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

>>>>>>> Input

    bam file = heart.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) = 66,316,235 / 66,313,855
    read pairs aligned  = 66,278,065
    total alignments = 144,781,076
    secondary alignments = 12,150,986
    non-unique alignments = 20,639,611
    aligned to genes  = 40,861,023
    ambiguous alignments = 89
    no feature assigned = 83,280,353
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  40,861,023 (32.91%)
    intronic = 21,741,193 (17.51%)
    intergenic = 61,539,160 (49.57%)
    overlapping exon = 8,843,360 (7.12%)


>>>>>>> Transcript coverage profile

    5' bias = 0.6
    3' bias = 0.53
    5'-3' bias = 1.05


>>>>>>> Junction analysis

    reads at junctions = 40,179,761

    AGGT : 5.99%
    ACCT : 5.56%
    AGAT : 3.11%
    CCCT : 2.99%
    ATCT : 2.99%
    TCCT : 2.97%
    AGGA : 2.6%
    AGCT : 2.37%
    AGAA : 2.13%
    AGGC : 1.93%
    AGGG : 1.8%