Annotation status display

The manual annotation in Vega includes:

• Chromosomes that were annotated clone by clone.
• Sections of chromosomes (one or more clones) that were fully annotated.
• Individual loci that were annotated.

Unannotated regions of genomes are indicated with either (i) grey shading on vertical views such as chromosome summary or (ii) grey coloured tracks on horizontal location views. These can be switched off via the Configuration panel. Annotated or unassembled regions of the genome do not have these indicators.

There are species specific differences as to the type of annotated region present.

Human

• All reference and non-reference chromosomes, for example MHC regions and GRC haplotype patches, have undergone a first pass manual annotation.

Mouse

• Contains twelve chromosomes (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and X) that were fully annotated on a clone by clone basis. In addition it contains distinct regions of interest were fully annotated on a clone by clone basis - the del36H region on chromosome 13, and candidate Idd regions on a number of chromosomes.
• The chromosome images on the mouse home page show the karyotype bands for all full length chromosomes overlaid with grey shading to indicate the regions that have not been annotated. Note that the karyotype bands, usually shown in shades of grey in Vega, are recoloured on this page in shades of blue to distinguish them from the annotation status shading.
• Location based views show computationally derived features for all parts of the assembled genome.

Zebrafish

• Contains fully annotated clones, non-annotated clones, and loci that were annotated on a case by case basis. Location based views show computationally derived features for all parts of the assembled genome.

Rat

• Annotation of Rnor6.0 was approached on a locus by locus basis with the exceptions of the MHC and chromosome Y which were fully annotated. Computationally derived features are shown for all parts of the genome.

Pig

• Chromosomes 7-LW, X-WTSI and Y-WTSI contain only fully annotated clones. Other chromosomes may have regions where the clones were completely annotated (eg the MHC region on chromosome 7, LRC region on chromosome 6) but mostly show annotation of individual loci. No karyotype bands are shown for pig. Location based views show computationally derived features for all parts of the genome.

Gorilla

• The Vega database for gorilla contains only fully annotated clones for specific regions of chromosome 6 and 19.

Chimpanzee

• The Vega database for chimpanzee contains only fully annotated clones for a specific region of chromosome 6.

Wallaby

• The Vega database for wallaby contains only fully annotated clones for a specific region of chromosome 2.

Dog

• The Vega database for dog contains 700 kbp of the MHC region on chromosome 12, consisting of fully annotated clones only.

Tasmanian Devil

• The Vega database for tasmanian devil contains seven fully annotated contigs spanning about 1.2 Mbp of the MHC region on chromosome 4.