Mercurial > repos > iuc > breseq

view test-data/report.html @ 3:0d18a3ba2d1c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
author iuc
date Mon, 04 Apr 2022 08:30:52 +0000
parents 82fb5e3bb93e
children
line wrap: on
line source

<!DOCTYPE html
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<html>
<head>
<title>smallest :: BRESEQ :: Mutation Predictions</title>
<style type = "text/css">
body {font-family: sans-serif; font-size: 11pt;}
th {background-color: rgb(0,0,0); color: rgb(255,255,255);}
table {background-color: rgb(1,0,0); color: rgb(0,0,0);}
tr {background-color: rgb(255,255,255);}
.mutation_in_codon {color:red; text-decoration : underline;}
.snp_type_synonymous{color:green;}
.snp_type_nonsynonymous{color:blue;}
.snp_type_nonsense{color:red;}
.mutation_header_row {background-color: rgb(0,130,0);}
.read_alignment_header_row {background-color: rgb(255,0,0);}
.missing_coverage_header_row {background-color: rgb(0,100,100);}
.new_junction_header_row {background-color: rgb(0,0,155);}
.copy_number_header_row {background-color: rgb(153,102,0);}
.alternate_table_row_0 {background-color: rgb(255,255,255);}
.alternate_table_row_1 {background-color: rgb(235,235,235);}
.gray_table_row {background-color: rgb(230,230,245);}
.polymorphism_table_row {background-color: rgb(160,255,160);}
.highlight_table_row {background-color: rgb(192,255,255);}
.reject_table_row {background-color: rgb(255,200,165);}
.user_defined_table_row {background-color: rgb(255,255,0);}
.information_table_row {background-color: rgb(200,255,255);}
.junction_repeat {background-color: rgb(255,165,0)}
.junction_gene {}
.hidden { display: none; }
.unhidden { display: block; }

</style>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<script type="text/javascript">
  function hideTog(divID) {
    var item = document.getElementById(divID);
    if (item) {
      item.className=(item.className=='hidden')?'unhidden':'hidden';
    }
  }
  function showTog(butID) {
    var button = document.getElementById(butID);
    if (button) {
      button.value=(button.value=='Show')?'Hide':'Show';
    }
  }
</script>

</head>
<body>
<table width="100%" border="0" cellspacing="0" cellpadding="3">
<tr>
<td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td>
<td width="100%">
<b><i>breseq</i></b>&nbsp;&nbsp;version 0.35.5&nbsp;&nbsp;
<br><a href="index.html">mutation predictions</a> | 
<a href="marginal.html">marginal predictions</a> | 
<a href="summary.html">summary statistics</a> | 
<a href="output.gd">genome diff</a> | 
<a href="log.txt">command line log</a>
</td></tr></table>

<p>
<!--Mutation Predictions -->
<p>
<!--Output Html_Mutation_Table_String-->
<table border="0" cellspacing="1" cellpadding="3">
<tr><th colspan="6" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr>
<th>evidence</th>
<th>position</th>
<th>mutation</th>
<th>annotation</th>
<th>gene</th>
<th width="100%">description</th>
</tr>

<!-- Item Lines -->

<!-- Print The Table Row -->
<tr class="normal_table_row">
<td align="center"><a href="evidence/JC_9.html">JC</a></td><!-- Evidence -->
<td align="right">41,405</td><!-- Position -->
<td align="center">(GCG)<sub>2&rarr;5</sub></td><!-- Cell Mutation -->
<td align="center">coding&nbsp;(325/873&nbsp;nt)</td>
<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
<td align="left">NinC protein</td>
</tr>
<!-- End Table Row -->

<!-- Print The Table Row -->
<tr class="normal_table_row">
<td align="center"><a href="evidence/MC_PLOT_6.html">MC</a>&nbsp;<a href="evidence/JC_10.html">JC</a></td><!-- Evidence -->
<td align="right">41,601</td><!-- Position -->
<td align="center">(AAC)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
<td align="center">coding&nbsp;(521&#8209;523/873&nbsp;nt)</td>
<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
<td align="left">NinC protein</td>
</tr>
<!-- End Table Row -->

<!-- Print The Table Row -->
<tr class="normal_table_row">
<td align="center"><a href="evidence/SNP_3.html">RA</a></td><!-- Evidence -->
<td align="right">47,317</td><!-- Position -->
<td align="center">N&rarr;T</td><!-- Cell Mutation -->
<td align="center"><span style="white-space: nowrap"><font class="snp_type_nonsynonymous">?87I</font>&nbsp;(<font class="mutation_in_codon">N</font>TC&rarr;<font class="mutation_in_codon">A</font>TC)&nbsp;</span></td>
<td align="center"><i>lambdap78</i>&nbsp;&larr;</td>
<td align="left">putative envelope protein</td>
</tr>
<!-- End Table Row -->
</table>
<p>
<table border="0" cellspacing="1" cellpadding="3" width="100%">
<tr><th colspan="11" align="left" class="missing_coverage_header_row">Unassigned missing coverage evidence</th></tr>
<tr><th>&nbsp;</th><th>&nbsp;</th><th>&nbsp;</th><th>seq&nbsp;id</th>
<th>start</th>
<th>end</th>
<th>size</th>
<th>&larr;reads</th>
<th>reads&rarr;</th>
<th>gene</th>
<th width="100%">description</th>
</tr>
<tr>
<td><a href="evidence/MC_SIDE_1_5.html">*</a></td>
<td><a href="evidence/MC_SIDE_2_5.html">*</a></td>
<td><a href="evidence/MC_PLOT_5.html">&divide;</a></td>
<td>NC_001416</td>
<td align="right">1</td>
<td align="right">38811</td>
<td align="right">38811</td>
<td align="center">NA&nbsp;[0]</td>
<td align="center">[1]&nbsp;2</td>
<td align="center"><i>nu1&#8211;[O]</i></td>
<td align="left">nu1,A,W,B,C,nu3,D,E,Fi,Fii,Z,U,V,G,T,H,M,L,K,I,J,lom,orf&#8209;401,orf206b,orf&#8209;314,orf&#8209;194,ea47,ea31,ea59,int,xis,lambdap35,ea8.5,ea22,orf61,orf63,orf60a,exo,bet,gam,kil,cIII,ea10,ral,orf28,lambdap48,N,rexb,rexa,cI,cro,cII,[O]</td>
</tr>
<tr>
<td><a href="evidence/MC_SIDE_1_7.html">*</a></td>
<td><a href="evidence/MC_SIDE_2_7.html">*</a></td>
<td><a href="evidence/MC_PLOT_7.html">&divide;</a></td>
<td>NC_001416</td>
<td align="right">48305</td>
<td align="right">48312</td>
<td align="right">8</td>
<td align="center">2&nbsp;[1]</td>
<td align="center">[1]&nbsp;2</td>
<td align="center"><i>lambdap79/&#8211;</i></td>
<td align="left">hypothetical protein/&#8211;</td>
</tr>
<tr>
<td><a href="evidence/MC_SIDE_1_8.html">*</a></td>
<td><a href="evidence/MC_SIDE_2_8.html">*</a></td>
<td><a href="evidence/MC_PLOT_8.html">&divide;</a></td>
<td>NC_001416</td>
<td align="right">48485</td>
<td align="right">48502</td>
<td align="right">18</td>
<td align="center">2&nbsp;[1]</td>
<td align="center">[0]&nbsp;NA</td>
<td align="center"><i>lambdap79/&#8211;</i></td>
<td align="left">hypothetical protein/&#8211;</td>
</tr>
</table>
</body></html>