Displaced fragment length distribution in ATAC-seq

Question

[enanoide]

Hi, I'm fairly new to ATAC-seq and I would like to ask the community about the fragment length distribution that my results have yielded.

Following numerous guidelines and tutorials in the field, I would have expected a first peak corresponding to nucleosome-free signal, and the decreasing peaks corresponding to mono/di nucleosomes, etc

How could a figure like this one be interpreted? The largest peak is the second one, right? Does it mean that the transposition has not worked as it should and the nucleosome signal is larger than nucleosome-free signal? Could it be that the nucleosome-free signal is displaced as this a non-model organism? But then what would be the first peak be?

Any insights, would be much appreciated, thanks for your time

[ATpoint]

Which protocol was used for the experiment (OmniATAC?) and which celltype is that? Have mitochondrial alignments been removed? Looks odd in the sense that you don't really see a banding ladder. The first peak is excessively high, indicating either overdigestion or excess of mitochondrial reads.