For the BACT1 genome
(where $N$ = 1,947,597),
there are $J$ = 1,250,228 possible synonymous and
$K$ = 4,592,563 possible nonsynonymous single-nucleotide mutations.
(Note that $J + K = 3N$.)
%
Using the mutation frequency threshold $p = 0.5\%$,
the BACT1 genome contains
$X$ = 8,838 synonymous and
$Y$ = 3,378 nonsynonymous rare single-nucleotide mutations.
%
Thus, the ratio of observed to possible synonymous single-nucleotide mutations
($R_S = X / J = \frac{8,838}{1,250,228}
\approx 0.00707$)
is an order of magnitude larger than the ratio of observed to possible nonsynonymous single-nucleotide mutations
($R_N = Y / K = \frac{3,378}{4,592,563}
\approx 0.00074$)
for BACT1.
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