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BT18.vep_summary.html 15.62 KiB
<html>
<head>
  <title>VEP summary</title>
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var var_cons_table = drawTable('var_cons_table', 'Consequences (most severe)', google.visualization.arrayToDataTable([['Consequence type','Count'],['splice_donor_variant',33],['splice_acceptor_variant',43],['stop_gained',53],['frameshift_variant',85],['stop_lost',3],['initiator_codon_variant',9],['inframe_insertion',16],['inframe_deletion',28],['missense_variant',3391],['splice_region_variant',619],['synonymous_variant',3340],['stop_retained_variant',3],['coding_sequence_variant',23],['mature_miRNA_variant',6],['5_prime_UTR_variant',377],['3_prime_UTR_variant',1558],['non_coding_transcript_exon_variant',224],['intron_variant',121565],['non_coding_transcript_variant',3],['upstream_gene_variant',28710],['downstream_gene_variant',23499],['intergenic_variant',262169]]));

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var consequences_table = drawTable('consequences_table', 'Consequences (all)', google.visualization.arrayToDataTable([['Consequence type','Count'],['splice_donor_variant',8],['splice_acceptor_variant',16],['stop_gained',58],['frameshift_variant',96],['stop_lost',3],['initiator_codon_variant',11],['inframe_insertion',18],['inframe_deletion',31],['missense_variant',3853],['splice_region_variant',214],['stop_retained_variant',3],['synonymous_variant',3858],['coding_sequence_variant',50],['intron_variant',12]]));

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            google.visualization.events.addListener(consequences_table, 'select', function() {
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          var coding_pie = drawPie('coding_pie', 'Coding consequences', google.visualization.arrayToDataTable([['Consequence type','Count'],['stop_gained',58],['frameshift_variant',96],['stop_lost',3],['inframe_insertion',18],['inframe_deletion',31],['missense_variant',3853],['synonymous_variant',3858],['coding_sequence_variant',50]]), {slices: [{color: "#ff0000"}, {color: "#ff69b4"}, {color: "#ff0000"}, {color: "#ff69b4"}, {color: "#ff69b4"}, {color: "#ffd700"}, {color: "#76ee00"}, {color: "#458b00"}]});
var coding_table = drawTable('coding_table', 'Coding consequences', google.visualization.arrayToDataTable([['Consequence type','Count'],['stop_gained',58],['frameshift_variant',96],['stop_lost',3],['inframe_insertion',18],['inframe_deletion',31],['missense_variant',3853],['synonymous_variant',3858],['coding_sequence_variant',50]]));

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var sift_table = drawTable('sift_table', 'SIFT summary', google.visualization.arrayToDataTable([['Prediction','Count'],['deleterious',754],['tolerated',2689]]));

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var chr_table = drawTable('chr_table', 'Variants by chromosome', google.visualization.arrayToDataTable([['Chromosome','Count'],['18',445757]]));

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var protein_bar = drawBar('protein_bar', 'Position in protein', google.visualization.arrayToDataTable([['Position in protein (percentile)','Count'],['00-10%',764],['10-20%',840],['20-30%',851],['30-40%',853],['40-50%',800],['50-60%',730],['60-70%',813],['70-80%',715],['80-90%',800],['90-100%',786]]), {hAxis: {title: "Position in protein (percentile)", textStyle: {fontSize: 10}}, legend: {position: "none"}});

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</head>
<body>
<div id="masthead" class="masthead">
  <div style="float: left; display: inline; padding: 10px; height: 80px;">
    <a href="http://www.ensembl.org/"><img src="http://static.ensembl.org/i/e-ensembl.png"></a>
  </div>
  
  <div style="float: right; display: inline; height: 80px; background: white; padding: 10px;">
    <a href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html"><img src="http://www.ensembl.org/img/vep_logo.png"></a>
  </div>
  <div class="gradient">
  </div>
</div>
<div class="main">
<div class="sidemenu"><div class="sidemenu_head">Links</div> <div class="sidemenu_body"><ul><li><a href="#masthead">Top of page</a></li> <li><a href="#run_stats">VEP run statistics</a></li> <li><a href="#gen_stats">General statistics</a></li> <li><a href="#var_class">Variant classes</a></li> <li><a href="#var_cons">Consequences (most severe)</a></li> <li><a href="#consequences">Consequences (all)</a></li> <li><a href="#coding">Coding consequences</a></li> <li><a href="#sift">SIFT summary</a></li> <li><a href="#chr">Variants by chromosome</a></li> <li><a href="#protein">Position in protein</a></li></ul></div></div><div class='main_content'><h3 id="run_stats">VEP run statistics</h3><table class="stats_table"><tr><td>VEP version (API)</td> <td>78 (78)</td></tr> <tr><td>Cache/Database</td> <td>/home/formacion/COMUNES/IAMZ/data/CIHEAM/ReferenceGenome/VEP//bos_taurus/78_UMD3.1</td></tr> <tr><td>Species</td> <td>bos_taurus</td></tr> <tr><td>Command line options</td> <td><pre>--dir /home/formacion/COMUNES/IAMZ/data/CIHEAM/ReferenceGenome/VEP/ --species bos_taurus -o BT18.vep --fork 4 --canonical --sift b --coding_only --no_intergenic --offline --force_overwrite</pre></td></tr> <tr><td>Start time</td> <td>2015-03-07 21:16:54</td></tr> <tr><td>End time</td> <td>2015-03-07 21:19:40</td></tr> <tr><td>Run time</td> <td>166 seconds</td></tr> <tr><td>Input file (format)</td> <td> (VCF)</td></tr> <tr><td>Output file</td> <td>BT18.vep <a href="BT18.vep">[text]</a></td></tr></table><h3 id="gen_stats">General statistics</h3><table class="stats_table"><tr><td>Lines of input read</td> <td>445813</td></tr> <tr><td>Variants processed</td> <td>445757</td></tr> <tr><td>Variants remaining after filtering</td> <td>445757</td></tr> <tr><td>Lines of output written</td> <td>7982</td></tr> <tr><td>Novel / existing variants</td> <td>-</td></tr> <tr><td>Overlapped genes</td> <td>916</td></tr> <tr><td>Overlapped transcripts</td> <td>1019</td></tr> <tr><td>Overlapped regulatory features</td> <td>-</td></tr></table><hr /><h3 id="var_class">Variant classes</h3><div style="width: 800px; height: 200px" id="var_class_pie">&nbsp;</div><div style="width: 800px; height: 200px" id="var_class_table">&nbsp;</div><hr /><h3 id="var_cons">Consequences (most severe)</h3><div style="width: 800px; height: 400px" id="var_cons_pie">&nbsp;</div><div style="width: 800px; height: 200px" id="var_cons_table">&nbsp;</div><hr /><h3 id="consequences">Consequences (all)</h3><div id="consequences_pie" style="width: 800px; height: 400px">&nbsp;</div><div id="consequences_table" style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="coding">Coding consequences</h3><div style="width: 800px; height: 400px" id="coding_pie">&nbsp;</div><div style="width: 800px; height: 200px" id="coding_table">&nbsp;</div><hr /><h3 id="sift">SIFT summary</h3><div id="sift_pie" style="width: 800px; height: 200px">&nbsp;</div><div style="width: 800px; height: 200px" id="sift_table">&nbsp;</div><hr /><h3 id="chr">Variants by chromosome</h3><div id="chr_bar" style="width: 800px; height: 200px">&nbsp;</div><div id="chr_table" style="width: 800px; height: 200px">&nbsp;</div><hr /><h3 id="chr_18">Distribution of variants on chromosome 18</h3><div style="width: 800px; height: 200px" id="chr_18_area">&nbsp;</div><hr /><h3 id="protein">Position in protein</h3><div id="protein_bar" style="width: 800px; height: 200px">&nbsp;</div></div>
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