Variant calling in RNA-Seq is similar to DNA variant calling and often employs the same tools (including SAMtools mpileup[124] and GATK HaplotypeCaller[125]) with adjustments to account for splicing. One unique dimension for RNA variants is allele-specific expression (ASE): the vairants from only one haplotype might be preferentially expressed due to regulatory effects including imprinting and expression quantitative trait loci, and noncoding rare variants.[126][127] Limitations of RNA variant identification include that it only reflects expressed regions (in humans, <5% of the genome) and has lower quality when compared to direct DNA sequencing.