Marker Order Variable

Use this field to specify the variable containing numeric values that define the order of the markers for calculating genetic distance within each linkage group.

If this variable is specified, marker order optimization will not be performed; instead marker order is determined solely by this variable. Genetic distances are computed between the markers based on the sorted order of this variable. If this field is left blank, the marker order optimization algorithm is used to predict marker order based on the structure in the pairwise recombination fraction matrix.

Note: To avoid unexpected results, a variable specified here should not contain any missing values. In such a case, the variable should instead be specified as a Framework Order Variable.

To Specify the Marker Order Variable:

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Specify the Order Data Set.

All of the variables in the specified order data set are displayed in the Available Variables field.

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Examine the list of available variables.

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Highlight the variable whose values specify the order of the markers.

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Click to add the highlighted variable to the Marker Order Variable field, as shown below:

Note: If the variable that you wish to order the markers by exists in the input data set, the input data set can be re-used as the order data set to select the variable.