RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354217.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) = 27,974,458 / 27,965,686 read pairs aligned = 27,964,013 total alignments = 59,592,577 secondary alignments = 3,652,433 non-unique alignments = 5,906,644 aligned to genes = 46,545,332 ambiguous alignments = 158,744 no feature assigned = 6,591,651 not aligned = 881,478 >>>>>>> Reads genomic origin exonic = 46,545,332 (87.59%) intronic = 3,610,375 (6.79%) intergenic = 2,981,276 (5.61%) overlapping exon = 1,850,262 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.28 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 15,938,000 ACCT : 5% AGGT : 4.8% TCCT : 3.54% AGGA : 3.53% ATCT : 3.49% GCCT : 3.11% AGCT : 2.77% CCCT : 2.58% AGGC : 2.44% TTCT : 2.13% AGAT : 2.08%