At $p=0.5$\%, NaiveFreq identified 249, 17,069, and 1,632 rare $p$-mutations in the CAMP, BACT1, and BACT2 MAGs, respectively. This illustrates that there exists a difference of nearly two orders of magnitude in mutation rates across these MAGs ($6.4 \times 10^{-5}$, $2.6 \times 10^{-3}$, and $1.9 \times 10^{-4}$ for CAMP, BACT1, and BACT2, respectively). If the CAMP MAG, which has a relatively low mutation rate, is selected as a decoy, then the FDR for the BACT1 MAG at $p=0.5\%$ is estimated as $\frac{6.4 \times 10^{-5}}{2.6 \times 10^{-3}} \approx 2.4\%$.\endinput