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

>>>>>>> Input

    bam file = /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/IFE_2/IFE_2Aligned.sortedByCoord.out.bam
    gff file = /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/supporting_files/annotation/mus_musculus/grcm38_gencode_M25/data/gencode.vM25.basic.annotation.filtered.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = strand-specific-forward


>>>>>>> Reads alignment

    reads aligned  = 66,829,685
    total alignments = 72,456,922
    secondary alignments = 5,627,237
    non-unique alignments = 9,090,161
    aligned to genes  = 46,982,107
    ambiguous alignments = 405,274
    no feature assigned = 15,864,451
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  46,982,107 (74.76%)
    intronic = 10,619,028 (16.9%)
    intergenic = 5,245,423 (8.35%)
    overlapping exon = 4,767,259 (7.59%)


>>>>>>> Transcript coverage profile

    5' bias = 0.71
    3' bias = 0.42
    5'-3' bias = 1.36


>>>>>>> Junction analysis

    reads at junctions = 26,858,711

    ACCT : 5.28%
    TCCT : 4.74%
    AGGT : 4.56%
    AGGA : 3.39%
    GCCT : 3.09%
    AGCT : 2.75%
    ATCT : 2.67%
    AGGC : 2.56%
    AGGG : 2.49%
    CCCT : 2.28%
    AGAT : 2.22%