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

>>>>>>> Input

    bam file = DE-7.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) = 68,589,471 / 68,569,869
    read pairs aligned  = 68,549,432
    total alignments = 153,734,631
    secondary alignments = 16,575,291
    non-unique alignments = 24,189,422
    aligned to genes  = 70,425,497
    ambiguous alignments = 488,388
    no feature assigned = 58,623,404
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  70,425,497 (54.57%)
    intronic = 46,558,520 (36.08%)
    intergenic = 12,064,884 (9.35%)
    overlapping exon = 3,454,924 (2.68%)


>>>>>>> Transcript coverage profile

    5' bias = 0.57
    3' bias = 0.36
    5'-3' bias = 1.31


>>>>>>> Junction analysis

    reads at junctions = 40,457,753

    AGGT : 9.24%
    ACCT : 4.99%
    AGGA : 3.31%
    TCCT : 3.27%
    AGCT : 2.96%
    ATCT : 2.91%
    AGGC : 2.67%
    GCCT : 2.54%
    CCCT : 2.24%
    AGGG : 2.21%
    AGAT : 2.14%