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What human genome assembly and coordinate system is Ensembl using?

Ensembl uses a one-based coordinate system. (UCSC use a zero-based coordinate system.)

Ensembl uses the most recently updated human genome housed at the GRC. This current major assembly releas e is called GRCh37. NCBI and UCSC use the same genome. (UCSC refers to the recent human genome as GRCh37/hg19).

Linking back to a previous Ensembl release:

If you are looking for an older genome, try the Ensembl archive sites. The previous human assembly NCBI36 is the same as UCSC's hg18.

To link to a specific Ensembl archive site, remember to use the Permanent Link (found at the bottom left of each page) eg. http://jun2013.archive.ensembl.org/Homo_sapiens/Info/Index.

Finding the new coordinates for your region of interest

You may have stored a genomic location on NCBI36, and want to know where the equivalent region is on GRCh37. Simply add the old assembly name into the address bar. eg. www.ensembl.org/Homo_sapiens/Location/View?db=core;r=13:32889611-32973805;a=ncbi36. This will redirect you to new coordinates with the message "Your request for 13:32889611-32973805 in NCBI36 has been mapped to the new GRCh37 coordinates 13:33991611-34075805".

Assembly updates

The GRC produce minor assembly releases to GRCh37 on a regular basis, approximately every three months. We incorporate these assembly updates, known as "patches" into GRCh37. By default, the chromosome coordinates do not change when we update the human assembly to the most recent minor release. Instead, we're adding additional alternate sequences to the assembly that can be swapped in on request.

When we update GRCh37 to the latest patch release, the assembly name is appended with the patch number. For example, the second minor assembly release for GRCh37 was called GRCh37.p2. The seventh minor assembly release for GRCh37 was called GRCh37.p7. Find more information about human patches and haplotypes here.


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