TCR clonotypes () and BCR clonotypes () show by default a table with the following columns:
Table for Clonotypes
- Clonotype #: A unique number identifying the clonotype.
- Chain: Which chain type the clonotype belongs to: TRA (), TRB (), TRG () and TRD () for TCR, or IGH (heavy), IGK (light ), and IGL (light ) for BCR. Note that other light BCR chain types are currently not supported.
- V, D, J and C: The identified V, D, J and C reference segment(s). If a single unambiguous V / D / J / C segment could not be identified, the segments will be listed separated by a comma.
- CDR3 nucleotide sequence: The nucleotide sequence for CDR3 including the V and J segment-encoded conserved amino acids.
- CDR3 amino acid sequence: The translated amino acid sequence for the CDR3 nucleotide sequence provided that it is in-frame.
- CDR3 length: The length of the CDR3 nucleotide sequence.
- Count: The number of times the specific clonotype was detected.
- Frequency (%): The count given as a percentage relative to the sum of all counts. Note that filtering can affect frequencies, see Filter Immune Repertoire.
One of three categories are used to characterize the CDR3 nucleotide sequences:
- Productive: sequences that are in frame and do not contain a premature stop codon;
- Out-of-frame: sequences that have a length that is not a multiple of three;
- Premature stop codon: sequences that are in-frame but contain a premature stop codon.
The clonotypes are sorted by count in decreasing order.