On the quantity and quality of single nucleotide polymorphisms in the human genome

Single nucleotide polymorphisms (SNPs) are useful markers for locating genes since they occur throughout the human genome and thousands can be scored at once using DNA microarrays. Here, we use branching processes and coalescent theory to show that if one uses Kruglyakʹs (Nature Gen. 12 (1999) 139–144) model of the growth of the human population and one assumes an average mutation rate of 1×10−8 per nucleotide per generation then there are about 5.7 million SNPʹs in the human genome, or one every 526 base pairs. We also obtain results for the number of SNPs that will be found in samples of sizes n⩾2 to gain insight into the number that will be found by various experimental procedures.