1624 lines
46 KiB
Text
1624 lines
46 KiB
Text
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<!DOCTYPE html>
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<html>
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<head>
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<title>Zebrafish Genome Assembly GRCz11 - 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="Zebrafish Genome Assembly GRCz11" />
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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/zebrafish" id="organismOverviewMenuItem">Zebrafish Overview</a></li>
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<li><a href="/grc/zebrafish/issues" id="issueListMenuItem">Zebrafish Genome Issues</a></li>
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<li><a href="/grc/zebrafish/data" id="assemblyDataMenuItem">Zebrafish Assembly Data</a></li>
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<!-- <li><a href="/zebrafish/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/zebrafish" 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>Zebrafish Genome Assembly GRCz11</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="GRCz10">GRCz10</option>
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<option value="Zv9">Zv9</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>59,578,282</td>
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<td><a href="/nucleotide/CM002885.2">CM002885.2</a></td>
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<td><a href="/nucleotide/NC_007112.7">NC_007112.7</a></td>
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</tr>
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<tr>
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<td>2</td>
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<td>59,640,629</td>
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<td><a href="/nucleotide/CM002886.2">CM002886.2</a></td>
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<td><a href="/nucleotide/NC_007113.7">NC_007113.7</a></td>
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</tr>
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<tr>
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<td>3</td>
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<td>62,628,489</td>
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<td><a href="/nucleotide/CM002887.2">CM002887.2</a></td>
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<td><a href="/nucleotide/NC_007114.7">NC_007114.7</a></td>
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</tr>
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<tr>
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<td>4</td>
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<td>78,093,715</td>
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<td><a href="/nucleotide/CM002888.2">CM002888.2</a></td>
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<td><a href="/nucleotide/NC_007115.7">NC_007115.7</a></td>
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</tr>
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<tr>
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<td>5</td>
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<td>72,500,376</td>
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<td><a href="/nucleotide/CM002889.2">CM002889.2</a></td>
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<td><a href="/nucleotide/NC_007116.7">NC_007116.7</a></td>
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</tr>
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<tr>
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<td>6</td>
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<td>60,270,059</td>
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<td><a href="/nucleotide/CM002890.2">CM002890.2</a></td>
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<td><a href="/nucleotide/NC_007117.7">NC_007117.7</a></td>
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</tr>
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<tr>
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<td>7</td>
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<td>74,282,399</td>
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<td><a href="/nucleotide/CM002891.2">CM002891.2</a></td>
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<td><a href="/nucleotide/NC_007118.7">NC_007118.7</a></td>
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</tr>
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<tr>
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<td>8</td>
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<td>54,304,671</td>
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<td><a href="/nucleotide/CM002892.2">CM002892.2</a></td>
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<td><a href="/nucleotide/NC_007119.7">NC_007119.7</a></td>
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</tr>
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<tr>
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<td>9</td>
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<td>56,459,846</td>
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<td><a href="/nucleotide/CM002893.2">CM002893.2</a></td>
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<td><a href="/nucleotide/NC_007120.7">NC_007120.7</a></td>
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</tr>
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<tr>
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<td>10</td>
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<td>45,420,867</td>
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<td><a href="/nucleotide/CM002894.2">CM002894.2</a></td>
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<td><a href="/nucleotide/NC_007121.7">NC_007121.7</a></td>
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</tr>
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<tr>
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<td>11</td>
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<td>45,484,837</td>
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<td><a href="/nucleotide/CM002895.2">CM002895.2</a></td>
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<td><a href="/nucleotide/NC_007122.7">NC_007122.7</a></td>
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</tr>
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<tr>
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<td>12</td>
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<td>49,182,954</td>
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<td><a href="/nucleotide/CM002896.2">CM002896.2</a></td>
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<td><a href="/nucleotide/NC_007123.7">NC_007123.7</a></td>
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</tr>
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<tr>
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<td>13</td>
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<td>52,186,027</td>
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<td><a href="/nucleotide/CM002897.2">CM002897.2</a></td>
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<td><a href="/nucleotide/NC_007124.7">NC_007124.7</a></td>
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</tr>
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<tr>
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<td>14</td>
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<td>52,660,232</td>
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<td><a href="/nucleotide/CM002898.2">CM002898.2</a></td>
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<td><a href="/nucleotide/NC_007125.7">NC_007125.7</a></td>
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</tr>
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<tr>
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<td>15</td>
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<td>48,040,578</td>
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<td><a href="/nucleotide/CM002899.2">CM002899.2</a></td>
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<td><a href="/nucleotide/NC_007126.7">NC_007126.7</a></td>
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</tr>
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<tr>
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<td>16</td>
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<td>55,266,484</td>
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<td><a href="/nucleotide/CM002900.2">CM002900.2</a></td>
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<td><a href="/nucleotide/NC_007127.7">NC_007127.7</a></td>
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</tr>
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<tr>
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<td>17</td>
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<td>53,461,100</td>
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<td><a href="/nucleotide/CM002901.2">CM002901.2</a></td>
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<td><a href="/nucleotide/NC_007128.7">NC_007128.7</a></td>
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</tr>
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<tr>
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<td>18</td>
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<td>51,023,478</td>
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<td><a href="/nucleotide/CM002902.2">CM002902.2</a></td>
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<td><a href="/nucleotide/NC_007129.7">NC_007129.7</a></td>
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</tr>
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<tr>
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<td>19</td>
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<td>48,449,771</td>
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<td><a href="/nucleotide/CM002903.2">CM002903.2</a></td>
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<td><a href="/nucleotide/NC_007130.7">NC_007130.7</a></td>
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</tr>
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<tr>
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<td>20</td>
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<td>55,201,332</td>
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<td><a href="/nucleotide/CM002904.2">CM002904.2</a></td>
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<td><a href="/nucleotide/NC_007131.7">NC_007131.7</a></td>
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</tr>
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|
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<tr>
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<td>21</td>
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<td>45,934,066</td>
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<td><a href="/nucleotide/CM002905.2">CM002905.2</a></td>
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<td><a href="/nucleotide/NC_007132.7">NC_007132.7</a></td>
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</tr>
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|
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<tr>
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<td>22</td>
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<td>39,133,080</td>
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<td><a href="/nucleotide/CM002906.2">CM002906.2</a></td>
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<td><a href="/nucleotide/NC_007133.7">NC_007133.7</a></td>
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</tr>
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<tr>
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<td>23</td>
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<td>46,223,584</td>
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<td><a href="/nucleotide/CM002907.2">CM002907.2</a></td>
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<td><a href="/nucleotide/NC_007134.7">NC_007134.7</a></td>
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</tr>
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<tr>
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<td>24</td>
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<td>42,172,926</td>
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<td><a href="/nucleotide/CM002908.2">CM002908.2</a></td>
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<td><a href="/nucleotide/NC_007135.7">NC_007135.7</a></td>
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</tr>
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<tr>
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<td>25</td>
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<td>37,502,051</td>
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<td><a href="/nucleotide/CM002909.2">CM002909.2</a></td>
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<td><a href="/nucleotide/NC_007136.7">NC_007136.7</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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<tr>
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<td>1</td>
|
|
<td>59,578,282</td>
|
|
<td>59,578,282</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>59,640,629</td>
|
|
<td>59,640,629</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>62,628,489</td>
|
|
<td>62,628,489</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>78,093,715</td>
|
|
<td>78,093,715</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>72,500,376</td>
|
|
<td>72,500,376</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>60,270,059</td>
|
|
<td>60,270,059</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>74,282,399</td>
|
|
<td>74,282,399</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>54,304,671</td>
|
|
<td>54,304,671</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>56,459,846</td>
|
|
<td>56,459,846</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>45,420,867</td>
|
|
<td>45,420,867</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>45,484,837</td>
|
|
<td>45,484,837</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>49,182,954</td>
|
|
<td>49,182,954</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>52,186,027</td>
|
|
<td>52,186,027</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>52,660,232</td>
|
|
<td>52,660,232</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>48,040,578</td>
|
|
<td>48,040,578</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>55,266,484</td>
|
|
<td>55,266,484</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>53,461,100</td>
|
|
<td>53,461,100</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>51,023,478</td>
|
|
<td>51,023,478</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>48,449,771</td>
|
|
<td>48,449,771</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>55,201,332</td>
|
|
<td>55,201,332</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>21</td>
|
|
<td>45,934,066</td>
|
|
<td>45,934,066</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>22</td>
|
|
<td>39,133,080</td>
|
|
<td>39,133,080</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>23</td>
|
|
<td>46,223,584</td>
|
|
<td>46,223,584</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>24</td>
|
|
<td>42,172,926</td>
|
|
<td>42,172,926</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>25</td>
|
|
<td>37,502,051</td>
|
|
<td>37,502,051</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Un</td>
|
|
<td>28,352,955</td>
|
|
<td>na</td>
|
|
<td>28,352,955</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>1,373,454,788</td>
|
|
<td>1,345,101,833</td>
|
|
<td>28,352,955</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>4,818,344</td>
|
|
<td>4,818,344</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>5,197,540</td>
|
|
<td>5,197,540</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>4,572,487</td>
|
|
<td>4,572,487</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>7,379,053</td>
|
|
<td>7,379,053</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>13,500,411</td>
|
|
<td>13,500,411</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>9,977,335</td>
|
|
<td>9,977,335</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>5,009,329</td>
|
|
<td>5,009,329</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>8,083,138</td>
|
|
<td>8,083,138</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>32,000,149</td>
|
|
<td>32,000,149</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>4,706,895</td>
|
|
<td>4,706,895</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>7,242,237</td>
|
|
<td>7,242,237</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>32,399,083</td>
|
|
<td>32,399,083</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>8,482,599</td>
|
|
<td>8,482,599</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>28,653,342</td>
|
|
<td>28,653,342</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>29,777,154</td>
|
|
<td>29,777,154</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>14,334,442</td>
|
|
<td>14,334,442</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>5,946,312</td>
|
|
<td>5,946,312</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>15,551,655</td>
|
|
<td>15,551,655</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>11,329,993</td>
|
|
<td>11,329,993</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>9,260,504</td>
|
|
<td>9,260,504</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>21</td>
|
|
<td>4,066,630</td>
|
|
<td>4,066,630</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>22</td>
|
|
<td>5,145,648</td>
|
|
<td>5,145,648</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>23</td>
|
|
<td>3,380,090</td>
|
|
<td>3,380,090</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>24</td>
|
|
<td>4,737,936</td>
|
|
<td>4,737,936</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>25</td>
|
|
<td>4,876,667</td>
|
|
<td>4,876,667</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Un</td>
|
|
<td>48,672</td>
|
|
<td>na</td>
|
|
<td>48,672</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>7,379,053</td>
|
|
<td>7,538,642</td>
|
|
<td>48,672</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>59,518,204</td>
|
|
<td>59,518,204</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>59,561,129</td>
|
|
<td>59,561,129</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>62,565,097</td>
|
|
<td>62,565,097</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>75,268,643</td>
|
|
<td>75,268,643</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>72,411,310</td>
|
|
<td>72,411,310</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>60,194,477</td>
|
|
<td>60,194,477</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>74,193,585</td>
|
|
<td>74,193,585</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>54,255,784</td>
|
|
<td>54,255,784</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>56,393,308</td>
|
|
<td>56,393,308</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>45,373,267</td>
|
|
<td>45,373,267</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>45,418,283</td>
|
|
<td>45,418,283</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>49,092,027</td>
|
|
<td>49,092,027</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>52,124,602</td>
|
|
<td>52,124,602</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>52,604,632</td>
|
|
<td>52,604,632</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>47,971,581</td>
|
|
<td>47,971,581</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>55,207,672</td>
|
|
<td>55,207,672</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>53,387,590</td>
|
|
<td>53,387,590</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>50,931,061</td>
|
|
<td>50,931,061</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>48,391,784</td>
|
|
<td>48,391,784</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>55,132,661</td>
|
|
<td>55,132,661</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>21</td>
|
|
<td>45,869,123</td>
|
|
<td>45,869,123</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>22</td>
|
|
<td>39,045,925</td>
|
|
<td>39,045,925</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>23</td>
|
|
<td>46,157,041</td>
|
|
<td>46,157,041</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>24</td>
|
|
<td>42,107,172</td>
|
|
<td>42,107,172</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>25</td>
|
|
<td>37,439,205</td>
|
|
<td>37,439,205</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Un</td>
|
|
<td>28,150,343</td>
|
|
<td>na</td>
|
|
<td>28,150,343</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>1,368,765,506</td>
|
|
<td>1,340,615,163</td>
|
|
<td>28,150,343</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>561</td>
|
|
<td>561</td>
|
|
<td>0</td>
|
|
<td>35</td>
|
|
<td>35</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>741</td>
|
|
<td>741</td>
|
|
<td>0</td>
|
|
<td>54</td>
|
|
<td>54</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>594</td>
|
|
<td>594</td>
|
|
<td>0</td>
|
|
<td>38</td>
|
|
<td>38</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>440</td>
|
|
<td>440</td>
|
|
<td>0</td>
|
|
<td>48</td>
|
|
<td>48</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>824</td>
|
|
<td>824</td>
|
|
<td>0</td>
|
|
<td>71</td>
|
|
<td>71</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>722</td>
|
|
<td>722</td>
|
|
<td>0</td>
|
|
<td>35</td>
|
|
<td>35</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>835</td>
|
|
<td>835</td>
|
|
<td>0</td>
|
|
<td>54</td>
|
|
<td>54</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>460</td>
|
|
<td>460</td>
|
|
<td>0</td>
|
|
<td>27</td>
|
|
<td>27</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>642</td>
|
|
<td>642</td>
|
|
<td>0</td>
|
|
<td>25</td>
|
|
<td>25</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>446</td>
|
|
<td>446</td>
|
|
<td>0</td>
|
|
<td>30</td>
|
|
<td>30</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>626</td>
|
|
<td>626</td>
|
|
<td>0</td>
|
|
<td>40</td>
|
|
<td>40</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>881</td>
|
|
<td>881</td>
|
|
<td>0</td>
|
|
<td>29</td>
|
|
<td>29</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>582</td>
|
|
<td>582</td>
|
|
<td>0</td>
|
|
<td>33</td>
|
|
<td>33</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>528</td>
|
|
<td>528</td>
|
|
<td>0</td>
|
|
<td>28</td>
|
|
<td>28</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>663</td>
|
|
<td>663</td>
|
|
<td>0</td>
|
|
<td>28</td>
|
|
<td>28</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>559</td>
|
|
<td>559</td>
|
|
<td>0</td>
|
|
<td>29</td>
|
|
<td>29</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>695</td>
|
|
<td>695</td>
|
|
<td>0</td>
|
|
<td>41</td>
|
|
<td>41</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>897</td>
|
|
<td>897</td>
|
|
<td>0</td>
|
|
<td>22</td>
|
|
<td>22</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>545</td>
|
|
<td>545</td>
|
|
<td>0</td>
|
|
<td>35</td>
|
|
<td>35</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>645</td>
|
|
<td>645</td>
|
|
<td>0</td>
|
|
<td>43</td>
|
|
<td>43</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>21</td>
|
|
<td>603</td>
|
|
<td>603</td>
|
|
<td>0</td>
|
|
<td>48</td>
|
|
<td>48</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>22</td>
|
|
<td>454</td>
|
|
<td>454</td>
|
|
<td>0</td>
|
|
<td>23</td>
|
|
<td>23</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>23</td>
|
|
<td>635</td>
|
|
<td>635</td>
|
|
<td>0</td>
|
|
<td>30</td>
|
|
<td>30</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>24</td>
|
|
<td>622</td>
|
|
<td>622</td>
|
|
<td>0</td>
|
|
<td>35</td>
|
|
<td>35</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>25</td>
|
|
<td>584</td>
|
|
<td>584</td>
|
|
<td>0</td>
|
|
<td>44</td>
|
|
<td>44</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Un</td>
|
|
<td>2,027</td>
|
|
<td>na</td>
|
|
<td>2,027</td>
|
|
<td>0</td>
|
|
<td>na</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>17,811</td>
|
|
<td>15,784</td>
|
|
<td>2,027</td>
|
|
<td>925</td>
|
|
<td>925</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>36</td>
|
|
<td>36</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>2</td>
|
|
<td>55</td>
|
|
<td>55</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>3</td>
|
|
<td>39</td>
|
|
<td>39</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>4</td>
|
|
<td>49</td>
|
|
<td>49</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>5</td>
|
|
<td>72</td>
|
|
<td>72</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>6</td>
|
|
<td>36</td>
|
|
<td>36</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>7</td>
|
|
<td>55</td>
|
|
<td>55</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>8</td>
|
|
<td>28</td>
|
|
<td>28</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>9</td>
|
|
<td>26</td>
|
|
<td>26</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>10</td>
|
|
<td>31</td>
|
|
<td>31</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>11</td>
|
|
<td>41</td>
|
|
<td>41</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>12</td>
|
|
<td>30</td>
|
|
<td>30</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>13</td>
|
|
<td>34</td>
|
|
<td>34</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>14</td>
|
|
<td>29</td>
|
|
<td>29</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>15</td>
|
|
<td>29</td>
|
|
<td>29</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>16</td>
|
|
<td>30</td>
|
|
<td>30</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>17</td>
|
|
<td>42</td>
|
|
<td>42</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>18</td>
|
|
<td>23</td>
|
|
<td>23</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>19</td>
|
|
<td>36</td>
|
|
<td>36</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>20</td>
|
|
<td>44</td>
|
|
<td>44</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>21</td>
|
|
<td>49</td>
|
|
<td>49</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>22</td>
|
|
<td>24</td>
|
|
<td>24</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>23</td>
|
|
<td>31</td>
|
|
<td>31</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>24</td>
|
|
<td>36</td>
|
|
<td>36</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>25</td>
|
|
<td>45</td>
|
|
<td>45</td>
|
|
<td>0</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Un</td>
|
|
<td>967</td>
|
|
<td>na</td>
|
|
<td>967</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Genome</td>
|
|
<td>1,917</td>
|
|
<td>950</td>
|
|
<td>967</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>GRCz11</td></tr>
|
|
<tr><td>Release date</td><td>2017-05-09</td></tr>
|
|
<tr><td>Assembly type</td><td>haploid-with-alt-loci</td></tr>
|
|
<tr><td>Release type</td><td>major</td></tr>
|
|
<tr><td>Assembly units</td><td>5</td></tr>
|
|
<tr><td>Total bases</td><td>1,679,186,873</td></tr>
|
|
<tr><td>Total non-N bases</td><td>1,674,495,211</td></tr>
|
|
<tr><td>Primary assembly N50</td><td>7,379,053</td></tr>
|
|
</tbody>
|
|
</table>
|
|
<table>
|
|
<thead>
|
|
<tr><th colspan="2">Regions</th></tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr><td>Total regions</td><td>607</td></tr>
|
|
<tr><td>Regions with alternate loci</td><td>607</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>930</td></tr>
|
|
<tr><td>Alternate loci aligned to primary assembly</td><td>930</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">
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|
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|
</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>
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