I ran HOMER's findPeaks.pl on a tissue sample and uncovered 46,811 total peaks. Running annotatePeaks.pl on this peak file yielded me 56,948 annotated regions in the output file. The breakdown of the annotated regions is as follows:

exon: 8712

Intergenic: 15450

intron: 21387

promoter-TSS: 9285

TTS: 2114

I'm not sure the breakdown is important here, but I was hoping to perhaps find some explanation as to why these results are the way that they are? Cheers,