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) = 19,683,023 / 19,669,307
    read pairs aligned  = 18,106,988
    total alignments = 46,335,718
    secondary alignments = 6,983,388
    non-unique alignments = 9,908,533
    aligned to genes  = 32,192,411
    ambiguous alignments = 250,743
    no feature assigned = 3,983,909
    not aligned = 947,972
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  32,192,411 (88.99%)
    intronic = 1,940,692 (5.36%)
    intergenic = 2,043,217 (5.65%)
    overlapping exon = 683,579 (1.89%)


>>>>>>> Transcript coverage profile

    5' bias = 0.67
    3' bias = 0.31
    5'-3' bias = 1.48


>>>>>>> Junction analysis

    reads at junctions = 22,155,657

    ACCT : 4.7%
    AGGT : 4.27%
    ATCT : 3.44%
    AGCT : 3.44%
    TCCT : 3.42%
    AGGG : 3.18%
    GCCT : 3.13%
    AGGC : 3.04%
    AGGA : 2.94%
    CCCT : 2.38%
    AGAT : 2.06%