This is an illustration of a permutation test: To assess whether a given LOD score is sufficiently large to indicate evidence of a QTL, we compare it to the distribution of the genome-wide maximum LOD score under the null hypothesis of no QTL.
The null distribution of the genome-wide maximum LOD is estimated by permuting the phenotypes relative to the genotypes.
Click the green button to shuffle the phenotypes and re-draw the LOD curves; click the pink “back” button to go back.
The code is on github.