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) = 20,799,690 / 20,781,980
    read pairs aligned  = 19,191,138
    total alignments = 48,457,315
    secondary alignments = 6,875,645
    non-unique alignments = 9,849,799
    aligned to genes  = 34,372,582
    ambiguous alignments = 260,455
    no feature assigned = 3,974,407
    not aligned = 1,051,878
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  34,372,582 (89.64%)
    intronic = 1,757,524 (4.58%)
    intergenic = 2,216,883 (5.78%)
    overlapping exon = 719,239 (1.88%)


>>>>>>> Transcript coverage profile

    5' bias = 0.67
    3' bias = 0.33
    5'-3' bias = 1.45


>>>>>>> Junction analysis

    reads at junctions = 23,741,627

    ACCT : 4.73%
    AGGT : 4.36%
    TCCT : 3.44%
    AGCT : 3.4%
    ATCT : 3.36%
    AGGA : 3.05%
    GCCT : 3.03%
    AGGG : 3.02%
    AGGC : 2.96%
    CCCT : 2.33%
    AGAT : 2.12%