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GRCg6

Description:
Genome Reference Consortium Chicken Build 6
Organism name:
Gallus gallus (chicken)
Infraspecific name:
Breed: Red Jungle fowl, inbred line UCD001
Isolate:
RJF #256
Sex:
female
BioSample:
SAMN02981218
BioProject:
PRJNA13342
Submitter:
Genome Reference Consortium
Date:
2018/02/02
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000002315.4 (replaced)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
AADN05
Assembly method:
FALCON-integrate v. 1.7.5
Genome coverage:
82x
Sequencing technology:
Pacific Biosciences RSII (P6-C4 and P5-C3 chemistry)

IDs: 1556721 [UID] 6002248 [GenBank]

See Genome Information for Gallus gallus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The current red jungle fowl (Gallus gallus) genome assembly, GRCg6a, was sequenced and assembled with single molecule real time (SMRT) sequencing technology to a depth of approximately 80x. The same DNA reference source, a female known as "RJF #256" ... from an inbred line (UCD 001), was sequenced on the Pacific Biosciences RSII instrument (a relatively equal split of P6 and P5 chemistry reads) and all reads were assembled with the FALCON assembler. In recognition of the need for improvement in assembly contiguity and representation of chromosomes we generated a high chromatin proximity map to aid in the order and orientation of assembled sequences. The creation of the improved chromosomal sequences proceeded in a way similar to that described for the Gallus_gallus-5.0 release. To avoid loss of sequence in the transition from Gallus_gallus-5.0 to GRCg6a, finished RJF BAC clones found in the former assembly were incorporated into the final chromosomal sequences, replacing underlying WGS contigs where appropriate. For more information see: https://www.ncbi.nlm.nih.gov/grc/chicken. Funding for the sequence characterization of the chicken genome was provided by the USDA, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) and Cobb Vantress.
GRCg6a differs from the earlier GRCg6 version only in the elimination of four redundant unlocalized scaffolds.  more

Global statistics

Total sequence length1,140,108,455
Total assembly gap length9,804,060
Gaps between scaffolds68
Number of scaffolds528
Scaffold N5023,063,781
Scaffold L5013
Number of contigs1,602
Contig N5016,739,324
Contig L5022
Total number of chromosomes and plasmids34
Number of component sequences (WGS or clone)2,443

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
Assembly Unit: Primary Assembly (GCA_000000185.4)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000093.5n/an/a7
Chromosome 2CM000094.5n/an/a0
Chromosome 3CM000095.5n/an/a4
Chromosome 4CM000096.5n/an/a0
Chromosome 5CM000097.5n/an/a0
Chromosome 6CM000098.5n/an/a6
Chromosome 7CM000099.5n/an/a0
Chromosome 8CM000100.5n/an/a0
Chromosome 9CM000101.5n/an/a1
Chromosome 10CM000102.5n/an/a0
Chromosome 11CM000103.5n/an/a0
Chromosome 12CM000104.5n/an/a0
Chromosome 13CM000105.5n/an/a1
Chromosome 14CM000106.5n/an/a1
Chromosome 15CM000107.5n/an/a1
Chromosome 16CM000108.5n/an/a1
Chromosome 17CM000109.5n/an/a0
Chromosome 18CM000110.5n/an/a0
Chromosome 19CM000111.5n/an/a1
Chromosome 20CM000112.5n/an/a0
Chromosome 21CM000113.5n/an/a0
Chromosome 22CM000114.5n/an/a1
Chromosome 23CM000115.5n/an/a6
Chromosome 24CM000116.5n/an/a0
Chromosome 25CM000124.5n/an/a1
Chromosome 26CM000117.5n/an/a0
Chromosome 27CM000118.5n/an/a0
Chromosome 28CM000119.5n/an/a1
Chromosome 30CM003637.2n/an/a0
Chromosome 31CM003638.2n/an/a3
Chromosome 32CM000120.4n/an/a0
Chromosome 33CM000123.5n/an/a1
Chromosome WCM000121.5n/an/a54
Chromosome ZCM000122.5n/an/a3
unplacedn/an/an/a340

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule1,140,108,4555281,130,304,39523,063,7811,07468
Chromosome 1AllAssembled moleculeUnlocalized scaffolds197,677,740197,608,38669,35424177197,166,990197,097,63669,35426,445,46126,445,46121,511106106016160
Chromosome 2Assembled molecule149,682,0493149,178,23977,922,350382
Chromosome 3AllAssembled moleculeUnlocalized scaffolds110,854,228110,838,41815,810844110,352,808110,336,99815,81088,985,37088,985,3706,27214140330
Chromosome 4Assembled molecule91,315,245290,814,34572,053,44191
Chromosome 5Assembled molecule59,809,098359,308,18842,721,69692
Chromosome 6AllAssembled moleculeUnlocalized scaffolds36,428,95736,374,70154,25682635,925,74735,871,49154,25620,451,86220,451,86210,92832320220
Chromosome 7Assembled molecule36,742,308236,241,90828,910,77541
Chromosome 8Assembled molecule30,219,446229,717,14620,392,703231
Chromosome 9AllAssembled moleculeUnlocalized scaffolds24,181,04924,153,08627,96332123,680,53923,652,57627,96323,063,78123,063,78127,963550220
Chromosome 10Assembled molecule21,119,840120,618,24020,619,840161
Chromosome 11Assembled molecule20,200,042219,699,34216,969,29871
Chromosome 12Assembled molecule20,387,278120,385,97820,387,278130
Chromosome 13AllAssembled moleculeUnlocalized scaffolds19,168,87119,166,7142,15721118,666,07118,663,9142,15718,666,71418,666,7142,15728280110
Chromosome 14AllAssembled moleculeUnlocalized scaffolds16,220,07316,219,30876532115,718,57315,717,80876515,478,99815,478,99876515150110
Chromosome 15AllAssembled moleculeUnlocalized scaffolds13,064,21813,062,1842,03421113,062,51813,060,4842,03413,062,18413,062,1842,03417170000
Chromosome 16AllAssembled moleculeUnlocalized scaffolds2,994,1042,844,601149,5034312,491,6842,342,281149,4031,519,6991,519,699149,50324231330
Chromosome 17Assembled molecule10,762,512110,262,41210,262,51211
Chromosome 18Assembled molecule11,373,140111,371,44011,373,140170
Chromosome 19AllAssembled moleculeUnlocalized scaffolds10,324,34310,323,2121,13121110,323,24310,322,1121,13110,323,21210,323,2121,13111110000
Chromosome 20Assembled molecule13,897,287113,897,28713,897,28700
Chromosome 21Assembled molecule6,844,97916,844,9796,844,97900
Chromosome 22AllAssembled moleculeUnlocalized scaffolds5,460,3805,459,4629184314,959,4704,958,5529183,070,9963,070,996918990220
Chromosome 23AllAssembled moleculeUnlocalized scaffolds6,202,9106,149,58053,3307166,201,8106,148,48053,3306,149,5806,149,58016,15711110000
Chromosome 24Assembled molecule6,491,22216,490,9226,491,22230
Chromosome 25AllAssembled moleculeUnlocalized scaffolds3,982,4943,980,6101,8849813,478,6343,476,7501,884576,389576,3891,88438380770
Chromosome 26Assembled molecule6,055,71015,555,3105,555,71041
Chromosome 27Assembled molecule8,080,43228,076,2228,008,924421
Chromosome 28AllAssembled moleculeUnlocalized scaffolds5,118,4015,116,8821,5192115,118,2015,116,6821,5195,116,8825,116,8821,519220000
Chromosome 30Assembled molecule1,818,52551,815,385379,495314
Chromosome 31AllAssembled moleculeUnlocalized scaffolds6,185,1606,153,03432,1264136,178,1606,146,03432,1266,153,0346,153,03411,30570700000
Chromosome 32Assembled molecule725,8313725,311408,42352
Chromosome 33AllAssembled moleculeUnlocalized scaffolds7,821,8487,821,6661826517,815,2087,815,0261821,769,4461,769,44618266660440
Chromosome WAllAssembled moleculeUnlocalized scaffolds12,958,0466,813,1146,144,9325515412,708,6136,571,5816,137,0326,813,1146,813,1143,461,7851032479000
Chromosome ZAllAssembled moleculeUnlocalized scaffolds151,835,32082,529,92169,305,39913103151,366,10382,072,40469,293,69925,612,42411,090,20541,007,8961214117990
unplacedAssembled molecule14,105,36934014,087,3691,222,1951800
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