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

>>>>>>> Input

    bam file = DE-1.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) = 87,309,921 / 87,286,398
    read pairs aligned  = 87,258,574
    total alignments = 196,872,006
    secondary alignments = 22,275,687
    non-unique alignments = 33,760,422
    aligned to genes  = 94,622,666
    ambiguous alignments = 704,333
    no feature assigned = 67,777,956
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  94,622,666 (58.26%)
    intronic = 54,624,925 (33.64%)
    intergenic = 13,153,031 (8.1%)
    overlapping exon = 4,515,279 (2.78%)


>>>>>>> Transcript coverage profile

    5' bias = 0.56
    3' bias = 0.38
    5'-3' bias = 1.25


>>>>>>> Junction analysis

    reads at junctions = 55,579,144

    ACCT : 5.77%
    AGGT : 4.93%
    AGGA : 3.62%
    TCCT : 3.43%
    AGGC : 3.04%
    AGCT : 3.04%
    ATCT : 2.96%
    GCCT : 2.65%
    CCCT : 2.43%
    AGAT : 2.3%
    AGGG : 2.28%