Example of a qualimap RNAseq report for paired-end data

rnaseq_qc_results.txt

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

>>>>>>> Input

    bam file = /tmp/07122375.bam
    gff file = /mnt/annotation.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = strand-specific-forward


>>>>>>> Reads alignment

    reads aligned (left/right) = 3,295,794 / 3,295,797
    read pairs aligned  = 3,295,792
    total alignments = 7,758,876
    secondary alignments = 1,167,285
    non-unique alignments = 1,511,158
    aligned to genes  = 1,329,862
    ambiguous alignments = 28,642
    no feature assigned = 1,650,052
    not aligned = 2,596,101


>>>>>>> Reads genomic origin

    exonic =  1,329,862 (44.63%)
    intronic = 1,032,186 (34.64%)
    intergenic = 617,866 (20.73%)
    overlapping exon = 156,843 (5.26%)


>>>>>>> Transcript coverage profile

    5' bias = 0.82
    3' bias = 0.67
    5'-3' bias = 1.18


>>>>>>> Junction analysis

    reads at junctions = 1,434,012

    ACCT : 4.86%
    AGGT : 4.8%
    AGGA : 3.61%
    TCCT : 3.49%
    ATCT : 3.2%
    AGCT : 3.09%
    AGGC : 2.55%
    GCCT : 2.51%
    CCCT : 2.46%
    AGAT : 2.38%
    AGGG : 2.19%