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Genotyping experiment 2017_WheatCAP_UCD


Experiment Short NameWheatCap
Platformsequence capture
Data ProgramKansas State University - Akhunov Lab (KSA)
Breeding ProgramUC Davis (UCD)
OPA Namenone
Processing Date11/12/17
Software versionnone
CommentsGenotype data from exome capture of all parents of bi-parental families being used for fine mapping of yield component QTL in the Wheat CAP project. Variant calling done using the GATK. Filtered to remove multiallelic SNPs, removed heterozygous sites, and keep only those singletons that had depth of coverage of 10x. The data will be used to determine the predicted effect of polymorphisms in the coding regions using SIFT and tools developed by T3. The data was aligned to IWGSC WGA v1.0.

1043576 markers were assayed for 60 lines.

(lines and markers)


Removed by filteringRemaining
284856 markers have a minor allele frequency (MAF) less than 5%
560847 markers are missing more than 10% of data
683462 markers removed
360114 markers

Maximum Missing Data: %     Minimum MAF: %    

Additional files available

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