I would like to ask you about an issue am facing. While doing exome sequencing I earlier did an estimation to what extent my reads were falling on the target regions, ie the target intervals that are used for target enrichment and I found for my samples the reads were around 75% spanning the exonic region. But now when am translating them into the variants and trying to find the somatic variants and annotating the somatic variants with all 3 annovar, oncotator and snpEff I find only 30% SNPs(novel ones which are not in dbSNP) are actually on the exons. The rest are spanning the intronic,intergenic,splice ,UTRs etc. Is this a likely scenario? How often do you see the SNPs mostly annotated in the non-exonic regions even when you use the exome sequencing provided your reads have high coverage in the exonic intervals used for target enrichment? I would like to know your advice in such cases.