We aligned 1,728,270 human reads, individual C (see Venter JC, et al, The Sequence of the Human Genome, Science Feb 16 2001: 1304-1351), to build34 of the human genome, available at ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/, using ssahaSNP. The settings
for ssahaSNP were such that the candidate SNP base in the read was at least Phred Q=23, that its neighbouring 5 bases on either side of the candidate SNP all had Phred quality values of >=15 and at least 9 of the 10 neighbours match. If the number of det
ected SNPs for the aligned segment of a read exceeded a rate of 15 SNPs per 1000 bases then that read alignment was ignored. If a read aligned to more than one place in the genome, then only the longest alignment with the fewest SNPs was reported.