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Table 2 The relative contribution of enzyme combinations to cDNA pool coverage.

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

Source Num df Den df F Sig. Partial R2
Model 58 2248.56 134.76 <0.001 77.66
Total pool size (bp) 1 85.40 14.25 <0.001 14.30
Average sequence length 1 86.29 52.87 <0.001 37.99
GC content 1 86.60 34.89 <0.001 28.72
Non-ACGT content 1 84.49 0.05 0.823 <0.01
Enzyme combination 27 2428.48 199.26 <0.001 68.90
Enzyme combination*GC content 27 2428.48 112.38 <0.001 55.55
  1. Variance partitioning addressing the contribution of enzyme combination (28 combinations) on pool coverage for 92 eukaryotic species (see additional file 1). Species was included as a random factor in a mixed model analysis which aimed to determine the influence of individual factors or interactions (Source). cDNA pool coverage was weighted by the number of sequences per species to account for variation in available sequence data. The numerator and denominator (Kenward-Roger corrected) degrees of freedom (Num df/Den df) are provided. F statistics (F) and the significance (Sig.) of the overall model, factors and interactions are reported. The proportion of the variation in cDNA pool coverage which is explained by each factor/interaction is indicated as Partial R-square values [27].