Table 1 Large structural variations defined in this study
From: Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
Type of variation | Definition |
|---|---|
Large deletion | A genomic sequence revealed as a gap between adjacent and co-linear aligned segments or HSPs (Figure 5a) |
Type-A insertion | An unaligned portion of a read that is flanked by two HSPs of the same read, (Figure 6a) |
Type-B insertion | The flanking regions of two or more convergent reads are not aligned to the genome. These unaligned flanking regions might represent the 5′ and 3′ ends of a putative large insertion (Figure 6c) |
Deletions associated with type-A insertions | Co-occurring deletion and type-A insertion where the deletion is equal or larger than the type-A insertion at the same breakpoint (Figure 8a, left) |
Type-A insertions associated with deletions | Co-occurring type-A insertion and deletion where the type-A insertion is larger than the deletion at the same breakpoint (Figure 8a, right) |
Type-B insertions associated with deletions | Co-occurring type-B insertion and deletion where the type-B insertion pattern for which the convergent reads are at a distance larger than zero (Figure 8b) |