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_1/IFE_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  = 87,479,467
    total alignments = 93,844,220
    secondary alignments = 6,364,753
    non-unique alignments = 10,073,871
    aligned to genes  = 62,546,916
    ambiguous alignments = 483,640
    no feature assigned = 20,610,920
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  62,546,916 (75.21%)
    intronic = 16,097,606 (19.36%)
    intergenic = 4,513,314 (5.43%)
    overlapping exon = 6,447,581 (7.75%)


>>>>>>> Transcript coverage profile

    5' bias = 0.78
    3' bias = 0.48
    5'-3' bias = 1.3


>>>>>>> Junction analysis

    reads at junctions = 37,057,873

    ACCT : 5.35%
    AGGT : 4.72%
    TCCT : 4.61%
    AGGA : 3.47%
    GCCT : 3.02%
    AGCT : 2.9%
    ATCT : 2.79%
    AGGC : 2.48%
    AGGG : 2.42%
    AGAT : 2.32%
    CCCT : 2.32%