Establishing a cut-off for reliable clonal detection. For each replicate (A: CDR3, B: VDJ), starting with the highest frequency clones, clones were tested for their simultaneous presence in the respective two other replicates. For each clone, presence or absence in the other two replicates were recorded. We regarded all those clones as "reliably detected" that belonged to the highest frequency set of clones with a ratio of presence to absence ≥99%. The percentage of clones passing the detection threshold is indicated by vertical red bars. Absolute numbers of reliably detected clones for CDR3-1M were (1427, 862, 791), and for CDR3-9M were (9414, 9485, 9460). For VDJ, 1M and 9M absolute numbers were (10741, 10731, 11055) and (18765, 18928, 18466), respectively. For a graphical overview of the method of reliable detection, please refer to Menzel et al..