Windows QTL Cartographer 2.5 - FTP Directory Listing

© 2010 N.C. State University, Bioinformatics Research Center
WinQTLCart Procedures 41
r (Recombination frequency) - If you choose this parameter, then token -function should be 3
(Morgan)
Token –chromosome (Line 10)
Indicates total number of chromosomes for source data.
Token –maximum (Line 11)
Indicates the maximum number of markers for a chromosome for all of the source data.
Token –named (Line 12)
Either yes or no.
Yes means markers have names
No means markers will not have names.
Token –start and –end (Line 13 and Line 55)
Use these tokens to start and end the marker position data of all chromosomes.
Token –Chromosome (Line 14, 28, and 41)
Indicates chromosome name. The marker position data for this chromosome will start with the next line.
Token #bycross (Line 56)
Indicates that cross information is to begin.
Token –SampleSize (Line 57)
Indicates sample size or individual number.
Token –Cross (Line 58)
Indicates codes for crosstype mating design (see the following table).
Code Design Examples
Bi Backcross to Pi B1, B2
Bij Backcross j times to Pi B13, B25
SFi Selfed generation i intercross SF2, SF6
RFi Randomly mated generation i intercross RF2, RF3
RI0 Doubled haploid RI0
RI1 Recombinant inbred via selfing RI1
RI2 Recombinant inbred via sib mating RI2
T(Bi)SFj Testcross of SFi to Pj T(B1)SF3
T(SFi+j)SFi Testcross of SFi for j generations T(SF4)SF3
T(Bj)RFi Testcross of RFi to Pj T(B1)RF3
T(D3)SFi Design III T(D3)SF5
Token –traits (Line 59)
Indicates trait number of source data.
Token –otraits (Line 60)
Indicates other trait number of source data. Other trait (also called a categorical trait) is the trait with
qualitative or categorical values, such as sex; color, and so on. Other traits can be used as factors that
can be "regressed out" in regression analysis. This means a regression of the quantitative trait of
interest on the categorical trait will have been performed and the residuals used as the phenotypes in the
analysis.