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Simple models of genomic variation in human SNP density

Authors
Journal
BMC Genomics
1471-2164
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Volume
8
Issue
1
Identifiers
DOI: 10.1186/1471-2164-8-146
Keywords
  • Research Article
Disciplines
  • Biology
  • Mathematics

Abstract

Background Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome. Results Using empirical estimates of recombination rate across the human genome and the observed SNP density distribution, we produce a maximum likelihood estimate of the genomic heterogeneity in the scaled mutation rate θ. Such models produce significantly better fits to the observed SNP density distribution than those that ignore the empirically observed recombinational heterogeneities. Conclusion Accounting for mutational and recombinational heterogeneities can allow for empirically sound null distributions in genome scans for "outliers", when the alternative hypotheses include fundamentally historical and unobserved phenomena.

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