Mercurial > repos > iuc > breseq

comparison test-data/report.html @ 0:a7735dbd58ee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
author iuc
date Thu, 31 Oct 2019 19:40:15 -0400
parents
children d515d94db821
comparison
equal deleted inserted replaced
-1:000000000000 0:a7735dbd58ee
1 <!DOCTYPE html
2 PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
3 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
4 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
5 <html>
6 <head>
7 <title>smallest :: BRESEQ :: Mutation Predictions</title>
8 <style type = "text/css">
9 body {font-family: sans-serif; font-size: 11pt;}
10 th {background-color: rgb(0,0,0); color: rgb(255,255,255);}
11 table {background-color: rgb(1,0,0); color: rgb(0,0,0);}
12 tr {background-color: rgb(255,255,255);}
13 .mutation_in_codon {color:red; text-decoration : underline;}
14 .snp_type_synonymous{color:green;}
15 .snp_type_nonsynonymous{color:blue;}
16 .snp_type_nonsense{color:red;}
17 .mutation_header_row {background-color: rgb(0,130,0);}
18 .read_alignment_header_row {background-color: rgb(255,0,0);}
19 .missing_coverage_header_row {background-color: rgb(0,100,100);}
20 .new_junction_header_row {background-color: rgb(0,0,155);}
21 .copy_number_header_row {background-color: rgb(153,102,0);}
22 .alternate_table_row_0 {background-color: rgb(255,255,255);}
23 .alternate_table_row_1 {background-color: rgb(235,235,235);}
24 .gray_table_row {background-color: rgb(230,230,245);}
25 .polymorphism_table_row {background-color: rgb(160,255,160);}
26 .highlight_table_row {background-color: rgb(192,255,255);}
27 .reject_table_row {background-color: rgb(255,200,165);}
28 .user_defined_table_row {background-color: rgb(255,255,0);}
29 .information_table_row {background-color: rgb(200,255,255);}
30 .junction_repeat {background-color: rgb(255,165,0)}
31 .junction_gene {}
32 .hidden { display: none; }
33 .unhidden { display: block; }
34
35 </style>
36 <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
37 <script type="text/javascript">
38 function hideTog(divID) {
39 var item = document.getElementById(divID);
40 if (item) {
41 item.className=(item.className=='hidden')?'unhidden':'hidden';
42 }
43 }
44 function showTog(butID) {
45 var button = document.getElementById(butID);
46 if (button) {
47 button.value=(button.value=='Show')?'Hide':'Show';
48 }
49 }
50 </script>
51
52 </head>
53 <body>
54 <table width="100%" border="0" cellspacing="0" cellpadding="3">
55 <tr>
56 <td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td>
57 <td width="100%">
58 <b><i>breseq</i></b>&nbsp;&nbsp;version 0.34.0&nbsp;&nbsp;
59 <br><a href="index.html">mutation predictions</a> |
60 <a href="marginal.html">marginal predictions</a> |
61 <a href="summary.html">summary statistics</a> |
62 <a href="output.gd">genome diff</a> |
63 <a href="log.txt">command line log</a>
64 </td></tr></table>
65
66 <p>
67 <!--Mutation Predictions -->
68 <p>
69 <!--Output Html_Mutation_Table_String-->
70 <table border="0" cellspacing="1" cellpadding="3">
71 <tr><th colspan="6" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr>
72 <th>evidence</th>
73 <th>position</th>
74 <th>mutation</th>
75 <th>annotation</th>
76 <th>gene</th>
77 <th width="100%">description</th>
78 </tr>
79
80 <!-- Item Lines -->
81
82 <!-- Print The Table Row -->
83 <tr class="normal_table_row">
84 <td align="center"><a href="evidence/JC_11.html">JC</a></td><!-- Evidence -->
85 <td align="right">41,405</td><!-- Position -->
86 <td align="center">(GCG)<sub>2&rarr;5</sub></td><!-- Cell Mutation -->
87 <td align="center">coding&nbsp;(325/873&nbsp;nt)</td>
88 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
89 <td align="left">NinC protein</td>
90 </tr>
91 <!-- End Table Row -->
92
93 <!-- Print The Table Row -->
94 <tr class="normal_table_row">
95 <td align="center"><a href="evidence/MC_PLOT_8.html">MC</a>&nbsp;<a href="evidence/JC_12.html">JC</a></td><!-- Evidence -->
96 <td align="right">41,601</td><!-- Position -->
97 <td align="center">(AAC)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
98 <td align="center">coding&nbsp;(521&#8209;523/873&nbsp;nt)</td>
99 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
100 <td align="left">NinC protein</td>
101 </tr>
102 <!-- End Table Row -->
103
104 <!-- Print The Table Row -->
105 <tr class="normal_table_row">
106 <td align="center"><a href="evidence/JC_13.html">JC</a></td><!-- Evidence -->
107 <td align="right">41,716</td><!-- Position -->
108 <td align="center">(T)<sub>5&rarr;9</sub></td><!-- Cell Mutation -->
109 <td align="center">coding&nbsp;(636/873&nbsp;nt)</td>
110 <td align="center"><i>NinC</i>&nbsp;&rarr;</td>
111 <td align="left">NinC protein</td>
112 </tr>
113 <!-- End Table Row -->
114
115 <!-- Print The Table Row -->
116 <tr class="normal_table_row">
117 <td align="center"><a href="evidence/MC_PLOT_9.html">MC</a>&nbsp;<a href="evidence/JC_14.html">JC</a></td><!-- Evidence -->
118 <td align="right">44,075</td><!-- Position -->
119 <td align="center">(CAAA)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
120 <td align="center">coding&nbsp;(190&#8209;193/624&nbsp;nt)</td>
121 <td align="center"><i>Q</i>&nbsp;&rarr;</td>
122 <td align="left">late gene regulator</td>
123 </tr>
124 <!-- End Table Row -->
125
126 <!-- Print The Table Row -->
127 <tr class="normal_table_row">
128 <td align="center"><a href="evidence/SNP_5.html">RA</a></td><!-- Evidence -->
129 <td align="right">47,317</td><!-- Position -->
130 <td align="center">N&rarr;T</td><!-- Cell Mutation -->
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>
132 <td align="center"><i>lambdap78</i>&nbsp;&larr;</td>
133 <td align="left">putative envelope protein</td>
134 </tr>
135 <!-- End Table Row -->
136 </table>
137 <p>
138 <table border="0" cellspacing="1" cellpadding="3" width="100%">
139 <tr><th colspan="11" align="left" class="missing_coverage_header_row">Unassigned missing coverage evidence</th></tr>
140 <tr><th>&nbsp;</th><th>&nbsp;</th><th>&nbsp;</th><th>seq&nbsp;id</th>
141 <th>start</th>
142 <th>end</th>
143 <th>size</th>
144 <th>&larr;reads</th>
145 <th>reads&rarr;</th>
146 <th>gene</th>
147 <th width="100%">description</th>
148 </tr>
149 <tr>
150 <td><a href="evidence/MC_SIDE_1_7.html">*</a></td>
151 <td><a href="evidence/MC_SIDE_2_7.html">*</a></td>
152 <td><a href="evidence/MC_PLOT_7.html">&divide;</a></td>
153 <td>NC_001416</td>
154 <td align="right">1</td>
155 <td align="right">38810</td>
156 <td align="right">38810</td>
157 <td align="center">NA&nbsp;[0]</td>
158 <td align="center">[10]&nbsp;13</td>
159 <td align="center"><i>nu1&#8211;[O]</i></td>
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>
161 </tr>
162 <tr>
163 <td><a href="evidence/MC_SIDE_1_10.html">*</a></td>
164 <td><a href="evidence/MC_SIDE_2_10.html">*</a></td>
165 <td><a href="evidence/MC_PLOT_10.html">&divide;</a></td>
166 <td>NC_001416</td>
167 <td align="right">48475</td>
168 <td align="right">48502</td>
169 <td align="right">28</td>
170 <td align="center">12&nbsp;[10]</td>
171 <td align="center">[0]&nbsp;NA</td>
172 <td align="center"><i>lambdap79/&#8211;</i></td>
173 <td align="left">hypothetical protein/&#8211;</td>
174 </tr>
175 </table>
176 </body></html>