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Oar_v3.1

Organism name:
Ovis aries (sheep)
Infraspecific name:
Breed: Texel
BioSample:
SAMN00116405
BioProject:
PRJNA169880
Submitter:
International Sheep Genome Consortium
Date:
2012/09/24
Synonyms:
oviAri3
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000298735.1 (replaced)
RefSeq assembly accession:
GCF_000298735.1 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
AMGL01
Assembly method:
SOAPdenovo v. 1.03
Sequencing technology:
Illumina GAII; 454

IDs: 457978 [UID] 426968 [GenBank] 457978 [RefSeq]

See Genome Information for Ovis aries

There are 4 assemblies for this organism

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History (Show revision history)

Comment

The 454 data was from a Texel ram collected by Tim Smith of (US Meat Animal Research Center (USMARC)) at the Clay Center in Nebraska, USA. Sex: male, Breed : Texel, Isolate number: 200118011, Country of Origin: USA, Isolation ... Source: Blood, Collection Date: Late 2009. Most of the Illumina data was from a 6-month old ewe collected by Dr. Jacob B. Hansen of the University of Copenhagen. Sex: female, Breed: Texel, Isolate number: N/A, Country of Origin: Denmark, Isolation Source: Blood, Collection Date: Late 2009.

A single Texel ewe and a single Texel ram were sequenced and the 75-fold coverage by Illumina reads of the Texel ewe were assembled de novo into contigs and scaffolds with SOAPdenovo. Then 120-fold coverage Illumina sequences from both the ewe and the ram were used for a round of gap-filling. At this point, the N50 length of contigs was 18 kb, and the N50 length of the assembled scaffolds was 1.1Mb, achieving a total length of 2.64 Gb and leaving 6.9% gaps. This assembly was the previous Oar v2.0. The current assembly, Oar_v3.1, was created with another round of gap-filling by adding 21-fold coverage of GC content unbiased Illumina sequencing data from the male and 3 Gb MeDIP-seq for high GC content sequence from the female to the original datasets. Approximately 200,000 gaps were filled, including about 5000 that were filled using CHORI-243 BAC library sequences and 454 reads generated for the Oar v1.0 assembly (ACIV000000000, BioProject PRJNA33937). Segmental duplicates were identified by Whole Genome Assembly Comparison (WAGC), and their read coverage checked by GC content adjustment. Probable artificial tandem duplicates were identified using the larger insert 454 and BAC libraries and comparison to the UMD3 bovine genome assembly, and one copy of the tandem pairs was removed. The assembly of 775 overlapping scaffold ends were revised and these adjacent scaffold pairs were linked together. Artificial duplicated copies that had been generated by multiple gap-filling steps using gapcloser were removed, and erroneously assembled scaffolds identified during the error checking were manually split. A high-density RH map with 39,042 SNP markers and Ovine SNP50 genotyping linkage data were used to check scaffold integrity and to anchor scaffolds and super-scaffolds to chromosomes, leaving roughly 5700 unplaced scaffolds.
For more information about the International Sheep Genomics Consortium (ISGC) and the sheep assembly, see http://www.sheephapmap.org/  more

Global statistics

Total sequence length2,619,054,388
Total ungapped length2,534,344,180
Gaps between scaffolds0
Number of scaffolds5,698
Scaffold N50100,079,507
Scaffold L508
Number of contigs130,765
Contig N5040,376
Contig L5018,404
Total number of chromosomes and plasmids28
Number of component sequences (WGS or clone)130,765

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_000298745.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM001582.1=NC_019458.10
Chromosome 2CM001583.1=NC_019459.10
Chromosome 3CM001584.1=NC_019460.10
Chromosome 4CM001585.1=NC_019461.10
Chromosome 5CM001586.1=NC_019462.10
Chromosome 6CM001587.1=NC_019463.10
Chromosome 7CM001588.1=NC_019464.10
Chromosome 8CM001589.1=NC_019465.10
Chromosome 9CM001590.1=NC_019466.10
Chromosome 10CM001591.1=NC_019467.10
Chromosome 11CM001592.1=NC_019468.10
Chromosome 12CM001593.1=NC_019469.10
Chromosome 13CM001594.1=NC_019470.10
Chromosome 14CM001595.1=NC_019471.10
Chromosome 15CM001596.1=NC_019472.10
Chromosome 16CM001597.1=NC_019473.10
Chromosome 17CM001598.1=NC_019474.10
Chromosome 18CM001599.1=NC_019475.10
Chromosome 19CM001600.1=NC_019476.10
Chromosome 20CM001601.1=NC_019477.10
Chromosome 21CM001602.1=NC_019478.10
Chromosome 22CM001603.1=NC_019479.10
Chromosome 23CM001604.1=NC_019480.10
Chromosome 24CM001605.1=NC_019481.10
Chromosome 25CM001606.1=NC_019482.10
Chromosome 26CM001607.1=NC_019483.10
Chromosome XCM001608.1=NC_019484.10
unplacedn/an/an/a5,670

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All2,619,037,7725,6972,534,327,564100,079,507125,0670
Chromosome 1275,612,8951266,811,716275,612,89512,8840
Chromosome 2248,993,8461241,471,245248,993,84611,2100
Chromosome 3224,283,2301216,749,049224,283,23011,1290
Chromosome 4119,255,6331115,434,016119,255,6335,4990
Chromosome 5107,901,6881104,779,382107,901,6884,9880
Chromosome 6117,031,4721113,069,016117,031,4725,7520
Chromosome 7100,079,507197,332,220100,079,5074,1220
Chromosome 890,695,168188,112,25190,695,1683,8550
Chromosome 994,726,778191,748,84994,726,7784,2090
Chromosome 1086,447,213183,765,37986,447,2133,9120
Chromosome 1162,248,096160,533,82462,248,0962,9770
Chromosome 1279,100,223176,773,55579,100,2233,6050
Chromosome 1383,079,144180,776,63383,079,1443,3520
Chromosome 1462,722,625160,463,38562,722,6253,3650
Chromosome 1580,923,592178,241,25580,923,5923,7140
Chromosome 1671,719,816169,791,57671,719,8163,0670
Chromosome 1772,286,588169,979,98072,286,5883,6290
Chromosome 1868,604,602166,361,34968,604,6023,2670
Chromosome 1960,464,314158,886,04460,464,3142,7360
Chromosome 2051,176,841149,578,45251,176,8412,3520
Chromosome 2150,073,674148,243,24850,073,6742,6400
Chromosome 2250,832,532149,278,97150,832,5322,3500
Chromosome 2362,330,649160,616,70462,330,6492,5720
Chromosome 2442,034,648140,569,19942,034,6482,6020
Chromosome 2545,367,442143,924,12345,367,4421,8700
Chromosome 2644,077,779143,012,85644,077,7791,6880
Chromosome X135,437,0881130,455,255135,437,0886,4130
unplaced31,530,6895,67027,568,0329,1035,3080
MoleculeTotal
Length
Mitochondrion MT16,616
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