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Hi Mahmood<br>
<br>
The human genome was produced by the genome reference consortium:<br>
<a class="moz-txt-link-freetext" href="https://www.ncbi.nlm.nih.gov/grc/human">https://www.ncbi.nlm.nih.gov/grc/human</a><br>
<br>
It was produced by cloning genome segments from a number of
individuals into BACs, sequencing the BACs then arranging the BACs
together. The BACs are now represented in the genome as contigs, and
each contig represents sequence from a single individual. Contigs
with the same two-letter prefix come from the same individual. The
GRC may have more information on the ethnic make-up of the
individuals used, but I know that a lot of the genome comes from a
man identified as RP11, who was African American. The individuals
used for the genome were healthy.<br>
<br>
Since each sequence is an individual sequence, sometimes a minor, or
even private, allele can be reference allele. The transcript
haplotype page shows you the CDS and protein sequences found in
actual 1000 Genomes individuals, listing the frequency of these
sequences in different ethnic groups, eg:<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?db=core;g=ENSG00000072110;r=14:68874143-68979440;t=ENST00000193403">http://www.ensembl.org/Homo_sapiens/Transcript/Haplotypes?db=core;g=ENSG00000072110;r=14:68874143-68979440;t=ENST00000193403</a><br>
<br>
The 1000 Genomes individuals all self-reported as healthy.<br>
<br>
All the best<br>
<br>
Emily<br>
<br>
<div class="moz-cite-prefix">On 18/08/2017 11:34, Mahmood Naderan
wrote:<br>
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<blockquote type="cite"
cite="mid:CADa2P2WWOBY+fHKypemoHrd9zYrsb2kokFPUU7GjL7jwbWB2SQ@mail.gmail.com">
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<div class="gmail_default" style="font-family:tahoma,sans-serif">Hi,<br>
</div>
<div class="gmail_default" style="font-family:tahoma,sans-serif">Question
is how much realistic is the sequences presented as
"reference" in the Ensembl database? In other words, is the
reference sequence of a gene relates to a healthy human?!
Perhaps no! Are the sequences relates to a group of humans?
Then which side of the world or ethnic? <br>
<br>
I appreciate any feedback on this question.<br>
<br clear="all">
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<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr"><font face="tahoma,sans-serif">Regards,<br>
Mahmood</font><br>
<br>
<br>
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<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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