= Solution
Define the evaluation universe first, including which sufficiently covered loci were eligible for both methods. Relative to the reference assay's labels,
$$
\boxed{\operatorname{TPR}=\frac{TP}{TP+FN},\qquad\operatorname{FPR}=\frac{FP}{FP+TN}.}
$$
The <true positive rate> is the fraction of reference-positive loci retained by <xPore>; the <false positive rate> is the fraction of reference-negative loci incorrectly retained. The latter is not the fraction of <xPore> calls that fail validation.
An imperfect reference assay can miss real modifications. “False positive” here therefore <means> disagreement with that reference, not independently demonstrated absence of a modification. Restricting the universe differently for the two denominators would invalidate the comparison.
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