Question: What are "HET" regions in a genome?
0
gravatar for alanh
21 days ago by
alanh50
alanh50 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 • 125 views
ADD COMMENTlink modified 21 days ago by h.mon25k • written 21 days ago by alanh50

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

ADD REPLYlink modified 21 days ago • written 21 days ago by h.mon25k

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 21 days ago • written 21 days ago by alanh50
4
gravatar for h.mon
21 days ago by
h.mon25k
Brazil
h.mon25k 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 21 days ago by h.mon25k
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