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

>>>>>>> Input

    bam file = DE-6.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) = 89,064,449 / 89,032,378
    read pairs aligned  = 89,001,182
    total alignments = 203,249,203
    secondary alignments = 25,152,376
    non-unique alignments = 36,338,769
    aligned to genes  = 85,197,788
    ambiguous alignments = 600,203
    no feature assigned = 81,101,841
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  85,197,788 (51.23%)
    intronic = 65,873,809 (39.61%)
    intergenic = 15,228,032 (9.16%)
    overlapping exon = 4,426,978 (2.66%)


>>>>>>> Transcript coverage profile

    5' bias = 0.48
    3' bias = 0.29
    5'-3' bias = 1.43


>>>>>>> Junction analysis

    reads at junctions = 50,118,718

    AGGT : 8.44%
    ACCT : 5.11%
    AGGA : 3.52%
    TCCT : 3.46%
    AGGC : 3.24%
    AGCT : 3%
    ATCT : 2.93%
    GCCT : 2.51%
    CCCT : 2.29%
    AGAT : 2.25%
    AGGG : 2.23%