The remaining output is more readable and is appropriate if the experimenter is not interested in doing further simulations. The positions of the QTL are given in Morgans from the telomere rather than recombination frequencies from the flanking markers.
Eqtl also appends some output to the SRmapqtl.out file. Once putative QTL are identified, Eqtl determines which markers are closest to these QTL and writes them to the SRmapqtl.out file. These markers will be in a table similar to the output of SRmapqtl itself. They can be read by Zmapqtl when running model 8.
In addition to reformatting the output of Zmapqtl, Eqtl will automatically detect whether a permutation test, jackknife or bootstrap experiment had been done. If such results exist, Eqtl will open and summarize them. For example, if you do a permutation test with Zmapqtl using interval mapping, an interim file qtlcart.z3e is created and appended to for each permutation. Eqtl will read this file and calculate experimentwise threshold values from it. Standard significance thresholds will be written to the log file. The user can specify a type I error rate (size) and Eqtl will calculate a threshold value relevant to it. Once done, the threshold value will be remembered and used by subsequent runs of Eqtl or Preplot.
For bootstrap results from Zmapqtl using interval mapping, Eqtl looks for a file qtlcart.z3a. If found, Eqtl will read in the sums and sums of squares of the likelihood ratio, additive effect and dominance effect at each position and print the mean and sample standard deviations into a summary file (qtlcart.z3d). Eqtl does similar calculations for the jackknife results that would be in qtlcart.z3i.
Table 4.1 shows the command line options specific to Eqtl.