RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354123.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) = 45,024,402 / 44,986,366 read pairs aligned = 44,957,766 total alignments = 101,623,516 secondary alignments = 11,612,748 non-unique alignments = 13,014,608 aligned to genes = 72,713,122 ambiguous alignments = 270,558 no feature assigned = 11,845,704 not aligned = 2,173,854 >>>>>>> Reads genomic origin exonic = 72,713,122 (85.99%) intronic = 8,729,747 (10.32%) intergenic = 3,115,957 (3.68%) overlapping exon = 3,556,107 (4.21%) >>>>>>> Transcript coverage profile 5' bias = 0.47 3' bias = 0.19 5'-3' bias = 1.91 >>>>>>> Junction analysis reads at junctions = 28,119,339 ACCT : 5.23% AGGT : 4.75% AGGA : 3.57% TCCT : 3.55% ATCT : 3.53% GCCT : 2.85% AGCT : 2.78% CCCT : 2.47% AGGC : 2.41% AGAT : 2.3% TTCT : 2.24%