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Part 1: Document Description
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Citation |
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Title: |
Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France |
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Identification Number: |
doi:10.15454/E2DFNJ |
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Distributor: |
Portail Data INRAE |
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Date of Distribution: |
2020-06-30 |
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Version: |
1 |
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Bibliographic Citation: |
Bouffartigue, Cathy; Sandrine Debille; Ana Maria Ramos Cabrer; Olivier Fabreguettes; Santiago Pereira-Lorenzo; Timothée Flutre; Luc Harvengt, 2020, "Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France", https://doi.org/10.15454/E2DFNJ, Portail Data INRAE, V1, UNF:6:0lpmASDvoFi+pHtRkZQiEw== [fileUNF] |
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Citation |
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Title: |
Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France |
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Identification Number: |
doi:10.15454/E2DFNJ |
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Authoring Entity: |
Bouffartigue, Cathy (INRA - IAGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN Castanet Tolosan, France) |
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Sandrine Debille (Genetics and Biotechnology team, Biotech and Advanced Forestry Department, FCBA tech institute, Campus Recherche Forêt-Bois de Pierroton, 71 route d'Arcachon, 33610 Cestas, France) |
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Ana Maria Ramos Cabrer (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.) |
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Olivier Fabreguettes (INRA - Université de Bordeaux, UMR 1202 BIOGECO Biodiversité, Gènes et Communautés. Centre de recherche Nouvelle-Aquitaine-Bordeaux, Cestas, France. INRA - Bordeaux Sciences Agro, UMR 1065 SAVE Santé et Agroécologie du Vignoble. Centre de recherche de Bordeaux Aquitaine, Villenave D'Ornon, France.) |
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Santiago Pereira-Lorenzo (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.) |
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Timothée Flutre (Departamento de Producción Vegetal y Proyectos de Ingeniería, Escola PolitécnicaSuperior, Campus de Lugo, Universidade de Santiago de Compostela, Lugo, Spain.) |
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Luc Harvengt (Genetics and Biotechnology team, Biotech and Advanced Forestry Department, FCBA tech institute, Campus Recherche Forêt-Bois de Pierroton, 71 route d'Arcachon, 33610 Cestas, France) |
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Distributor: |
Portail Data INRAE |
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Access Authority: |
Bouffartigue, Cathy |
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Depositor: |
Bouffartigue, Cathy |
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Date of Deposit: |
2019-09-28 |
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Study Scope |
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Keywords: |
Genetic Resource, ; chestnut; genetic diversity; genetic structure; microsatellite markers; landraces |
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Abstract: |
To ensure methodological reproducibility the datasets used in "Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France", Rmd and bash files used to perform all analyses used in the article, are stored here. Please start by reading 0_README.html |
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Kind of Data: |
Dataset |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Notes: |
<img src="https://www.etalab.gouv.fr/wp-content/uploads/2011/10/licence-ouverte-open-licence.gif" alt="Licence Ouverte" height="100"><a href="https://www.etalab.gouv.fr/licence-ouverte-open-licence">Licence Ouverte / Open Licence Version 2.0</a> compatible CC BY |
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Other Study Description Materials |
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File Description--f99985 |
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File: avgQmatrix_13_2.tab |
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Notes: |
UNF:6:5Wko+WRSc49qbqVcGP8Y4g== |
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File Description--f99977 |
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File: avgQmatrix_13_6.tab |
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Notes: |
UNF:6:ce523HRYGim5jMIwuggxOA== |
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File Description--f99986 |
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File: avgQmatrix_13conEs_2.tab |
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Notes: |
UNF:6:eE+H2lYLWQRcKLTzpuppxA== |
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File Description--f99978 |
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File: avgQmatrix_13conEs_6.tab |
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Notes: |
UNF:6:gN5u2Sh69pMwKyIJZs09kQ== |
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File Description--f99979 |
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File: avgQmatrix_13cult_3.tab |
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Notes: |
UNF:6:NYtYt5RL3hB/Om2YnuHBfA== |
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File Description--f99980 |
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File: avgQmatrix_13for_4.tab |
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Notes: |
UNF:6:UTksl5JZbg0iI9FPmFpFXg== |
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File Description--f99981 |
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File: avgQmatrix_24_2.tab |
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Notes: |
UNF:6:C05z/jbegned1+9jOiIImQ== |
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File Description--f99982 |
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File: avgQmatrix_24conEs_2.tab |
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Notes: |
UNF:6:jqx8lAOJbKfycuukDrEVDA== |
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File Description--f99983 |
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File: avgQmatrix_24cult_4.tab |
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Notes: |
UNF:6:BBQbnuPTXUtaKsiLL7fPzA== |
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File Description--f99984 |
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File: avgQmatrix_24for_4.tab |
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Notes: |
UNF:6:mT25GFfRP0laTi3OSMVp0w== |
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List of Variables: |
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Variables |
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f99985 Location: |
Variable Format: character Notes: UNF:6:ec49wQtrdjBA4+5t5xEphw== |
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f99985 Location: |
Variable Format: character Notes: UNF:6:sX8YEcHJn9sYLSwlz6aiSA== |
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f99985 Location: |
Summary Statistics: StDev 0.3249994867796225; Mean 0.5834578095238095; Valid 1050.0; Max. 0.9725; Min. 0.0178 Variable Format: numeric Notes: UNF:6:DpIUhiDwkxpZ155z/JY5Dg== |
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f99985 Location: |
Summary Statistics: StDev 0.3249994867796224; Mean 0.4165421904761904; Min. 0.0275; Max. 0.9822; Valid 1050.0 Variable Format: numeric Notes: UNF:6:ndBlhwtK3AOTbud7OMurew== |
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f99977 Location: |
Variable Format: character Notes: UNF:6:ec49wQtrdjBA4+5t5xEphw== |
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f99977 Location: |
Variable Format: character Notes: UNF:6:sX8YEcHJn9sYLSwlz6aiSA== |
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f99977 Location: |
Summary Statistics: Mean 0.1508540952380952; Valid 1050.0; Min. 0.004; StDev 0.29148706339916064; Max. 0.975 Variable Format: numeric Notes: UNF:6:pdG7Mv3cK7W8lXjtK5GW2g== |
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f99977 Location: |
Summary Statistics: Max. 0.961; StDev 0.28519374208675; Valid 1050.0; Mean 0.19200523809523806; Min. 0.004; Variable Format: numeric Notes: UNF:6:wOB+aejOUP+xQa0RztGJKQ== |
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f99977 Location: |
Summary Statistics: StDev 0.21022620247952173; Valid 1050.0; Max. 0.9809; Mean 0.08320400000000007; Min. 0.003; Variable Format: numeric Notes: UNF:6:H0ZdycPUea8qHaQMLsdvWA== |
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f99977 Location: |
Summary Statistics: StDev 0.31034378841623894; Valid 1050.0; Min. 0.003; Mean 0.2164464761904762; Max. 0.9667; Variable Format: numeric Notes: UNF:6:6rl3pgnKIUmwtruC4JUUAQ== |
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f99977 Location: |
Summary Statistics: Max. 0.9651; StDev 0.30239573696714456; Min. 0.004; Valid 1050.0; Mean 0.19068980952380954 Variable Format: numeric Notes: UNF:6:1PnmHSdtOM5Yw9k0GOm1Iw== |
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f99977 Location: |
Summary Statistics: Valid 1050.0; Max. 0.9609; Mean 0.16680066666666665; StDev 0.2633177160573152; Min. 0.0032 Variable Format: numeric Notes: UNF:6:vnIH2ld0Oa5rjYOiLjpn2w== |
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f99986 Location: |
Variable Format: character Notes: UNF:6:yUuQJAKx7aaF75jg8tsJHw== |
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f99986 Location: |
Variable Format: character Notes: UNF:6:tEO8Pmq4N+UPcUZ9VwVudg== |
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f99986 Location: |
Summary Statistics: Mean 0.582280188679245; Min. 0.0195; StDev 0.32496450493168916; Valid 1060.0; Max. 0.9705 Variable Format: numeric Notes: UNF:6:K0lnW6SVIArCf+ZzFIk7jQ== |
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f99986 Location: |
Summary Statistics: StDev 0.3249645049316892; Max. 0.9805; Min. 0.0295; Valid 1060.0; Mean 0.4177198113207549 Variable Format: numeric Notes: UNF:6:xnpvxwBX9Iw3Ax78jEt3YQ== |
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f99978 Location: |
Variable Format: character Notes: UNF:6:yUuQJAKx7aaF75jg8tsJHw== |
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f99978 Location: |
Variable Format: character Notes: UNF:6:tEO8Pmq4N+UPcUZ9VwVudg== |
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f99978 Location: |
Summary Statistics: Valid 1060.0; Max. 0.9607; Mean 0.19099716981132078; Min. 0.004; StDev 0.2843965065007472 Variable Format: numeric Notes: UNF:6:H1pbySkva9+QzIY47kowDA== |
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f99978 Location: |
Summary Statistics: Min. 0.003; Mean 0.08334415094339619; Max. 0.98; StDev 0.20925386101820279; Valid 1060.0 Variable Format: numeric Notes: UNF:6:4Rh9nbktnH8GEwPHIVChHQ== |
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f99978 Location: |
Summary Statistics: Min. 0.004; Mean 0.190181037735849; Valid 1060.0; Max. 0.9646; StDev 0.30171654059342856 Variable Format: numeric Notes: UNF:6:UZ80+iWzKqCct8cSUPSt5Q== |
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f99978 Location: |
Summary Statistics: Max. 0.9662; Mean 0.21426424528301885; Min. 0.003; Valid 1060.0; StDev 0.30806950581105347 Variable Format: numeric Notes: UNF:6:KJt4FsBJnhVifvOFmGSpEA== |
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f99978 Location: |
Summary Statistics: Min. 0.004; Valid 1060.0; Max. 0.9749; StDev 0.2913188886994171; Mean 0.15272707547169811; Variable Format: numeric Notes: UNF:6:M8/dkH0izrh4sV8xUCUQOA== |
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f99978 Location: |
Summary Statistics: Valid 1060.0; Min. 0.0035; Mean 0.16848594339622638; Max. 0.9598; StDev 0.2637256674069682 Variable Format: numeric Notes: UNF:6:RoEXAaw1oQSRSbQJTH2eUg== |
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f99979 Location: |
Variable Format: character Notes: UNF:6:r6me4RlKJQD8sWePELCJ1A== |
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f99979 Location: |
Variable Format: character Notes: UNF:6:qEAbvxusG4sH71ePtb6qAw== |
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f99979 Location: |
Summary Statistics: Min. 0.0103; Mean 0.3436939102564103; Valid 312.0; StDev 0.3581266745764433; Max. 0.9711 Variable Format: numeric Notes: UNF:6:KOn5bdYujTfbI26K/N2SXA== |
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f99979 Location: |
Summary Statistics: Valid 312.0; StDev 0.3610421834390576; Min. 0.0103; Mean 0.3019897435897436; Max. 0.9783; Variable Format: numeric Notes: UNF:6:zpj0EFI8qUn4dila5oCIQA== |
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f99979 Location: |
Summary Statistics: StDev 0.36835231404771246; Mean 0.35431506410256414; Valid 312.0; Min. 0.0099; Max. 0.9745; Variable Format: numeric Notes: UNF:6:whH7FotvwKh2rnvq3TfeEg== |
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f99980 Location: |
Variable Format: character Notes: UNF:6:Za0D4ECSKxqlCw37flQs+A== |
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f99980 Location: |
Variable Format: character Notes: UNF:6:PrDymBTY5DQrgFB+LqMcUw== |
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f99980 Location: |
Summary Statistics: StDev 0.37265886971187145; Max. 0.98; Min. 0.0042; Valid 717.0; Mean 0.2786697350069735 Variable Format: numeric Notes: UNF:6:/R0vB6wfvJNVL5EAjnKtCA== |
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f99980 Location: |
Summary Statistics: Max. 0.9798; Min. 0.004; StDev 0.3805168473346671; Valid 717.0; Mean 0.31121046025104604 Variable Format: numeric Notes: UNF:6:08ZsbxnRGafNKHO4EG8Giw== |
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f99980 Location: |
Summary Statistics: Mean 0.1802195258019527; Min. 0.005; Valid 717.0; Max. 0.9868; StDev 0.3270022631314207 Variable Format: numeric Notes: UNF:6:cADG2T9hRjWgp2JO4/rwCQ== |
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f99980 Location: |
Summary Statistics: Mean 0.22989818688981875; Valid 717.0; StDev 0.3399886246200151; Min. 0.004; Max. 0.984; Variable Format: numeric Notes: UNF:6:6cDh4piAygGN01CgKBW5hw== |
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f99981 Location: |
Variable Format: character Notes: UNF:6:NXagC6hAFnJvD3VEhHhPrg== |
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f99981 Location: |
Variable Format: character Notes: UNF:6:QPLZDG2Nh5DQY5uuKjDV6g== |
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f99981 Location: |
Summary Statistics: StDev 0.3941375933024861; Mean 0.6469734615384616; Min. 0.009; Valid 520.0; Max. 0.991 Variable Format: numeric Notes: UNF:6:rM4Tzmy8zQ56V8fWNvUuPw== |
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f99981 Location: |
Summary Statistics: Valid 520.0; Max. 0.991; Mean 0.3530265384615385; StDev 0.3941375933024861; Min. 0.009; Variable Format: numeric Notes: UNF:6:GMOtJINpJy2gKjc1ctC1lw== |
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f99982 Location: |
Variable Format: character Notes: UNF:6:ee8AxMxu/sF7yQt3eu+RTA== |
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f99982 Location: |
Variable Format: character Notes: UNF:6:U3pabnW6oNpR1u7IltxU/Q== |
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f99982 Location: |
Summary Statistics: Min. 0.0108; Max. 0.99; Mean 0.3613102079395084; Valid 529.0; StDev 0.38851293435451056 Variable Format: numeric Notes: UNF:6:CTuo0+C1snlj7bU/8fiF4Q== |
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f99982 Location: |
Summary Statistics: Max. 0.9892; Valid 529.0; StDev 0.3885129343545105; Mean 0.6386897920604916; Min. 0.01; Variable Format: numeric Notes: UNF:6:vyyN7Ysod3uJaq0W7eLRqA== |
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f99983 Location: |
Variable Format: character Notes: UNF:6:3xyKOYIcMVXKgOIcMBvhFg== |
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f99983 Location: |
Variable Format: character Notes: UNF:6:n1Ka6Kus3sq7LxmPkUQ2sQ== |
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f99983 Location: |
Summary Statistics: Min. 0.004; StDev 0.3588134485510939; Max. 0.986; Valid 212.0; Mean 0.2260849056603774 Variable Format: numeric Notes: UNF:6:rmbMX6AwPQk2Ff2aHBkbjw== |
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f99983 Location: |
Summary Statistics: Mean 0.3574702830188679; StDev 0.4164276278148489; Min. 0.005; Valid 212.0; Max. 0.9819 Variable Format: numeric Notes: UNF:6:aME+K2voY4UiJayfyf5EiQ== |
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f99983 Location: |
Summary Statistics: Max. 0.9858; StDev 0.34551019579639997; Mean 0.21194811320754708; Valid 212.0; Min. 0.003; Variable Format: numeric Notes: UNF:6:KLna1YFZXZfGJw1gXLDjsA== |
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f99983 Location: |
Summary Statistics: Valid 212.0; StDev 0.34715489542598144; Max. 0.9849; Min. 0.003; Mean 0.20449811320754716 Variable Format: numeric Notes: UNF:6:Wm7HJUo4ps40uXOzpxt65Q== |
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f99984 Location: |
Variable Format: character Notes: UNF:6:pFM1S3zkBS/KUxM/azLmPA== |
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f99984 Location: |
Variable Format: character Notes: UNF:6:7wkwxXQBYNpHMrdlrhJhzg== |
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f99984 Location: |
Summary Statistics: Max. 0.9804; StDev 0.33540815097228777; Min. 0.003; Mean 0.25703986710963456; Valid 301.0 Variable Format: numeric Notes: UNF:6:zb9wKuFcnQFJ1aTQ4s/TNQ== |
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f99984 Location: |
Summary Statistics: Mean 0.32151561461794026; StDev 0.39423153221007645; Min. 0.0031; Valid 301.0; Max. 0.9845 Variable Format: numeric Notes: UNF:6:iGNFTHFGaLk5nZg775SjYg== |
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f99984 Location: |
Summary Statistics: StDev 0.18065958449400343; Min. 0.0035; Mean 0.12272225913621267; Max. 0.5933; Valid 301.0 Variable Format: numeric Notes: UNF:6:87th6GUyRpJNB05OZ2bfAQ== |
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f99984 Location: |
Summary Statistics: StDev 0.38226020680520134; Max. 0.9893; Min. 0.0035; Valid 301.0; Mean 0.29872691029900333; Variable Format: numeric Notes: UNF:6:maMvu39xlxDV3df4/fJ0Bw== |
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0_README_reproducible_analysis.html |
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Text: |
README html |
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text/html |
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0_README_reproducible_analysis.md |
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README |
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application/octet-stream |
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CLUMPP.Rmd |
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application/octet-stream |
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df.13conEs.tsv |
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text/tsv |
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df.13cult.tsv |
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text/tsv |
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df.13for.tsv |
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text/tsv |
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df.13.tsv |
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text/tsv |
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df.24conEs.tsv |
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text/tsv |
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df.24cult.tsv |
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df.24for.tsv |
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text/tsv |
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df.24.tsv |
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text/tsv |
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launch_reprod.bash |
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application/octet-stream |
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launch_structure.bash |
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plot_DeltaK.R |
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type/x-r-syntax |
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plot_Q_matrix.R |
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reprod_Private_13conEsSSRs_K2_run2_v2.html |
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text/html |
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reprod_Private_13conEsSSRs_K6_run2_v2.html |
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text/html |
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reprod_Private_13cultSSRs_K3_run2.html |
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reprod_Private_13forSSRs_K4_run2.html |
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reprod_Private_13SSRs_K2_run2_v2.html |
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reprod_Private_13SSRs_K6_run2_v2.html |
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reprod_Private_24conEsSSRs_K2_run2_v2.html |
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reprod_Private_24cultSSRs_K4_run2.html |
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reprod_Private_24forSSRs_K4_run2.html |
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reprod_Private_24SSRs_K2_run2_v2.html |
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structure2clumpp.R |
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STRUCTURE.Rmd |
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application/octet-stream |