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annotate test-data/report.html @ 0:f848a7f97332 draft

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"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
author iuc
date Thu, 31 Oct 2019 19:40:40 -0400
parents
children 82fb5e3bb93e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <!DOCTYPE html
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2 PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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3 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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4 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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5 <html>
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6 <head>
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7 <title>smallest :: BRESEQ :: Mutation Predictions</title>
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8 <style type = "text/css">
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9 body {font-family: sans-serif; font-size: 11pt;}
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10 th {background-color: rgb(0,0,0); color: rgb(255,255,255);}
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11 table {background-color: rgb(1,0,0); color: rgb(0,0,0);}
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12 tr {background-color: rgb(255,255,255);}
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13 .mutation_in_codon {color:red; text-decoration : underline;}
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14 .snp_type_synonymous{color:green;}
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15 .snp_type_nonsynonymous{color:blue;}
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16 .snp_type_nonsense{color:red;}
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17 .mutation_header_row {background-color: rgb(0,130,0);}
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18 .read_alignment_header_row {background-color: rgb(255,0,0);}
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19 .missing_coverage_header_row {background-color: rgb(0,100,100);}
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20 .new_junction_header_row {background-color: rgb(0,0,155);}
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21 .copy_number_header_row {background-color: rgb(153,102,0);}
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22 .alternate_table_row_0 {background-color: rgb(255,255,255);}
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23 .alternate_table_row_1 {background-color: rgb(235,235,235);}
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24 .gray_table_row {background-color: rgb(230,230,245);}
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25 .polymorphism_table_row {background-color: rgb(160,255,160);}
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26 .highlight_table_row {background-color: rgb(192,255,255);}
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27 .reject_table_row {background-color: rgb(255,200,165);}
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28 .user_defined_table_row {background-color: rgb(255,255,0);}
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29 .information_table_row {background-color: rgb(200,255,255);}
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30 .junction_repeat {background-color: rgb(255,165,0)}
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31 .junction_gene {}
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32 .hidden { display: none; }
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33 .unhidden { display: block; }
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34
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35 </style>
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36 <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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37 <script type="text/javascript">
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38 function hideTog(divID) {
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39 var item = document.getElementById(divID);
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40 if (item) {
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41 item.className=(item.className=='hidden')?'unhidden':'hidden';
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42 }
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43 }
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44 function showTog(butID) {
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45 var button = document.getElementById(butID);
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46 if (button) {
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47 button.value=(button.value=='Show')?'Hide':'Show';
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48 }
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49 }
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50 </script>
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51
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52 </head>
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53 <body>
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54 <table width="100%" border="0" cellspacing="0" cellpadding="3">
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55 <tr>
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56 <td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td>
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57 <td width="100%">
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58 <b><i>breseq</i></b>&nbsp;&nbsp;version 0.34.0&nbsp;&nbsp;
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59 <br><a href="index.html">mutation predictions</a> |
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60 <a href="marginal.html">marginal predictions</a> |
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61 <a href="summary.html">summary statistics</a> |
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62 <a href="output.gd">genome diff</a> |
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63 <a href="log.txt">command line log</a>
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64 </td></tr></table>
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65
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66 <p>
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67 <!--Mutation Predictions -->
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68 <p>
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69 <!--Output Html_Mutation_Table_String-->
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70 <table border="0" cellspacing="1" cellpadding="3">
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71 <tr><th colspan="6" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr>
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72 <th>evidence</th>
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73 <th>position</th>
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74 <th>mutation</th>
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75 <th>annotation</th>
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76 <th>gene</th>
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77 <th width="100%">description</th>
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78 </tr>
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79
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80 <!-- Item Lines -->
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81
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82 <!-- Print The Table Row -->
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83 <tr class="normal_table_row">
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84 <td align="center"><a href="evidence/JC_11.html">JC</a></td><!-- Evidence -->
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85 <td align="right">41,405</td><!-- Position -->
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86 <td align="center">(GCG)<sub>2&rarr;5</sub></td><!-- Cell Mutation -->
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87 <td align="center">coding&nbsp;(325/873&nbsp;nt)</td>
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88 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
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89 <td align="left">NinC protein</td>
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90 </tr>
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91 <!-- End Table Row -->
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92
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93 <!-- Print The Table Row -->
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94 <tr class="normal_table_row">
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95 <td align="center"><a href="evidence/MC_PLOT_8.html">MC</a>&nbsp;<a href="evidence/JC_12.html">JC</a></td><!-- Evidence -->
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96 <td align="right">41,601</td><!-- Position -->
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97 <td align="center">(AAC)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
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98 <td align="center">coding&nbsp;(521&#8209;523/873&nbsp;nt)</td>
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99 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
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100 <td align="left">NinC protein</td>
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101 </tr>
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102 <!-- End Table Row -->
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103
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104 <!-- Print The Table Row -->
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105 <tr class="normal_table_row">
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106 <td align="center"><a href="evidence/JC_13.html">JC</a></td><!-- Evidence -->
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107 <td align="right">41,716</td><!-- Position -->
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108 <td align="center">(T)<sub>5&rarr;9</sub></td><!-- Cell Mutation -->
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109 <td align="center">coding&nbsp;(636/873&nbsp;nt)</td>
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110 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
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111 <td align="left">NinC protein</td>
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112 </tr>
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113 <!-- End Table Row -->
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114
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115 <!-- Print The Table Row -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
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parents:
diff changeset
116 <tr class="normal_table_row">
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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117 <td align="center"><a href="evidence/MC_PLOT_9.html">MC</a>&nbsp;<a href="evidence/JC_14.html">JC</a></td><!-- Evidence -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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118 <td align="right">44,075</td><!-- Position -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
119 <td align="center">(CAAA)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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120 <td align="center">coding&nbsp;(190&#8209;193/624&nbsp;nt)</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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121 <td align="center"><i>Q</i>&nbsp;&rarr;</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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122 <td align="left">late gene regulator</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
123 </tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
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parents:
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124 <!-- End Table Row -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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125
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
126 <!-- Print The Table Row -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
127 <tr class="normal_table_row">
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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128 <td align="center"><a href="evidence/SNP_5.html">RA</a></td><!-- Evidence -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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129 <td align="right">47,317</td><!-- Position -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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130 <td align="center">N&rarr;T</td><!-- Cell Mutation -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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131 <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>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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132 <td align="center"><i>lambdap78</i>&nbsp;&larr;</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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133 <td align="left">putative envelope protein</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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134 </tr>
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parents:
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135 <!-- End Table Row -->
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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136 </table>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
137 <p>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
138 <table border="0" cellspacing="1" cellpadding="3" width="100%">
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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139 <tr><th colspan="11" align="left" class="missing_coverage_header_row">Unassigned missing coverage evidence</th></tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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140 <tr><th>&nbsp;</th><th>&nbsp;</th><th>&nbsp;</th><th>seq&nbsp;id</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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141 <th>start</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
142 <th>end</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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143 <th>size</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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144 <th>&larr;reads</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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145 <th>reads&rarr;</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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146 <th>gene</th>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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147 <th width="100%">description</th>
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iuc
parents:
diff changeset
148 </tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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149 <tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
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parents:
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150 <td><a href="evidence/MC_SIDE_1_7.html">*</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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151 <td><a href="evidence/MC_SIDE_2_7.html">*</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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152 <td><a href="evidence/MC_PLOT_7.html">&divide;</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
153 <td>NC_001416</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
154 <td align="right">1</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
155 <td align="right">38810</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
156 <td align="right">38810</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
157 <td align="center">NA&nbsp;[0]</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
158 <td align="center">[10]&nbsp;13</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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159 <td align="center"><i>nu1&#8211;[O]</i></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
160 <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>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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161 </tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
162 <tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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163 <td><a href="evidence/MC_SIDE_1_10.html">*</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
164 <td><a href="evidence/MC_SIDE_2_10.html">*</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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165 <td><a href="evidence/MC_PLOT_10.html">&divide;</a></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
166 <td>NC_001416</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
167 <td align="right">48475</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
168 <td align="right">48502</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
169 <td align="right">28</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
170 <td align="center">12&nbsp;[10]</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
171 <td align="center">[0]&nbsp;NA</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
172 <td align="center"><i>lambdap79/&#8211;</i></td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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173 <td align="left">hypothetical protein/&#8211;</td>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
diff changeset
174 </tr>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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175 </table>
f848a7f97332 "planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
iuc
parents:
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176 </body></html>