htsworkflow/pipelines/test/testdata/sample_summary_1_12.htm

   1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
   2 <html xmlns:casava="http://www.illumina.com/casava/alignment">
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   4 <body>
   5 <p>Sample Summary Information For Experiment (12564_index6)</p>
   6 <p>Project Summary</p>
   7 <table border="1" cellpadding="5">
   8 <tr>
   9 <td>Project Name</td>
  10 <td>12564_index6</td>
  11 </tr>
  12 <tr>
  13 <td>Machine</td>
  14 <td>HWI-ST0787</td>
  15 </tr>
  16 <tr>
  17 <td>Run Folder</td>
  18 <td>111221_SN787_0107_AD0CV5ACXX</td>
  19 </tr>
  20 <tr>
  21 <td>Flow Cell ID</td>
  22 <td>D0CV5ACXX</td>
  23 </tr>
  24 <tr>
  25 <td>Platform</td>
  26 <td></td>
  27 </tr>
  28 <tr>
  29 <td>Control Software</td>
  30 <td>HiSeq Control Software 1.4.8</td>
  31 </tr>
  32 <tr>
  33 <td>Primary Analysis</td>
  34 <td>RTA 1.12.4.2</td>
  35 </tr>
  36 <tr>
  37 <td>Secondary Analysis</td>
  38 <td>CASAVA-1.8.1</td>
  39 </tr>
  40 </table>
  41 <p>Project Results Summary</p>
  42 <table border="1" cellpadding="5">
  43 <tr>
  44 <th>Clusters (Raw)</th>
  45 <th>Clusters(PF)</th>
  46 <th>Yield (MBases)</th>
  47 </tr>
  48 <tr>
  49 <td>658,174</td>
  50 <td>475,618</td>
  51 <td>23</td>
  52 </tr>
  53 </table>
  54 <p>Barcode-Lane summary</p>
  55 <div ID="ScrollableTableHeaderDiv"><table width="100%">
  56 <col>
  57 <col width="8%">
  58 <col width="10%">
  59 <col width="4%">
  60 <col width="20%">
  61 <col width="6%">
  62 <col width="6%">
  63 <col width="4%">
  64 <col width="30%">
  65 <tr>
  66 <th>Barcode-Lane</th>
  67 <th>Sample</th>
  68 <th>Barcode</th>
  69 <th>Lane</th>
  70 <th>Species</th>
  71 <th>Analysis Type</th>
  72 <th>Length</th>
  73 <th>Num Tiles</th>
  74 <th>Genome Directory</th>
  75 </tr>
  76 </table></div>
  77 <div ID="ScrollableTableBodyDiv"><table width="100%">
  78 <col>
  79 <col width="8%">
  80 <col width="10%">
  81 <col width="4%">
  82 <col width="20%">
  83 <col width="6%">
  84 <col width="6%">
  85 <col width="4%">
  86 <col width="30%">
  87 <tr>
  88 <td>12564_GCCAAT_L5</td>
  89 <td>12564</td>
  90 <td>GCCAAT</td>
  91 <td>5</td>
  92 <td>Homo_sapiens</td>
  93 <td>eland extended</td>
  94 <td>49 </td>
  95 <td>48</td>
  96 <td>/mmjggl/nicodemus/data01/genomes/hg18/chromosomes//*.fa</td>
  97 </tr>
  98 </table></div>
  99 <p>Sample Results Summary : Read 1</p>
 100 <div ID="ScrollableTableHeaderDiv"><table width="100%">
 101 <col>
 102 <col width="7%">
 103 <col width="8%">
 104 <col width="8%">
 105 <col width="12%">
 106 <col width="12%">
 107 <col width="8%">
 108 <col width="7%">
 109 <col width="9%">
 110 <col width="8%">
 111 <col width="6%">
 112 <col width="6%">
 113 <tr><th colspan="12">Sample Info</th></tr>
 114 <tr>
 115 <th>Sample</th>
 116 <th>Sample Yield (Mbases)</th>
 117 <th>Clusters (raw)</th>
 118 <th>Clusters (PF)</th>
 119 <th>1st Cycle Int (PF)</th>
 120 <th>% intensity after 20 cycles (PF)</th>
 121 <th>% PF Clusters</th>
 122 <th>% Align (PF)</th>
 123 <th>Alignment Score (PF)</th>
 124 <th>% Mismatch Rate (PF)</th>
 125 <th>% &gt;=Q30 bases (PF)</th>
 126 <th>Mean Quality SCore (PF)</th>
 127 </tr>
 128 </table></div>
 129 <div ID="ScrollableTableBodyDiv"><table width="100%">
 130 <col>
 131 <col width="7%">
 132 <col width="8%">
 133 <col width="8%">
 134 <col width="12%">
 135 <col width="12%">
 136 <col width="8%">
 137 <col width="7%">
 138 <col width="9%">
 139 <col width="8%">
 140 <col width="6%">
 141 <col width="6%">
 142 <tr>
 143 <td>12564</td>
 144 <td>23</td>
 145 <td>658,174</td>
 146 <td>475,618</td>
 147 <td>1100</td>
 148 <td>89.39</td>
 149 <td>72.26</td>
 150 <td>76.89</td>
 151 <td>128.73</td>
 152 <td>0.40</td>
 153 <td>88.79</td>
 154 <td>35.13</td>
 155 </tr>
 156 </table></div>
 157 <p>Sample Results Summary : Read 2</p>
 158 <div ID="ScrollableTableHeaderDiv"><table width="100%">
 159 <col>
 160 <col width="7%">
 161 <col width="8%">
 162 <col width="8%">
 163 <col width="12%">
 164 <col width="12%">
 165 <col width="8%">
 166 <col width="7%">
 167 <col width="9%">
 168 <col width="8%">
 169 <col width="6%">
 170 <col width="6%">
 171 <tr><th colspan="12">Sample Info</th></tr>
 172 <tr>
 173 <th>Sample</th>
 174 <th>Sample Yield (Mbases)</th>
 175 <th>Clusters (raw)</th>
 176 <th>Clusters (PF)</th>
 177 <th>1st Cycle Int (PF)</th>
 178 <th>% intensity after 20 cycles (PF)</th>
 179 <th>% PF Clusters</th>
 180 <th>% Align (PF)</th>
 181 <th>Alignment Score (PF)</th>
 182 <th>% Mismatch Rate (PF)</th>
 183 <th>% &gt;=Q30 bases (PF)</th>
 184 <th>Mean Quality SCore (PF)</th>
 185 </tr>
 186 </table></div>
 187 <div ID="ScrollableTableBodyDiv"><table width="100%">
 188 <col>
 189 <col width="7%">
 190 <col width="8%">
 191 <col width="8%">
 192 <col width="12%">
 193 <col width="12%">
 194 <col width="8%">
 195 <col width="7%">
 196 <col width="9%">
 197 <col width="8%">
 198 <col width="6%">
 199 <col width="6%">
 200 <tr>
 201 <td>12564</td>
 202 <td>0</td>
 203 <td>0</td>
 204 <td>0</td>
 205 <td>0</td>
 206 <td>0</td>
 207 <td></td>
 208 <td></td>
 209 <td></td>
 210 <td></td>
 211 <td></td>
 212 <td></td>
 213 </tr>
 214 </table></div>
 215 <p>Expanded Sample Summary : Read 1</p>
 216 <div ID="ScrollableTableHeaderDiv"><table width="100%">
 217 <col>
 218 <col width="7%">
 219 <col width="8%">
 220 <col width="8%">
 221 <col width="8%">
 222 <col width="6%">
 223 <col width="10%">
 224 <col width="10%">
 225 <col width="9%">
 226 <col width="5%">
 227 <col width="8%">
 228 <col width="6%">
 229 <col width="6%">
 230 <tr>
 231 <th colspan="2">Sample Info</th>
 232 <th colspan="2">Phasing Info</th>
 233 <th colspan="1">Raw data</th>
 234 <th colspan="8">Filtered data</th>
 235 </tr>
 236 <tr>
 237 <th>Sample</th>
 238 <th>Clusters (raw)</th>
 239 <th>% Phasing</th>
 240 <th>% Prephasing</th>
 241 <th>% Mismatch Rate (raw)</th>
 242 <th>% PF Clusters</th>
 243 <th>Cycle 2-4 Av Int (PF)</th>
 244 <th>Cycle 2-10 Av % Loss (PF)</th>
 245 <th>Cycle 10-20 Av % Loss (PF)</th>
 246 <th>% Align (PF)</th>
 247 <th>% Mismatch Rate (PF)</th>
 248 <th>% &gt;=Q30 bases (PF)</th>
 249 <th>Mean Quality SCore (PF)</th>
 250 </tr>
 251 </table></div>
 252 <div ID="ScrollableTableBodyDiv"><table width="100%">
 253 <col>
 254 <col width="7%">
 255 <col width="8%">
 256 <col width="8%">
 257 <col width="8%">
 258 <col width="6%">
 259 <col width="10%">
 260 <col width="10%">
 261 <col width="9%">
 262 <col width="5%">
 263 <col width="8%">
 264 <col width="6%">
 265 <col width="6%">
 266 <tr>
 267 <td>12564</td>
 268 <td>658,174</td>
 269 <td>0.19</td>
 270 <td>0.31</td>
 271 <td>0.77</td>
 272 <td>72.26</td>
 273 <td>1083.00</td>
 274 <td>-84.76</td>
 275 <td>0.48</td>
 276 <td>76.89</td>
 277 <td>0.40</td>
 278 <td>88.79</td>
 279 <td>35.13</td>
 280 </tr>
 281 </table></div>
 282 <p>Expanded Sample Summary : Read 2</p>
 283 <div ID="ScrollableTableHeaderDiv"><table width="100%">
 284 <col>
 285 <col width="7%">
 286 <col width="8%">
 287 <col width="8%">
 288 <col width="8%">
 289 <col width="6%">
 290 <col width="10%">
 291 <col width="10%">
 292 <col width="9%">
 293 <col width="5%">
 294 <col width="8%">
 295 <col width="6%">
 296 <col width="6%">
 297 <tr>
 298 <th colspan="2">Sample Info</th>
 299 <th colspan="2">Phasing Info</th>
 300 <th colspan="1">Raw data</th>
 301 <th colspan="8">Filtered data</th>
 302 </tr>
 303 <tr>
 304 <th>Sample</th>
 305 <th>Clusters (raw)</th>
 306 <th>% Phasing</th>
 307 <th>% Prephasing</th>
 308 <th>% Mismatch Rate (raw)</th>
 309 <th>% PF Clusters</th>
 310 <th>Cycle 2-4 Av Int (PF)</th>
 311 <th>Cycle 2-10 Av % Loss (PF)</th>
 312 <th>Cycle 10-20 Av % Loss (PF)</th>
 313 <th>% Align (PF)</th>
 314 <th>% Mismatch Rate (PF)</th>
 315 <th>% &gt;=Q30 bases (PF)</th>
 316 <th>Mean Quality SCore (PF)</th>
 317 </tr>
 318 </table></div>
 319 <div ID="ScrollableTableBodyDiv"><table width="100%">
 320 <col>
 321 <col width="7%">
 322 <col width="8%">
 323 <col width="8%">
 324 <col width="8%">
 325 <col width="6%">
 326 <col width="10%">
 327 <col width="10%">
 328 <col width="9%">
 329 <col width="5%">
 330 <col width="8%">
 331 <col width="6%">
 332 <col width="6%">
 333 <tr>
 334 <td>12564</td>
 335 <td>0</td>
 336 <td>0</td>
 337 <td>0</td>
 338 <td></td>
 339 <td></td>
 340 <td>0</td>
 341 <td>0</td>
 342 <td>0</td>
 343 <td></td>
 344 <td></td>
 345 <td></td>
 346 <td></td>
 347 </tr>
 348 </table></div>
 349 <p>IVC Plots</p>
 350 <a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/IVC.htm">
 351 click here
 352 </a><p>All Intensity Plots</p>
 353 <a href="/mmjggl/nicodemus/data01/sequencer/111221_SN787_0107_AD0CV5ACXX/Unaligned/Basecall_Stats_D0CV5ACXX/All.htm">
 354 click here
 355 </a><p>Mismatch Graphs</p>
 356 <a href="FullMismatch.htm">
 357 click here
 358 </a><p>Mismatch Curves</p>
 359 <a href="FullPerfect.htm">
 360 click here
 361 </a><p>Additional Paired Statistics</p>
 362 <div ID="ScrollableTableHeaderDiv"><table width="100%">
 363 <col>
 364 <col width="7%">
 365 <col width="7%">
 366 <col width="7%">
 367 <col width="7%">
 368 <col width="6%">
 369 <col width="6%">
 370 <col width="6%">
 371 <col width="6%">
 372 <col width="6%">
 373 <col width="6%">
 374 <col width="6%">
 375 <col width="6%">
 376 <col width="9%">
 377 <tr>
 378 <th colspan="1">Sample Info</th>
 379 <th colspan="5">Relative Orientation Statistics</th>
 380 <th colspan="5">Insert Size Statistics (for relative orientation R+)</th>
 381 <th colspan="3">Insert Statistics (% of individually uniquely alignable pairs)</th>
 382 </tr>
 383 <tr>
 384 <th>Sample</th>
 385 <th>F-:<br>&gt;R2 R1&gt;</th>
 386 <th>F+:<br>&gt;R1 R2&gt;</th>
 387 <th>R-:<br>&lt;R2 R1&gt;</th>
 388 <th>R+:<br>&gt;R1 R2&lt;</th>
 389 <th>Total</th>
 390 <th>Median</th>
 391 <th>Below-median SD</th>
 392 <th>Above-median SD</th>
 393 <th>Low thresh.</th>
 394 <th>High thresh.</th>
 395 <th>Too small</th>
 396 <th>Too large</th>
 397 <th>Orientation and size OK</th>
 398 </tr>
 399 </table></div>
 400 <div ID="ScrollableTableBodyDiv"><table width="100%">
 401 <col>
 402 <col width="7%">
 403 <col width="7%">
 404 <col width="7%">
 405 <col width="7%">
 406 <col width="6%">
 407 <col width="6%">
 408 <col width="6%">
 409 <col width="6%">
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 413 <col width="6%">
 414 <col width="9%">
 415 <tr>
 416 <td>12564</td>
 417 <td></td>
 418 <td></td>
 419 <td></td>
 420 <td></td>
 421 <td>0</td>
 422 <td></td>
 423 <td></td>
 424 <td></td>
 425 <td></td>
 426 <td></td>
 427 <td></td>
 428 <td></td>
 429 <td></td>
 430 </tr>
 431 </table></div>
 432 <p>CASAVA-1.8.1</p>
 433 </body>
 434 </html>