Main Window – Variants

Variant <Gene Name>_<Amplicon>:<Chr>:<Pos>:<Allele>
Function Function Annotations (e.g., coding)
Protein Protein nomenclature of variant
Coding impact Impact Annotations (e.g., missense)
ClinVar Annotations from ClinVar version 20170801
‘.’ indicates no associated ClinVar entry
‘1’ indicates one associated ClinVar entry
DANN DANN score with a range of 0 (low pathogenicity) – 1 (high pathogenicity).
Whitelist Logical value that indicates whether a variant is included in an optionally uploaded white list (TRUE) or not (FALSE).
 # of Genotyped Cells
  • Number and percentage of filtered cells across all samples with genotype information.
  • Number and percentage of filtered cells across all samples with mutant genotype calls (heterozygous, homozygous).
Sample Column
[Sample 1]
  • Number and percentage of filtered cells across [Sample 1] with genotype information.
  • Number and percentage of filtered cells across [Sample 1] with mutant genotype calls (heterozygous, homozygous)
  • Aggregated variant allele frequency (VAF) of filtered cells across [Sample 1] based on genotype information (diploidy assumed)
  • Aggregated VAF of filtered cells across [Sample 1] based on sequencing read information (comparable to bulk sequencing)
  • The Subclones table may be exported by clicking the icon on the top right corner of the table:  
Additional information about each variant can be found by highlighting the variant in the table (KRAS:p.G12A in image) and review the variant summary to the right side of the table. Clicking the blue hyperlink will provide additional annotation information via the VARSOME database.