Clone Summary table

The Clone Summary table lists the identified clones in rank order from the most frequently occurring to least frequent. Each row represents an individual clone. Select Clone Summary from the Views list to see the table.

For each clone, the identified variable and joining region are listed as well as the amino acid (CDR3 AA) and nucleotide (CDR3 NT) sequences of the CDR3 region. The variable gene mutation, the isotype (Oncomine™ BCR IGH‑LR Assay only), and the clonal lineage assignment (Lineage ID) are also listed.

Click the column heading cells to sort the table. Frequency = # of reads for the identified clone (Count) / total reported reads (sum of Count column).

For multi‑sample analyses the Clone Summary table lists the frequency of each clone that is identified in any of the samples. The table is sorted in descending order that is based on the frequency of the clones in the leftmost column for each sample in the analysis. Although you can compare across multiple repertoire analysis workflows (that is, BCR IGH‑SR versus BCR IGH‑LR), in some instances BCR IGH‑SR analysis results can include multiple variable gene assignments.

  1. Sample 1

  2. Sample 2

The following table lists and describes the information that is available in the Clone Summary table.

Column name

Description

Lineage ID [1]

Lineage ID represents the rank order of the clonal lineage abundance. Calculated as the sum of the frequencies of all members of the clonal lineage. Lineage 1 corresponds to the most abundant lineage, followed by Lineage 2, until the least abundant lineage is reached.

Variable

The best matching IMGT variable gene of the rearrangement.

Joining

The best matching IMGT joining gene of the rearrangement.

CDR3 AA

The CDR3 amino acid sequence of the rearrangement, denoted using the IMGT definition of the CDR3 region.

CDR3 NT

The CDR3 nucleotide sequence of the rearrangement, denoted using the IMGT definition of the CDR3 region.

Variable Mutation

The fraction of bases within the variable gene that differ from the best-matching IMGT variable gene. In B cells, such mismatching bases are largely derived from somatic hypermutation.

Count

The total number of reads mapping to the rearrangement after quality filtering.

Frequency

The frequency of the rearrangement as a proportion of total reads passing quality filtering.

Rank

The frequency rank of the rearrangement.

Isotype

The isotype identified for the clone[2].

1 This data is available only for the Oncomine™ BCR IGH‑LR Assay and Oncomine™ BCR IGH‑SR Assay.
2 Isotype identification with the Oncomine™ BCR IGH‑LR Assay assay only.

Note: Additional details are available by downloading the Clone Summary table.