A subclone is a group of cells that has the same mutation. Small subclones contain less than X % of the total number of cells in the variant. This threshold is adjustable and defaults to 1 %. Missing GT subclones are subclones with missing genotypes in one or more of the selected variants.
This table is segmented into two sections – Variant subclones and Relative fractions of subclones. Clicking in the horizontal bar with the word Subclones displays the information in a larger window.
Settings: Click the 
icon to filter the subclones.
Ignore zygosity
Selecting this option disregards mutant genotype information. Cells with heterozygous and homozygous genotype calls are treated equally.
Default: Unchecked
Remove subclones with < X % of cells
Removes subclones with a select percentage of cells from the Subclones Table. All removed subclones are listed in the Small Subclones column. Adjust the number by using the arrows or entering a new number.
Default: Checked with a value of 1 %
Remove subclones with missing genotypes
Removes subclones that contain missing genotypes (NA) in at least one selected variant used for subclone identification.
Default: Checked
Show VAF
Lists the average variant allele frequencies (VAF) per subclone across all loaded samples in the Subclones Table.
Default: Checked
Auto Name Clones
Subclones are automatically named. By default, the subclones are named C1, C2, C3, etc. Clicking this button updates the subclone names to reflect the variants that are part of it. Subclones are auto-named using these rules:
-
- Auto-generated subclone names must have less than 25 characters.
- Variants must have a gene name.
- None of the variants should have missing genotypes.
- For two variants from the same gene, the protein name or variant position is added to the subclone name.
- When the Ignore zygosity filter is off, the zygosity state in the form of Hom/Het is added to the subclone name.
Names are automatically reset whenever there is a change in subclone population due to a change in selected variants or change of one of the filters. To auto rename subclones, click the button.
Variant subclones
The top section of the Subclones Table displays the subclones associated with the selected variants in the Variants Table.
Variant
Lists the selected variants from the Variants Table using the format <gene
name>:<chromosome number>:<position>:<allele>.
Subclone
A column displays for each subclone. By default, subclone names are C1, C2, etc. "C" stands for clone. To edit the name, click the 
icon.
Subclone-associated variants are identified as either (1) WT, Het (heterozygous), Hom (homozygous) (zygosity included) or (2) WT, Mut (zygosity ignored). NA represents missing genotype information.
The percentage in parentheses reflects the average VAF of a given variant in that clone across all loaded samples. The variant-clone identity and percentage update with each variant list update.
Summarizes all subclones with small percentages, meaning they contain less than X % of the total number of cells in the variant. The number in parentheses in the column header represents the total number of small subclones.
Missing GT Subclones
Lists all subclones with a missing value (NA) in at least one selected variant. The number in parentheses in the column header represents the total number of subclones with missing genotype (GT) information.
Relative fractions of subclones
The bottom section of the Subclones Table summarizes the relative fractions of subclones per loaded sample.
For each sample, it shows the total number of cells and percentage per subclone, small subclone, and missing GT subclones as well as an overall accounting for the entire analysis.
Note: Subclone percentage numbers are relative and include subclones that are grouped as small subclones and missing GT subclones.