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1 <!DOCTYPE html><html><head><title>EURL VTEC Typer summary report</title>
2 <style type="text/css">
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21 </style> <meta charset='utf-8'>
22 <body><div style="border: 1px solid #73ad21;max-width:940px;text-align:center;margin:auto;"></br>
23 <table class="table table-head"><tr><td width="25%"><img src='https://aries.iss.it/static/images/aries.jpg' alt='ARIES' style='float:left;width:50%;padding-left:0.5cm;'>
24 <img src='https://aries.iss.it/static/images/isseurlvtec.png' alt='ISS-EURL VTEC' style='float:left;width:30%'></td>
25 <td><h1>EURL VTEC Typer</h1><h2>Report for Strain_1_L2.fastq</h2>2018-05-17 11:16 UTC</td><td style='width: 25%; padding-left: 0.2cm; text-align: left;'><h4>Istituto Superiore di Sanità</h4>
26 Department of Food Safety, Nutrition and Veterinary Public Health<br/>European Union Reference Laboratory for <i>E. coli</i></td></tr></table>
27 <h3>Summary</h3>
28 O26:H11<br/>ST21<br/><p>eae, ehxa, stx1a, stx1b
29 </p>
30 <br/><hr/><h3>Raw data quality check</h3>
31 <p>FASTQC result: <a href='https://galaxy.iss.it/datasets/4b25789cdf945d7e/display/?preview=True'>Webpage</a></p>
32 <br/><hr/><h3>Trimming analysis</h3>
33 <table cellpadding="4" class="table table-rep">
34 <tr><td>Maximum length trimming</td><td>360</td></tr>
35 <tr><td>Left-side trimming</td><td>10</td></tr>
36 <tr><td>Right-side trimming</td><td>0</td></tr>
37 <tr><td>Minimum Phred quality score for right-side trimming</td><td>25</td></tr>
38 <tr><td>Average Phred quality score for right-side trimming</td><td>27</td></tr>
39 <tr><td>Minimum length filtering</td><td>50</td></tr>
40 </table><br/><hr/><h3>Assembly statistics</h3>
41 <table cellpadding="4" class="table table-rep">
42 <tr><td>Estimated genome size:</td><td>5000000 bp
43 </td></tr>
44 <tr><td>Assembled nucleotides:</td><td>5493390 bp
45 </td></tr>
46 <tr><td>Estimated coverage:</td><td>1.1 x
47 </td></tr>
48 <tr><td>N. contigs:</td><td>315
49 </td></tr>
50 <tr><td>Average contig length:</td><td>17439
51 </td></tr>
52 <tr><td>Median contig length:</td><td>4504
53 </td></tr>
54 <tr><td>Maximum contig length:</td><td>164788
55 </td></tr>
56 <tr><td>N. contigs >= 200 bp:</td><td>315 (100.0 %)
57 </td></tr>
58 <tr><td>N. contigs >= 2,000 bp:</td><td>224 (71.1 %)
59 </td></tr>
60 <tr><td>N50:</td><td>52450
61 </td></tr>
62 <tr><td>NG50:</td><td>59152
63 </td></tr>
64 </table><br/><hr/><h3>Serotyping</h3>
65 <table cellpadding="4" class="table table-rep">
66 <tr><th>sseqid</th><th>pident</th><th>length</th><th>positive
67 </th></tr>
68 <tr><td>wzx_208_AF529080_O26</td><td>100.00</td><td>1263</td><td>1263
69 </td></tr>
70 <tr><td>wzy_192_AF529080_O26</td><td>100.00</td><td>1023</td><td>1023
71 </td></tr>
72 <tr><td>fliC_269_AY337465_H11</td><td>99.93</td><td>1459</td><td>1458
73 </td></tr>
74 <tr><td>fliC_276_AY337472_H11</td><td>99.79</td><td>1459</td><td>1456
75 </td></tr>
76 </table><br/><hr/><h3>Multi Locus Sequence Typing</h3>
77 <table cellpadding="4" class="table table-rep">
78 <tr><th>Sample</th><th>ST</th><th>adk</th><th>fumC</th><th>gyrB</th><th>icd</th><th>mdh</th><th>purA</th><th>recA</th><th>mismatches</th><th>uncertainty</th><th>depth</th><th>maxMAF
79 </th></tr>
80 <tr><td>dataset_10081</td><td>21</td><td>16</td><td>4</td><td>12</td><td>16</td><td>9</td><td>7</td><td>7</td><td>0</td><td>-</td><td>31.5927142857</td><td>0.333333333333
81 </td></tr>
82 </table><br/><hr/><h3>Virulotyping</h3>
83 <p>This table is filtered for results with >90% gene coverage, unfiltered results can be found <a href='https://galaxy.iss.it/datasets/977c7565c45fc8c2/display/?preview=True'>here</a></p>
84 <table cellpadding="4" class="table table-cross">
85 <tr><th>#gene</th><th>percentage gene coverage</th><th>gene mean read coverage</th><th>percentage gene identity
86 </th></tr>
87 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/hm138194'>ehxa_7_hm138194</a></td><td>100.0</td><td>22.75</td><td>100.0
88 </td></tr>
89 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ae005174'>nlea_8_ae005174</a></td><td>99.92</td><td>27.36</td><td>99.85
90 </td></tr>
91 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af540491'>celb_8_af540491</a></td><td>100.0</td><td>254.92</td><td>98.61
92 </td></tr>
93 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cu928160'>iss_13_cu928160</a></td><td>100.0</td><td>28.49</td><td>99.71
94 </td></tr>
95 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cp001164'>nlea_7_cp001164</a></td><td>99.92</td><td>17.8</td><td>99.85
96 </td></tr>
97 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010960'>nlea_13_ap010960</a></td><td>93.95</td><td>14.56</td><td>99.92
98 </td></tr>
99 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab011549'>katp_1_ab011549</a></td><td>100.0</td><td>108.79</td><td>100.0
100 </td></tr>
101 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af054421'>espb_13_af054421</a></td><td>93.12</td><td>10.91</td><td>99.89
102 </td></tr>
103 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab456530'>toxb_3_ab456530</a></td><td>100.0</td><td>27.15</td><td>99.98
104 </td></tr>
105 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am230663'>stx1b_14_am230663_a</a></td><td>100.0</td><td>18.51</td><td>100.0
106 </td></tr>
107 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x06119'>celb_9_x06119</a></td><td>100.0</td><td>177.13</td><td>99.31
108 </td></tr>
109 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>iha_5_ap010953</a></td><td>100.0</td><td>38.17</td><td>100.0
110 </td></tr>
111 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>espp_3_gq259888</a></td><td>100.0</td><td>41.34</td><td>100.0
112 </td></tr>
113 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af461168'>stx1a_15_af461168_a</a></td><td>99.89</td><td>20.92</td><td>99.79
114 </td></tr>
115 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/aj225018'>espa_23_aj225018</a></td><td>100.0</td><td>9.57</td><td>100.0
116 </td></tr>
117 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010960'>nlec_6_ap010960</a></td><td>100.0</td><td>18.57</td><td>99.8
118 </td></tr>
119 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>lpfa_3_ap010953</a></td><td>100.0</td><td>15.77</td><td>100.0
120 </td></tr>
121 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/af453441'>nleb_11_af453441</a></td><td>97.58</td><td>12.94</td><td>99.9
122 </td></tr>
123 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>toxb_4_fj386569</a></td><td>100.0</td><td>25.5</td><td>99.97
124 </td></tr>
125 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ae014075'>iss_11_ae014075</a></td><td>100.0</td><td>15.83</td><td>97.66
126 </td></tr>
127 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/x94129'>ehxa_4_x94129</a></td><td>93.56</td><td>16.28</td><td>99.71
128 </td></tr>
129 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>espa_22_fm201463</a></td><td>100.0</td><td>18.99</td><td>100.0
130 </td></tr>
131 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/am422003'>nlea_12_am422003</a></td><td>100.0</td><td>21.17</td><td>100.0
132 </td></tr>
133 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab071620'>stx1b_11_ab071620_c</a></td><td>100.0</td><td>11.84</td><td>99.63
134 </td></tr>
135 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ecu59503'>eae_45_ecu59503</a></td><td>92.62</td><td>28.63</td><td>99.85
136 </td></tr>
137 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab011549'>espp_4_ab011549</a></td><td>95.62</td><td>29.83</td><td>99.87
138 </td></tr>
139 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/hm138194'>espp_1_hm138194</a></td><td>99.03</td><td>37.41</td><td>99.97
140 </td></tr>
141 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128535'>cif_2_ay128535</a></td><td>99.88</td><td>19.24</td><td>99.88
142 </td></tr>
143 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ay128537'>cif_1_ay128537</a></td><td>99.88</td><td>18.14</td><td>99.88
144 </td></tr>
145 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ab303060'>espj_1_ab303060</a></td><td>100.0</td><td>63.45</td><td>100.0
146 </td></tr>
147 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fm201463'>nleb_12_fm201463</a></td><td>93.54</td><td>16.32</td><td>99.57
148 </td></tr>
149 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/ap010953'>nlec_3_ap010953</a></td><td>94.53</td><td>20.93</td><td>99.46
150 </td></tr>
151 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/fj386569'>ehxa_5_fj386569</a></td><td>99.63</td><td>23.12</td><td>99.97
152 </td></tr>
153 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/cu928158'>iss_12_cu928158</a></td><td>100.0</td><td>23.77</td><td>99.42
154 </td></tr>
155 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/d00021'>celb_10_d00021</a></td><td>100.0</td><td>150.01</td><td>98.61
156 </td></tr>
157 <tr><td><a href='https://www.ncbi.nlm.nih.gov/nuccore/gq259888'>toxb_2_gq259888</a></td><td>99.29</td><td>24.57</td><td>99.98
158 </td></tr>
159 </table><br/></div></body></html>
160