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In the literature, duplication rate is a combination of the duplicating mutation and fixation rates.
Few of these genes, however, were duplicated specifically in K. capsulata as evidenced by the low duplication rate found in this genome (0.15 duplication per gene, fig. 4).
Quality control of these libraries focuses on duplication rate and potential contamination by bacteria and fungi, whose % are easily visualized on the report.
This may result from high genomic duplication rate and extensive copy number variation within and between newt populations, consistent with the reported ca. 10% differences in genome size between closely related lineages of L. vulgaris and L. montandoni34.
When segmental duplications are not taken into account, the gene duplication rate is overestimated.
This could be due to either low gene duplication rate compared to divergence time, or negative selection that prevents certain gene families from changing their copy numbers.
The viral DNA duplication rate has to be chosen of the same order of magnitude of the bacterial duplication rate, otherwise either the viral content would explode and the host-parasite couple disappears, or the virus would be diluted out (15).
Still, all the libraries show a considerably high duplication rate.
The duplication rate varied between 56 and 87%.
The duplication rate was quantified using MarkDuplicates from Picard [ 32].
Therefore, the long-term average duplication rate rdup used in Eqs. 2, 6 is in fact considerably lower than the raw duplication rate r dup ∗.
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