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  T3/Wheat

Genotyping experiment 2014_SRWW_YNVP

Description

Experiment Short NameSRWW_GBS
PlatformGBS restriction site
Data ProgramKansas State Genotyping Lab (KSG)
Breeding ProgramKansas State University (KSM)
OPA Namenone
Processing Date1/7/15
SoftwareIllumina Genome Studio, TASSEL GBS
Software versionnone
CommentsYield Validation Panel, used to verify results of 2012_ElitePanel. Soft Red Winter Wheat, cut with PstI. The marker sequence is from the IWGSC Whole Chromosome Survey Sequence (WCSS) using 64 bases before the SNP and 63 bases after the SNP giving a total of 128 bases. The markers were anchored to the WCSS by the Akhunov lab. Because of the large number of markers the genotype data can only be accessed as a single genotype experiment not a consensus genotype experiment. The markers where filtered with max missing 0.5 and MAF 0.03 before loading. If no map is selected then the location information is the position on unordered contigs. ABB Analysis Plan.

112307 markers were assayed for 308 lines.

(lines and markers)

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Removed by filteringRemaining
3234 markers have a minor allele frequency (MAF) less than 5%
93396 markers are missing more than 10% of data
93934 markers removed
18373 markers

Maximum Missing Data: %     Minimum MAF: %    



Additional files available

Samples (germplasm lines)
Manifest (markers used)Project_2014TCAPYNVP_SNPs_Maxmissing0.5_MAF0.03_hmp.txt
Cluster File
Raw dataProject_2014TCAPYNVP_SNPs_hmp.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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