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  T3/Wheat

Genotyping experiment HWWAMP_GBS_2014

Description

Experiment Short NameHWWAMP_GBS
PlatformGBS restriction site
Data ProgramKansas State Genotyping Lab (KSG)
Breeding ProgramKansas State University (KSM)
OPA Namen/a
Processing Date04/11/2014
SoftwareAkhunov Lab Pipeline
Software versionn/a
CommentsHard Red Winter Wheat AM panel, cut with PstI and MseI. Map for each chromosome arm created by ordering contigs using GenomeZipper and POPSEQ. Science 18 July 2014 Vol 345 Issue 6194. 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. The contig coordinates file list the location of the SNP in the contig. Genotype calls from the VCF file where converted from (0,1,2) format to (-1,0,1) and (A,C,T,G) format. 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 marker location information is the position on the WCSS assembly.

1263570 markers were assayed for 311 lines.

(lines and markers)

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Removed by filteringRemaining
518362 markers have a minor allele frequency (MAF) less than 5%
1226804 markers are missing more than 10% of data
1231244 markers removed
12090 markers

Maximum Missing Data: %     Minimum MAF: %    



Additional files available

Samples (germplasm lines)
Manifest (markers used)all_chr_300acc_SNPs_min50acc_rmMultiAllele_addHeader.vcf
Cluster File
Raw dataContigs_coordinates_in_concatenated.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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