Windows QTL Cartographer 2.5 - FTP Directory Listing

file with Windows notepad.
© 2010 N.C. State University, Bioinformatics Research Center
WinQTLCart Procedures 73
Control File. Click Control File button to change the control filename and click + button to open the
control file with Windows notepad. The control file includes all initial parameters setting in the dialog,
detail please to see Mt-MIM Control File 74 .
Population Group. Total population refers to the total population number in the source data.
Selected number indicates how many populations will be in the QTL mapping model. To use Index
edit box to indicate the index of selected populations comparing to all populations in original source
data.
Parameter setting for current population Group. Click the spin dial beside the Current population
value to set current population number first. Then to fill other parameters in the rest of group.
Note: The current population number depends on selected population number only. For example, if the
selected population number is 3, then the current population will be 1, 2, and 3 despite where these
population is located in source data file.
For each current population:
Total traits in current population. The number refers to the total traits (or environments) in the source
data.
Selected traits in current population. The number indicates that how many traits will be in the QTL
mapping model.
index. The number string indicates the index of selected traits.
Selected QTLs in current population. Click the spin dial to set the QTL number for current
population.
Chromosome String. Chromosome number for QTL1, QTL2, ...
Position (cM) String. Positions for QTL1, QTL2, ...
Selected Epistasis in current population. Click the spin dial to set the QTL interaction terms for
current population.
QTL-1. QTL number list. They are the first QTL number between two QTL interaction.
QTL-2. QTL number list. They are the second QTL number between two QTL interaction.
Pleiotropy vs. Close Linkage Test Group. The purpose of the test is to see that two or more QTL is
the same or not statistically. The QTL number list is in QTL Number String edit box. Please notice that
you can do the test for one or more population all together.
Genome wide test of QTL effects. The purpose of the test is to see that two group of QTL effects (QTL
main effect or epistatic effect) are the same or not statistically. Effect number is the QTL effect
numbers in a effect group. Effect1 and Effect2 indicate group 1 effects and group 2 effect respectively.
Each QTL effect includes three number that are population number, trait number and QTL effect number.
Trait Pair wise Test. Click Trait Pair wise Test button to open the control file and click + button to
open the control file with Windows notepad.
Refine Model Group. Click the pull-down menu to select a function (please to see Mt-MIM Functions
75
) and click Go button to start calculation. Modifying Step Edit Box to indicate the walk step in cM
while searching through chromosomes.
Update. Click the button after changing parameters setting.
Finish. Click the button to finish Mt-MIM analysis and the software will remind you to save the
parameters setting into a new control file.