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The GATK automatically incorporates base and alignment quality scores when calculating these probabilities.
This mapping quality score incorporates base qualities, number of mismatches, and the repeat structure.
SolSNP, an individual sample variant detector (classifier) implemented in Java does the variant calling based on a modified Kolmogorov-Smirnov like statistic, which incorporates base quality scores.
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Its an old argument that has a simple retort: State control of corporate governance has lead to a "race to the bottom" where management has been able to pick and chose where to incorporate based on the States with the weakest protections for shareholders.
In a recent review, Beisel and Storz (2010) described the specific regulatory circuits that incorporate base-pairing sRNAs.
We first describe two specific regulatory circuits that incorporate base-pairing microRNAs and show their fine-tuning roles in the modulation of periodic behavior.
Measures of family functioning during childhood were incorporated based on previous studies showing the relationships between parental conflict, parent-child hostility and psychosocial maladjustment in childhood [ 11] and later in adulthood [ 50].
This model incorporates unequal base composition and different transition and transversion rates.
The best results are seen with photo-MOs that incorporate base pair mismatches on both sides of the photo-element (Fig. 1K).
The proposed model incorporates time based aging on that trust value.
This scatter search algorithm incorporates procedures based on different strategies, such as local search, GRASP, and path relinking.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com