selection of the window for searching candidate genes

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venkat rami reddy

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Feb 28, 2024, 2:34:01 PMFeb 28

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After QTL mapping for a DH maize population with 500 permutations for detecting the thresholds and i have the peaks with sig. SNPS, it is important to identify the candidate genes for further analysis. What is the criteria to select the candidate genes window in from and to the peak SNP?

Thanks in advance

Regards

Rami

Karl Broman

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Feb 29, 2024, 11:31:26 AMFeb 29

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The usual methods for defining a QTL interval are 1.5-LOD support intervals (the function lod_int), and 95% Bayesian credible intervals (the function bayes_int). Neither approach is entirely satisfactory.