snpEff_summary.html

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<!--==========================================================================
	Index
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<center>
<div class="main">

<center> <h3> SnpEff: Variant analysis </h3> </center>

<div style="margin-left: .5em">
<table class="toc"><tr><td>
	<center><b>Contents</b></center>
	<a href="#summary">Summary</a><br>
	<a href="#changeRateChr"> Variant rate by chromosome</a><br>
	<a href="#changesByType">Variants by type</a><br>
	<a href="#effectsImpact"> Number of variants by impact </a><br>
	<a href="#effectsImpact"> Number of variants by functional class </a><br>
	<a href="#effects"> Number of variants by effect </a><br>
	<a href="#quality">Quality histogram</a><br>
	<a href="#indels">InDel length histogram</a><br>
	<a href="#baseChages">Base variant table</a><br>
	<a href="#tstv">Transition vs transversions (ts/tv)</a><br>
	<a href="#alleleFreq"> Allele frequency </a><br>
	<a href="#alleleCount"> Allele Count </a><br>
	<a href="#codonChanges"> Codon change table </a><br>
	<a href="#aaChanges"> Amino acid change table </a><br>
	<a href="#chrChanges"> Chromosome variants plots </a><br>
	<a href="snpEff_genes.txt"> Details by gene </a><br>
</tr></td></table>
</div>


<!--==========================================================================
	Summary table 
	========================================================================== -->

<hr>
<a name="summary">
<center>
<b>Summary</b><p>

<table border=0>
	<tr bgcolor=ffffff> 
		<td valign=top> <b> Genome </b> </td>
		<td> testHg3775Chr1 </td>
	</tr>
	<tr bgcolor=dddddd> 
		<td valign=top> <b> Date </b> </td>
		<td> 2016-07-03 08:09 </td>
	</tr>
	<tr bgcolor=ffffff> 
		<td valign=top> <b> SnpEff version </b> </td>
		<td> <pre>SnpEff 4.3 (build 2016-06-25 15:57), by Pablo Cingolani</pre> </td>
	</tr>
	<tr bgcolor=dddddd> 
		<td valign=top> <b> Command line arguments </b> </td>
		<td> <pre>SnpEff  testHg3775Chr1 tests/test_non_variants.vcf 
</pre> </td>
	</tr>
	<tr bgcolor=ffffff> 
		<td valign=top> <b> Warnings </b> </td>
		 
		<td bgcolor="#ffffff"> 0 </td>
	</tr>	
	<tr bgcolor=dddddd> 
		<td valign=top> <b> Errors </b> </td>
		 
		<td bgcolor="#dddddd"> 0 </td>
	</tr>	
	<tr bgcolor=ffffff>
		<td valign=top> <b> Number of lines (input file) </b> </td>
		<td> 882 </td>
	</tr>
	<tr bgcolor=dddddd>
		<td valign=top> <b> Number of variants (before filter) </b> </td>
		<td> 882 </td>
	</tr>
	<tr bgcolor=ffffff>
		<td valign=top> <b> Number of not variants <br>(i.e. reference equals alternative) </b> </td>
		<td> 0 </td>
	</tr>
	<tr bgcolor=dddddd>
		<td valign=top> <b> Number of variants processed <br> (i.e. after filter and non-variants) </b> </td>
		<td> 0 </td>
	</tr>
	<tr bgcolor=ffffff>
		<td valign=top> <b> Number of known variants <br>(i.e. non-empty ID) </b> </td>
		<td> 
		0
		( 0% ) 
		</td>
	</tr>
	<tr bgcolor=ffffff>
		<td valign=top> <b> Number of multi-allelic VCF entries <br>(i.e. more than two alleles) </b> </td>
		<td> 
		0
		</td>
	</tr>
	<tr bgcolor=dddddd>
		<td valign=top> <b> Number of effects </b> </td>
		<td> 0 </td>
	</tr>
	<tr bgcolor=ffffff>
		<td valign=top> <b> Genome total length </b> </td>
		<td> 249,250,621 </td>
	</tr>
	<tr bgcolor=dddddd>
		<td valign=top> <b> Genome effective length </b> </td>
		<td> 0 </td>
	</tr>
	<tr bgcolor=ffffff>
		<td valign=top> <b> Variant rate </b> </td>
		<td> 1 variant every 0 bases </td>
	</tr>
</table>
<p>
</center>

<!--==========================================================================
	Variant rate by chromosome
	========================================================================== -->

<hr> 
<a name="changeRateChr"> 

<center>
<b> Variants rate details </b><p>

<table border=1>
	<tr><th> Chromosome </th><th> Length </th><th> Variants </th><th> Variants rate </th></tr> 
	<tr>
		<th> Total </th>
		<th class="numeric"> 0 </th>
		<th class="numeric"> 0 </th>
		<th class="numeric"> 0 </th>
	</tr> 
</table> 
</center>

<!--==========================================================================
	Variantss by type
	========================================================================== -->

<hr> 
<a name="changesByType"> 
<center>
<b> Number variantss by type</b><p>

<table border=1>
	<thead>
		<tr>
			<th> <b> Type   </b> </th>
			<th> <b> Total  </b> </th>
		</tr>
	</thead>
    <tbody>
	    <tr>
	    	<td> <b> SNP </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> MNP </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> INS </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> DEL </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> MIXED </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> INV </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> DUP </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> BND </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
	    <tr>
	    	<td> <b> INTERVAL </b> </td>
	    	<td class="numeric" bgcolor="ffffff"> 0 </td>
	    </tr>
    </tbody>
    <tfoot>
	    <tr>
	    	<th><b>Total </b> </th>
	    	<th class="numeric"> 0 </th>
	    </tr>
    </tfoot>
</table>
</center>

<!--==========================================================================
	Effects by impact
	========================================================================== -->

<hr> 
<a name="effectsImpact"> 
<center>
<b> Number of effects by impact </b> <p> 

<table border=0>
	<thead>
		<tr> 
			<th><b> Type (alphabetical order)  </b></th>
			<th> &nbsp; </th>
			<th> Count </th>
			<th> Percent </th>
		</tr>
	</thead>
</table><br>
<p>
</center>

<!--==========================================================================
	Effects by functional class
	========================================================================== -->

<hr> 
<a name="effectsFuncClass"> 
<center>
<b> Number of effects by functional class </b> <p> 

<table border=0>
	<thead>
		<tr> 
			<th><b> Type (alphabetical order)  </b></th>
			<th> &nbsp; </th>
			<th> Count </th>
			<th> Percent </th>
		</tr>
	</thead>
</table><br>
<p>

Missense / Silent ratio: 0

</center>

<!--==========================================================================
	Effects stats
	========================================================================== -->

<hr> 
<a name="effects"> 
<center>
<b> Number of effects by type and region </b> <p> 

<table border=0>
	<tr>
		<th> Type </th>
		<th> Region </th>
	</tr>
	<tr>
		<td> <table border=0>
	<thead>
		<tr> 
			<th><b> Type (alphabetical order)  </b></th>
			<th> &nbsp; </th>
			<th> Count </th>
			<th> Percent </th>
		</tr>
	</thead>
</table><br>
 </td>
		<td> <table border=0>
	<thead>
		<tr> 
			<th><b> Type (alphabetical order)  </b></th>
			<th> &nbsp; </th>
			<th> Count </th>
			<th> Percent </th>
		</tr>
	</thead>
</table><br>
 </td>
	</tr>
</table>
<p>

<img src="http://chart.apis.google.com/chart?cht=bvs&chs=800x300&chbh=50,4,8&chxt=y,y,x,x&chtt=Variations&chxp=1,50.0|3,50.0&chxr=0,0.0,0.0|1,0.0,100.0|3,0.0,100.0&chco=00FFFF,FA8072,FF0000,A52A2A,FFA500,DEB887,E9967A,7FFFD4,808080&chdl=Upstream|5%27UTR|Exon|Splice+Donor|Intron|Splice+Acceptor|3%27UTR|Downstream|Intergenic&chxl=1:|%25|2:|Intergenic|Up|5%27UTR|Exon|Donor|Intron|Acceptor|Exon|3%27UTR|Down|Intergenic|3:|&chd=e:AA__AAAAAAAAAAAAAAAAAA,AAAA__AAAAAAAAAAAAAAAA,AAAAAA__AAAAAA__AAAAAA,AAAAAAAA__AAAAAAAAAAAA,AAAAAAAAAA__AAAAAAAAAA,AAAAAAAAAAAA__AAAAAAAA,AAAAAAAAAAAAAAAA__AAAA,AAAAAAAAAAAAAAAAAA__AA,__AAAAAAAAAAAAAAAAAA__" border=1><p>

</center>

<!--==========================================================================
	Quality
	========================================================================== -->

<hr> 
<a name="quality"> 
<b> Quality:</b> 
<p>
<pre>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Quality+histogram&chxl=1:|Count|3:|Quality&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
</pre>

<!--==========================================================================
	InDels
	========================================================================== -->

<hr> 
<a name="indels"> 
<b> Insertions and deletions length:</b> 
<p>
<pre>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chxl=1:|Count|3:|Length&chtt=Insertion+deletion+length+histogram&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
</pre>

<!--==========================================================================
	Base changes
	========================================================================== -->

<hr> 
<a name="baseChages"> 
<center>
<b> Base changes (SNPs) </b> <p>

<table border=1>
    <tr>
    	<td> &nbsp; </td>  <th> <b> A </b> </th> <th> <b> C </b> </th> <th> <b> G </b> </th> <th> <b> T </b> </th>
    </tr>
	    <tr> <th> <b> A </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr>
	    <tr> <th> <b> C </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr>
	    <tr> <th> <b> G </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr>
	    <tr> <th> <b> T </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr>
</table>
</center>

<p>

<!--==========================================================================
	Ts/Tv
	========================================================================== -->

<hr> 
<a name="tstv">
<center> <b> Ts/Tv (transitions / transversions) </b> <p> </center>

<small>
<b>Note:</b> Only SNPs are used for this statistic.<br>
<b>Note:</b> This Ts/Tv ratio is a 'raw' ratio (ratio of observed events).
</small>
<p>

<center>
<table border=1>
	<tr> <th> Transitions </th><td class="numeric"> 0 </td> </tr>
	<tr> <th> Transversions </th><td class="numeric"> 0 </td> </tr>
	<tr> <th> Ts/Tv ratio </th><td class="numeric"> 0 </td> </tr>
</table>
</center>
<p>

	<b>All variants:</b>
	<pre>No results available (empty input?)</pre>
	<p>
	<b>Only known variants</b> (i.e. the ones having a non-empty ID field):
	<pre>No results available (empty input?)</pre>
<p>

<!--==========================================================================
	Allele frequency
	========================================================================== -->

<hr> 
<a name="alleleFreq">
<center> <b> Allele frequency </b> <p> </center>

	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Allele+Frequency+%25&chxl=1:|Count|3:|Alleles+frequency&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
<p>
	
<!--==========================================================================
	Allele Count
	========================================================================== -->

<hr> 
<a name="alleleCount">
<center> <b> Allele Count </b> <p> </center>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chtt=Allele+Count&chxp=1,50.0|3,50.0&chxl=1:|Count|3:|Allele+Count&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
<p>


<!--==========================================================================
	Hom/Het table
	========================================================================== -->

<hr> 
<a name="homHet">
<center> <b> Hom/Het per sample </b> <p> </center>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Heterozygous+genotypes&chxl=1:|Heterozygous+count|3:|Sample+number&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Homozygous+%28ALT%29+genotypes&chxl=1:|Homozygous+count|3:|Sample+number&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
	<img src="http://chart.apis.google.com/chart?chd=e:&cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Missing+genotypes&chxl=1:|Missing+count|3:|Sample+number&chxr=0,2.147483647E9,-2.147483648E9|1,0.0,100.0|3,0.0,100.0"><br>
	
	<pre>Sample_names 
Reference 
Het 
Hom 
Missing 
</pre>
<p>

<!--==========================================================================
	Codon change table
	========================================================================== -->
	
<hr> 
<a name="codonChanges">
<center>
<b> Codon changes</b> <p>

	<div class="note">
		How to read this table: <br>
		- Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.<br>
		- Red background colors indicate that more changes happened (heat-map).<br>
		- Diagonals are indicated using grey background color <br> 
		- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).<br>
		<p>
	</div><p>

  
<table border=1>
	<thead>
		<tr> 
			<th> &nbsp; </th>
			
		</tr>
	</thead>
</table>
</center>

<!--==========================================================================
	Amino acid change table
	========================================================================== -->

<hr> 
<a name="aaChanges">
<center>
<b> Amino acid changes</b><p> 

	<div class="note">
		How to read this table: <br>
		- Rows are reference amino acids and columns are changed amino acids. E.g. Row 'A' column 'E' indicates how many 'A' amino acids have been replaced by 'E' amino acids.<br>
		- Red background colors indicate that more changes happened (heat-map).<br>
		- Diagonals are indicated using grey background color <br> 
		- WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).<br>
		<p>
	</div><p>

<table border=1>
	<thead>
		<tr> 
			<th> &nbsp; </th>
			
		</tr>
	</thead>
</table>
</center>

<!--==========================================================================
	Chromosome variants table
	========================================================================== -->

<hr> 
<a name="chrChanges">
<center>
<b> Variants by chromosome</b><p> 

<center>
</center>

<!--==========================================================================
	Variants by gene 
	========================================================================== -->

<center>
	<hr>
	<b> Details by gene </b><p>
	<p>
	<b><a href="snpEff_genes.txt">Here</a></b> you can find a tab-separated table.
</center>
</div>
</center>