Number of Permutations to Compute

Select the number of Monte Carlo permutations to use to estimate comparisonwise and experimentwise LOD thresholds as well as exact p-values for the LOD scores at each QTL testing point.

Note: This option is available only when performing Haley-Knott Regression.

For each iteration, the trait are randomly permuted and used in the interval mapping model to generate an empirical distribution for the LOD scores.

Refer to Churchill and Doerge (Genetics, 1994)¹ for additional information about this method.

When set to 0, only observed LOD scores are reported and a LOD threshold reference line can be specified manually in the LOD Threshold [1,10] parameter field.

Caution: Permutations can be computationally time-consuming.

To Specify the Number of Permutations to Compute:

Choose Haley-Knott Regression as the QTL Mapping Model Algorithm.

Type the number of permutations into the text box.

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1

Churchill, G.A., and R.W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics 138:963-971.