Results (IM and CIM Analysis)

The Results tab is shown below:

The Results tab contains the following elements:

•

A set of overlay LOD score plots for each chromosome/ linkage group and, optionally, trait.

These Overlay Plots show the computed LOD score from the QTL model (on the y-axis) for each QTL testing interval (on the x-axis, measured in genetic distance) for each chromosome/linkage group. If the EM Algorithm was chosen as the QTL Mapping Model Algorithm, or if permutation testing was not used to computed empirical LOD thresholds, then LOD score plots are overlaid for multiple traits.

Black diamonds and upside-down read triangles near the x-axis in the LOD score plot indicate the position of markers and mapped QTL, respectively, and they are displayed when the option to Display markers and Display QTL location, respectively, have been checked in the Options tab from the QTL IM, CIM and MIM Analysis application process.

A modified Results tab is generated when the Haley-Knott Regression mapping algorithm is chosen and a Number of Permutations to Compute is specified on the process dialog, then the results of this tab are split out into separate plots for each trait, as shown below:

•

In this case, each plot shows a black line indicating the experimentwise computed LOD threshold (calculated from permutation testing) as well as the individual (location specific) comparisonwise LOD thresholds represented by the gray dashed line. The comparisonwise thresholds are also reported in the output data set. Text above the plots for each trait specifies the value where the experimentwise LOD threshold was drawn. These lines are computed empirically from the data to be used to highlight LOD scores that could be deemed significant evidence of a QTL (shown as peaks that rise above the lines).