CNV graphs
The information that is displayed on the CNV graphs is different for the two comparison methods, Dispersion and HMM SNP-Based Normalization with smoothing.
Dispersion and HMM
• All Chromosomes graph – Displays all the regions across all the chromosomes in the project. Duplications are displayed in green. Deletions are displayed in red. Normal regions, or regions where the data was insufficient for making a call, are displayed in gray. The horizontal red and green lines represent the coverage ratios for duplications and deletions, respectively, in an ideal project without noise.
• Raw Data Dispersion graph – Displays the coverage ratios for all the raw data points. The red lines indicate the confidence interval of the data based on the expected CNV% for the data.
• Filtering Points Dispersion graph –Displays the dispersion value for each filtering point at the indicated coverage level.
The graphs are interactive:
Option | Description |
|---|---|
Zoom in | Hold down the left mouse button and draw a box from the upper left hand corner of any region in a graph towards the lower right hand corner. A box is formed around the area that is being reduced for viewing. |
Zoom out | Hold down the left mouse button and draw a box from the lower right hand corner of any region in the graph towards the upper left hand corner. The magnification for zooming out is always 100%. |
Highlight ROI | Click Select ROI to open the Regions of Interest dialog box that displays all the chromosomes in the project on which ROIs are located. Select a chromosome, and then click OK. The All Chromosomes graph is zoomed in on the selected ROI and all the raw data points in the selected ROI are highlighted in purple in the Raw Data Dispersion graph. |
Saving the graph to a file | Right-click any graph, and then select Save Picture to save the graph as PNG file. You must name the graph and select a location in which to save the graph. |
SNP-Based Normalization with smoothing
• Log2Ratio graph (Top graph) – Based on the coverage ratios for the CNV regions. Insertions are displayed in green. Deletions are displayed in red. Normal regions, or regions where the data was insufficient for making a call, are displayed in gray. SNP Regions (regions of interest for the purpose of checking allele ratios to visualize copy number) as designated in the region of interest BED file are displayed in blue. The horizontal red and green lines represent the coverage ratios for insertions and deletions, respectively. The differently colored solid lines that are displayed below the Log2Ratio graph indicate the consecutive regions summarized for each call.
• Allele Ratio graph (Bottom graph) – Based on the allele frequency ratios for the CNV regions. By default, when the graph first opens, it displays all the allele frequency ratios across all the chromosomes in the project.
 | The SNP-based Normalization with Smoothing algorithm evaluates SNPs that overall are heterozygous with allele frequency ratios that range from approximately 50-50 to 40-60. The typical ratio for a normal region (no CNV) falls within this 40-60 range. The Allele Ratio graph helps to visualize the samples that fall outside this typical range, and therefore identify a potential CNV. |
The graphs are interactive:
Option | Description |
|---|---|
Log2Ratio graph | |
Toggle the display through Low Resolution, High Resolution, and if applicable, Custom Resolution | Click Toggle Resolution. |
Toggle the Y axis between Log2Ratio and Sample Fraction | Click Toggle Ratio. |
Toggle the display of specific Regions of Interest for the purpose of checking allele ratios to visualize copy number as defined by the user in a BED file. | Click Toggle SNP Regions |
Allele Frequency graph | |
Toggle the display to show the following: • Allele frequencies for only the sample (solid blue dots). • Both the sample and the control sample (open blue dots). • Only the control sample. | Click Toggle Sample/Control. |
Move the display through the allele frequency ratio for each individual chromosome in the project. | Click the Next Chromosome and Previous Chromosome buttons. |
For both graphs | |
Zoom in | Hold down the left mouse button and draw a box from the upper left hand corner of any region in a graph towards the lower right hand corner. A box is formed around the area that is being reduced for viewing. |
Zoom out | Hold down the left mouse button and draw a box from the lower right hand corner of any region in the graph towards the upper left hand corner. The magnification for zooming out is always 100%. |
Saving the graph to a file | Right-click any graph, and then select Save Picture to save the graph as PNG file. You must name the graph and select a location in which to save the graph. |