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

>>>>>>> Input

    bam file = juvenile.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) = 210,304,183 / 210,278,128
    read pairs aligned  = 210,168,928
    total alignments = 461,972,496
    secondary alignments = 41,390,185
    non-unique alignments = 69,977,096
    aligned to genes  = 100,442,329
    ambiguous alignments = 9,449
    no feature assigned = 291,543,622
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  100,442,329 (25.62%)
    intronic = 68,230,885 (17.41%)
    intergenic = 223,312,737 (56.97%)
    overlapping exon = 30,291,613 (7.73%)


>>>>>>> Transcript coverage profile

    5' bias = 0.55
    3' bias = 0.58
    5'-3' bias = 0.93


>>>>>>> Junction analysis

    reads at junctions = 119,877,069

    AGGT : 6.36%
    ACCT : 5.5%
    AGAT : 3.2%
    TCCT : 3.14%
    ATCT : 2.92%
    AGCT : 2.52%
    AGGA : 2.33%
    AGAA : 1.99%
    AGGG : 1.89%
    TTCT : 1.82%
    AGGC : 1.77%