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<html><head><meta http-equiv="content-type" content="text/html;charset=utf-8" />
<title>Linked-read report at 2021-04-09 09:32:08 </title><script src='http://opengene.org/plotly-1.2.0.min.js'></script>
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</head><body><div id='container'><h1 style='text-align:left;'><a href='https://github.com/CicyYeung/LRTK' target='_blank' style='color:#56461f;text-decoration:none;'>Linked-read report</a</h1>
<div style='font-size:10px;font-weight:normal;text-align:left;color:#666666;padding:5px;'>Created by <a href=' https://github.com/CicyYeung/LRTK' style='color:#1F77B4'>Linked Read ToolKits</a> v1.0, a unified and versatile toolkit for analyzing Linked-Read sequencing data</div>
<div class='section_div_p1'>
<div class='section_title' onclick=showOrHide('result')><a name='result'>Quality </td></tr> on sequencing reads <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='result'>
<div id='detection_result'>
<table class='summary_table' style='width:800px'>
<tr><td class='col1'>Number of total reads before filtering:</td><td class='col2'>4,945,058</td></tr>
<tr><td class='col1'>Number of reads per barcode before filtering:</td><td class='col2'>192</td></tr>
<tr><td class='col1'>Read length before filtering:</td><td class='col2'>150 bp</td></tr>
<tr><td class='col1'>Q20 before filtering:</td><td class='col2'>95.7%</td></tr>
<tr><td class='col1'>Q30 before filtering:</td><td class='col2'>91.18%</td></tr>
<tr><td class='col1'>GC content before filtering:</td><td class='col2'>44.69%</td></tr>
<tr><td class='col1'>Number of total reads after filtering:</td><td class='col2'>4,578,758</td></tr>
<tr><td class='col1'>Number of reads per barcodes after filtering:</td><td class='col2'>192</td></tr>
<tr><td class='col1'>Read length after filtering:</td><td class='col2'>150 bp</td></tr>
<tr><td class='col1'>Q20 after filtering:</td><td class='col2'>96.73%</td></tr>
<tr><td class='col1'>Q30 after filtering:</td><td class='col2'>92.56%</td></tr>
<tr><td class='col1'>GC content after filtering:</td><td class='col2'>42.84%</td></tr>
</table>
</div>
</div>
</div>
<div class='section_div_p2'>
<div class='section_title' onclick=showOrHide('pbsq')><a name='summary'> Per base sequencing quality scores<font color='#56461f' > (click to show/hide) </font></a></div>
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var layout={title:'Base quality for read2', xaxis:{title:'position'}, yaxis:{title:'quality'} };
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<div class='section_div_p3'>
<div class='section_title' onclick=showOrHide('pbsc')><a name='summary'> Per base GC-content <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='pbsc' style='display:none'>
<div id='pbsc_figure'>
<div class='figure' id='plot_pbgc1' style='height:400px;width:800px'></div>
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</div>
<div class='section_div_p4'>
<div class='section_title' onclick=showOrHide('summary')><a name='summary'>Barcode-aware read alignment <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='summary'>
<div class='subsection_title' onclick=showOrHide('general')>Summary Table</div>
<div id='general'>
<table class='summary_table'>
<tr><td class='col1'> Number of barcodes before error correction:</td><td class='col2'>4578758</td></tr>
<tr><td class='col1'> Number of barcodes after error correction:</td><td class='col2'>4230077</td></tr>
<tr><td class='col1'> Percentage of validated barcodes:</td><td class='col2'>92.38%</td></tr>
<tr><td class='col1'> Duplication rate:</td><td class='col2'>1.4%</td></tr>
<tr><td class='col1'> Average phasical coverage of long fragments (C<sub>F</sub>):</td><td class='col2'>137.21 X</td></tr>
<tr><td class='col1'> Average short-read coverage per fragment (C<sub>R</sub>):</td><td class='col2'>0.21 X</td></tr>
<tr><td class='col1'> Mean depth:</td><td class='col2'>28.25 X</td></tr>
<tr><td class='col1'> Average fragment length (u<sub>FL</sub>):</td><td class='col2'>48376.3 bp</td></tr>
<tr><td class='col1'> Weighted average fragment length (Wu<sub>FL</sub>):</td><td class='col2'>162388 bp</td></tr>
<tr><td class='col1'> Number of fragments per barcode (N<sub>F/P</sub>):</td><td class='col2'>39.90</td></tr>
<tr><td class='col1'> Median insert size:</td><td class='col2'>219 bp</td></tr>
</table>
</div>
</div>
</div>
<div class='section_div_p5'>
<div class='section_title' onclick=showOrHide('insert_size')><a name='summary'> Number of fragment per barcode <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='insert_size' style='display:none'>
<div id='insert_size_figure'>
<div class='figure' id='plot_insert_size' style='height:400px;width:800px;'></div>
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</div>
<div class='section_div_p6'>
<div class='section_title' onclick=showOrHide('insert_size_1')><a name='summary'> Fragment length <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='insert_size_1' style='display:none'>
<div id='insert_size_figure_1'>
<div class='figure' id='plot_insert_size_1' style='height:400px;width:800px;'></div>
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</div>
<div class='section_div_p7'>
<div class='section_title' onclick=showOrHide('insert_size_2')><a name='summary'> Coverage of reads per fragment <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='insert_size_2' style='display:none'>
<div id='insert_size_figure_2'>
<div class='figure' id='plot_insert_size_2' style='height:400px;width:800px;'></div>
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</div>
</div>
<div class='section_div_p8'>
<div class='section_title' onclick=showOrHide('insert_size_3')><a name='summary'> Sequencing depth <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='insert_size_3' style='display:none'>
<div id='insert_size_figure_3'>
<div class='figure' id='plot_depth' style='height:400px;width:600px;'></div>
</div>
<script type="text/javascript">
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</div>
</div>
<div class='section_div_p9'>
<div class='section_title' onclick=showOrHide('insert_size_4')><a name='summary'> Insert sizes <font color='#56461f' > (click to show/hide) </font></a></div>
<div id='insert_size_4' style='display:none'>
<div id='insert_size_figure_4'>
<div class='figure' id='plot_insert_size_4' style='height:400px;width:600px;'></div>
</div>
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'Percentage (%) ',type:'bar',line:{color:'rgba(128,0,128,1.0)', width:1}
}];
var layout={title:'Insert size distribution', xaxis:{title:'Insert size (bp)'}, yaxis:{title:'Read percentage (%)'}};
Plotly.newPlot('plot_insert_size_4', data, layout);
</script>
</div>
</div>
<div class='section_div_p10'>
<div class='section_title' onclick=showOrHide('result_2')><a name='result_2'>Genetic variant (SNVs, INDELs, SVs)<font color='#56461f' > (click to show/hide) </font></a></div>
<div id='result_2'>
<div id='detection_result_2'>
<table class='summary_table_2' style='width:800px'>
<tr><td class='col1'>Number of SNVs / small INDELs / large SVs:</td><td class='col2'><B>3270981 / 430765 / 19573<B></td></tr>
</table>
</div>
<div id='kmer_hits_figure_2'>
<div class='figure' id='plot_kmer_hits_2' style='height:500px;width:800px'></div>
</div>
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var layout={title:'Deletion size distribution', xaxis:{title:'Deletion size (bp)'}, yaxis:{title:'Percentages (%)'}};
Plotly.newPlot('plot_kmer_hits_2', data, layout);
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'Percentages (%) ',type:'bar',line:{color:'rgba(128,0,128,1.0)', width:1}
}];
var layout={title:'Insertion size distribution', xaxis:{title:'Insertion size (bp)'}, yaxis:{title:'Percentages (%)'}};
Plotly.newPlot('plot_kmer_hits_3', data, layout);
</script>
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