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) = 20,747,769 / 20,700,578
    read pairs aligned  = 19,171,152
    total alignments = 46,682,199
    secondary alignments = 5,233,852
    non-unique alignments = 7,926,964
    aligned to genes  = 34,097,009
    ambiguous alignments = 249,429
    no feature assigned = 4,408,700
    not aligned = 977,517
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  34,097,009 (88.55%)
    intronic = 2,290,021 (5.95%)
    intergenic = 2,118,679 (5.5%)
    overlapping exon = 749,521 (1.95%)


>>>>>>> Transcript coverage profile

    5' bias = 0.65
    3' bias = 0.3
    5'-3' bias = 1.39


>>>>>>> Junction analysis

    reads at junctions = 24,148,556

    ACCT : 4.56%
    AGGT : 4.22%
    AGCT : 3.59%
    ATCT : 3.43%
    TCCT : 3.32%
    AGGG : 3.09%
    AGGA : 2.99%
    GCCT : 2.89%
    AGGC : 2.87%
    CCCT : 2.26%
    AGAT : 2.11%