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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

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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Phenotype chr1.1 chr2.8 chr3.12 chr4.12 chr4.55 chr7.88 chr9.55 chr10.1 chrX.1 chrX.5 Purple AA AT Purple AA AT F F GG GC 80 CC CC TT TT TT CT 80 CC CC AT TT TT CT 8 CC CC AT AT GG CT GC TT CC AT AT GT 10 CT Yellow AA AT TT GC Purple and AA TT Yellow F Purple AA AT AA GG TT GC AT TT TT CT Purple AA AT AA GG TT GC AT TT TT CT Purple AA AT AA Purple AA AT AA 80 CC TT GG AT TT TT TT 646 GG CC GG AT TT TT TT Purple and AA TT AT CC 80 Yellow 80 CC GG AT AT GT TT Purple AA AT AT CC CC GC AT F TT TT TT E Purple AA AT AT CC TT GC AT TT TT CC Purple AA AT E 00 CC TT GG AT TT TT CC Yellow AA AT AT GC TT 00 CC AT AT GG CC 80 TT E AT AT GC CC CC AT AT GG TT Yellow AA AT AT GG CC CC AT AT GG Yellow AA ধ 80 CC CC AT AT GT TT GG TT GG AT AT GG TT Purple and AA AA AT GG Yellow Yellow AA AA F 80 CC GG AT TT TT CC 80 GC CC GG AT AT GT CC Purple AA AA AT GC Purple and AT AA Yellow Purple AA AA F F GG 80 CC GG AA TT GT CC
Transcribed Image Text:Phenotype chr1.1 chr2.8 chr3.12 chr4.12 chr4.55 chr7.88 chr9.55 chr10.1 chrX.1 chrX.5 Purple AA AT Purple AA AT F F GG GC 80 CC CC TT TT TT CT 80 CC CC AT TT TT CT 8 CC CC AT AT GG CT GC TT CC AT AT GT 10 CT Yellow AA AT TT GC Purple and AA TT Yellow F Purple AA AT AA GG TT GC AT TT TT CT Purple AA AT AA GG TT GC AT TT TT CT Purple AA AT AA Purple AA AT AA 80 CC TT GG AT TT TT TT 646 GG CC GG AT TT TT TT Purple and AA TT AT CC 80 Yellow 80 CC GG AT AT GT TT Purple AA AT AT CC CC GC AT F TT TT TT E Purple AA AT AT CC TT GC AT TT TT CC Purple AA AT E 00 CC TT GG AT TT TT CC Yellow AA AT AT GC TT 00 CC AT AT GG CC 80 TT E AT AT GC CC CC AT AT GG TT Yellow AA AT AT GG CC CC AT AT GG Yellow AA ধ 80 CC CC AT AT GT TT GG TT GG AT AT GG TT Purple and AA AA AT GG Yellow Yellow AA AA F 80 CC GG AT TT TT CC 80 GC CC GG AT AT GT CC Purple AA AA AT GC Purple and AT AA Yellow Purple AA AA F F GG 80 CC GG AA TT GT CC
А C C AA BB OODD -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 6 4 10 8 6 A (d)01601- 10 8 2 3 4 5 6 7 8 9 10 X 2 3 4 5 6 7 8 9 10 X Chromosome Chromosome ...C 10- 8 1 2 4 5 6 7 8 9 10 X Chromosome logo(p) 2 6 1 2 3 4 5 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
Transcribed Image Text:А C C AA BB OODD -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 6 4 10 8 6 A (d)01601- 10 8 2 3 4 5 6 7 8 9 10 X 2 3 4 5 6 7 8 9 10 X Chromosome Chromosome ...C 10- 8 1 2 4 5 6 7 8 9 10 X Chromosome logo(p) 2 6 1 2 3 4 5 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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