The total gap size between contigs was estimated by fluorescence in situ hybridization (Additional file 4) to be 9,598,219 bp and 7,290,600 bp by optical mapping (Additional file 5) resulting in a total assembly size of 382,771,738 bp and 380,464,119 bp, respectively.
The lengths of sequence gaps between contigs are estimated from the expected insert sizes and are usually filled with a stretch of Ns.
Based on the end-sequence data from the obtained libraries, direct linkages between the contigs were estimated using CAT software, and linking cosmid clones were selected from the large-insert library.
From the alignment the orientation, order and distance between the contigs was estimated.
There were 42,970 unique bands in the contigs and the total physical length of contigs was estimated to be 151,469 Mb with an average of 304 kb per contig.
The N50 size of the contigs was estimated to be ~1,494 kb and the longest contig was ~5,562 kb.
The relative positions and orientations of these contigs are estimated by paired reads that land in different contigs.
The N50 size of the contigs was estimated to be ~1,494 kb.
The contigs were then mapped on to the version 2.0 of the bovine assembly (BosTau2.0, The Bovine Genome Sequencing Project Consortium) and the length of the between-contig gaps were estimated (which ranged between 79 to 519 bp, while one gap could not be estimated with the current depth of the genomic assembly).
Similarities between contigs or libraries were estimated using Pearson's correlation coefficient.
