Figure 5

The success rate and score distribution of V, D, and J alignments for simulated rearrangements with mutation probability: a) 0% b) 20% c) 30% and d) 50%. The success rate is a function of the alignment score and mutation probability. The success rate (circles with dashed lines) is the frequency at which a V-, D-, or J-alignments in the simulated sequences are correct. The score distribution is calculated from the number of times an alignment score occurs in 10,000 simulated sequences. Scores that occur less than 10 times (out of the 10,000 simulations) are not shown to prevent discontinuities. V-segments scores are normalized by the length to account for differences in the size of the V-germlines, which may have 5’ or 3’ truncations. The solid vertical line in the D-alignment score at score = 9 corresponds to the suggested minimum length for the size of a D-match in JOINSOLVER. The increase in the success rate of low scoring J-matches is a result of ties in which most or all J germlines are selected.