Analysis Output | Sample Analysis Reports | Small Variants Summary

Small Variants Summary

This table provides metrics about the number of SNVs, deletions, and insertions.

Table 4 Small Variants Summary Table
Statistic	Definition
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 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).

Table 5 Variants by Sequence Context Table
Statistic	Definition
Number in Genes	The number of variants that fall into a gene.
Number in Exons	The number of variants that fall into an exon.
Number in Coding Regions	The number of variants that fall into a coding region.
Number in UTR Regions	The number of variants that fall into an untranslated region (UTR).
Number in Splice Site Regions	The number of variants that fall into a splice site region.

To view the guidelines for calculating variation consequences, visit the Ensembl website: uswest.ensembl.org/info/genome/variation/predicted_data.html#consequences.

Table 6 Variants by Consequence Table
Statistic	Definition
Frameshifts	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.