Alternate sequences in UCSC and Ensembl
If you go to the UCSC Genome Browser and type “vars” in the “gene” text box (human genome, 2009 assembly), you’ll notice something different. The chromosome region listed is “chr6_apd_hap1:3,060,047-3,078,462″ Those are the haplotype sequence coordinates. With the addition of the hg19 assembly, now provided by GRC, additional alternative sequences were included: haplotypes, alternative loci and patches.
Now type in “vars” in the “position or search term” box, or “chr6:30,000,000-31,000,000″ and submit.
Now to go the Mapping and Sequencing tracks and change the “GRC Patch Release” Menu to “pack.” Click the title link and you’ll see you can turn on either the haplotypes or the patch releases.
Once you do that, click refresh.
Here you will be able to see all those alternative sequences provided by the GRC.
It will look something like the the screenshot below.
Click on any of the sequence icons and get more information about that sequence. You can read more about the GRC haplotype and patch release at the site.
The Ensembl browser too of course has these alternative sequences included. Instead of going through how to access them here, I’ll point you to their very informative blog post on that very subject.