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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

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