TABLE 3.
Basic statistics for Mutect2 variants in Polizzello ancient sequences.
| Sample | TP | TN | FP | FN | PPV | SN | SPC | FNR | FPR | NPV | FDR | FOR | ACC |
| Pol-1 | 34 | 16528 | 1 | 6 | 0.97 | 0.85 | 1.00 | 0.15 | 6.0E-05 | 1.00 | 0.03 | 3.63E-04 | 1.00 |
| Pol-2 | 30 | 16534 | 1 | 4 | 0.97 | 0.88 | 1.00 | 0.12 | 6.0E-05 | 1.00 | 0.03 | 2.42E-04 | 1.00 |
| Pol-3 | 26 | 16536 | 2 | 5 | 0.93 | 0.84 | 1.00 | 0.16 | 1.2E-04 | 1.00 | 0.07 | 3.02E-04 | 1.00 |
| Pol-4 | 8 | 16557 | 0 | 4 | 1.00 | 0.67 | 1.00 | 0.33 | 0.0E+00 | 1.00 | 0.00 | 2.42E-04 | 1.00 |
| Pol-5 | 8 | 16559 | 0 | 2 | 1.00 | 0.80 | 1.00 | 0.20 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-6 | 34 | 16531 | 1 | 3 | 0.97 | 0.92 | 1.00 | 0.08 | 6.0E-05 | 1.00 | 0.03 | 1.81E-04 | 1.00 |
| Pol-7 | 33 | 16534 | 0 | 2 | 1.00 | 0.94 | 1.00 | 0.06 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-9 | 25 | 16542 | 0 | 2 | 1.00 | 0.93 | 1.00 | 0.07 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-10 | 11 | 16553 | 1 | 4 | 0.92 | 0.73 | 1.00 | 0.27 | 6.0E-05 | 1.00 | 0.08 | 2.42E-04 | 1.00 |
| Pol-11 | 35 | 16527 | 0 | 7 | 1.00 | 0.83 | 1.00 | 0.17 | 0.0E+00 | 1.00 | 0.00 | 4.23E-04 | 1.00 |
| Pol-12 | 32 | 16533 | 1 | 3 | 0.97 | 0.91 | 1.00 | 0.09 | 6.0E-05 | 1.00 | 0.03 | 1.81E-04 | 1.00 |
| Pol-13 | 11 | 16556 | 0 | 2 | 1.00 | 0.85 | 1.00 | 0.15 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-14 | 7 | 16560 | 0 | 2 | 1.00 | 0.78 | 1.00 | 0.22 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-15 | 13 | 16553 | 0 | 3 | 1.00 | 0.81 | 1.00 | 0.19 | 0.0E+00 | 1.00 | 0.00 | 1.81E-04 | 1.00 |
| Pol-16 | 18 | 16547 | 0 | 4 | 1.00 | 0.82 | 1.00 | 0.18 | 0.0E+00 | 1.00 | 0.00 | 2.42E-04 | 1.00 |
| Pol-17 | 25 | 16536 | 1 | 7 | 0.96 | 0.78 | 1.00 | 0.22 | 6.0E-05 | 1.00 | 0.04 | 4.23E-04 | 1.00 |
| Pol-18 | 26 | 16535 | 2 | 6 | 0.93 | 0.81 | 1.00 | 0.19 | 1.2E-04 | 1.00 | 0.07 | 3.63E-04 | 1.00 |
| Pol-21 | 23 | 16539 | 1 | 6 | 0.96 | 0.79 | 1.00 | 0.21 | 6.0E-05 | 1.00 | 0.04 | 3.63E-04 | 1.00 |
| Pol-22 | 8 | 16555 | 3 | 3 | 0.73 | 0.73 | 1.00 | 0.27 | 1.8E-04 | 1.00 | 0.27 | 1.81E-04 | 1.00 |
| Pol-23 | 30 | 16534 | 0 | 5 | 1.00 | 0.86 | 1.00 | 0.14 | 0.0E+00 | 1.00 | 0.00 | 3.02E-04 | 1.00 |
| Pol-24 | 11 | 16554 | 1 | 3 | 0.92 | 0.79 | 1.00 | 0.21 | 6.0E-05 | 1.00 | 0.08 | 1.81E-04 | 1.00 |
| Pol-25 | 8 | 16556 | 0 | 5 | 1.00 | 0.62 | 1.00 | 0.38 | 0.0E+00 | 1.00 | 0.00 | 3.02E-04 | 1.00 |
| Pol-26 | 30 | 16536 | 0 | 3 | 1.00 | 0.91 | 1.00 | 0.09 | 0.0E+00 | 1.00 | 0.00 | 1.81E-04 | 1.00 |
| Pol-27 | 28 | 16538 | 1 | 2 | 0.97 | 0.93 | 1.00 | 0.07 | 6.0E-05 | 1.00 | 0.03 | 1.21E-04 | 1.00 |
| Pol-28 | 10 | 16557 | 0 | 2 | 1.00 | 0.83 | 1.00 | 0.17 | 0.0E+00 | 1.00 | 0.00 | 1.21E-04 | 1.00 |
| Pol-29 | 8 | 16556 | 0 | 5 | 1.00 | 0.62 | 1.00 | 0.38 | 0.0E+00 | 1.00 | 0.00 | 3.02E-04 | 1.00 |
| Pol-30 | 19 | 16547 | 0 | 3 | 1.00 | 0.86 | 1.00 | 0.14 | 0.0E+00 | 1.00 | 0.00 | 1.81E-04 | 1.00 |
| Mean | 20.41 | 16544.19 | 0.59 | 3.81 | 0.97 | 0.82 | 1.00 | 0.18 | 0.00 | 1.00 | 0.03 | 2.31E-04 | 1.00 |
| Median | 23.00 | 16542.00 | 0.00 | 3.00 | 1.00 | 0.83 | 1.00 | 0.17 | 0.00 | 1.00 | 0.00 | 1.81E-04 | 1.00 |
Basic statistics related to the variants detected in each sample by means of Mutect2 and our filtering protocol [including minimum allele depth (AD) = 10 and minimum allele fraction (AF) = 50%] were obtained by taking as reference variants those inserted by schmutzi in the endogenous consensus sequences. TP, true positives (all variants detected by Mutect2 and retained by our filtering process, also detected in schmutzi consensus sequences); TN, true negatives (all non-variant and non-callable sites according to both methods); FP, false positives (reliable variants detected exclusively by Mutect2); FN, false negatives (variants detected exclusively by schmutzi, without considering those detected by Mutect2 and discarded by our filtering pipeline); PPV, positive predictive value or precision; SN, true positive rate or sensitivity (recall); SPC, true negative rate or specificity; FNR, false negative rate or miss rate; FPR, false positive rate or fallout; NPV, negative predictive value; FDR, false discovery rate; FOR, false omission rate; ACC, accuracy. Mean and median are also reported for the whole dataset.