Figure 2. Alignment of Coccidioides immitis whole-genome sequence reads flanking a confirmed single-nucleotide polymorphism (RSv3 supercontig 1, position 6729646, highlighted in blue in panel B) among the 3 cluster isolates. Isolates from patients X, Y, and Z, who had coccidioidomycosis, are shown in panels A, B, and C, respectively. The alignment was created by using SolScape, a short-read sequence-alignment viewer developed in house (J. Pearson et al., unpub. data; tool available upon request). Reference sequence position is given at the top of each panel; actual reference sequence is highlighted in white at the center of each panel. Bases differing from the reference sequence are highlighted in pink, green, or yellow.