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The additional fragment from the first Neandertal then provides an estimate of contamination in combination with heterozygosity at this class of sites (Table 1).
Using these data (SOM Text 7), we derive a maximum likelihood estimate of contamination of 0.7% with an upper 95% bound of 0.8%.
If one takes the entire excess of nuclear fragments to represent contamination, that is, assumes that the contamination was exclusively of mtDNA-free nuclear DNA, this yields an estimate of contamination of 41% in that proof-of-principle data.
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In addition to the low estimates of contamination, there are two reasons that contamination cannot explain our results.
The findings provide the first comprehensive estimates of contamination across Japan following the nuclear accident in 2011.
However, the magnitude of contamination necessary to explain the CEU-YRI and ASN-YRI comparisons are both over 10% and thus inconsistent with our estimates of contamination in the Neandertal data, which are all below 1% (Table 1).
Estimates of contamination in commercially available lots of recombinant Taq polymerase range from 10 1000 genome equivalents of bacterial DNA per Unit of enzyme [1], [4] [6].
This approach is therefore unlikely to yield realistic estimates of contamination.
Table I shows estimates of contamination using these 133 sites from several Neandertal libraries as well as estimates directly from the extracts from which they were prepared.
To achieve reliable nuclear DNA sequences from Neandertals, it is therefore necessary to develop direct nuclear estimates of contamination similar to those for mtDNA.
Thus, estimates of contamination and other parameters can be determined once and applied to the library as it is being used for further sequencing or other experiments.
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CEO of Professional Science Editing for Scientists @ prosciediting.com