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) = 19,826,623 / 19,574,453
    read pairs aligned  = 18,224,337
    total alignments = 42,678,299
    secondary alignments = 3,277,223
    non-unique alignments = 5,039,281
    aligned to genes  = 33,721,525
    ambiguous alignments = 439,997
    no feature assigned = 3,477,027
    not aligned = 2,299,220
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  33,721,525 (90.65%)
    intronic = 2,312,544 (6.22%)
    intergenic = 1,164,483 (3.13%)
    overlapping exon = 885,091 (2.38%)


>>>>>>> Transcript coverage profile

    5' bias = 0.42
    3' bias = 0.33
    5'-3' bias = 1.53


>>>>>>> Junction analysis

    reads at junctions = 18,557,074

    AGGT : 4.77%
    ACCT : 4.16%
    AGGA : 3.42%
    CCCT : 3.32%
    AGAA : 3.16%
    TCCT : 3%
    AGGG : 2.66%
    AGAT : 2.57%
    GCCT : 2.49%
    AGCT : 2.47%
    AGGC : 2.29%