Reading Manhattan and Q-Q Plots from a GWAS

The two diagnostic pictures. Q-Q inflation is how stratification is detected in practice.

Questions this Concept answers

Why does a Q-Q plot that deviates upward from the diagonal across most of its range (not just the extreme tail) suggest a problem with the GWAS?

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Manhattan Plot and QQ Plot in R for GWAS Data

A Manhattan plot displays genome-wide association study (GWAS) results by plotting each variant's genomic position (chromosome and base-pair coordinate) against its statistical significance, conventi…