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Genotyping experiment 2015GBS_MN


Experiment Short NameMN_GBS_S15
PlatformGBS restriction site
Data ProgramUSDA-ARS Fargo, ND (NDG)
Breeding ProgramUniversity of Minnesota - Agronomy (MN)
Processing Date12/15/15
SoftwareFastQC, Fastx Toolkit, Cutadapt, Bowtie2, SAMTools, GATK, VCFTools, same protocol at Poland et al (2012)
Software version0.11.2, 0.0.14, 1.8.1, 2.2.4, 0.1.18, 3.4-46, 0.1.14
CommentsIllumina Hi-Seq 2000, VCF file filtered for: QUAL gte 40, GQ gte 40, DP gte 5, mean DP gte 10

235216 markers were assayed for 1498 lines.

(lines and markers)


Removed by filteringRemaining
191103 markers have a minor allele frequency (MAF) less than 5%
232543 markers are missing more than 10% of data
234105 markers removed
1111 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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