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  T3/Wheat

Genotyping experiment 2014_HapMap_WEC

Description

Experiment Short NameHapMap
Platformsequence capture
Data ProgramKansas State University - Akhunov Lab (KSA)
Breeding ProgramKansas State University (KSM)
OPA Namenone
Processing Date9/26/2014
SoftwareBowtie
Software versionnone
CommentsThe data were generated by re-sequencing 62 diverse wheat lines using whole exome capture (WEC) approach. The panel of wheat lines was selected to capture the genetic diversity of the major global wheat growing regions and included landraces and cultivars. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology 2015, 16:48

1341162 markers were assayed for 62 lines.

(lines and markers)

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Removed by filteringRemaining
236149 markers have a minor allele frequency (MAF) less than 5%
722445 markers are missing more than 10% of data
879080 markers removed
462082 markers

Maximum Missing Data: %     Minimum MAF: %    



Additional files available

Samples (germplasm lines)
Manifest (markers used)WEC_filtered_SNPs.vcf
Cluster File
Raw data2014_HapMap_WEC

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement

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