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Наверное правильное написать не гомозиготен (тогда бы у него была два генотипа в локусах), а гаплоиден.Гаплоидизация сэмплов связана с особенностями типирования, которое применялось в лаборатории Райха.
We find that to get decent diploidcalls we need about 20x coverage.Most of these samples have much less.Note though that for F_st workusing smartpca or f_3 stats usingqp3Pop (ADMIXTOOLS) you get validestimates using inbreed: YES
Именно. Есть еще исходники http://www.ebi.ac.uk/ena/data/view/ERP009526 , может, оттуда что-то вытащится.
Цитата: Srkz от 05 Март 2015, 18:07:04Именно. Есть еще исходники http://www.ebi.ac.uk/ena/data/view/ERP009526 , может, оттуда что-то вытащится.Совместно с FenriR вытащили оттуда более качественную версию (но все равно, снипов маловато). Новый номер кита - M652848Забавно, теперь у меня с ним аж два сегмента более 7 сМ Minimum threshold size to be included in total = 100 SNPsMismatch-bunching Limit = 50 SNPsMinimum segment cM to be included in total = 7.0 cMChr Start Location End Location Centimorgans (cM) SNPs16 77794409 80315964 7.6 33122 16687634 20841719 8.9 215Largest segment = 8.9 cM
А North-Caucasus у кого и в каком проценте максимален?
Mismatch-bunching Limit = 50 SNPs Для "древних" образцов с низкой плотностью снипов на одну килобазу это слишком много. Думаю, что нужно уменьшить это значнение
M652848 (EHG_Oleniy_Ostrov I0061)Minimum threshold size to be included in total = 100 SNPsMismatch-bunching Limit = 25 SNPsMinimum segment cM to be included in total = 7.0 cMChr Start Location End Location Centimorgans (cM) SNPs7 152956591 155687863 9.7 18217 13422178 15272242 8.9 18518 448505 3210857 8.6 18822 43881493 47038544 8.6 262Largest segment = 9.7 cMTotal of segments > 7 cM = 35.8 cMM020637 (Yamnaya_Sok_River I0443)Minimum threshold size to be included in total = 100 SNPsMismatch-bunching Limit = 25 SNPsMinimum segment cM to be included in total = 7.0 cMChr Start Location End Location Centimorgans (cM) SNPs4 186983950 189670284 7.8 1889 135171669 136913377 7.9 10519 8044054 13225012 9.6 31421 15243812 18355365 7.7 205Largest segment = 9.6 cMTotal of segments > 7 cM = 33.0 cM
И ожидаемо огромное количество Гедрозии в К27: 0.00% Nilotic-Omotic 0.00% Ancestral-South-Indi 46.28% North-European-Balti 7.48% Uralic 0.17% Australo-Melanesian 0.00% East-Siberean 0.00% Ancestral-Yayoi 0.00% Caucasian-Near-Easte 0.00% Tibeto-Burman 0.00% Austronesian 0.00% Central-African-Pygm 0.10% Central-African-Hunt 0.00% Nilo-Saharian 0.00% North-African 26.86% Gedrosia-Caucasian 0.00% Cushitic 0.00% Congo-Pygmean 0.00% Bushmen 0.06% South-Meso-Amerindia 3.31% South-West-European 2.25% North-Amerindian 0.00% Arabic 0.24% North-Circumpolar 6.45% Kalash 0.63% Papuan-Australian 6.17% Baltic-Finnic 0.00% BantuВот кто ее немцам притащил
Polish 69,45 ---//Confidence: very highMoksha 69,44 ---//Confidence: low Finnish 68,7 ---//Confidence: low Veps 66,99 ---//Confidence: medium Russian-North-Kargopol 66,84 ---//Confidence: very highBelarusian 64,93 ---//Confidence: very highMari 64,93 ---//Confidence: high Russian-West 64,83 ---//Confidence: very highTatar-Volga 64,66 ---//Confidence: high Russian-South 64,65 ---//Confidence: very highUkrainian-East-and-Center 64,43 ---//Confidence: high Russian-North-East 63,86 ---//Confidence: very highKarelian 63,42 ---//Confidence: high Balt 63,23 ---//Confidence: high Estonian 61,98 ---//Confidence: high Chuvash 61,84 ---//Confidence: very highSwedish 61,76 ---//Confidence: high British 60,88 ---//Confidence: very highUkrainian-West-and-Center 60,7 ---//Confidence: high Norwegian 60,41 ---//Confidence: high Udmurt 60,34 ---//Confidence: high Komi 59,8 ---//Confidence: high French 57,8 ---//Confidence: very highErzya 57,59 ---//Confidence: medium German 57,49 ---//Confidence: medium Saami 57,24 ---//Confidence: medium Ust-Ishim 57,14 ---//Confidence: very lowSerbian 55,48 ---//Confidence: high Romanian 55,09 ---//Confidence: medium Bosnian 54,69 ---//Confidence: medium Croatian 54,51 ---//Confidence: very highTatar_Lithuanian 52,88 ---//Confidence: very lowMontenegrian 52,1 ---//Confidence: medium Tadjik 51,87 ---//Confidence: high Hungarian 51,83 ---//Confidence: very highMansi 51,54 ---//Confidence: low Italian 49,96 ---//Confidence: very highMacedonian 49,73 ---//Confidence: medium Chechen 49,3 ---//Confidence: very highBulgarian 48,72 ---//Confidence: high Spanish 48,13 ---//Confidence: very highGreek_Azov 47,65 ---//Confidence: low Tatar-Crimean 47,47 ---//Confidence: low Basque 47,46 ---//Confidence: very highGagauz 46,86 ---//Confidence: medium Bashkir 46,84 ---//Confidence: very highKosovar 46,56 ---//Confidence: medium Lezgin 46,16 ---//Confidence: very highShor 46,15 ---//Confidence: very lowTurkmen 45,46 ---//Confidence: very highSicilian 45,42 ---//Confidence: very highAdygei 44,65 ---//Confidence: high Ossetian 44,48 ---//Confidence: high Kumyk 44,22 ---//Confidence: high Pathan 43,4 ---//Confidence: very highNogay 43,33 ---//Confidence: high Ket 43,02 ---//Confidence: low Uttar-Pradesh-HC 42,84 ---//Confidence: high Kalash 42,4 ---//Confidence: very highKurd 41,62 ---//Confidence: low Uzbek 41,53 ---//Confidence: high Greek 41,3 ---//Confidence: very highSelkup 40,63 ---//Confidence: high Burusho 40,53 ---//Confidence: very highHakas 40,25 ---//Confidence: medium Ashkenazi 40,14 ---//Confidence: high Sindhi 39,77 ---//Confidence: very highAzerbaijani 39,68 ---//Confidence: high Balochi 39,51 ---//Confidence: very highSephard 38,68 ---//Confidence: high Balkarian 38,64 ---//Confidence: very highIranian 38,16 ---//Confidence: very highAltaian 37,95 ---//Confidence: high Syrian 37,7 ---//Confidence: high Kazah 37,62 ---//Confidence: high Brahui 37,47 ---//Confidence: very highNenets 36,71 ---//Confidence: high Turkish 36,61 ---//Confidence: very highHazara 35,28 ---//Confidence: very highItalian-South 35,02 ---//Confidence: high Abkhazian 34,77 ---//Confidence: very highSardinian 34,56 ---//Confidence: very highCypriot 34,32 ---//Confidence: medium Georgian 33,86 ---//Confidence: very highDruze 33,28 ---//Confidence: very highEgyptian 33,22 ---//Confidence: medium Armenian 32,97 ---//Confidence: high Kirgiz 32,93 ---//Confidence: very highMakrani 32,84 ---//Confidence: very highDolgan 31,43 ---//Confidence: medium UAE 31,27 ---//Confidence: medium Kanjar 31,01 ---//Confidence: low Jordanian 30,47 ---//Confidence: very highAndhra-Pradesh 30,3 ---//Confidence: medium Uygur 30 ---//Confidence: medium Karnataka 29,67 ---//Confidence: medium Uttar-Pradesh 29,27 ---//Confidence: very highMongol 28,81 ---//Confidence: medium Palestinian 28,41 ---//Confidence: very highTuvinian 28,41 ---//Confidence: high Tunisian 28,06 ---//Confidence: medium Kalmyk 27,94 ---//Confidence: medium Gujarati 27,93 ---//Confidence: very highSaud 27,92 ---//Confidence: very highKol 27,46 ---//Confidence: high Loschbour 27,35 ---//Confidence: very lowMaya 26,47 ---//Confidence: very highMoroccan 26,34 ---//Confidence: very highBedouin 26,03 ---//Confidence: very highLBK 25,68 ---//Confidence: very lowBR2 25,43 ---//Confidence: very lowYakut 25,32 ---//Confidence: very highBuryat 25,27 ---//Confidence: very highNganassan 24,78 ---//Confidence: high Kerala 24,08 ---//Confidence: medium Tamil-Nadu 21,85 ---//Confidence: high Evenk 19,94 ---//Confidence: high NE1 19,87 ---//Confidence: very lowNivh 19,03 ---//Confidence: very lowMunda 18,83 ---//Confidence: very highXibo 18,03 ---//Confidence: medium Even 17,93 ---//Confidence: medium Yemenite 16,96 ---//Confidence: medium Mongola 16,49 ---//Confidence: medium Hezhen 15,88 ---//Confidence: low Lahu 14,59 ---//Confidence: low Tu 14,42 ---//Confidence: low Ethiopian 14,3 ---//Confidence: high Miao 14,1 ---//Confidence: medium Karitiana 13,99 ---//Confidence: medium Burmese 13,32 ---//Confidence: high Han-North 13,13 ---//Confidence: medium Daur 13,1 ---//Confidence: medium Han 12,37 ---//Confidence: very highDai 12,31 ---//Confidence: medium Japanese 11,96 ---//Confidence: very highCambodian 11,95 ---//Confidence: medium She 11,95 ---//Confidence: medium Naxi 11,6 ---//Confidence: low Oroqen 11,59 ---//Confidence: medium Yi 10,99 ---//Confidence: medium Naga 10,24 ---//Confidence: very lowTujia 8,56 ---//Confidence: medium Papuan 8 ---//Confidence: low Melanesian 7,76 ---//Confidence: low BiakaPygmy 5,57 ---//Confidence: very lowMotala12 5,43 ---//Confidence: very lowBantuKenia 5,41 ---//Confidence: low MbutiPygmy 4,52 ---//Confidence: very low
Ямник I0443 (Лопатино-II) загружен, как M020637UPD Ух, К36 какой у него:Amerindian 1.36%East_Central_Euro 5.41%Eastern_Euro 16.34%Fennoscandian 11.09%North_Atlantic 15.65%North_Caucasian 20.00%North_Sea 14.04%South_Central_Asian 10.74%Volga-Ural 5.36%Ничего ближневосточного, зато Северный Кавказ и Средняя Азия. А также забавно высокое содержание North Sea (о чем подозревалось)Компонент Eastern Euro выведен на базе северных русских, эрзи и мокши
Тема: дДНК ямной культуры (Прочитано 171206 раз)