Useful Facts about Quality Control in Exome Sequencing (Ts/Tv)
http://www.biostars.org/post/show/4751/titv-ratio-confirms-snp-discovery-is-this-a-general-rule/ QT:”
The transition transversion ratio in human is observed to be around 2.1 and this can be used as a confirmation for the filtering in a snp discovery project.
”
http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties
QT:”
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 dbSNP.
….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….
Transition to Transversion Ratio
…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. ….
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. “