On the images of the chromosomes in the Chromosome Browser, some places are darkened. Why is that?
In the Chromosome Browser we show areas as darkened when they are SNP Poor. That is, the microarray chip does not include enough data points in this area to make scientifically sound judgment about whether matches are parts of Identical By Descent (IBD) segments or not. When segments that cross these areas are evaluated for IBD status they are treated as two segments, one on each side of the SNP Poor area.
