SHM in FRs and CDRs. (A) Representative Env-specific lineages traced in the Rep-seq data generated from the blood post-2, post-4, and post-6 time points, with the number of identified somatic variants for each lineage indicated. The columns labeled FR1, CDR1, FR2, CDR2, and FR3 denotes the different subregions of the Ab V region. For every lineage, the percentage average SHM (nucleotide level) for each subregion was calculated from the number of variants identified at a given time point. The percentage average SHM for a given subregion from different time points is indicated with different shades, where darker and lighter gray correspond to higher and lower SHM levels, respectively (representative data from one independent experiment analyzed at least twice). (B) SHM (nucleotide level) in subregions (FR1–4 and CDR1–3) plotted relative to the total SHM in the corresponding full VDJ region (upper right schematic) for lineages where unmutated, or close to unmutated, sequences were identified in the Rep-seq data. Ten variants ranging from low to high SHM levels are shown for each lineage (representative data from one independent experiment analyzed at least twice).