We consider the BACT1 genome at the threshold $p = 0.5\%$.
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In this genome, there are $N'$ = 1,942,314 nucleotides
located throughout all sense codons (we ignore stop codons in the reference genome).
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BACT1 has $J$ = 5,525,851 possible non-nonsense and
$K$ = 301,091 possible nonsense single-nucleotide mutations.
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Using $p = 0.5\%$, BACT1 contains
$X$ = 12,185 non-nonsense and
$Y$ = 15 nonsense rare single-nucleotide mutations.
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At $p = 0.5\%$, then, the ratio of observed to possible non-nonsense single-nucleotide mutations
($R_{NNS} = X / J = \frac{12,185}{5,525,851}
\approx 0.00221$)
is larger than the ratio of observed to possible nonsynonymous single-nucleotide mutations
($R_{NS} = Y / K = \frac{15}{301,091}
\approx 0.00005$)
for BACT1.
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