Table 3.
Scaffolded assembly statistics after Hi-C analysis on HapSolo assemblies, for three primary assemblies for each of three species
| Species | Chardonnay | Mosquito | Thorny Skatef | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Assembly type | No HapSoloa | HapSolo −HCb | HapSolo +HCc | No HapSolo | HapSolo −HC | HapSolo +HC | No HapSolo | HapSolo −HC | HapSolo +HC |
| # of Scaffolds | 1332 | 2748 | 2403 | 1211 | 603 | 611 | 14,238 | 12,269 | 10,009 |
| % of Genome in k largest scaffoldsd,e | 52.0% | 89.0% | 84.0% | 61.9% | 68.3% | 85.7% | 31.5% | 104.7% | 106.3% |
| % of Genome in Scaffolds > 10Mbe | 44.0% | 94.0% | 94.0% | 93.5% | 94.7% | 94.1% | 40.4% | 103.3% | 105.5% |
| Scaffold assembly size (Mb) | 656.1 | 570.4 | 540.1 | 212.5 | 200.8 | 200.3 | 3240 | 3158 | 3039 |
| Largest scaffold (Mb) | 19.1 | 32.6 | 36.5 | 43.6 | 53.0 | 95.0 | 170.0 | 208.4 | 250.5 |
| Scaffold N50 (Mb) | 7.2 | 23.5 | 20.7 | 37.9 | 41.5 | 41.6 | 62.1 | 65.5 | 69.8 |
| Scaffold L50 | 28 | 11 | 11 | 3 | 3 | 2 | 16 | 35 | 13 |
aResults in this column were based on the primary assembly without application of HapSolo
bResults in this column were based on application of HapSolo without hill climbing (−HC) and default parameters of ID, Q and QR
cResults in this column were based on application of HapSolo with 50,000 cycles of hill climbing (+HC)
dPercentage of genome in the largest k scaffolds, where k is equal to the number of chromosomes expected for each species
ePercentages normalized using expected genome sizes of 490 Mb, 200 Mb and 2560 Mb for chardonnay, mosquito and thorny skate respectively
fResults for HapSolo were generated using minimap2