АвторТема: Анализ однородности генома  (Прочитано 23234 раз)

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Re: Анализ однородности генома
« Ответ #90 : 21 Май 2010, 00:24:38 »
ну, вам виднее (я статей не читал). Если же вдруг опять увидите - что можно как-то вытащить родство из-каких нибудь "краевых эффектов" на ROH или чего ещё - дайте знать (калькулятор есть, регионы вытаскивать умеем, надо только научится вытащить информацию из них - если она там есть). Потом, ведь можно вводить какие-нибудь поправки - для родителей идентичных гаплотипов, и различных гаплотипов (Молчу, молчу, я здесь не компетентен).

Ну, гаплоблоки можно и сейчас искать. Правда тут два неудобства- этих алгоритмов поиска блоков существует множество (и все они дают разные результаты), второе -большинство этих общих гаплоблоков настолько древние, что выходят за любой мыслимый горизонт генеалогических событий. :)

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Re: Анализ однородности генома
« Ответ #91 : 30 Июнь 2010, 20:58:53 »
прогон данных моего отца, немца Поволжья.

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.

Chr  1 has a ROH of length  301 from position  42420501 to position  44327044 (1.91 Mb)
Chr  2 has a ROH of length  220 from position 165739074 to position 166656351 (0.92 Mb)
Chr  3 has a ROH of length  245 from position 167350172 to position 169189729 (1.84 Mb)
Chr  6 has a ROH of length  200 from position  50873311 to position  51930256 (1.06 Mb)
Chr  6 has a No-Call run of length 13 from position  79031111 to position  79081009 (49.90 Kb)
Chr  8 has a ROH of length  208 from position  15609497 to position  15984805 (0.38 Mb)
Chr  9 has a ROH of length 2170 from position  16308055 to position  23996322 (7.69 Mb)
Chr  9 has a ROH of length  243 from position 131364187 to position 132340429 (0.98 Mb)
Chr 10 has a ROH of length  220 from position  57977755 to position  59092753 (1.11 Mb)
Chr 10 has a ROH of length  259 from position  66773246 to position  67741619 (0.97 Mb)
Chr 11 has a ROH of length  212 from position  55420386 to position  56416314 (1.00 Mb)

Chr  1:  68.596 % (30163 of 43972 SNPs) are homozygous, 121 No-Calls
Chr  2:  69.271 % (32137 of 46393 SNPs) are homozygous, 118 No-Calls
Chr  3:  68.129 % (26222 of 38489 SNPs) are homozygous,  97 No-Calls
Chr  4:  68.458 % (23436 of 34234 SNPs) are homozygous, 106 No-Calls
Chr  5:  68.595 % (23887 of 34823 SNPs) are homozygous, 102 No-Calls
Chr  6:  67.944 % (25780 of 37943 SNPs) are homozygous, 111 No-Calls
Chr  7:  68.468 % (21308 of 31121 SNPs) are homozygous,  91 No-Calls
Chr  8:  68.439 % (21702 of 31710 SNPs) are homozygous, 101 No-Calls
Chr  9:  69.386 % (18778 of 27063 SNPs) are homozygous,  85 No-Calls
Chr 10:  69.531 % (20849 of 29985 SNPs) are homozygous,  87 No-Calls
Chr 11:  67.671 % (18956 of 28012 SNPs) are homozygous,  88 No-Calls
Chr 12:  66.936 % (18795 of 28079 SNPs) are homozygous,  91 No-Calls
Chr 13:  69.068 % (14795 of 21421 SNPs) are homozygous,  45 No-Calls
Chr 14:  67.143 % (12596 of 18760 SNPs) are homozygous,  56 No-Calls
Chr 15:  68.700 % (11745 of 17096 SNPs) are homozygous,  41 No-Calls
Chr 16:  66.478 % (11500 of 17299 SNPs) are homozygous,  50 No-Calls
Chr 17:  68.789 % (10500 of 15264 SNPs) are homozygous,  44 No-Calls
Chr 18:  67.062 % (11375 of 16962 SNPs) are homozygous,  47 No-Calls
Chr 19:  66.935 % ( 6818 of 10186 SNPs) are homozygous,  42 No-Calls
Chr 20:  67.945 % ( 9812 of 14441 SNPs) are homozygous,  47 No-Calls
Chr 21:  66.416 % ( 5575 of  8394 SNPs) are homozygous,  26 No-Calls
Chr 22:  64.772 % ( 5663 of  8743 SNPs) are homozygous,  30 No-Calls

Chr  X:  13876 SNPs, 101 No-Calls
Chr  Y:   1921 SNPs,  34 No-Calls
mtDNA :   2132 SNPs,  16 No-Calls

Total autosomal (Chr 1-22):   68.237 % (382392 of 560390 SNPs) are homozygous, 1626 No-Calls

Re ROH on Chr 9:
Один участник дискуссии на https://www.23andme.com/you/community/thread/3093/ подтверждает наличие общего прадеда у своих родителей при ROH=3000 на одной из хромосом.

Значит в случае родителей моего отца это был несколько более далекий предок, скажем прапрадед, некто, ориентировочно, 1790 г.р.

К сожалению, не могу подтвердить этого документально, т.к. метрики по колонии Franzosen (Россоши, Сосновской волости Камышинского уезда Саратовской губернии), откуда родом патрилинеальная бабка отца по фамилии Гельд (Heldt), не сохранились.

Его матрилинеальная ветка - из колонии Grimm (Лесной Карамыш, той же волости/уезда), ТОГО ЖЕ кирхеншпиля, т.е. жители обеих колоний (удаленность 7 км) были прихожанами одной и той же кирхи. По линии матери отца (ее фамилия была Фрицлер (Fritzler)), в 4 поколениях из 16 возможных фамилий мне известны только 7.

Одна из известных - фамилия Эбель (Ebel). Катарина Эбель 1816 г.р (кто родители и откуда она - не знаю), в 1835 г. в колонии Гримм выходит замуж за Якоба Фрицлера.

По переписи населения 1834 в колонии Францозен из известных мне по Гримму встречается только фамилия Эбель, в составе трех семей, все отмечены как переселенцы из колонии Штефан (Stephan). В одном случае некто Johann Conrad Ebel 1806 г.р женится на Христине Варваре Гельд 1810 г.р.

Если допустить что Катарина Эбель из Гримм - сестра Кондрата Эбеля из Францозен, то их отец был бы общим пра-прадедом родителей моего отца - Якоба Киндсфатер и Раель Фрицлер, как в аптеке - 4 поколения.

Поспрашиваю на WD форуме по Штефану, может найду подтверждение по Эбелям.


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Re: Анализ однородности генома
« Ответ #92 : 30 Июнь 2010, 21:09:14 »
а вот это неожиданность. прогон по моей маме:


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.

Chr  1 has a ROH of length  279 from position 225075125 to position 226921326 (1.85 Mb)
Chr  3 has a ROH of length  446 from position  35686440 to position  37979665 (2.29 Mb)
Chr  3 has a ROH of length  491 from position 112772517 to position 114809359 (2.04 Mb)
Chr  3 has a ROH of length 1063 from position 119457845 to position 124924378 (5.47 Mb)
Chr  4 has a ROH of length  217 from position 182555439 to position 183201406 (0.65 Mb)
Chr  6 has a No-Call run of length 17 from position  79031111 to position  79088461 (57.35 Kb)
Chr  8 has a ROH of length  204 from position  50895122 to position  52320132 (1.43 Mb)
Chr 11 has a ROH of length  278 from position  47011024 to position  54649547 (7.64 Mb)
Chr 19 has a ROH of length  221 from position  43170120 to position  44071746 (0.90 Mb)
Chr  Y has a ROH of length 1921 from position   2715180 to position  57441719 (54.73 Mb)
Chr  Y has a No-Call run of length 1921 from position   2715180 to position  57441719 (54726.54 Kb)

Chr  1:  68.930 % (30310 of 43972 SNPs) are homozygous,  91 No-Calls
Chr  2:  67.284 % (31215 of 46393 SNPs) are homozygous, 106 No-Calls
Chr  3:  70.023 % (26951 of 38489 SNPs) are homozygous,  95 No-Calls
Chr  4:  68.076 % (23305 of 34234 SNPs) are homozygous,  92 No-Calls
Chr  5:  67.364 % (23458 of 34823 SNPs) are homozygous,  87 No-Calls
Chr  6:  68.513 % (25996 of 37943 SNPs) are homozygous, 108 No-Calls
Chr  7:  68.581 % (21343 of 31121 SNPs) are homozygous,  85 No-Calls
Chr  8:  67.297 % (21340 of 31710 SNPs) are homozygous, 121 No-Calls
Chr  9:  68.366 % (18502 of 27063 SNPs) are homozygous,  65 No-Calls
Chr 10:  67.924 % (20367 of 29985 SNPs) are homozygous,  83 No-Calls
Chr 11:  68.931 % (19309 of 28012 SNPs) are homozygous,  93 No-Calls
Chr 12:  68.756 % (19306 of 28079 SNPs) are homozygous,  78 No-Calls
Chr 13:  69.609 % (14911 of 21421 SNPs) are homozygous,  45 No-Calls
Chr 14:  69.392 % (13018 of 18760 SNPs) are homozygous,  41 No-Calls
Chr 15:  66.986 % (11452 of 17096 SNPs) are homozygous,  27 No-Calls
Chr 16:  66.588 % (11519 of 17299 SNPs) are homozygous,  42 No-Calls
Chr 17:  66.614 % (10168 of 15264 SNPs) are homozygous,  34 No-Calls
Chr 18:  66.802 % (11331 of 16962 SNPs) are homozygous,  29 No-Calls
Chr 19:  67.220 % ( 6847 of 10186 SNPs) are homozygous,  25 No-Calls
Chr 20:  68.146 % ( 9841 of 14441 SNPs) are homozygous,  46 No-Calls
Chr 21:  68.144 % ( 5720 of  8394 SNPs) are homozygous,  20 No-Calls
Chr 22:  66.453 % ( 5810 of  8743 SNPs) are homozygous,  20 No-Calls

Chr  X:  69.905 % ( 9700 of 13876 SNPs) are homozygous,  21 No-Calls
Chr  Y:   1921 SNPs, 1921 No-Calls
mtDNA :   2133 SNPs,  13 No-Calls

Total autosomal (Chr 1-22):   68.170 % (382019 of 560390 SNPs) are homozygous, 1433 No-Calls

Дело в том, что ее родители, вообще-то из разных этносов. Отец - украинец по фамилии Запорожец (и как раз по его линии я нашел запись о браке Якова Запорожца с Марией, дочерью Онисима Запорожца в 1830, т.е. могли быть родственниками). Они были православными.

Мамина материнская линия из великороссов, осевших в Иркутске в течение 19 века, впрочем, известно, что одна из маминых прабабушек была полькой, но судя по отчеству - католичкой.

« Последнее редактирование: 30 Июнь 2010, 23:34:02 от kindsvaters »

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Re: Анализ однородности генома
« Ответ #93 : 30 Июнь 2010, 21:13:13 »
для сравнения - мои результаты. Тут уже ничего особенно не бросается в глаза.

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.

Chr  2 has a ROH of length  243 from position 152204772 to position 153626373 (1.42 Mb)
Chr  2 has a ROH of length  213 from position 177863367 to position 178941287 (1.08 Mb)
Chr  3 has a ROH of length  254 from position  90355016 to position  97561554 (7.21 Mb)
Chr  4 has a ROH of length  377 from position 150908137 to position 153767487 (2.86 Mb)
Chr  5 has a ROH of length  274 from position 130215289 to position 131895601 (1.68 Mb)
Chr  6 has a No-Call run of length 10 from position  79069674 to position  79086086 (16.41 Kb)
Chr  6 has a ROH of length  252 from position 130585380 to position 131664173 (1.08 Mb)
Chr  8 has a ROH of length  242 from position  10459377 to position  11289115 (0.83 Mb)
Chr  9 has a ROH of length  216 from position 106099767 to position 106667080 (0.57 Mb)
Chr 11 has a ROH of length  212 from position  55420386 to position  56416314 (1.00 Mb)
Chr 14 has a ROH of length  231 from position  91384529 to position  92036873 (0.65 Mb)

Chr  1:  68.025 % (29912 of 43972 SNPs) are homozygous, 119 No-Calls
Chr  2:  67.877 % (31490 of 46393 SNPs) are homozygous, 115 No-Calls
Chr  3:  67.778 % (26087 of 38489 SNPs) are homozygous,  89 No-Calls
Chr  4:  68.257 % (23367 of 34234 SNPs) are homozygous,  88 No-Calls
Chr  5:  68.509 % (23857 of 34823 SNPs) are homozygous,  77 No-Calls
Chr  6:  68.229 % (25888 of 37943 SNPs) are homozygous, 114 No-Calls
Chr  7:  68.073 % (21185 of 31121 SNPs) are homozygous,  89 No-Calls
Chr  8:  68.858 % (21835 of 31710 SNPs) are homozygous, 100 No-Calls
Chr  9:  68.289 % (18481 of 27063 SNPs) are homozygous,  66 No-Calls
Chr 10:  68.671 % (20591 of 29985 SNPs) are homozygous,  86 No-Calls
Chr 11:  67.825 % (18999 of 28012 SNPs) are homozygous,  66 No-Calls
Chr 12:  68.090 % (19119 of 28079 SNPs) are homozygous,  70 No-Calls
Chr 13:  68.428 % (14658 of 21421 SNPs) are homozygous,  31 No-Calls
Chr 14:  66.999 % (12569 of 18760 SNPs) are homozygous,  34 No-Calls
Chr 15:  66.852 % (11429 of 17096 SNPs) are homozygous,  38 No-Calls
Chr 16:  67.108 % (11609 of 17299 SNPs) are homozygous,  48 No-Calls
Chr 17:  67.374 % (10284 of 15264 SNPs) are homozygous,  43 No-Calls
Chr 18:  67.557 % (11459 of 16962 SNPs) are homozygous,  38 No-Calls
Chr 19:  66.277 % ( 6751 of 10186 SNPs) are homozygous,  49 No-Calls
Chr 20:  68.721 % ( 9924 of 14441 SNPs) are homozygous,  41 No-Calls
Chr 21:  66.702 % ( 5599 of  8394 SNPs) are homozygous,  28 No-Calls
Chr 22:  66.270 % ( 5794 of  8743 SNPs) are homozygous,  37 No-Calls

Chr  X:  13876 SNPs,  81 No-Calls
Chr  Y:   1921 SNPs,  11 No-Calls
mtDNA :   2132 SNPs,  11 No-Calls

Total autosomal (Chr 1-22):   67.968 % (380887 of 560390 SNPs) are homozygous, 1466 No-Calls



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Re: Анализ однородности генома
« Ответ #94 : 21 Апрель 2011, 22:29:13 »
Подниму тему из небытия. 

Chr  1 has a ROH of length   226 from position  65651840 to position  66161685 ( 0.51 Mb)
Chr  1 has a ROH of length   399 from position  94274883 to position  94451100 ( 0.18 Mb)
Chr  1 has a ROH of length   299 from position 153077751 to position 154117182 ( 1.04 Mb)
Chr  1 has a ROH of length   229 from position 234752210 to position 235200934 ( 0.45 Mb)
Chr  2 has a ROH of length   255 from position  26591404 to position  27484644 ( 0.89 Mb)
Chr  2 has a ROH of length   319 from position  83104451 to position  84393432 ( 1.29 Mb)
Chr  2 has a ROH of length   359 from position  88627739 to position  96907428 ( 8.28 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  3 has a ROH of length   260 from position  20558205 to position  21274609 ( 0.72 Mb)
Chr  3 has a ROH of length   429 from position  36969238 to position  37429062 ( 0.46 Mb)
Chr  3 has a ROH of length   264 from position  48481226 to position  49627152 ( 1.15 Mb)
Chr  3 has a ROH of length   204 from position 159187915 to position 160133656 ( 0.95 Mb)
Chr  4 has a ROH of length   263 from position  27707183 to position  28535419 ( 0.83 Mb)
Chr  4 has a ROH of length   221 from position  73636388 to position  74515344 ( 0.88 Mb)
Chr  4 has a ROH of length   207 from position 100220270 to position 100462032 ( 0.24 Mb)
Chr  5 has a ROH of length   233 from position 153008030 to position 153717333 ( 0.71 Mb)
Chr  6 has a ROH of length   244 from position  20634996 to position  21263882 ( 0.63 Mb)
Chr  6 has a ROH of length   799 from position  29839766 to position  30315474 ( 0.48 Mb)
Chr  6 has a ROH of length   298 from position  62743552 to position  64411606 ( 1.67 Mb)
Chr  6 has a ROH of length   283 from position 133041265 to position 133796900 ( 0.76 Mb)
Chr  6 has a ROH of length   319 from position 139888074 to position 141504287 ( 1.62 Mb)
Chr  7 has a ROH of length   278 from position  86320624 to position  86968333 ( 0.65 Mb)
Chr  7 has a ROH of length   238 from position 108505722 to position 109432103 ( 0.93 Mb)
Chr  8 has a ROH of length   251 from position  20338150 to position  20840920 ( 0.50 Mb)
Chr  8 has a ROH of length   229 from position  52451712 to position  53173571 ( 0.72 Mb)
Chr  9 has a ROH of length   203 from position   7131418 to position   7365925 ( 0.23 Mb)
Chr 11 has a ROH of length   285 from position  72634968 to position  73759149 ( 1.12 Mb)
Chr 12 has a ROH of length   202 from position  84274938 to position  85219843 ( 0.94 Mb)
Chr 14 has a ROH of length   348 from position  72345198 to position  73068729 ( 0.72 Mb)
Chr 15 has a ROH of length   221 from position  69889150 to position  70753857 ( 0.86 Mb)
Chr 16 has a ROH of length   550 from position   2025998 to position   2169888 ( 0.14 Mb)   (2 heterozygous SNPs treated as homozygous)
Chr 16 has a ROH of length   274 from position  30123122 to position  31173042 ( 1.05 Mb)
Chr 16 has a ROH of length   480 from position  31804809 to position  47463980 (15.66 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr 17 has a ROH of length   200 from position  45624338 to position  45644069 ( 0.02 Mb)
Chr 18 has a ROH of length   220 from position  27324711 to position  27815666 ( 0.49 Mb)
Chr 19 has a ROH of length   220 from position  43416470 to position  43825658 ( 0.41 Mb)
Chr 20 has a ROH of length   303 from position  31843016 to position  33282831 ( 1.44 Mb)
Chr  X has a ROH of length   310 from position  63081957 to position  66858535 ( 3.78 Mb)
Chr  X has a ROH of length   211 from position 130589710 to position 132119749 ( 1.53 Mb)
Chr  X has a ROH of length   225 from position 153424778 to position 153901293 ( 0.48 Mb)
Chr  Y has a ROH of length  3483 from position   2709694 to position  57442197 (54.73 Mb)

Chr  1:  71.676 % (55355 of 77230 SNPs) are homozygous,   356 No-Calls
Chr  2:  70.563 % (54821 of 77691 SNPs) are homozygous,   274 No-Calls
Chr  3:  69.578 % (44198 of 63523 SNPs) are homozygous,   258 No-Calls
Chr  4:  69.858 % (38633 of 55302 SNPs) are homozygous,   256 No-Calls
Chr  5:  68.649 % (38628 of 56269 SNPs) are homozygous,   227 No-Calls
Chr  6:  72.892 % (46362 of 63604 SNPs) are homozygous,   338 No-Calls
Chr  7:  70.045 % (35927 of 51291 SNPs) are homozygous,   296 No-Calls
Chr  8:  69.629 % (34412 of 49422 SNPs) are homozygous,   200 No-Calls
Chr  9:  68.443 % (29531 of 43147 SNPs) are homozygous,   164 No-Calls
Chr 10:  70.427 % (35577 of 50516 SNPs) are homozygous,   208 No-Calls
Chr 11:  70.688 % (34016 of 48121 SNPs) are homozygous,   168 No-Calls
Chr 12:  71.604 % (33893 of 47334 SNPs) are homozygous,   195 No-Calls
Chr 13:  70.668 % (25589 of 36210 SNPs) are homozygous,   121 No-Calls
Chr 14:  70.143 % (21689 of 30921 SNPs) are homozygous,   107 No-Calls
Chr 15:  68.374 % (19507 of 28530 SNPs) are homozygous,   125 No-Calls
Chr 16:  71.426 % (21637 of 30293 SNPs) are homozygous,   164 No-Calls
Chr 17:  71.883 % (19335 of 26898 SNPs) are homozygous,   170 No-Calls
Chr 18:  69.583 % (19525 of 28060 SNPs) are homozygous,    78 No-Calls
Chr 19:  72.662 % (13566 of 18670 SNPs) are homozygous,   142 No-Calls
Chr 20:  71.713 % (17156 of 23923 SNPs) are homozygous,    92 No-Call
Chr 21:  71.618 % ( 9647 of 13470 SNPs) are homozygous,    54 No-Calls
Chr 22:  70.130 % ( 9990 of 14245 SNPs) are homozygous,   116 No-Calls

Chr  X:  72.891 % (19015 of 26087 SNPs) are homozygous,   120 No-Calls
Chr  Y:   3483 SNPs,  3483 No-Calls
mtDNA :   2737 SNPs,   136 No-Calls

Total autosomal (Chr 1-22):  70.506 % (658994 of 934670 SNPs) are Homozygous   (this tally includes 4 heterozygous SNPs that were treated as homozygous)

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Re: Анализ однородности генома
« Ответ #95 : 03 Октябрь 2011, 06:34:07 »
Коли вспомнили про гетерозоготность сегодня.
Хочу особо отметить, что кросс-лабораторные сравнения могут вводить в заблуждение.

Прогнал файл отца: 70.076 %. Его файл - из фтдна.
Мой же вышеприведённый результат от 23андме (67.767 %) может только привести к конфузу, так как я большая смесь, чем отец, а процент у меня меньше. В точности до наоборот.

Теперь я запускаю свой результат, но уже из фтдна. Получаю 71.386 %. Всё нормально, больший процент гетерозиготности - чем у отца.

Кстати, вот как результаты отличаются для одного и того же человека:

для файла от 23андме:
Chr  1 has a ROH of length   271 from position  96006413 to position  97498267 ( 1.49 Mb)
Chr  2 has a ROH of length   204 from position 135016952 to position 136509584 ( 1.49 Mb)
Chr  3 has a ROH of length   254 from position   3562732 to position   4377649 ( 0.81 Mb)
Chr  3 has a ROH of length   301 from position 111443884 to position 113204782 ( 1.76 Mb)
Chr  7 has a ROH of length   234 from position  83124094 to position  84575619 ( 1.45 Mb)
Chr 10 has a ROH of length   298 from position  80052642 to position  81888175 ( 1.84 Mb)
Chr 10 has a ROH of length   202 from position  93328580 to position  94835536 ( 1.51 Mb)
Chr 12 has a ROH of length   283 from position  20776581 to position  21393223 ( 0.62 Mb)
Chr 15 has a ROH of length   300 from position  97885993 to position  99026864 ( 1.14 Mb)
Chr 18 has a ROH of length   249 from position  33268044 to position  34360094 ( 1.09 Mb)

Total autosomal (Chr 1-22):   0.220 % (  1234 of 560386 SNPs) are NoCalls
Total autosomal (Chr 1-22):  32.233 % (180627 of 560386 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  67.767 % (379759 of 560386 SNPs) are Homozygous   (this tally includes 0 heterozygous SNPs that were treated as homozygous)

а теперь для файла от ФТДНА:
Chr  1 has a ROH of length   224 from position  96021382 to position  97325716 ( 1.30 Mb)
Chr  1 has a ROH of length   203 from position 156331063 to position 157170738 ( 0.84 Mb)
Chr  2 has a ROH of length   244 from position 155099251 to position 156474113 ( 1.37 Mb)
Chr  3 has a ROH of length   286 from position   3563042 to position   4380021 ( 0.82 Mb)
Chr  6 has a ROH of length   416 from position  31329328 to position  31427267 ( 0.10 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  6 has a ROH of length   756 from position  32299317 to position  32535726 ( 0.24 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  6 has a ROH of length   211 from position  33144667 to position  33190018 ( 0.05 Mb)
Chr 10 has a ROH of length   246 from position  79766533 to position  81883857 ( 2.12 Mb)
Chr 15 has a ROH of length   269 from position  98072569 to position  99053999 ( 0.98 Mb)
Chr 18 has a ROH of length   229 from position  33265115 to position  34360094 ( 1.09 Mb)

Total autosomal (Chr 1-22):   0.417 % (  2285 of 548011 SNPs) are NoCalls
Total autosomal (Chr 1-22):  28.614 % (156810 of 548011 SNPs) are Heterozygous (this tally excludes 2 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  71.386 % (391201 of 548011 SNPs) are Homozygous   (this tally includes 2 heterozygous SNPs that were treated as homozygous)

Оффлайн kaa76

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Re: Анализ однородности генома
« Ответ #96 : 22 Август 2013, 18:23:59 »
Подниму тему из подвала...

Прогнал мои данные (FTDNA) через утилиту Search for Runs of Homozygosity (ROHs):

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  1 has a ROH of length   204 from position  97946561 to position  98438713 ( 0.49 Mb)
Chr  1 has a ROH of length   202 from position 169311941 to position 169490371 ( 0.18 Mb)
Chr  2 has a ROH of length   215 from position 182464465 to position 183411209 ( 0.95 Mb)
Chr  5 has a ROH of length   269 from position  79578880 to position  80514920 ( 0.94 Mb)
Chr  6 has a ROH of length   201 from position  25863494 to position  26256290 ( 0.39 Mb)
Chr  6 has a ROH of length   362 from position  27994809 to position  28596013 ( 0.60 Mb)
Chr  6 has a ROH of length   284 from position  29463897 to position  29717900 ( 0.25 Mb)
Chr  6 has a ROH of length   237 from position  31677499 to position  31838993 ( 0.16 Mb)
Chr  6 has a ROH of length   307 from position  31978305 to position  32269302 ( 0.29 Mb)
Chr  6 has a ROH of length   261 from position  32295583 to position  32449697 ( 0.15 Mb)
Chr  6 has a ROH of length   308 from position  58155613 to position  64116524 ( 5.96 Mb)
Chr  7 has a ROH of length   220 from position  98569948 to position  99301754 ( 0.73 Mb)
Chr  8 has a ROH of length   239 from position  42320244 to position  48244020 ( 5.92 Mb)
Chr  8 has a ROH of length   250 from position  79880560 to position  80945258 ( 1.06 Mb)
Chr 10 has a ROH of length   205 from position  93082285 to position  94372930 ( 1.29 Mb)
Chr 11 has a ROH of length   271 from position   9864934 to position  10866286 ( 1.00 Mb)
Chr 11 has a ROH of length   204 from position  39276279 to position  40161976 ( 0.89 Mb)
Chr 13 has a ROH of length   233 from position  94462890 to position  94618853 ( 0.16 Mb)
Chr 14 has a ROH of length   257 from position  72109648 to position  73064488 ( 0.95 Mb)
Chr 19 has a ROH of length   220 from position  10487769 to position  11304733 ( 0.82 Mb)
Chr 22 has a ROH of length   295 from position  39405489 to position  41018668 ( 1.61 Mb)

Chr  1:  71.995 % (42084 of 58454 SNPs) are homozygous,    37 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  2:  70.415 % (40109 of 56961 SNPs) are homozygous,    29 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  3:  69.089 % (32201 of 46608 SNPs) are homozygous,    40 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  4:  70.199 % (28043 of 39948 SNPs) are homozygous,    17 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  5:  70.013 % (29113 of 41582 SNPs) are homozygous,    23 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  6:  71.174 % (33785 of 47468 SNPs) are homozygous,    24 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  7:  70.039 % (26339 of 37606 SNPs) are homozygous,    26 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  8:  69.574 % (25428 of 36548 SNPs) are homozygous,    27 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  9:  69.208 % (22426 of 32404 SNPs) are homozygous,    21 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 10:  70.693 % (27310 of 38632 SNPs) are homozygous,    18 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 11:  70.174 % (25363 of 36143 SNPs) are homozygous,    26 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 12:  71.202 % (24979 of 35082 SNPs) are homozygous,    28 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 13:  70.823 % (19484 of 27511 SNPs) are homozygous,    17 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 14:  70.804 % (16285 of 23000 SNPs) are homozygous,    12 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 15:  71.979 % (15402 of 21398 SNPs) are homozygous,    10 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 16:  70.469 % (15838 of 22475 SNPs) are homozygous,    20 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 17:  71.740 % (14325 of 19968 SNPs) are homozygous,     8 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 18:  69.543 % (14940 of 21483 SNPs) are homozygous,    15 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 19:  70.554 % (10490 of 14868 SNPs) are homozygous,    13 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 20:  70.208 % (12780 of 18203 SNPs) are homozygous,     7 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 21:  68.875 % ( 6964 of 10111 SNPs) are homozygous,     3 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 22:  70.347 % ( 7245 of 10299 SNPs) are homozygous,     8 No-Calls,   0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22):   0.062 % (   429 of 696752 SNPs) are NoCalls
Total autosomal (Chr 1-22):  29.540 % (205819 of 696752 SNPs) are Heterozygous (this tally excludes 0 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  70.460 % (490933 of 696752 SNPs) are Homozygous   (this tally includes 0 heterozygous SNPs that were treated as homozygous)

Оффлайн grimsvotn

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  • Neolithic Era
    • I1-L1248 haplogroup project
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Re: Анализ однородности генома
« Ответ #97 : 11 Сентябрь 2013, 18:28:28 »
Вторю уважаемому Александру - также прогнал свой и отцов геномы через утилиту.

Помогите разобраться :)

Мои данные:


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  2 has a No-Call run of length 10 from position  41238644 to position  41248468 ( 9.82 Kb)
Chr  Y has a No-Call run of length 21 from position   2897433 to position   3004873 (107.44 Kb)
Chr  Y has a No-Call run of length 32 from position   3077483 to position   3245636 (168.15 Kb)
Chr  Y has a No-Call run of length 16 from position   3310270 to position   3401707 (91.44 Kb)
Chr  Y has a No-Call run of length 29 from position   3436718 to position   3490038 (53.32 Kb)
Chr  Y has a No-Call run of length 35 from position   3547060 to position   3682867 (135.81 Kb)
Chr  Y has a No-Call run of length 11 from position   3697126 to position   3711649 (14.52 Kb)
Chr  Y has a No-Call run of length 11 from position   3721230 to position   3764211 (42.98 Kb)
Chr  Y has a No-Call run of length 47 from position   3781791 to position   4065381 (283.59 Kb)
Chr  Y has a No-Call run of length 34 from position   4084431 to position   4239428 (155.00 Kb)
Chr  Y has a No-Call run of length 64 from position   4262761 to position   4527871 (265.11 Kb)
Chr  Y has a No-Call run of length 44 from position   4559101 to position   4723799 (164.70 Kb)
Chr  Y has a No-Call run of length 18 from position   4749584 to position   4800467 (50.88 Kb)
Chr  Y has a No-Call run of length 38 from position   4804521 to position   4871809 (67.29 Kb)
Chr  Y has a No-Call run of length 24 from position   4882982 to position   4925084 (42.10 Kb)
Chr  Y has a No-Call run of length 26 from position   4927998 to position   4956740 (28.74 Kb)
Chr  Y has a No-Call run of length 41 from position   4957608 to position   5012099 (54.49 Kb)
Chr  Y has a No-Call run of length 12 from position   5025304 to position   5060531 (35.23 Kb)
Chr  Y has a No-Call run of length 46 from position   5060885 to position   5187330 (126.44 Kb)
Chr  Y has a No-Call run of length 39 from position   5191781 to position   5292479 (100.70 Kb)
Chr  Y has a No-Call run of length 42 from position   5298470 to position   5366585 (68.11 Kb)
Chr  Y has a No-Call run of length 89 from position   5370861 to position   5558366 (187.50 Kb)
Chr  Y has a No-Call run of length 79 from position   5577743 to position   5908658 (330.92 Kb)
Chr  Y has a No-Call run of length 14 from position   5949606 to position   6006768 (57.16 Kb)
Chr  Y has a No-Call run of length 13 from position   6019917 to position   6073852 (53.94 Kb)
Chr  Y has a No-Call run of length 38 from position   6082930 to position   6736154 (653.22 Kb)
Chr  Y has a No-Call run of length 10 from position  13938496 to position  13982729 (44.23 Kb)
Chr  Y has a No-Call run of length 10 from position  28495550 to position  28539062 (43.51 Kb)

Chr  1 has a ROH of length   204 from position  11814631 to position  12153188 ( 0.34 Mb)
Chr  1 has a ROH of length   228 from position 155043325 to position 155852008 ( 0.81 Mb)
Chr  2 has a ROH of length   204 from position  75656149 to position  76091891 ( 0.44 Mb)
Chr  2 has a ROH of length   202 from position  81607450 to position  82432988 ( 0.83 Mb)
Chr  2 has a ROH of length   232 from position 152224940 to position 153219178 ( 0.99 Mb)
Chr  2 has a ROH of length   246 from position 181035163 to position 181813765 ( 0.78 Mb)
Chr  2 has a ROH of length   653 from position 209162775 to position 211864403 ( 2.70 Mb)
Chr  2 has a ROH of length   237 from position 226251703 to position 227199263 ( 0.95 Mb)
Chr  3 has a ROH of length   267 from position  22628123 to position  23650884 ( 1.02 Mb)
Chr  3 has a ROH of length   250 from position 130105223 to position 131060915 ( 0.96 Mb)
Chr  3 has a ROH of length   264 from position 156699828 to position 157581467 ( 0.88 Mb)
Chr  4 has a ROH of length   286 from position  27966505 to position  28872833 ( 0.91 Mb)
Chr  4 has a ROH of length   432 from position  31405546 to position  33200267 ( 1.79 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  5 has a ROH of length   268 from position  12003910 to position  13482159 ( 1.48 Mb)
Chr  5 has a ROH of length   362 from position 119379252 to position 120622200 ( 1.24 Mb)
Chr  6 has a ROH of length   410 from position  23909811 to position  24620913 ( 0.71 Mb)
Chr  6 has a ROH of length  1112 from position  26341301 to position  28610734 ( 2.27 Mb)
Chr  6 has a ROH of length   345 from position  46437221 to position  47095744 ( 0.66 Mb)
Chr  6 has a ROH of length   244 from position  65837939 to position  66624531 ( 0.79 Mb)
Chr  6 has a ROH of length   238 from position  78381834 to position  79174120 ( 0.79 Mb)
Chr  7 has a ROH of length   266 from position  94032753 to position  94180691 ( 0.15 Mb)
Chr  7 has a ROH of length   327 from position  94653626 to position  95078175 ( 0.42 Mb)
Chr  7 has a ROH of length   248 from position 118355075 to position 120156307 ( 1.80 Mb)
Chr  8 has a ROH of length   305 from position   9231661 to position   9969692 ( 0.74 Mb)
Chr  9 has a ROH of length   237 from position  25274255 to position  25719019 ( 0.44 Mb)
Chr  9 has a ROH of length   234 from position 106493088 to position 107267304 ( 0.77 Mb)
Chr  9 has a ROH of length   245 from position 108413323 to position 109270732 ( 0.86 Mb)
Chr 10 has a ROH of length   235 from position  60160226 to position  61068522 ( 0.91 Mb)
Chr 10 has a ROH of length   248 from position 121062068 to position 121739257 ( 0.68 Mb)
Chr 11 has a ROH of length   324 from position   5246512 to position   5296732 ( 0.05 Mb)
Chr 11 has a ROH of length   225 from position  17306223 to position  17499547 ( 0.19 Mb)
Chr 11 has a ROH of length   328 from position  27932280 to position  29460313 ( 1.53 Mb)
Chr 11 has a ROH of length   302 from position  48097480 to position  50517487 ( 2.42 Mb)
Chr 12 has a ROH of length   399 from position  20709733 to position  21334059 ( 0.62 Mb)
Chr 12 has a ROH of length   306 from position  59611521 to position  60859665 ( 1.25 Mb)
Chr 12 has a ROH of length   383 from position  99294499 to position 100739614 ( 1.45 Mb)
Chr 12 has a ROH of length   261 from position 104129802 to position 104759331 ( 0.63 Mb)
Chr 14 has a ROH of length   248 from position  56380452 to position  56887937 ( 0.51 Mb)
Chr 15 has a ROH of length   237 from position  72054830 to position  72974647 ( 0.92 Mb)
Chr 16 has a ROH of length   212 from position    193586 to position    333138 ( 0.14 Mb)
Chr 17 has a ROH of length   339 from position  48255183 to position  48275866 ( 0.02 Mb)
Chr 18 has a ROH of length   231 from position  22117430 to position  22546515 ( 0.43 Mb)
Chr 20 has a ROH of length   205 from position  19528138 to position  19832870 ( 0.30 Mb)
Chr 20 has a ROH of length   206 from position  44417363 to position  44824624 ( 0.41 Mb)
Chr 21 has a ROH of length   204 from position  25583058 to position  26091601 ( 0.51 Mb)

Chr  1:  71.388 % (54904 of 76909 SNPs) are homozygous,  2699 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  2:  72.161 % (55814 of 77346 SNPs) are homozygous,  2564 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  3:  70.674 % (44726 of 63285 SNPs) are homozygous,  2076 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  4:  71.233 % (39190 of 55017 SNPs) are homozygous,  1914 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  5:  69.598 % (38988 of 56019 SNPs) are homozygous,  1887 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  6:  72.454 % (45823 of 63244 SNPs) are homozygous,  2336 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  7:  72.073 % (36732 of 50965 SNPs) are homozygous,  1858 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  8:  70.867 % (34877 of 49215 SNPs) are homozygous,  1705 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  9:  70.604 % (30338 of 42969 SNPs) are homozygous,  1519 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 10:  71.190 % (35824 of 50322 SNPs) are homozygous,  1705 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 11:  72.328 % (34697 of 47972 SNPs) are homozygous,  1682 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 12:  72.274 % (34059 of 47125 SNPs) are homozygous,  1641 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 13:  70.664 % (25494 of 36078 SNPs) are homozygous,  1240 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 14:  72.299 % (22281 of 30818 SNPs) are homozygous,  1095 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 15:  69.250 % (19667 of 28400 SNPs) are homozygous,   931 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 16:  72.387 % (21837 of 30167 SNPs) are homozygous,  1197 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 17:  72.422 % (19328 of 26688 SNPs) are homozygous,  1051 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 18:  71.127 % (19895 of 27971 SNPs) are homozygous,   899 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 19:  72.460 % (13429 of 18533 SNPs) are homozygous,   891 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 20:  72.472 % (17273 of 23834 SNPs) are homozygous,   758 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 21:  72.501 % ( 9718 of 13404 SNPs) are homozygous,   505 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 22:  72.702 % (10251 of 14100 SNPs) are homozygous,   653 No-Calls,   0 heterozygous SNPs treated as homozygous

Chr  X:  10.374 % ( 2698 of 26007 SNPs) are homozygous,  2377 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  Y:   1766 SNPs,  1044 No-Calls,   0 heterozygous SNPs treated as homozygous
mtDNA :   2459 SNPs,   135 No-Calls,   0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22):   3.526 % ( 32806 of 930381 SNPs) are NoCalls
Total autosomal (Chr 1-22):  28.508 % (265236 of 930381 SNPs) are Heterozygous (this tally excludes 1 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  71.492 % (665145 of 930381 SNPs) are Homozygous   (this tally includes 1 heterozygous SNPs that


Отца:


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  2 has a No-Call run of length 10 from position  41238644 to position  41248468 ( 9.82 Kb)
Chr  Y has a No-Call run of length 20 from position   2920925 to position   3004873 (83.95 Kb)
Chr  Y has a No-Call run of length 45 from position   3011019 to position   3262129 (251.11 Kb)
Chr  Y has a No-Call run of length 16 from position   3310270 to position   3401707 (91.44 Kb)
Chr  Y has a No-Call run of length 29 from position   3436718 to position   3490038 (53.32 Kb)
Chr  Y has a No-Call run of length 17 from position   3547060 to position   3627909 (80.85 Kb)
Chr  Y has a No-Call run of length 17 from position   3640050 to position   3682867 (42.82 Kb)
Chr  Y has a No-Call run of length 37 from position   3697126 to position   3764211 (67.08 Kb)
Chr  Y has a No-Call run of length 36 from position   3781791 to position   4017487 (235.70 Kb)
Chr  Y has a No-Call run of length 10 from position   4026698 to position   4065381 (38.68 Kb)
Chr  Y has a No-Call run of length 34 from position   4084431 to position   4239428 (155.00 Kb)
Chr  Y has a No-Call run of length 64 from position   4262761 to position   4527871 (265.11 Kb)
Chr  Y has a No-Call run of length 44 from position   4559101 to position   4723799 (164.70 Kb)
Chr  Y has a No-Call run of length 18 from position   4749584 to position   4800467 (50.88 Kb)
Chr  Y has a No-Call run of length 38 from position   4804521 to position   4871809 (67.29 Kb)
Chr  Y has a No-Call run of length 15 from position   4882982 to position   4907409 (24.43 Kb)
Chr  Y has a No-Call run of length 26 from position   4927998 to position   4956740 (28.74 Kb)
Chr  Y has a No-Call run of length 41 from position   4957608 to position   5012099 (54.49 Kb)
Chr  Y has a No-Call run of length 59 from position   5025304 to position   5187330 (162.03 Kb)
Chr  Y has a No-Call run of length 82 from position   5191781 to position   5366585 (174.80 Kb)
Chr  Y has a No-Call run of length 94 from position   5370861 to position   5574967 (204.11 Kb)
Chr  Y has a No-Call run of length 28 from position   5577743 to position   5672315 (94.57 Kb)
Chr  Y has a No-Call run of length 20 from position   5680126 to position   5754102 (73.98 Kb)
Chr  Y has a No-Call run of length 29 from position   5755943 to position   5908658 (152.72 Kb)
Chr  Y has a No-Call run of length 14 from position   5949606 to position   6006768 (57.16 Kb)
Chr  Y has a No-Call run of length 13 from position   6019917 to position   6073852 (53.94 Kb)
Chr  Y has a No-Call run of length 38 from position   6082930 to position   6736154 (653.22 Kb)
Chr  Y has a No-Call run of length 10 from position  13938496 to position  13982729 (44.23 Kb)
Chr  Y has a No-Call run of length 10 from position  28495550 to position  28539062 (43.51 Kb)

Chr  1 has a ROH of length   224 from position  31687958 to position  32315147 ( 0.63 Mb)
Chr  1 has a ROH of length   613 from position  94451747 to position  94581125 ( 0.13 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  1 has a ROH of length   212 from position 100116850 to position 100744798 ( 0.63 Mb)
Chr  1 has a ROH of length   373 from position 173500243 to position 175281020 ( 1.78 Mb)
Chr  2 has a ROH of length   227 from position  18743344 to position  19497218 ( 0.75 Mb)
Chr  2 has a ROH of length   233 from position  53861427 to position  54630346 ( 0.77 Mb)
Chr  2 has a ROH of length   221 from position 137338721 to position 137868740 ( 0.53 Mb)
Chr  2 has a ROH of length   304 from position 219205471 to position 220084902 ( 0.88 Mb)
Chr  3 has a ROH of length   233 from position  20033962 to position  20644662 ( 0.61 Mb)
Chr  3 has a ROH of length   276 from position  37045903 to position  37125699 ( 0.08 Mb)
Chr  3 has a ROH of length   211 from position  48628014 to position  49641049 ( 1.01 Mb)
Chr  3 has a ROH of length   203 from position 126097849 to position 126732159 ( 0.63 Mb)
Chr  3 has a ROH of length   237 from position 160580103 to position 161435382 ( 0.86 Mb)
Chr  4 has a ROH of length   204 from position  39442960 to position  40244347 ( 0.80 Mb)
Chr  4 has a ROH of length   204 from position  78161506 to position  78968798 ( 0.81 Mb)
Chr  4 has a ROH of length   234 from position 155007625 to position 155545072 ( 0.54 Mb)
Chr  5 has a ROH of length   204 from position 131567924 to position 131729935 ( 0.16 Mb)
Chr  5 has a ROH of length   559 from position 142792990 to position 144688529 ( 1.90 Mb)
Chr  6 has a ROH of length  1385 from position    155815 to position   3000303 ( 2.84 Mb)
Chr  6 has a ROH of length   728 from position  27279877 to position  28610734 ( 1.33 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  6 has a ROH of length   600 from position  28669315 to position  29518934 ( 0.85 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  6 has a ROH of length   241 from position  88721653 to position  89314769 ( 0.59 Mb)
Chr  6 has a ROH of length   232 from position 169663638 to position 170414285 ( 0.75 Mb)
Chr  7 has a ROH of length   585 from position  86639826 to position  87606246 ( 0.97 Mb)
Chr  7 has a ROH of length   291 from position  94840916 to position  95078175 ( 0.24 Mb)
Chr  8 has a ROH of length  4030 from position   1918352 to position   6434895 ( 4.52 Mb)
Chr  9 has a ROH of length   302 from position  26318151 to position  27120369 ( 0.80 Mb)
Chr 10 has a ROH of length   638 from position  30881362 to position  33227477 ( 2.35 Mb)
Chr 11 has a ROH of length   343 from position   5207389 to position   5296732 ( 0.09 Mb)
Chr 11 has a ROH of length   273 from position  12048496 to position  12371595 ( 0.32 Mb)
Chr 11 has a ROH of length   467 from position  27451759 to position  29460313 ( 2.01 Mb)
Chr 11 has a ROH of length   238 from position  66721028 to position  67442661 ( 0.72 Mb)
Chr 11 has a ROH of length   301 from position  95762146 to position  96579907 ( 0.82 Mb)
Chr 12 has a ROH of length   221 from position  43570625 to position  44368839 ( 0.80 Mb)
Chr 12 has a ROH of length   200 from position  45217957 to position  45977587 ( 0.76 Mb)
Chr 12 has a ROH of length   424 from position  47286631 to position  48276432 ( 0.99 Mb)
Chr 12 has a ROH of length   391 from position  81287312 to position  82578417 ( 1.29 Mb)
Chr 12 has a ROH of length   200 from position  98365558 to position  98982066 ( 0.62 Mb)
Chr 12 has a ROH of length   319 from position 111716718 to position 113267819 ( 1.55 Mb)
Chr 13 has a ROH of length   208 from position  95581052 to position  95740500 ( 0.16 Mb)
Chr 13 has a ROH of length   251 from position 107498032 to position 108016375 ( 0.52 Mb)
Chr 15 has a ROH of length   206 from position  45090821 to position  45758379 ( 0.67 Mb)
Chr 15 has a ROH of length   306 from position  74524730 to position  75246945 ( 0.72 Mb)
Chr 16 has a ROH of length   355 from position   2088312 to position   2132583 ( 0.04 Mb)
Chr 17 has a ROH of length   279 from position  40971770 to position  41693608 ( 0.72 Mb)
Chr 18 has a ROH of length   231 from position  22117430 to position  22546515 ( 0.43 Mb)
Chr 20 has a ROH of length   219 from position  21011236 to position  21967950 ( 0.96 Mb)

Chr  1:  72.175 % (55509 of 76909 SNPs) are homozygous,  1583 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  2:  71.837 % (55563 of 77346 SNPs) are homozygous,  1501 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  3:  70.908 % (44874 of 63285 SNPs) are homozygous,  1322 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  4:  70.000 % (38512 of 55017 SNPs) are homozygous,  1138 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  5:  71.456 % (40029 of 56019 SNPs) are homozygous,  1173 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  6:  71.188 % (45022 of 63244 SNPs) are homozygous,  1468 No-Calls,   2 heterozygous SNPs treated as homozygous
Chr  7:  70.327 % (35842 of 50965 SNPs) are homozygous,  1142 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  8:  72.169 % (35518 of 49215 SNPs) are homozygous,  1066 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  9:  70.220 % (30173 of 42969 SNPs) are homozygous,   884 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 10:  72.008 % (36236 of 50322 SNPs) are homozygous,  1033 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 11:  72.307 % (34687 of 47972 SNPs) are homozygous,  1062 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 12:  72.997 % (34400 of 47125 SNPs) are homozygous,  1025 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 13:  71.284 % (25718 of 36078 SNPs) are homozygous,   766 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 14:  71.737 % (22108 of 30818 SNPs) are homozygous,   697 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 15:  70.799 % (20107 of 28400 SNPs) are homozygous,   586 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 16:  72.364 % (21830 of 30167 SNPs) are homozygous,   654 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 17:  72.205 % (19270 of 26688 SNPs) are homozygous,   613 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 18:  69.980 % (19574 of 27971 SNPs) are homozygous,   557 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 19:  71.899 % (13325 of 18533 SNPs) are homozygous,   537 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 20:  71.100 % (16946 of 23834 SNPs) are homozygous,   440 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 21:  70.725 % ( 9480 of 13404 SNPs) are homozygous,   272 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 22:  72.284 % (10192 of 14100 SNPs) are homozygous,   429 No-Calls,   0 heterozygous SNPs treated as homozygous

Chr  X:  5.033 % ( 1309 of 26007 SNPs) are homozygous,   993 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  Y:   1766 SNPs,  1042 No-Calls,   0 heterozygous SNPs treated as homozygous
mtDNA :   2459 SNPs,    51 No-Calls,   0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22):   2.144 % ( 19948 of 930381 SNPs) are NoCalls
Total autosomal (Chr 1-22):  28.533 % (265466 of 930381 SNPs) are Heterozygous (this tally excludes 3 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  71.467 % (664915 of 930381 SNPs) are Homozygous   (this tally includes 3 heterozygous SNPs that

Оффлайн valera27

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  • Y - R1a1a-YP682(xYP1260,YP612,YP1696); mt - H1a
Re: Анализ однородности генома
« Ответ #98 : 20 Июнь 2016, 23:02:02 »
У меня:

Total autosomal (Chr 1-22):   2.293 % ( 21338 of 930382 SNPs) are NoCalls
Total autosomal (Chr 1-22):  28.895 % (268830 of 930382 SNPs) are Heterozygous (this tally excludes 1 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  71.105 % (661552 of 930382 SNPs) are Homozygous   (this tally includes 1 heterozygous SNPs that were treated as homozygous)

У деда (из моих "подопечных" пока что он рекордсмен по "родству" родителей - и определяемому утилитами, и документальному):
Total autosomal (Chr 1-22):   1.224 % (  7171 of 585811 SNPs) are NoCalls
Total autosomal (Chr 1-22):  27.457 % (160846 of 585811 SNPs) are Heterozygous (this tally excludes 5 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  72.543 % (424965 of 585811 SNPs) are Homozygous   (this tally includes 5 heterozygous SNPs that were treated as homozygous)

Оффлайн Lieschen

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Re: Анализ однородности генома
« Ответ #99 : 19 Сентябрь 2016, 13:36:35 »
Добавлю и от себя данных:
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  6 has a No-Call run of length 14 from position  79029649 to position  79086086 (56.44 Kb)
Chr 11 has a No-Call run of length 19 from position  55122337 to position  55184276 (61.94 Kb)
Chr 15 has a No-Call run of length 12 from position  32505886 to position  32595143 (89.26 Kb)
Chr 22 has a No-Call run of length 10 from position  21023069 to position  21061758 (38.69 Kb)
Chr 22 has a No-Call run of length 31 from position  21070855 to position  21400912 (330.06 Kb)

Chr  3 has a ROH of length   422 from position  48532643 to position  51373998 ( 2.84 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  5 has a ROH of length   556 from position  19772707 to position  23189319 ( 3.42 Mb)   (1 heterozygous SNPs treated as homozygous)
Chr  5 has a ROH of length   226 from position  68760674 to position  71519868 ( 2.76 Mb)
Chr  6 has a ROH of length   435 from position  27994809 to position  28753149 ( 0.76 Mb)
Chr  6 has a ROH of length   252 from position  30563899 to position  30824698 ( 0.26 Mb)
Chr  6 has a ROH of length   326 from position  31650122 to position  31853065 ( 0.20 Mb)
Chr  6 has a ROH of length   432 from position  32299435 to position  32535767 ( 0.24 Mb)
Chr  6 has a ROH of length   243 from position  92703806 to position  93783434 ( 1.08 Mb)
Chr  7 has a ROH of length   220 from position  94677512 to position  94873702 ( 0.20 Mb)
Chr 11 has a ROH of length   209 from position   5309382 to position   5578877 ( 0.27 Mb)
Chr 12 has a ROH of length   206 from position  31768556 to position  32255018 ( 0.49 Mb)
Chr 12 has a ROH of length   341 from position  71634812 to position  73440076 ( 1.81 Mb)
Chr 16 has a ROH of length   296 from position  31284350 to position  46579336 (15.29 Mb)
Chr 16 has a ROH of length   250 from position  82184321 to position  82587057 ( 0.40 Mb)
Chr 18 has a ROH of length   327 from position  66476708 to position  67469280 ( 0.99 Mb)
Total Mb:  31.00

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

Chr  1:  72.150 % (42518 of 58930 SNPs) are homozygous,  1378 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  2:  72.029 % (41352 of 57410 SNPs) are homozygous,  1465 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  3:  71.016 % (33362 of 46978 SNPs) are homozygous,  1204 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  4:  69.665 % (28057 of 40274 SNPs) are homozygous,  1159 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  5:  70.836 % (29681 of 41901 SNPs) are homozygous,  1023 No-Calls,   1 heterozygous SNPs treated as homozygous
Chr  6:  71.624 % (34333 of 47935 SNPs) are homozygous,  1311 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  7:  69.938 % (26512 of 37908 SNPs) are homozygous,  1084 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  8:  70.016 % (25801 of 36850 SNPs) are homozygous,   984 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr  9:  70.561 % (23036 of 32647 SNPs) are homozygous,   807 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 10:  72.386 % (28156 of 38897 SNPs) are homozygous,   951 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 11:  72.302 % (26367 of 36468 SNPs) are homozygous,   899 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 12:  72.304 % (25582 of 35381 SNPs) are homozygous,   970 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 13:  71.465 % (19813 of 27724 SNPs) are homozygous,   710 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 14:  71.064 % (16506 of 23227 SNPs) are homozygous,   615 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 15:  72.042 % (15515 of 21536 SNPs) are homozygous,   502 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 16:  70.745 % (16038 of 22670 SNPs) are homozygous,   541 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 17:  72.624 % (14641 of 20160 SNPs) are homozygous,   470 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 18:  72.906 % (15771 of 21632 SNPs) are homozygous,   509 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 19:  71.068 % (10651 of 14987 SNPs) are homozygous,   516 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 20:  70.819 % (12979 of 18327 SNPs) are homozygous,   411 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 21:  70.905 % ( 7221 of 10184 SNPs) are homozygous,   259 No-Calls,   0 heterozygous SNPs treated as homozygous
Chr 22:  71.776 % ( 7487 of 10431 SNPs) are homozygous,   369 No-Calls,   0 heterozygous SNPs treated as homozygous

Total autosomal (Chr 1-22):   2.582 % ( 18137 of 702457 SNPs) are NoCalls
Total autosomal (Chr 1-22):  28.625 % (201078 of 702457 SNPs) are Heterozygous (this tally excludes 2 heterozygous SNPs that were treated as homozygous)
Total autosomal (Chr 1-22):  71.375 % (501379 of 702457 SNPs) are Homozygous   (this tally includes 2 heterozygous SNPs that were treated as homozygous)


Значит ли это, что родители были скорее из одного этноса, чем из разных?  (происхождение отца покрыто мраком, мама псковско-смоленская)

 

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