0ef6a13f063c246c1339f59e0d3f7f2c07a840de
Home.md
| ... | ... | @@ -188,11 +188,11 @@ MCL-exome, Zhang 2014, 28 |
| 188 | 188 | |
| 189 | 189 | ### Studies with QC completed |
| 190 | 190 | |
| 191 | -[@loveGeneticLandscapeMutations2012](papers/loveGeneticLandscapeMutations2012) |
|
| 192 | - |
|
| 193 | -[@reddyGeneticFunctionalDrivers2017](papers/reddyGeneticFunctionalDrivers2017) |
|
| 194 | - |
|
| 195 | -[@paneaWholeGenomeLandscape2019](papers/paneaWholeGenomeLandscape2019) |
|
| 191 | +|Study|Novel genes failing QC| |
|
| 192 | +|:-:|:-:| |
|
| 193 | +|[@loveGeneticLandscapeMutations2012](papers/loveGeneticLandscapeMutations2012)|80%| |
|
| 194 | +|[@reddyGeneticFunctionalDrivers2017](papers/reddyGeneticFunctionalDrivers2017)|48%| |
|
| 195 | +|[@paneaWholeGenomeLandscape2019](papers/paneaWholeGenomeLandscape2019)|55%| |
|
| 196 | 196 | |
| 197 | 197 | ## B-cell lymphoma mutation browser |
| 198 | 198 |
papers/paneaWholeGenomeLandscape2019.pdf
papers/paneaWholeGenomeLandscape2019_tmp.html
| ... | ... | @@ -1,665 +0,0 @@ |
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| 368 | -<h1 id="paneawholegenomelandscape2019">@paneaWholeGenomeLandscape2019</h1> |
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| 369 | -<h2 id="summary-of-novel-genes">Summary of novel genes</h2> |
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| 370 | -<table> |
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| 371 | -<thead> |
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| 372 | -<tr> |
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| 373 | -<th style="text-align:center">Entity</th> |
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| 374 | -<th style="text-align:center">Total</th> |
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| 375 | -<th style="text-align:center">Tier 1</th> |
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| 376 | -<th style="text-align:center">Tier 2</th> |
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| 377 | -<th style="text-align:center">Tier 2 Pass</th> |
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| 378 | -<th style="text-align:center">Tier 2 Fail</th> |
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| 379 | -<th style="text-align:center">Fail Rate</th> |
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| 380 | -</tr> |
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| 381 | -</thead> |
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| 382 | -<tbody> |
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| 383 | -<tr> |
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| 384 | -<td style="text-align:center">BL</td> |
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| 385 | -<td style="text-align:center">40</td> |
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| 386 | -<td style="text-align:center">4</td> |
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| 387 | -<td style="text-align:center">35</td> |
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| 388 | -<td style="text-align:center">13</td> |
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| 389 | -<td style="text-align:center">22</td> |
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| 390 | -<td style="text-align:center">55%</td> |
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| 391 | -</tr> |
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| 392 | -</tbody> |
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| 393 | -</table> |
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| 394 | -<pre><code class="language-mermaid"><div class="mermaid">--- |
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| 395 | -config: |
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| 396 | - sankey: |
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| 397 | - showValues: true |
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| 398 | - linkColor: target |
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| 399 | - width: 600 |
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| 400 | - height: 300 |
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| 401 | - nodeAlignment: right |
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| 402 | - prefix: '(' |
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| 403 | - suffix: ' genes)' |
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| 404 | ---- |
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| 405 | -sankey-beta |
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| 406 | -New to this study, BL Tier 1, 4 |
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| 407 | -New to this study, BL Tier 2, 36 |
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| 408 | -BL Tier 2, Pass QC, 13 |
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| 409 | -BL Tier 2, Fail QC, 23 |
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| 410 | -</div></code></pre> |
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| 411 | -<h2 id="novel-genes-reported-in-this-study">Novel genes reported in this study</h2> |
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| 412 | -<h3 id="tier-1">Tier 1</h3> |
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| 413 | -<table> |
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| 414 | -<thead> |
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| 415 | -<tr> |
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| 416 | -<th style="text-align:left">Novel gene</th> |
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| 417 | -<th style="text-align:center">BL tier</th> |
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| 418 | -</tr> |
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| 419 | -</thead> |
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| 420 | -<tbody> |
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| 421 | -<tr> |
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| 422 | -<td style="text-align:left"><a href="../BMP7">BMP7</a></td> |
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| 423 | -<td style="text-align:center">1</td> |
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| 424 | -</tr> |
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| 425 | -<tr> |
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| 426 | -<td style="text-align:left"><a href="../EIF4A1">EIF4A1</a></td> |
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| 427 | -<td style="text-align:center">1</td> |
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| 428 | -</tr> |
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| 429 | -<tr> |
|
| 430 | -<td style="text-align:left"><a href="../EPPK1">EPPK1</a></td> |
|
| 431 | -<td style="text-align:center">1</td> |
|
| 432 | -</tr> |
|
| 433 | -<tr> |
|
| 434 | -<td style="text-align:left"><a href="../HNRNPU">HNRNPU</a></td> |
|
| 435 | -<td style="text-align:center">1</td> |
|
| 436 | -</tr> |
|
| 437 | -</tbody> |
|
| 438 | -</table> |
|
| 439 | -<h3 id="tier-2">Tier 2</h3> |
|
| 440 | -<table> |
|
| 441 | -<thead> |
|
| 442 | -<tr> |
|
| 443 | -<th style="text-align:left">Novel Gene</th> |
|
| 444 | -<th style="text-align:center">BL tier</th> |
|
| 445 | -<th style="text-align:center">Average variant quality</th> |
|
| 446 | -<th style="text-align:center">QC outcome</th> |
|
| 447 | -</tr> |
|
| 448 | -</thead> |
|
| 449 | -<tbody> |
|
| 450 | -<tr> |
|
| 451 | -<td style="text-align:left"><a href="../HIST1H3I">HIST1H3I</a></td> |
|
| 452 | -<td style="text-align:center">2</td> |
|
| 453 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 454 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 455 | -</tr> |
|
| 456 | -<tr> |
|
| 457 | -<td style="text-align:left"><a href="../CXCR4">CXCR4</a></td> |
|
| 458 | -<td style="text-align:center">2</td> |
|
| 459 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 460 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 461 | -</tr> |
|
| 462 | -<tr> |
|
| 463 | -<td style="text-align:left"><a href="../IRF8">IRF8</a></td> |
|
| 464 | -<td style="text-align:center">2</td> |
|
| 465 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 466 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 467 | -</tr> |
|
| 468 | -<tr> |
|
| 469 | -<td style="text-align:left"><a href="../MCL1">MCL1</a></td> |
|
| 470 | -<td style="text-align:center">2</td> |
|
| 471 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 472 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 473 | -</tr> |
|
| 474 | -<tr> |
|
| 475 | -<td style="text-align:left"><a href="../CD83">CD83</a></td> |
|
| 476 | -<td style="text-align:center">2</td> |
|
| 477 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 478 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 479 | -</tr> |
|
| 480 | -<tr> |
|
| 481 | -<td style="text-align:left"><a href="../PLCG2">PLCG2</a></td> |
|
| 482 | -<td style="text-align:center">2</td> |
|
| 483 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 484 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 485 | -</tr> |
|
| 486 | -<tr> |
|
| 487 | -<td style="text-align:left"><a href="../IGLL5">IGLL5</a></td> |
|
| 488 | -<td style="text-align:center">2</td> |
|
| 489 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 490 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 491 | -</tr> |
|
| 492 | -<tr> |
|
| 493 | -<td style="text-align:left"><a href="../HIST1H3D">HIST1H3D</a></td> |
|
| 494 | -<td style="text-align:center">2</td> |
|
| 495 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 496 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 497 | -</tr> |
|
| 498 | -<tr> |
|
| 499 | -<td style="text-align:left"><a href="../WNK2">WNK2</a></td> |
|
| 500 | -<td style="text-align:center">2</td> |
|
| 501 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 502 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 503 | -</tr> |
|
| 504 | -<tr> |
|
| 505 | -<td style="text-align:left"><a href="../HIST1H4J">HIST1H4J</a></td> |
|
| 506 | -<td style="text-align:center">2</td> |
|
| 507 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 508 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 509 | -</tr> |
|
| 510 | -<tr> |
|
| 511 | -<td style="text-align:left"><a href="../IKZF3">IKZF3</a></td> |
|
| 512 | -<td style="text-align:center">2</td> |
|
| 513 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 514 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 515 | -</tr> |
|
| 516 | -<tr> |
|
| 517 | -<td style="text-align:left"><a href="../ZFP36L1">ZFP36L1</a></td> |
|
| 518 | -<td style="text-align:center">2</td> |
|
| 519 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 520 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 521 | -</tr> |
|
| 522 | -<tr> |
|
| 523 | -<td style="text-align:left"><a href="../RNF144B">RNF144B</a></td> |
|
| 524 | -<td style="text-align:center">2</td> |
|
| 525 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 526 | -<td style="text-align:center"><strong>Pass</strong></td> |
|
| 527 | -</tr> |
|
| 528 | -<tr> |
|
| 529 | -<td style="text-align:left"><a href="../ALPK2">ALPK2</a></td> |
|
| 530 | -<td style="text-align:center">2</td> |
|
| 531 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 532 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 533 | -</tr> |
|
| 534 | -<tr> |
|
| 535 | -<td style="text-align:left"><a href="../CD79B">CD79B</a></td> |
|
| 536 | -<td style="text-align:center">2</td> |
|
| 537 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 538 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 539 | -</tr> |
|
| 540 | -<tr> |
|
| 541 | -<td style="text-align:left"><a href="../CTCF">CTCF</a></td> |
|
| 542 | -<td style="text-align:center">2</td> |
|
| 543 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 544 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 545 | -</tr> |
|
| 546 | -<tr> |
|
| 547 | -<td style="text-align:left"><a href="../DNMT1">DNMT1</a></td> |
|
| 548 | -<td style="text-align:center">2</td> |
|
| 549 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 550 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 551 | -</tr> |
|
| 552 | -<tr> |
|
| 553 | -<td style="text-align:left"><a href="../ETS1">ETS1</a></td> |
|
| 554 | -<td style="text-align:center">2</td> |
|
| 555 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 556 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 557 | -</tr> |
|
| 558 | -<tr> |
|
| 559 | -<td style="text-align:left"><a href="../FZD3">FZD3</a></td> |
|
| 560 | -<td style="text-align:center">2</td> |
|
| 561 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 562 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 563 | -</tr> |
|
| 564 | -<tr> |
|
| 565 | -<td style="text-align:left"><a href="../HIST1H1C">HIST1H1C</a></td> |
|
| 566 | -<td style="text-align:center">2</td> |
|
| 567 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 568 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 569 | -</tr> |
|
| 570 | -<tr> |
|
| 571 | -<td style="text-align:left"><a href="../HIST1H2AG">HIST1H2AG</a></td> |
|
| 572 | -<td style="text-align:center">2</td> |
|
| 573 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 574 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 575 | -</tr> |
|
| 576 | -<tr> |
|
| 577 | -<td style="text-align:left"><a href="../HIST1H2BK">HIST1H2BK</a></td> |
|
| 578 | -<td style="text-align:center">2</td> |
|
| 579 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 580 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 581 | -</tr> |
|
| 582 | -<tr> |
|
| 583 | -<td style="text-align:left"><a href="../KCNK10">KCNK10</a></td> |
|
| 584 | -<td style="text-align:center">2</td> |
|
| 585 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 586 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 587 | -</tr> |
|
| 588 | -<tr> |
|
| 589 | -<td style="text-align:left"><a href="../MME">MME</a></td> |
|
| 590 | -<td style="text-align:center">2</td> |
|
| 591 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 592 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 593 | -</tr> |
|
| 594 | -<tr> |
|
| 595 | -<td style="text-align:left"><a href="../MTOR">MTOR</a></td> |
|
| 596 | -<td style="text-align:center">2</td> |
|
| 597 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 598 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 599 | -</tr> |
|
| 600 | -<tr> |
|
| 601 | -<td style="text-align:left"><a href="../PABPC4L">PABPC4L</a></td> |
|
| 602 | -<td style="text-align:center">2</td> |
|
| 603 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 604 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 605 | -</tr> |
|
| 606 | -<tr> |
|
| 607 | -<td style="text-align:left"><a href="../PCDHA11">PCDHA11</a></td> |
|
| 608 | -<td style="text-align:center">2</td> |
|
| 609 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 610 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 611 | -</tr> |
|
| 612 | -<tr> |
|
| 613 | -<td style="text-align:left"><a href="../PDZRN3">PDZRN3</a></td> |
|
| 614 | -<td style="text-align:center">2</td> |
|
| 615 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 616 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 617 | -</tr> |
|
| 618 | -<tr> |
|
| 619 | -<td style="text-align:left"><a href="../PIK3R1">PIK3R1</a></td> |
|
| 620 | -<td style="text-align:center">2</td> |
|
| 621 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 622 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 623 | -</tr> |
|
| 624 | -<tr> |
|
| 625 | -<td style="text-align:left"><a href="../PXDNL">PXDNL</a></td> |
|
| 626 | -<td style="text-align:center">2</td> |
|
| 627 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 628 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 629 | -</tr> |
|
| 630 | -<tr> |
|
| 631 | -<td style="text-align:left"><a href="../SNTB2">SNTB2</a></td> |
|
| 632 | -<td style="text-align:center">2</td> |
|
| 633 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 634 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 635 | -</tr> |
|
| 636 | -<tr> |
|
| 637 | -<td style="text-align:left"><a href="../WDR7">WDR7</a></td> |
|
| 638 | -<td style="text-align:center">2</td> |
|
| 639 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 640 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 641 | -</tr> |
|
| 642 | -<tr> |
|
| 643 | -<td style="text-align:left"><a href="../HIST1H3H">HIST1H3H</a></td> |
|
| 644 | -<td style="text-align:center">2</td> |
|
| 645 | -<td style="text-align:center">☆ ☆ ☆ ☆ ☆</td> |
|
| 646 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 647 | -</tr> |
|
| 648 | -<tr> |
|
| 649 | -<td style="text-align:left"><a href="../HIST1H3J">HIST1H3J</a></td> |
|
| 650 | -<td style="text-align:center">2</td> |
|
| 651 | -<td style="text-align:center">☆ ☆ ☆ ☆ ☆</td> |
|
| 652 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 653 | -</tr> |
|
| 654 | -<tr> |
|
| 655 | -<td style="text-align:left"><a href="../HIST1H2AM">HIST1H2AM</a></td> |
|
| 656 | -<td style="text-align:center">2</td> |
|
| 657 | -<td style="text-align:center">☆ ☆ ☆ ☆ ☆</td> |
|
| 658 | -<td style="text-align:center"><strong>Fail</strong></td> |
|
| 659 | -</tr> |
|
| 660 | -</tbody> |
|
| 661 | -</table> |
|
| 662 | -<h1 id="details">Details</h1> |
|
| 663 | -
|
|
| 664 | -</body>
|
|
| 665 | -</html>
|