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  T3 Barley Sandbox

Genotyping experiment 2016_HapMap_WEC


Experiment Short NameJH_HapMap
Platformexome capture
Data ProgramLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Breeding ProgramJames Hutton (JH)
OPA Namenone
Processing Date2/23/16
SoftwareGenome Analysis Toolkit (GATK)
Software version2.7.4
CommentsThe data was generated from exome sequence of 267 barley accessions, primarily wild material and landraces that were purified by two rounds of single-seed descent (SSD). A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in the data set. Nature Genetics 48, 1024-1030 (2016)


1167749 markers were assayed for 267 lines.
(lines and markers)

Removed by filteringRemaining
852489 markers have a minor allele frequency (MAF) less than 5%
0 markers are missing more than 10% of data
852489 markers removed
315260 markers

Maximum Missing Data: %     Minimum MAF: %    

Additional files available

Samples (germplasm lines)
Manifest (markers used)
Cluster File
Raw data

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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