Тема: Проект Magnus Ducatus Lituaniae (Прочитано 215858 раз)

I2a1a · « : 17 Апрель 2011, 00:30:56 »

Это предварительный анонс проекта Magnus Ducatus Lituaniae.
Блог проекта - Magnus Ducatus Lituaniae Project

Рациональная цель проекта - этно-популяционно-стратификационный анализ генотипы (входные данные в формате 23andme) лиц, с документированной родословной из регионов входивших в состав ВКЛ после Люблинской унии. По мере расширения проекта, планируется подключение потомков жителей Волыни, Киевщины, Мазовии, Брянщины и Черниговщины.

Первая фаза проекта (примерно 50 участников):
1) подключение референсов белорусской, литовской и польских популяций
2) создание мастер-файла в Рlink
3) обработка данных в Plink -вычисление IBS матрицы, расчеты данных гомозиготности (группировка по совпадающим сегментам, кластеризация), структуризация, выявление "глубоких" IBD (HIR)-сегментов и их кластеризации, выявление гаплоблоков и пр.
4) создание MDS-графика с отображением участников проекта.
4) анализ IBD-сегментов в AIS-convert.
5) фазирование гентотипов в Beagle
6) вывод данных в Structure и анализ структуры (admixture) участников проекта

По мере решения проблем с Germline, планируется расширенный анализ гаплотипных IBD-сегментов, а также по мере получения доступа к Linux-машине -admixture-анализ генотипов в программе Admixture.

На выходе участники проекта получат всевозможные данные, в том числе и следущие графики

татиа · « **Ответ #1 :** 17 Апрель 2011, 00:42:42 »

Очень жаль, что происхождение моей мамы из этого региона не документированная реальность((

I2a1a · « **Ответ #2 :** 17 Апрель 2011, 00:56:27 »

Вот так будет выглядеть отчет о пересекающихся сегементах гомозиготности

POOL   FID   IID   PHE   CHR   SNP1   SNP2   BP1   BP2   KB   NSNP   NSIM   GRP
S1   FAM001   ID002   -9   5   rs7713458   rs10941803   43672990   46384240   2711.25   233   1   1
S1   FAM001   ID001   -9   5   rs7713458   rs12517615   43672990   45402545   1729.56   159   1   1*
S1   FAM002   ID001   -9   5   rs10512852   rs17344896   44429326   45649982   1220.66   119   0   2*
S1   CON   3   0:03   5   rs10512852   rs12517615   44429326   45402545   973.219   101   NA   NA
S1   UNION   3   0:03   5   rs7713458   rs10941803   43672990   46384240   2711.25   233   NA   NA

S2   FAM001   ID001   -9   15   rs8026748   rs11072382   69757818   70783089   1025.27   139   1   1
S2   FAM001   ID002   -9   15   rs2279787   rs12372979   69714177   70802813   1088.64   155   1   1*
S2   CON   2   0:02   15   rs8026748   rs11072382   69757818   70783089   1025.27   139   NA   NA
S2   UNION   2   0:02   15   rs2279787   rs12372979   69714177   70802813   1088.64   155   NA   NA

S3   FAM001   ID001   -9   9   rs10987852   rs1075650   129859395   130978734   1119.34   121   1   1
S3   FAM001   ID002   -9   9   rs1571142   rs11564101   129700631   130839082   1138.45   125   1   1*
S3   CON   2   0:02   9   rs10987852   rs11564101   129859395   130839082   979.687   101   NA   NA
S3   UNION   2   0:02   9   rs1571142   rs1075650   129700631   130978734   1278.1   145   NA   NA

S4   FAM001   ID001   -9   8   rs7836486   rs16938743   47062007   49846738   2784.73   203   1   1
S4   FAM002   ID001   -9   8   rs7836486   rs4521758   47062007   48904123   1842.12   111   1   1*
S4   CON   2   0:02   8   rs7836486   rs4521758   47062007   48904123   1842.12   111   NA   NA
S4   UNION   2   0:02   8   rs7836486   rs16938743   47062007   49846738   2784.73   203   NA   NA

S7   FAM002   ID001   -9   3   rs13433898   rs17430092   83105077   84922139   1817.06   188   1   1
S7   FAM001   ID002   -9   3   rs2132599   rs11719954   82911048   84002320   1091.27   111   1   1*
S7   CON   2   0:02   3   rs13433898   rs11719954   83105077   84002320   897.243   84   NA   NA
S7   UNION   2   0:02   3   rs2132599   rs17430092   82911048   84922139   2011.09   215   NA   NA

S8   FAM001   ID002   -9   3   rs2526388   rs9840336   50149890   51892650   1742.76   117   0   1*
S8   FAM002   ID001   -9   3   rs2072053   rs9817653   50172096   52123273   1951.18   131   0   2*
S8   CON   2   0:02   3   rs2072053   rs9840336   50172096   51892650   1720.55   114   NA   NA
S8   UNION   2   0:02   3   rs2526388   rs9817653   50149890   52123273   1973.38   134   NA   NA

I2a1a · « **Ответ #3 :** 17 Апрель 2011, 01:00:20 »

Отчет о IBD-сегментах, после удаления сцепленных снипов и снипов в низкой степенью генотипирования

FID1 IID1 FID2 IID2 PHE CHR BP1 BP2 SNP1 SNP2 NSNP KB
FAM001 ID002 FAM002 ID001 -1 1 12654159 14129451 rs2265709 rs1005301 122 1475.29
FAM001 ID002 FAM002 ID001 -1 1 34867458 36866408 rs6425904 rs743015 133 1998.95
FAM001 ID002 FAM002 ID001 -1 1 43171574 44266382 rs3768029 rs7523468 123 1094.81
FAM001 ID002 FAM002 ID001 -1 1 44783332 46429551 rs11211012 rs11584024 142 1646.22
FAM001 ID002 FAM002 ID001 -1 1 67033654 68193675 rs12408354 rs2419044 197 1160.02
FAM001 ID002 FAM002 ID001 -1 1 68279982 69692921 rs12076293 rs1926268 204 1412.94
FAM001 ID002 FAM002 ID001 -1 1 71013820 72288875 rs7547597 rs1026997 202 1275.06
FAM001 ID002 FAM002 ID001 -1 1 80088813 82134490 rs11162840 rs1948395 305 2045.68
FAM001 ID002 FAM002 ID001 -1 1 88169152 89548821 rs4655859 rs10801723 129 1379.67
FAM001 ID002 FAM002 ID001 -1 1 94354117 95927332 rs3789443 rs2700338 274 1573.21
FAM001 ID002 FAM002 ID001 -1 1 99733258 100816738 rs10493914 rs10875316 125 1083.48
FAM001 ID002 FAM002 ID001 -1 1 102194302 103534051 rs10493966 rs17127731 135 1339.75
FAM001 ID002 FAM002 ID001 -1 1 105827987 107460385 rs7415139 rs1335051 156 1632.4
FAM001 ID002 FAM002 ID001 -1 1 113150093 114346954 rs11804649 rs6656609 123 1196.86
FAM001 ID002 FAM002 ID001 -1 1 117296343 118656353 rs4128518 rs2490197 177 1360.01
FAM001 ID002 FAM002 ID001 -1 1 171480558 173289029 rs2795288 rs10489329 120 1808.47
FAM001 ID002 FAM002 ID001 -1 1 173393468 174620749 rs1057285 rs1503124 126 1227.28
FAM001 ID002 FAM002 ID001 -1 1 185439838 187001959 rs2025513 rs10754227 149 1562.12
FAM001 ID002 FAM002 ID001 -1 1 206706517 207829498 rs7520798 rs11587591 172 1122.98
FAM001 ID002 FAM003 ID001 -1 1 37097270 38430471 rs3738081 rs1564119 138 1333.2
FAM001 ID002 FAM003 ID001 -1 1 42197181 43318791 rs653944 rs492763 114 1121.61
FAM001 ID002 FAM003 ID001 -1 1 61217156 63177277 rs12047847 rs10889392 288 1960.12
FAM001 ID002 FAM003 ID001 -1 1 71852486 74101956 rs10493486 rs1340440 164 2249.47
FAM001 ID002 FAM003 ID001 -1 1 74799846 75840867 rs17095579 rs6662665 155 1041.02
FAM001 ID002 FAM003 ID001 -1 1 84020018 87809161 rs6576943 rs12410191 580 3789.14
FAM001 ID002 FAM003 ID001 -1 1 91884155 93166306 rs2478178 rs7515257 148 1282.15
FAM001 ID002 FAM003 ID001 -1 1 106141008 108157301 rs1163518 rs10494078 228 2016.29
FAM001 ID002 FAM003 ID001 -1 1 114675894 115870562 rs627205 rs552279 138 1194.67
FAM001 ID002 FAM003 ID001 -1 1 145025789 146209659 rs4950361 rs1814653 148 1183.87
FAM001 ID002 FAM003 ID001 -1 1 161230524 162599273 rs2841998 rs2077405 217 1368.75
FAM001 ID002 FAM003 ID001 -1 1 178492287 179626503 rs99174 rs634225 154 1134.22
FAM001 ID002 FAM003 ID001 -1 1 180249584 181356634 rs4418557 rs3768622 130 1107.05
FAM001 ID002 FAM003 ID001 -1 1 189885788 192196600 rs7551667 rs642668 203 2310.81
FAM001 ID002 FAM003 ID001 -1 1 192748927 193798046 rs2494129 rs1890645 144 1049.12
FAM001 ID001 FAM003 ID001 -1 1 182249110 183602155 rs1952251 rs7512337 152 1353.05
FAM002 ID001 FAM003 ID001 -1 1 79109195 80359581 rs2996691 rs4384179 151 1250.39
FAM001 ID002 FAM002 ID001 -1 2 13567369 16263326 rs494516 rs687584 372 2695.96
FAM001 ID002 FAM002 ID001 -1 2 21123314 23080927 rs589566 rs4665534 195 1957.61
FAM001 ID002 FAM002 ID001 -1 2 31299299 33004436 rs13386968 rs897509 173 1705.14
FAM001 ID002 FAM002 ID001 -1 2 46107466 47405781 rs6748835 rs6712843 330 1298.32
FAM001 ID002 FAM002 ID001 -1 2 47898276 48899488 rs2651766 rs11690419 113 1001.21
FAM001 ID002 FAM002 ID001 -1 2 53232993 54400129 rs1364676 rs985773 185 1167.14
FAM001 ID002 FAM002 ID001 -1 2 56457489 57796491 rs13432055 rs10496076 180 1339
FAM001 ID002 FAM002 ID001 -1 2 62292185 63486947 rs4671416 rs12470121 100 1194.76
FAM001 ID002 FAM002 ID001 -1 2 82090863 84273243 rs7355329 rs10496308 182 2182.38
FAM001 ID002 FAM002 ID001 -1 2 85383492 86594374 rs13001442 rs1015117 170 1210.88
FAM001 ID002 FAM002 ID001 -1 2 102304821 103366006 rs1420089 rs7565678 163 1061.18
FAM001 ID002 FAM002 ID001 -1 2 103714645 105198625 rs6543232 rs11683715 172 1483.98
FAM001 ID002 FAM002 ID001 -1 2 113833982 115038151 rs6739740 rs10514812 121 1204.17
FAM001 ID002 FAM002 ID001 -1 2 115404426 117433098 rs4849358 rs2118392 227 2028.67
FAM001 ID002 FAM002 ID001 -1 2 121684884 123022591 rs4073806 rs10211068 117 1337.71
FAM001 ID002 FAM002 ID001 -1 2 125141023 126678911 rs6721614 rs1484448 152 1537.89
FAM001 ID002 FAM002 ID001 -1 2 136937213 138477637 rs47150 rs1455167 194 1540.42
FAM001 ID002 FAM002 ID001 -1 2 149650765 150656949 rs11900448 rs330630 120 1006.18
FAM001 ID002 FAM002 ID001 -1 2 171375243 172577431 rs6755814 rs6718013 147 1202.19
FAM001 ID002 FAM002 ID001 -1 2 178205612 179872719 rs2365619 rs7558234 226 1667.11
FAM001 ID002 FAM002 ID001 -1 2 199250963 200644644 rs1455335 rs3115418 124 1393.68
FAM001 ID002 FAM002 ID001 -1 2 222854475 224304863 rs4674642 rs10498153 179 1450.39
FAM001 ID002 FAM003 ID001 -1 2 8647744 9747170 rs3912049 rs4311040 129 1099.43
FAM001 ID002 FAM003 ID001 -1 2 23731432 25963647 rs3795932 rs3856394 176 2232.22
FAM001 ID002 FAM003 ID001 -1 2 37292497 38589594 rs1137437 rs4670876 247 1297.1
FAM001 ID002 FAM003 ID001 -1 2 57791248 58954047 rs11125728 rs734926 114 1162.8
FAM001 ID002 FAM003 ID001 -1 2 60590341 62283712 rs6724431 rs1008725 150 1693.37
FAM001 ID002 FAM003 ID001 -1 2 63287683 64715559 rs6758966 rs2070063 153 1427.88
FAM001 ID002 FAM003 ID001 -1 2 75033179 76093768 rs7594760 rs441584 204 1060.59
FAM001 ID002 FAM003 ID001 -1 2 82961206 84457271 rs10184915 rs4832076 134 1496.07
FAM001 ID002 FAM003 ID001 -1 2 107523945 111453746 rs6744070 rs17041670 228 3929.8
FAM001 ID002 FAM003 ID001 -1 2 112134446 113256443 rs4848138 rs2856838 110 1122
FAM001 ID002 FAM003 ID001 -1 2 117443515 119162500 rs4848429 rs332104 169 1718.98
FAM001 ID002 FAM003 ID001 -1 2 148918245 149978935 rs1446553 rs7556835 106 1060.69
FAM001 ID002 FAM003 ID001 -1 2 151845207 153631051 rs3856557 rs1946677 202 1785.84
FAM001 ID002 FAM003 ID001 -1 2 153872190 154933281 rs1347927 rs1527867 156 1061.09
FAM001 ID002 FAM003 ID001 -1 2 183915935 185476099 rs444319 rs1366840 176 1560.16
FAM001 ID002 FAM003 ID001 -1 2 187394307 188577005 rs11891963 rs2033838 103 1182.7
FAM001 ID002 FAM003 ID001 -1 2 197857012 200067380 rs12619296 rs7608290 149 2210.37
FAM001 ID002 FAM003 ID001 -1 2 213280784 214500142 rs10188254 rs1588455 137 1219.36
FAM001 ID002 FAM003 ID001 -1 2 224966817 227079969 rs12992690 rs11674718 295 2113.15
FAM001 ID002 FAM002 ID001 -1 3 4646835 5800657 rs902983 rs1897958 267 1153.82
FAM001 ID002 FAM002 ID001 -1 3 14501542 16377563 rs1062540 rs690014 304 1876.02
FAM001 ID002 FAM002 ID001 -1 3 30761522 31826730 rs6550012 rs6773772 152 1065.21
FAM001 ID002 FAM002 ID001 -1 3 60456499 61544793 rs2197751 rs1320172 271 1088.29
FAM001 ID002 FAM002 ID001 -1 3 63224648 64258539 rs6445336 rs2263039 219 1033.89
FAM001 ID002 FAM002 ID001 -1 3 69599010 70689611 rs1001498 rs11927332 142 1090.6
FAM001 ID002 FAM002 ID001 -1 3 71912709 73123205 rs10865660 rs6776264 209 1210.5
FAM001 ID002 FAM002 ID001 -1 3 73320419 74613336 rs9850430 rs6799372 253 1292.92
FAM001 ID002 FAM002 ID001 -1 3 76009081 77120883 rs4856006 rs7617945 138 1111.8
FAM001 ID002 FAM002 ID001 -1 3 78314071 79787521 rs17015805 rs9882126 138 1473.45
FAM001 ID002 FAM002 ID001 -1 3 89251573 97523082 rs7642606 rs9843398 212 8271.51
FAM001 ID002 FAM002 ID001 -1 3 104315821 105589393 rs4643721 rs2398966 139 1273.57
FAM001 ID002 FAM002 ID001 -1 3 111969774 113133975 rs4610259 rs754914 107 1164.2
FAM001 ID002 FAM002 ID001 -1 3 117957761 119311368 rs2116574 rs6780942 196 1353.61
FAM001 ID002 FAM002 ID001 -1 3 139616102 141318227 rs1564406 rs4683801 216 1702.12
FAM001 ID002 FAM002 ID001 -1 3 168127619 169664229 rs11928994 rs11926516 152 1536.61
FAM001 ID002 FAM002 ID001 -1 3 178157980 179415628 rs10936922 rs6762634 115 1257.65
FAM001 ID002 FAM002 ID001 -1 3 179856359 180858986 rs10513758 rs9874079 113 1002.63
FAM001 ID002 FAM003 ID001 -1 3 17107009 18552212 rs11549705 rs1828729 119 1445.2
FAM001 ID002 FAM003 ID001 -1 3 28101599 29457330 rs1156909 rs17666612 228 1355.73
FAM001 ID002 FAM003 ID001 -1 3 43067294 45152010 rs557418 rs10490812 202 2084.72
FAM001 ID002 FAM003 ID001 -1 3 46919278 51893268 rs1138518 rs1587922 172 4973.99
FAM001 ID002 FAM003 ID001 -1 3 57643241 60723766 rs6806730 rs4974227 610 3080.53
FAM001 ID002 FAM003 ID001 -1 3 65926792 67869427 rs1430416 rs1459912 263 1942.63
FAM001 ID002 FAM003 ID001 -1 3 98062005 99440970 rs13070471 rs9828347 111 1378.96
FAM001 ID002 FAM003 ID001 -1 3 99969330 101217279 rs9832986 rs9827744 121 1247.95
FAM001 ID002 FAM003 ID001 -1 3 103678370 105069675 rs7627117 rs1673874 128 1391.31
FAM001 ID002 FAM003 ID001 -1 3 109641264 111168865 rs3996040 rs9824654 170 1527.6
FAM001 ID002 FAM003 ID001 -1 3 127881519 129110017 rs9289282 rs9865083 161 1228.5
FAM001 ID002 FAM003 ID001 -1 3 129672262 131291559 rs2953128 rs7622131 132 1619.3
FAM001 ID002 FAM003 ID001 -1 3 132037742 133355666 rs12493708 rs6772218 144 1317.92
FAM001 ID002 FAM003 ID001 -1 3 137290299 138784201 rs9810089 rs10804653 132 1493.9
FAM001 ID002 FAM003 ID001 -1 3 144980320 146367022 rs4839608 rs7622285 118 1386.7
FAM001 ID002 FAM003 ID001 -1 3 147247925 148840489 rs12635752 rs1318446 202 1592.56
FAM001 ID002 FAM003 ID001 -1 3 153460876 154505470 rs323623 rs9824588 115 1044.59
FAM001 ID002 FAM003 ID001 -1 3 160617634 161726767 rs12485627 rs6441322 124 1109.13
FAM001 ID002 FAM003 ID001 -1 3 178749444 179860573 rs10470510 rs9864924 106 1111.13
FAM001 ID001 FAM003 ID001 -1 3 16723971 17827925 rs9856652 rs12495352 108 1103.95
FAM001 ID001 FAM003 ID001 -1 3 43067294 44111428 rs557418 rs7625991 106 1044.13
FAM002 ID001 FAM003 ID001 -1 3 55617546 56760596 rs17055498 rs6792241 140 1143.05
FAM001 ID002 FAM002 ID001 -1 4 17155479 18684976 rs6843189 rs207311 116 1529.5
FAM001 ID002 FAM002 ID001 -1 4 20722041 22441780 rs1821330 rs439863 250 1719.74
FAM001 ID002 FAM002 ID001 -1 4 32583628 35735842 rs7436505 rs11935245 178 3152.21
FAM001 ID002 FAM002 ID001 -1 4 42533105 43931165 rs1562840 rs7699496 158 1398.06
FAM001 ID002 FAM002 ID001 -1 4 54187138 55500312 rs2572289 rs2067951 181 1313.17
FAM001 ID002 FAM002 ID001 -1 4 76999967 78012039 rs1013588 rs237616 178 1012.07
FAM001 ID002 FAM002 ID001 -1 4 83078508 84771944 rs10008190 rs6818782 181 1693.44
FAM001 ID002 FAM002 ID001 -1 4 87399136 88925317 rs11725943 rs2732167 172 1526.18
FAM001 ID002 FAM002 ID001 -1 4 105522604 106668349 rs4306954 rs4082504 128 1145.74
FAM001 ID002 FAM002 ID001 -1 4 110076525 111085957 rs1364842 rs4698800 132 1009.43
FAM001 ID002 FAM002 ID001 -1 4 119682133 121566817 rs2200517 rs705103 247 1884.68
FAM001 ID002 FAM002 ID001 -1 4 122837616 124511396 rs28651243 rs300550 174 1673.78
FAM001 ID002 FAM002 ID001 -1 4 127844385 130365626 rs313048 rs1757939 220 2521.24
FAM001 ID002 FAM002 ID001 -1 4 140112137 141255371 rs4600866 rs2139926 182 1143.23
FAM001 ID002 FAM002 ID001 -1 4 150507561 152463768 rs7653957 rs7655373 113 1956.21
FAM001 ID002 FAM002 ID001 -1 4 157381701 158876103 rs6844119 rs1004310 167 1494.4

I2a1a · « **Ответ #4 :** 17 Апрель 2011, 01:01:14 »

FID1 IID1 FID2 IID2 PHE CHR BP1 BP2 SNP1 SNP2 NSNP KB
FAM001 ID002 FAM002 ID001 -1 1 222927066 234686152 rs12133496 rs1253615 13 11759.1
FAM001 ID002 FAM002 ID001 -1 2 2582345 10348167 rs1451198 rs13422172 11 7765.82
FAM001 ID002 FAM002 ID001 -1 2 79257340 88808762 rs1368960 rs335115 10 9551.42
FAM001 ID002 FAM002 ID001 -1 2 206481747 217516448 rs7592297 rs1011502 13 11034.7
FAM001 ID002 FAM002 ID001 -1 3 71578698 85487473 rs6771130 rs2117152 13 13908.8
FAM001 ID002 FAM002 ID001 -1 3 104283065 115432817 rs10937267 rs2062834 12 11149.8
FAM001 ID002 FAM002 ID001 -1 5 94601083 109016440 rs385225 rs187462 13 14415.4
FAM001 ID002 FAM001 ID001 -1 5 1229601 44434453 rs4975536 rs10941665 46 43204.9
FAM001 ID002 FAM001 ID001 -1 5 44434453 77164410 rs10941665 rs10514122 27 32730
FAM001 ID002 FAM001 ID001 -1 5 77164410 134537886 rs10514122 rs1122171 51 57373.5
FAM001 ID002 FAM001 ID001 -1 5 134537886 144682989 rs1122171 rs157858 10 10145.1
FAM001 ID002 FAM001 ID001 -1 5 144682989 179788872 rs157858 rs1828172 41 35105.9
FAM001 ID002 FAM002 ID001 -1 6 68004709 87194644 rs9454109 rs1876527 19 19189.9
FAM001 ID002 FAM002 ID001 -1 7 11481390 16875070 rs17164640 rs2471907 10 5393.68
FAM001 ID002 FAM002 ID001 -1 7 108526859 120706464 rs1513914 rs1541509 11 12179.6
FAM001 ID002 FAM001 ID001 -1 7 95323458 158456556 rs2600566 rs2657389 60 63133.1
FAM001 ID002 FAM002 ID001 -1 8 18718011 25948059 rs2638663 rs11135910 12 7230.05
FAM001 ID002 FAM002 ID001 -1 8 70738684 87175826 rs4738017 rs7846145 17 16437.1
FAM001 ID002 FAM002 ID001 -1 8 103113852 116257839 rs1269707 rs1519084 13 13144
FAM001 ID002 FAM001 ID001 -1 8 179030 13313779 rs2906330 rs17092948 27 13134.7
FAM001 ID002 FAM001 ID001 -1 8 13313779 53172159 rs17092948 rs3849810 44 39858.4
FAM001 ID002 FAM001 ID001 -1 8 53172159 145475151 rs3849810 rs7838717 95 92303
FAM001 ID002 FAM002 ID001 -1 9 116202074 124749144 rs10759693 rs10818768 13 8547.07
FAM001 ID002 FAM001 ID001 -1 9 123945860 139093641 rs4147659 rs7037849 18 15147.8
FAM001 ID002 FAM001 ID001 -1 10 97386460 134821592 rs4417206 rs4326710 45 37435.1
FAM001 ID002 FAM001 ID001 -1 11 239131 78266089 rs11601356 rs11237644 71 78027
FAM001 ID002 FAM001 ID001 -1 11 78266089 99075724 rs11237644 rs631773 23 20809.6
FAM001 ID002 FAM001 ID001 -1 11 99075724 127525578 rs631773 rs1477577 35 28449.9
FAM001 ID002 FAM001 ID001 -1 11 128791122 134323841 rs11607460 rs11224099 10 5532.72
FAM001 ID002 FAM002 ID001 -1 12 93605693 102466844 rs7138248 rs4540923 11 8861.15
FAM001 ID002 FAM001 ID001 -1 12 3523568 41734204 rs4766137 rs1656535 45 38210.6
FAM001 ID002 FAM001 ID001 -1 12 41734204 131536633 rs1656535 rs2091731 87 89802.4
FAM001 ID002 FAM002 ID001 -1 13 82160171 94926858 rs2329247 rs7984974 15 12766.7
FAM001 ID002 FAM001 ID001 -1 13 18108426 68460886 rs4293225 rs9541678 52 50352.5
FAM001 ID002 FAM001 ID001 -1 13 68460886 112050604 rs9541678 rs9577340 53 43589.7
FAM001 ID002 FAM002 ID001 -1 14 34193684 47376530 rs7145220 rs1956328 14 13182.8
FAM001 ID002 FAM001 ID001 -1 14 19782162 80540892 rs11851004 rs17545310 71 60758.7
FAM001 ID002 FAM001 ID001 -1 14 80540892 103624674 rs17545310 rs1744280 27 23083.8
FAM001 ID002 FAM002 ID001 -1 15 89814906 96731004 rs8043364 rs3923686 11 6916.1
FAM001 ID002 FAM001 ID001 -1 16 332462 23260349 rs370681 rs239349 27 22927.9
FAM001 ID002 FAM001 ID001 -1 16 27066373 55282311 rs12444461 rs4784714 12 28215.9
FAM001 ID002 FAM001 ID001 -1 16 55282311 67255962 rs4784714 rs1111721 12 11973.7
FAM001 ID002 FAM001 ID001 -1 16 67255962 77566282 rs1111721 rs8060634 12 10310.3
FAM001 ID002 FAM001 ID001 -1 16 77566282 88596560 rs8060634 rs9936896 22 11030.3
FAM001 ID002 FAM001 ID001 -1 17 51088 6981602 rs4890183 rs314245 10 6930.51
FAM001 ID002 FAM001 ID001 -1 17 6981602 13716102 rs314245 rs746590 12 6734.5
FAM001 ID002 FAM001 ID001 -1 17 13716102 64903636 rs746590 rs100043 43 51187.5
FAM001 ID002 FAM001 ID001 -1 17 69040691 78181864 rs11656549 rs2306755 12 9141.17
FAM001 ID002 FAM001 ID001 -1 18 323739 8820080 rs11081025 rs627543 13 8496.34
FAM001 ID002 FAM001 ID001 -1 18 18474290 73145738 rs4990483 rs11660621 63 54671.4
FAM001 ID002 FAM001 ID001 -1 19 291700 48527610 rs882572 rs12461712 37 48235.9
FAM001 ID002 FAM001 ID001 -1 20 16749 54725886 rs6086616 rs2426643 61 54709.1
FAM001 ID002 FAM001 ID001 -1 20 54725886 61874860 rs2426643 rs6062521 11 7148.97
FAM001 ID002 FAM001 ID001 -1 21 20199522 46761215 rs1475873 rs6518299 39 26561.7
FAM001 ID002 FAM001 ID001 -1 22 20393337 29676752 rs5749696 rs1003480 14 9283.42
FAM001 ID002 FAM001 ID001 -1 22 29676752 43035946 rs1003480 rs9614231 16 13359.2
FAM001 ID002 FAM001 ID001 -1 22 43035946 49330921 rs9614231 rs5770775 12 6294.98

I2a1a · « **Ответ #5 :** 17 Апрель 2011, 01:02:58 »

Данные о совпадающих сегментах
FID1 IID2 FID1 IID2 PHE NSEG KB KBAVG
FAM001 ID001 FAM002 ID001 -1 4 4511.33 1127.83
FAM001 ID001 FAM003 ID001 -1 11 25500.9 2318.26
FAM002 ID001 FAM003 ID001 -1 12 15648.7 1304.06
FAM001 ID002 FAM001 ID001 -1 24 59780.3 2490.85
FAM001 ID002 FAM002 ID001 -1 245 389124 1588.26
FAM001 ID002 FAM003 ID001 -1 223 371831 1667.4

I2a1a · « **Ответ #6 :** 17 Апрель 2011, 01:08:24 »

Кластеризация

SOL-0    FAM001_ID002 FAM001_ID001 FAM002_ID001

FAM001 ID002   0 0 0 0
FAM001 ID001   1 0 0 0
FAM002 ID001   2 1 1 0
FAM003 ID001   3 2 0 0

FAM001 ID002   0 0 0
FAM002 ID001   1 1 0
FAM001 ID001   2 0 0

I2a1a · « **Ответ #7 :** 17 Апрель 2011, 01:09:28 »

Пересекающиеся IBD-сегменты

POOL FID1 IID1 FID2 IID2 PHE CHR SNP1 SNP2 BP1 BP2 KB NSNP NSIM GRP
POOL FID IID PHE CHR SNP1 SNP2 BP1 BP2 KB NSNP NSIM GRP
S1 FAM001 ID002 FAM001 ID001 NA 22 rs1003480 rs9614231 29676752 43035946 13359.2 16 0 1*
S1 FAM001 ID002 FAM001 ID001 NA 22 rs9614231 rs5770775 43035946 49330921 6294.98 12 0 2*
S1 CON 2 NA NA 0:0 22 rs9614231 rs9614231 43035946 43035946 0 1 NA NA
S1 UNION 2 NA NA 0:0 22 rs1003480 rs5770775 29676752 49330921 19654.2 27 NA NA

S2 FAM001 ID002 FAM001 ID001 NA 22 rs5749696 rs1003480 20393337 29676752 9283.42 14 0 1*
S2 FAM001 ID002 FAM001 ID001 NA 22 rs1003480 rs9614231 29676752 43035946 13359.2 16 0 2*
S2 CON 2 NA NA 0:0 22 rs1003480 rs1003480 29676752 29676752 0 1 NA NA
S2 UNION 2 NA NA 0:0 22 rs5749696 rs9614231 20393337 43035946 22642.6 29 NA NA

S3 FAM001 ID002 FAM001 ID001 NA 20 rs6086616 rs2426643 16749 54725886 54709.1 61 0 1*
S3 FAM001 ID002 FAM001 ID001 NA 20 rs2426643 rs6062521 54725886 61874860 7148.97 11 0 2*
S3 CON 2 NA NA 0:0 20 rs2426643 rs2426643 54725886 54725886 0 1 NA NA
S3 UNION 2 NA NA 0:0 20 rs6086616 rs6062521 16749 61874860 61858.1 71 NA NA

S4 FAM001 ID002 FAM001 ID001 NA 17 rs314245 rs746590 6981602 13716102 6734.5 12 0 1*
S4 FAM001 ID002 FAM001 ID001 NA 17 rs746590 rs100043 13716102 64903636 51187.5 43 0 2*
S4 CON 2 NA NA 0:0 17 rs746590 rs746590 13716102 13716102 0 1 NA NA
S4 UNION 2 NA NA 0:0 17 rs314245 rs100043 6981602 64903636 57922 54 NA NA

S5 FAM001 ID002 FAM001 ID001 NA 17 rs4890183 rs314245 51088 6981602 6930.51 10 0 1*
S5 FAM001 ID002 FAM001 ID001 NA 17 rs314245 rs746590 6981602 13716102 6734.5 12 0 2*
S5 CON 2 NA NA 0:0 17 rs314245 rs314245 6981602 6981602 0 1 NA NA
S5 UNION 2 NA NA 0:0 17 rs4890183 rs746590 51088 13716102 13665 21 NA NA

S6 FAM001 ID002 FAM001 ID001 NA 16 rs1111721 rs8060634 67255962 77566282 10310.3 12 0 1*
S6 FAM001 ID002 FAM001 ID001 NA 16 rs8060634 rs9936896 77566282 88596560 11030.3 22 0 2*
S6 CON 2 NA NA 0:0 16 rs8060634 rs8060634 77566282 77566282 0 1 NA NA
S6 UNION 2 NA NA 0:0 16 rs1111721 rs9936896 67255962 88596560 21340.6 33 NA NA

S7 FAM001 ID002 FAM001 ID001 NA 16 rs4784714 rs1111721 55282311 67255962 11973.7 12 0 1*
S7 FAM001 ID002 FAM001 ID001 NA 16 rs1111721 rs8060634 67255962 77566282 10310.3 12 0 2*
S7 CON 2 NA NA 0:0 16 rs1111721 rs1111721 67255962 67255962 0 1 NA NA
S7 UNION 2 NA NA 0:0 16 rs4784714 rs8060634 55282311 77566282 22284 23 NA NA

S8 FAM001 ID002 FAM001 ID001 NA 16 rs12444461 rs4784714 27066373 55282311 28215.9 12 0 1*
S8 FAM001 ID002 FAM001 ID001 NA 16 rs4784714 rs1111721 55282311 67255962 11973.7 12 0 2*
S8 CON 2 NA NA 0:0 16 rs4784714 rs4784714 55282311 55282311 0 1 NA NA
S8 UNION 2 NA NA 0:0 16 rs12444461 rs1111721 27066373 67255962 40189.6 23 NA NA

S9 FAM001 ID002 FAM001 ID001 NA 14 rs11851004 rs17545310 19782162 80540892 60758.7 71 0 1*
S9 FAM001 ID002 FAM001 ID001 NA 14 rs17545310 rs1744280 80540892 103624674 23083.8 27 0 2*
S9 CON 2 NA NA 0:0 14 rs17545310 rs17545310 80540892 80540892 0 1 NA NA
S9 UNION 2 NA NA 0:0 14 rs11851004 rs1744280 19782162 103624674 83842.5 97 NA NA

S10 FAM001 ID002 FAM001 ID001 NA 14 rs11851004 rs17545310 19782162 80540892 60758.7 71 0 1*
S10 FAM001 ID002 FAM002 ID001 NA 14 rs7145220 rs1956328 34193684 47376530 13182.8 14 0 2*
S10 CON 2 NA NA 0:0 14 rs7145220 rs1956328 34193684 47376530 13182.8 14 NA NA
S10 UNION 2 NA NA 0:0 14 rs11851004 rs17545310 19782162 80540892 60758.7 71 NA NA

S11 FAM001 ID002 FAM001 ID001 NA 13 rs9541678 rs9577340 68460886 112050604 43589.7 53 0 1*
S11 FAM001 ID002 FAM002 ID001 NA 13 rs2329247 rs7984974 82160171 94926858 12766.7 15 0 2*
S11 CON 2 NA NA 0:0 13 rs2329247 rs7984974 82160171 94926858 12766.7 15 NA NA
S11 UNION 2 NA NA 0:0 13 rs9541678 rs9577340 68460886 112050604 43589.7 53 NA NA

S12 FAM001 ID002 FAM001 ID001 NA 13 rs4293225 rs9541678 18108426 68460886 50352.5 52 0 1*
S12 FAM001 ID002 FAM001 ID001 NA 13 rs9541678 rs9577340 68460886 112050604 43589.7 53 0 2*
S12 CON 2 NA NA 0:0 13 rs9541678 rs9541678 68460886 68460886 0 1 NA NA
S12 UNION 2 NA NA 0:0 13 rs4293225 rs9577340 18108426 112050604 93942.2 104 NA NA

S13 FAM001 ID002 FAM001 ID001 NA 12 rs1656535 rs2091731 41734204 131536633 89802.4 87 0 1*
S13 FAM001 ID002 FAM002 ID001 NA 12 rs7138248 rs4540923 93605693 102466844 8861.15 11 0 2*
S13 CON 2 NA NA 0:0 12 rs7138248 rs4540923 93605693 102466844 8861.15 11 NA NA
S13 UNION 2 NA NA 0:0 12 rs1656535 rs2091731 41734204 131536633 89802.4 87 NA NA

S14 FAM001 ID002 FAM001 ID001 NA 12 rs4766137 rs1656535 3523568 41734204 38210.6 45 0 1*
S14 FAM001 ID002 FAM001 ID001 NA 12 rs1656535 rs2091731 41734204 131536633 89802.4 87 0 2*
S14 CON 2 NA NA 0:0 12 rs1656535 rs1656535 41734204 41734204 0 1 NA NA
S14 UNION 2 NA NA 0:0 12 rs4766137 rs2091731 3523568 131536633 128013 131 NA NA

S15 FAM001 ID002 FAM001 ID001 NA 11 rs11237644 rs631773 78266089 99075724 20809.6 23 0 1*
S15 FAM001 ID002 FAM001 ID001 NA 11 rs631773 rs1477577 99075724 127525578 28449.9 35 0 2*
S15 CON 2 NA NA 0:0 11 rs631773 rs631773 99075724 99075724 0 1 NA NA
S15 UNION 2 NA NA 0:0 11 rs11237644 rs1477577 78266089 127525578 49259.5 57 NA NA

S16 FAM001 ID002 FAM001 ID001 NA 11 rs11601356 rs11237644 239131 78266089 78027 71 0 1*
S16 FAM001 ID002 FAM001 ID001 NA 11 rs11237644 rs631773 78266089 99075724 20809.6 23 0 2*
S16 CON 2 NA NA 0:0 11 rs11237644 rs11237644 78266089 78266089 0 1 NA NA
S16 UNION 2 NA NA 0:0 11 rs11601356 rs631773 239131 99075724 98836.6 93 NA NA

S17 FAM001 ID002 FAM002 ID001 NA 9 rs10759693 rs10818768 116202074 124749144 8547.07 13 0 1*
S17 FAM001 ID002 FAM001 ID001 NA 9 rs4147659 rs7037849 123945860 139093641 15147.8 18 0 2*
S17 CON 2 NA NA 0:0 9 rs4147659 rs10818768 123945860 124749144 803.284 2 NA NA
S17 UNION 2 NA NA 0:0 9 rs10759693 rs7037849 116202074 139093641 22891.6 29 NA NA

S18 FAM001 ID002 FAM001 ID001 NA 8 rs3849810 rs7838717 53172159 145475151 92303 95 0 1*
S18 FAM001 ID002 FAM002 ID001 NA 8 rs1269707 rs1519084 103113852 116257839 13144 13 0 2*
S18 CON 2 NA NA 0:0 8 rs1269707 rs1519084 103113852 116257839 13144 13 NA NA
S18 UNION 2 NA NA 0:0 8 rs3849810 rs7838717 53172159 145475151 92303 95 NA NA

S19 FAM001 ID002 FAM001 ID001 NA 8 rs3849810 rs7838717 53172159 145475151 92303 95 0 1*
S19 FAM001 ID002 FAM002 ID001 NA 8 rs4738017 rs7846145 70738684 87175826 16437.1 17 0 2*
S19 CON 2 NA NA 0:0 8 rs4738017 rs7846145 70738684 87175826 16437.1 17 NA NA
S19 UNION 2 NA NA 0:0 8 rs3849810 rs7838717 53172159 145475151 92303 95 NA NA

S20 FAM001 ID002 FAM001 ID001 NA 8 rs17092948 rs3849810 13313779 53172159 39858.4 44 0 1*
S20 FAM001 ID002 FAM001 ID001 NA 8 rs3849810 rs7838717 53172159 145475151 92303 95 0 2*
S20 CON 2 NA NA 0:0 8 rs3849810 rs3849810 53172159 53172159 0 1 NA NA
S20 UNION 2 NA NA 0:0 8 rs17092948 rs7838717 13313779 145475151 132161 138 NA NA

S21 FAM001 ID002 FAM001 ID001 NA 8 rs17092948 rs3849810 13313779 53172159 39858.4 44 0 1*
S21 FAM001 ID002 FAM002 ID001 NA 8 rs2638663 rs11135910 18718011 25948059 7230.05 12 0 2*
S21 CON 2 NA NA 0:0 8 rs2638663 rs11135910 18718011 25948059 7230.05 12 NA NA
S21 UNION 2 NA NA 0:0 8 rs17092948 rs3849810 13313779 53172159 39858.4 44 NA NA

S22 FAM001 ID002 FAM001 ID001 NA 8 rs2906330 rs17092948 179030 13313779 13134.7 27 0 1*
S22 FAM001 ID002 FAM001 ID001 NA 8 rs17092948 rs3849810 13313779 53172159 39858.4 44 0 2*
S22 CON 2 NA NA 0:0 8 rs17092948 rs17092948 13313779 13313779 0 1 NA NA
S22 UNION 2 NA NA 0:0 8 rs2906330 rs3849810 179030 53172159 52993.1 70 NA NA

S23 FAM001 ID002 FAM001 ID001 NA 7 rs2600566 rs2657389 95323458 158456556 63133.1 60 0 1*
S23 FAM001 ID002 FAM002 ID001 NA 7 rs1513914 rs1541509 108526859 120706464 12179.6 11 0 2*
S23 CON 2 NA NA 0:0 7 rs1513914 rs1541509 108526859 120706464 12179.6 11 NA NA
S23 UNION 2 NA NA 0:0 7 rs2600566 rs2657389 95323458 158456556 63133.1 60 NA NA

S24 FAM001 ID002 FAM001 ID001 NA 5 rs1122171 rs157858 134537886 144682989 10145.1 10 0 1*
S24 FAM001 ID002 FAM001 ID001 NA 5 rs157858 rs1828172 144682989 179788872 35105.9 41 0 2*
S24 CON 2 NA NA 0:0 5 rs157858 rs157858 144682989 144682989 0 1 NA NA
S24 UNION 2 NA NA 0:0 5 rs1122171 rs1828172 134537886 179788872 45251 50 NA NA

S25 FAM001 ID002 FAM001 ID001 NA 5 rs10514122 rs1122171 77164410 134537886 57373.5 51 0 1*
S25 FAM001 ID002 FAM001 ID001 NA 5 rs1122171 rs157858 134537886 144682989 10145.1 10 0 2*
S25 CON 2 NA NA 0:0 5 rs1122171 rs1122171 134537886 134537886 0 1 NA NA
S25 UNION 2 NA NA 0:0 5 rs10514122 rs157858 77164410 144682989 67518.6 60 NA NA

S26 FAM001 ID002 FAM001 ID001 NA 5 rs10514122 rs1122171 77164410 134537886 57373.5 51 0 1*
S26 FAM001 ID002 FAM002 ID001 NA 5 rs385225 rs187462 94601083 109016440 14415.4 13 0 2*
S26 CON 2 NA NA 0:0 5 rs385225 rs187462 94601083 109016440 14415.4 13 NA NA
S26 UNION 2 NA NA 0:0 5 rs10514122 rs1122171 77164410 134537886 57373.5 51 NA NA

S27 FAM001 ID002 FAM001 ID001 NA 5 rs10941665 rs10514122 44434453 77164410 32730 27 0 1*
S27 FAM001 ID002 FAM001 ID001 NA 5 rs10514122 rs1122171 77164410 134537886 57373.5 51 0 2*
S27 CON 2 NA NA 0:0 5 rs10514122 rs10514122 77164410 77164410 0 1 NA NA
S27 UNION 2 NA NA 0:0 5 rs10941665 rs1122171 44434453 134537886 90103.4 77 NA NA

S28 FAM001 ID002 FAM001 ID001 NA 5 rs4975536 rs10941665 1229601 44434453 43204.9 46 0 1*
S28 FAM001 ID002 FAM001 ID001 NA 5 rs10941665 rs10514122 44434453 77164410 32730 27 0 2*
S28 CON 2 NA NA 0:0 5 rs10941665 rs10941665 44434453 44434453 0 1 NA NA
S28 UNION 2 NA NA 0:0 5 rs4975536 rs10514122 1229601 77164410 75934.8 72 NA NA

I2a1a · « **Ответ #8 :** 17 Апрель 2011, 01:11:25 »

Данные по числу и средней длине участков гомозиготности

FID IID PHE NSEG KB KBAVG
FAM001 ID002 -9 25 35896.5 1435.86
FAM002 ID001 -9 27 39950.8 1479.66
FAM001 ID001 -9 29 41770.3 1440.35

I2a1a · « **Ответ #9 :** 17 Апрель 2011, 01:15:35 »

IBDsegments -общее число

FID1 IID2 FID1 IID2 PHE NSEG KB KBAVG
FAM001 ID002 FAM002 ID001 -1 18 203433 11301.8
FAM001 ID002 FAM001 ID001 -1 39 1.2654e+006 32446.2

I2a1a · « **Ответ #10 :** 17 Апрель 2011, 01:17:22 »

Отфазированные генотипы

rs3094315 A G 1 0 0 0 1 0 0 1 0
rs12562034 G - 1 0 0 1 0 0 1 0 0
rs3934834 C - 1 0 0 1 0 0 1 0 0
rs9442372 G A 1 0 0 0 1 0 1 0 0
rs3737728 G A 1 0 0 0 1 0 1 0 0
rs11260588 G - 1 0 0 1 0 0 1 0 0
rs6687776 C T 1 0 0 1 0 0 0 1 0
rs9651273 G A 1 0 0 0 1 0 1 0 0
rs4970405 A G 1 0 0 1 0 0 0 1 0
rs12726255 A G 1 0 0 1 0 0 0 1 0
rs11807848 T C 0 1 0 0 0 1 0 1 0
rs9442373 A C 0 1 0 0 0 1 0 1 0
rs2298217 C T 1 0 0 1 0 0 0 1 0
rs12145826 G - 1 0 0 1 0 0 1 0 0
rs9442380 C - 1 0 0 1 0 0 1 0 0
rs7553429 A - 1 0 0 1 0 0 1 0 0
rs4970362 G - 1 0 0 1 0 0 1 0 0
rs9660710 C - 1 0 0 1 0 0 1 0 0
rs4970420 A G 0 1 0 0 1 0 0 0 1
rs1320565 T C 0 1 0 0 0 1 0 1 0
rs11260549 G - 1 0 0 1 0 0 1 0 0
rs9729550 C A 0 1 0 0 0 1 0 1 0
rs11721 C - 1 0 0 1 0 0 1 0 0
rs2887286 T - 1 0 0 1 0 0 1 0 0
rs3813199 G - 1 0 0 1 0 0 1 0 0
rs3766186 C - 1 0 0 1 0 0 1 0 0
rs7515488 T C 0 1 0 0 0 1 0 1 0
rs715643 C T 1 0 0 1 0 0 0 1 0
rs6675798 T C 0 1 0 0 1 0 0 1 0
rs7524470 G A 0 1 0 0 0 1 0 1 0
rs11804831 T C 0 1 0 0 1 0 0 1 0
rs6685064 T C 0 1 0 0 0 1 0 1 0
rs2229831 A - 1 0 0 1 0 0 1 0 0
rs3737717 A - 1 0 0 1 0 0 1 0 0
rs12142199 G A 0 1 0 0 1 0 0 1 0
rs10949 A - 1 0 0 1 0 0 1 0 0
rs2765033 C - 1 0 0 1 0 0 1 0 0
rs2649588 C T 0 1 0 0 0 1 0 1 0
rs819980 C T 0 1 0 0 0 1 0 1 0
rs9439462 C - 1 0 0 1 0 0 1 0 0
rs3766178 T C 1 0 0 0 1 0 0 1 0
rs2031709 C - 1 0 0 1 0 0 1 0 0
rs3128342 C A 0 1 0 0 1 0 0 0 1
rs880051 G A 1 0 0 1 0 0 0 1 0
rs2296716 C T 1 0 0 1 0 0 0 1 0
rs6603793 C T 1 0 0 0 1 0 0 1 0
rs7520996 T C 1 0 0 0 1 0 0 1 0
rs6603811 C - 1 0 0 1 0 0 1 0 0
rs7531583 A G 0 1 0 0 0 1 0 1 0
rs16825336 G A 1 0 0 1 0 0 0 1 0
rs2180311 T C 0 1 0 0 0 1 0 1 0
rs6681938 C T 0 1 0 0 1 0 0 0 1
rs10907192 G - 1 0 0 1 0 0 1 0 0
rs4648592 G - 1 0 0 1 0 0 1 0 0
rs7525092 C - 1 0 0 1 0 0 1 0 0
rs2474460 C T 0 1 0 0 0 1 0 1 0
rs12758705 G - 1 0 0 1 0 0 1 0 0
rs2803329 A G 0 1 0 0 0 1 0 1 0
rs3820011 C - 1 0 0 1 0 0 1 0 0
rs2803291 C - 1 0 0 1 0 0 1 0 0
rs41307846 G A 1 0 0 0 1 0 1 0 0
rs1878745 A G 1 0 0 1 0 0 0 1 0
rs2292861 A G 0 1 0 0 0 1 0 1 0
rs2459994 C T 1 0 0 1 0 0 0 1 0
rs12755035 A G 0 1 0 0 0 1 0 1 0
rs884080 G A 0 1 0 0 0 1 1 0 0
rs908742 G A 1 0 0 1 0 0 0 1 0
rs4648808 C - 1 0 0 1 0 0 1 0 0
rs6603813 T - 1 0 0 1 0 0 1 0 0
rs3107151 G - 1 0 0 1 0 0 1 0 0
rs3128291 G - 1 0 0 1 0 0 1 0 0
rs3128296 T G 1 0 0 0 1 0 1 0 0
rs3753242 C - 1 0 0 1 0 0 1 0 0
rs424079 A - 1 0 0 1 0 0 1 0 0
rs262669 G - 1 0 0 1 0 0 1 0 0
rs2257182 T - 1 0 0 1 0 0 1 0 0
rs262654 G - 1 0 0 1 0 0 1 0 0
rs3052 C - 1 0 0 1 0 0 1 0 0
rs262688 T - 1 0 0 1 0 0 1 0 0
rs2460002 G A 0 1 0 0 1 0 0 1 0
rs6665593 G - 1 0 0 1 0 0 1 0 0
rs7512482 T - 1 0 0 1 0 0 1 0 0
rs262683 C - 1 0 0 1 0 0 1 0 0
rs2460000 G A 0 1 0 0 1 0 0 0 1
rs263526 T - 1 0 0 1 0 0 1 0 0
rs10910034 T C 0 1 0 0 1 0 0 0 1
rs1713712 T C 0 1 0 0 1 0 0 0 1
rs260513 A G 0 1 0 0 1 0 0 0 1
rs260512 A G 0 1 0 0 1 0 0 0 1
rs10797417 A - 1 0 0 1 0 0 1 0 0
rs7547453 C - 1 0 0 1 0 0 1 0 0
rs11588312 T C 0 1 0 0 1 0 0 0 1
rs6673129 C - 1 0 0 1 0 0 1 0 0
rs7553178 A G 0 1 0 0 1 0 0 0 1
rs4648819 A G 1 0 0 1 0 0 0 1 0
rs10910047 G A 0 1 0 0 1 0 0 0 1
rs12119470 C T 1 0 0 0 1 0 1 0 0
rs2017143 T C 0 1 0 0 1 0 0 1 0
rs2643885 A C 1 0 0 0 1 0 1 0 0
rs903919 C T 1 0 0 0 1 0 1 0 0
rs884941 T C 0 1 0 0 0 1 0 1 0
rs884940 T C 0 1 0 0 0 1 0 1 0
rs12743493 A G 0 1 0 0 0 1 0 0 1
rs10910050 C A 0 1 0 1 0 0 0 0 1

I2a1a · « **Ответ #11 :** 17 Апрель 2011, 01:27:53 »

Фазирование генотипов в гаплотипы (Beagle)

Level   Marker   Parent   Child   Allele   Count   Haplotype identifiers...

0   rs3094315   0   0   A   4   0   1   2   4
0   rs3094315   0   0   G   2   3   5

1   rs12562034   0   0   G   6   0   1   2   3   4   5

2   rs3934834   0   0   C   6   0   1   2   3   4   5

3   rs9442372   0   0   G   5   0   1   3   4   5
3   rs9442372   0   0   A   1   2

4   rs3737728   0   0   G   5   0   1   3   4   5
4   rs3737728   0   0   A   1   2

5   rs11260588   0   0   G   6   0   1   2   3   4   5

6   rs6687776   0   0   C   5   0   1   2   3   5
6   rs6687776   0   0   T   1   4

7   rs9651273   0   0   G   5   0   1   3   4   5
7   rs9651273   0   0   A   1   2

8   rs4970405   0   0   A   5   0   1   2   3   5
8   rs4970405   0   0   G   1   4

9   rs12726255   0   0   A   5   0   1   2   3   5
9   rs12726255   0   0   G   1   4

10   rs11807848   0   0   T   2   0   4
10   rs11807848   0   0   C   4   1   2   3   5

11   rs9442373   0   0   A   2   0   4
11   rs9442373   0   0   C   4   1   2   3   5

12   rs2298217   0   0   C   5   0   1   2   3   5
12   rs2298217   0   0   T   1   4

13   rs12145826   0   0   G   6   0   1   2   3   4   5

14   rs9442380   0   0   C   6   0   1   2   3   4   5

15   rs7553429   0   0   A   6   0   1   2   3   4   5

16   rs4970362   0   0   G   6   0   1   2   3   4   5

17   rs9660710   0   0   C   6   0   1   2   3   4   5

18   rs4970420   0   0   A   2   0   2
18   rs4970420   0   0   G   4   1   3   4   5

19   rs1320565   0   0   T   2   0   4
19   rs1320565   0   0   C   4   1   2   3   5

20   rs11260549   0   0   G   6   0   1   2   3   4   5

21   rs9729550   0   0   C   2   0   4
21   rs9729550   0   0   A   4   1   2   3   5

22   rs11721   0   0   C   6   0   1   2   3   4   5

23   rs2887286   0   0   T   6   0   1   2   3   4   5

24   rs3813199   0   0   G   6   0   1   2   3   4   5

25   rs3766186   0   0   C   6   0   1   2   3   4   5

26   rs7515488   0   0   T   2   0   4
26   rs7515488   0   0   C   4   1   2   3   5

27   rs715643   0   0   C   5   0   1   2   3   5
27   rs715643   0   0   T   1   4

28   rs6675798   0   0   T   3   0   2   4
28   rs6675798   0   0   C   3   1   3   5

29   rs7524470   0   0   G   2   0   4
29   rs7524470   0   0   A   4   1   2   3   5

......

I2a1a · « **Ответ #12 :** 17 Апрель 2011, 01:29:45 »

Отфазированные генотипы

M rs3094315 A A A G G A
M rs12562034 G G G G G G
M rs3934834 C C C C C C
M rs9442372 G G G A G G
M rs3737728 G G G A G G
M rs11260588 G G G G G G
M rs6687776 C C C C T C
M rs9651273 G G G A G G
M rs4970405 A A A A G A
M rs12726255 A A A A A G
M rs11807848 T C C C T C
M rs9442373 C A C C C A
M rs2298217 C C C C C T
M rs12145826 G G G G G G
M rs9442380 C C C C C C
M rs7553429 A A A A A A
M rs4970362 G G G G G G
M rs9660710 C C C C C C
M rs4970420 A G G A G G
M rs1320565 C T C C T C
M rs11260549 G G G G G G
M rs9729550 A C A A C A
M rs11721 C C C C C C
M rs2887286 T T T T T T
M rs3813199 G G G G G G
M rs3766186 C C C C C C
M rs7515488 C T C C C T
M rs715643 C C C C C T
M rs6675798 C T C T C T
.......
......

I2a1a · « **Ответ #13 :** 17 Апрель 2011, 01:40:54 »

Данные по IBD сегментам (Germline)
FAM001 ID002   FAM001 ID001   1   41866612 49243353   rs6656183 rs3121518   1280   5.87   cM   0   0   0
FAM001 ID002   FAM001 ID001   1   144270181 155289901   rs17352281 rs7515836   1280   10.63   cM   0   0   0
FAM001 ID002   FAM001 ID001   1   182642126 190426897   rs6696161 rs1416490   1152   5.26   cM   0   0   0
FAM001 ID002   FAM001 ID001   1   208904314 217644245   rs10746432 rs12123734   1920   10.38   cM   0   0   0
FAM002 ID001   FAM001 ID001   10   135284293 135284293   rs11101905 rs11101905   128   179.10   cM   0   0   0
FAM001 ID002   FAM001 ID001   10   135284293 135284293   rs11101905 rs11101905   1152   179.10   cM   0   0   0
FAM001 ID002   FAM001 ID001   10   135284293 135284293   rs11101905 rs11101905   1408   179.10   cM   0   0   0
FAM002 ID001   FAM001 ID001   10   135284293 135284293   rs11101905 rs11101905   128   179.10   cM   0   0   0
FAM001 ID002   FAM001 ID001   10   135284293 135284293   rs11101905 rs11101905   384   179.10   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM001 ID002   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   384   159.54   cM   0   0   0
FAM001 ID002   FAM002 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0
FAM002 ID001   FAM001 ID001   11   134445626 134445626   rs11224228 rs11224228   128   159.54   cM   0   0   0

I2a1a · « **Ответ #14 :** 17 Апрель 2011, 02:20:22 »

Наконец, карта хромосом трех участников с указанием (RHHmapper) регионов редких гомозиготных и гетерозиготныз генотипов.

АвторТема: Проект Magnus Ducatus Lituaniae (Прочитано 215858 раз)

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