,71623990900
Chromosome 6AllAssembled moleculeUnlocalized scaffolds183,259,016173,908,6129,350,4041,401801,321173,510,581164,705,7428,804,83923,444,54523,444,54547,84510,1569,45070681810
Chromosome 7AllAssembled moleculeUnlocalized scaffolds167,472,413160,261,4437,210,9701,4162191,197157,687,316151,077,6946,609,62211,262,25611,262,25614,82910,5109,7677432202200
Chromosome 8AllAssembled moleculeUnlocalized scaffolds152,351,737145,085,8687,265,8691,112811,031145,049,592138,158,4856,891,10712,907,57512,907,5753,887,0698,5938,07152282820
Chromosome 9AllAssembled moleculeUnlocalized scaffolds146,219,147138,509,9917,709,1561,214246968116,349,503109,302,3927,047,1118,897,6058,897,60521,0298,0257,2108152472470
Chromosome 10AllAssembled moleculeUnlocalized scaffolds143,367,436135,001,9958,365,4411,6051201,485133,156,315125,703,6657,452,6509,728,9669,884,62810,6149,0798,1679121211210
Chromosome 11AllAssembled moleculeUnlocalized scaffolds142,596,467134,204,7648,391,70390075825131,565,729123,603,6287,962,10116,974,78016,974,7805,484,1388,7888,13964976760
Chromosome 12AllAssembled moleculeUnlocalized scaffolds137,611,705135,371,3362,240,36985368785131,911,809129,875,2712,036,53813,878,15113,878,1512,9079,0038,83217169690
Chromosome 13AllAssembled moleculeUnlocalized scaffolds125,086,051115,868,4569,217,5955905153996,726,87987,798,7358,928,1447,897,2258,218,5627,579,0745,1804,65053052520
Chromosome 14AllAssembled moleculeUnlocalized scaffolds109,444,494107,349,1582,095,3365895253788,171,73286,255,5401,916,19211,478,16211,478,1625,0785,8065,63317353530
Chromosome 15AllAssembled moleculeUnlocalized scaffolds103,136,698100,063,4223,073,2766408855279,849,64476,976,1002,873,5447,419,1137,419,11313,8765,2464,99425289890
Chromosome 16AllAssembled moleculeUnlocalized scaffolds97,032,67490,682,3766,350,2981,07025981180,268,70174,510,3465,758,3553,011,5643,106,02019,1897,1616,3787832602600
Chromosome 17AllAssembled moleculeUnlocalized scaffolds88,448,45283,384,2105,064,24270913757278,179,67073,435,5644,744,1064,963,8024,963,80255,1817,5567,0994571381380
Chromosome 18AllAssembled moleculeUnlocalized scaffolds79,091,31677,261,7461,829,5705222749575,845,57174,184,8121,660,75911,030,25711,030,2574,6974,1654,00915628280
Chromosome 19AllAssembled moleculeUnlocalized scaffolds66,869,99964,473,4372,396,56257214442854,075,63352,002,9862,072,6472,766,3372,939,6169,8747,7187,4023161451450
Chromosome 20AllAssembled moleculeUnlocalized scaffolds64,076,43362,293,5721,782,8614254438159,735,70658,105,6561,630,05010,103,65110,103,6518,3564,7454,59515045450
Chromosome 21Assembled molecule46,489,110332,706,06927,632,627204
Chromosome 22AllAssembled moleculeUnlocalized scaffolds51,342,46550,165,5581,176,90732910622333,421,15432,343,9141,077,2402,831,9012,831,90114,8233,6913,5881031071070
Chromosome XAllAssembled moleculeUnlocalized scaffolds158,892,513155,361,3573,531,1561,310607703133,747,617130,951,0932,796,5241,285,8081,330,5066,74028,44227,7806626086080
Chromosome YAllAssembled moleculeUnlocalized scaffolds24,725,38123,952,694772,6871714323,463,20922,691,222771,9872,480,0952,480,095276,0704538713130
unplacedAssembled molecule58,331,0909,95850,395,43112,3488,9910
MoleculeTotal
Length
Mitochondrion MT16,554
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
chr6_hla_hap146,3686,3681,8980
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