i annotated my vcf file (resulted from samtools) using snpEff and output of snpEff confused me. in html output the "number of SNPs" is 2.5 million while "number of effects" is 3.8 million. this case about indels is higher even, number of indels is 350,256 while "number of effects" is 9 million. what happened? is it normal result? if i want that number of variant and "number of effects" be equal, what should i do?
thanks in advance