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) = 23,013,618 / 22,710,420
    read pairs aligned  = 19,857,866
    total alignments = 48,632,676
    secondary alignments = 2,908,638
    non-unique alignments = 4,597,542
    aligned to genes  = 39,481,459
    ambiguous alignments = 370,092
    no feature assigned = 4,183,236
    not aligned = 2,021,978
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  39,481,459 (90.42%)
    intronic = 2,939,120 (6.73%)
    intergenic = 1,244,116 (2.85%)
    overlapping exon = 1,081,657 (2.48%)


>>>>>>> Transcript coverage profile

    5' bias = 0.69
    3' bias = 0.29
    5'-3' bias = 1.46


>>>>>>> Junction analysis

    reads at junctions = 25,136,813

    AGGT : 4.43%
    ACCT : 4.32%
    AGGA : 3.6%
    AGGG : 3.06%
    CCCT : 2.94%
    TCCT : 2.94%
    AGCT : 2.77%
    AGAA : 2.62%
    AGAT : 2.56%
    AGGC : 2.39%
    ATCT : 2.34%