If Zmapqtl was used to do a bootstrap experiment or a permutation test, then there will be interim results files. With the default filename stem and model 3, there will be files qtlcart.z3c and qtlcart.z3e if a permutation test was done, and qtlcart.z3a if a bootstrap was done. Using the work code PBZM will direct Eqtl to detect these files and processes their results. It will open a qtlcart.z3e file and determine an experimentwise threshold based on the size specified with the -a option.
If the qtlcart.z3a file exists, then Eqtl opens it and computes the means and standard deviations, at each test site, of the likelihood ratio test statistic, additive effect and dominance effect. The results are printed to qtlcart.z3b.
The jackknife procedure produces a qtlcart.z3i file. Adding a J to the work code directs Eqtl to computes the means and standard deviations of the likelihood ratio test statistic, additive effect and dominance effect at each test site. The results are printed to qtlcart.z3j.