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