Human mutations don't occur randomly. In fact, transitions (changes from A G and C T) are expected to occur twice as frequently as transversions (changes from A C, A T, G C or G T). Thus, another useful diagnostic is the ratio of transitions to transversions in a particular set of SNP calls. This ratio is often evaluated separately for previously discovered and novel SNPs.
Across the entire genome the ratio of transitions to transversions is typically around 2. In protein coding regions, this ratio is typically higher, often a little above 3. The higher ratio occurs because, especially when they occur in the third base of a codon, transversions are much more likely to change the encoded amino acid. A refinement to this analysis, in protein coding regions, is to examine the transition to transversion ratio separately for non-degenerate, two-fold degenerate, three-fold degenerate and four-fold degenerate sites.