The
Results
tab is shown below:
The
Results
tab contains the following elements:
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These
Overlay Plot
s 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:
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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).
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