We report a systematic investigation on c-axis point-contact Andreev reflection (PCAR) in BaFe$_{2-x}$Ni$_x$As$_2$ superconducting single crystals from underdoped to overdoped regions (0.075 $leq xleq 0.15$). At optimal doping ($x=0.1$) the PCAR spectrum feature the structures of two superconducting gap and electron-boson coupling mode. In the $spm$ scenario, quantitative analysis using a generalized Blonder-Tinkham-Klapwijk (BTK) formalism with two gaps: one isotropic and another angle dependent, suggest a nodeless state in strong-coupling limit with gap minima on the Fermi surfaces. Upon crossing above the optimal doping ($x > 0.1$), the PCAR spectrum show an in-gap sharp narrow peak at low bias, in contrast to the case of underdoped samples ($x < 0.1$), signaling the onset of deepened gap minima or nodes in the superconducting gap. This result provides evidence of the modulation of the gap amplitude with doping concentration, consistent with the calculations for the orbital dependent pair interaction mediated by the antiferromagnetic spin fluctuations.
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