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3_Genotyping_AmaizingDentPublic_ImputedBeagle_354I_978134L.tsv
Version 1.0
File Citation
Nicolas, Stephane; Negro, Sandra; Madur, Delphine; Clipet, Camille; Combes, Valérie; Bauland, Cyril; Tardieu, François; Charcosset, Alain; Moreau, Laurence, 2020, "3_Genotyping_AmaizingDentPublic_ImputedBeagle_354I_978134L.tsv", Amaizing Dent Panel Genotyping Dataset (354 Public Lines), https://doi.org/10.15454/GAHEU0/OOMKEZ, Portail Data INRAE, V1

This file is part of "Amaizing Dent Panel Genotyping Dataset (354 Public Lines)".

Dataset Citation
Nicolas, Stephane; Negro, Sandra; Madur, Delphine; Clipet, Camille; Combes, Valérie; Bauland, Cyril; Tardieu, François; Charcosset, Alain; Moreau, Laurence, 2020, "Amaizing Dent Panel Genotyping Dataset (354 Public Lines)", https://doi.org/10.15454/GAHEU0, Portail Data INRAE, V1, UNF:6:xDkI2MetKCmc6/d1u04ZkA== [fileUNF]
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2 Downloads
File Metadata  
doi:10.15454/GAHEU0/OOMKEZ
db08c38de1cff98c135ef3408e10dd79
2020-01-10
671.9 MB
text/tsv
Genotyping matrix with inbred lines in row and markers in columns (354 rows x 978,135 columns). The first columns indicates the variety name. The header of genotyping matrix indicates names of markers. Genotyping data matrix were coded in allelic dose (0,1,2) and all markers is bi-allelic. Correspondences between genotypes 0 and 2 (homozygous genotypes) and nucleotides of single nucleotide polymorphisms (SNP) or insertion/deletion were provided in "2_Table_Locus_AmaizingDentePublic_978134L.tsv". Missing data were imputed after assembling four sub-matrices genotyping matrix from 50K, 600K, GBS and kaspar markers using Beagle V3.3.2 (Browning and Browning, 2007, Am J Hum Genet 81:210-223). Duplicated loci were removed based on their physical position considering the technologies providing the least missing data for this loci (600K then 50K then GBS).
2019-11-25
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