Focal copy number alterations in IGV

Question

[neuro3030]

I am visualizing a segmented copy number file (.seg) from the TCGA in IGV.

From the example screenshot below, the gene RAC2 shows loss in a few samples (blue). Assuming all of the samples that are blue for RAC2 are significant using GISTIC, how do you interpret the sample with a portion of the gene in blue (sample is about midway down)?

For instance, assuming the raw score for the blue portion is -0.6552, and the white portion (corresponding to the other half of the gene) is -0.0054, how can you determine which portion of the gene is significantly deleted? Are both the blue and the white? Just the blue portion?

thanks and any help would be great

[Ram]

Did you try looking at the raw SCNA data from TCGA?