Windows QTL Cartographer 2.5 - FTP Directory Listing

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Windows QTL Cartographer 2.5
file. (You can view this summary in a larger window by clicking the Result button in the Statistical
Summary group box, just to the left of the information pane.)
5. In the Single Marker Analysis group box, click Result to view the analysis result for the selected
trait. You can change the font used by the display window to make the results easier to read.
Click the Save… button in this group to save the marker analysis results to a text file.
6. In the Statistical Summary group box, click Result to view the summary in a larger display
window. Click the Save… button to save the statistical results to a text file.
The statistical summary includes:
Basic summary of the data
A histogram for the quantitative trait
WinQTLCart's summary of missing individuals that should be present, as indicated by the
data. If markers show 0% data, there was likely an import problem.
Summary of marker segregation
Combines LR map QTL and Q stats
7. Click the Graphic File… button to save the results to a QTL mapping result file (*.QRT). You can
open this .QRT file later to view the results as a graph.
8. Click Close to end the single-marker analysis session and return to the Form View of Source
Data.
Qstats show some important results:
Tells you that the data were imported correctly. If a marker has 0% data, that indicates a problem
(likely an import problem). For example, the original marker may be *Marker_1, but QTL sees
that as *Marker-1, and the values won't match.
Tests for segregation distortion
Setting threshold levels (IM & CIM)
Both Interval Mapping 58 and Composite Interval Mapping 60 use threshold values to determine QTLs. If
you don't know the threshold value for a trait, you can have WinQTLCart find them out and use them as
inputs for the QTL search.
The threshold levels control the rate of Type 1 errors (false positives). A lower threshold value means
more false positives; but a higher value means you may miss more QTLs.
When you look at a result graph 17
, the horizontal line you see running across the graph is the
threshold level. When the graph peaks over the threshold level, that is good evidence for a QTL. So,
setting the threshold level in this form controls how high or low that line will sit on the graph. Too high
and you'll see no QTLs; too low and you'll see too many. (The threshold value can be changed later in
the Graph window.)
Getting a very accurate threshold level may take a long time. Recommendations are included in the
threshold procedures.
1. Follow the instructions for the form you're working with (either IM or CIM). Be sure to select a trait
or all traits for which you want to set a threshold level.
2. The Threshold group box on the right of the form controls inputting or obtaining mapping threshold
© 2010 N.C. State University, Bioinformatics Research Center