-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathreport.html
More file actions
601 lines (583 loc) · 22.9 KB
/
report.html
File metadata and controls
601 lines (583 loc) · 22.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
<!–– Rscript -e "library(knitr); knit('report.Rhtml', output='report.html')" $PARAMS ––>
<!DOCTYPE html>
<html>
<head>
<style type="text/css">
.knitr .inline {
background-color: #f7f7f7;
border:solid 1px #B0B0B0;
}
.error {
font-weight: bold;
color: #FF0000;
}
.warning {
font-weight: bold;
}
.message {
font-style: italic;
}
.source, .output, .warning, .error, .message {
padding: 0 1em;
border:solid 1px #F7F7F7;
}
.source {
background-color: #f5f5f5;
}
.rimage .left {
text-align: left;
}
.rimage .right {
text-align: right;
}
.rimage .center {
text-align: center;
}
.hl.num {
color: #AF0F91;
}
.hl.str {
color: #317ECC;
}
.hl.com {
color: #AD95AF;
font-style: italic;
}
.hl.opt {
color: #000000;
}
.hl.std {
color: #585858;
}
.hl.kwa {
color: #295F94;
font-weight: bold;
}
.hl.kwb {
color: #B05A65;
}
.hl.kwc {
color: #55aa55;
}
.hl.kwd {
color: #BC5A65;
font-weight: bold;
}
</style>
<title>Report of the quality control (QC) of the genotyping data</title>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap-theme.min.css" integrity="sha384-rHyoN1iRsVXV4nD0JutlnGaslCJuC7uwjduW9SVrLvRYooPp2bWYgmgJQIXwl/Sp" crossorigin="anonymous">
<link href="bootstrap-3.3.7-dist/css/bootstrap.min.css" rel="stylesheet">
<link href="bootstrap-3.3.7-dist/css/bootstrap-theme.min.css" rel="stylesheet">
</head>
<body>
<h1> Report of the quality control (QC) of the genotyping data </h1>
<p>QC was performed on 14906 samples distributed across 52 batches.</p>
<p>Input data was read from the following files: </p>
<p>n1.zcall, n2.zcall, n3.zcall, n4.zcall, n5.zcall, n6.zcall, n7.zcall, n8.zcall, n9.zcall, n10.zcall, n11.zcall, n12.zcall, n13.zcall, n14.zcall, n15.zcall, n16.zcall, n17.zcall, n18.zcall, n19.zcall, n20.zcall, n21.zcall, n22.zcall, n23.zcall, n24.zcall, n25.zcall, n26.zcall, n27.zcall, n28.zcall, n29.zcall, n30.zcall, n31.zcall, n32.zcall, n33.zcall, n34.zcall, n35.zcall, n36.zcall, n37.zcall, n38.zcall, n39.zcall, n40.zcall, n41.zcall, n42.zcall, n43.zcall, n44.zcall, n45.zcall, n46.zcall, n47.zcall, n48.zcall, n49.zcall, n50.zcall, n51.zcall, n52.zcall</p><p>The files were in this folder:</p><p>/groupvol/med-bio/epiUKB/Airwave//coreExome_zcall</p>
<h2> Sample QC </h2>
<hr/>
<p>Per-sample QC of GWA data consisted of four steps: (1) identification of individuals with discordant sex information, (2) identification of samples with outlying missing genotype or heterozygosity rates, (3) identification of duplicated or related individuals and (4) identification of individuals of divergent ancestry. Steps 2 and 3 were carried out per-batch individually, whereas steps 3 and 4 were applied on the whole sample set.</p>
<h3> Samples with outlying missing genotype or heterozygosity rates </h3>
<p>Large variations exist in DNA sample quality and these can have substantial effects on genotype call rate and genotype accuracy. Samples of low DNA quality or concentration often have below-average call rates and genotype accuracy. The genotype failure rate and heterozygosity rate per individual are both measures of DNA sample quality. Therefore, individuals with more than 3% missing genotypes were removed. Those with an excessive or reduced proportion of heterozygote genotypes (3 SDs from the batch mean), which may be indicative of DNA sample contamination, inbreeding or differing population, were equally removed.</p>
<?xml version="1.0" encoding="UTF-8"?>
<table class="table table-striped table-hover table-condensed table-responsive" style="width: auto !important; margin-left: auto; margin-right: auto;">
<thead>
<tr><th style="border-bottom:hidden"/><th style="border-bottom:hidden"/><th style="border-bottom:hidden"/><th style="border-bottom:hidden"/><th style="text-align:center; border-bottom:hidden; padding-bottom:0; padding-left:3px;padding-right:3px;" colspan="3"><div style="border-bottom: 1px solid #ddd;padding-bottom: 5px;">Filters</div></th></tr><tr>
<th style="text-align:left;"> BATCH </th>
<th style="text-align:left;"> total </th>
<th style="text-align:left;"> kept </th>
<th style="text-align:left;"> excluded </th>
<th style="text-align:left;"> high_imiss </th>
<th style="text-align:left;"> high_het </th>
<th style="text-align:left;"> low_het </th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;font-weight: bold;"> ALL </td>
<td style="text-align:left;font-weight: bold;"> 14906 </td>
<td style="text-align:left;font-weight: bold;"> 14698 </td>
<td style="text-align:left;font-weight: bold;"> 208 </td>
<td style="text-align:left;font-weight: bold;"> 75 </td>
<td style="text-align:left;font-weight: bold;"> 159 </td>
<td style="text-align:left;font-weight: bold;"> 26 </td>
</tr>
<tr>
<td style="text-align:left;"> n1 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n2 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n3 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n4 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
</tr>
<tr>
<td style="text-align:left;"> n5 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 281 </td>
<td style="text-align:left;"> 7 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 6 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n6 </td>
<td style="text-align:left;"> 240 </td>
<td style="text-align:left;"> 237 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n7 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 279 </td>
<td style="text-align:left;"> 9 </td>
<td style="text-align:left;"> 9 </td>
<td style="text-align:left;"> 6 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n8 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n9 </td>
<td style="text-align:left;"> 276 </td>
<td style="text-align:left;"> 275 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n10 </td>
<td style="text-align:left;"> 276 </td>
<td style="text-align:left;"> 274 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n11 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 283 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n12 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 281 </td>
<td style="text-align:left;"> 7 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 4 </td>
</tr>
<tr>
<td style="text-align:left;"> n13 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n14 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n15 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n16 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 283 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n17 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n18 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n19 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n20 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 2 </td>
</tr>
<tr>
<td style="text-align:left;"> n21 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n22 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n23 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 275 </td>
<td style="text-align:left;"> 12 </td>
<td style="text-align:left;"> 12 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n24 </td>
<td style="text-align:left;"> 249 </td>
<td style="text-align:left;"> 245 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n25 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n26 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n27 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n28 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n29 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 283 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n30 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n31 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n32 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n33 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n34 </td>
<td style="text-align:left;"> 576 </td>
<td style="text-align:left;"> 563 </td>
<td style="text-align:left;"> 13 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 10 </td>
<td style="text-align:left;"> 2 </td>
</tr>
<tr>
<td style="text-align:left;"> n35 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n36 </td>
<td style="text-align:left;"> 283 </td>
<td style="text-align:left;"> 278 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n37 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n38 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n39 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n40 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 280 </td>
<td style="text-align:left;"> 8 </td>
<td style="text-align:left;"> 6 </td>
<td style="text-align:left;"> 7 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n41 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n42 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 286 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n43 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n44 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 2 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n45 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n46 </td>
<td style="text-align:left;"> 287 </td>
<td style="text-align:left;"> 270 </td>
<td style="text-align:left;"> 17 </td>
<td style="text-align:left;"> 17 </td>
<td style="text-align:left;"> 8 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n47 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n48 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 283 </td>
<td style="text-align:left;"> 5 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n49 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 284 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 4 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n50 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 285 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 3 </td>
<td style="text-align:left;"> 0 </td>
</tr>
<tr>
<td style="text-align:left;"> n51 </td>
<td style="text-align:left;"> 288 </td>
<td style="text-align:left;"> 281 </td>
<td style="text-align:left;"> 7 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 6 </td>
<td style="text-align:left;"> 1 </td>
</tr>
<tr>
<td style="text-align:left;"> n52 </td>
<td style="text-align:left;"> 48 </td>
<td style="text-align:left;"> 47 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
<td style="text-align:left;"> 1 </td>
<td style="text-align:left;"> 0 </td>
</tr>
</tbody>
</table>
<h3> Duplicated or related individuals </h3>
<p>If duplicates, high-degree relatives are present, a bias may be introduced in the study because the genotypes within families will be overrepresented, and thus the sample may no longer be a fair reflection of the allele frequencies in the entire population. To identify duplicate and related individuals, identity by state (IBS) was calculated for each pair of individuals based on the average proportion of alleles shared in common at genotyped SNPs. Because the method works best when only independent SNPs are included in the analysis, regions of extended linkage disequilibrium (LD) were removed remaining regions were pruned so that no pair of SNPs within a 50 kb window wre correlated at r2 > 0.2. The degree of recent shared ancestry for a pair of individuals (identity by descent, IBD) was then estimated with genome-wide IBS data.</p>
<h3> Individuals of divergent ancestry</h3>
<p>In genetic studies, a major source of confounding is population stratification, in which genotypic differences between cases and controls are generated because of different population origins rather than because of any effect on disease risk. Efforts were made to reduce the effect of population stratification through the removal of individuals of divergent ancestry. For this purpose, principal component analysis (PCA) was used, a multivariate statistical method used here to derive uncorrelated variables from the overall set of (correlated) markers. The principal component model was built using pruned genome-wide genotype data from populations of known ancestry, namely, the HapMap genotype data from Europe (CEU), Asia (CHB + JPT) and Africa (YRI). The PCA was then applied to predict principal component scores for the sample set, thus allowing them to be clustered in terms of ancestry alongside the HapMap samples. Regions of extended high LD (including the HLA region) were removed before the analysis because these can overly influence the principal component model.</p>
<p>The CEU population was the closest to the majority of individuals in the sample set. A maximum Euclidean distance of 0.005 from the this population in the first to principal components was set as a threshold to remove individuals with divergent ancestry.</p>
<img src='/groupvol/med-bio/epiUKB/Airwave//QC/illumina_b37_maf0.01/ancestry.png'/>
</body>
</html>