Normalization The Normalization section gives information about the sample-level and chromosome-level coverages. Any chromosomes with disproportionate coverages are noted; targets on these chromosomes were ignored when setting up the statistical models.
Target-level log2-ratios The target-level coverage log-ratios are presented as a graph. Double click on it to see it in full view and access data points in a table.
An example is shown in figure 29.29. On the horizontal axis, the targets are placed in the order in which they appear in the genome. On the vertical axis, the adjusted coverage log-ratio of each target is plotted. The black line represents the actually observed mean adjusted log-ratio of coverage for each target. The cyan and red lines represent the 95% confidence intervals of the expected mean adjusted log-ratios of coverages, based on the statistical model. Chromosome boundaries are indicated as vertical lines.
Figure 29.29: An example graph showing the mean adjusted log-ratios of coverages in the report produced by the Copy Number Variant Detection tool. In this example, the second and ninth chromosomes are amplified, and the log-ratios of coverages of targets on these chromosome are significantly higher than for targets on other chromosomes. The black line in these regions is outside the boundaries defined by the cyan and red lines.
CNV statistics The last section in the report provides some information about the number of CNVs called in the region-level prediction results. If a gene track is provided as input, it also shows the number of genes affected by CNVs. It is possible for a gene to be affected by both a deletion and an amplification, if the gene overlap two different regions from the Region-level CNV results track. The number of uncalled or filtered regions are also shown.