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planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:40:19 -0400
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<!DOCTYPE HTML>
<html>
	<head>
		<link rel="stylesheet" href="css/agogo.css" type="text/css" />
		<link rel="stylesheet" href="css/report.css" type="text/css" />
	<title>Qualimap report: BAM QC</title>

	</head>
<body>
	<div class="header-wrapper">
		<div class="header">
		<p class="logo"><a href="http://qualimap.bioinfo.cipf.es/">
		<img class="logo" src="css/qualimap_logo_small.png" alt="Logo"/>
		</a></p>
<div class="headertitle"><a href="">Qualimap Report: BAM QC</a></div>
	</div>
</div>

<div class="content-wrapper">
<div class="content">
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<div class=section>
<h2>Input data and parameters<a class="headerlink" name="input" title="Permalink to this headline">&nbsp;</a></h2>
<div class=summary>


<div class=table-summary>
<h3>QualiMap command line</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>qualimap bamqc -bam ../qualimap2/test-data/test.bam -nw 400 -hm 3</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Alignment</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Command line: </td>
<td class=column2>bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Draw chromosome limits: </td>
<td class=column2>no
</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Analyze overlapping paired-end reads:</td>
<td class=column2>no
</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Program: </td>
<td class=column2>bwamem (0.7.15-r1140)</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Analysis date: </td>
<td class=column2>Thu Jul 26 16:33:35 EDT 2018</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Size of a homopolymer: </td>
<td class=column2>3</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Skip duplicate alignments: </td>
<td class=column2>no
</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number of windows: </td>
<td class=column2>400</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>BAM file: </td>
<td class=column2>../qualimap2/test-data/test.bam</td>
</tr>
</table>
</div>

</div>
</div> <!-- summary section -->

<div class=section>
<h2>Summary<a class="headerlink" name="summary" title="Permalink to this headline">&nbsp;</a></h2>
<div class=summary>


<div class=table-summary>
<h3>Globals</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Reference size</td>
<td class=column2>3,101,976,562</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number of reads</td>
<td class=column2>61,169</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads</td>
<td class=column2>60,246 / 98.49%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Unmapped reads</td>
<td class=column2>923 / 1.51%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped paired reads</td>
<td class=column2>60,246 / 98.49%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads, first in pair</td>
<td class=column2>30,268 / 49.48%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads,  second in pair</td>
<td class=column2>29,978 / 49.01%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads, both in pair</td>
<td class=column2>59,810 / 97.78%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads, singletons</td>
<td class=column2>436 / 0.71%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Secondary alignments</td>
<td class=column2>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Supplementary alignments</td>
<td class=column2>1,169 / 1.91%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Read min/max/mean length</td>
<td class=column2>250 / 250 / 250</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Duplicated reads (flagged)</td>
<td class=column2>48 / 0.08%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Clipped reads</td>
<td class=column2>33,606 / 54.94%</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>ACGT Content</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number/percentage of A's</td>
<td class=column2>3,912,917 / 29.53%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number/percentage of C's</td>
<td class=column2>2,699,395 / 20.37%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number/percentage of T's</td>
<td class=column2>3,942,019 / 29.75%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number/percentage of G's</td>
<td class=column2>2,694,640 / 20.34%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Number/percentage of N's</td>
<td class=column2>14,397 / 0.11%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>GC Percentage</td>
<td class=column2>40.71%</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Coverage</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mean</td>
<td class=column2>0.0043</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Standard Deviation</td>
<td class=column2>0.0869</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Mapping Quality</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mean Mapping Quality</td>
<td class=column2>49.97</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Insert size</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mean</td>
<td class=column2>75,226.79</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Standard Deviation</td>
<td class=column2>2,849,315.96</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>P25/Median/P75</td>
<td class=column2>339 / 427 / 535</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Mismatches and indels</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>General error rate</td>
<td class=column2>1.49%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mismatches</td>
<td class=column2>190,508</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Insertions</td>
<td class=column2>2,279</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads with at least one insertion</td>
<td class=column2>3.3%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Deletions</td>
<td class=column2>2,316</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Mapped reads with at least one deletion</td>
<td class=column2>3.41%</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td class=column1>Homopolymer indels</td>
<td class=column2>50.79%</td>
</tr>
</table>
</div>


<div class=table-summary>
<h3>Chromosome stats</h3>
<table class="summary hovertable">
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td><b>Name</b></td>
<td><b>Length</b></td>
<td><b>Mapped bases</b></td>
<td><b>Mean coverage</b></td>
<td><b>Standard deviation</b></td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>1</td>
<td>249250621</td>
<td>1063202</td>
<td>0.0043</td>
<td>0.1147</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>2</td>
<td>243199373</td>
<td>1091086</td>
<td>0.0045</td>
<td>0.082</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>3</td>
<td>198022430</td>
<td>906302</td>
<td>0.0046</td>
<td>0.0765</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>4</td>
<td>191154276</td>
<td>899976</td>
<td>0.0047</td>
<td>0.088</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>5</td>
<td>180915260</td>
<td>759318</td>
<td>0.0042</td>
<td>0.0739</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>6</td>
<td>171115067</td>
<td>734471</td>
<td>0.0043</td>
<td>0.0752</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>7</td>
<td>159138663</td>
<td>654165</td>
<td>0.0041</td>
<td>0.0773</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>8</td>
<td>146364022</td>
<td>676934</td>
<td>0.0046</td>
<td>0.1184</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>9</td>
<td>141213431</td>
<td>525097</td>
<td>0.0037</td>
<td>0.0766</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>10</td>
<td>135534747</td>
<td>724777</td>
<td>0.0053</td>
<td>0.1311</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>11</td>
<td>135006516</td>
<td>589118</td>
<td>0.0044</td>
<td>0.082</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>12</td>
<td>133851895</td>
<td>581268</td>
<td>0.0043</td>
<td>0.0745</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>13</td>
<td>115169878</td>
<td>424915</td>
<td>0.0037</td>
<td>0.0689</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>14</td>
<td>107349540</td>
<td>385363</td>
<td>0.0036</td>
<td>0.068</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>15</td>
<td>102531392</td>
<td>361006</td>
<td>0.0035</td>
<td>0.0671</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>16</td>
<td>90354753</td>
<td>405846</td>
<td>0.0045</td>
<td>0.0833</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>17</td>
<td>81195210</td>
<td>351366</td>
<td>0.0043</td>
<td>0.0765</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>18</td>
<td>78077248</td>
<td>355035</td>
<td>0.0045</td>
<td>0.0817</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>19</td>
<td>59128983</td>
<td>263166</td>
<td>0.0045</td>
<td>0.0888</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>20</td>
<td>63025520</td>
<td>262814</td>
<td>0.0042</td>
<td>0.0805</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>21</td>
<td>48129895</td>
<td>179259</td>
<td>0.0037</td>
<td>0.0748</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>22</td>
<td>51304566</td>
<td>150578</td>
<td>0.0029</td>
<td>0.0612</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>X</td>
<td>155270560</td>
<td>669025</td>
<td>0.0043</td>
<td>0.0753</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>Y</td>
<td>59373566</td>
<td>28998</td>
<td>0.0005</td>
<td>0.049</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>MT</td>
<td>16569</td>
<td>56251</td>
<td>3.395</td>
<td>2.0903</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000207.1</td>
<td>4262</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000226.1</td>
<td>15008</td>
<td>21953</td>
<td>1.4628</td>
<td>1.7817</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000229.1</td>
<td>19913</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000231.1</td>
<td>27386</td>
<td>1169</td>
<td>0.0427</td>
<td>0.2278</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000210.1</td>
<td>27682</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000239.1</td>
<td>33824</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000235.1</td>
<td>34474</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000201.1</td>
<td>36148</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000247.1</td>
<td>36422</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000245.1</td>
<td>36651</td>
<td>481</td>
<td>0.0131</td>
<td>0.1138</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000197.1</td>
<td>37175</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000203.1</td>
<td>37498</td>
<td>459</td>
<td>0.0122</td>
<td>0.1178</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000246.1</td>
<td>38154</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000249.1</td>
<td>38502</td>
<td>483</td>
<td>0.0125</td>
<td>0.1113</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000196.1</td>
<td>38914</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000248.1</td>
<td>39786</td>
<td>456</td>
<td>0.0115</td>
<td>0.1064</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000244.1</td>
<td>39929</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000238.1</td>
<td>39939</td>
<td>410</td>
<td>0.0103</td>
<td>0.1008</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000202.1</td>
<td>40103</td>
<td>423</td>
<td>0.0105</td>
<td>0.1417</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000234.1</td>
<td>40531</td>
<td>733</td>
<td>0.0181</td>
<td>0.1675</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000232.1</td>
<td>40652</td>
<td>543</td>
<td>0.0134</td>
<td>0.1194</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000206.1</td>
<td>41001</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000240.1</td>
<td>41933</td>
<td>475</td>
<td>0.0113</td>
<td>0.1056</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000236.1</td>
<td>41934</td>
<td>924</td>
<td>0.022</td>
<td>0.1466</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000241.1</td>
<td>42152</td>
<td>930</td>
<td>0.0221</td>
<td>0.1716</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000243.1</td>
<td>43341</td>
<td>110</td>
<td>0.0025</td>
<td>0.0503</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000242.1</td>
<td>43523</td>
<td>444</td>
<td>0.0102</td>
<td>0.1005</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000230.1</td>
<td>43691</td>
<td>939</td>
<td>0.0215</td>
<td>0.1544</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000237.1</td>
<td>45867</td>
<td>852</td>
<td>0.0186</td>
<td>0.135</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000233.1</td>
<td>45941</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000204.1</td>
<td>81310</td>
<td>1345</td>
<td>0.0165</td>
<td>0.1549</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000198.1</td>
<td>90085</td>
<td>1750</td>
<td>0.0194</td>
<td>0.1441</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000208.1</td>
<td>92689</td>
<td>3998</td>
<td>0.0431</td>
<td>0.2697</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000191.1</td>
<td>106433</td>
<td>0</td>
<td>0</td>
<td>0</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000227.1</td>
<td>128374</td>
<td>476</td>
<td>0.0037</td>
<td>0.0608</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000228.1</td>
<td>129120</td>
<td>4339</td>
<td>0.0336</td>
<td>0.3105</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000214.1</td>
<td>137718</td>
<td>2220</td>
<td>0.0161</td>
<td>0.1342</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000221.1</td>
<td>155397</td>
<td>2809</td>
<td>0.0181</td>
<td>0.174</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000209.1</td>
<td>159169</td>
<td>463</td>
<td>0.0029</td>
<td>0.0574</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000218.1</td>
<td>161147</td>
<td>1369</td>
<td>0.0085</td>
<td>0.1116</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000220.1</td>
<td>161802</td>
<td>40235</td>
<td>0.2487</td>
<td>0.6522</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000213.1</td>
<td>164239</td>
<td>490</td>
<td>0.003</td>
<td>0.0545</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000211.1</td>
<td>166566</td>
<td>384</td>
<td>0.0023</td>
<td>0.0679</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000199.1</td>
<td>169874</td>
<td>21154</td>
<td>0.1245</td>
<td>0.5192</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000217.1</td>
<td>172149</td>
<td>2403</td>
<td>0.014</td>
<td>0.1307</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000216.1</td>
<td>172294</td>
<td>13420</td>
<td>0.0779</td>
<td>0.4454</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000215.1</td>
<td>172545</td>
<td>960</td>
<td>0.0056</td>
<td>0.0995</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000205.1</td>
<td>174588</td>
<td>1778</td>
<td>0.0102</td>
<td>0.1251</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000219.1</td>
<td>179198</td>
<td>1205</td>
<td>0.0067</td>
<td>0.092</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000224.1</td>
<td>179693</td>
<td>2523</td>
<td>0.014</td>
<td>0.1396</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000223.1</td>
<td>180455</td>
<td>622</td>
<td>0.0034</td>
<td>0.0586</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000195.1</td>
<td>182896</td>
<td>2173</td>
<td>0.0119</td>
<td>0.1236</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000212.1</td>
<td>186858</td>
<td>1274</td>
<td>0.0068</td>
<td>0.1243</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000222.1</td>
<td>186861</td>
<td>437</td>
<td>0.0023</td>
<td>0.0482</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000200.1</td>
<td>187035</td>
<td>370</td>
<td>0.002</td>
<td>0.0629</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000193.1</td>
<td>189789</td>
<td>3642</td>
<td>0.0192</td>
<td>0.1547</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000194.1</td>
<td>191469</td>
<td>1260</td>
<td>0.0066</td>
<td>0.0909</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000225.1</td>
<td>211173</td>
<td>10094</td>
<td>0.0478</td>
<td>0.2717</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>GL000192.1</td>
<td>547496</td>
<td>3452</td>
<td>0.0063</td>
<td>0.0849</td>
</tr>
<tr onmouseover="this.style.backgroundColor='#EEEEEC';" onmouseout="this.style.backgroundColor='#FFFFFF';">
<td>NC_007605</td>
<td>171823</td>
<td>12864</td>
<td>0.0749</td>
<td>0.298</td>
</tr>
</table>
</div>

</div>
</div> <!-- summary section -->



<div class=section>

<h2>Coverage across reference<a class="headerlink" name="genome_coverage_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_coverage_across_reference.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Coverage Histogram<a class="headerlink" name="genome_coverage_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_coverage_histogram.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Coverage Histogram (0-50X)<a class="headerlink" name="genome_coverage_0to50_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_coverage_0to50_histogram.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Genome Fraction Coverage<a class="headerlink" name="genome_coverage_quotes.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_coverage_quotes.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Duplication Rate Histogram<a class="headerlink" name="genome_uniq_read_starts_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_uniq_read_starts_histogram.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Mapped Reads Nucleotide Content<a class="headerlink" name="genome_reads_content_per_read_position.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_reads_content_per_read_position.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Mapped Reads GC-content Distribution<a class="headerlink" name="genome_gc_content_per_window.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_gc_content_per_window.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Mapped Reads Clipping Profile<a class="headerlink" name="genome_reads_clipping_profile.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_reads_clipping_profile.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Homopolymer Indels<a class="headerlink" name="genome_homopolymer_indels" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_homopolymer_indels.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Mapping Quality Across Reference<a class="headerlink" name="genome_mapping_quality_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_mapping_quality_across_reference.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Mapping Quality Histogram<a class="headerlink" name="genome_mapping_quality_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_mapping_quality_histogram.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Insert Size Across Reference<a class="headerlink" name="genome_insert_size_across_reference.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_insert_size_across_reference.png"></div>

</div><!-- graph section -->


<div class=section>

<h2>Insert Size Histogram<a class="headerlink" name="genome_insert_size_histogram.png" title="Permalink to this headline">&nbsp;</a></h2>

<div><img width=100% src="images_qualimapReport/genome_insert_size_histogram.png"></div>

</div><!-- graph section -->


</div>

</div>

</div>

</div>


<div class="sidebar">
<h3>Contents</h3>
<li class="toctree-l1"><a class="reference internal" href="#input">Input data & parameters</a></li>
<li class="toctree-l1"><a class="reference internal" href="#summary">Summary</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_across_reference.png">Coverage across reference</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_histogram.png">Coverage Histogram</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_0to50_histogram.png">Coverage Histogram (0-50X)</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_coverage_quotes.png">Genome Fraction Coverage</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_uniq_read_starts_histogram.png">Duplication Rate Histogram</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_reads_content_per_read_position.png">Mapped Reads Nucleotide Content</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_gc_content_per_window.png">Mapped Reads GC-content Distribution</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_reads_clipping_profile.png">Mapped Reads Clipping Profile</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_homopolymer_indels">Homopolymer Indels</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_across_reference.png">Mapping Quality Across Reference</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_mapping_quality_histogram.png">Mapping Quality Histogram</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_across_reference.png">Insert Size Across Reference</a></li>
<li class="toctree-l1"><a class="reference internal" href="#genome_insert_size_histogram.png">Insert Size Histogram</a></li>
</div> <!-- sidebar -->

<div class="clearer"></div>
</div>

</div>


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<div class="footer">
2018/07/26 16:33:36
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Generated by QualiMap v.2.2.2-dev
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