When a Structural Variation event occurs, often the result is that reads that are aligned to a region have a high number of mismatches in a localized region that is located to one side of the event. When analyzing next generation sequencing data for Structural Variation events, NextGENe splits a read that has a high level of mismatches that is localized to one side of the possible event in to two separate reads and then remaps both reads to the reference.The location at which the reads are split is referred to as the breakpoint for the reads and the split reads are referred to as Linked Reads. The read that is on the left side of the breakpoint is Position 1 with Orientation 1. The read that is on the right side of the breakpoint is Position 2 with Orientation 2. You can generate a Structural Variation report to detail both positions on either side of the breakpoints for all reads that were split between two reference locations across the entire reference genome and identify the event as one of the following:

Two subjective options—Scaled reads and a Median Score—are provided for evaluating a potential Structural Variation event, and determining if the event should be considered a true event and included in the report.