Figure 5.

Complex mutation event leading to multiple duplications and deletions in the MA subline CYC-17. Arrows denote the left and right Illumina read pairs (with arrows not signifying left or right, specifically) and provide evidence for complex de novo events on scaffold 18 in CYC-17, including a large-scale deletion (center of figure) and multiple smaller duplications and deletions. While distance between read pairs should only be a few hundred base pairs, the arrows show read pairs with drastic differences in mapping distance and are indicative of indel activity. The sequence coverage track represents the normalized depth of sequencing coverage, relative to the other CYC MA sublines, where lighter color represents lower relative coverage (e.g., the 401-kb deletion). Also, −logP is plotted for each consecutive sliding window (i.e., the probability of a region deviating from 1:1 coverage ratios by chance, or the probability of an indel), and higher values relative to lower values represent increasing probability of CNV (see Methods).