Per chromosome imputation report for cohort SampleQCReport.
Chromosome index, 22 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
Property | Value |
---|---|
FORMAT | OXFORD |
UPLOADED | 17/02/2016 |
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 |
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 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by 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 |
Variants binned by 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 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering