RNA-Seq QC report
-----------------------------------

>>>>>>> Input

    bam file = DE-3C.markdup.sorted.bam
    gff file = genes.filtered.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = strand-specific-reverse
    5'-3' bias region size = 100
    5'-3' bias number of top transcripts = 1000


>>>>>>> Reads alignment

    reads aligned (left/right) = 78,856,641 / 78,834,962
    read pairs aligned  = 78,811,152
    total alignments = 176,633,950
    secondary alignments = 18,942,347
    non-unique alignments = 27,805,748
    aligned to genes  = 84,674,432
    ambiguous alignments = 633,267
    no feature assigned = 63,513,059
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  84,674,432 (57.14%)
    intronic = 50,221,592 (33.89%)
    intergenic = 13,291,467 (8.97%)
    overlapping exon = 4,285,356 (2.89%)


>>>>>>> Transcript coverage profile

    5' bias = 0.58
    3' bias = 0.37
    5'-3' bias = 1.3


>>>>>>> Junction analysis

    reads at junctions = 49,959,947

    AGGT : 8.58%
    ACCT : 5.22%
    AGGA : 3.36%
    TCCT : 3.33%
    ATCT : 3.03%
    AGCT : 2.91%
    GCCT : 2.63%
    AGGC : 2.54%
    CCCT : 2.34%
    AGAT : 2.17%
    AGGG : 2.16%