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) = 20,131,787 / 20,097,847
    read pairs aligned  = 18,594,499
    total alignments = 47,792,822
    secondary alignments = 7,563,188
    non-unique alignments = 10,793,565
    aligned to genes  = 32,192,089
    ambiguous alignments = 272,327
    no feature assigned = 4,534,745
    not aligned = 1,110,620
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  32,192,089 (87.65%)
    intronic = 1,946,110 (5.3%)
    intergenic = 2,588,635 (7.05%)
    overlapping exon = 717,075 (1.95%)


>>>>>>> Transcript coverage profile

    5' bias = 0.56
    3' bias = 0.38
    5'-3' bias = 1.41


>>>>>>> Junction analysis

    reads at junctions = 21,419,511

    ACCT : 4.53%
    AGGT : 4.13%
    ATCT : 3.63%
    AGGG : 3.55%
    AGGC : 3.42%
    TCCT : 3.39%
    AGCT : 3.28%
    GCCT : 3.18%
    AGGA : 3%
    CCCT : 2.34%
    GCCA : 2.12%