Mercurial > repos > cpt > cpt_phageqc_annotations
diff cpt_phageqc_annotation/test-data/PhageQC_Out.html @ 0:c3140b08d703 draft default tip
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| author | cpt |
|---|---|
| date | Fri, 17 Jun 2022 13:00:50 +0000 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_phageqc_annotation/test-data/PhageQC_Out.html Fri Jun 17 13:00:50 2022 +0000 @@ -0,0 +1,1142 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> + <meta http-equiv="X-UA-Compatible" content="IE=edge"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <!-- The above 3 meta tags *must* come first in the head; any other head content must come *after* these tags --> + <meta name="description" content=""> + <meta name="author" content=""> + <title>Phage QC on AY216660.2 - 76</title> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap-theme.min.css"> + + <style type="text/css"> +/* + * Base structure + */ + +/* Move down content because we have a fixed navbar that is 50px tall */ +body { + padding-top: 50px; +} + +h3:before { + display: block; + content: " "; + margin-top: -50px; + height: 50px; + visibility: hidden; +} + +/* + * Global add-ons + */ + +.sub-header { + padding-bottom: 10px; + border-bottom: 1px solid #eee; +} + +/* + * Top navigation + * Hide default border to remove 1px line. + */ +.navbar-fixed-top { + border: 0; +} + +/* + * Sidebar + */ + +/* Hide for mobile, show later */ +.sidebar { + display: none; +} +@media (min-width: 768px) { + .sidebar { + position: fixed; + top: 51px; + bottom: 0; + left: 0; + z-index: 1000; + display: block; + padding: 20px; + overflow-x: hidden; + overflow-y: auto; /* Scrollable contents if viewport is shorter than content. */ + background-color: #f5f5f5; + border-right: 1px solid #eee; + } +} + +/* Sidebar navigation */ +.nav-sidebar { + margin-right: -21px; /* 20px padding + 1px border */ + margin-bottom: 20px; + margin-left: -20px; +} +.nav-sidebar > li > a { + padding-right: 20px; + padding-left: 20px; +} +.nav-sidebar > .active > a, +.nav-sidebar > .active > a:hover, +.nav-sidebar > .active > a:focus { + color: #fff; + background-color: #428bca; +} + + +/* + * Main content + */ + +.main { + padding: 20px; +} +@media (min-width: 768px) { + .main { + padding-right: 40px; + padding-left: 40px; + } +} +.main .page-header { + margin-top: 0; +} + + +/* + * Placeholder dashboard ideas + */ + +.placeholders { + margin-bottom: 30px; + text-align: center; +} +.placeholders h4 { + margin-bottom: 0; +} +.placeholder { + margin-bottom: 20px; +} +.placeholder img { + display: inline-block; + border-radius: 50%; +} + +td.moron { + font-size: 150%; + padding: 0px; + color: gray; +} +.strand_emph { + text-decoration: underline; + color: black; +} + + </style> + <!-- HTML5 shim and Respond.js for IE8 support of HTML5 elements and media queries --> + <!--[if lt IE 9]> + <script src="//oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script> + <script src="//oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> + <![endif]--> + </head> + <body> + + <nav class="navbar navbar-inverse navbar-fixed-top"> + <div class="container-fluid"> + <div class="navbar-header"> + <a class="navbar-brand" href="#">Phage QC on AY216660.2</a> + </div> + </div> + </nav> + + <div class="container-fluid"> + <div class="row"> + <div class="col-sm-3 col-md-2 sidebar"> + <ul class="nav nav-sidebar"> + <li><a href="#main"><b>Overview</b></a></li> + <li><a href="#bad_gene_starts"><b>Bad Gene Starts</b></a></li> + <li><a href="#missing_rbs"><small>Missing RBS</small></a></li> + <li><a href="#weird_starts"><small>Unusual Start Codons</small></a></li> + <li><a href="#excessive_gaps"><small>Excessive Gaps</small></a></li> + <li><a href="#excessive_overlap"><small>Excessive Overlaps</small></a></li> + <!--<li><a href="#coding_density"><small>Coding Density</small></a></li>--> + <li><a href="#antisense"><b>Antisense Genes</b></a></li> + <li><a href="#morons"><small>Possible Morons</small></a></li> + <li><a href="#annotations"><b>Annotation Issues</b></a></li> + <li><a href="#missing_product"><small>Missing Product Tags</small></a></li> + </ul> + </div> + <div class="col-sm-9 col-sm-offset-3 col-md-10 col-md-offset-2 main" id="main"> + <div class="jumbotron"> + <div class="row"> + <div class="col-sm-7"> + <h1>Phage AY216660.2</h1> + <!--<h2>Score: 76/100</h2>--> + </div> + <!--<div class="col-sm-5"> + <table class="table table-striped"> + <thead> + <tr> + <th>Section</th> + <th>Score</th> + </tr> + </thead> + <tbody> + <tr><td>Missing RBS</td><td>0%</td></tr> + <tr><td>Excessive Gaps</td><td>76%</td></tr> + <tr><td>Excessive Overlap</td><td>76%</td></tr> + <tr><td>Coding Density Score</td><td>99%</td></tr> + <tr><td>Possible Morons</td><td>98%</td></tr> + <tr><td>Missing Product Tags</td><td>100%</td></tr> + </tbody> + </table> + </div>--> + </div> + </div> + + <h2 class="sub-header" id="bad_gene_starts">Gene Starts</h2> + <h3 id="missing_rbs">Genes missing RBS <small>0 / 79</small></h3> + <p>The following genes have issues with their RBS.</p> + <p> + Since you have not annotated any possible RBSs, this does not count off from your overall score. + </p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature Type</th> + <th>ID</th> + <th>Location</th> + <th>Error</th> + <th>Upstream (-15 .. -5)</th> + </tr> + </thead> + <tbody> + <tr> + <td>gene</td> + <td>CPT-T1_001.gene</td> + <td>40..576 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">taaatgttaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_002.gene</td> + <td>589..2184 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">taacttt AGG </span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_003.gene</td> + <td>2230..3522 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">acggcccttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_004.gene</td> + <td>3496..4273 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">cc GGAG ccgg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_005.gene</td> + <td>4264..5388 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tccagacttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_006.gene</td> + <td>5389..5876 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">agcaaagtaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_007.gene</td> + <td>5926..6705 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tagtcctttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_008.gene</td> + <td>6784..7755 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ttttttatta</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_009.gene</td> + <td>7794..8093 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gtcccttttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_010.gene</td> + <td>8127..8548 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">agcgcctttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_011.gene</td> + <td>8534..8919 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">atgac AGGA c</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_012.gene</td> + <td>8897..9355 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">atcgtccagt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_013.gene</td> + <td>9332..9743 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gcaatcaagc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_014.gene</td> + <td>9733..10414 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">tac GAG taga</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_015.gene</td> + <td>10516..10845 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgctatcaac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_016.gene</td> + <td>10516..11162 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgctatcaac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_017.gene</td> + <td>11192..14076 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gttttttcgt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_018.gene</td> + <td>14067..14432 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">cattc AGGA a</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_019.gene</td> + <td>14500..15294 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">gttgc AGGT a</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_020.gene</td> + <td>15279..16025 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgtcgcttca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_021.gene</td> + <td>16009..16621 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">taatcgttcg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_022.gene</td> + <td>16688..20217 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ataaatagca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_023.gene</td> + <td>20251..20568 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">atgccctttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_024.gene</td> + <td>20556..21257 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cttaatagca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_025.gene</td> + <td>21279..21518 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">aatcacacta</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_026.gene</td> + <td>21755..21906 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgtatatcgt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_027.gene</td> + <td>22020..23098 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">attcatcgta</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_028.gene</td> + <td>23129..23820 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">aaacaaataa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_029.gene</td> + <td>23854..24289 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcgcccataa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_030.gene</td> + <td>24351..26550 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cgtgctattt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_031.gene</td> + <td>26447..26600 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgcccattgc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_032.gene</td> + <td>26638..27585 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cgcgtttttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_033.gene</td> + <td>27635..28098 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gcaaaaagtg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_034.gene</td> + <td>28168..30199 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gttacaacga</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_035.gene</td> + <td>30181..30612 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">caaagacttc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_036.gene</td> + <td>30669..31393 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">atctcaccaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_037.gene</td> + <td>31377..31641 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">aaaacaaacg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_038.gene</td> + <td>31695..31917 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcatagaaac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_039.gene</td> + <td>31881..32167 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cttcatctct</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_040.gene</td> + <td>32099..32399 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace"> GAG ttttacc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_041.gene</td> + <td>32467..33611 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tttcattatc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_042.gene</td> + <td>33673..34166 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ttttatagaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_043.gene</td> + <td>34226..34415 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">accacatcga</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_044.gene</td> + <td>34525..34749 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gttcaaaaaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_045.gene</td> + <td>34739..35237 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace"> AGG cgcttaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_046.gene</td> + <td>35227..35638 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">acgcatattg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_047.gene</td> + <td>35761..36179 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">caatcctcga</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_048.gene</td> + <td>36173..37755 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcacgccgtc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_049.gene</td> + <td>37741..38294 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gacggcacaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_050.gene</td> + <td>38277..38706 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcaagataac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_051.gene</td> + <td>38774..38994 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tttacattaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_052.gene</td> + <td>38987..39222 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">taccaaacaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_053.gene</td> + <td>39289..39444 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ggcatatcaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_054.gene</td> + <td>39429..39758 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tatcctgact</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_055.gene</td> + <td>39766..39978 [-1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">tagc GGA tcg</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_056.gene</td> + <td>39959..40342 [-1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">acatcaacag</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_057.gene</td> + <td>41020..41606 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tgtatattga</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_058.gene</td> + <td>41606..41945 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">aaaatgt GGA </span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_059.gene</td> + <td>42013..42254 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">ac GAG atacc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_060.gene</td> + <td>42247..42487 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcagcacttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_061.gene</td> + <td>42473..42594 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ggcgacaaca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_062.gene</td> + <td>42580..42764 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ttgctactgt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_063.gene</td> + <td>42824..43324 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ccatcgacaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_064.gene</td> + <td>43385..43881 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">acatcaacca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_065.gene</td> + <td>43870..44030 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">actcttgtcc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_066.gene</td> + <td>44098..44485 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gcacgacaac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_067.gene</td> + <td>44527..44649 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gttccccttt</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_068.gene</td> + <td>44625..44852 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gacattatct</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_069.gene</td> + <td>44898..45356 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cctacaccaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_070.gene</td> + <td>45428..45970 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ttaagcaacc</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_071.gene</td> + <td>45941..46451 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gcctgtgata</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_072.gene</td> + <td>46444..47026 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">tcacaaaaag</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_073.gene</td> + <td>47085..47308 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ctcatcgaca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_074.gene</td> + <td>47293..47649 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">cccgatcgaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_075.gene</td> + <td>47637..47879 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">aagtttttca</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_076.gene</td> + <td>47864..48082 [1]</td> + <td>Unannotated but valid RBS</td> + <td><span style="font-family:monospace">cgt AGGT aac</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_077.gene</td> + <td>48235..48408 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">gcggcaacaa</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_078.gene</td> + <td>48377..48574 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">ctggcgttat</span></td> + </tr> + <tr> + <td>gene</td> + <td>CPT-T1_079.gene</td> + <td>48564..48803 [1]</td> + <td>No RBS annotated, None found</td> + <td><span style="font-family:monospace">atattgaatt</span></td> + </tr> + </tbody> + </table> + </div> + + <h3 id="weird_starts">Start Codon Usage</h3> + <p>This section covers genes with unusual start codons</p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Start Codon</th> + <th>Count</th> + </tr> + </thead> + <tbody> + <tr><td>ATG</td><td>74</td></tr> + <tr><td>GTG</td><td>3</td></tr> + <tr><td>TTG</td><td>2</td></tr> + </tbody> + </table> + </div> + + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature Type</th> + <th>ID</th> + <th>Location</th> + <th>Error</th> + </tr> + </thead> + <tbody> + </tbody> + </table> + </div> + + <h3 id="excessive_gaps">Intergenic Gaps</h3> + <p>Phage genomes are under pressure to maintain high coding density. Large intergenic gaps may be a sign of incorrect gene starts or missing genes.</p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Region</th> + <th>Size</th> + <th>Bounding Gene Transcription Direction</th> + <th>Message</th> + </tr> + </thead> + <tbody> + <tr> + <td>2184 .. 2238</td> + <td>54</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>5876 .. 5937</td> + <td>61</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>6705 .. 6795</td> + <td>90</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>10414 .. 10527</td> + <td>113</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>14432 .. 14511</td> + <td>79</td> + <td>→ →</td> + <td> + 2 ORFs found in this region + </td> + </tr> + <tr> + <td>16621 .. 16698</td> + <td>77</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>21506 .. 21765</td> + <td>259</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>21906 .. 22033</td> + <td>127</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>24289 .. 24350</td> + <td>61</td> + <td>→ →</td> + <td> + 1 ORFs found in this region + </td> + </tr> + <tr> + <td>27573 .. 27634</td> + <td>61</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>28087 .. 28180</td> + <td>93</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>30612 .. 30679</td> + <td>67</td> + <td>→ →</td> + <td> + 1 ORFs found in this region + </td> + </tr> + <tr> + <td>31641 .. 31707</td> + <td>66</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>32399 .. 32477</td> + <td>78</td> + <td>→ →</td> + <td> + 1 ORFs found in this region + </td> + </tr> + <tr> + <td>33611 .. 33683</td> + <td>72</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>34166 .. 34238</td> + <td>72</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>34415 .. 34533</td> + <td>118</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>35638 .. 35760</td> + <td>122</td> + <td>→ →</td> + <td> + 2 ORFs found in this region + </td> + </tr> + <tr> + <td>38693 .. 38773</td> + <td>80</td> + <td>→ →</td> + <td> + 2 ORFs found in this region + </td> + </tr> + <tr> + <td>39211 .. 39288</td> + <td>77</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>40330 .. 41030</td> + <td>700</td> + <td>→ →</td> + <td> + 7 ORFs found in this region + </td> + </tr> + <tr> + <td>41945 .. 42023</td> + <td>78</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>42764 .. 42835</td> + <td>71</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>43324 .. 43395</td> + <td>71</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>44030 .. 44110</td> + <td>80</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>44485 .. 44538</td> + <td>53</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>44852 .. 44909</td> + <td>57</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>45356 .. 45439</td> + <td>83</td> + <td>→ →</td> + <td> + 6 ORFs found in this region + </td> + </tr> + <tr> + <td>47026 .. 47098</td> + <td>72</td> + <td>→ →</td> + <td> + </td> + </tr> + <tr> + <td>48082 .. 48246</td> + <td>164</td> + <td>→ →</td> + <td> + 2 ORFs found in this region + </td> + </tr> + </tbody> + </table> + </div> + + <h3 id="excessive_overlap">Overlapping Genes </h3> + <p>Large gene overlaps may indicate an incorrect gene start or miscalled gene.</p> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature A</th> + <th>Feature B</th> + <th>Shared Region</th> + <th>Overlap Length</th> + </tr> + </thead> + <tbody> + <tr> + <td>CPT-T1_015.gene ([10516:10845](+))</td> + <td>CPT-T1_016.gene ([10516:11162](+))</td> + <td>10527..10844</td> + <td>317 bp</td> + </tr> + <tr> + <td>CPT-T1_030.gene ([24351:26550](-))</td> + <td>CPT-T1_031.gene ([26447:26600](-))</td> + <td>26446..26536</td> + <td>90 bp</td> + </tr> + <tr> + <td>CPT-T1_039.gene ([31881:32167](+))</td> + <td>CPT-T1_040.gene ([32099:32399](+))</td> + <td>32111..32166</td> + <td>55 bp</td> + </tr> + </tbody> + </table> + </div> + <!--<h3 id="coding_density">Coding Density Issues <small>99 / 100</small></h3> + <div class="table-responsive"> + <p> + You have a coding density of 93 which scores + 99 / 100. Most genomes should be in the 90% to + 100% coding density range + </p> + </div>--> + + <h2 class="sub-header" id="antisense">Antisense Genes</h2> + <h3 id="morons">Possible Morons <small>78 / 79 (Doesn't count towards score)</small></h3> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature</th> + <th>RBS</th> + <th>Surrounding Features</th> + </tr> + </thead> + <tbody> + <tr> + <td>CPT-T1_025.gene</td> + <td>No RBS Available</td> + <td class="moron"> + → + → + <span class="strand_emph">←</span> + → + → + </div> + </td> + </tr> + </tbody> + </table> + </div> + + + <h2 class="sub-header" id="annotations">Annotation Issues</h2> + <h3 id="missing_product">Missing Product Tags <small>79 / 79</small></h3> + <div class="table-responsive"> + <table class="table table-striped"> + <thead> + <tr> + <th>Feature</th> + <th>Qualifiers</th> + </tr> + </thead> + <tbody> + </tbody> + </table> + </div> + + + + + + </div> + </div> + </div> + + + <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script> + </body> +</html>