read coverage improves with iteration and recapitulates Sanger sequence upon convergence. (A) Coverage plots demonstrate influence of mapper selection and iteration for MiSeq data (50 base reads) of an IGH amplicon from a Hodgkin lymphoma specimen to its clonal IGHV region, IGHV1-69-2. The FR1-FR3 regions of this gene starts at location 143 and ends at 430. (B) Sequence alignment of the 100 nt region of highest divergence (21%) of HL-IGHV sequence from its corresponding germline sequence: IGHV1-69-2, the independently converged sequence from CUSHAW3 and SHRiMP2, along with the Sanger sequence from IGH amplicon from this specimen. Initial coverage of this region is low in part or all of this region for all four mappers shown and remains low after iteration in the highest density portion with the default settings for BWA-MEM and Novoalign.