Imputation Report For Cohort: 07_imputation_check

Per chromosome imputation report for cohort 07_imputation_check.

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC

UPLOADED 12.3.2020

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 34417086 87.952
0.1 1242685 3.176
0.2 820374 2.096
0.3 610392 1.560
0.4 493353 1.261
0.5 400604 1.024
0.6 339075 0.866
0.7 284170 0.726
0.8 239889 0.613
0.9 283950 0.726
Total 39131578 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.0 7219928 18.450
0.1 2052775 5.246
0.2 1493111 3.816
0.3 1458689 3.728
0.4 1710329 4.371
0.5 2285036 5.839
0.6 3178816 8.123
0.7 4377653 11.187
0.8 6146715 15.708
0.9 9197319 23.504
1.0 11207 0.029
Total 39131578 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 2706949 88.1762
0.1 94974 3.0937
0.2 61426 2.0009
0.3 44454 1.4480
0.4 38760 1.2626
0.5 31905 1.0393
0.6 25937 0.8449
0.7 22047 0.7182
0.8 18995 0.6187
0.9 24484 0.7975
Total 3069931

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 564799 18.3978
0.1 163714 5.3328
0.2 119106 3.8798
0.3 116767 3.8036
0.4 134785 4.3905
0.5 182534 5.9459
0.6 251721 8.1996
0.7 344342 11.2166
0.8 484253 15.7741
0.9 707303 23.0397
1.0 607 0.0198
Total 3069931

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 2996835 88.3439
0.1 105819 3.1194
0.2 68390 2.0161
0.3 49453 1.4578
0.4 40910 1.2060
0.5 32563 0.9599
0.6 28340 0.8354
0.7 23939 0.7057
0.8 20360 0.6002
0.9 25628 0.7555
Total 3392237

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 630319 18.5812
0.1 178188 5.2528
0.2 130272 3.8403
0.3 125698 3.7055
0.4 145624 4.2929
0.5 193861 5.7148
0.6 271247 7.9961
0.7 375705 11.0754
0.8 528764 15.5875
0.9 811687 23.9278
1.0 872 0.0257
Total 3392237

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 2484463 88.0424
0.1 90370 3.2025
0.2 58056 2.0573
0.3 43652 1.5469
0.4 35413 1.2549
0.5 29479 1.0447
0.6 23921 0.8477
0.7 20458 0.7250
0.8 17096 0.6058
0.9 18986 0.6728
Total 2821894

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 516098 18.2891
0.1 143552 5.0871
0.2 103742 3.6763
0.3 99997 3.5436
0.4 117240 4.1547
0.5 159458 5.6507
0.6 224834 7.9675
0.7 312578 11.0769
0.8 446075 15.8076
0.9 697617 24.7216
1.0 703 0.0249
Total 2821894

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 2435671 87.3758
0.1 87861 3.1519
0.2 63669 2.2840
0.3 45434 1.6299
0.4 34934 1.2532
0.5 28165 1.0104
0.6 25195 0.9038
0.7 21752 0.7803
0.8 19911 0.7143
0.9 24989 0.8964
Total 2787581

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 499234 17.9092
0.1 142349 5.1065
0.2 103400 3.7093
0.3 100248 3.5962
0.4 119242 4.2776
0.5 160212 5.7473
0.6 225699 8.0966
0.7 317943 11.4057
0.8 454250 16.2955
0.9 664454 23.8362
1.0 550 0.0197
Total 2787581

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 2284815 88.2792
0.1 79945 3.0889
0.2 55003 2.1252
0.3 40456 1.5631
0.4 31690 1.2244
0.5 25814 0.9974
0.6 22076 0.8530
0.7 18688 0.7221
0.8 15109 0.5838
0.9 14572 0.5630
Total 2588168

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 474092 18.3177
0.1 132549 5.1213
0.2 95158 3.6767
0.3 92955 3.5915
0.4 107679 4.1604
0.5 146563 5.6628
0.6 208863 8.0699
0.7 296122 11.4414
0.8 421845 16.2990
0.9 611761 23.6368
1.0 581 0.0224
Total 2588168

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 2151038 87.4366
0.1 84564 3.4374
0.2 54494 2.2151
0.3 40133 1.6313
0.4 34200 1.3902
0.5 26404 1.0733
0.6 22484 0.9139
0.7 17366 0.7059
0.8 15122 0.6147
0.9 14306 0.5815
Total 2460111

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 437877 17.7991
0.1 122225 4.9683
0.2 87464 3.5553
0.3 85748 3.4855
0.4 99048 4.0262
0.5 133298 5.4184
0.6 189926 7.7202
0.7 264199 10.7393
0.8 379838 15.4399
0.9 657192 26.7139
1.0 3296 0.1340
Total 2460111

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 2014441 87.9936
0.1 73894 3.2278
0.2 48084 2.1004
0.3 36731 1.6045
0.4 29797 1.3016
0.5 23402 1.0222
0.6 19421 0.8483
0.7 16366 0.7149
0.8 12310 0.5377
0.9 14859 0.6491
Total 2289305

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 425548 18.5885
0.1 119581 5.2235
0.2 85472 3.7335
0.3 83429 3.6443
0.4 96288 4.2060
0.5 128191 5.5996
0.6 182443 7.9694
0.7 252480 11.0287
0.8 359320 15.6956
0.9 555984 24.2861
1.0 569 0.0249
Total 2289305

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 1983602 88.4469
0.1 67090 2.9915
0.2 46053 2.0535
0.3 34057 1.5186
0.4 28072 1.2517
0.5 22573 1.0065
0.6 18435 0.8220
0.7 16001 0.7135
0.8 13311 0.5935
0.9 13511 0.6024
Total 2242705

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 412815 18.4070
0.1 114428 5.1022
0.2 83535 3.7247
0.3 80212 3.5766
0.4 94068 4.1944
0.5 124640 5.5576
0.6 175596 7.8297
0.7 246096 10.9732
0.8 359416 16.0260
0.9 551477 24.5898
1.0 422 0.0188
Total 2242705

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 1484915 88.0487
0.1 55494 3.2905
0.2 35265 2.0911
0.3 25577 1.5166
0.4 20229 1.1995
0.5 16709 0.9908
0.6 14610 0.8663
0.7 11998 0.7114
0.8 10196 0.6046
0.9 11478 0.6806
Total 1686471

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 316681 18.7777
0.1 88053 5.2211
0.2 64109 3.8014
0.3 62371 3.6983
0.4 73678 4.3688
0.5 98259 5.8263
0.6 135890 8.0577
0.7 187122 11.0955
0.8 265538 15.7452
0.9 394425 23.3876
1.0 345 0.0205
Total 1686471

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 1687975 87.5731
0.1 63875 3.3139
0.2 41125 2.1336
0.3 29692 1.5404
0.4 24941 1.2940
0.5 21405 1.1105
0.6 16564 0.8594
0.7 14372 0.7456
0.8 12873 0.6679
0.9 14681 0.7617
Total 1927503

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 345433 17.9213
0.1 98606 5.1157
0.2 72420 3.7572
0.3 69890 3.6259
0.4 81942 4.2512
0.5 107466 5.5754
0.6 150766 7.8218
0.7 210778 10.9353
0.8 305112 15.8294
0.9 484456 25.1339
1.0 634 0.0329
Total 1927503

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 1699205 87.7240
0.1 59816 3.0881
0.2 39466 2.0375
0.3 30716 1.5858
0.4 24000 1.2390
0.5 21023 1.0853
0.6 18508 0.9555
0.7 14066 0.7262
0.8 12485 0.6446
0.9 17705 0.9140
Total 1936990

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 348180 17.9753
0.1 97767 5.0474
0.2 69921 3.6098
0.3 68215 3.5217
0.4 79402 4.0992
0.5 107448 5.5472
0.6 151441 7.8184
0.7 211792 10.9341
0.8 311224 16.0674
0.9 491134 25.3555
1.0 466 0.0241
Total 1936990

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 1622296 87.7810
0.1 59553 3.2224
0.2 36945 1.9991
0.3 30883 1.6711
0.4 23295 1.2605
0.5 18880 1.0216
0.6 16171 0.8750
0.7 13335 0.7215
0.8 12018 0.6503
0.9 14741 0.7976
Total 1848117

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 333083 18.0228
0.1 94791 5.1291
0.2 68795 3.7224
0.3 67212 3.6368
0.4 78823 4.2650
0.5 103788 5.6159
0.6 143726 7.7769
0.7 200283 10.8371
0.8 284130 15.3740
0.9 473058 25.5968
1.0 428 0.0232
Total 1848117

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 1204734 86.9572
0.1 44425 3.2066
0.2 29801 2.1510
0.3 22549 1.6276
0.4 18088 1.3056
0.5 15861 1.1448
0.6 12700 0.9167
0.7 10902 0.7869
0.8 10170 0.7341
0.9 16203 1.1695
Total 1385433

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 242984 17.5385
0.1 71264 5.1438
0.2 51687 3.7307
0.3 50124 3.6179
0.4 58169 4.1986
0.5 78508 5.6667
0.6 111121 8.0207
0.7 153628 11.0888
0.8 221818 16.0107
0.9 345741 24.9554
1.0 389 0.0281
Total 1385433

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 1117691 87.9770
0.1 40359 3.1768
0.2 27746 2.1840
0.3 19319 1.5207
0.4 16193 1.2746
0.5 11370 0.8950
0.6 10528 0.8287
0.7 9481 0.7463
0.8 7969 0.6273
0.9 9780 0.7698
Total 1270436

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 233932 18.4135
0.1 67770 5.3344
0.2 48628 3.8277
0.3 47818 3.7639
0.4 55943 4.4034
0.5 74105 5.8330
0.6 100218 7.8885
0.7 137416 10.8164
0.8 196020 15.4293
0.9 308341 24.2705
1.0 245 0.0193
Total 1270436

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 1002752 88.0213
0.1 34591 3.0364
0.2 23653 2.0763
0.3 17848 1.5667
0.4 14975 1.3145
0.5 11064 0.9712
0.6 9473 0.8315
0.7 7656 0.6720
0.8 6815 0.5982
0.9 10388 0.9119
Total 1139215

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 214437 18.8232
0.1 62449 5.4818
0.2 45802 4.0205
0.3 46157 4.0516
0.4 54136 4.7520
0.5 71050 6.2368
0.6 95069 8.3451
0.7 129333 11.3528
0.8 176234 15.4698
0.9 244274 21.4423
1.0 274 0.0241
Total 1139215

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 1136179 88.6741
0.1 38695 3.0200
0.2 24943 1.9467
0.3 19565 1.5270
0.4 14108 1.1011
0.5 12601 0.9835
0.6 11208 0.8747
0.7 8821 0.6884
0.8 6831 0.5331
0.9 8346 0.6514
Total 1281297

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 260485 20.3298
0.1 72573 5.6640
0.2 53878 4.2050
0.3 52496 4.0971
0.4 61922 4.8328
0.5 81772 6.3820
0.6 109578 8.5521
0.7 145135 11.3272
0.8 194741 15.1987
0.9 248496 19.3941
1.0 221 0.0172
Total 1281297

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 964380 88.4694
0.1 32264 2.9598
0.2 23313 2.1387
0.3 15628 1.4337
0.4 14156 1.2986
0.5 11327 1.0391
0.6 9167 0.8410
0.7 7980 0.7321
0.8 5460 0.5009
0.9 6397 0.5868
Total 1090072

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 210829 19.3408
0.1 62218 5.7077
0.2 46507 4.2664
0.3 46194 4.2377
0.4 55383 5.0807
0.5 73187 6.7140
0.6 98713 9.0556
0.7 130663 11.9866
0.8 168563 15.4635
0.9 197670 18.1337
1.0 145 0.0133
Total 1090072

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 966819 87.5143
0.1 35769 3.2377
0.2 23593 2.1356
0.3 18387 1.6644
0.4 14302 1.2946
0.5 10822 0.9796
0.6 9639 0.8725
0.7 7975 0.7219
0.8 7035 0.6368
0.9 10414 0.9427
Total 1104755

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 203341 18.4060
0.1 59711 5.4049
0.2 44080 3.9900
0.3 43187 3.9092
0.4 51241 4.6382
0.5 69558 6.2962
0.6 95715 8.6639
0.7 131812 11.9313
0.8 172961 15.6561
0.9 233017 21.0922
1.0 132 0.0119
Total 1104755

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 763541 87.9094
0.1 31251 3.5980
0.2 19132 2.2027
0.3 14143 1.6283
0.4 9817 1.1303
0.5 8276 0.9528
0.6 7477 0.8609
0.7 6280 0.7230
0.8 4479 0.5157
0.9 4158 0.4787
Total 868554

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 173671 19.9954
0.1 50443 5.8077
0.2 37551 4.3234
0.3 38366 4.4172
0.4 47173 5.4312
0.5 61662 7.0994
0.6 82405 9.4876
0.7 102957 11.8538
0.8 124594 14.3450
0.9 149597 17.2237
1.0 135 0.0155
Total 868554

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 780948 88.2444
0.1 28603 3.2320
0.2 18305 2.0684
0.3 14319 1.6180
0.4 11037 1.2471
0.5 9388 1.0608
0.6 7262 0.8206
0.7 6272 0.7087
0.8 4575 0.5170
0.9 4274 0.4829
Total 884983

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 167931 18.9756
0.1 49396 5.5816
0.2 36062 4.0749
0.3 36029 4.0712
0.4 43848 4.9547
0.5 57997 6.5535
0.6 79300 8.9606
0.7 105145 11.8810
0.8 135078 15.2633
0.9 174081 19.6705
1.0 116 0.0131
Total 884983

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 464984 87.5221
0.1 16847 3.1710
0.2 10627 2.0003
0.3 9194 1.7306
0.4 7513 1.4141
0.5 6137 1.1551
0.6 5061 0.9526
0.7 4654 0.8760
0.8 3837 0.7222
0.9 2422 0.4559
Total 531276

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 104712 19.7095
0.1 30359 5.7144
0.2 22078 4.1557
0.3 22052 4.1508
0.4 26490 4.9861
0.5 35214 6.6282
0.6 47412 8.9242
0.7 62725 11.8065
0.8 81420 15.3254
0.9 98779 18.5928
1.0 35 0.0066
Total 531276

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

Back to top

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 462853 88.2391
0.1 16626 3.1696
0.2 11285 2.1514
0.3 8202 1.5636
0.4 6923 1.3198
0.5 5436 1.0363
0.6 4898 0.9338
0.7 3761 0.7170
0.8 2932 0.5590
0.9 1628 0.3104
Total 524544

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 103447 19.7213
0.1 30789 5.8697
0.2 23444 4.4694
0.3 23524 4.4847
0.4 28205 5.3771
0.5 36265 6.9136
0.6 47133 8.9855
0.7 59399 11.3239
0.8 75521 14.3975
0.9 96775 18.4494
1.0 42 0.0080
Total 524544

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