Vega Genome Assemblies
The genome assemblies in Vega can differ from those in Ensembl (and other browsers such as UCSC) to differing degrees depending on the species:
The reference chromosomes in Vega are identical to the human GRCh38 build. The GRC haplotype patches are treated in two ways (i) the LRC and MHC haplotye regions are represented as distinct chromosomes (rather than as haplotype patch regions as they are in Ensembl), and (ii) the remainder of the haplotypes are stored only as patches and are therefore not presented as distinct chromosomes. The coordinates of features on all of the haplotype patches are always relative to the patch itself rather than the reference chromosome.
The mouse Vega genome assembly is identical to GRCm38 but Vega also contains strains not present in GRCm38, namely candidate Insulin Dependent diabetes (Idd) regions in NOD/MrkTac (Non-Obese Diabetic), NOD/ShiLtJ, and 129 strains.
The Vega zebrafish assembly is identical to GRCz10 but also contains the AB chromosome consisting of PAC clones from the AB strain.
Vega contains 18 chromosomes on the Sscrofa10.2 (chr X is not present), and three (7-LW, X-WTSI, Y-WTSI) on other assemblies unique to Vega.
Vega contains the Rnor6.0 assembly.
This gorilla assembly and annotation is unique to Vega.
This chimpanzee assembly and annotation is unique to Vega.
The wallaby assembly and annotation is unique to Vega.
Vega has an assembly and annotation on the MHC region of chromosome 12 for a different breed of dog (Doberman) to that in Ensembl.
The tasmanian devil assembly and annotation is unique to Vega.