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

>>>>>>> Input

    bam file = /dev/stdin
    gff file = /home/bayegy/Databases/transcriptome/references/mmu/GCF_000001635.27_GRCm39_genomic.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = non-strand-specific
    5'-3' bias region size = 100
    5'-3' bias number of top transcripts = 1000


>>>>>>> Reads alignment

    reads aligned (left/right) = 20,241,997 / 19,998,124
    read pairs aligned  = 18,008,415
    total alignments = 42,822,310
    secondary alignments = 2,582,189
    non-unique alignments = 4,092,794
    aligned to genes  = 34,505,260
    ambiguous alignments = 309,986
    no feature assigned = 3,914,055
    not aligned = 1,384,617
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  34,505,260 (89.81%)
    intronic = 2,752,361 (7.16%)
    intergenic = 1,161,694 (3.02%)
    overlapping exon = 813,128 (2.12%)


>>>>>>> Transcript coverage profile

    5' bias = 0.64
    3' bias = 0.22
    5'-3' bias = 1.6


>>>>>>> Junction analysis

    reads at junctions = 21,890,626

    AGGT : 4.51%
    ACCT : 4.42%
    AGGA : 3.62%
    AGGG : 3.02%
    TCCT : 2.93%
    AGCT : 2.87%
    CCCT : 2.67%
    AGAT : 2.58%
    AGAA : 2.46%
    ATCT : 2.42%
    AGGC : 2.39%