Analysis Output | Sample Summary Reports | Somatic Analysis Summary | Variants Summary

Variants Summary

Table 2 Somatic Small Variants Summary
Statistic	Definition
Total	The total number of variants present in the data set that pass the quality filters.
Number in Genes	The number of variants in a gene.
Number in Exons	The number of variants in an exon.
Number in Coding Regions	The number of variants in a coding region.
Splice Site Region	The number of variants in a splice site region.
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.
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 within a coding region but do not cause an amino acid change.
Mature miRNA	The number of variants in a mature miRNA.
UTR Region	The number of variants in an untranslated region (UTR).
dbSNP	The number of variants present in dbSNP.

Table 3 Somatic Small Variants
Statistics	Definition
Chr	Name of reference chromosome.
Pos	The reference position within chromosome.
Depth	The number of reads aligned at this position.
Ref	The reference allele.
Alt	The alternative allele.
Alt Freq	The proportion of the alternative allele among all alleles being considered.
Type	The type of small variant (SNV, Insertion, Deletion).
Consequence	Predicted transcript consequence.
dsSNP	The numeric identifier developed by the National Center for Biotechnology Information (NCBI) for the Single Nucleotide Polymorphism Database (dbSNP).
COSMIC	The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database.
ClinVar	A public archive of reports of the relationships among human variations and phenotypes.

Table 4 Somatic Structural Variants Summary
Variant Class	Notes
CNV	The method to determine copy number variations is described in Copy Number Aberrations (SENECA)
Deletions	For more information regarding the criteria used to determine these structural variants, see Large Indel and Structural Variant Calls.
Tandem duplications
Insertions, inversions
Translocation breakends
Duplications (DUP)

Table 5 Somatic Structural Variants
Statistics	Definition
Chr	Name of reference chromosome.
Pos	Position within reference chromosome.
Len	Length difference between reference allele and alternative allele.
Type	Structural variant type.
Qual	Structural variant quality score.

Table 6 Somatic Copy Number Variants
Statistics	Definition
Chr	Name of reference chromosome.
Pos	The reference position within chromosome.
Len	The estimated length of the copy number variant.
Qual	The quality score of the copy number variant.
Copy Number	The number of copies of the copy number variant.
LOH	Loss of heterozygosity of the copy number variant.

Table 7 Somatic Translocation Variants
Statistics	Definition
Chr	Name of reference chromosome.
Pos	Position within reference chromosome.
Ref	The reference allele.
Alt	The alt allele.
Qual	Structural variant quality score.