We determine the contribution to the anomalous magnetic moment of the muon from the $alpha^2_{mathrm{QED}}$ hadronic vacuum polarization diagram using full lattice QCD and including $u/d$ quarks with physical masses for the first time. We use gluon field configurations that include $u$, $d$, $s$ and $c$ quarks in the sea at multiple values of the lattice spacing, multiple $u/d$ masses and multiple volumes that allow us to include an analysis of finite-volume effects. We obtain a result for $a_{mu}^{mathrm{HVP,LO}}$ of $667(6)(12)$, where the first error is from the lattice calculation and the second includes systematic errors from missing QED and isospin-breaking effects and from quark-line disconnected diagrams. Our result implies a discrepancy between the experimental determination of $a_{mu}$ and the Standard Model of 3$sigma$.
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