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Table 5 Effects of taxonomic grouping and enzyme combination on pool coverage.

From: Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

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
  1. 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].