RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354109.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 45,462,120 / 45,413,785 read pairs aligned = 45,401,913 total alignments = 96,206,842 secondary alignments = 5,330,937 non-unique alignments = 8,757,011 aligned to genes = 75,424,820 ambiguous alignments = 236,025 no feature assigned = 11,338,793 not aligned = 8,587,413 >>>>>>> Reads genomic origin exonic = 75,424,820 (86.93%) intronic = 6,582,804 (7.59%) intergenic = 4,755,989 (5.48%) overlapping exon = 3,386,627 (3.9%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.16 5'-3' bias = 1.78 >>>>>>> Junction analysis reads at junctions = 23,191,804 ACCT : 5.2% AGGT : 4.69% ATCT : 3.68% AGGA : 3.66% TCCT : 3.33% GCCT : 3.07% AGCT : 2.84% AGGC : 2.37% CCCT : 2.37% AGAT : 2.28% TTCT : 2.21%