Open Access Highly Accessed Research article

Bos taurus genome assembly

Yue Liu1, Xiang Qin1, Xing-Zhi Henry Song1, Huaiyang Jiang1, Yufeng Shen12, K James Durbin13, Sigbjørn Lien4, Matthew Peter Kent4, Marte Sodeland4, Yanru Ren1, Lan Zhang1, Erica Sodergren15, Paul Havlak16, Kim C Worley1*, George M Weinstock15 and Richard A Gibbs1

Author Affiliations

1 Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA

2 Department of Computer Science and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA

3 Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA, 95064, USA

4 Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, Ås, 1432, Norway

5 Washington University St Louis, MO, USA

6 Department of Computer Science, University of Houston, 4800 Calhoun Road, Houston, TX 77204-3010, USA

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BMC Genomics 2009, 10:180  doi:10.1186/1471-2164-10-180

Published: 24 April 2009

Additional files

Additional file 1:

Completeness of assembly compared to unassembled reads. Table provides completeness statistics for 4 assemblies compared to finished BACs, markers, ESTs, and BAC end sequences.

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Additional file 2:

Detailed comparisons of Independent Maps. Table for comparison of independent maps of chromosomes 6, 19 and 29. Each column gives the order of the scaffolds in the map. Column 1 is the scaffold name, column 2 is the order in the chromosome map used as the gold standard evidence, column 3 is the order in the Btau_4.0 assembly, column 4 is the order in the Integrated Bovine Map[11], column 5 is the order in the Btau_3.1 assembly.

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Additional file 3:

SNP distribution before and after repositioning. Figure shows the locations of the small fraction of SNPs (135 SNPs, or 0.8%) whose LOD scores were found to improve with repositioning are shown. The SNPs were grouped into local 1 Mb sized bins. Bins with more than one SNP are identified with different indicators on the graphs. (A) The locations of the SNPs before repositioning. (B) The locations the SNPs after repositioning.

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Additional file 4:

SNPs with linkage position different from Btau_4.0 assembly postion. Table provides list of SNPs with linkage positions that disagree with Btau_4.0 assembly, also provides the identity and position of the most closely linked SNP. Columns include SNP name, chromosome, position in Btau_4.0, and best two-point hit, with the chromosome and position for that linked SNP.

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Additional file 5:

Additional SNP placement by linkage analysis. The locations of 568 SNPs with previously unassigned position in Btau_4.0 whose location was determined by identifying the pairwise comparison between the unknown SNP and all the mapped SNPs that produced the highest LOD score using the twopoint option of CRIMAP.

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Additional file 6:

Placement of unplaced scaffolds using linkage information. Table provides placement information for unplaced scaffolds based on linked markers. Columns include SNP, unplaced Contig, location in unplaced contig, chromosome placement, linked SNP, location in chromosome.

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