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What haplotypes and assembly patches can I see for human?

Where do haplotypes and patches come from?

The GRC provides haplotypic regions along with the Primary assembly for human. In addition to haplotypes, which are regions with known variations to the Primary assembly, the GRC provides assembly patches on a regular basis.

There are two types of assembly patches: Novel patches and Fix patches. Novel patches are additional sequence for alternate alleles that are not represented on the primary assembly. Fix patches are additional sequence that will replace regions the known regions of misassembly in GRCh37 when the next major assembly update (GRCh38) is released.

How is this shown on the browser?

You might notice some strange-looking chromosome names, or regions of the genome that have red or green highlighting. Red regions represent regions of the genome where there is a haplotype or novel patch. Green regions represent regions of the genome where there is a fix patch. For an example, see the top image in Region in Detail. You can jump to haplotypes and patches by clicking on those highlighted regions. Other access points include BioMart (see the Region: Chromosome filter), and the Perl API.

What haplotypes are available with GRCh37?

A list of haplotypes and patches can be found on the GRC human overview page. Specifically, these haplotypes are found in Ensembl:

  • Haplotype on chromosome 4: HSCHR4_1
  • Haplotypes on chromosome 6 in the MHC region
  • Haplotype on chromosome 17: HSCHR17_1

For more about patches and haplotypes, see our blog post.

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