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Genotyping experiment UMN_NSGC_GWAS


Experiment Short NameMN_GWAS
PlatformGBS restriction site
Data ProgramUniversity of Minnesota Genomics (UMG)
Breeding ProgramUniversity of Minnesota - Agronomy (MN)
OPA Name
Processing Date1/1/2018
SoftwareTASSEL 5 and Illumina Genome Studio
Software versionTASSEL 5 and Illumina 2.0.2
CommentsGBS and 50K SNP datasets where merged and missing data imputed using LD-kNNi in TASSEL 5


69607 markers were assayed for 748 lines.
(lines and markers)

Removed by filteringRemaining
8391 markers have a minor allele frequency (MAF) less than 5%
0 markers are missing more than 10% of data
8391 markers removed
61215 markers

Maximum Missing Data: %     Minimum MAF: %    

Additional files available

Samples (germplasm lines)
Manifest (markers used)
Cluster File
Raw data50K_GBS_Merged_Filtered_Imputed_SNPs.txt

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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