Model 6 requires two additional parameters. One is the number of markers to control for the genetic background , and the other is a window size . When invoked, the program will read in the results of a prior run of SRmapqtl to pick the most important markers to control for the genetic background. Then, when testing at any point on the genome, it will use up to of these markers. If SRmapqtl didn't rank as many markers as specified with , then is reset to the number of markers ranked. The window size will block out a region of the genome on either side of the markers flanking the test site. Since these flanking regions are tightly linked to the testing site, if we were to use them as background markers we would then be eliminating the signal from the test site itself.
Note that if and equals the total number of markers, then Model 6 reduces to Model 1. If is large (say the size of the largest chromosome) and equals the number of markers, then Model 2 is the result. If is zero, then Model 3 is the result. In the future, we will recommend that people use model 3 or model 6 for analysis. The default values of 5 for and 10 for should be good starting points for Model 6. Increasing will allow better resolution for mapping linked QTLs.