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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].