Can someone help with explanations of allele estimates (SNP) which were produced using TASSEL 3.0 (Association analysis)?

10 October 2013 1 5K Report

When I did association analysis using TASSEL, I found the allele estimates of one of significant marker (which associated with a QTLs) had 3 allele G, A, and R (G:A) (ee attachment). how can I interpret this in association table? I mean that there are two allels one increases the trait, while, the other decrease the trait. Here I have G and A with negative sign. Can anybody help me?

Ahmed Sallam

thanks for replying. do you recommend with the deletion of hetero haplotype R and deal with it as a missing value?.

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