Tassel-GBS Import Engine

Running this process for the gbs_2xbc1geno sample setting generates the Results window shown below. Refer to the Tassel-GBS Import Engine process description for more information.

The Results window contains the following panes:

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

The following tab is generated by this process:

•	Selected Marker Counts Plot : Shows a plot of selected marker counts. Note : This tab is generated only when Outcross in NOT selected as the Cross Type .

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Genotype Color Plots : This tab displays a cell plot for each individual (in the rows) colored by the genotypes of markers (in the columns). These plots are useful to detect potential genotyping errors in the data and genotype messiness. Note : This tab only is displayed when the Display marker genotype cell color plots check box option is checked.

•	Marker Type Counts Plot : This tab that shows a plot of selected markers counts for each cross type from a bi-parental cross of outbred parents. Note : This tab is generated only when Outcross is selected as the Cross Type .

•	P-Value Plots of Test I : This tab shows the raw p-values of a chi-square test that is conditional on the genotypes of parents. Note : This tab is generated only when Outcross is selected as the Cross Type .

•	P-Value Plots of Test II : This tab shows the raw p -values of a chi -square test that is NOT conditional on the genotypes of parents. Note : This tab is generated only when Outcross is selected as the Cross Type .

Output Data

This process generates the following output data sets:

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Genotypes Data Set of Selected Markers : This data set contains the Marker ID Variable , Parent 1 ID Variable , Parent 2 ID Variable , Individual Variables , and Variables to Keep in Output Data Set that were specified on the General tab. Columns of relevant summary statistics as well as coded genotypes for each selected marker are also included. Variables that have _testI or _testII in their names come from the Chi -square Test I or Chi -square Test II, respectively. Note : The Chi -square Test I is conditional on the genotypes of parents, the Chi -square Test II is not.

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Annotation Data Set of Selected Markers : This data set contains relevant columns of summary statistics for the subset of markers selected from the analyses, plus all columns from the Annotation SAS Data Set (provided one has been specified. Variables that have _testI or _testII in their names come from the Chi -square Test I or Chi -square Test II, respectively. The Chi -square Test I is conditional on the genotypes of parents, the Chi-square Test II is not.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets .

Launch Follow-up Processes

•	Marker Properties : Click Marker Properties to launch the Marker Properties process with the Genotypes and annotation data sets specified as input.

General

•	Click View Data to reveal the underlying data table associated with the current tab.

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Create Report to generate a pdf - or rtf -formatted report containing the plots and charts of selected tabs.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.