Figure 4: IMGT clonotype (AA) and (nt) characterization.

This figure represents screenshots from IMGT/HighV-QUEST online. (a) IMGT clonotypes (AA). ‘Exp. ID’ is the identifier of the ‘IMGT clonotype (AA)’ in the data set. The IMGT clonotype (AA) definition includes the names of the V, D, J genes and alleles, the CDR3-IMGT length (AA), the CDR3-IMGT sequence (AA) and the anchors 104 and 118 of the junction ‘C, F’ (for 2nd-CYS 104 and J-PHE F118 for V-BETA, respectively). ‘V%’ indicates the percentage identity of the V-REGION of the representative sequence with the closest germline V-REGION, the sequence length in nucleotides is provided and a link gives access to the sequence in FASTA format; 'nb' indicates the number of sequences '1 copy' and 'More than 1' assigned to the clonotype, and the total. In the ‘IMGT clonotypes (nt)’ column, ‘Sequences file’ gives access to a file containing the '1 copy' sequences assigned to a given IMGT clonotype (AA), in FASTA format. An asterisk (#17083) indicates an example of IMGT clonotype (AA) with a TRBV20-1*02-TRBD1*01-TRBJ1-6*02 rearrangement as described in the genotype and haplotype identification. This figure shows a very small part of the list of the 22,234 unique IMGT clonotypes (AA) identified in this case study. (b) IMGT clonotypes (nt). The nb of different CDR3-IMGT (nt) indicates the nb of IMGT clonotypes (nt) for a given IMGT clonotype (AA) (for example, 2 for #17379). The CDR3-IMGT sequence (nt) is shown with the nb of different nt (nb diff nt). ‘0’ indicates that the CDR3-IMGT (nt) is identical to that of the IMGT clonotype (AA) representative sequence. For #17379, there is an IMGT clonotype (nt) with 1 nt difference (‘c’ instead of ‘t’ at the third position, compared with the CDR3-IMGT of the representative sequence). #17379 also shows an example of ‘several alleles’ (for V and J) assigned to an IMGT clonotype (AA).