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) = 19,638,224 / 19,400,291
    read pairs aligned  = 17,448,415
    total alignments = 41,576,869
    secondary alignments = 2,538,354
    non-unique alignments = 4,014,499
    aligned to genes  = 33,552,491
    ambiguous alignments = 319,971
    no feature assigned = 3,689,669
    not aligned = 1,681,519
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  33,552,491 (90.09%)
    intronic = 2,504,852 (6.73%)
    intergenic = 1,184,817 (3.18%)
    overlapping exon = 846,106 (2.27%)


>>>>>>> Transcript coverage profile

    5' bias = 0.67
    3' bias = 0.25
    5'-3' bias = 1.58


>>>>>>> Junction analysis

    reads at junctions = 21,301,122

    AGGT : 4.43%
    ACCT : 4.35%
    AGGA : 3.51%
    AGGG : 3.11%
    TCCT : 2.92%
    CCCT : 2.86%
    AGCT : 2.84%
    AGAT : 2.57%
    AGAA : 2.46%
    ATCT : 2.38%
    AGGC : 2.34%