Data from: Genomic variation in recently collected maize landraces from Mexico

Arteaga MC, Moreno-Letelier A, Mastretta-Yanes A, Vázquez-Lobo A, Breña-Ochoa A, Moreno-Estrada A, Eguiarte LE, Piñero D

Date Published: November 19, 2015

DOI: http://dx.doi.org/10.5061/dryad.4t20n

 

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Title Scripts for analyses and plots
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Description Content: 'admixtureplot.R' to plot admixture analyses, 'maices_estimatingpopgenstats_wrapall.R' R code for estimating He, Ho, and Fst, 'maices_PCAs_plots.html' and 'maices_PCAs_plots.Rmd' show a Rmarkdown document used to plot the PCA, NJ trees and maps. 'runadmixture.sh' code used to run admixture. These scripts need the data and metada available at the DataandMetadata.zip section of this repository
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Title Admixture output
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Description Contains the log, .Q, .P and se files of the admixture analyses. For command line used and code for plotting see the Scripts section of this repo.
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Title Data and Meta
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Description 'data/SNPs' contains SNP data provided in plink and gds format along with a README of how each file was produced. 'data/spatial' contains the shapefiles used for the maps. Please uncompress each one before use. 'meta/maizteocintle_SNP50k_meta_extended.txt' is a text file containing sampling locality, lat, long, and other metadata of each of the samples. Columns correspond to the data collected as part of the Global Maize Proyect and are further detailed at http://www.biodiversidad.gob.mx/genes/pdf/proyecto/Anexo13_Base %20de%20datos/Contenido%20y%20observaciones%20de%20la%20BdeD.pdf
Download DataandMeta.zip (26.86 Mb)
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When using this data, please cite the original publication:

Arteaga MC, Moreno-Letelier A, Mastretta-Yanes A, Vázquez-Lobo A, Breña-Ochoa A, Moreno-Estrada A, Eguiarte LE, Piñero D (2015) Genomic variation in recently collected maize landraces from Mexico. Genomics Data 7: 38–45. http://dx.doi.org/10.1016/j.gdata.2015.11.002

Additionally, please cite the Dryad data package:

Arteaga MC, Moreno-Letelier A, Mastretta-Yanes A, Vázquez-Lobo A, Breña-Ochoa A, Moreno-Estrada A, Eguiarte LE, Piñero D (2015) Data from: Genomic variation in recently collected maize landraces from Mexico. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4t20n
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