Table 2.
Variant calling performance with different reference genomes.
| Dataset | Reference Genome | #True-pos | #False-pos | #False-neg |
|---|---|---|---|---|
| HG001 (60X) | GRCh38 | 3,478,662 | 12,819 | 63,679 |
| GRCh38 + CPG | 3,478,639 | 12,206 (4.78% lower) | 63,702 | |
| HG002 (60X) | GRCh38 | 3,443,252 | 16,575 | 61,707 |
| GRCh38 + CPG | 3,443,250 | 16,025 (3.32% lower) | 61,709 | |
| HG005 (60X) | GRCh38 | 3,249,098 | 9895 | 59,116 |
| GRCh38 + CPG | 3,249,085 | 9,427 (4.73% lower) | 59,129 | |
| HG005 (300X) | GRCh38 | 3,252,032 | 6900 | 56,182 |
| GRCh38 + CPG | 3,252,026 | 6542 (5.19% lower) | 56,189 |
“CPG” represents the 46.646 Mbp common sequences.