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<p>Hi Bin Xu,</p>
<p>The human reference genome is a composite genome, derived from
the sequence of several different anonymous individuals. The size
is not an average, but a total of all chromosomal sequence
(autosomes, plus X and Y).</p>
<p>More information can be found on the following pages:</p>
<p><a class="moz-txt-link-freetext" href="https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals">https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals</a><br>
</p>
<p>Best wishes</p>
<p>Ben<br>
</p>
<div class="moz-cite-prefix">On 11/12/2023 14:50, Bin Xu wrote:<br>
</div>
<blockquote type="cite"
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<p class="MsoNormal">Hi Ben,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for your message!<o:p></o:p></p>
<p class="MsoNormal">Do you mean that the human haploid genome
size 3,099,750,718 is the average or median size of male and
female haploid genome?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Bin Xu, PhD<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div
style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Dev
<a class="moz-txt-link-rfc2396E" href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> <b>On Behalf Of </b>
Benjamin Moore<br>
<b>Sent:</b> Monday, December 11, 2023 6:50 AM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Subject:</b> Re: [ensembl-dev] ***SPAM*** RE: REVEL
Pluging in VEP 110<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Bin Xu,<o:p></o:p></p>
<p>The genome size quoted on the species-specific hompages on
the Ensembl websites refers to the length of the haploid
genome size for that species, in the case of human, including
sequences from both the X and Y chromosome. The genome
assembly was generated by the Genome Reference Consortium
(GRC). You can read more about the genome assemblies and
associated data/methods on the documentation:<o:p></o:p></p>
<p><a href="https://www.ncbi.nlm.nih.gov/grc/human"
moz-do-not-send="true" class="moz-txt-link-freetext">https://www.ncbi.nlm.nih.gov/grc/human</a><o:p></o:p></p>
<p>Best wishes<o:p></o:p></p>
<p>Ben<o:p></o:p></p>
<div>
<p class="MsoNormal">On 08/12/2023 17:24, Bin Xu wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoPlainText">Dear Ensembl Team,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">I am looking at the human genome size
in your web page below, but it does not specify the base
pairs 3,099,750,718 as either male, or female, or average of
male and female.<o:p></o:p></p>
<p class="MsoPlainText">The same are the other species. As I
know the female genome size is about 1.6% more than male.<o:p></o:p></p>
<p class="MsoPlainText">Could you please help to update the
data by presenting female and male genome size respectively.<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"><a
href="https://useast.ensembl.org/Homo_sapiens/Info/Annotation"
moz-do-not-send="true" class="moz-txt-link-freetext">https://useast.ensembl.org/Homo_sapiens/Info/Annotation</a><o:p></o:p></p>
<p class="MsoPlainText"><span style="mso-ligatures:none"><img
style="width:6.3472in;height:3.0277in"
id="Picture_x0020_1"
src="cid:part1.0i08VWTn.dQIIaLkh@ebi.ac.uk" class=""
width="609" height="291" border="0"></span><o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Best regards,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Bin Xu, PhD <o:p></o:p></p>
<p class="MsoPlainText">Vice President<o:p></o:p></p>
<p class="MsoPlainText">O: 732-783-7398 | C: 267-318-5247<o:p></o:p></p>
<p class="MsoPlainText"><a
href="mailto:bin.xu@accurantbiotech.com"
moz-do-not-send="true" class="moz-txt-link-freetext">bin.xu@accurantbiotech.com</a>
<o:p></o:p></p>
<p class="MsoPlainText">259 Prospect Plains Rd, Cranbury, NJ
08512<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">-----Original Message-----<br>
From: Dev <a href="mailto:dev-bounces@ensembl.org"
moz-do-not-send="true"><dev-bounces@ensembl.org></a>
On Behalf Of Diana Lemos<br>
Sent: Friday, December 8, 2023 4:44 AM<br>
To: Souhila Amanzougarene <a
href="mailto:souhila.amanzougarene@cnrs.fr"
moz-do-not-send="true"><souhila.amanzougarene@cnrs.fr></a><br>
Cc: Ensembl developers list <a
href="mailto:dev@ensembl.org" moz-do-not-send="true"><dev@ensembl.org></a><br>
Subject: Re: [ensembl-dev] REVEL Pluging in VEP 110<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Hi,<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">The plugin was updated after release
108 which could have caused differences in the output.<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Can you please send an example of your
input file with variants that were expected to have a REVEL
score but didn't with version 110?<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">Also, when did you download the REVEL
file?<o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">On 08/12/2023 08:15, Souhila
Amanzougarene wrote:<o:p></o:p></p>
<p class="MsoPlainText">> Dear Ensembl Team,<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> I'm using VEP tool version 110 to
annotate a VCF file (hg38) with the
<o:p></o:p></p>
<p class="MsoPlainText">> REVEL plugin. I processed it by
running the following command :<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> ./vep -i variations.vcf
--assembly GRCh38 --plugin <o:p>
</o:p></p>
<p class="MsoPlainText">>
REVEL,file=/path/to/revel/data.tsv.gz<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> This command runs without any
errors, but the REVEL column is empty in
<o:p></o:p></p>
<p class="MsoPlainText">> the annotated VCF.<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> I attempted to run VEP 110 using
the REVEL.pm file from VEP 108, and
<o:p></o:p></p>
<p class="MsoPlainText">> it worked, I now have scores in
the REVEL column.<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> Thak you for your assisatnce !<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText">> Best regards,<o:p></o:p></p>
<p class="MsoPlainText">> <o:p></o:p></p>
<p class="MsoPlainText"> <o:p></o:p></p>
<p class="MsoPlainText">_______________________________________________<o:p></o:p></p>
<p class="MsoPlainText">Dev mailing list <a
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style="color:windowtext;text-decoration:none">Dev@ensembl.org</span></a><o:p></o:p></p>
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<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org"
moz-do-not-send="true" class="moz-txt-link-freetext">Dev@ensembl.org</a><o:p></o:p></pre>
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moz-do-not-send="true" class="moz-txt-link-freetext">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><o:p></o:p></pre>
<pre>Ensembl Blog: <a href="http://www.ensembl.info/"
moz-do-not-send="true" class="moz-txt-link-freetext">http://www.ensembl.info/</a><o:p></o:p></pre>
</blockquote>
<pre>-- <o:p></o:p></pre>
<pre>Dr. Ben Moore (he/him)<o:p></o:p></pre>
<pre>Ensembl Outreach Manager<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></pre>
<pre>European Molecular Biology Laboratory<o:p></o:p></pre>
<pre>Wellcome Trust Genome Campus<o:p></o:p></pre>
<pre>Hinxton<o:p></o:p></pre>
<pre>Cambridge<o:p></o:p></pre>
<pre>CB10 1SD<o:p></o:p></pre>
<pre>UK<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a href="mailto:bmoore@ebi.ac.uk" moz-do-not-send="true"
class="moz-txt-link-freetext">bmoore@ebi.ac.uk</a><o:p></o:p></pre>
<pre>+44 (0)1223 494265<o:p></o:p></pre>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Ben Moore (he/him)
Ensembl Outreach Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK
<a class="moz-txt-link-abbreviated" href="mailto:bmoore@ebi.ac.uk">bmoore@ebi.ac.uk</a>
+44 (0)1223 494265</pre>
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