Association Analysis Options (Multiple Environments)

Use this to specify options for a single trait association analysis in multi-environment trials.

Display

This specifies which items of output are to be produced by the analysis.

Summary	Produces a summary of the QTLs that are retained in the model
Progress	Produces monitoring output detailing the progress of the analysis

Threshold

Specify the threshold value for significant linkage disequilibrium to use on the -log10 scale.

Model part for PCA scores or subpopulation factor

Specifies whether the principal components scores when using an eigenanalysis relationship model or the subpopulations factor when using a subpopulations relationship model are included as Random or Fixed terms.

Frequency of minor alleles

Specify the frequency q below which alleles are considered rare. Rare alleles are automatically pooled together. Markers whose major frequency allele is greater than or equal to 1-q are considered close to fixation and are not used in the analysis.

Scale the scores by the square roots of their singular values

When selected the marker scores are scaled by the square roots of their singular values.

Standardize the marker scores according to their frequencies

When selected the marker scores are standardized according to their frequencies.

Select best variance-covariance model using

This option specifies whether to assess the different variance-covariance structures to use for the random genetic effects in different environments by using the Schwarz information criterion (SIC), which is also known as the Bayesian Information Criterion (BIC), or by using the Akaike information criterion (AIC).

Graphics

This specifies whether plots are to be produced by the analysis.

Plot genome wide profile of the test statistic	Plots a genome wide profile of the test statistic.
Plot QTL positions on genetic map	Plots the significant QTLs on a genetic map.

Action buttons

OK	Stores the option settings and closes the dialog.
Cancel	Close the dialog without making any changes.
Defaults	Sets the options to their default settings.

Action Icons

	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.