Table 5.
Effects of taxonomic grouping and enzyme combination on pool coverage.
| Source | Num df | Den df | F | Sig. | Partial R2 |
|---|---|---|---|---|---|
| Model | 254 | 1485.02 | 87.57 | <0.001 | 93.74 |
| Taxonomic group | 7 | 57.37 | 13.48 | <0.001 | 62.19 |
| Total pool size (bp) | 1 | 55.88 | 5.00 | 0.029 | 8.22 |
| Average sequence length | 1 | 56.31 | 66.16 | <0.001 | 54.02 |
| GC content | 1 | 56.56 | 12.12 | 0.001 | 17.65 |
| Non-ACGT content | 1 | 56.59 | 0.75 | 0.389 | 1.31 |
| Enzyme combination | 27 | 1593.69 | 230.17 | <0.001 | 79.59 |
| Enzyme combination * GC content | 27 | 1593.69 | 142.71 | <0.001 | 70.74 |
| Enzyme combination * Taxonomic group | 189 | 1593.69 | 21.05 | <0.001 | 71.40 |
Variance partitioning addressing the influence of enzyme combination (28 combinations) and taxonomic grouping on pool coverage for 68 species (see additional file 2). Species was included as a random factor and cDNA pool coverage was weighted by the number of sequences per species to account for variation in available sequence data. Denominator degrees of freedom were Kenward-Roger corrected. Partial R-square indicates the proportion of the variation in cDNA pool coverage which is explained by each factor/interaction [27].