In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string $\widetilde{\bf X}$. Earlier works have proved that if each $x_k$ is deleted with the same probability $q\in[0,1)$, then $\exp(O(n^{1/3}))$ independent copies of the contracted string $\widetilde{\bf X}$ suffice to reconstruct $\bf x$ with high probability. We extend this upper bound to the setting where the deletion probabilities vary, assuming certain regularity conditions. First we consider the case where $x_k$ is deleted with some known probability $q_k$. Then we consider the case where each letter $ζ\in \{0,1,...,m-1\}$ is associated with some possibly unknown deletion probability $q_ζ$.