The Breakpoints track (BP):
The breakpoints track contains a row for each called breakpoint with the following information:- 'Chromosome': The chromosome on which the breakpoint is located.
- 'Region': The location on the chromosome of the breakpoint.
- 'Name': The type of the breakpoint ('left breakpoint' or 'right breakpoint').
- 'p-value': The p-value (in the Binomial distribution) of the unaligned end breakpoint.
- 'Unaligned': The consensus sequence of the unaligned ends at the breakpoint.
- 'Unaligned length': The length of the consensus sequence of the unaligned ends at the breakpoint.
- 'Mapped to self': If the unaligned end sequence at the breakpoint was found to map back to the reference in the vicinity of the breakpoint itself, a 'Deletion' or 'Insertion' based on 'self-mapping' evidence is called. This column will contain 'Deletion' or 'Insertion' if that is the case, or be empty if the unaligned end did not map back to the reference in the vicinity of the breakpoint itself.
- 'Perfect mapped': The number of 'perfect mapped' reads. This number is intended as a proxy for the number of reads that fit with the reference sequence. When calculating this number we consider all reads that extend across the breakpoint. We ignore reads that are non-specifically mapped, in a broken pair, or has more than the maximum number of mismatches. A read is perfectly mapped if (1) it has no insertions or deletions (mismatches are allowed) and (2) it has no unaligned end.
- 'Not perfect mapped': The number of 'not perfect mapped' reads. This number is intended as a proxy for the number of reads that fit with the predicted indel. When calculating this number we consider all reads that extend across the breakpoint or that has an unaligned end starting at the breakpoint. We ignore reads that are non-specifically mapped, in a broken pair, or has more than the maximum number of mismatches. A read is not perfect mapped if (1) it has an insertion or deletion or (2) it has an unaligned end.
- 'Fraction non-perfectly mapped': the 'Non perfect mapped' divided by the 'Non perfect mapped' + 'Perfect mapped'.
- 'Sequence complexity': The sequence complexity of the unaligned end of the breakpoint (see section 25.2.7 for how the sequence complexity is calculated).
- 'Reads': The number of reads supporting the breakpoint.
Note that typically, breakpoints will be found for which it is not possible to infer a structural variant. There may be a number of reasons for that: (1) the unaligned ends from which the breakpoint signature was derived might not be caused by an underlying structural variant, but merely be due to read mapping issues or noise, or (2) the breakpoint(s) which the detected breakpoint should have been matched to was/were not detected, and therefore no matching breakpoint(s) were found. Breakpoints may go un-detected either because of lack of coverage in the breakpoint region or because they are located within regions with exclusively non-uniquely mapped reads (only unaligned ends of uniquely mapping reads are used).