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Thresholds of reference and to be aligned images were varied.
We list a part of the whole list of thresholds for reference.
Thirteen studies reported adequate data on the threshold of the reference standard for inclusion in this analysis.
We exposed mice to three doses that span several orders of magnitude, and the lower two doses are considered "low-dose" by two well-accepted definitions: a dose that does not exceed the threshold of the U.S. Environmental Protection Agency reference dose of 50 μg/kg BW/day and a dose that is within the range of observed human environmental exposure levels (Vandenberg et al. 2013).
On the other hand, when there is a large allele frequency difference between lines, one line will have a high frequency of a non-reference allele, which increases the probability to reach over the SNP detection threshold of three non-reference reads in resequencing.
Table 7 Performances obtained using Euclidean distance by combining the two methodologies with the two sets of reference (threshold with α=2) ComplOverlap Eucl + All Output×G T 1 70 83 Output×G T 2 77 83.
Table 4 Performance obtained with statistical value χ 2 by combining the two methodologies with two sets of reference (threshold with α=1) ComplOverlap χ 2 + All Output×G T 1 50 47 Output×G T 2 43 43.
Table 6 Performances obtained using Euclidean distance by combining the two methodologies with the two sets of reference (threshold with α=1) ComplOverlap Eucl + All Output×G T 1 50 43 Output×G T 2 43 47. Figure 14 shows the results from using thresholds with α=2.
The second diagram used as references the images manually segmented by individual 2 (G T 2) Table 5 Performances obtained with the statistical value χ 2by combining the two methodologies with two sets of reference (threshold with α=2) ComplOverlap χ 2 + All Output×G T 1 70 70 Output×G T 2 77 63.
By defining core proteins using a low threshold for the number of reference proteins with conserved CDS, we are able to identify sets of proteins with conserved CDS to at least a few other orthologs, typically from the closest species, without requiring such high level of conservation over all pairs of proteins.
Using a SNP detection threshold of three non-reference reads for each pool, a total of approximately 3.7 SNPs/kb were found in the resequencing data.
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