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) = 20,030,500 / 19,999,212
    read pairs aligned  = 18,400,279
    total alignments = 46,209,787
    secondary alignments = 6,180,075
    non-unique alignments = 8,931,065
    aligned to genes  = 32,832,744
    ambiguous alignments = 259,983
    no feature assigned = 4,185,917
    not aligned = 1,009,496
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  32,832,744 (88.69%)
    intronic = 2,078,444 (5.61%)
    intergenic = 2,107,473 (5.69%)
    overlapping exon = 733,524 (1.98%)


>>>>>>> Transcript coverage profile

    5' bias = 0.66
    3' bias = 0.3
    5'-3' bias = 1.48


>>>>>>> Junction analysis

    reads at junctions = 22,586,187

    ACCT : 4.68%
    AGGT : 4.37%
    TCCT : 3.43%
    AGCT : 3.4%
    ATCT : 3.38%
    GCCT : 3.07%
    AGGG : 3.06%
    AGGA : 3.03%
    AGGC : 3%
    CCCT : 2.37%
    AGAT : 2.11%