What do the names in Ensembl for clones, contigs and scaffolds mean?
All clones and whole genome shotgun contigs in the integrated assembly in Ensembl are identified by their EMBL accessions. In the case of the WGS contigs, these accessions always start with CABZ. Clones and WGS contigs are grouped into “scaffolds”. A scaffold corresponds to a single fingerprint contig of clones, which has had its gaps filled in using WGS contigs placed using sequence alignment. Scaffolds on chromosomes also occur which consist purely of WGS contigs; these are WGS contigs which have been placed using marker information. Scaffolds are given names which begin with Zv9_scaffold, followed by a number. The first scaffold on chromosome 1 is Zv9_scaffold1, the second is Zv9_scaffold2, and so on up till the end of chromosome 25. There are also scaffolds which are not placed on chromosomes. Some of these are based on fingerprint contigs of clones whose parent chromosome could not be identified. These have scaffold names which are Zv9_scaffold followed by a number, just like scaf
