The Structural variants track contains a row for each of the called Structural variants that is not already reported in the InDel track.
It contains the following information:
- Chromosome: The chromosome on which the structural variant is located.
- Region: The location on the chromosome of the structural variant.
- Name: The type of the structural variant ('deletion', 'insertion', 'inversion', 'replacement', 'translocation' or 'complex').
- Evidence: The breakpoint mapping evidence ('that is, the 'unaligned end 'signature') on which the call of the structural variant was based. This may be either 'Self mapped', 'Paired breakpoint', 'Cross mapped breakpoints', 'Cross mapped breakpoints (invalid orientation)', 'Close breakpoints', 'Multiple breakpoints' or 'Tandem duplication', depending on which type of signature that was found.
- Length: the length of the allele sequence of the structural variant. Note that the length of variants for which the allele sequence could not be determined is reported as 0 (e.g insertions inferred from 'Close breakpoints').
- Reference sequence': The sequence of the reference in the region of the structural variant.
- Variant sequence: The allele sequence of the structural variant if it is known. If not, the column will be empty.
- Repeat: The same as in the InDel track.
- Variant ratio: The same as in the InDel track.
- Signatures: The number of unaligned breakpoints involved in the signature of the structural variant. In most cases these will be pairs of breakpoints, and the value is 2, however some structural variants that have signatures involving more than two breakpoint (See section 25.2.6). Typically structural variants of type 'complex' will be inferred from more than 2 breakpoint signatures.
- Left breakpoints: The positions of the 'Left breakpoints' involved in the signature of the structural variant.
- Right breakpoints: The positions of the 'Right breakpoints' involved in the signature of the structural variant.
- Mapping scores fraction: The mapping scores of the unaligned ends for each of the breakpoints. These are the similarity values between the unaligned end and the region of the reference to which it was mapped. The values lie between 0 and 1. The closer the value is to 1, the better the match, suggesting better reliability of the inferred variant.
- Reads: The total number of reads supporting the breakpoints from which the indels was constructed.
- Sequence complexity: The sequence complexity of the unaligned end of the breakpoint (see section 25.2.7).
- Split group: Some structural variants extend over a very large a region. For these visualization is challenging, and instead of reporting them in a single row we split them in multiple rows - one for each 'end' of the variant. To allow the user to see which of these 'split features' belong together, we give features that belong to the same structural variant a common 'split group' identifier. If the column is empty the structural variant is not split, but contained within a single row.