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

>>>>>>> Input

    bam file = DE-2.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) = 83,069,646 / 83,046,675
    read pairs aligned  = 83,017,779
    total alignments = 181,107,831
    secondary alignments = 14,991,510
    non-unique alignments = 23,121,669
    aligned to genes  = 82,091,802
    ambiguous alignments = 599,490
    no feature assigned = 75,286,151
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  82,091,802 (52.16%)
    intronic = 62,939,845 (39.99%)
    intergenic = 12,346,306 (7.85%)
    overlapping exon = 4,385,610 (2.79%)


>>>>>>> Transcript coverage profile

    5' bias = 0.55
    3' bias = 0.34
    5'-3' bias = 1.3


>>>>>>> Junction analysis

    reads at junctions = 46,959,895

    ACCT : 5.61%
    AGGT : 4.94%
    TCCT : 3.53%
    AGGA : 3.5%
    ATCT : 3.09%
    AGCT : 3.04%
    GCCT : 2.7%
    AGGC : 2.64%
    CCCT : 2.48%
    AGAT : 2.29%
    AGGG : 2.26%