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We correlate phase-contrast microscopy of modification tracks induced by tightly focused single ultrashort and short laser pulses inside fused silica with numerical simulations of nonlinear laser excitation footprints. Different pulse durations on the femtosecond and picosecond range are compared in order to validate the experimental and theoretical observations on the subsequent refractive index variations in a regime where linear and nonlinear contributions play a comparable role. The nature of the laser-induced structural changes depends essentially on the characteristics of pulse propagation in different regions of the irradiated zone. Numerical simulations of laser pulse propagation in the excited region show that accumulation of excess energy and swift nonlinear absorption contribute to the formation of either positive or negative phase-shift regions within the same single-pulse-induced damage trace. The decrease in the refractive index can be unambiguously correlated with the regions of maximum energy deposition during prolonged exposure times.