RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354146.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) = 41,826,372 / 41,785,163 read pairs aligned = 41,758,058 total alignments = 89,989,708 secondary alignments = 6,378,173 non-unique alignments = 10,190,399 aligned to genes = 68,429,947 ambiguous alignments = 312,558 no feature assigned = 10,549,570 not aligned = 1,498,271 >>>>>>> Reads genomic origin exonic = 68,429,947 (86.64%) intronic = 8,381,224 (10.61%) intergenic = 2,168,346 (2.75%) overlapping exon = 3,736,947 (4.73%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.23 5'-3' bias = 1.84 >>>>>>> Junction analysis reads at junctions = 29,140,470 ACCT : 5.28% AGGT : 4.68% TCCT : 3.64% AGGA : 3.49% ATCT : 3.37% GCCT : 3% AGCT : 2.74% CCCT : 2.57% AGGC : 2.52% AGGG : 2.04% AGAT : 2.04%