Here is an example of the data input file:
# 1002909319 -filetype JZmapqtl.zr # # QTL Cartographer v. 1.15e, October 2001 # This output file (qtlcart.zr) was # created by JZmapqtl... # # It is 13:55:19 on Friday, 12 October 2001 # # # This output of JZmapqtl is meant to be used # with MultiRegress -walk 2.00 Interval distance in cM -cross B1 Cross -otraits 1 Number of explanatory variables -traits 2 Number of Traits -positions 39 Number of positions -n 9 Sample Size -Trait 1 Trait.1 5 5.3 6.2 4.1 5.5 5.8 6.7 6.1 6.4 -Trait 2 Trait.2 15 15.3 16.2 24.1 25.5 25.8 16.7 26.1 16.4 -Otrait 1 Sex 1 2 1 1 1 2 2 1 2 -Site 1 -parameter additive -chromosome 1 -marker 1 -name c1m1 -position 0.000100 -values 0.5 0.5 0.5 0.499 0.499 -0.5 -0.5 -0.5 -0.5 -Site 2 -parameter additive -chromosome 1 -marker 1 -name c1m1 -position 0.020100 -values 0.4984 0.4984 0.4984 0.3026 0.3026 -0.4984 -0.4984 -0.4984 -0.4984 -Site 3 ......
The data file above was created by JZmapqtl with model 9. The header of the file is similar to the qtlcart.cro format: The first line has a long integer and specifies the filetype as JZmapqtl.zr. Some header information is followed by parameter definitions that include the distances between sites (same as the walking speed in Zmapqtl, JZmapqtl and MImapqtl), the cross, numbers of categorical traits and quantitative traits, positions (or sites) and sample size (n). The data set above has a sample size of 9 for two traits, one categorical trait and 39 genotype sites. The cross and walk parameters are not needed by MultiRegress: They are provided as a reminder of how the data set was created. The genotypes are expected QTL types based on flanking marker information.
After the parameters, the traits are listed. For each trait, there will be a token -Trait followed by the trait number, trait name and n real values. After the traits come the categorical traits in the same format: The token -Otrait is followed by the categorical trait number, name and then n integer values.
Finally, data for each of the sites are presented. Site data start with the token -Site followed by information about the site. The token -parameter is followed by the word additive or dominance indicating what expected value is calculated. The other tokens indicate which chromosome and left-flanking marker define the site, and the position is from the left telomere of the chromosome. The token -values is followed by n expected values of the QTL genotype at the site. This structure is repeated for each site.