1447 lines
41 KiB
Text
1447 lines
41 KiB
Text
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<!DOCTYPE html>
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<html>
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<head>
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<title>Rat Genome Assembly GRCr8 - Genome Reference Consortium</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name="ncbi_app" content="grc" />
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<meta name="ncbi_db" content="none" />
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<meta name="ncbi_pdid" content="screen_default" />
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<meta name="ncbi_pagename" content="assemblyDataPage" />
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<meta name="ncbi_pagetitle" content="Rat Genome Assembly GRCr8" />
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<link rel="stylesheet" type="text/css" href="/grc/static/grc/css/grc.css" />
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<style>
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#menu ul#primary a#dataMenuItem {
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border: 1px solid #666;
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border-bottom: none;
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background: #333;
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padding-bottom: 6px;
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margin-top: 0;
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color: #ff9933;
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text-decoration: none;
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}
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#menu ul#secondary li a#data-assemblyDataMenuItem {
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color: #EFEFEF;
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}
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</style>
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<link rel="stylesheet" type="text/css" href="/core/jig/1.14.8/css/jig.min.css" />
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<script type="text/javascript" src="/core/jig/1.14.8/js/jig.min.js"></script>
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<script type="text/javascript" src="/grc/static/grc/js/grc.js"></script>
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</head>
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<body>
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<noscript>
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<p>
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<b>Warning:</b> this web site requires JavaScript to function. <a href="/guide/browsers#js_settings">more...</a>
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</p>
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</noscript>
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<div id="header-container">
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<a href="/grc">
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<div id="header">
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<img alt="GRC logo" src="/grc/static/grc/img/GRC_logo_reasonably_small.png" /><img src="/grc/static/grc/img/TitleBanner.png" alt="Genome Reference Consortium" /></a>
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</div>
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</div>
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<div id="page">
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<a id="skipnav" href="#main">Skip navigation and go to main content</a>
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<div id="menu">
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<ul id="primary">
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<li><a href="/grc" title="GRC home" id="homeMenuItem">GRC Home</a></li>
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<li><a href="/grc/data" title="Data" id="dataMenuItem">Data</a>
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<ul id="secondary">
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<li><a href="/grc/rat" id="organismOverviewMenuItem">Rat Overview</a></li>
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<li><a href="/grc/rat/issues" id="issueListMenuItem">Rat Genome Issues</a></li>
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<li><a href="/grc/rat/data" id="assemblyDataMenuItem">Rat Assembly Data</a></li>
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<!-- <li><a href="/rat/report-an-issue">Report a Problem</a></li> -->
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</ul>
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</li>
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<li><a href="/grc/help" title="Information and help" id="helpMenuItem">Help</a></li>
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<li><a href="/grc/report-an-issue" title="Report a problem" id="reportAnIssueMenuItem">Report an Issue</a></li>
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<li><a href="/grc/contact-us" title="contact us" id="contactUsMenuItem">Contact Us</a></li>
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<li><a href="/grc/credits" title="credits" id="creditsMenuItem">Credits</a></li>
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<li><a href="/projects/genome/assembly/grc/curation/rat" title="Curators only, authentication required" id="curatorsOnlyMenuItem">Curators Only</a></li>
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</ul>
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</div><!--end menu-->
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<div id="main"><a name="main"></a>
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<div id="assemblyDataPage">
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<div id="contents" style="overflow:hidden;">
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<h1>Rat Genome Assembly GRCr8</h1>
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<p>
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Information on tiling path files (TPFs) for the
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assembly is available at
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<a href="/grc/tpf">TPF Overview</a>.
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</p>
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Other assembly versions:
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<select id="assembly_select" name="assembly_select">
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<option>Select one</option>
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<option value="mRatBN7.2">mRatBN7.2</option>
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</select>
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<div class="cleaner"></div>
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<div id="tabs" class="ui-tabs ui-widget ui-widget-content ui-corner-all">
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<ul class="ui-tabs-nav ui-helper-reset ui-helper-clearfix ui-widget-header ui-corner-all">
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<li class="ui-state-default ui-corner-top ui-tabs-selected ui-state-active ui-tabs-active"><a class="ui-tabs-anchor" href="#chromosome_lengths">Chromosome lengths</a></li>
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<li class="ui-state-default ui-corner-top"><a class="ui-tabs-anchor" href="#total_lengths">Total lengths</a></li>
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<li class="ui-state-default ui-corner-top"><a class="ui-tabs-anchor" href="#ungapped_lengths">Ungapped lengths</a></li>
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<li class="ui-state-default ui-corner-top"><a class="ui-tabs-anchor" href="#n50s">N50s</a></li>
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<li class="ui-state-default ui-corner-top"><a class="ui-tabs-anchor" href="#gaps">Gaps</a></li>
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<li class="ui-state-default ui-corner-top"><a class="ui-tabs-anchor" href="#counts">Counts</a></li>
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</ul>
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<div id="chromosome_lengths" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
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Chromosome lengths are calculated by summing the length of the placed scaffolds and estimated gaps.
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<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
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<div class="ui-ncbigrid-inner-div" tabindex="0">
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<table
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class="ui-ncbigrid"
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data-jig="ncbigrid"
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data-jigconfig="
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isPageToolbarHideable: false,
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isSortable: true, columnTypes: [null, 'numComma', 'str', null, 'numComma', 'numComma', 'str'], sortFunctions: [sortChromosomeIDs, null, null, null, null, null, null]">
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<thead>
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<tr>
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<th>Chromosome</th>
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<th>Total length (bp)</th>
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<th>GenBank accession</th>
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<th>RefSeq accession</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>1</td>
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<td>270,518,180</td>
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<td><a href="/nucleotide/CM070391.1">CM070391.1</a></td>
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<td><a href="/nucleotide/NC_086019.1">NC_086019.1</a></td>
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</tr>
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<tr>
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<td>2</td>
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<td>251,712,708</td>
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<td><a href="/nucleotide/CM070392.1">CM070392.1</a></td>
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<td><a href="/nucleotide/NC_086020.1">NC_086020.1</a></td>
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</tr>
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<tr>
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<td>3</td>
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<td>189,428,310</td>
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<td><a href="/nucleotide/CM070393.1">CM070393.1</a></td>
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<td><a href="/nucleotide/NC_086021.1">NC_086021.1</a></td>
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</tr>
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<tr>
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<td>4</td>
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<td>184,426,481</td>
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<td><a href="/nucleotide/CM070394.1">CM070394.1</a></td>
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<td><a href="/nucleotide/NC_086022.1">NC_086022.1</a></td>
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</tr>
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<tr>
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<td>5</td>
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<td>172,190,305</td>
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<td><a href="/nucleotide/CM070395.1">CM070395.1</a></td>
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<td><a href="/nucleotide/NC_086023.1">NC_086023.1</a></td>
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</tr>
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<tr>
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<td>6</td>
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<td>147,156,653</td>
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<td><a href="/nucleotide/CM070396.1">CM070396.1</a></td>
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<td><a href="/nucleotide/NC_086024.1">NC_086024.1</a></td>
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</tr>
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<tr>
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<td>7</td>
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<td>137,014,596</td>
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<td><a href="/nucleotide/CM070397.1">CM070397.1</a></td>
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<td><a href="/nucleotide/NC_086025.1">NC_086025.1</a></td>
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</tr>
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<tr>
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<td>8</td>
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<td>132,782,436</td>
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<td><a href="/nucleotide/CM070398.1">CM070398.1</a></td>
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<td><a href="/nucleotide/NC_086026.1">NC_086026.1</a></td>
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</tr>
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<tr>
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<td>9</td>
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<td>121,768,150</td>
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<td><a href="/nucleotide/CM070399.1">CM070399.1</a></td>
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<td><a href="/nucleotide/NC_086027.1">NC_086027.1</a></td>
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</tr>
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<tr>
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<td>10</td>
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<td>107,713,808</td>
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<td><a href="/nucleotide/CM070400.1">CM070400.1</a></td>
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<td><a href="/nucleotide/NC_086028.1">NC_086028.1</a></td>
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</tr>
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<tr>
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<td>11</td>
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<td>99,753,367</td>
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<td><a href="/nucleotide/CM070401.1">CM070401.1</a></td>
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<td><a href="/nucleotide/NC_086029.1">NC_086029.1</a></td>
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</tr>
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<tr>
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<td>12</td>
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<td>52,308,831</td>
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<td><a href="/nucleotide/CM070402.1">CM070402.1</a></td>
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<td><a href="/nucleotide/NC_086030.1">NC_086030.1</a></td>
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</tr>
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<tr>
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<td>13</td>
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<td>109,350,286</td>
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<td><a href="/nucleotide/CM070403.1">CM070403.1</a></td>
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<td><a href="/nucleotide/NC_086031.1">NC_086031.1</a></td>
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</tr>
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<tr>
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<td>14</td>
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<td>109,089,856</td>
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<td><a href="/nucleotide/CM070404.1">CM070404.1</a></td>
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<td><a href="/nucleotide/NC_086032.1">NC_086032.1</a></td>
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</tr>
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<tr>
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<td>15</td>
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<td>108,192,169</td>
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<td><a href="/nucleotide/CM070405.1">CM070405.1</a></td>
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<td><a href="/nucleotide/NC_086033.1">NC_086033.1</a></td>
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</tr>
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<tr>
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<td>16</td>
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<td>91,442,908</td>
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<td><a href="/nucleotide/CM070406.1">CM070406.1</a></td>
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<td><a href="/nucleotide/NC_086034.1">NC_086034.1</a></td>
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</tr>
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<tr>
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<td>17</td>
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<td>93,515,804</td>
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<td><a href="/nucleotide/CM070407.1">CM070407.1</a></td>
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<td><a href="/nucleotide/NC_086035.1">NC_086035.1</a></td>
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</tr>
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<tr>
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<td>18</td>
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<td>86,134,022</td>
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<td><a href="/nucleotide/CM070408.1">CM070408.1</a></td>
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<td><a href="/nucleotide/NC_086036.1">NC_086036.1</a></td>
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</tr>
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<tr>
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<td>19</td>
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<td>74,246,245</td>
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<td><a href="/nucleotide/CM070409.1">CM070409.1</a></td>
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<td><a href="/nucleotide/NC_086037.1">NC_086037.1</a></td>
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</tr>
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<tr>
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<td>20</td>
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<td>56,021,148</td>
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<td><a href="/nucleotide/CM070410.1">CM070410.1</a></td>
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<td><a href="/nucleotide/NC_086038.1">NC_086038.1</a></td>
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</tr>
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|
|
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<tr>
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<td>X</td>
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<td>157,758,123</td>
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<td><a href="/nucleotide/CM070411.1">CM070411.1</a></td>
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<td><a href="/nucleotide/NC_086039.1">NC_086039.1</a></td>
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</tr>
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<tr>
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<td>Y</td>
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<td>59,846,084</td>
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<td><a href="/nucleotide/CM070412.1">CM070412.1</a></td>
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<td><a href="/nucleotide/NC_086040.1">NC_086040.1</a></td>
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</tr>
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</tbody>
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</table>
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</div>
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</div>
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</div>
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<div id="total_lengths" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
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Total lengths are calculated by summing the length of the sequenced bases and estimated gaps.
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<div id="total_lengths_inner_tabs" data-jig="ncbitabs">
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<div id="total_lengths_primary" >
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<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
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<div class="ui-ncbigrid-inner-div" tabindex="0">
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<table class="ui-ncbigrid"
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data-jig="ncbigrid"
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data-jigconfig="
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isPageToolbarHideable: false,
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isSortable: true, columnTypes: [null, 'numComma', 'str', null, 'numComma', 'numComma', 'str'], sortFunctions: [sortChromosomeIDs, null, null, null, null, null, null]">
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<thead>
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<th>Chromosome</th>
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<th>All scaffolds</th>
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<th>Placed scaffolds</th>
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<th>Unplaced scaffolds</th>
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</thead>
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<tbody>
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|
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<tr>
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<td>1</td>
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<td>270,518,180</td>
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<td>270,518,180</td>
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<td>0</td>
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</tr>
|
|
|
|
<tr>
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<td>2</td>
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<td>251,712,708</td>
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<td>251,712,708</td>
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<td>0</td>
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</tr>
|
|
|
|
<tr>
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<td>3</td>
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<td>193,850,820</td>
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<td>189,428,310</td>
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<td>4,422,510</td>
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</tr>
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|
|
|
<tr>
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<td>4</td>
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|
<td>184,426,481</td>
|
|
<td>184,426,481</td>
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<td>0</td>
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</tr>
|
|
|
|
<tr>
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|
<td>5</td>
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|
<td>172,190,305</td>
|
|
<td>172,190,305</td>
|
|
<td>0</td>
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|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>147,156,653</td>
|
|
<td>147,156,653</td>
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<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>137,014,596</td>
|
|
<td>137,014,596</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>132,782,436</td>
|
|
<td>132,782,436</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>121,768,150</td>
|
|
<td>121,768,150</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>107,713,808</td>
|
|
<td>107,713,808</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>99,753,367</td>
|
|
<td>99,753,367</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>52,308,831</td>
|
|
<td>52,308,831</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>109,350,286</td>
|
|
<td>109,350,286</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>109,089,856</td>
|
|
<td>109,089,856</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>108,192,169</td>
|
|
<td>108,192,169</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>91,442,908</td>
|
|
<td>91,442,908</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>93,515,804</td>
|
|
<td>93,515,804</td>
|
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<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
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<td>18</td>
|
|
<td>86,134,022</td>
|
|
<td>86,134,022</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>74,246,245</td>
|
|
<td>74,246,245</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
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<td>20</td>
|
|
<td>56,021,148</td>
|
|
<td>56,021,148</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>X</td>
|
|
<td>157,758,123</td>
|
|
<td>157,758,123</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Y</td>
|
|
<td>92,364,546</td>
|
|
<td>59,846,084</td>
|
|
<td>32,518,462</td>
|
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</tr>
|
|
|
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<tr>
|
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<td>Genome</td>
|
|
<td>2,849,581,192</td>
|
|
<td>2,812,370,470</td>
|
|
<td>37,210,722</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<div id="n50s" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
|
|
|
|
|
|
N50 is a measure of contiguity. 50% of the bases reside in a scaffold of this length or greater.
|
|
|
|
|
|
<div id="n50s_inner_tabs" data-jig="ncbitabs">
|
|
|
|
|
|
<div id="n50s_primary" >
|
|
<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
|
|
<div class="ui-ncbigrid-inner-div" tabindex="0">
|
|
<table class="ui-ncbigrid"
|
|
data-jig="ncbigrid"
|
|
data-jigconfig="
|
|
isPageToolbarHideable: false,
|
|
isSortable: true, columnTypes: [null, 'numComma', 'str', null, 'numComma', 'numComma', 'str'], sortFunctions: [sortChromosomeIDs, null, null, null, null, null, null]">
|
|
<thead>
|
|
|
|
<th>Chromosome</th>
|
|
<th>All scaffolds</th>
|
|
<th>Placed scaffolds</th>
|
|
<th>Unplaced scaffolds</th>
|
|
|
|
</thead>
|
|
<tbody>
|
|
|
|
<tr>
|
|
<td>1</td>
|
|
<td>270,518,180</td>
|
|
<td>270,518,180</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>251,712,708</td>
|
|
<td>251,712,708</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>189,428,310</td>
|
|
<td>189,428,310</td>
|
|
<td>2,449,928</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>184,426,481</td>
|
|
<td>184,426,481</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>172,190,305</td>
|
|
<td>172,190,305</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>147,156,653</td>
|
|
<td>147,156,653</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>137,014,596</td>
|
|
<td>137,014,596</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>132,782,436</td>
|
|
<td>132,782,436</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>121,768,150</td>
|
|
<td>121,768,150</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>107,713,808</td>
|
|
<td>107,713,808</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>99,753,367</td>
|
|
<td>99,753,367</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>52,308,831</td>
|
|
<td>52,308,831</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>109,350,286</td>
|
|
<td>109,350,286</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>109,089,856</td>
|
|
<td>109,089,856</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>108,192,169</td>
|
|
<td>108,192,169</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>91,442,908</td>
|
|
<td>91,442,908</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>93,515,804</td>
|
|
<td>93,515,804</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>86,134,022</td>
|
|
<td>86,134,022</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>74,246,245</td>
|
|
<td>74,246,245</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>56,021,148</td>
|
|
<td>56,021,148</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>X</td>
|
|
<td>157,758,123</td>
|
|
<td>157,758,123</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Y</td>
|
|
<td>59,846,084</td>
|
|
<td>59,846,084</td>
|
|
<td>903,984</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>137,014,596</td>
|
|
<td>137,014,596</td>
|
|
<td>903,984</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<div id="ungapped_lengths" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
|
|
|
|
|
|
Ungapped lengths are calculated by summing the length of sequenced bases only. 'Ns' are excluded.
|
|
|
|
|
|
<div id="ungapped_lengths_inner_tabs" data-jig="ncbitabs">
|
|
|
|
|
|
<div id="ungapped_lengths_primary" >
|
|
<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
|
|
<div class="ui-ncbigrid-inner-div" tabindex="0">
|
|
<table class="ui-ncbigrid"
|
|
data-jig="ncbigrid"
|
|
data-jigconfig="
|
|
isPageToolbarHideable: false,
|
|
isSortable: true, columnTypes: [null, 'numComma', 'str', null, 'numComma', 'numComma', 'str'], sortFunctions: [sortChromosomeIDs, null, null, null, null, null, null]">
|
|
<thead>
|
|
|
|
<th>Chromosome</th>
|
|
<th>All scaffolds</th>
|
|
<th>Placed scaffolds</th>
|
|
<th>Unplaced scaffolds</th>
|
|
|
|
</thead>
|
|
<tbody>
|
|
|
|
<tr>
|
|
<td>1</td>
|
|
<td>270,167,028</td>
|
|
<td>270,167,028</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>251,671,381</td>
|
|
<td>251,671,381</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>193,790,736</td>
|
|
<td>189,368,226</td>
|
|
<td>4,422,510</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>184,252,369</td>
|
|
<td>184,252,369</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>172,120,554</td>
|
|
<td>172,120,554</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>147,155,907</td>
|
|
<td>147,155,907</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>136,990,387</td>
|
|
<td>136,990,387</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>132,742,312</td>
|
|
<td>132,742,312</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>121,767,304</td>
|
|
<td>121,767,304</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>107,713,808</td>
|
|
<td>107,713,808</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>99,751,644</td>
|
|
<td>99,751,644</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>52,308,308</td>
|
|
<td>52,308,308</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>109,344,646</td>
|
|
<td>109,344,646</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>109,063,146</td>
|
|
<td>109,063,146</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>107,526,243</td>
|
|
<td>107,526,243</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>91,428,241</td>
|
|
<td>91,428,241</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>93,515,704</td>
|
|
<td>93,515,704</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>86,132,090</td>
|
|
<td>86,132,090</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>73,926,054</td>
|
|
<td>73,926,054</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>56,018,448</td>
|
|
<td>56,018,448</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>X</td>
|
|
<td>157,468,448</td>
|
|
<td>157,468,448</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Y</td>
|
|
<td>90,326,107</td>
|
|
<td>59,836,953</td>
|
|
<td>30,489,154</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>2,845,450,615</td>
|
|
<td>2,810,269,201</td>
|
|
<td>35,181,414</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<div id="gaps" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
|
|
|
|
Spanned gaps are found within scaffolds and there is some evidence suggesting linkage
|
|
between the two sequences flanking the gap. Unspanned gaps are found between scaffolds and
|
|
there is no evidence of linkage.
|
|
|
|
<div id="gaps_inner_tabs" data-jig="ncbitabs">
|
|
|
|
|
|
<div id="gaps_primary" >
|
|
<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
|
|
<div class="ui-ncbigrid-inner-div" tabindex="0">
|
|
<table class="ui-ncbigrid"
|
|
data-jig="ncbigrid"
|
|
data-jigconfig="
|
|
isPageToolbarHideable: false,
|
|
">
|
|
|
|
<thead>
|
|
<tr>
|
|
<th></th>
|
|
<th colspan="3">Spanned gaps</th>
|
|
<th colspan="3">Unspanned gaps</th>
|
|
</tr>
|
|
<tr>
|
|
<th>Chromosome </th>
|
|
<th>All scaffolds</th>
|
|
<th>Placed scaffolds</th>
|
|
<th>Unplaced scaffolds</th>
|
|
<th>All scaffolds</th>
|
|
<th>Placed scaffolds</th>
|
|
<th>Unplaced scaffolds</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
|
|
<tr>
|
|
<td>1</td>
|
|
<td>21</td>
|
|
<td>21</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>6</td>
|
|
<td>6</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>17</td>
|
|
<td>17</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>13</td>
|
|
<td>13</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>4</td>
|
|
<td>4</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>7</td>
|
|
<td>7</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>8</td>
|
|
<td>8</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>5</td>
|
|
<td>5</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>7</td>
|
|
<td>7</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>4</td>
|
|
<td>4</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>2</td>
|
|
<td>2</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>2</td>
|
|
<td>2</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>11</td>
|
|
<td>11</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>4</td>
|
|
<td>4</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>2</td>
|
|
<td>2</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>9</td>
|
|
<td>9</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>X</td>
|
|
<td>10</td>
|
|
<td>10</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Y</td>
|
|
<td>85</td>
|
|
<td>29</td>
|
|
<td>56</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>220</td>
|
|
<td>164</td>
|
|
<td>56</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
|
|
</table>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<div id="counts" class="ui-tabs-panel ui-widget-content ui-corner-bottom">
|
|
|
|
|
|
Scaffold counts.
|
|
|
|
|
|
<div id="counts_inner_tabs" data-jig="ncbitabs">
|
|
|
|
|
|
<div id="counts_primary" >
|
|
<div class="ui-ncbigrid-outer-div caption-exists" role="grid" tabindex="0">
|
|
<div class="ui-ncbigrid-inner-div" tabindex="0">
|
|
<table class="ui-ncbigrid"
|
|
data-jig="ncbigrid"
|
|
data-jigconfig="
|
|
isPageToolbarHideable: false,
|
|
isSortable: true, columnTypes: [null, 'numComma', 'str', null, 'numComma', 'numComma', 'str'], sortFunctions: [sortChromosomeIDs, null, null, null, null, null, null]">
|
|
<thead>
|
|
|
|
<th>Chromosome</th>
|
|
<th>All scaffolds</th>
|
|
<th>Placed scaffolds</th>
|
|
<th>Unplaced scaffolds</th>
|
|
|
|
</thead>
|
|
<tbody>
|
|
|
|
<tr>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>6</td>
|
|
<td>1</td>
|
|
<td>5</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>X</td>
|
|
<td>1</td>
|
|
<td>1</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Y</td>
|
|
<td>47</td>
|
|
<td>1</td>
|
|
<td>46</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>76</td>
|
|
<td>22</td>
|
|
<td>54</td>
|
|
</tr>
|
|
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
</div>
|
|
|
|
<div id="global_stats">
|
|
<table>
|
|
<thead>
|
|
<tr><th colspan="2">General</th></tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr><td>Assembly name</td><td>GRCr8</td></tr>
|
|
<tr><td>Release date</td><td>2024-01-31</td></tr>
|
|
<tr><td>Assembly type</td><td>haploid</td></tr>
|
|
<tr><td>Release type</td><td>major</td></tr>
|
|
<tr><td>Assembly units</td><td>2</td></tr>
|
|
<tr><td>Total bases</td><td>2,849,597,507</td></tr>
|
|
<tr><td>Total non-N bases</td><td>2,845,466,930</td></tr>
|
|
<tr><td>Primary assembly N50</td><td>137,014,596</td></tr>
|
|
</tbody>
|
|
</table>
|
|
<table>
|
|
<thead>
|
|
<tr><th colspan="2">Regions</th></tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr><td>Total regions</td><td>0</td></tr>
|
|
<tr><td>Regions with alternate loci</td><td>0</td></tr>
|
|
<tr><td>Regions with FIX patches</td><td>0</td></tr>
|
|
<tr><td>Regions with NOVEL patches</td><td>0</td></tr>
|
|
<tr><td>Regions as PAR</td><td>0</td></tr>
|
|
</tbody>
|
|
<table>
|
|
<thead>
|
|
<tr><th colspan="2">Alternate loci and patches</th></tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr><td>Alternate loci</td><td>0</td></tr>
|
|
<tr><td>Alternate loci aligned to primary assembly</td><td>0</td></tr>
|
|
<tr><td>FIX patches</td><td>0</td></tr>
|
|
<tr><td>FIX patches aligned to primary assembly</td><td>0</td></tr>
|
|
<tr><td>NOVEL patches</td><td>0</td></tr>
|
|
<tr><td>NOVEL patches aligned to primary assembly</td><td>0</td></tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
<script type="text/javascript">
|
|
|
|
jQuery(function(){
|
|
jQuery("#tabs").tabs();
|
|
});
|
|
|
|
</script>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<div class="cleaner"></div>
|
|
<div id="footer">
|
|
<ul>
|
|
<li><a title="Get GRC data via FTP" href="https://ftp.ncbi.nlm.nih.gov/pub/grc/">FTP</a></li>
|
|
<li><a target="_blank" href="https://www.genome.gov">NHGRI</a></li>
|
|
<li><a target="_blank" href="http://www.wellcome.ac.uk">Wellcome Sanger Institute</a></li>
|
|
<li><a target="_blank" href="https://www.hhs.gov">HHS</a></li>
|
|
<li><a target="_blank" href="https://www.nih.gov">NIH</a></li>
|
|
<li><a target="_blank" href="https://www.nih.gov/web-policies-notices">Accessibility</a></li>
|
|
<li class="last"><a target="_blank" href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html">HHS Vulnerability Disclosure</a></li>
|
|
</ul>
|
|
</div>
|
|
</div>
|
|
</div><!-- end page -->
|
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|
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<script type="text/javascript" src="/grc/static/grc/js/stats.js"></script>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
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