Population Admixture

Running this process for the MoroccoExample sample setting generates the tabbed Results window shown below. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, etc. that facilitate your analysis.

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 tabs are generated by this process:

•	Individual Admixture: This tab displays graphs of the estimated ancestral population admixture probabilities for each individual.

•	Individual Cluster: This tab displays a dendrogram of clusters of individuals based on their ancestral population admixture probabilities.

•	SNP Genotype Frequency: This tab displays a graph of estimated frequency of the reference allele of each marker in each ancestral population.

•	SNP Cluster: This tab displays a dendrogram of clusters of markers based on the frequency of the reference allele of each marker in the ancestral populations.

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Scree Plot (Population Admixture): This tab displays a graph of eigenvalues in the y-axis and putative number of ancestral populations in the x-axis. This graph can be used to help determining the number of ancestral populations when this parameter is unknown. This graph usually has an elbow shape, and the x-value in the region of the elbow is considered a good estimate for the number of ancestral populations.

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Stability Point: This tab displays a graph of the estimated number of ancestral populations and their respective estimated variances. This graph can be used to help determining the number of ancestral populations when this parameter is unknown. The second region from the left to right where the variance flats down and finds a minimum is considered a good estimate for the number of ancestral populations.

Output Data

This process generates the following output data sets:

P Matrix from Population Admixture: This data set contains markers in the rows and estimated frequency of reference allele for each marker in each ancestral population in the columns.

Q Matrix from Population Admixture: This data set contains individuals in the rows and estimated admixture probabilities of ancestral populations for each individual in the columns.

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

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window.

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.