Table 2.
Simulations of mapping errors with MEM seeds.
| k | N | Not seeded | Seeded, not best | Relative error |
|---|---|---|---|---|
| 50 | 1 | 1.7 · 10−4 | 4.9 · 10−4 | 3.9 |
| 50 | 10 | 1.6 · 10−3 | 4.7 · 10−3 | 3.9 |
| 50 | 100 | 7.9 · 10−3 | 4.4 · 10−2 | 6.6 |
| 100 | 1 | 4.4 · 10−8 | 2.3 · 10−5 | 523.7 |
| 100 | 10 | 3.5 · 10−7 | 2.3 · 10−4 | 658.1 |
| 100 | 100 | 1.0 · 10−6 | 2.3 · 10−3 | 2301.0 |
Ideal reads were randomly generated 1,000,000 times with sequencing error rate p = 0.01, divergence rate μ = 0.06, varying the read size k and number N of duplicates as indicated, using skip-9 seeds of size γ = 19. The meanings of the columns are the same as in Table 1.