Table 6.
SNP detection in sequenced samples
| Variant filtering conditions | Sample name | Number of SNPs | Precision | Sensitivity |
|---|---|---|---|---|
| VQSLOD > 0 | EOM (13) | 12,734 | 65.25% | 45.09% |
| LOM (10) | 12,730 | 67.16% | 46.40% | |
| ENM (1) | 2269 | 84.93% | 10.49% | |
| LNM (1) | 9235 | 67.29% | 33.83% | |
| Dd2 bulk (1) | 18,369 | – | – | |
| COM (2) | 8851 | 31.55% | 15.22% | |
| VQSLOD > 6 | EOM (13) | 6917 | 91.75% | 46.22% |
| LOM (10) | 6990 | 92.40% | 47.05% | |
| ENM (1) | 1375 | 96.58% | 9.68% | |
| LNM (1) | 4902 | 95.17% | 33.99% | |
| Dd2 bulk (1) | 13,725 | – | – | |
| COM (2) | 3162 | 66.69% | 15.37% | |
| VQSLOD > 6, read depth > 10 | EOM (13) | 3937 | 99.48% | 29.74% |
| LOM (10) | 4360 | 99.41% | 32.92% | |
| ENM (1) | 252 | 97.62% | 1.87% | |
| LNM (1) | 2575 | 98.87% | 19.33% | |
| Dd2 bulk (1) | 13,168 | – | – | |
| COM (2) | 1021 | 79.28% | 6.13% |
*Precision and sensitivity are calculated by using SNPs detected in Dd2 bulk sample as the standard SNP set