The results of a genome scan are depicted graphically, where the locations of the markers are given on the x-axis (black triangles), and the result of the statistical test is indicated on the y-axis (here a likelihood ratio test). The significance threshold is given by the horizontal line parallel to the x-axis and intersecting the y-axis at the appropriate value. The significance threshold has been adjusted to account for the number of independent tests performed, and was determined by a permutation test. Evidence for linkage of a QTL with markers occurs when the test for linkage generates a significance level that exceeds the permutation threshold. The best estimate of the QTL location is the position on the x-axis corresponding to the greatest significance level.
Mackay Journal of Biology 2009 8:23 doi:10.1186/jbiol133