An example of significant eQTL identified using SeqGene. The HapMap individuals were stratified based on their genotypes at rs1042927 (dbSNP entry nubmer). We found 52 individuals are of genotype 'AA' and the other eight samples are of genotype 'AC'. We compared the expression levels of the gene KB-1839H6.1 in the two groups. (A). The KB-1839H6.1 gene expression level (RPKM) in the two groups (with 'AA' or 'AC' genotype at rs1042927). The expression levels were quantified using SeqGene's 'rpkm' function. (B). The aggregated coverage in the two groups illustrated on the gene model. The coverage is normalized to 'Coverage per Million Reads'. This plot was generated using the SeqGene's 'snpview' function. Gene models for every transcript were displayed at the bottom as flanking regions (gray), UTRs (orange), CDS (green) and introns (lines).