I am trying to check if this low freq variant is ineresting, if it is also mosaic.
AC=1;AF=0.5;AN=2;DP=910; 0/1:99:910:0.095:99:549,0,17114:824,86 and QD=0.57;SF=8f.
The region around it has similar coverage, some snps is low frequent AD like
2/910 or 6/906 or 0/910, this is what I see from IGV.
It is in GC percentage
60% which is high GC.
What I can't understand is this black bar which seems to be a downsampling.
Could this downsampling be the reason behind the low the ALT allele counts?
Hoovering over says in this interval [-] 356 reads has been removed.
My goal is to be sure whether to discard this variant or accept it as possible mosaic. I don't also if there is another meaning for the orange area rather than it is the region targeted by downsampling? Image here: