RNA-Seq QC report
-----------------------------------

>>>>>>> Input

    bam file = SRX7354125.markdup.sorted.bam
    gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = strand-specific-reverse
    5'-3' bias region size = 100
    5'-3' bias number of top transcripts = 1000


>>>>>>> Reads alignment

    reads aligned (left/right) = 33,148,599 / 33,119,413
    read pairs aligned  = 33,115,303
    total alignments = 70,490,484
    secondary alignments = 4,222,472
    non-unique alignments = 6,977,656
    aligned to genes  = 55,242,940
    ambiguous alignments = 223,402
    no feature assigned = 7,745,307
    not aligned = 7,596,120


>>>>>>> Reads genomic origin

    exonic =  55,242,940 (87.7%)
    intronic = 5,167,106 (8.2%)
    intergenic = 2,578,201 (4.09%)
    overlapping exon = 2,155,217 (3.42%)


>>>>>>> Transcript coverage profile

    5' bias = 0.39
    3' bias = 0.21
    5'-3' bias = 2


>>>>>>> Junction analysis

    reads at junctions = 19,262,918

    ACCT : 5.32%
    AGGT : 4.9%
    ATCT : 3.63%
    AGGA : 3.51%
    TCCT : 3.44%
    GCCT : 3.1%
    AGCT : 2.79%
    CCCT : 2.53%
    AGGC : 2.48%
    AGAT : 2.13%
    TTCT : 2.07%