Table A1.
Primary analysis: Distribution of variants with the mutserve variant calling method (VCM).
| Variant Description | PCP | TSS | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Broad Classification |
Detailed Classification |
N | Mean Observed VL | Mean Primary VL | Mean Absolute Difference in VLs | N | Mean Observed VL | Mean Primary VL | Mean Absolute Difference in VLs |
| [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | ||||
| Grade A variant found | including exome | 79 | 99.73% [98.50%–100.00%] |
99.61% [97.03%–100.00%] |
0.44% [0.00%–2.73%] |
77 | 99.43% [98.20%–100.00%] |
99.60% [97.03%–100.00%] |
0.65% [0.00%–2.77%] |
| Grade B variant found | including exome | 5 | 26.06% [3.50%–92.50%] |
28.59% [2.57%–94.77%] |
2.91% [0.93%–7.47%] |
2 | 55.65% [19.60%–91.70%] |
58.57% [22.37%–94.77%] |
2.92% [2.77%–3.07%] |
| excluding exome | 8 | 7.07% [2.50%–28.40%] |
6.36% [1.10%–28.35%] |
0.79% [0.05%–2.10%] |
1 | 28.30% | 28.35% | 0.05% | |
| Grade C variant found | from highCov | - | - | - | - | 1 | 21.70% | 0.40% | 21.30% |
| Grade A variant lost | including exome | - | - | - | - | 2 | - | 100.00% [100.00%–100.00%] |
- |
| Grade B variant lost | including exome | 4 | - | 0.88% [0.50%–1.27%] |
- | 7 | - | 4.19% [0.50%–17.37%] |
- |
| excluding exome | 34 | - | 1.10% [0.40%–5.75%] |
- | 41 | - | 1.46% [0.40%–6.20%] |
- | |
| from lowCov and exome | 2 | - | 0.48% [0.45%–0.50%] |
- | 2 | - | 0.48% [0.45%–0.50%] |
- | |
| Grade C variant lost | from highCov | 177 | - | 0.82% [0.40%–5.80%] |
- | 176 | - | 0.83% [0.40%–5.80%] |
- |
| from lowCov | 12 | - | 0.93% [0.40%–3.80%] |
- | 12 | - | 0.93% [0.40%–3.80%] |
- | |
| from exome | 4 | - | 0.70% [0.40%–1.00%] |
- | 4 | - | 0.70% [0.40%–1.00%] |
- | |
| Novel variant | Only present in Ion Torrent | 1 | 2.70% | - | - | 2 | 25.15% [19.30%–31.00%] |
- | - |
Abbreviations: PCP—PrecisionCallerPipeline; TSS—Ion Torrent Suite™ Software; N—number; VL—variant level; Min—minimum; Max—maximum.