When BreakPointer finshes it creates a tab delimited file with 12 columns described below:
1. Serial number of the breakpoint.
2. Line number in the "rearrangement_predictions" input file.
3. First chromosome.
4. Predicted location on first chromosome.
5. Second chromosome.
6. Predicted location on second chromosome.
7. Is this rearrangement an inversion? (0 = No inversion; 1 = An inversion).
8. The number of split reads BreakPointer found that support this rearrangement (since BreakPointer stops after aligning "align_enough_reads" reads, it is never more than that).
9. The average score of the alignment of all supporting reads found.
10. Which sequence comes first in the rearranged genome (0 = First sequence; 1 = Second sequence).
11. The length of non template DNA inserted at the breakpoint.
12. The non template DNA inserted at the breakpoint.