I did some variant calling on a 9MB genome we assembled and compared to another genome. We just got a few SNPs and single nucleotide indels.
With SnpEff I assessed the severity of the variants. We just got a few indels in genes.
Interestingly most of the indels are close to the stop codon. And most of them are in areas where we did not find known motifs with InterProScan...
I want to further assess the severity of the indels which are in genes. Any papers or other suggestions?
It is realy interesting that I see a strong bias of indels towards the end of the genes. Did you ever observe the same picture?