Figure 4.

Analysis of Illumina sequencing data. A set of high confidence variants was called using the somatic command in VarScan (dark gray), with reads from the mapping strain treated as “normal” data and reads from merged bulks treated as “tumor” data. Allele frequencies were then estimated for these sites in the low fluorescence and high fluorescence bulks with Popoolation2 (light gray). Differences between these two bulks were assessed using G-tests.