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

>>>>>>> Input

    bam file = DE-3.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) = 80,822,391 / 80,796,797
    read pairs aligned  = 80,767,510
    total alignments = 179,036,830
    secondary alignments = 17,417,642
    non-unique alignments = 25,432,890
    aligned to genes  = 78,217,196
    ambiguous alignments = 579,030
    no feature assigned = 74,799,522
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  78,217,196 (51.12%)
    intronic = 61,570,472 (40.24%)
    intergenic = 13,229,050 (8.65%)
    overlapping exon = 4,235,563 (2.77%)


>>>>>>> Transcript coverage profile

    5' bias = 0.58
    3' bias = 0.36
    5'-3' bias = 1.31


>>>>>>> Junction analysis

    reads at junctions = 45,530,061

    AGGT : 8.09%
    ACCT : 5.28%
    AGGA : 3.38%
    TCCT : 3.36%
    ATCT : 3.07%
    AGCT : 2.94%
    GCCT : 2.68%
    AGGC : 2.62%
    CCCT : 2.33%
    AGAT : 2.2%
    AGGG : 2.16%