ABSTRACT Quantum Chromodynamics predicts phase transition from hadronic matter to quark matter at high density, which is highly probable in astrophysical systems like binary neutron star mergers. To explore the critical density where such phase transition can occur, we performed numerical relativity simulations of binary neutron star mergers with various masses (equal and unequal binaries). We aim to understand the effect of the onset of phase transition on the merger dynamics and gravitational wave spectra. We generated a set of equations of states by agnostically changing the onset of phase transition, having the hadronic matter part and quark matter part fixed. This particular arrangement of the equation of states explores the scenario of mergers where mixed phases of matter are achieved before or during the merger. Under these circumstances, if the matter properties with hadronic and quark degrees differ significantly, it is reflected in the stability of the final merger product for the intermediate mass binary. We performed a case study on mixed species merger, where one of the binary companions is hybrid star. If quark matter appears at low densities, we observe significant change in post-merger gravitational wave analysis in terms of higher peak frequencies and post-merger frequencies in power spectral density. We report indications expressed as spikes in phase difference plots at merger time for mixed mergers. We found that the expression of phase transition in post-merger gravitational wave signals is more significant for unequal mass binary than for equal mass binary having the same total baryonic mass.