We delineate equilibrium phase structure and topological charge distribution of dense two-colour QCD at low temperature by using a lattice simulation with two-flavour Wilson fermions that has a chemical potential $mu$ and a diquark source $j$ incorporated. We systematically measure the diquark condensate, the Polyakov loop, the quark number density and the chiral condensate with improved accuracy and $jto0$ extrapolation over earlier publications; the known qualitative features of the low temperature phase diagram, which is composed of the hadronic, Bose-Einstein condensed (BEC) and BCS phases, are reproduced. In addition, we newly find that around the boundary between the hadronic and BEC phases, nonzero quark number density occurs even in the hadronic phase in contrast to the prediction of the chiral perturbation theory (ChPT), while the diquark condensate approaches zero in a manner that is consistent with the ChPT prediction. At the highest $mu$, which is of order the inverse of the lattice spacing, all the above observables change drastically, which implies a lattice artifact. Finally, at temperature of order $0.45T_c$, where $T_c$ is the chiral transition temperature at zero chemical potential, the topological susceptibility is calculated from a gradient-flow method and found to be almost constant for all the values of $mu$ ranging from the hadronic to BCS phase. This is a contrast to the case of $0.89T_c$ in which the topological susceptibility becomes small as the hadronic phase changes into the quark-gluon plasma phase.
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