trunk/htsworkflow/pipelines/test/testdata/Summary-pipeline100.htm

   1 <!--RUN_TIME Wed Jul  2 06:47:44 2008 -->
   2 <!--SOFTWARE_VERSION @(#) $Id: jerboa.pl,v 1.94 2007/12/04 09:59:07 rshaw Exp $-->
   3 <html>
   4 <body>
   5
   6 <a name="Top"><h2><title>080627_HWI-EAS229_0036_3055HAXX Summary</title></h2></a>
   7 <h1>Summary Information For Experiment 080627_HWI-EAS229_0036_3055HAXX on Machine HWI-EAS229</h1>
   8 <h2><br></br>Chip Summary<br></br></h2>
   9 <table border="1" cellpadding="5">
  10 <tr><td>Machine</td><td>HWI-EAS229</td></tr>
  11 <tr><td>Run Folder</td><td>080627_HWI-EAS229_0036_3055HAXX</td></tr>
  12 <tr><td>Chip ID</td><td>unknown</td></tr>
  13 </table>
  14 <h2><br></br>Chip Results Summary<br></br></h2>
  15 <table border="1" cellpadding="5">
  16 <tr>
  17 <td>Clusters</td>
  18 <td>Clusters (PF)</td>
  19 <td>Yield (kbases)</td>
  20 </tr>
  21 <tr><td>80933224</td>
  22 <td>43577803</td>
  23 <td>1133022</td>
  24 </tr>
  25 </table>
  26 <h2><br></br>Lane Parameter Summary<br></br></h2>
  27 <table border="1" cellpadding="5">
  28 <tr>
  29 <td>Lane</td>
  30 <td>Sample ID</td>
  31 <td>Sample Target</td>
  32 <td>Sample Type</td>
  33 <td>Length</td>
  34 <td>Filter</td>
  35 <td>Num Tiles</td>
  36 <td>Tiles</td>
  37 </tr>
  38 <tr>
  39 <td>1</td>
  40 <td>unknown</td>
  41 <td>mm9</td>
  42 <td>ELAND</td>
  43 <td>26</td>
  44 <td>'((CHASTITY>=0.6))'</td>
  45 <td>100</td>
  46 <td><a href="#Lane1">Lane 1</a></td>
  47 </tr>
  48 <tr>
  49 <td>2</td>
  50 <td>unknown</td>
  51 <td>mm9</td>
  52 <td>ELAND</td>
  53 <td>26</td>
  54 <td>'((CHASTITY>=0.6))'</td>
  55 <td>100</td>
  56 <td><a href="#Lane2">Lane 2</a></td>
  57 </tr>
  58 <tr>
  59 <td>3</td>
  60 <td>unknown</td>
  61 <td>mm9</td>
  62 <td>ELAND</td>
  63 <td>26</td>
  64 <td>'((CHASTITY>=0.6))'</td>
  65 <td>100</td>
  66 <td><a href="#Lane3">Lane 3</a></td>
  67 </tr>
  68 <tr>
  69 <td>4</td>
  70 <td>unknown</td>
  71 <td>elegans170</td>
  72 <td>ELAND</td>
  73 <td>26</td>
  74 <td>'((CHASTITY>=0.6))'</td>
  75 <td>100</td>
  76 <td><a href="#Lane4">Lane 4</a></td>
  77 </tr>
  78 <tr>
  79 <td>5</td>
  80 <td>unknown</td>
  81 <td>elegans170</td>
  82 <td>ELAND</td>
  83 <td>26</td>
  84 <td>'((CHASTITY>=0.6))'</td>
  85 <td>100</td>
  86 <td><a href="#Lane5">Lane 5</a></td>
  87 </tr>
  88 <tr>
  89 <td>6</td>
  90 <td>unknown</td>
  91 <td>elegans170</td>
  92 <td>ELAND</td>
  93 <td>26</td>
  94 <td>'((CHASTITY>=0.6))'</td>
  95 <td>100</td>
  96 <td><a href="#Lane6">Lane 6</a></td>
  97 </tr>
  98 <tr>
  99 <td>7</td>
 100 <td>unknown</td>
 101 <td>elegans170</td>
 102 <td>ELAND</td>
 103 <td>26</td>
 104 <td>'((CHASTITY>=0.6))'</td>
 105 <td>100</td>
 106 <td><a href="#Lane7">Lane 7</a></td>
 107 </tr>
 108 <tr>
 109 <td>8</td>
 110 <td>unknown</td>
 111 <td>elegans170</td>
 112 <td>ELAND</td>
 113 <td>26</td>
 114 <td>'((CHASTITY>=0.6))'</td>
 115 <td>100</td>
 116 <td><a href="#Lane8">Lane 8</a></td>
 117 </tr>
 118 </table>
 119 <h2><br></br>Lane Results Summary<br></br></h2>
 120 <table border="1" cellpadding="5">
 121 <tr>
 122 <td colspan="2">Lane Info</td>
 123 <td colspan="8">Tile Mean +/- SD for Lane</td>
 124 </tr>
 125 <tr>
 126 <td>Lane </td>
 127 <td>Lane Yield (kbases) </td>
 128 <td>Clusters (raw)</td>
 129 <td>Clusters (PF) </td>
 130 <td>1st Cycle Int (PF) </td>
 131 <td>% intensity after 20 cycles (PF) </td>
 132 <td>% PF Clusters </td>
 133 <td>% Align (PF) </td>
 134 <td>Alignment Score (PF) </td>
 135 <td> % Error Rate (PF) </td>
 136 </tr>
 137 <tr>
 138 <td>1</td>
 139 <td>158046</td>
 140 <td>96483 +/- 9074</td>
 141 <td>60787 +/- 4240</td>
 142 <td>329 +/- 35</td>
 143 <td>101.88 +/- 6.03</td>
 144 <td>63.21 +/- 3.29</td>
 145 <td>70.33 +/- 0.24</td>
 146 <td>9054.08 +/- 59.16</td>
 147 <td>0.46 +/- 0.18</td>
 148 </tr>
 149 <tr>
 150 <td>2</td>
 151 <td>156564</td>
 152 <td>133738 +/- 7938</td>
 153 <td>60217 +/- 1926</td>
 154 <td>444 +/- 39</td>
 155 <td>92.62 +/- 7.58</td>
 156 <td>45.20 +/- 3.31</td>
 157 <td>51.98 +/- 0.74</td>
 158 <td>6692.04 +/- 92.49</td>
 159 <td>0.46 +/- 0.09</td>
 160 </tr>
 161 <tr>
 162 <td>3</td>
 163 <td>185818</td>
 164 <td>152142 +/- 10002</td>
 165 <td>71468 +/- 2827</td>
 166 <td>366 +/- 36</td>
 167 <td>91.53 +/- 8.66</td>
 168 <td>47.19 +/- 3.80</td>
 169 <td>82.24 +/- 0.44</td>
 170 <td>10598.68 +/- 64.13</td>
 171 <td>0.41 +/- 0.04</td>
 172 </tr>
 173 <tr>
 174 <td>4</td>
 175 <td>34953</td>
 176 <td>15784 +/- 2162</td>
 177 <td>13443 +/- 1728</td>
 178 <td>328 +/- 40</td>
 179 <td>97.53 +/- 9.87</td>
 180 <td>85.29 +/- 1.91</td>
 181 <td>80.02 +/- 0.53</td>
 182 <td>10368.82 +/- 71.08</td>
 183 <td>0.15 +/- 0.05</td>
 184 </tr>
 185 <tr>
 186 <td>5</td>
 187 <td>167936</td>
 188 <td>119735 +/- 8465</td>
 189 <td>64590 +/- 2529</td>
 190 <td>417 +/- 37</td>
 191 <td>88.69 +/- 14.79</td>
 192 <td>54.10 +/- 2.59</td>
 193 <td>76.95 +/- 0.32</td>
 194 <td>9936.47 +/- 65.75</td>
 195 <td>0.28 +/- 0.02</td>
 196 </tr>
 197 <tr>
 198 <td>6</td>
 199 <td>173463</td>
 200 <td>152177 +/- 8146</td>
 201 <td>66716 +/- 2493</td>
 202 <td>372 +/- 39</td>
 203 <td>87.06 +/- 9.86</td>
 204 <td>43.98 +/- 3.12</td>
 205 <td>78.80 +/- 0.43</td>
 206 <td>10162.28 +/- 49.65</td>
 207 <td>0.38 +/- 0.03</td>
 208 </tr>
 209 <tr>
 210 <td>7</td>
 211 <td>149287</td>
 212 <td>84649 +/- 7325</td>
 213 <td>57418 +/- 3617</td>
 214 <td>295 +/- 28</td>
 215 <td>89.40 +/- 8.23</td>
 216 <td>67.97 +/- 1.82</td>
 217 <td>33.38 +/- 0.25</td>
 218 <td>4247.92 +/- 32.37</td>
 219 <td>1.00 +/- 0.03</td>
 220 </tr>
 221 <tr>
 222 <td>8</td>
 223 <td>106953</td>
 224 <td>54622 +/- 4812</td>
 225 <td>41136 +/- 3309</td>
 226 <td>284 +/- 37</td>
 227 <td>90.21 +/- 9.10</td>
 228 <td>75.39 +/- 2.27</td>
 229 <td>48.33 +/- 0.29</td>
 230 <td>6169.21 +/- 169.50</td>
 231 <td>0.86 +/- 1.22</td>
 232 </tr>
 233 <tr><td colspan="13">Tile mean across chip</td></tr>
 234 <tr>
 235 <td>Av.</td>
 236 <td></td>
 237 <td>101166</td>
 238 <td>54472</td>
 239 <td>354</td>
 240 <td>92.36</td>
 241 <td>60.29</td>
 242 <td>65.25</td>
 243 <td>8403.69</td>
 244 <td>0.50</td>
 245 </tr>
 246 </table>
 247 <h2><br></br>Expanded Lane Summary<br></br></h2>
 248 <table border="1" cellpadding="5">
 249 <tr>
 250
 251 <tr><td colspan="2">Lane Info</td>
 252 <td colspan="2">Phasing Info</td>
 253 <td colspan="2">Raw Data (tile mean)</td>
 254 <td colspan="7">Filtered Data (tile mean)</td></tr>
 255 <td>Lane </td>
 256 <td>Clusters (tile mean) (raw)</td>
 257 <td>% Phasing </td>
 258 <td>% Prephasing </td>
 259 <td>% Error Rate (raw) </td>
 260 <td> Equiv Perfect Clusters (raw) </td>
 261 <td>% retained </td>
 262 <td>Cycle 2-4 Av Int (PF) </td>
 263 <td>Cycle 2-10 Av % Loss (PF) </td>
 264 <td>Cycle 10-20 Av % Loss (PF) </td>
 265 <td>% Align (PF) </td>
 266 <td>% Error Rate (PF) </td>
 267 <td> Equiv Perfect Clusters (PF) </td>
 268 </tr>
 269 <tr>
 270 <td>1</td>
 271 <td>96483</td>
 272 <td>0.7700</td>
 273 <td>0.3100</td>
 274 <td>1.00</td>
 275 <td>49676</td>
 276 <td>63.21</td>
 277 <td>317 +/- 32</td>
 278 <td>0.13 +/- 0.44</td>
 279 <td>-1.14 +/- 0.34</td>
 280 <td>70.33</td>
 281 <td>0.46</td>
 282 <td>41758</td>
 283 </tr>
 284 <tr>
 285 <td>2</td>
 286 <td>133738</td>
 287 <td>0.7700</td>
 288 <td>0.3100</td>
 289 <td>1.22</td>
 290 <td>40467</td>
 291 <td>45.20</td>
 292 <td>415 +/- 33</td>
 293 <td>0.29 +/- 0.40</td>
 294 <td>-0.79 +/- 0.35</td>
 295 <td>51.98</td>
 296 <td>0.46</td>
 297 <td>30615</td>
 298 </tr>
 299 <tr>
 300 <td>3</td>
 301 <td>152142</td>
 302 <td>0.7700</td>
 303 <td>0.3100</td>
 304 <td>1.30</td>
 305 <td>78588</td>
 306 <td>47.19</td>
 307 <td>344 +/- 26</td>
 308 <td>0.68 +/- 0.51</td>
 309 <td>-0.77 +/- 0.42</td>
 310 <td>82.24</td>
 311 <td>0.41</td>
 312 <td>57552</td>
 313 </tr>
 314 <tr>
 315 <td>4</td>
 316 <td>15784</td>
 317 <td>0.7700</td>
 318 <td>0.3100</td>
 319 <td>0.29</td>
 320 <td>11095</td>
 321 <td>85.29</td>
 322 <td>306 +/- 34</td>
 323 <td>0.20 +/- 0.69</td>
 324 <td>-1.28 +/- 0.66</td>
 325 <td>80.02</td>
 326 <td>0.15</td>
 327 <td>10671</td>
 328 </tr>
 329 <tr>
 330 <td>5</td>
 331 <td>119735</td>
 332 <td>0.7700</td>
 333 <td>0.3100</td>
 334 <td>0.85</td>
 335 <td>60335</td>
 336 <td>54.10</td>
 337 <td>380 +/- 32</td>
 338 <td>0.34 +/- 0.49</td>
 339 <td>-1.55 +/- 4.69</td>
 340 <td>76.95</td>
 341 <td>0.28</td>
 342 <td>49015</td>
 343 </tr>
 344 <tr>
 345 <td>6</td>
 346 <td>152177</td>
 347 <td>0.7700</td>
 348 <td>0.3100</td>
 349 <td>1.21</td>
 350 <td>70905</td>
 351 <td>43.98</td>
 352 <td>333 +/- 27</td>
 353 <td>0.57 +/- 0.50</td>
 354 <td>-0.91 +/- 0.39</td>
 355 <td>78.80</td>
 356 <td>0.38</td>
 357 <td>51663</td>
 358 </tr>
 359 <tr>
 360 <td>7</td>
 361 <td>84649</td>
 362 <td>0.7700</td>
 363 <td>0.3100</td>
 364 <td>1.38</td>
 365 <td>21069</td>
 366 <td>67.97</td>
 367 <td>272 +/- 20</td>
 368 <td>1.15 +/- 0.52</td>
 369 <td>-0.84 +/- 0.58</td>
 370 <td>33.38</td>
 371 <td>1.00</td>
 372 <td>18265</td>
 373 </tr>
 374 <tr>
 375 <td>8</td>
 376 <td>54622</td>
 377 <td>0.7700</td>
 378 <td>0.3100</td>
 379 <td>1.17</td>
 380 <td>21335</td>
 381 <td>75.39</td>
 382 <td>262 +/- 31</td>
 383 <td>1.10 +/- 0.59</td>
 384 <td>-1.01 +/- 0.47</td>
 385 <td>48.33</td>
 386 <td>0.86</td>
 387 <td>19104</td>
 388 </tr>
 389 </table>
 390 <b><br></br>IVC Plots</b>
 391 <p> <a href='IVC.htm' target="_blank"> IVC.htm
 392  </a></p>
 393 <b><br></br>All Intensity Plots</b>
 394 <p> <a href='All.htm' target="_blank"> All.htm
 395  </a></p>
 396 <b><br></br>Error graphs: </b>
 397 <p> <a href='Error.htm' target="_blank"> Error.htm
 398  </a></p>
 399 <td><a href="#Top">Back to top</a></td>
 400 <a name="Lane1"><h2><br></br>Lane 1<br></br></h2></a>
 401 <table border="1" cellpadding="5">
 402 <tr>
 403 <td>Lane </td>
 404 <td>Tile </td>
 405 <td>Clusters (raw)</td>
 406 <td>Av 1st Cycle Int (PF) </td>
 407 <td>Av % intensity after 20 cycles (PF) </td>
 408 <td>% PF Clusters </td>
 409 <td>% Align (PF) </td>
 410 <td>Av Alignment Score (PF) </td>
 411 <td>% Error Rate (PF) </td>
 412 </tr>
 413 <tr>
 414 <td>1</td>
 415 <td>0001</td>
 416 <td>114972</td>
 417 <td>326.48</td>
 418 <td>94.39</td>
 419 <td>57.44</td>
 420 <td>70.2</td>
 421 <td>9038.6</td>
 422 <td>0.44</td>
 423 </tr>
 424 </table>
 425 <td><a href="#Top">Back to top</a></td>
 426 <a name="Lane2"><h2><br></br>Lane 2<br></br></h2></a>
 427 <table border="1" cellpadding="5">
 428 <tr>
 429 <td>Lane </td>
 430 <td>Tile </td>
 431 <td>Clusters (raw)</td>
 432 <td>Av 1st Cycle Int (PF) </td>
 433 <td>Av % intensity after 20 cycles (PF) </td>
 434 <td>% PF Clusters </td>
 435 <td>% Align (PF) </td>
 436 <td>Av Alignment Score (PF) </td>
 437 <td>% Error Rate (PF) </td>
 438 </tr>
 439 <tr>
 440 <td>2</td>
 441 <td>0001</td>
 442 <td>147793</td>
 443 <td>448.12</td>
 444 <td>83.68</td>
 445 <td>38.57</td>
 446 <td>53.7</td>
 447 <td>6905.4</td>
 448 <td>0.54</td>
 449 </tr>
 450 </table>
 451 <td><a href="#Top">Back to top</a></td>
 452 <a name="Lane3"><h2><br></br>Lane 3<br></br></h2></a>
 453 <table border="1" cellpadding="5">
 454 <tr>
 455 <td>Lane </td>
 456 <td>Tile </td>
 457 <td>Clusters (raw)</td>
 458 <td>Av 1st Cycle Int (PF) </td>
 459 <td>Av % intensity after 20 cycles (PF) </td>
 460 <td>% PF Clusters </td>
 461 <td>% Align (PF) </td>
 462 <td>Av Alignment Score (PF) </td>
 463 <td>% Error Rate (PF) </td>
 464 </tr>
 465 <tr>
 466 <td>3</td>
 467 <td>0001</td>
 468 <td>167904</td>
 469 <td>374.05</td>
 470 <td>86.91</td>
 471 <td>40.36</td>
 472 <td>81.3</td>
 473 <td>10465.0</td>
 474 <td>0.47</td>
 475 </tr>
 476 </table>
 477 <td><a href="#Top">Back to top</a></td>
 478 <a name="Lane4"><h2><br></br>Lane 4<br></br></h2></a>
 479 <table border="1" cellpadding="5">
 480 <tr>
 481 <td>Lane </td>
 482 <td>Tile </td>
 483 <td>Clusters (raw)</td>
 484 <td>Av 1st Cycle Int (PF) </td>
 485 <td>Av % intensity after 20 cycles (PF) </td>
 486 <td>% PF Clusters </td>
 487 <td>% Align (PF) </td>
 488 <td>Av Alignment Score (PF) </td>
 489 <td>% Error Rate (PF) </td>
 490 </tr>
 491 <tr>
 492 <td>4</td>
 493 <td>0001</td>
 494 <td>20308</td>
 495 <td>276.85</td>
 496 <td>92.87</td>
 497 <td>84.26</td>
 498 <td>80.4</td>
 499 <td>10413.8</td>
 500 <td>0.16</td>
 501 </tr>
 502 </table>
 503 <td><a href="#Top">Back to top</a></td>
 504 <a name="Lane5"><h2><br></br>Lane 5<br></br></h2></a>
 505 <table border="1" cellpadding="5">
 506 <tr>
 507 <td>Lane </td>
 508 <td>Tile </td>
 509 <td>Clusters (raw)</td>
 510 <td>Av 1st Cycle Int (PF) </td>
 511 <td>Av % intensity after 20 cycles (PF) </td>
 512 <td>% PF Clusters </td>
 513 <td>% Align (PF) </td>
 514 <td>Av Alignment Score (PF) </td>
 515 <td>% Error Rate (PF) </td>
 516 </tr>
 517 </table>
 518 <td><a href="#Top">Back to top</a></td>
 519 <a name="Lane6"><h2><br></br>Lane 6<br></br></h2></a>
 520 <table border="1" cellpadding="5">
 521 <tr>
 522 <td>Lane </td>
 523 <td>Tile </td>
 524 <td>Clusters (raw)</td>
 525 <td>Av 1st Cycle Int (PF) </td>
 526 <td>Av % intensity after 20 cycles (PF) </td>
 527 <td>% PF Clusters </td>
 528 <td>% Align (PF) </td>
 529 <td>Av Alignment Score (PF) </td>
 530 <td>% Error Rate (PF) </td>
 531 </tr>
 532 <tr>
 533 <td>6</td>
 534 <td>0001</td>
 535 <td>166844</td>
 536 <td>348.12</td>
 537 <td>77.59</td>
 538 <td>38.13</td>
 539 <td>79.7</td>
 540 <td>10264.4</td>
 541 <td>0.44</td>
 542 </tr>
 543 </table>
 544 <td><a href="#Top">Back to top</a></td>
 545 <a name="Lane7"><h2><br></br>Lane 7<br></br></h2></a>
 546 <table border="1" cellpadding="5">
 547 <tr>
 548 <td>Lane </td>
 549 <td>Tile </td>
 550 <td>Clusters (raw)</td>
 551 <td>Av 1st Cycle Int (PF) </td>
 552 <td>Av % intensity after 20 cycles (PF) </td>
 553 <td>% PF Clusters </td>
 554 <td>% Align (PF) </td>
 555 <td>Av Alignment Score (PF) </td>
 556 <td>% Error Rate (PF) </td>
 557 </tr>
 558 <tr>
 559 <td>7</td>
 560 <td>0001</td>
 561 <td>98913</td>
 562 <td>269.90</td>
 563 <td>86.66</td>
 564 <td>64.55</td>
 565 <td>33.2</td>
 566 <td>4217.5</td>
 567 <td>1.02</td>
 568 </tr>
 569 </table>
 570 <td><a href="#Top">Back to top</a></td>
 571 <a name="Lane8"><h2><br></br>Lane 8<br></br></h2></a>
 572 <table border="1" cellpadding="5">
 573 <tr>
 574 <td>Lane </td>
 575 <td>Tile </td>
 576 <td>Clusters (raw)</td>
 577 <td>Av 1st Cycle Int (PF) </td>
 578 <td>Av % intensity after 20 cycles (PF) </td>
 579 <td>% PF Clusters </td>
 580 <td>% Align (PF) </td>
 581 <td>Av Alignment Score (PF) </td>
 582 <td>% Error Rate (PF) </td>
 583 </tr>
 584 <tr>
 585 <td>8</td>
 586 <td>0001</td>
 587 <td>64972</td>
 588 <td>243.60</td>
 589 <td>89.40</td>
 590 <td>73.17</td>
 591 <td>48.3</td>
 592 <td>6182.8</td>
 593 <td>0.71</td>
 594 </tr>
 595 </table>
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