Chromosome index, 22 in total. Skip to the section for a particular chromosome using the buttons below.

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT OXFORD

UPLOADED 17/02/2016

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 34550271 88.131
0.1 1183640 3.019
0.2 784645 2.001
0.3 597669 1.525
0.4 481965 1.229
0.5 393259 1.003
0.6 340346 0.868
0.7 282896 0.722
0.8 239372 0.611
0.9 335496 0.856
1.0 13580 0.035
Total 39203139 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.0 8189606 20.890
0.1 2519897 6.428
0.2 1771425 4.519
0.3 1572599 4.011
0.4 1682161 4.291
0.5 1929613 4.922
0.6 2365593 6.034
0.7 2735890 6.979
0.8 2933246 7.482
0.9 7879712 20.100
1.0 5623397 14.344
Total 39203139 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2710694 88.3215
0.1 89876 2.9284
0.2 57673 1.8791
0.3 45299 1.4760
0.4 37595 1.2249
0.5 30222 0.9847
0.6 27396 0.8926
0.7 22100 0.7201
0.8 18508 0.6030
0.9 28594 0.9317
1.0 1165 0.0380
Total 3069122

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 642258 20.9264
0.1 199842 6.5114
0.2 141613 4.6141
0.3 125590 4.0920
0.4 134353 4.3776
0.5 152256 4.9609
0.6 186148 6.0652
0.7 216085 7.0406
0.8 232537 7.5767
0.9 604522 19.6969
1.0 433918 14.1382
Total 3069122

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2998336 88.4841
0.1 100636 2.9699
0.2 65455 1.9316
0.3 49477 1.4601
0.4 38846 1.1464
0.5 32546 0.9605
0.6 28952 0.8544
0.7 22938 0.6769
0.8 20385 0.6016
0.9 29637 0.8746
1.0 1350 0.0398
Total 3388558

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 714294 21.0796
0.1 222347 6.5617
0.2 153533 4.5309
0.3 134632 3.9731
0.4 141796 4.1846
0.5 160571 4.7386
0.6 197769 5.8364
0.7 230438 6.8005
0.8 246196 7.2655
0.9 680396 20.0792
1.0 506586 14.9499
Total 3388558

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2489743 88.1857
0.1 86662 3.0695
0.2 55700 1.9729
0.3 42168 1.4936
0.4 35845 1.2696
0.5 28638 1.0143
0.6 24572 0.8703
0.7 20369 0.7215
0.8 17066 0.6045
0.9 21754 0.7705
1.0 778 0.0276
Total 2823295

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 607102 21.5033
0.1 180911 6.4078
0.2 124979 4.4267
0.3 108555 3.8450
0.4 114877 4.0689
0.5 132093 4.6787
0.6 163217 5.7811
0.7 192232 6.8088
0.8 206958 7.3304
0.9 576155 20.4072
1.0 416216 14.7422
Total 2823295

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2442803 87.5880
0.1 81682 2.9288
0.2 60434 2.1669
0.3 45241 1.6221
0.4 34343 1.2314
0.5 27660 0.9918
0.6 24628 0.8831
0.7 21610 0.7748
0.8 19502 0.6993
0.9 29626 1.0623
1.0 1440 0.0516
Total 2788969

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 571312 20.4847
0.1 184138 6.6024
0.2 129288 4.6357
0.3 115372 4.1367
0.4 120739 4.3292
0.5 134775 4.8324
0.6 161952 5.8069
0.7 185274 6.6431
0.8 199917 7.1681
0.9 580576 20.8169
1.0 405626 14.5439
Total 2788969

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2289474 88.4265
0.1 76476 2.9537
0.2 52133 2.0135
0.3 40501 1.5643
0.4 31545 1.2184
0.5 24584 0.9495
0.6 22489 0.8686
0.7 18100 0.6991
0.8 15063 0.5818
0.9 18187 0.7024
1.0 574 0.0222
Total 2589126

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 542524 20.9539
0.1 162109 6.2611
0.2 112357 4.3396
0.3 98934 3.8211
0.4 105633 4.0799
0.5 117624 4.5430
0.6 147748 5.7065
0.7 175771 6.7888
0.8 194420 7.5091
0.9 532807 20.5786
1.0 399199 15.4183
Total 2589126

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2155454 87.5758
0.1 81889 3.3271
0.2 52890 2.1489
0.3 40391 1.6411
0.4 32200 1.3083
0.5 26147 1.0623
0.6 22197 0.9019
0.7 17744 0.7209
0.8 15378 0.6248
0.9 16430 0.6675
1.0 525 0.0213
Total 2461245

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 502264 20.4069
0.1 149517 6.0749
0.2 104564 4.2484
0.3 92579 3.7615
0.4 98097 3.9857
0.5 110677 4.4968
0.6 139387 5.6633
0.7 166391 6.7604
0.8 181776 7.3855
0.9 551709 22.4159
1.0 364284 14.8008
Total 2461245

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 2019968 88.1921
0.1 68945 3.0101
0.2 47841 2.0887
0.3 35131 1.5338
0.4 28655 1.2511
0.5 23701 1.0348
0.6 19288 0.8421
0.7 16750 0.7313
0.8 12320 0.5379
0.9 17249 0.7531
1.0 571 0.0249
Total 2290419

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 492675 21.5103
0.1 149217 6.5148
0.2 105245 4.5950
0.3 94411 4.1220
0.4 100495 4.3876
0.5 114052 4.9795
0.6 136317 5.9516
0.7 156231 6.8211
0.8 168116 7.3400
0.9 458810 20.0317
1.0 314850 13.7464
Total 2290419

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1989189 88.6533
0.1 64036 2.8539
0.2 44453 1.9812
0.3 31980 1.4253
0.4 27680 1.2336
0.5 21460 0.9564
0.6 18976 0.8457
0.7 15848 0.7063
0.8 12942 0.5768
0.9 16738 0.7460
1.0 483 0.0215
Total 2243785

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 475269 21.1816
0.1 140202 6.2485
0.2 96956 4.3211
0.3 85539 3.8123
0.4 90228 4.0212
0.5 102545 4.5702
0.6 125819 5.6074
0.7 150435 6.7045
0.8 168871 7.5262
0.9 466531 20.7921
1.0 341390 15.2149
Total 2243785

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1485849 88.1734
0.1 53661 3.1844
0.2 34050 2.0206
0.3 24592 1.4593
0.4 20387 1.2098
0.5 15902 0.9437
0.6 14557 0.8638
0.7 12055 0.7154
0.8 9524 0.5652
0.9 14093 0.8363
1.0 475 0.0282
Total 1685145

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 322904 19.1618
0.1 99722 5.9177
0.2 70930 4.2091
0.3 63695 3.7798
0.4 69327 4.1140
0.5 79909 4.7420
0.6 102915 6.1072
0.7 123516 7.3297
0.8 140940 8.3637
0.9 356572 21.1597
1.0 254715 15.1153
Total 1685145

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1702238 87.8221
0.1 60528 3.1228
0.2 39551 2.0405
0.3 28599 1.4755
0.4 24056 1.2411
0.5 21286 1.0982
0.6 17186 0.8867
0.7 13842 0.7141
0.8 13006 0.6710
0.9 17305 0.8928
1.0 683 0.0352
Total 1938280

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 395590 20.4093
0.1 117188 6.0460
0.2 79937 4.1241
0.3 70068 3.6150
0.4 74144 3.8252
0.5 85817 4.4275
0.6 110589 5.7055
0.7 136258 7.0298
0.8 153853 7.9376
0.9 425212 21.9376
1.0 289624 14.9423
Total 1938280

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1713579 87.8692
0.1 59060 3.0285
0.2 35900 1.8409
0.3 30953 1.5872
0.4 23640 1.2122
0.5 20950 1.0743
0.6 17843 0.9150
0.7 14140 0.7251
0.8 12629 0.6476
0.9 20420 1.0471
1.0 1034 0.0530
Total 1950148

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 412440 21.1492
0.1 120762 6.1925
0.2 83495 4.2815
0.3 73564 3.7722
0.4 77953 3.9973
0.5 89216 4.5748
0.6 113000 5.7944
0.7 135090 6.9272
0.8 146323 7.5032
0.9 401175 20.5715
1.0 297130 15.2363
Total 1950148

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1636625 88.0116
0.1 56208 3.0227
0.2 35375 1.9023
0.3 30352 1.6322
0.4 23071 1.2407
0.5 18642 1.0025
0.6 16635 0.8946
0.7 12668 0.6812
0.8 12525 0.6735
0.9 16796 0.9032
1.0 658 0.0354
Total 1859555

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 394926 21.2377
0.1 117120 6.2983
0.2 83541 4.4925
0.3 72968 3.9239
0.4 77802 4.1839
0.5 87564 4.7089
0.6 107761 5.7950
0.7 127635 6.8637
0.8 140106 7.5344
0.9 384329 20.6678
1.0 265803 14.2939
Total 1859555

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1214943 87.1459
0.1 43083 3.0903
0.2 27701 1.9869
0.3 22591 1.6204
0.4 17463 1.2526
0.5 15406 1.1050
0.6 12567 0.9014
0.7 11102 0.7963
0.8 10035 0.7198
0.9 18303 1.3128
1.0 954 0.0684
Total 1394148

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 276735 19.8498
0.1 85464 6.1302
0.2 59670 4.2800
0.3 53339 3.8259
0.4 56933 4.0837
0.5 66462 4.7672
0.6 83607 5.9970
0.7 100560 7.2130
0.8 106564 7.6437
0.9 296284 21.2520
1.0 208530 14.9575
Total 1394148

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1130042 88.2060
0.1 39206 3.0602
0.2 26181 2.0436
0.3 18343 1.4318
0.4 15675 1.2235
0.5 12070 0.9421
0.6 9939 0.7758
0.7 9253 0.7222
0.8 8072 0.6301
0.9 11816 0.9223
1.0 542 0.0423
Total 1281139

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 265917 20.7563
0.1 85793 6.6966
0.2 60229 4.7012
0.3 54891 4.2845
0.4 58257 4.5473
0.5 65228 5.0914
0.6 78776 6.1489
0.7 89397 6.9779
0.8 91648 7.1536
0.9 252776 19.7306
1.0 178227 13.9116
Total 1281139

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1023590 88.3617
0.1 33220 2.8677
0.2 22043 1.9029
0.3 16753 1.4462
0.4 14309 1.2352
0.5 11719 1.0116
0.6 9158 0.7906
0.7 8101 0.6993
0.8 6398 0.5523
0.9 12577 1.0857
1.0 541 0.0467
Total 1158409

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 249723 21.5574
0.1 76540 6.6073
0.2 54761 4.7273
0.3 49386 4.2633
0.4 52259 4.5113
0.5 61530 5.3116
0.6 72488 6.2575
0.7 80702 6.9666
0.8 83836 7.2372
0.9 215490 18.6022
1.0 161694 13.9583
Total 1158409

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1131543 88.7856
0.1 37471 2.9401
0.2 22684 1.7799
0.3 18947 1.4867
0.4 14619 1.1471
0.5 11829 0.9282
0.6 10709 0.8403
0.7 9640 0.7564
0.8 6917 0.5427
0.9 9579 0.7516
1.0 529 0.0415
Total 1274467

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 280554 22.0134
0.1 81904 6.4265
0.2 57692 4.5268
0.3 52286 4.1026
0.4 54887 4.3067
0.5 63275 4.9648
0.6 79762 6.2585
0.7 92794 7.2810
0.8 101160 7.9374
0.9 230692 18.1011
1.0 179461 14.0813
Total 1274467

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 972189 88.7018
0.1 29936 2.7313
0.2 23101 2.1077
0.3 15121 1.3796
0.4 13557 1.2369
0.5 11007 1.0043
0.6 9068 0.8274
0.7 7986 0.7286
0.8 6102 0.5567
0.9 7714 0.7038
1.0 239 0.0218
Total 1096020

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 240481 21.9413
0.1 82602 7.5365
0.2 60695 5.5378
0.3 53832 4.9116
0.4 60382 5.5092
0.5 71920 6.5619
0.6 81437 7.4302
0.7 81769 7.4605
0.8 77001 7.0255
0.9 168802 15.4014
1.0 117099 10.6840
Total 1096020

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 969005 87.6617
0.1 33790 3.0568
0.2 23300 2.1079
0.3 17725 1.6035
0.4 13774 1.2461
0.5 10986 0.9939
0.6 9419 0.8521
0.7 8123 0.7349
0.8 6585 0.5957
0.9 11895 1.0761
1.0 789 0.0714
Total 1105391

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 214114 19.3700
0.1 66975 6.0589
0.2 47046 4.2561
0.3 41127 3.7206
0.4 45815 4.1447
0.5 56421 5.1042
0.6 72263 6.5373
0.7 85029 7.6922
0.8 88665 8.0211
0.9 223763 20.2429
1.0 164173 14.8520
Total 1105391

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 766617 88.2211
0.1 28359 3.2635
0.2 18928 2.1782
0.3 13450 1.5478
0.4 9592 1.1038
0.5 8478 0.9756
0.6 7329 0.8434
0.7 6082 0.6999
0.8 4526 0.5208
0.9 5595 0.6439
1.0 16 0.0018
Total 868972

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 194066 22.3328
0.1 72781 8.3755
0.2 56607 6.5142
0.3 52129 5.9989
0.4 58675 6.7522
0.5 68842 7.9222
0.6 68190 7.8472
0.7 60732 6.9889
0.8 53892 6.2018
0.9 113006 13.0046
1.0 70052 8.0615
Total 868972

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 783041 88.4388
0.1 27120 3.0630
0.2 17990 2.0318
0.3 13288 1.5008
0.4 11175 1.2621
0.5 8804 0.9943
0.6 7794 0.8803
0.7 6050 0.6833
0.8 4687 0.5294
0.9 5312 0.6000
1.0 143 0.0162
Total 885404

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 179927 20.3215
0.1 55041 6.2165
0.2 39059 4.4114
0.3 34759 3.9258
0.4 38170 4.3110
0.5 47108 5.3205
0.6 60237 6.8033
0.7 66999 7.5671
0.8 69237 7.8198
0.9 166321 18.7848
1.0 128546 14.5183
Total 885404

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 461674 87.6356
0.1 15835 3.0058
0.2 10315 1.9580
0.3 8888 1.6871
0.4 7034 1.3352
0.5 6006 1.1401
0.6 4922 0.9343
0.7 4397 0.8346
0.8 4189 0.7952
0.9 3462 0.6572
1.0 89 0.0169
Total 526811

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 103968 19.7354
0.1 32608 6.1897
0.2 23110 4.3868
0.3 20788 3.9460
0.4 23469 4.4549
0.5 28264 5.3651
0.6 36432 6.9156
0.7 41097 7.8011
0.8 41704 7.9163
0.9 103873 19.7173
1.0 71498 13.5719
Total 526811

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 463675 88.3643
0.1 15961 3.0417
0.2 10947 2.0862
0.3 7879 1.5015
0.4 6904 1.3157
0.5 5216 0.9940
0.6 4722 0.8999
0.7 3998 0.7619
0.8 3013 0.5742
0.9 2414 0.4600
1.0 2 0.0004
Total 524731

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.0 110563 21.0704
0.1 37114 7.0730
0.2 26118 4.9774
0.3 24155 4.6033
0.4 27870 5.3113
0.5 33464 6.3774
0.6 39779 7.5808
0.7 41455 7.9002
0.8 39526 7.5326
0.9 89911 17.1347
1.0 54776 10.4389
Total 524731

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering