|Title||Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.|
|Publication Type||Journal Article|
|Year of Publication||2012|
|Authors||Zimin, AV, Kelley, DR, Roberts, M, Marçais, G, Salzberg, SL, Yorke, JA|
|Keywords||Animals, Cattle, Genome, Humans, Reproducibility of Results, Segmental Duplications, Genomic|
We analyzed the whole genome sequence coverage in two versions of the Bos taurus genome and identified all regions longer than five kilobases (Kbp) that are duplicated within chromosomes with >99% sequence fidelity in both copies. We call these regions High Fidelity Duplications (HFDs). The two assemblies were Btau 4.2, produced by the Human Genome Sequencing Center at Baylor College of Medicine, and UMD Bos taurus 3.1 (UMD 3.1), produced by our group at the University of Maryland. We found that Btau 4.2 has a far greater number of HFDs, 3111 versus only 69 in UMD 3.1. Read coverage analysis shows that 39 million base pairs (Mbp) of sequence in HFDs in Btau 4.2 appear to be a result of a mis-assembly and therefore cannot be qualified as segmental duplications. UMD 3.1 has only 0.41 Mbp of sequence in HFDs that are due to a mis-assembly.
|Alternate Journal||PLoS ONE|
|PubMed Central ID||PMC3411808|
|Grant List||R01 GM083873 / GM / NIGMS NIH HHS / United States |
R01 HG006102 / HG / NHGRI NIH HHS / United States
R01 HG006677 / HG / NHGRI NIH HHS / United States
R01HG0294501 / HG / NHGRI NIH HHS / United States
Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.
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