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  T3/Oat Sandbox

Genotyping experiment Oliver_2013_OTANA/PI260616

Description

Experiment Short NameOliver_OP
PlatformGolden Gate OPA
Data ProgramUSDA-ARS Fargo: data (FND-GD)
Breeding ProgramAAFC Ottawa, ON-CAN: mapping (OTW-M)
OPA NameOOPA1
Processing Date2011
SoftwareIllumina Genome Studio
Software version2011.1
CommentsOriginal SNP scores for oat population OTANA/PI260616 as published in Oliver RE, Tinker NA, Lazo GR, et al. SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species. Xu M, ed. PLoS ONE. 2013;8(3):e58068. Note: progeny OP-57, OP-64, OP-97, OP-106, OP-109, OP-111, OP-123, and OP-124 were dropped from the data for quality reasons during mapping. OPOOPA1 was a legacy platform that led to the oat 6K Infinium assay.

475 markers were assayed for 100 lines.

(lines and markers)

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Removed by filteringRemaining
6 markers have a minor allele frequency (MAF) less than 5%
8 markers are missing more than 10% of data
9 markers removed
466 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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