Therefore, we hypothesize the relationship before and after certain structural breakpoints are statistically different.
Figure 1b shows a plot of transpiration rate versus vapor pressure deficit for two genotypes with contrasting responses to high VPD: a linear increase in transpiration rate with increasing VPD and a limited-transpiration rate above a certain VPD breakpoint.
This can sometimes make identification of the indel breakpoints less certain.
The PCF algorithms may be generalized to allow breakpoints only at certain prespecified positions.
Ritz et al. use all identified CN profiles of an individual to detect breakpoints with a certain probability.
Evolutionary adaptation takes place in evolutionary breakpoint regions, where certain gene categories and specific repetitive elements are significantly enriched.
First, if reference sequence annotations of type "repeat sequence" or "mobile element" are present, and the breakpoint is within a certain distance of the end of one of these features (default: 20 bases), then the breakpoint is shifted to exactly align to the end of the annotated feature.
Looking at the position of the regions that code for the necessary protein domains, and considering the reading frames of the various exons involved, it becomes clear that an oncogenic fusion protein will only be generated if breakpoints are located within certain introns.
Fraction of coverage indicates the fraction of ChIP-seq peaks falling into a certain distance range from the SM breakpoints.
