Changes

== Proportion of dbSNPs ==

== Proportion of dbSNPs ==

Most of the genetic variants in any one individual have been previously observed in other individuals. Thus, it is usually a good diagnostic to investigate what fraction of variants in an individual genome have been previously described in [[www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP]].  

Most of the genetic variants in any one individual have been previously observed in other individuals. Thus, it is usually a good diagnostic to investigate what fraction of variants in an individual genome have been previously described in [http://www.ncbi.nlm.nih.gov/projects/SNP/ dbSNP].  

The expected proportion of previously discovered SNPs (those already catalogued in dbSNP) and novel SNPs (those that haven't been previously discovered) will change overtime. The dbSNP database is being constantly updated so that currently (mid-2010) we'd expect >90% of the variants in an individual genome to have been previously discovered.  

The expected proportion of previously discovered SNPs (those already catalogued in dbSNP) and novel SNPs (those that haven't been previously discovered) will change overtime. The dbSNP database is being constantly updated so that currently (mid-2010) we'd expect >90% of the variants in an individual genome to have been previously discovered.  

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.

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, transitions 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.

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.

== Why Are Reciprocal Changes Not Equally Frequent? ==

== Why Are Reciprocal Changes Not Equally Frequent? ==