Evidence for negative selection in the large expanded clone. (a) High frequency of silent mutations in members of the large expanded clone. Each sequence variant (member) of the clone was compared with the germline sequence to determine the numbers and kinds of mutations it contained. The heights of the bars represent the number of mutations, and the proportions of the bars that correspond to replacement (R, red) or silent (S, blue) mutations are shown. Sequence variant numbers are given on the x-axis, as are their corresponding time points. Nucleotide positions 10-381 (ImMunoGeneTics, or IMGT) were used for the alignment. (b) Graphical output of BASELINe analysis  (see Methods). Negative values indicate negative selection, and positive values indicate positive selection. Confidence in the magnitude of selection is depicted by the width of the curve; the narrower the curve, the more confident we are of the results. Both the complementarity-determining region (CDR) and the framework region (FWR) show strong negative selection. The CDR shows evidence of significantly more negative selection than the FWR (P ≤0.0031).