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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Those were the statuses I was referring to
Will.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Which leads me to ask – what were
the statuses that Andrea listed?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Gavin<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Will McLaren<br>
<b><span style='font-weight:bold'>Sent:</span></b> 04 February 2011 15:04<br>
<b><span style='font-weight:bold'>To:</span></b> Andrea Edwards<br>
<b><span style='font-weight:bold'>Cc:</span></b> Dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re:
[ensembl-dev] Transcript variation alleles - - Bayesian Filter detected spam</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hello,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I think there are some crossed wires here - validation_status is a
property of a variation supplied to us by dbSNP.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Their descriptions are here:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a
href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation">http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation</a><br>
<br>
The pictures are, in order:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>cluster<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>freq<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>submitter<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>doublehit<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>hapmap<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>1000Genome<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 4 February 2011 14:14, Andrea Edwards <<a
href="mailto:edwardsa@cs.man.ac.uk">edwardsa@cs.man.ac.uk</a>> wrote:<o:p></o:p></span></font></p>
<div text="#000000" bgcolor="#ffffff">
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
Gavin<br>
<br>
I believe the validatation statuses are just pass and fail <br>
<br>
If you query the variation schema directly you can find the reasons for failure
when a variation is imported from say dbSNP<br>
<br>
mysql> select description from failed_description;<br>
+--------------------------------------------------------+<br>
| description
|<br>
+--------------------------------------------------------+<br>
| Variation maps to more than 3 different
locations |<br>
| None of the variant alleles match the reference allele |<br>
| Variation has more than 3 different alleles
|<br>
| Loci with no observed variant alleles in
dbSNP |<br>
| Variation does not map to the
genome
|<br>
| Variation has no associated
sequence
|<br>
+--------------------------------------------------------+<br>
6 rows in set (0.06 sec)<br>
<br>
As will has said, they map all variants to the positive strand and make sure at
least one of the variant alleles exists at the base position in the forward
strand. If this failed you would get the error 'None of the variant alleles match
the reference allele.' I think the others are fairly self explanatory though
i'm not sure how a variant could have no associated sequence if it was imported
from dbSNP<br>
<br>
<br>
<br>
<br>
<br>
<br>
On 02/02/2011 15:20, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName>
wrote: <o:p></o:p></span></font></p>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>Thanks Graham - <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Can you also tell me where to find information on the meaning of the<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>possible validation statuses?<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>-----Original Message-----<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>From: Graham Ritchie [<a
href="mailto:grsr@ebi.ac.uk" target="_blank">mailto:grsr@ebi.ac.uk</a>] <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Sent: 02 February 2011 15:12<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>To: <st1:PersonName
w:st="on">Oliver, Gavin</st1:PersonName><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Cc: <a
href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Subject: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>found in subject<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Hi Gavin,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>The alleles of a transcript variation always represent the genomic base<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>change.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Cheers,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Graham<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Ensembl variation<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>On 2 Feb 2011, at 15:02, <st1:PersonName
w:st="on">Oliver, Gavin</st1:PersonName> wrote:<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Hi,<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>When I pull transcript variation alleles via the API, does the allele<o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>shown (e.g. A/T) represent the genomic base change, or the<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>transcriptomic one?<o:p></o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Gavin<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>The contents of this message and any attachments to it are<o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>confidential and may be legally privileged. If you have received this<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>message in error, you should delete it from your system immediately and<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>advise the sender.<o:p></o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Almac Group (UK) Limited, registered no. NI061368. Almac Sciences<o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>Limited, registered no. NI041550. Almac Discovery Limited, registered<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>no. NI046249. Almac Pharma Services Limited, registered no. NI045055.<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Almac Clinical Services Limited, registered no. NI041905. Almac<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Clinical Technologies Limited, registered no. NI061202. Almac<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Diagnostics Limited, registered no. NI043067. All preceding companies<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>are registered in <st1:country-region
w:st="on"><st1:place w:st="on">Northern Ireland</st1:place></st1:country-region> with a registered office address of<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Almac House, 20 Seagoe Industrial Estate, <st1:place
w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region
w:st="on">UK</st1:country-region></st1:place>. <o:p></o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Almac Sciences (<st1:country-region
w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region
w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no.<o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>SC154034.<o:p></o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'> <o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac<o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are<o:p></o:p></span></font></pre><pre><st1:State
w:st="on"><st1:place w:st="on"><font size=2 face="Courier New"><span
style='font-size:10.0pt'>Delaware</span></font></st1:place></st1:State> limited liability companies and Almac Group Incorporated is a<o:p></o:p></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Delaware Corporation. More information on the Almac Group can be found<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>on the Almac website: <a
href="http://www.almacgroup.com" target="_blank">www.almacgroup.com</a><o:p></o:p></span></font></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>_______________________________________________<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Dev mailing list<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><a
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><a
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></span></font></pre></blockquote>
<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>mailman/listinfo/dev<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>_______________________________________________<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>Dev mailing list<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><a
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'><a
href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></span></font></pre>
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face="Times New Roman"><span style='font-size:12.0pt'><br>
_______________________________________________<br>
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<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: <A href="http://www.almacgroup.com">www.almacgroup.com</A><o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
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