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"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
author iuc
date Thu, 31 Oct 2019 19:40:40 -0400
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children 82fb5e3bb93e
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<title>smallest :: BRESEQ :: Mutation Predictions</title>
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</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 0.34.0&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_11.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>
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<td align="center"><a href="evidence/MC_PLOT_8.html">MC</a>&nbsp;<a href="evidence/JC_12.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 -->

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<tr class="normal_table_row">
<td align="center"><a href="evidence/JC_13.html">JC</a></td><!-- Evidence -->
<td align="right">41,716</td><!-- Position -->
<td align="center">(T)<sub>5&rarr;9</sub></td><!-- Cell Mutation -->
<td align="center">coding&nbsp;(636/873&nbsp;nt)</td>
<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
<td align="left">NinC protein</td>
</tr>
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<td align="center"><a href="evidence/MC_PLOT_9.html">MC</a>&nbsp;<a href="evidence/JC_14.html">JC</a></td><!-- Evidence -->
<td align="right">44,075</td><!-- Position -->
<td align="center">(CAAA)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
<td align="center">coding&nbsp;(190&#8209;193/624&nbsp;nt)</td>
<td align="center"><i>Q</i>&nbsp;&rarr;</td>
<td align="left">late gene regulator</td>
</tr>
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<td align="center"><a href="evidence/SNP_5.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>
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</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_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">1</td>
<td align="right">38810</td>
<td align="right">38810</td>
<td align="center">NA&nbsp;[0]</td>
<td align="center">[10]&nbsp;13</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_10.html">*</a></td>
<td><a href="evidence/MC_SIDE_2_10.html">*</a></td>
<td><a href="evidence/MC_PLOT_10.html">&divide;</a></td>
<td>NC_001416</td>
<td align="right">48475</td>
<td align="right">48502</td>
<td align="right">28</td>
<td align="center">12&nbsp;[10]</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>
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