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Tuesday, September 6, 2016

Note that this utility requires the input file to be unzipped. If a zipped file is provided, the utility may appear to freeze.

File to be processed: dna-data-2016-09-06.zip

ROHs of length at least 200 will be reported.
No-Call runs of length at least 10 will be reported.
No-Calls will be treated as homozygous.
Heterozygous SNPs that are at least 150 SNPs away from the nearest heterozygous SNP will be treated as homozygous.
Note that this utility requires the input file to be unzipped.  If a zipped file is provided, the utility may appear to freeze.

File to be processed:  AncestryDNA.txt

ROHs of length at least 200 will be reported.

No-Call runs of length at least 10 will be reported.

No-Calls will be treated as homozygous.
Heterozygous SNPs that are at least 150 SNPs away from the nearest heterozygous SNP will be treated as homozygous.

Chr  Y has a No-Call run of length 12 from position   2655180 to position   2655371 ( 0.19 Kb)
Chr  Y has a No-Call run of length 17 from position   2655436 to position   2669716 (14.28 Kb)
Chr  Y has a No-Call run of length 21 from position   2697625 to position   2756519 (58.89 Kb)
Chr  Y has a No-Call run of length 17 from position   2837192 to position   2888392 (51.20 Kb)
Chr  Y has a No-Call run of length 10 from position   3199276 to position   4716925 (1517.65 Kb)
Chr  Y has a No-Call run of length 24 from position   6635162 to position   6796065 (160.90 Kb)
Chr  Y has a No-Call run of length 21 from position   6846615 to position   6894819 (48.20 Kb)
Chr  Y has a No-Call run of length 18 from position   6931809 to position   6976734 (44.93 Kb)
Chr  Y has a No-Call run of length 11 from position   7035520 to position   7087279 (51.76 Kb)
Chr  Y has a No-Call run of length 10 from position   7134120 to position   7162736 (28.62 Kb)
Chr  Y has a No-Call run of length 23 from position   7401585 to position   7611416 (209.83 Kb)
Chr  Y has a No-Call run of length 17 from position   7626710 to position   7697222 (70.51 Kb)
Chr  Y has a No-Call run of length 28 from position   7801788 to position   7989319 (187.53 Kb)
Chr  Y has a No-Call run of length 15 from position   8020092 to position   8149348 (129.26 Kb)
Chr  Y has a No-Call run of length 76 from position   8194310 to position   8714022 (519.71 Kb)
Chr  Y has a No-Call run of length 25 from position   8758629 to position   9376415 (617.79 Kb)
Chr  Y has a No-Call run of length 20 from position   9417393 to position   9968357 (550.96 Kb)
Chr  Y has a No-Call run of length 24 from position  13864428 to position  14140277 (275.85 Kb)
Chr  Y has a No-Call run of length 14 from position  14149772 to position  14231555 (81.78 Kb)
Chr  Y has a No-Call run of length 13 from position  14245444 to position  14345705 (100.26 Kb)
Chr  Y has a No-Call run of length 12 from position  14491671 to position  14515265 (23.59 Kb)
Chr  Y has a No-Call run of length 58 from position  14734176 to position  14922817 (188.64 Kb)
Chr  Y has a No-Call run of length 10 from position  14968449 to position  14994820 (26.37 Kb)
Chr  Y has a No-Call run of length 29 from position  15014550 to position  15043778 (29.23 Kb)
Chr  Y has a No-Call run of length 44 from position  15116138 to position  15467824 (351.69 Kb)
Chr  Y has a No-Call run of length 42 from position  15469740 to position  15668070 (198.33 Kb)
Chr  Y has a No-Call run of length 13 from position  15779994 to position  15842844 (62.85 Kb)
Chr  Y has a No-Call run of length 16 from position  15980942 to position  16202544 (221.60 Kb)
Chr  Y has a No-Call run of length 14 from position  16213100 to position  16315153 (102.05 Kb)
Chr  Y has a No-Call run of length 12 from position  16331558 to position  16404607 (73.05 Kb)
Chr  Y has a No-Call run of length 11 from position  16519057 to position  16601300 (82.24 Kb)
Chr  Y has a No-Call run of length 45 from position  16849994 to position  17201259 (351.27 Kb)
Chr  Y has a No-Call run of length 12 from position  17275043 to position  17353144 (78.10 Kb)
Chr  Y has a No-Call run of length 12 from position  17389379 to position  17436200 (46.82 Kb)
Chr  Y has a No-Call run of length 13 from position  17446588 to position  17510373 (63.79 Kb)
Chr  Y has a No-Call run of length 13 from position  17537643 to position  17614366 (76.72 Kb)
Chr  Y has a No-Call run of length 15 from position  17782178 to position  17912084 (129.91 Kb)
Chr  Y has a No-Call run of length 20 from position  17936279 to position  18066156 (129.88 Kb)
Chr  Y has a No-Call run of length 13 from position  18097249 to position  18180446 (83.20 Kb)
Chr  Y has a No-Call run of length 10 from position  18394634 to position  18600862 (206.23 Kb)
Chr  Y has a No-Call run of length 17 from position  18617596 to position  18747493 (129.90 Kb)
Chr  Y has a No-Call run of length 23 from position  18759669 to position  18927898 (168.23 Kb)
Chr  Y has a No-Call run of length 42 from position  19033817 to position  19244931 (211.11 Kb)
Chr  Y has a No-Call run of length 14 from position  19255890 to position  19375294 (119.40 Kb)
Chr  Y has a No-Call run of length 21 from position  19469989 to position  21100759 (1630.77 Kb)
Chr  Y has a No-Call run of length 10 from position  21117888 to position  21242391 (124.50 Kb)
Chr  Y has a No-Call run of length 10 from position  21253443 to position  21288728 (35.29 Kb)
Chr  Y has a No-Call run of length 22 from position  21385724 to position  21570974 (185.25 Kb)
Chr  Y has a No-Call run of length 82 from position  21590100 to position  21784286 (194.19 Kb)
Chr  Y has a No-Call run of length 87 from position  21801722 to position  22072340 (270.62 Kb)
Chr  Y has a No-Call run of length 11 from position  22094491 to position  22191144 (96.65 Kb)
Chr  Y has a No-Call run of length 14 from position  22214221 to position  22601068 (386.85 Kb)
Chr  Y has a No-Call run of length 44 from position  22634764 to position  22843448 (208.68 Kb)
Chr  Y has a No-Call run of length 15 from position  22866703 to position  22944601 (77.90 Kb)
Chr  Y has a No-Call run of length 17 from position  22968980 to position  23069523 (100.54 Kb)
Chr  Y has a No-Call run of length 11 from position  23156865 to position  23248930 (92.07 Kb)
Chr  Y has a No-Call run of length 25 from position  23383729 to position  23791923 (408.19 Kb)
Chr  Y has a No-Call run of length 15 from position  23801764 to position  24366649 (564.89 Kb)
Chr  Y has a No-Call run of length 11 from position  24401940 to position  28538592 (4136.65 Kb)

Chr  1 has a ROH of length   223 from position  45742914 to position  45978675 ( 0.24 Mb)
Chr  1 has a ROH of length   259 from position 156083468 to position 156108924 ( 0.03 Mb)
Chr  2 has a ROH of length   784 from position  47520035 to position  47780865 ( 0.26 Mb)
Chr  2 has a ROH of length   655 from position  48009816 to position  48461993 ( 0.45 Mb)
Chr  2 has a ROH of length  1279 from position 179396885 to position 179582853 ( 0.19 Mb)   (2 heterozygous SNPs treated as homozygous)
Chr  2 has a ROH of length   591 from position 179586698 to position 179649461 ( 0.06 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  2 has a ROH of length   279 from position 215574279 to position 215888624 ( 0.31 Mb)
Chr  3 has a ROH of length   476 from position  38513431 to position  38659795 ( 0.15 Mb)
Chr  5 has a ROH of length   300 from position 131801726 to position 131953510 ( 0.15 Mb)
Chr  5 has a ROH of length   257 from position 176541937 to position 176833020 ( 0.29 Mb)
Chr  6 has a ROH of length   880 from position  30193577 to position  30940387 ( 0.75 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  7 has a ROH of length   217 from position 117170943 to position 117199533 ( 0.03 Mb)
Chr  7 has a ROH of length   559 from position 117218381 to position 117476763 ( 0.26 Mb)
Chr  7 has a ROH of length   232 from position 134013464 to position 134944544 ( 0.93 Mb)
Chr  9 has a ROH of length   219 from position  34637265 to position  34677857 ( 0.04 Mb)
Chr  9 has a ROH of length   527 from position 135616700 to position 135849248 ( 0.23 Mb)
Chr 11 has a ROH of length   210 from position  76861379 to position  76918426 ( 0.06 Mb)
Chr 13 has a ROH of length  1790 from position  32894738 to position  32915344 ( 0.02 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr 13 has a ROH of length   666 from position  32929242 to position  32956757 ( 0.03 Mb)   (2 heterozygous SNPs treated as homozygous)
Chr 14 has a ROH of length   409 from position  23885041 to position  23898990 ( 0.01 Mb)
Chr 16 has a ROH of length  1267 from position   2088585 to position   2199788 ( 0.11 Mb)
Chr 16 has a ROH of length   417 from position  23607079 to position  23713813 ( 0.11 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr 16 has a ROH of length   462 from position  68713730 to position  69000588 ( 0.29 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr 17 has a ROH of length  1683 from position  41173086 to position  41246476 ( 0.07 Mb)
Chr 17 has a ROH of length   463 from position  41246482 to position  41462229 ( 0.22 Mb)
Chr 19 has a ROH of length   205 from position   1192769 to position   1250109 ( 0.06 Mb)
Chr  X has a ROH of length   283 from position  98446580 to position 100127101 ( 1.68 Mb)
Chr  X has a ROH of length   406 from position 100563546 to position 102663922 ( 2.10 Mb)
Chr  X has a ROH of length   277 from position 149537834 to position 149943008 ( 0.41 Mb)
Chr  X has a ROH of length   248 from position 153294996 to position 153297142 ( 0.00 Mb)
Chr  X has a ROH of length   511 from position 153546556 to position 154229403 ( 0.68 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  Y has a ROH of length  1691 from position   2655180 to position  28817458 (26.16 Mb)   (2 heterozygous SNPs treated as homozygous)
Total Mb:  36.37

The following percentages are for individual homozygous SNPs, not just those in lengthy ROHs.

Chr  1:  70.171 % (35519 of 50618 SNPs) are homozygous,    44 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  2:  70.999 % (37247 of 52461 SNPs) are homozygous,    56 No-Calls,   3 heterozygous SNPs treated as homozygous
Chr  3:  69.895 % (28705 of 41069 SNPs) are homozygous,    37 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  4:  67.399 % (24160 of 35846 SNPs) are homozygous,    37 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  5:  70.579 % (27050 of 38326 SNPs) are homozygous,    35 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  6:  70.495 % (28876 of 40962 SNPs) are homozygous,    59 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  7:  70.704 % (24760 of 35019 SNPs) are homozygous,    34 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  8:  67.943 % (21381 of 31469 SNPs) are homozygous,    35 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  9:  69.696 % (20570 of 29514 SNPs) are homozygous,    27 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 10:  69.291 % (22550 of 32544 SNPs) are homozygous,    37 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 11:  71.538 % (23164 of 32380 SNPs) are homozygous,    29 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 12:  70.265 % (22347 of 31804 SNPs) are homozygous,    40 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 13:  71.739 % (17553 of 24468 SNPs) are homozygous,    28 No-Calls,   3 heterozygous SNPs treated as homozygous
Chr 14:  70.766 % (14817 of 20938 SNPs) are homozygous,    16 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 15:  71.141 % (14687 of 20645 SNPs) are homozygous,    18 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 16:  73.575 % (17561 of 23868 SNPs) are homozygous,    28 No-Calls,   2 heterozygous SNPs treated as homozygous
Chr 17:  74.123 % (17310 of 23353 SNPs) are homozygous,    22 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 18:  70.418 % (13240 of 18802 SNPs) are homozygous,    17 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 19:  73.055 % (11908 of 16300 SNPs) are homozygous,    21 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 20:  70.669 % (12061 of 17067 SNPs) are homozygous,    17 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 21:  69.333 % ( 6744 of  9727 SNPs) are homozygous,    10 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 22:  70.676 % ( 7392 of 10459 SNPs) are homozygous,    10 No-Calls,   0 heterozygous SNPs treated as homozygous

Chr  X:  78.067 % (22555 of 28892 SNPs) are homozygous,    31 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  Y:   1691 SNPs,  1557 No-Calls,   2 heterozygous SNPs treated as homozygous
Chr XY:    525 SNPs,     1 No-Calls,   0 heterozygous SNPs treated as homozygous
mtDNA :    195 SNPs,     0 No-Calls,   0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22):   0.103 % (   657 of 637639 SNPs) are NoCalls
Total autosomal (Chr 1-22):  29.490 % (188037 of 637639 SNPs) are Heterozygous (this tally excludes 9 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  70.510 % (449602 of 637639 SNPs) are Homozygous   (this tally includes 9 heterozygous SNPs that were treated as homozygous)
Processing Completed.

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