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Abstract We consider the compactifcation of 5d non-simply laced fractional quiver gauge theory constructed in [1]. In contrast to the simply laced quivers, here two Ω-background parameters play different roles, so that we can take two possible Nekrasov-Shatashvili limits. We demonstrate how different quantum integrable systems can emerge from these two limits, using BC 2-quiver as the simplest illustrative example for our general results. We also comment possible connections with compactified 3d non-simply laced quiver gauge theory.