A statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. SNVer reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained. Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation. SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data.