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.




3 thoughts on “Alternate sequences in UCSC and Ensembl

  1. GenomeRef

    I think it is great that you are trying to point how to find the non-chromosomal alternate paths that are part of the assembly. However, I think there are some terminology issues to be sorted. First, these are references sequences, and they are full fledged members of the assembly- they are just not part of the chromosome assembly. Second, I’m not sure that I would call these ‘haplotypic regions’. These sequences represent alternate paths from those found on the chromosome, but they may not always represent a specific haplotype in the ‘HapMap’ sense of the word. In some cases, like the MAPT or MHC locus they do, but a lot of careful experimental work has gone into ensuring these represent a true haplotype. That same level of work has not occurred at all regions and so I think we want to be very careful about referring to them as haplotypic.
    For more information on the terminology preferred by the GRC, try this page:

  2. Trey

    Thank you for the clarification. I’ve changed the title of the post. I was using the terminology that Ensembl used in their blog post (I hadn’t used ‘haplotypic regions’ that is their terminology) and that UCSC uses to an extent in the track description, but your explanation does clarify this. I’ll make appropriate changes. Thank you very much.

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