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author youngkim
date Thu, 31 Mar 2016 10:10:37 -0400
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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Strict//EN">
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2 <html>
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3 <head><title>ezBAMQC Report</title>
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4 <style type="text/css">
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5 html,body{margin:0;padding:0;height:100%;width:1500px}
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6 div#header{background-color:#F3F2ED;}
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7 div#header h1{text-align:center; height:80px;line-height:80px;margin:0;padding-left:10px;}
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8 div#container{text-align:left;height:100%;width:1500px}
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9 div#navigation{background:#F6F0E0;}
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10 div#navigation{float:left;width:200px;height:100%}
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11 .menu-item ul {
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12 background: #F6F0E0;
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13 font-size: 13px;
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14 line-height: 30px;
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15 height: 0px;
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17 padding: 0px; }
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18 .menu-item:hover ul { height: 220px; }
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19 table{ margin:0;padding:0;width:1300px;table-layout:fixed;text-align:left; }
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20 table > thead > tr.tableizer-firstrow > th { padding: 10px; background: lavenderblush;}
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21 table > tbody > tr > td{ padding: 10px; background: #f8f8f8; word-wrap: break word; }
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22 div#footer{background:#BFBD93;}
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23 div#footer p{margin:0;padding:5px 10px}
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24 div#footer{clear:both;width:100%;text-align:center}
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25 div#main{float:right;width:1300px}
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26 a{text-decoration:none; color:#000000;}
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27 a:hover {text-decoration: underline; }
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28 </style> </head>
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29 <body>
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30 <div id ="container">
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31 <div id="header"><h1>ezBAMQC Report</h1><p text-align="left">Created On: 03-24-2016</p></div>
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32 <div id="wrapper">
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33 <div class="summary" id="navigation">
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34 <h2>Summary</h2>
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35 <ul>
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36 <li><div class="menu-item">
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37 <h4>smp0</h4>
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38 <ul>
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39 <li><a href="#M00">Basic Statistics</a></li>
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40 <li><a href="#M01">Read Distribution</a></li>
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41 <li><a href="#M02">Mappability</a></li>
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42 <li><a href="#M03">Coverage</a></li>
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43 <li><a href="#M04">Read Length and Insertion Size</a></li>
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44 </ul></div></li>
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45 <li><div class="menu-item">
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46 <h4>smp1</h4>
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47 <ul>
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48 <li><a href="#M10">Basic Statistics</a></li>
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49 <li><a href="#M11">Read Distribution</a></li>
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50 <li><a href="#M12">Mappability</a></li>
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51 <li><a href="#M13">Coverage</a></li>
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52 <li><a href="#M14">Read Length and Insertion Size</a></li>
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53 </ul></div></li>
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54 <li><div class="menu-item">
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55 <h4>smp2</h4>
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56 <ul>
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57 <li><a href="#M20">Basic Statistics</a></li>
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58 <li><a href="#M21">Read Distribution</a></li>
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59 <li><a href="#M22">Mappability</a></li>
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60 <li><a href="#M23">Coverage</a></li>
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61 <li><a href="#M24">Read Length and Insertion Size</a></li>
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62 </ul></div></li>
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63 <li><div class="menu-item"><a href="#M115"><h4>Sample Correlation</h4></a></div></li>
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64 </ul>
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65 </div>
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66 <div id="main" >
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67 <h2>smp0</h2>
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68 <div class="module"><h2 id="M00">Basic Statistics</h2>
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69 <table>
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70 <thead><tr class="tableizer-firstrow">
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71 <th>Measure</th><th>Value</th></tr></thead>
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72 <tbody><tr><td>Total Reads</td><td>77686</td></tr>
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73 <tr><td>Unique Reads</td><td>64349</td></tr>
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74 <tr><td>Multi-reads</td><td>13337</td></tr>
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75 <tr><td>Unmapped Reads</td><td>0</td></tr>
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76 <tr><td>Low Quality Reads</td><td>0</td></tr>
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77 <tr><td>Forward Reads</td><td>31875</td></tr>
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78 <tr><td>Reverse Reads</td><td>32474</td></tr>
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79 <tr><td>Splice Reads</td><td>13900</td></tr>
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80 <tr><td>Non-Splice Reads</td><td>50449</td></tr>
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81 <tr><td>rRNA Reads</td><td>8521</td></tr></tbody></table></div>
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82 <div class="module"><h2 id="M01">Read Distribution</h2>
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83 <p><img class="indented" src="./figs/smp0.read_distr.png" alt="Read Distribution"><img class="indented" src="./figs/smp0.read_distr_pie.png" alt="Read Distribution"></p></div>
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84 <div class="module"><h2 id="M02">Mappability</h2>
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85 <p><img class="indented" src="./figs/smp0.clipping_profile.png" alt="Mappablity Profile"> <img class="indented" src="./figs/smp0.mapq_profile.png" alt="MapQ Profile"></p></div>
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86 <div class="module"><h2 id="M03">Coverage</h2>
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87 <p><img class="indented" src="./figs/smp0.geneBodyCoverage.png" alt="Read Coverage"> <img class="indented" src="./figs/smp0.TransCoverage.png" alt="Read Coverage"></p></div>
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88 <div class="module"><h2 id="M04">Read Length</h2>
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89 <p><img class="indented" src="./figs/smp0.readlen_profile.png" alt="Read Length"></p></div>
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90 <h2>smp1</h2>
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91 <div class="module"><h2 id="M10">Basic Statistics</h2>
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92 <table>
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93 <thead><tr class="tableizer-firstrow">
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94 <th>Measure</th><th>Value</th></tr></thead>
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95 <tbody><tr><td>Total Reads</td><td>79258</td></tr>
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96 <tr><td>Unique Reads</td><td>66672</td></tr>
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97 <tr><td>Multi-reads</td><td>12586</td></tr>
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98 <tr><td>Unmapped Reads</td><td>0</td></tr>
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99 <tr><td>Low Quality Reads</td><td>0</td></tr>
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100 <tr><td>Forward Reads</td><td>33207</td></tr>
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101 <tr><td>Reverse Reads</td><td>33465</td></tr>
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102 <tr><td>Splice Reads</td><td>14459</td></tr>
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103 <tr><td>Non-Splice Reads</td><td>52213</td></tr>
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104 <tr><td>rRNA Reads</td><td>7563</td></tr></tbody></table></div>
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105 <div class="module"><h2 id="M11">Read Distribution</h2>
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106 <p><img class="indented" src="./figs/smp1.read_distr.png" alt="Read Distribution"><img class="indented" src="./figs/smp1.read_distr_pie.png" alt="Read Distribution"></p></div>
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107 <div class="module"><h2 id="M12">Mappability</h2>
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108 <p><img class="indented" src="./figs/smp1.clipping_profile.png" alt="Mappablity Profile"> <img class="indented" src="./figs/smp1.mapq_profile.png" alt="MapQ Profile"></p></div>
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109 <div class="module"><h2 id="M13">Coverage</h2>
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110 <p><img class="indented" src="./figs/smp1.geneBodyCoverage.png" alt="Read Coverage"> <img class="indented" src="./figs/smp1.TransCoverage.png" alt="Read Coverage"></p></div>
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111 <div class="module"><h2 id="M14">Read Length</h2>
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112 <p><img class="indented" src="./figs/smp1.readlen_profile.png" alt="Read Length"></p></div>
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113 <h2>smp2</h2>
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114 <div class="module"><h2 id="M20">Basic Statistics</h2>
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115 <table>
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116 <thead><tr class="tableizer-firstrow">
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117 <th>Measure</th><th>Value</th></tr></thead>
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118 <tbody><tr><td>Total Reads</td><td>80603</td></tr>
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119 <tr><td>Unique Reads</td><td>69389</td></tr>
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120 <tr><td>Multi-reads</td><td>11214</td></tr>
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121 <tr><td>Unmapped Reads</td><td>0</td></tr>
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122 <tr><td>Low Quality Reads</td><td>0</td></tr>
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123 <tr><td>Forward Reads</td><td>34065</td></tr>
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124 <tr><td>Reverse Reads</td><td>35324</td></tr>
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125 <tr><td>Splice Reads</td><td>12624</td></tr>
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126 <tr><td>Non-Splice Reads</td><td>56765</td></tr>
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127 <tr><td>rRNA Reads</td><td>5939</td></tr></tbody></table></div>
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128 <div class="module"><h2 id="M21">Read Distribution</h2>
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129 <p><img class="indented" src="./figs/smp2.read_distr.png" alt="Read Distribution"><img class="indented" src="./figs/smp2.read_distr_pie.png" alt="Read Distribution"></p></div>
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130 <div class="module"><h2 id="M22">Mappability</h2>
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131 <p><img class="indented" src="./figs/smp2.clipping_profile.png" alt="Mappablity Profile"> <img class="indented" src="./figs/smp2.mapq_profile.png" alt="MapQ Profile"></p></div>
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132 <div class="module"><h2 id="M23">Coverage</h2>
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133 <p><img class="indented" src="./figs/smp2.geneBodyCoverage.png" alt="Read Coverage"> <img class="indented" src="./figs/smp2.TransCoverage.png" alt="Read Coverage"></p></div>
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134 <div class="module"><h2 id="M24">Read Length</h2>
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135 <p><img class="indented" src="./figs/smp2.readlen_profile.png" alt="Read Length"></p></div>
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136 <div class="Smp_corr"><h2 id="M115">Sample Correlation and Quality</h2>
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137 <p><img class="indented" src="./figs/smp_corr.png" alt="Sample Correlation"><img class="indented" src="./figs/smp_qual.png" alt="Sample Correlation"></p>
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138 <h2 id="M115">Sample Coverage</h2>
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139 <p><img class="indented" src="./figs/smp_cov.png" alt="Sample Coverage"></p></div>
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140 <h2 id="M115">Sample Variation</h2>
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141 <p><img class="indented" src="./figs/smp_reproducibility.png" alt="Sample Variation"><img class="indented" src="./figs/smp_var.png" alt="Sample Variation"></p></div>
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142 </div>
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143 <div id="footer"><p>Produced by Bioinformatics Shared Resource at CSHL </p></div></div></div></body></html>
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144