I was wondering what is the range of SNP density across species and model organisms.

I.e., what would be a reasonable estimate for the SNP density (i.e., x SNPs for each 1 Kb) in:

  1. humans
  2. humans with the highest variation (i.e., Africans)
  3. flies
  4. mouse
  5. lab mice with highest variation (i.e., isogenic lab mouse 1 with isogenic lab mouse 2 with the highest variation)
  6. model organism with the highest snp density (could be lab or naturally occurring)

SNP Density

Human = ~1.18 SNPs per kbases

Based on CgsSNP, the average numbers of SNPs per 10 kb was 8.33, 8.44, and 8.09 in the human genome, in intergenic regions, and in genic regions, respectively.

Source: Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. by Zhao Z, Fu YX, Hewett-Emmett D, Boerwinkle E.

Drosophila melanogaster = ~0.02 SNP per kbases

FLYSNPdb provides high-resolution single nucleotide polymorphism (SNP) data of Drosophila melanogaster. The database currently contains 27 367 polymorphisms, including >3700 indels (insertions/deletions), covering all major chromsomes. These SNPs are clustered into 2238 markers, which are evenly distributed with an average density of one marker every 50.3 kb or 6.6 genes.

source: FLYSNPdb: a high-density SNP database of Drosophila melanogaster

Mouse(Mus musculus) = ~0.2 SNP per kbases

Source: Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse


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