Average time spent in an M/M/1 queue when incoming packets have a rejection probability.

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The mean time spent in an $M/M/1/\infty$ queue would be $\frac{1/\mu}{1-\rho}$, where $\rho = \lambda/\mu$ if I am not mistaken.

If the queue throws away incoming packets with probability $p=0.5$ how does the computation for the average time accepted packets spend in the system change?

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In this case you will have a Poisson process with rate $p\lambda$. And you can use the same expression for the performance measures.