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Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow
[htsworkflow.git] / htsworkflow / pipelines / test / testdata / sample_summary_1_12.htm
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html xmlns:casava="http://www.illumina.com/casava/alignment">
+<link rel="stylesheet" href="../../css/Reports.css" type="text/css">
+<body>
+<p>Sample Summary Information For Experiment (12564_index6)</p>
+<p>Project Summary</p>
+<table border="1" cellpadding="5">
+<tr>
+<td>Project Name</td>
+<td>12564_index6</td>
+</tr>
+<tr>
+<td>Machine</td>
+<td>HWI-ST0787</td>
+</tr>
+<tr>
+<td>Run Folder</td>
+<td>111221_SN787_0107_AD0CV5ACXX</td>
+</tr>
+<tr>
+<td>Flow Cell ID</td>
+<td>D0CV5ACXX</td>
+</tr>
+<tr>
+<td>Platform</td>
+<td></td>
+</tr>
+<tr>
+<td>Control Software</td>
+<td>HiSeq Control Software 1.4.8</td>
+</tr>
+<tr>
+<td>Primary Analysis</td>
+<td>RTA 1.12.4.2</td>
+</tr>
+<tr>
+<td>Secondary Analysis</td>
+<td>CASAVA-1.8.1</td>
+</tr>
+</table>
+<p>Project Results Summary</p>
+<table border="1" cellpadding="5">
+<tr>
+<th>Clusters (Raw)</th>
+<th>Clusters(PF)</th>
+<th>Yield (MBases)</th>
+</tr>
+<tr>
+<td>658,174</td>
+<td>475,618</td>
+<td>23</td>
+</tr>
+</table>
+<p>Barcode-Lane summary</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="8%">
+<col width="10%">
+<col width="4%">
+<col width="20%">
+<col width="6%">
+<col width="6%">
+<col width="4%">
+<col width="30%">
+<tr>
+<th>Barcode-Lane</th>
+<th>Sample</th>
+<th>Barcode</th>
+<th>Lane</th>
+<th>Species</th>
+<th>Analysis Type</th>
+<th>Length</th>
+<th>Num Tiles</th>
+<th>Genome Directory</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="8%">
+<col width="10%">
+<col width="4%">
+<col width="20%">
+<col width="6%">
+<col width="6%">
+<col width="4%">
+<col width="30%">
+<tr>
+<td>12564_GCCAAT_L5</td>
+<td>12564</td>
+<td>GCCAAT</td>
+<td>5</td>
+<td>Homo_sapiens</td>
+<td>eland extended</td>
+<td>49 </td>
+<td>48</td>
+<td>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes//*.fa</td>
+</tr>
+</table></div>
+<p>Sample Results Summary : Read 1</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr><th colspan="12">Sample Info</th></tr>
+<tr>
+<th>Sample</th>
+<th>Sample Yield (Mbases)</th>
+<th>Clusters (raw)</th>
+<th>Clusters (PF)</th>
+<th>1st Cycle Int (PF)</th>
+<th>% intensity after 20 cycles (PF)</th>
+<th>% PF Clusters</th>
+<th>% Align (PF)</th>
+<th>Alignment Score (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>23</td>
+<td>658,174</td>
+<td>475,618</td>
+<td>1100</td>
+<td>89.39</td>
+<td>72.26</td>
+<td>76.89</td>
+<td>128.73</td>
+<td>0.40</td>
+<td>88.79</td>
+<td>35.13</td>
+</tr>
+</table></div>
+<p>Sample Results Summary : Read 2</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr><th colspan="12">Sample Info</th></tr>
+<tr>
+<th>Sample</th>
+<th>Sample Yield (Mbases)</th>
+<th>Clusters (raw)</th>
+<th>Clusters (PF)</th>
+<th>1st Cycle Int (PF)</th>
+<th>% intensity after 20 cycles (PF)</th>
+<th>% PF Clusters</th>
+<th>% Align (PF)</th>
+<th>Alignment Score (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="12%">
+<col width="12%">
+<col width="8%">
+<col width="7%">
+<col width="9%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>Expanded Sample Summary : Read 1</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<th colspan="2">Sample Info</th>
+<th colspan="2">Phasing Info</th>
+<th colspan="1">Raw data</th>
+<th colspan="8">Filtered data</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>Clusters (raw)</th>
+<th>% Phasing</th>
+<th>% Prephasing</th>
+<th>% Mismatch Rate (raw)</th>
+<th>% PF Clusters</th>
+<th>Cycle 2-4 Av Int (PF)</th>
+<th>Cycle 2-10 Av % Loss (PF)</th>
+<th>Cycle 10-20 Av % Loss (PF)</th>
+<th>% Align (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>658,174</td>
+<td>0.19</td>
+<td>0.31</td>
+<td>0.77</td>
+<td>72.26</td>
+<td>1083.00</td>
+<td>-84.76</td>
+<td>0.48</td>
+<td>76.89</td>
+<td>0.40</td>
+<td>88.79</td>
+<td>35.13</td>
+</tr>
+</table></div>
+<p>Expanded Sample Summary : Read 2</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<th colspan="2">Sample Info</th>
+<th colspan="2">Phasing Info</th>
+<th colspan="1">Raw data</th>
+<th colspan="8">Filtered data</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>Clusters (raw)</th>
+<th>% Phasing</th>
+<th>% Prephasing</th>
+<th>% Mismatch Rate (raw)</th>
+<th>% PF Clusters</th>
+<th>Cycle 2-4 Av Int (PF)</th>
+<th>Cycle 2-10 Av % Loss (PF)</th>
+<th>Cycle 10-20 Av % Loss (PF)</th>
+<th>% Align (PF)</th>
+<th>% Mismatch Rate (PF)</th>
+<th>% &gt;=Q30 bases (PF)</th>
+<th>Mean Quality SCore (PF)</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="8%">
+<col width="8%">
+<col width="8%">
+<col width="6%">
+<col width="10%">
+<col width="10%">
+<col width="9%">
+<col width="5%">
+<col width="8%">
+<col width="6%">
+<col width="6%">
+<tr>
+<td>12564</td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td>0</td>
+<td>0</td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>IVC Plots</p>
+<a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/IVC.htm">
+click here
+</a><p>All Intensity Plots</p>
+<a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/All.htm">
+click here
+</a><p>Mismatch Graphs</p>
+<a href="FullMismatch.htm">
+click here
+</a><p>Mismatch Curves</p>
+<a href="FullPerfect.htm">
+click here
+</a><p>Additional Paired Statistics</p>
+<div ID="ScrollableTableHeaderDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="9%">
+<tr>
+<th colspan="1">Sample Info</th>
+<th colspan="5">Relative Orientation Statistics</th>
+<th colspan="5">Insert Size Statistics (for relative orientation R+)</th>
+<th colspan="3">Insert Statistics (% of individually uniquely alignable pairs)</th>
+</tr>
+<tr>
+<th>Sample</th>
+<th>F-:<br>&gt;R2 R1&gt;</th>
+<th>F+:<br>&gt;R1 R2&gt;</th>
+<th>R-:<br>&lt;R2 R1&gt;</th>
+<th>R+:<br>&gt;R1 R2&lt;</th>
+<th>Total</th>
+<th>Median</th>
+<th>Below-median SD</th>
+<th>Above-median SD</th>
+<th>Low thresh.</th>
+<th>High thresh.</th>
+<th>Too small</th>
+<th>Too large</th>
+<th>Orientation and size OK</th>
+</tr>
+</table></div>
+<div ID="ScrollableTableBodyDiv"><table width="100%">
+<col>
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="7%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="6%">
+<col width="9%">
+<tr>
+<td>12564</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td>0</td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+<td></td>
+</tr>
+</table></div>
+<p>CASAVA-1.8.1</p>
+</body>
+</html>
htsworkflow sequencing LIMS software