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Gallus_gallus-2.1

Organism name:
Gallus gallus (chicken)
Infraspecific name:
Breed: Red Jungle fowl, inbred line UCD001
Isolate:
#256
Sex:
female
BioSample:
SAMN02981218
Submitter:
International Chicken Genome Consortium
Date:
2006/11/01
Synonyms:
galGal3
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000002315.1 (replaced)
RefSeq assembly accession:
GCF_000002315.2 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
  • Different: 14 unplaced scaffolds.
  • Data displayed for RefSeq version
WGS Project:
AADN02
Genome coverage:
6.6x
Sequencing technology:
Sanger; 454

IDs: 238058 [UID] 309298 [GenBank] 238058 [RefSeq]

See Genome Information for Gallus gallus

History (Show revision history)

Comment

The chicken genome that was sequenced is from the inbred line UCD001, which was derived from a wild population of red jungle fowl in Malaysia in the late 1930s. There is the possible introgression of a limited amount of ... White Leghorn genome during the captive breeding history. All sequencing libraries were prepared from DNA of a single female of the inbred line to minimize heterozygosity and provide sequence for both sex chromosomes. (The female chicken is heterogametic (ZW) and the male is homogametic (ZZ).). The 01 version of the project was generated using PCAP from approximately 6.6X coverage in whole-genome shotgun reads and a combination of plasmid, fosmid and bacterial artificial chromosome (BAC)-end read pairs. From that assembly, 198,000 additional reads were ordered to cover all contig ends and regions of low quality. This 02 version is the result of a new PCAP assembly that was generated from the sequence improvement reads as well as the original 6.6X coverage. In addition, the original release markers have been added to the various maps (consensus linkage map, East Lansing map, radiation hybrid map, physical map). The creation of the new chromosomal sequences proceeded in a way similar to that described for the original release (International Chicken Genome Sequencing Consortium, 2004) but benefited from the additional reads, improved assembly methods, and the addition of the RH and East Lansing maps and the significantly improved genetic and physical maps. Furt  more

Global statistics

Total sequence length1,098,770,941
Total assembly gap length56,179,654
Gaps between scaffolds359
Number of scaffolds17,507
Scaffold N5011,063,745
Scaffold L5026
Number of contigs78,535
Contig N5046,345
Contig L505,653
Total number of chromosomes and plasmids34

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_000000185.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000093.2=NC_006088.25
Chromosome 2CM000094.2=NC_006089.29
Chromosome 3CM000095.2=NC_006090.20
Chromosome 4CM000096.2=NC_006091.24
Chromosome 5CM000097.2=NC_006092.22
Chromosome 6CM000098.2=NC_006093.23
Chromosome 7CM000099.2=NC_006094.23
Chromosome 8CM000100.2=NC_006095.22
Chromosome 9CM000101.2=NC_006096.20
Chromosome 10CM000102.2=NC_006097.21
Chromosome 11CM000103.2=NC_006098.21
Chromosome 12CM000104.2=NC_006099.21
Chromosome 13CM000105.2=NC_006100.24
Chromosome 14CM000106.2=NC_006101.20
Chromosome 15CM000107.2=NC_006102.20
Chromosome 16CM000108.2=NC_006103.224
Chromosome 17CM000109.2=NC_006104.21
Chromosome 18CM000110.2=NC_006105.21
Chromosome 19CM000111.2=NC_006106.20
Chromosome 20CM000112.2=NC_006107.22
Chromosome 21CM000113.2=NC_006108.20
Chromosome 22CM000114.2=NC_006109.23
Chromosome 23CM000115.2=NC_006110.20
Chromosome 24CM000116.2=NC_006111.20
Chromosome 25CM000124.2=NC_006112.11
Chromosome 26CM000117.2=NC_006113.20
Chromosome 27CM000118.2=NC_006114.20
Chromosome 28CM000119.2=NC_006115.21
Chromosome 32CM000120.2=NC_006119.20
Chromosome WCM000121.2=NC_006126.246
Chromosome ZCM000122.2=NC_006127.217
Linkage Group LGE22C19W28_E50C23CM000123.2=NC_008465.11
Linkage Group LGE64CM000367.1=NC_008466.11
unplacedn/an/an/a16,985

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule1,098,754,16617,5061,042,574,51211,063,74561,028359
Chromosome 1AllAssembled moleculeUnlocalized scaffolds201,215,710200,994,015221,69558535195,406,207195,192,289213,91821,916,69121,916,691128,3749,2029,1871552520
Chromosome 2AllAssembled moleculeUnlocalized scaffolds155,015,804154,873,767142,03734259150,486,393150,358,687127,70628,487,95928,487,95974,4136,9216,9051624240
Chromosome 3Assembled molecule113,657,78914110,205,32921,514,9443,83513
Chromosome 4AllAssembled moleculeUnlocalized scaffolds94,410,80894,230,402180,406128491,097,25690,936,578160,67818,898,37918,898,379149,1243,7673,73730770
Chromosome 5AllAssembled moleculeUnlocalized scaffolds62,266,73862,238,93127,8072018259,538,64259,513,00125,64132,733,14232,733,14220,7372,5242,520417170
Chromosome 6AllAssembled moleculeUnlocalized scaffolds37,434,45437,400,44234,0121512335,207,40935,176,21531,1948,639,9688,639,96817,4001,5241,521312120
Chromosome 7AllAssembled moleculeUnlocalized scaffolds38,488,56938,384,769103,80096336,311,71736,212,52599,19213,602,62513,602,62575,3081,2621,2557550
Chromosome 8AllAssembled moleculeUnlocalized scaffolds31,092,38830,671,729420,65964228,983,60628,570,315413,29118,941,92918,941,929419,5331,0711,05813330
Chromosome 9Assembled molecule25,554,352223,541,93712,990,5071,0002
Chromosome 10AllAssembled moleculeUnlocalized scaffolds22,570,11122,556,43213,67987120,498,61620,484,93713,6794,421,3324,421,33213,6791,3691,3690660
Chromosome 11AllAssembled moleculeUnlocalized scaffolds22,000,76221,928,09572,667109120,878,40220,811,33767,0655,811,8265,811,82672,6671,7191,70415880
Chromosome 12AllAssembled moleculeUnlocalized scaffolds20,543,74720,536,6877,06043119,578,83919,573,3675,47217,057,99617,057,9967,0608398381220
Chromosome 13AllAssembled moleculeUnlocalized scaffolds18,947,40918,911,93435,47595417,966,27817,932,29033,98810,359,57310,359,57324,6351,1351,1314550
Chromosome 14Assembled molecule15,819,469515,306,69211,975,5881,0294
Chromosome 15Assembled molecule12,968,165412,585,6176,861,0076573
Chromosome 16AllAssembled moleculeUnlocalized scaffolds676,935432,983243,952401624628,679405,348223,33194,83694,83663,18983572615150
Chromosome 17AllAssembled moleculeUnlocalized scaffolds11,185,43711,182,5262,91121110,341,00110,338,0902,91110,682,52610,682,5262,9117607600110
Chromosome 18AllAssembled moleculeUnlocalized scaffolds10,937,15210,925,26111,89132110,525,23810,513,34711,8919,214,0979,214,09711,8915615610110
Chromosome 19Assembled molecule9,939,72319,570,5389,939,7234800
Chromosome 20AllAssembled moleculeUnlocalized scaffolds14,061,23013,986,23574,99542213,628,98313,560,66068,32310,511,47510,511,47568,5876976889110
Chromosome 21Assembled molecule6,959,64246,657,0225,065,0164973
Chromosome 22AllAssembled moleculeUnlocalized scaffolds4,092,5903,936,574156,01612933,960,5183,809,688150,8301,295,0731,295,073150,09425023119880
Chromosome 23Assembled molecule6,042,21735,248,0813,357,3224272
Chromosome 24Assembled molecule6,400,10926,138,4845,078,7284421
Chromosome 25AllAssembled moleculeUnlocalized scaffolds2,112,1712,031,79980,372161511,437,3031,367,93369,370208,097208,09780,3722442301414140
Chromosome 26Assembled molecule5,102,43834,830,4103,133,6233752
Chromosome 27Assembled molecule4,841,970134,538,5491,415,54454512
Chromosome 28AllAssembled moleculeUnlocalized scaffolds4,617,4414,512,026105,4158713,802,6413,711,37991,262981,1061,004,515105,41541039416660
Chromosome 32Assembled molecule1,02811,0281,02800
Chromosome WAllAssembled moleculeUnlocalized scaffolds984,623259,642724,98149346858,993233,885625,10859,773182,06057,19416242120220
Chromosome ZAllAssembled moleculeUnlocalized scaffolds74,946,95474,602,320344,6341381211767,846,20967,536,373309,8361,795,0521,795,05234,2678,6438,582611201200
Linkage Group LGE22C19W28_E50C23AllAssembled moleculeUnlocalized scaffolds1,086,336895,237191,0991091992,218822,662169,556354,076457,032191,09915412529880
Linkage Group LGE64AllAssembled moleculeUnlocalized scaffolds607,48949,846557,643211575,26944,589530,680557,64349,846557,64351744000
unplacedAssembled molecule62,172,40616,98553,400,4086,0938,3930
MoleculeTotal
Length
Mitochondrion MT16,775
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