Genomic context analysis can indicate mutational mechanisms causing SVs.

<p>(A) DNA sequence and insertion frequency of the 10 most commonly inserted sequences identified within the control genome. For the tumor the tenth most frequently inserted sequence corresponds to CA with 897 insertions. For the sake of a clear representation the eleventh most frequently inserted sequence (AAA, 894 insertions) is shown. (B) The fraction of single base insertions within simple repeats consisting of the same base type, computed with respect to all single base insertions. Simple repeats of a minimum length of 4 were considered. (C) A genome browser view of a genomic locus containing two insertions (I/V), two deletions (II/IV) and one tandem duplication (III). As indicated by the discordant coverage and horizontal bars, these high-confidence SVs are both identified within the tumor and the control genomes, and have therefore been inherited from the parental strains.