TABLE 4.
Evaluation of assembly by variant calling. The values before the slash are generated by default parameters while values after are with “-squash-ploidy”, which allows matches that ignore the haplotyping difference.
| Variation type | Variation subtype | Metric | stLFRdenovo | NECAT | AsmMix |
|---|---|---|---|---|---|
| SNV | SNP | TP | 2,330,486/2,523,914 | 1,161,996/2,067,723 | 2,536,637/2,779,428 |
| FN | 698,572/505,144 | 1,867,062/961,337 | 492,421/249,635 | ||
| FP | 253,797/60,369 | 975,393/69,669 | 291,137/48,351 | ||
| Precision | 0.9018/0.9766 | 0.5437/0.9674 | 0.8970/0.9829 | ||
| Sensitivity | 0.7694/0.8332 | 0.4498/0.6826 | 0.8374/0.9176 | ||
| Indel | TP | 334,312/377,364 | 162,087/284,873 | 358,833/408,144 | |
| FN | 125,053/82,001 | 297,278/174,492 | 100,541/51,200 | ||
| FP | 72,872/29,827 | 355,587/232,840 | 97,589/48,279 | ||
| Precision | 0.8210/0.9268 | 0.3131/0.5502 | 0.7862/0.9842 | ||
| Sensitivity | 0.7278/0.8215 | 0.3529/0.6201 | 0.7811/0.8885 | ||
| SV | Insertion | TP | 1811 | 3,752 | 3,906 |
| FN | 3,631 | 1779 | 1,659 | ||
| FP | 539 | 343 | 627 | ||
| Precision | 0.7707 | 0.9162 | 0.8616 | ||
| Sensitivity | 0.3329 | 0.6784 | 0.7018 | ||
| Deletion | TP | 2,750 | 2,420 | 2,539 | |
| FN | 1,449 | 1,690 | 1,537 | ||
| FP | 5,983 | 763 | 1,223 | ||
| Precision | 0.3148 | 0.7603 | 0.6749 | ||
| Sensitivity | 0.6548 | 0.5888 | 0.6229 | ||
| Haplotyping | Phased SNP Ratio | 0.6881 | - | 0.7224 | |
| Short Switch Ratio | 0.0515 | - | 0.0502 | ||
| Long Switch Ratio | 0.0008 | - | 0.0007 | ||
| Phasing Block N50 | 4,802,248 | - | 5,015,779 | ||