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

>>>>>>> Input

    bam file = ctenidia.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) = 36,725,984 / 36,728,439
    read pairs aligned  = 36,685,637
    total alignments = 80,553,129
    secondary alignments = 7,098,706
    non-unique alignments = 11,599,239
    aligned to genes  = 16,806,775
    ambiguous alignments = 1,066
    no feature assigned = 52,146,049
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  16,806,775 (24.37%)
    intronic = 11,301,982 (16.39%)
    intergenic = 40,844,067 (59.23%)
    overlapping exon = 4,132,563 (5.99%)


>>>>>>> Transcript coverage profile

    5' bias = 0.52
    3' bias = 0.54
    5'-3' bias = 0.97


>>>>>>> Junction analysis

    reads at junctions = 17,270,876

    AGGT : 6.9%
    ACCT : 6.28%
    TCCT : 3.44%
    AGAT : 3.02%
    ATCT : 2.89%
    AGCT : 2.63%
    AGGA : 2.53%
    AGAA : 2.19%
    AGGG : 2.08%
    TTCT : 1.72%
    AGGC : 1.66%