We determine the nucleon axial, scalar and tensor charges within lattice Quantum Chromodynamics including all contributions from valence and sea quarks. We analyze three gauge ensembles simulated within the twisted mass formulation at approximately physical value of the pion mass. Two of these ensembles are simulated with two dynamical light quarks and lattice spacing $a=0.094$~fm and the third with $a=0.08$~fm includes in addition the strange and charm quarks in the sea. After comparing the results among these three ensembles, we quote as final values our most accurate analysis using the latter ensemble. For the nucleon isovector axial charge we find $1.286(23)$ in agreement with the experimental value. We provide the flavor decomposition of the intrinsic spin $frac{1}{2}DeltaSigma^q$ carried by quarks in the nucleon obtaining for the up, down, strange and charm quarks $frac{1}{2}DeltaSigma^{u}=0.431(8)$, $frac{1}{2}DeltaSigma^{d}=-0.212(8)$, $frac{1}{2}DeltaSigma^{s}=-0.023(4)$ and $frac{1}{2}DeltaSigma^{c}=-0.005(2)$, respectively. The corresponding values of the tensor and scalar charges for each quark flavor are also evaluated providing valuable input for experimental searches for beyond the standard model physics. In addition, we extract the nucleon $sigma$-terms and find for the light quark content $sigma_{pi N}=41.6(3.8)$~MeV and for the strange $sigma_{s}=45.6(6.2)$~MeV. The y-parameter that is used in phenomenological studies we find $y=0.078(7)$.
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