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

>>>>>>> Input

    bam file = HB.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) = 75,371,867 / 75,344,465
    read pairs aligned  = 75,319,060
    total alignments = 171,984,511
    secondary alignments = 21,268,179
    non-unique alignments = 30,836,676
    aligned to genes  = 74,866,738
    ambiguous alignments = 528,243
    no feature assigned = 65,742,906
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  74,866,738 (53.24%)
    intronic = 52,762,156 (37.52%)
    intergenic = 12,980,750 (9.23%)
    overlapping exon = 3,915,719 (2.78%)


>>>>>>> Transcript coverage profile

    5' bias = 0.56
    3' bias = 0.37
    5'-3' bias = 1.31


>>>>>>> Junction analysis

    reads at junctions = 41,983,162

    AGGT : 10.07%
    ACCT : 4.97%
    AGGA : 3.38%
    TCCT : 3.29%
    AGCT : 2.94%
    ATCT : 2.85%
    GCCT : 2.54%
    AGGC : 2.51%
    CCCT : 2.26%
    AGGG : 2.22%
    AGAT : 2.19%