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Table 11 Definitions used for metrics calculations

From: Comparison of the performance of an amplicon sequencing assay based on Oxford Nanopore technology to real-time PCR assays for detecting bacterial biodefense pathogens

Metric

Description

Function

True Positive (TP)

Result is positive, key is positive

 

True Negative (TN)

Result is negative, key is negative

 

False Positive (FP)

Result is positive, key is negative

 

False Negative (FN)

Result is negative, key is positive

 

Precision (PPV)

Positive Predictive Value; number of TP of result positives

TP/(TP + FP)

Recall (TPR)

Sensitivity; number of TP out of all key positives

TP/(TP + FN)

Specificity (TNR)

Number of TN out of all key negatives

TN/(FP + TN)

False Positive Rate (FPR)

Number of false positives out of all key negatives

FP/(FP + TN)

  1. Each sample from real-time PCR and sequencing was measured for a target assay (columns faceted along top of Figs. 7, 8, 9, 10). Under Description, ‘Result’ is in reference to a real-time PCR Ct value or a sequence mapped count above (negative for PCR, positive for sequencing) or below (positive for PCR, negative for sequencing) a particular threshold. These definitions were used to generate the Precision-recall (PR) and Receiver Operator Characteristic (ROC) curves in Figs. 7, 8, 9, 10. A range of thresholds was employed for the generation of PR and ROC curves