Evaluation of eQTL Window Sizes for Accurate Gene Location

Feb 28, 2025

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Compare 5, 10, and 20 cM window sizes to locate cis-eQTLs accurately using LRT traces for known transcripts. Results indicate 20 cM window as the most precise. Genes: At4g03060 AOP2, At4g03050 AOP3, At1g54040 Epithiospecifier, At3g14210 ESM1.

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eqtl window sizes
ciseqtls
lrt traces
gene positions
accurate localization

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Evaluation of eQTL Window Sizes for Accurate Gene Location

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Supplemental Figure 2: Evaluation of eQTL window or range sizes (5, 10, 20 cM) for their ability to correctly locate known cis-eQTLs. The LRT traces (in red) for four transcripts with known cis-eQTLs on the chromosomes where each encoding gene is physically located. The physical position of each gene (A-D) is indicated with a red arrow on the x-axis for each graph. The location of eQTLs identified using the 5, 10 and 20 cM windows are shown with green, orange, and blue arrowheads, respectively. In all four cases, the 20 cM window most accurately indicates the position of the known gene underlying the cis-eQTL. (A) At4g03060 – AOP2, (B) At4g03050 – AOP3, (C) At1g54040 – Epithiospecifier, (D) At3g14210 – ESM1.

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