Table 2.
Summary of a subset of results found in this analysis
| Short Name | Kapa | NEB | PBAT | Swift | Low NEB | Low Swift | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | A | B | A | B | A | B | A | B | A | B | A | B |
| # Sequenced Reads (Millions) | 347.5 | 607.9 | 355.6 | 389.9 | 127.9 | 124.1 | 395.8 | 368.2 | 453.7 | 408.6 | 392.7 | 449.8 |
| Low Quality Bases Trimmed (R1) | 2.3 | 1.8 | 1.0 | 1.0 | 0.9 | 0.9 | 0.6 | 0.6 | 1.2 | 1.1 | 1.1 | 0.8 |
| Low Quality Bases Trimmed (R2) | 2.0 | 1.7 | 1.1 | 1.0 | 5.9 | 3.4 | 0.7 | 0.7 | 1.2 | 1.2 | 1.0 | 0.8 |
| Insert Size | 208.1 | 228.0 | 285.4 | 297.8 | 299.3 | 300.6 | 222.1 | 225.0 | 291.4 | 290.8 | 217.9 | 223.8 |
| Duplicate Rate | 27.5 | 32.4 | 9.5 | 9.9 | 13.5 | 11.0 | 12.8 | 12.1 | 18.0 | 16.2 | 30.7 | 26.9 |
| % CpGs Covered | 74.0 | 72.3 | 87.5 | 87.6 | 81.8 | 82.6 | 85.6 | 85.2 | 87.6 | 87.6 | 85.5 | 85.3 |
| % CpG Retention | 81.6 | 79.0 | 78.5 | 75.6 | 74.0 | 71.1 | 80.3 | 77.5 | 77.8 | 74.8 | 79.4 | 76.9 |
All values shown are averaged across the two technical replicates, with the exception of PBAT, which only had one technical replicate. The first four rows are taken from the raw data, while the last three rows are taken from the subsampled data, where the BAMs were downsampled to be comparable to PBAT