In USMG5, inclusion of exon 2 is associated with increased transcript expression, and inclusion of exon 1a is associated with decreased transcript expression. The reference T allele of rs791148 is associated with inclusion of exon 1a, and the alternate G allele is associated with inclusion of exon 2. (A) Screenshots taken from Integrated Genome Viewer (IGV) illustrating the read coverage of the two samples in USMG5. The Y-axis for both tracks is scaled to a maximum read count of 1150 (measured as number of reads mapping to a given nucleotide). (B) The different USMG5 isoforms observed. (C) The percentage of each isoform (color-coded as in B) observed in the allele-specific alignment for both individuals. The height of each pie chart is representative of the gene expression for USMG5 as measured by the number of reads mapping to the exonic and intronic regions of the gene. The number of isoforms present in each individual was deduced by counting the number of splice junction reads spanning a unique splice junction for each of the isoforms (junction 1a-2 for isoform 1; junction1-3 for isoform 2; junction 1a-3 for isoform 3; and junction 1-2 for isoform 4).
