  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 $\frac{1}{2}\Delta\Sigma^q$ carried by quarks in the nucleon obtaining for
the up, down, strange and charm quarks $\frac{1}{2}\Delta\Sigma^{u}=0.431(8)$,
$\frac{1}{2}\Delta\Sigma^{d}=-0.212(8)$,
$\frac{1}{2}\Delta\Sigma^{s}=-0.023(4)$ and
$\frac{1}{2}\Delta\Sigma^{c}=-0.005(2)$, 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 $y=0.078(7)$.
