I have an interesting variant in a
very low GC content. The variant is segregating in affected and carriers' exome data (A=>G).
However, for one affected patient actually the proband , we have only a whole genome data not exome for him. The variant doesn't show in WG data.
I generated the BAM and looked the variant in IGV, we have 17 reads, 1 read disagree with reference (A=>C not even similar to variant in the other patients)
But it seems it is a flanking region. Many bases quality out of the 17 reads are low and many reads mapping are low too.
What is the effect of this flanking region?
Like if I state that this variant does not exist in this proband, this violates the variant. But if we don't have enough coverage ,bases quality? hard effects here for some reason, a bit different, maybe we can do something else to verify. It is a very low GC content which affect coverage, but is there any affect from a flanking region?
Attached is my IGV image: https://ibb.co/nafmO8