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Bos_taurus_UMD_3.0

Organism name:
Bos taurus (cattle)
Infraspecific name:
Breed: Hereford
Sex:
pooled male and female
BioSample:
SAMN02898106
Submitter:
Center for Bioinformatics and Computational Biology, University of Maryland
Date:
2009/09/09
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000003055.2 (replaced)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
DAAA02
Assembly method:
UMD Overlapper v. 2009; additional processing
Genome coverage:
9x
Sequencing technology:
Sanger

IDs: 4528 [UID] 4528 [GenBank]

See Genome Information for Bos taurus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

This assembly of the Bos taurus genome was created from the traces of BioProject PRJNA12555. This assembly closes thousands of gaps and corrects many inversions, deletions, translocations and single-nucleotide errors that were present on other assemblies, as determined by ... alignment to independent mapping data and to independently sequenced transcripts (full-length cDNAs). In this assembly synteny between the cow and human genomes and independent mapping data were used to assemble roughly 99% of the genome onto the 30 Bos taurus chromosomes.
Bos_taurus_UMD3.1 (UMD3.1) is an update to the UMD3 assembly that corrects errors in the gap types. The gap type changes join many placed scaffolds together but do not change the sequences of the chromosomes or the sequences of the unplaced scaffolds.
Annotation was produced by the NCBI Eukaryotic Genomes Annotation Pipeline Group using Gnomon, and added to the scaffolds in May 2010.
In June 2014 138 contigs were suppressed because they are contaminants, so the assembly name was updated to Bos_taurus_UMD_3.1.1, assembly GCA_000003055.4.
In November 2014 37 more contigs were suppressed because they are contaminants and two contigs (DAAA02065100 and DAAA02065112) were unsuppressed because they were determined to be Bos taurus. Therefore, a total of 173 contigs are suppressed. The assembly name remains Bos_taurus_UMD_3.1.1 but the assembly was incremented to GCA_000003055.5.  more

Global statistics

Total sequence length2,670,405,961
Total assembly gap length20,737,887
Gaps between scaffolds45,351
Number of scaffolds48,667
Scaffold N50187,719
Scaffold L504,233
Number of contigs75,790
Contig N5096,951
Contig L507,932
Total number of chromosomes and plasmids30

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_000001245.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1GK000001.2=AC_000158.10
Chromosome 2GK000002.2=AC_000159.10
Chromosome 3GK000003.2=AC_000160.10
Chromosome 4GK000004.2=AC_000161.10
Chromosome 5GK000005.2=AC_000162.10
Chromosome 6GK000006.2=AC_000163.10
Chromosome 7GK000007.2=AC_000164.10
Chromosome 8GK000008.2=AC_000165.10
Chromosome 9GK000009.2=AC_000166.10
Chromosome 10GK000010.2=AC_000167.10
Chromosome 11GK000011.2=AC_000168.10
Chromosome 12GK000012.2=AC_000169.10
Chromosome 13GK000013.2=AC_000170.10
Chromosome 14GK000014.2=AC_000171.10
Chromosome 15GK000015.2=AC_000172.10
Chromosome 16GK000016.2=AC_000173.10
Chromosome 17GK000017.2=AC_000174.10
Chromosome 18GK000018.2=AC_000175.10
Chromosome 19GK000019.2=AC_000176.10
Chromosome 20GK000020.2=AC_000177.10
Chromosome 21GK000021.2=AC_000178.10
Chromosome 22GK000022.2=AC_000179.10
Chromosome 23GK000023.2=AC_000180.10
Chromosome 24GK000024.2=AC_000181.10
Chromosome 25GK000025.2=AC_000182.10
Chromosome 26GK000026.2=AC_000183.10
Chromosome 27GK000027.2=AC_000184.10
Chromosome 28GK000028.2=AC_000185.10
Chromosome 29GK000029.2=AC_000186.10
Chromosome XGK000030.2=AC_000187.10
unplacedn/an/an/a3,286

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Chromosome 1158,337,0672,275157,294,391195,2781,5262,274
Chromosome 2137,060,4241,675136,217,273205,5461,2381,674
Chromosome 3121,430,4051,640120,643,505184,5221,2031,639
Chromosome 4120,829,6991,657120,067,824231,7871,0541,656
Chromosome 5121,191,4241,609120,321,769199,4641,2611,608
Chromosome 6119,458,7362,627118,527,296189,4191,1622,626
Chromosome 7112,638,6591,678110,832,556180,7831,1131,677
Chromosome 8113,384,8362,046112,606,715179,5431,0752,045
Chromosome 9105,708,2501,765104,985,054182,9851,0031,764
Chromosome 10104,305,0161,520103,634,539207,2209361,519
Chromosome 11107,310,7631,321106,541,332208,5661,1191,320
Chromosome 1291,163,1251,51090,441,598178,9419601,509
Chromosome 1384,240,3501,22783,698,834184,4027741,226
Chromosome 1484,648,3901,97784,018,133228,2487711,976
Chromosome 1585,296,6761,27184,522,042163,0888891,270
Chromosome 1681,724,6871,16681,044,388185,1099981,165
Chromosome 1775,158,59697574,594,691220,438834974
Chromosome 1866,004,0231,28665,448,904161,4508071,285
Chromosome 1964,057,4571,14563,557,252170,4007321,144
Chromosome 2072,042,65590971,551,568185,993783908
Chromosome 2171,599,0961,16071,052,926179,7587551,159
Chromosome 2261,435,87478061,077,594182,996537779
Chromosome 2352,530,06267552,134,867176,892564674
Chromosome 2462,714,93077262,346,081204,456535771
Chromosome 2542,904,17080142,619,964174,447382800
Chromosome 2651,681,46474651,326,006171,675522745
Chromosome 2745,407,9021,05944,947,593158,7244681,058
Chromosome 2846,312,54656645,994,213214,476453565
Chromosome 2951,505,22495351,074,834141,336581952
Chromosome X148,823,8996,590147,044,776172,8042,0886,589
unplaced9,499,5563,2869,499,5565,42500
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