Main Window – Subclones

The Subclone table is segmented into two sections:

  • The top section summarizes the number of subclones that are identified across all loaded samples. The cluster identity and cluster number changes every time the variant list is updated. Percentages shown in parenthesis after each cluster-variant pair denote the average VAF % across all loaded samples.
  • The bottom section summarizes the relative fractions of subclones per loaded sample. Integer numbers represent the number of cells per variant per subclone. Please note that subclone percentage numbers are relative and include subclones that are grouped as “Small Subclones” and “Missing GT Subclones”.

To assess relative subclone size within and across different samples we recommend reviewing the data in the REVIEW SUBCLONES page.

Variant Lists all selected variants as <Gene Name>_<Amplicon>:<Chr>:<Pos>:<Allele>
C1 Subclone 1. Subclone-associated variants are either WT, Het, Hom (zygosity included) or WT, Mut (zygosity ignored). NA represent missing genotype (GT) information.
The percentage in parentheses (Show VAF) reflect the average VAF of a given variant in that clone across all loaded samples.
Small Subclones (6) 0.51 % All subclones with small percentages summarized. Number in parentheses represents total number of Small Subclones. Percentage represents total fraction of Small Subclone-cells out of all cells pass-filter.

Missing GT Subclones (77) 46.87%
All subclones with a missing value (NA) in at least one selected variant summarized. Number in parentheses represents total number of Subclones with missing GT information. Percentage represents total fraction of Missing GT Subclones-cells out of all cells pass-filter.
  • Each subclone is labeled as C1, C2, etc. Subclones may be renamed by double-clicking in the column header of the subclone.
  • The Subclones table may be exported by clicking the icon on the top right corner of the table: