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/HF_1/HF_1Aligned.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  = 95,174,484
    total alignments = 101,979,109
    secondary alignments = 6,804,625
    non-unique alignments = 10,871,631
    aligned to genes  = 66,189,764
    ambiguous alignments = 539,609
    no feature assigned = 24,240,835
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  66,189,764 (73.19%)
    intronic = 19,343,087 (21.39%)
    intergenic = 4,897,748 (5.42%)
    overlapping exon = 7,050,933 (7.8%)


>>>>>>> Transcript coverage profile

    5' bias = 0.78
    3' bias = 0.5
    5'-3' bias = 1.29


>>>>>>> Junction analysis

    reads at junctions = 37,808,984

    ACCT : 5.29%
    AGGT : 4.79%
    TCCT : 4.49%
    AGGA : 3.45%
    AGCT : 3.06%
    GCCT : 2.9%
    ATCT : 2.59%
    AGGC : 2.54%
    AGAT : 2.39%
    AGGG : 2.35%
    CCCT : 2.35%