Importance of "independent" under-graduate research in graduate admissions
In an application, list all material that shows you in a positive light. Being able to perform successful research, both on your own and under supervision, is good. The fact that you engaged, on your own (or with friends) on research and were able to publish it (I assume in a peer-reviewed journal) is a plus for your application… unless the quality of the paper is really (visibly) bad.