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

>>>>>>> Input

    bam file = SRX7354090.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) = 35,951,248 / 35,923,173
    read pairs aligned  = 35,918,315
    total alignments = 77,329,337
    secondary alignments = 5,454,916
    non-unique alignments = 8,646,276
    aligned to genes  = 59,400,127
    ambiguous alignments = 227,016
    no feature assigned = 8,421,595
    not aligned = 3,428,711


>>>>>>> Reads genomic origin

    exonic =  59,400,127 (87.58%)
    intronic = 5,015,247 (7.39%)
    intergenic = 3,406,348 (5.02%)
    overlapping exon = 2,438,599 (3.6%)


>>>>>>> Transcript coverage profile

    5' bias = 0.31
    3' bias = 0.28
    5'-3' bias = 1.63


>>>>>>> Junction analysis

    reads at junctions = 22,125,176

    ACCT : 5.4%
    AGGT : 4.35%
    TCCT : 4.09%
    ATCT : 3.92%
    GCCT : 3.7%
    AGGA : 3.03%
    CCCT : 2.8%
    AGCT : 2.51%
    AGGC : 2.39%
    TTCT : 2.2%
    TCCC : 1.93%