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

>>>>>>> Input

    bam file = DE-5.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) = 79,518,941 / 79,489,396
    read pairs aligned  = 79,463,438
    total alignments = 179,299,009
    secondary alignments = 20,290,672
    non-unique alignments = 29,685,007
    aligned to genes  = 77,053,238
    ambiguous alignments = 548,580
    no feature assigned = 72,003,855
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  77,053,238 (51.69%)
    intronic = 58,629,076 (39.33%)
    intergenic = 13,374,779 (8.97%)
    overlapping exon = 3,979,962 (2.67%)


>>>>>>> Transcript coverage profile

    5' bias = 0.55
    3' bias = 0.35
    5'-3' bias = 1.35


>>>>>>> Junction analysis

    reads at junctions = 45,044,548

    AGGT : 9.79%
    ACCT : 5.1%
    TCCT : 3.39%
    AGGA : 3.38%
    ATCT : 3.02%
    AGCT : 2.95%
    GCCT : 2.56%
    AGGC : 2.44%
    CCCT : 2.37%
    AGAT : 2.16%
    AGGG : 2.14%