Figure 3

Iterative mapping increases accuracy of total SNV calls and frequency estimations from FL-128 BCL2 region. (A) Percent identity (35 base moving average) of BCL2 from FL-128 (Sanger sequence) to its GRCh37.p10 reference has a minimum value of 75% identity. (B) Local coverage relative to reference location for initial BFAST mapping (blue circle) and converged iterated BFAST mapping (red triangle) shows improved coverage in areas with lower percent identity; coverage in controls (black line), offset by 5,000, shows typical non-uniform coverage pattern. (C) Frequency of variants (# mutated reads/total # reads) called by analysis of initial BFAST (blue circle) and final iterated BFAST (red triangle) are plotted versus reference location using frequency along the horizontal axis to facilitate comparison to (D). These alignment data show a wide range of frequencies and a general increase in detected frequency with iterative mapping, most notable in regions where iteration increased coverage (circle). Iterative remapping also identified an additional 19 SNVs (22% increase). Note that a large number of mutations share a common frequency, representing the founder genotype of the current most frequent clone (MFC) in this population (black arrow). (D) Cumulative frequency distribution data plotted as rank (1 to 86 for initial BFAST, 1 to 105 for converged iterated BFAST, high to low frequency) versus variant frequency show the increase in the number of variants detected and a tighter distribution of MFC genotype frequencies upon iteration (black arrow). Two homozygous SNPs are present in this sample.