Median Score for a Structural Variation event
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. For each pseudo paired read that aligns at position 1 and position 2 of a possible Structural Variation event, the percentage of the read that matches is recorded and an initial score is calculated. The Median Score, which is defined as the median of the matching percentage for all pseudo paired reads that match at positions 1/2, is then calculated from all initial scores for the event. For example:
• For pseudo paired read #1 - For 100 bps, 100% aligned to each side of the event, so the initial score is set at 100%.
• For pseudo paired read #2 - For 100 bps, there is a 2 bp mismatch, so the initial score is set at 98%.
• For pseudo paired read #3 - For 100 bps, there is a 50 bp mismatch, so the initial score is set at 50%.
The Median Score for this potential Structural Variant event would therefore be 98%, and you might call this event a true Structural Variation event based on such a high value for the Median Score.