mRNA-seq data provides information about gene expression -- once sequenced reads from mRNA-seq libraries are aligned, the read coverage depth of a gene or transcript model reflects the expression level of that entity. Coverage can be normalized to give a relative measure of expression that allows comparison between genes of different lengths or between the same gene in libraries sequenced to different depths.  The data can also be used to measure relative expression of mutated sequence vs wildtype sequence for aberrations found in the genome.  Combining expression and mutational data (SNVs, indels and gene fusions) from mRNA-seq provides insight into transcriptional dysregulation and the effects of genomic and epigenetic interaction on transcription at a gene or exon level.
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