Small Variants Summary

Table 14 Small Variants Statistics
Statistic	Description
Total Passing	The total number of variants present in the data set that passed the variant quality filters.
Percent Found in dbSNP	100*(number of variants in dbSNP/Number of variants)
Het/Hom Ratio	Number of heterozygous variants/Number of homozygous variants.
Ts/Tv Ratio	Transition rate of SNVs that pass the quality filters divided by the transversion rate of SNVs that pass the quality filters. Transitions are interchanges of purines (A, G) or of pyrimidines (C, T). Transversions are interchanges between purine and pyrimidine bases (for example, A to T).
Mean Variant Frequency	Number of reads in which the variant was detected divided by the number of reads.

Table 15 Statistics for Variants by Sequence Context
Statistic	Description
Number in Genes	The number of variants that occur in a gene.
Number in Exons	The number of variants that occur in an exon.
Number in Coding Regions	The number of variants that occur in a coding region.
Number in UTR Region	The number of variants that occur in an untranslated region (UTR).
Number in Splice Site Regions	The number of variants that occur in a splice site region.

Table 16 Statistics for Variants by Consequence
Statistic	Description
Frameshift	The number of variants that cause a frameshift.
Non-synonymous	The number of variants that cause an amino acid change in a coding region.
Synonymous	The number of variants that are within a coding region, but do not cause an amino acid change.
Stop Gained	The number of variants that cause an additional stop codon.
Stop Lost	The number of variants that cause the loss of a stop codon.

For Research Use Only. Not for use in diagnostic procedures.