Question: What are "HET" regions in a genome?
0
gravatar for alanh
4 months ago by
alanh60
alanh60 wrote:

I was looking at a couple of the metadata files describing the regions of GRCh38 (e.g. centromeres, alternate scaffolds, etc.), and one of the lines is the following:

HET7 7 61377789 61528020 HET na na na

This is the only "HET" region in the human genome, and I can't find any details documenting this anywhere in Google, I checked the Genome Browser and there isn't any special indication about the region, and I asked some knowledgable colleagues and they didn't know either.

metadata genome • 233 views
ADD COMMENTlink modified 4 months ago by h.mon27k • written 4 months ago by alanh60

Where are these metadata files from? Which is the file in question?

ADD REPLYlink modified 4 months ago • written 4 months ago by h.mon27k

From https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.28

clicked on "Download the regions report" on the upper right, which yields this URL:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/GCA_000001405.28_GRCh38.p13_assembly_regions.txt

It's line 212 in that file.

ADD REPLYlink modified 4 months ago • written 4 months ago by alanh60
4
gravatar for h.mon
4 months ago by
h.mon27k
Brazil
h.mon27k wrote:

Apparently it is an heterochromatic region. It is listed at the table Modeled centromeres and heterochromatin regions found at the Genome Reference Consortium Human Genome Overview page. It doesn't have an "assembly unit", probably because it is composed of repetitive material and thus currently impossible to assemble.

ADD COMMENTlink written 4 months ago by h.mon27k
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