Well, thank you very much cmdcolin for taking the time to properly explain breakends! I am really thankful for that.
I will take a look into the resources that you provided.
Based on a more concrete example, I have results like the one below to interpret:
> CONTIG TYPE POS EVENTLENGTH REF ALT
> Chromosome_contig SYMBOLIC 2256635 -1 G G]plasmid_contig:17079]
> plasmid_contig SYMBOLIC 17079 -1 A A]Chromosome_contig:2256635]
Does that mean that an inversion occcured with the chromosome and plasmid contigs?
What bugs me is that the event lenght is -1 bp and the genomic coordinates associated do not match with that event length…
Read more here: Source link