It might be a basic question but I am having difficulty on finding the significant differences of phenotypes for a significant SNP. The phenotypic data I have is in the ordinal scale (1,2,3,4,5). I have done GWAS analysis found some significant SNPs. I am trying to see if the SNP is not false positive by evaluating the phenotypic difference among the accessions with SNP AA, AB and BB. But since the phenotypic data is in the ordinal scale, unlike quantitative traits, it is hard to see the statistical significance difference among the phenotypic data. I am wondering if there is a better way to see the significant difference in the phenotypic data than taking average for accessions having SNPs - AA, AB, BB. Is the chi-sq test reasonable to use? I would appreciate any suggestions.
Thanks
