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<p>Hi Bin,</p>
<p>Yes, it is true thast the haploid male and female genome sizes
are different. However, the reference human genome sequence is not
a 'male' or 'female' genome sequence. Instead it contains all
autosomes, plus both sex chromosomes. So, the genome size quoted
on the Ensembl site is the total of all 24 chromosomes (1-22 +X +
Y).</p>
<p>I hope this helps.<br>
</p>
<p>Best wishes</p>
<p>Ben<br>
</p>
<div class="moz-cite-prefix">On 11/12/2023 16:38, 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">The haploid genome sizes of male and female
are different, since X chromosome is longer than Y.<o:p></o:p></p>
<p class="MsoNormal">This is why I interpret that human haploid
genome size 3,099,750,718 is the average.<o:p></o:p></p>
<p class="MsoNormal">Could you explain if I am wrong?<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<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 10:17 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 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).<o:p></o:p></p>
<p>More information can be found on the following pages:<o:p></o:p></p>
<p><a
href="https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals"
moz-do-not-send="true" class="moz-txt-link-freetext">https://www.ncbi.nlm.nih.gov/grc/help/faq/#human-reference-genome-individuals</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 11/12/2023 14:50, Bin Xu wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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
href="mailto:dev-bounces@ensembl.org"
moz-do-not-send="true"><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 href="mailto:dev@ensembl.org"
moz-do-not-send="true" class="moz-txt-link-freetext">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.VayLsmbA.uFsCgYxV@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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<pre>Dr. Ben Moore (he/him)<o:p></o:p></pre>
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<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>
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<pre>UK<o:p></o:p></pre>
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<pre>+44 (0)1223 494265<o:p></o:p></pre>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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</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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