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