Table for Clonotype Sample Comparison
The default view on Clonotype Sample Comparison is a table with the following columns:
- Sample: The sample where the clonotype was identified. If the same clonotype is present in multiple samples, there will be one row for each sample.
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.
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.