Table 3. Reference strain relative abundances expected and computed by StrainFLAIR or Kraken2 for each simulated experiment with variable coverage of the BL21 strain, absent from the reference variation graph.
BL21 strain expected abundances are followed by an asterisk in the K-12 column. Best results are shown in bold. For StrainFLAIR, the proportion of specific genes detected is shown in parentheses. Complete results are presented Section S1.6.
| #reads BL21-DE3 |
Method | O104:H4 | IAI39 | K-12 | Sakai | SE15 | Santai | RM8426 |
|---|---|---|---|---|---|---|---|---|
| 1,000 | Expected | 59.88 | 39.92 | 0.2* | 0 | 0 | 0 | 0 |
| StrainFLAIR | 56.48 | 43.52 | 0 | 0 | 0 | 0 | 0 | |
| (0.995) | (0.989) | (0.254) | (0.189) | (0.151) | (0.192) | (0.214) | ||
| Kraken2 | 38.93 | 60.76 | 0.11 | 0.05 | 0.08 | 0.04 | 0.03 | |
| 25,000 | Expected | 57.14 | 38.1 | 4.76* | 0 | 0 | 0 | 0 |
| StrainFLAIR | 54.12 | 41.72 | 4.16 | 0 | 0 | 0 | 0 | |
| (0.995) | (0.989) | (0.584) | (0.266) | (0.177) | (0.282) | (0.298) | ||
| Kraken2 | 37.75 | 58.93 | 2.16 | 0.28 | 0.34 | 0.25 | 0.29 | |
| 200,000 | Expected | 42.86 | 28.57 | 28.57* | 0 | 0 | 0 | 0 |
| StrainFLAIR | 46.96 | 35.32 | 17.72 | 0 | 0 | 0 | 0 | |
| (0.993) | (0.988) | (0.711) | (0.318) | (0.211) | (0.346) | (0.351) | ||
| Kraken2 | 31.14 | 48.83 | 13.53 | 1.57 | 1.67 | 1.58 | 1.68 |