It would be useful to have more information about what exactly you're looking at or an example of your data output. The most common display of ChipSeq data shows peaks bound to a certain area of the genome (with the locus on the X axis). If this is what you're talking about, then the Y axis shows normalized read counts, which (very basically) represents the number of times an antibody bound to that specific sequence during the experiment. I.e., a larger peak indicates that this site is more commonly bound by the transcription factor you're analyzing. Multiple types of normalization can be used to get the final output depending on the software used and the preferences of the statistician, but the basic function of this is to elucidate which peaks are real and reduce background noise.

Does that help?

Dear Chani

Thank you for your answer. Ya it really helpful...