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

>>>>>>> Input

    bam file = larvae.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) = 44,605,420 / 44,607,755
    read pairs aligned  = 44,576,579
    total alignments = 98,429,234
    secondary alignments = 9,216,059
    non-unique alignments = 15,738,580
    aligned to genes  = 24,515,604
    ambiguous alignments = 212
    no feature assigned = 58,174,838
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  24,515,604 (29.65%)
    intronic = 15,293,538 (18.49%)
    intergenic = 42,881,300 (51.86%)
    overlapping exon = 6,829,552 (8.26%)


>>>>>>> Transcript coverage profile

    5' bias = 0.54
    3' bias = 0.56
    5'-3' bias = 0.94


>>>>>>> Junction analysis

    reads at junctions = 27,805,433

    AGGT : 5.86%
    ACCT : 5.18%
    ATCT : 3.03%
    TCCT : 2.98%
    AGAT : 2.86%
    AGCT : 2.29%
    AGGA : 2.23%
    TTCT : 1.78%
    GCCT : 1.73%
    AGGC : 1.66%
    ACCA : 1.56%