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) = 19,745,458 / 19,495,300
    read pairs aligned  = 17,454,061
    total alignments = 41,768,527
    secondary alignments = 2,527,769
    non-unique alignments = 3,996,225
    aligned to genes  = 33,662,690
    ambiguous alignments = 321,407
    no feature assigned = 3,787,980
    not aligned = 1,565,642
    SSP estimation (fwd/rev) = 0.5 / 0.5


>>>>>>> Reads genomic origin

    exonic =  33,662,690 (89.89%)
    intronic = 2,688,909 (7.18%)
    intergenic = 1,099,071 (2.93%)
    overlapping exon = 883,622 (2.36%)


>>>>>>> Transcript coverage profile

    5' bias = 0.68
    3' bias = 0.27
    5'-3' bias = 1.52


>>>>>>> Junction analysis

    reads at junctions = 21,421,630

    AGGT : 4.43%
    ACCT : 4.32%
    AGGA : 3.51%
    AGGG : 3.14%
    CCCT : 2.93%
    TCCT : 2.91%
    AGCT : 2.82%
    AGAT : 2.55%
    AGAA : 2.47%
    ATCT : 2.36%
    AGGC : 2.35%