I was looking at a simple visualization program that, among other things, visualized BED file with respect to the inputted FASTA ref sequence. I noticed that there were separate tracks for annotations and that there very many regions that were overlapping. I'm having a hard time understanding that, can someone explain to me how can coding regions overlap in a BED file?
edit: Since I see that I created somewhat of a confusion with my not-so-clear question, basically I'm asking if someone can explain to me how is it possible that coding regions overlap in a BED file.
For example, these are couple of lines from my
1 5262 5712 E4287_5.mRNA1 449 + . . . 1 450 0 mRNA 1 5262 5712 E4287_5 449 + . . . 1 450 0 gen ... 1 6729 7644 E4287_7 914 + . . . 1 915 0 gene 1 6729 7644 b0030 914 + . . . 1 915 0 CDS