Genome-wide SNP analysis of human genome
Allelic frequency difference across population can provide valuable insight into population differentiation in a variety of ways, and it is becoming increasingly popular nowadays with easy access to genome-wide allele frequency data. Using the 1000 Genomes Project phase I single nucleotide polymorphism (SNP) data, the fixation index was estimated to be 0.0308 for 14 populations sampled from 4 geographical regions. Relationship among populations was also examined by distinct allelic richness and private allelic richness for single population and population combination. We found that African populations have higher distinct and private allelic richness than populations outside Africa. In addition, ADD and ADD-DEL simulation studies identified that rare variants influence population parameter estimation by decreasing fixation index and distinct allelic richness, while increasing private allelic richness.
Mao, Huzhang, "Genome-wide SNP analysis of human genome" (2013). Texas Medical Center Dissertations (via ProQuest). AAI1549834.