2016/05/21 by Chang‐Yong Lee, Chang-Yong Lee, Lee, Chang-Yong
Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #Genomics (q-bio.GN) #Genomics and Chromatin Dynamics #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms #q-bio.GN
paper · pdf · doi:10.48550/arxiv.1605.06576
17 pages, 4 figures
arxiv created 2016/05/21 · openalex publication_date 2016/05/21 · arxiv updated 2016/05/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the closer proximity of existing SNPs. With the Hapmap SNP data, we empirically demonstrate that the preferential model is better for illustrating the clustered distribution of SNPs than the random model. Moreover, the model is applicable not only to autosomes but also to the X chromosome, although the X chromosome has different characteristics from autosomes. The analysis of the estimated parameters in the model can explain the pronounced population structure and the low genetic diversity of the X chromosome. In addition, correlation between the parameters reveals the population-wise difference of the mutation probability. These results support the mutational non-independence hypothesis against random mutation.