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Open Access Research article

Simple models of genomic variation in human SNP density

Raazesh Sainudiin12*, Andrew G Clark3 and Richard T Durrett2

Author Affiliations

1 Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK

2 Department of Mathematics, Cornell University, Ithaca, New York 14853, USA

3 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA

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BMC Genomics 2007, 8:146  doi:10.1186/1471-2164-8-146

Published: 6 June 2007



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.


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.


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.