AA BB CODD -log10(p) Now imagine that you've done a GWAS with those 10 SNPs, plus 7000 SNPs which are not associated with the phenotype. Here are 4 Manhattan plots log10(P) 10 8 4 10 8 6 A (d)01601- 10 8 1 2 3 4 5 6 7 8 9 10 X 2 3 4 5 6 7 8 9 10 X Chromosome Chromosome ...C 10 1 2 4 5 6 7 8 9 10 X Chromosome logo(p) 2 8 6 1 2 3 4 5 6 7 8 9 10 X Chromosome Which plot is most representative of what you found? Remember that the chromosomes are along the x axis, the log 10 pvalue is the y axis, and each point is an individual SNP. ..B D
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