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_3/IFE_3Aligned.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  = 142,635,553
    total alignments = 154,046,430
    secondary alignments = 11,410,877
    non-unique alignments = 17,996,805
    aligned to genes  = 102,092,447
    ambiguous alignments = 809,612
    no feature assigned = 32,931,423
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  102,092,447 (75.61%)
    intronic = 26,093,080 (19.32%)
    intergenic = 6,838,343 (5.06%)
    overlapping exon = 10,657,779 (7.89%)


>>>>>>> Transcript coverage profile

    5' bias = 0.79
    3' bias = 0.47
    5'-3' bias = 1.3


>>>>>>> Junction analysis

    reads at junctions = 58,897,281

    ACCT : 5.35%
    AGGT : 4.68%
    TCCT : 4.58%
    AGGA : 3.42%
    GCCT : 3.09%
    AGCT : 2.85%
    ATCT : 2.75%
    AGGC : 2.44%
    AGGG : 2.41%
    CCCT : 2.3%
    AGAT : 2.27%