Table A2.
Mixture analysis: Distribution of variants with the mutserve VCM.
| Variant Description | PCP | TSS | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Macro | Meso | Micro | N | Mean Observed VL | Within Platform |
Other Platforms |
N | Mean Observed VL | Within Platform |
Other Platforms |
| Mean Absolute Difference in VLs | Mean Absolute Difference in VLs | Mean Absolute Difference in VLs | Mean Absolute Difference in VLs | |||||||
| [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | [Min–Max] | |||||
| Found variants | Found variants | Major Grade A | 270 | 92.51% [51.50%–100.00%] |
3.51% [0.00%–22.90%] |
3.73% [0.00%–23.42%] |
260 | 92.10% [56.80%–100.00%] |
3.40% [0.10%–18.20%] |
3.55% [0.00%–18.15%] |
| Major Grade B | 39 | 20.82% [2.60%–94.30%] |
1.73% [0.16%–6.32%] |
2.09% [0.29%–6.10%] |
15 | 43.18% [11.80%–94.20%] |
2.26% [0.14%–6.29%] |
2.25% [0.08%–4.98%] |
||
| Major Grade C | - | - | - | - | 5 | 28.48% [22.30%–34.10%] |
8.65% [1.03%–13.49%] |
28.11% [21.91%–33.72%] |
||
| Minor Grade A | 133 | 16.95% [2.50%–52.90%] |
4.38% [0.02%–28.00%] |
4.41% [0.06%–28.20%] |
73 | 25.31% [11.00%–48.30%] |
5.73% [0.00%–23.50%] |
5.75% [0.02%–23.60%] |
||
| Minor Grade B | 8 | 7.54% [3.30%–26.00%] |
1.90% [0.32%–3.95%] |
1.72% [0.14%–4.18%] |
1 | 26.30% | 3.38% | 2.61% | ||
| Shared Grade A | 125 | 99.89% [99.20%–100.00%] |
0.09% [0.00%–0.40%] |
0.20% [0.00%–2.41%] |
125 | 99.64% [98.60%–100.00%] |
0.20% [0.00%–1.30%] |
0.45% [0.00%–2.71%] |
||
| Mixture found variants | Major Grade B | 9 | 4.08% [2.60%–5.70%] |
- | 0.44% [0.03%–1.69%] |
4 | 12.60% [11.90%–13.20%] |
- | 3.12% [0.83%–3.99%] |
|
| Lost variants | Mixture lost variants | Major Grade B | 26 | - | 2.77% [1.88%–3.56%] |
2.00% [0.83%–2.72%] |
- | - | - | - |
| Minor Grade A | 137 | - | 2.44% [0.98%–24.80%] |
2.44% [0.97%–24.98%] |
187 | - | 3.86% [0.98%–10.00%] |
3.87% [0.97%–10.00%] |
||
| Minor Grade B | 57 | - | 0.48% [0.03%–4.63%] |
0.48% [0.01%–4.74%] |
14 | - | 2.65% [0.20%–9.17%] |
2.78% [0.22%–9.48%] |
||
| Old lost variants | Major Grade A | - | - | - | - | 10 | - | - | 91.40% [75.00%–99.00%] |
|
| Major Grade B | 186 | - | - | 0.81% [0.30%–2.70%] |
241 | - | - | 1.44% [0.30%–16.50%] |
||
| Major Grade C | 430 | - | - | 0.72% [0.30%–5.74%] |
425 | - | - | 0.73% [0.30%–5.74%] |
||
| Minor Grade A | - | - | - | - | 10 | - | - | 8.60% [1.00%–25.00%] |
||
| Minor Grade B | 195 | - | - | 0.09% [0.00%–1.44%] |
245 | - | - | 0.16% [0.00%–4.34%] |
||
| Minor Grade C | 430 | - | - | 0.06% [0.00%–0.95%] |
425 | - | - | 0.06% [0.00%–0.95%] |
||
| Shared Grade C | 540 | - | - | 0.86% [0.40%–2.69%] |
540 | - | - | 0.86% [0.40%–2.69%] |
||
| Novel variants | Found variants | Minor novel | - | - | - | - | 5 | 21.24% [16.80%–26.00%] |
18.07% [11.98%–24.07%] |
- |
| Shared novel | - | - | - | - | 4 | 31.65% [28.00%–35.10%] |
12.10% [8.10%–15.78%] |
- | ||
| Novel variants | Novel variant: mixture | 12 | 27.26% [2.50%–99.20%] |
- | - | 9 | 13.92% [10.60%–21.10%] |
- | - | |
| Primary novel variants | Mixture lost variants | Major novel | 5 | - | 2.47% [2.02%–2.67%] |
- | 5 | - | 28.33% [23.25%–30.69%] |
- |
| Minor novel | 5 | - | 0.23% [0.03%–0.68%] |
- | 5 | - | 1.15% [0.19%–3.10%] |
- | ||
| Shared novel | - | - | - | - | 1 | - | 19.35% | - | ||
Abbreviations: PCP—PrecisionCallerPipeline; TSS—Ion Torrent Suite™ Software; N—number; VL—variant level; Min—minimum; Max—maximum.