publicdata/nih-gov
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions
nih-gov/www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html

848 lines
25 KiB
HTML
Raw Blame History

This file contains invisible Unicode characters

This file contains invisible Unicode characters that are indistinguishable to humans but may be processed differently by a computer. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>SNP Attributes</title>
<style type="text/css">
<!--
.excel1 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
}
.excel5 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel2 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel6 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel3 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel7 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:.5pt hairline windowtext;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel4 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:.5pt hairline windowtext;
border-left:none;
}
-->
</style>
<style type="text/css">
<!--
.excel8 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
}
.excel12 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel9 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel13 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel10 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel14 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:.5pt hairline windowtext;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel11 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:.5pt hairline windowtext;
border-left:none;
}
-->
</style>
<style type="text/css">
<!--
.excel15 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
}
.excel19 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel16 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel20 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel17 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:none;
border-left:none;
}
.excel21 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:.5pt hairline windowtext;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel18 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:.5pt hairline windowtext;
border-bottom:.5pt hairline windowtext;
border-left:none;
}
-->
</style>
<style type="text/css">
<!--
.excel22 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
}
.excel26 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:middle;
border:none;
white-space:nowrap;
background:#63AAFE;
}
.excel23 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:.5pt hairline windowtext;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel24 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:none;
border-left:.5pt hairline windowtext;
background:silver;
}
.excel25 {
padding-top:1px;
padding-right:1px;
padding-left:1px;
color:windowtext;
font-size:10.0pt;
font-weight:700;
font-style:normal;
text-decoration:none;
font-family:Verdana;
text-align:general;
vertical-align:bottom;
border:none;
white-space:nowrap;
border-top:none;
border-right:none;
border-bottom:.5pt hairline windowtext;
border-left:.5pt hairline windowtext;
background:silver;
}
-->
</style>
<style type="text/css">
<!--
p.MsoNormal {
margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:0in;
line-height:115%;
font-size:11.0pt;
font-family:"Times New Roman";
}
p.MsoListParagraph {
margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:.5in;
line-height:115%;
font-size:11.0pt;
font-family:"Times New Roman";
}
p.MsoListParagraphCxSpLast {
margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:.5in;
line-height:115%;
font-size:11.0pt;
font-family:"Times New Roman";
}
.a1 {
color: #3669CD;
}
-->
</style>
</head>
<body>
<table width="200" border="0">
<tr>
<td><h2 class="a1"><strong>New SNP Attributes</strong></h2>
<p>New attributes have been added to dbSNP to allow searching and filtering of human variation by the following characteristics. </p>
<p>Please contact <a href="mailto:snp-admin@ncbi.nlm.nih.gov">snp-admin@ncbi.nlm.nih.gov</a> if you have any questions or comments.</p>
<table width="615" border="0">
<tr>
<td width="525" align="center" bgcolor="#999999"><strong>Attribute</strong></td>
<td width="80" bgcolor="#999999"><strong>RS Count (Build 132)</strong></td>
</tr>
<tr>
<td><blockquote>
<p><span class="a1"><strong><a name="alleleorigin" id="alleleorigin"></a>Allele Origin:</strong></span><strong><span>&nbsp;&nbsp; </span></strong><span>The rs report summarizes the reported origin(s) of the variant allele </span>asserted by each submitter for the submitted SNP (ss) . Current values are germline, somatic, and unknown.&nbsp;&nbsp; Additional attributes will be added in the future release to include:<span> </span></p>
<ul>
<li><span>not-tested </span></li>
<li><span>tested-inconclusive</span></li>
<li><span>other</span></li>
</ul>
</blockquote>
<p>&nbsp;</p>
</td>
<td align="right" valign="top" bgcolor="#FFFFFF"><p>&nbsp;</p>
<p><strong>423</strong></p></td>
</tr>
<tr>
<td bgcolor="#CCCCCC"><blockquote>
<p><span class="a1"><strong><a name="clinical" id="clinical"></a>Clinical significance:</strong></span><strong><span>&nbsp;&nbsp; </span></strong><span>The significance of the indicated allele. </span></p>
<p><span class="MsoListParagraphCxSpLast" style="line-height:normal;">The supported values are:</span></p>
<ul>
<li><span>unknown </span></li>
<li><span>untested</span></li>
<li><span>non-pathogenic</span></li>
<li><span>probable-non-pathogenic</span></li>
<li><span>probable-pathogenic</span></li>
<li><span>pathogenic</span></li>
<li>drug-response</li>
<li>histocompatibility</li>
<li><span>other</span> </li>
</ul>
</blockquote>
<p>&nbsp;</p></td>
<td align="right" valign="top" bgcolor="#CCCCCC"><p>&nbsp;</p>
<p><strong>13105</strong></p></td>
</tr>
<tr>
<td bgcolor="#FFFFFF"><blockquote>
<p><span class="a1"><strong><a name="gmaf" id="gmaf"></a>Global minor allele frequency (MAF):</strong></span><strong><span>&nbsp; </span></strong><span>dbSNP is reporting the </span>minor allele frequency for each rs included in &nbsp;a default global population. Since this is being provided to distinguish common polymorphism from rare variants, the MAF is actually the second most frequent allele value. In other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and 0.01, the MAF will be reported as 0.49. The current default global population is <span>1000Genome phase 1 genotype data</span> from 629 worldwide individuals, released in the <a href="http://www.1000genomes.org/announcements/november-2010-data-release-2010-11-09">08-04-2010</a> dataset. </p>
<p>&nbsp;</p>
</blockquote>
</td>
<td align="right" valign="top" bgcolor="#FFFFFF"><p>&nbsp;</p>
<p><strong>14946243</strong></p></td>
</tr>
<tr>
<td bgcolor="#CCCCCC"><blockquote>
<p><span class="a1"><strong><a name="suspect" id="suspect"></a>Suspect:</strong></span><strong><span>&nbsp; </span></strong><span>Variation suspected to be false positive due to </span>artifacts of the presence of a paralogous sequence in the genome<span>&nbsp; (</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/19877174">Musumeci et al. 2010</a>) (</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/21030649">Sudmant et al. 2010</a>)<span> or evidence suggested sequencing error or computation artifacts.<strong>&nbsp; </strong></span></p>
</blockquote></td>
<td align="right" valign="top" bgcolor="#CCCCCC"><p>&nbsp;</p>
<p><strong>105630</strong></p></td>
</tr>
</table>
<p>Below are examples of the attributes shown on web pages and schema changes.<br />
</p></td>
</tr>
<tr>
<td><h3><a name="refsnp" id="refsnp"></a>RefSNP Summary (<a href="/projects/SNP/snp_ref.cgi?rs=rs11694">Example</a>)</h3></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><img name="RS_Char_FAQ_r2_c2" src="RS_Char_FAQ_r2_c2.png" border="0" id="RS_Char_FAQ_r2_c2" alt="" /></td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel1">
<col width="99" />
<col width="363" />
<tr>
<td class="excel5" width="99">A. Allele Origin</td>
<td class="excel2" width="363">Indicated as Germline or Somatic for each allele</td>
</tr>
<tr>
<td class="excel6">B. Clinical Significance</td>
<td class="excel3">Click on &quot;VarView&quot; or &quot;OMIM&quot; to view phenotype</td>
</tr>
<tr>
<td class="excel6">C. Global MAF</td>
<td class="excel3">The minor allele (G), frequency (0.003), and allele count (3) is shown</td>
</tr>
<tr>
<td class="excel7">D. Suspected</td>
<td class="excel4">A red &quot;?&quot; icon is shown for suspected SNP in the &quot;Validation&quot; row</td>
</tr>
</table></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><h3><a name="geneview" id="geneview"></a>SNP GeneView (<a href="/projects/SNP/snp_ref.cgi?chooseRs=coding&amp;go=Go&amp;locusId=4023">Example</a>)</h3></td>
</tr>
<tr>
<td><img name="RS_Char_FAQ_r4_c2" src="RS_Char_FAQ_r4_c2.png" width="926" height="227" border="0" id="RS_Char_FAQ_r4_c2" alt="" /></td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel8">
<col width="99" />
<col width="379" />
<tr>
<td class="excel12" width="99">A. Allele Origin</td>
<td class="excel9" width="379">Indicated as Germline or Somatic for each allele</td>
</tr>
<tr>
<td class="excel13">B. Clinical Significance</td>
<td class="excel10">Click on icon under &quot;Clinical Source&quot;&nbsp; to view effect in Variation Viewer</td>
</tr>
<tr>
<td class="excel13">C. Global MAF</td>
<td class="excel10">MAF is shown for the corresponding allele</td>
</tr>
<tr>
<td class="excel14">D. Suspected</td>
<td class="excel11">A red &quot;?&quot; icon is shown for suspected SNP under the &quot;Validation&quot; column </td>
</tr>
</table></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><h3><a name="varview" id="varview"></a>Variation Viewer
(<a href="/sites/varvu?gene=7399">Example</a>)</h3></td>
</tr>
<tr>
<td><img name="RS_Char_FAQ_r6_c2" src="RS_Char_FAQ_r6_c2.png" width="1112" height="183" border="0" id="RS_Char_FAQ_r6_c2" alt="" /></td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel15">
<col width="110" />
<col width="379" />
<tr>
<td class="excel19">A. Allele Origin</td>
<td class="excel16" width="379">Indicated as Germline or Somatic for the variation under &quot;Origin&quot; column</td>
</tr>
<tr>
<td class="excel20">B. Clinical Significance</td>
<td class="excel17">shown under &quot;Clinical Intrepretation&quot; column</td>
</tr>
<tr>
<td class="excel20">C. Global MAF</td>
<td class="excel17">frequency is shown under minor allele frequency (MAF) column</td>
</tr>
<tr>
<td class="excel21">D. Suspected</td>
<td class="excel18">A red &quot;?&quot; icon is shown for suspected SNP under the &quot;Suspect&quot; column </td>
</tr>
</table></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><h3><a name="docsum" id="docsum"></a>RS Docsum (<a href="/projects/SNP/docsum/docsum_doc.html">XML Schema</a>)</h3></td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel22">
<col width="110" />
<col width="169" />
<tr>
<td width="121" class="excel26">SNP Attribute</td>
<td class="excel26" width="247">XML Element</td>
</tr>
<tr>
<td class="excel23">A. Allele Origin</td>
<td><a href="/projects/SNP/docsum/docsum0.html#alleleorigin">Rs/AlleleOrigin</a></td>
</tr>
<tr>
<td class="excel24">B. Clinical Significance</td>
<td><a href="/projects/SNP/docsum/docsum0.html#phenotype">Rs/Phenotype</a></td>
</tr>
<tr>
<td class="excel24">C. Global MAF</td>
<td><a href="/projects/SNP/docsum/docsum0.html#frequency">Rs/Frequency</a></td>
</tr>
<tr>
<td class="excel25">D. Suspected</td>
<td><a href="/projects/SNP/docsum/docsum0.html#suspect">Rs/Validation/@name='suspect'</a></td>
</tr>
</table></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><h3><a name="entrez" id="entrez"></a>Entrez Search and Eutils Retrieval</h3></td>
</tr>
<tr>
<td><img name="RS_Char_FAQ_r8_c2" src="RS_Char_FAQ_r8_c2.png" width="945" height="295" border="0" id="RS_Char_FAQ_r8_c2" alt="" /></td>
</tr>
<tr>
<td><p>The SNP attributes can be search from the web using the field and terms below or selected from the <a href="http://www.ncbi.nlm.nih.gov/snp/limits">limit</a> page. The search can also be performed programatically using eUtils eSearch. Note: eUtils eFetch is currently being updated to support retrieval of variations with the new attributes. We'll let you know when the update is done.</p>
</td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel22">
<col width="110" />
<col width="169" />
<tr>
<td width="121" class="excel26">SNP Attribute</td>
<td class="excel26" width="247">Search Field (type)</td>
<td class="excel26" width="247">Search Terms</td>
</tr>
<tr>
<td class="excel23">A. Allele Origin</td>
<td>ALLELE_ORIGIN (text)</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=somatic[ALLELE_ORIGIN]">somatic</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=germline[ALLELE_ORIGIN]">germline</a></td>
</tr>
<tr>
<td class="excel24">B. Clinical Significance</td>
<td>CLINICAL_SIGNIFICANCE (text)</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22non pathogenic%22[CLINICAL_SIGNIFICANCE]">non pathogenic</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22other%22[CLINICAL_SIGNIFICANCE]">other</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22pathogenic%22[CLINICAL_SIGNIFICANCE]">pathogenic</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22probable non pathogenic%22[CLINICAL_SIGNIFICANCE]">probable non pathogenic</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22probable pathogenic%22[CLINICAL_SIGNIFICANCE]">probable pathogenic</a></td>
</tr>
<tr>
<td class="excel24">&nbsp;</td>
<td>&nbsp;</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%22unknown%22[CLINICAL_SIGNIFICANCE]">unknown</a></td>
</tr>
<tr>
<td class="excel24">C. Global MAF</td>
<td>GLOBAL_MAF (floating-point)</td>
<td>exact <a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=0.01[GLOBAL_MAF]">0.01[GLOBAL_MAF]</a> or range <a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=0.01:0.05[GLOBAL_MAF]">0.01:0.05[GLOBAL_MAF])</a></td>
</tr>
<tr>
<td class="excel25">D. Suspected</td>
<td>SUSPECTED (text)</td>
<td><a href="http://www.ncbi.nlm.nih.gov/snp?Db=snp&amp;Cmd=DetailsSearch&amp;Term=%paralog%22[SUSPECTED]">paralog</a></td>
</tr>
</table></td>
</tr>
<tr>
<td>&nbsp;</td>
</tr>
<tr>
<td><a name="vcf" id="entrez2"></a><strong>VCF</strong></td>
</tr>
<tr>
<td>The VCF four new tags of the attributes are described in the <a href="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/000-README.html">000-README</a> file on the FTP site (<a href="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/">ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/</a>) and in the VCF header.<br /></td>
</tr>
<tr>
<td><table cellspacing="0" cellpadding="0" class="excel22">
<col width="110" />
<col width="169" />
<tr>
<td width="121" class="excel26">SNP Attribute</td>
<td class="excel26" width="247">VCF Tag</td>
</tr>
<tr>
<td class="excel23">A. Allele Origin</td>
<td>##INFO=&lt;ID=SAO,Number=1,Type=Integer,Description=&quot;SNP Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both&quot;&gt;</td>
</tr>
<tr>
<td class="excel24">B. Clinical Significance</td>
<td>##INFO=&lt;ID=SCS,Number=1,Type=Integer,Description=&quot;SNP Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other&quot;&gt;</td>
</tr>
<tr>
<td class="excel24">C. Global MAF</td>
<td>##INFO=&lt;ID=GMAF,Number=1,Type=Float,Description=&quot;Global Minor Allele Frequency [0, 0.5]; global population is 1000GenomesProject phase 1 genotype data from 629 individuals, released in the 08-04-2010 dataset&quot;&gt;</td>
</tr>
<tr>
<td class="excel25">D. Suspected</td>
<td>##INFO=&lt;ID=SSR,Number=1,Type=Integer,Description=&quot;SNP Suspect Reason Code, 0 - unspecified, 1 - Paralog, 2 - byEST, 3 - Para_EST, 4 - oldAlign, 5 - other&quot;&gt;</td>
</tr>
</table></td>
</tr>
</table>
</body>
</html>
Reference in a new issue View git blame Copy permalink