Additional file 3.
Table S1, Additional file 3. SOLiD sequencing statistics. When using our new SOLiD data or prior data from the literature, our validation procedure only validated two alleles for any location, regardless of the data sets being compared. However, for some SNPs, neither of the two validated alleles matched the published reference allele. Some (8) of these are likely due to Indian-origin vs. Chinese-origin differences. For the vast majority, however, there are two possibilities, each of which explains an undefinable proportion of these SNPs: (1) a proportion of the reference allele (Sanger) calls are wrong, and (2) a small proportion of the apparent three allele SNPs represent true SNPs with three valid alleles in Indian-origin rhesus macaques.
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Fawcett et al. BMC Genomics 2011 12:311 doi:10.1186/1471-2164-12-311