We study the effects of flavor symmetry breaking on holographic dense matter and compact stars in the D4/D6 model. To this end, two light flavors and one intermediate mass flavor are considered. For two light quarks, we investigate how the strong isospin violation affects the properties of holographic dense matter and compact stars. We observe that quark-antiquark condensates are flavor dependent and show interesting behavior near the transition from dense matter with only one flavor to matter with two flavors. An intermediate mass quark is introduced to investigate the role of the third flavor. The mass-radius relations of holographic compact stars with three flavors show that the mass-radius curve changes drastically at a transition density from which the third flavor begins to appear in the matter.
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