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Although dentin generally contains a higher proportion of total human DNA than dental calculus, many dental calculus samples in this study have comparable proportions of human DNA to their dentin pair, with one dental calculus sample from the Netherlands (S454) having a higher proportion of DNA assigned to the human genome than its paired dentin sample (Supplementary Table S9).
Prokaryote genomes are considered compacted genomes with only small fractions of their genomic DNA assigned to intergenic regions [ 1].
To correct for the GO ascertainment bias, within the context of functional inference on non-coding elements, the probability of a given annotation term should be set proportional to the fraction of the length of non-coding DNA assigned to it, which is strongly correlated with the length of the locus that contains it, and is highly variable across different loci (Supplementary Fig. 1).
Alternative splicing also enables transcription to start at a gene and then continue transcribing another gene with another function or encoding a different protein, located remotely or even on another chromosome [ 24]. 4-5% of DNA, assigned to identified proteins is transcribed in this way.
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Unmapped reads representing non-PAO1 DNA and the mapped reads representing the PAO1 DNA were assigned to not-in-reference and in-reference read pools, respectively.
Next , 2,551DNA markers assigned to 15,683 BACs by overgo hybridization (Methods) were incorporated into the physical map contigs.
Our S1 linkage map covers about 280 Mb of the poplar genome or 90% of the DNA sequence assigned to linkage groups.
An additional DNA band assigned to cytosine is detected in the factor loadings shown in Fig. 5b, which also strengthens the previously identified phosphodiester DNA band assignment at about 1,090 cm−1 [ 24, 25].
(B) Authenticity test of DNA reads assigned to Triticum by Smith et al. using same empirical distributions as in A. The dotted lines indicate the location of the goodness-of-fit p-value from reads assigned to wheat in sedimentary ancient DNA.
10.7554/eLife.10005.004 Figure 2. Authenticity test of DNA reads assigned to Triticum by Smith et al. (A ) The histograms in the center panel show the empirical distributions of goodness-of-fit p-values of subsamples of 150 reads from ancient and modern DNA (same libraries as in Figure 1 ).
As expected, when we computed the P-values using a binomial distribution with parameters n (sample size) and, where is the probability of observing the total length of non-coding DNA indirectly assigned to a particular GO, we could not detect any particular GO category significant in 5% or more of the experiments.
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