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Bos_taurus_UMD_3.1

Organism name:
Bos taurus
Infraspecific name:
Breed: Hereford
Sex:
pooled male and female
BioSample:
SAMN02898106
Submitter:
Center for Bioinformatics and Computational Biology, University of Maryland
Date:
2009/12/01
Assembly level:
Chromosome
Genome representation:
full
GenBank Assembly ID:
GCA_000003055.3 (replaced)
RefSeq Assembly ID:
GCF_000003055.4 (replaced)
RefSeq Assembly and GenBank Assembly Identical:
no (show details)
  • Only in RefSeq: chromosome MT.
Data displayed for RefSeq version
WGS Project:
DAAA02
Assembly method:
UMD Overlapper v. 2009; additional processing
Genome coverage:
9x
Sequencing technology:
Sanger

IDs: 313678 [UID] 5348 [GenBank] 313678 [RefSeq]

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
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Global statistics

Total sequence length2,670,422,299
Total assembly gap length20,737,263
Gaps between scaffolds3,193
Number of scaffolds6,510
Scaffold N506,380,747
Number of contigs75,771
Contig N5096,955
Total number of chromosomes and plasmids31

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_000001245.3)
Molecule nameGenBank IDRefSeq IDUnlocalized
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 1158,337,067106157,294,6566,458,4203,690105
Chromosome 2137,060,42464136,217,3288,169,6752,84763
Chromosome 3121,430,40573120,643,50510,841,4852,77072
Chromosome 4120,829,69983120,067,8245,769,4852,62882
Chromosome 5121,191,424130120,321,7694,964,2562,740129
Chromosome 6119,458,736138118,527,2965,003,0013,651137
Chromosome 7112,638,659210110,832,5563,078,5482,581209
Chromosome 8113,384,836321112,606,7152,194,0302,800320
Chromosome 9105,708,250399104,985,0541,299,3862,369398
Chromosome 10104,305,01647103,634,53914,183,3142,40946
Chromosome 11107,310,76362106,541,33217,927,4362,37861
Chromosome 1291,163,12519890,441,5987,024,4952,272197
Chromosome 1384,240,3503483,698,89616,325,7721,96333
Chromosome 1484,648,3909384,018,13314,691,0232,65592
Chromosome 1585,296,6766584,522,0428,185,5642,09564
Chromosome 1681,724,6874381,044,53712,752,5782,11642
Chromosome 1775,158,5965474,594,6918,786,8141,75553
Chromosome 1866,004,0235865,448,9978,212,6992,03157
Chromosome 1964,057,4574963,557,2524,531,4201,82848
Chromosome 2072,042,6554871,551,5685,179,7151,64447
Chromosome 2171,599,0963571,052,92610,873,7171,88034
Chromosome 2261,435,8742061,077,59417,143,0071,29719
Chromosome 2352,530,0627352,134,8679,203,3531,16672
Chromosome 2462,714,9301862,346,08124,930,1381,28917
Chromosome 2542,904,1701942,619,96411,993,1871,16418
Chromosome 2651,681,4642451,326,0067,685,3721,24423
Chromosome 2745,407,9026944,947,5935,653,9601,45868
Chromosome 2846,312,5463245,994,2138,350,58198731
Chromosome 2951,505,2245951,074,8344,448,6371,47558
Chromosome X148,823,899599147,044,7763,493,8578,079598
unplaced9,499,5563,2869,499,5565,42500
MoleculeTotal
Length
Mitochondrion MT16,338
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