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

>>>>>>> Input

    bam file = gonad.markdup.sorted.bam
    gff file = Panopea-generosa-v1.0.a4_biotype-trna_strand_converted-no_RNAmmer.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) = 41,072,342 / 41,059,764
    read pairs aligned  = 41,017,159
    total alignments = 88,696,621
    secondary alignments = 6,564,515
    non-unique alignments = 11,027,828
    aligned to genes  = 20,060,305
    ambiguous alignments = 100
    no feature assigned = 57,608,388
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  20,060,305 (25.83%)
    intronic = 16,547,866 (21.31%)
    intergenic = 41,060,522 (52.87%)
    overlapping exon = 5,329,654 (6.86%)


>>>>>>> Transcript coverage profile

    5' bias = 0.56
    3' bias = 0.53
    5'-3' bias = 1.06


>>>>>>> Junction analysis

    reads at junctions = 28,937,910

    AGGT : 6.63%
    ACCT : 4.92%
    AGAT : 4.05%
    AGTT : 3.22%
    AGGA : 2.79%
    ATCT : 2.74%
    TCCT : 2.69%
    AGGC : 2.55%
    AGCT : 2.2%
    AGAG : 2.12%
    AGAA : 2.11%