RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354264.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) = 30,295,332 / 30,277,361 read pairs aligned = 30,273,897 total alignments = 64,293,821 secondary alignments = 3,721,128 non-unique alignments = 5,676,950 aligned to genes = 48,761,861 ambiguous alignments = 178,229 no feature assigned = 9,174,220 not aligned = 1,267,935 >>>>>>> Reads genomic origin exonic = 48,761,861 (84.16%) intronic = 6,293,625 (10.86%) intergenic = 2,880,595 (4.97%) overlapping exon = 2,238,650 (3.86%) >>>>>>> Transcript coverage profile 5' bias = 0.52 3' bias = 0.25 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 18,223,811 ACCT : 5.21% AGGT : 4.73% TCCT : 3.58% ATCT : 3.57% AGGA : 3.39% GCCT : 3.33% AGCT : 2.68% CCCT : 2.68% AGGC : 2.5% TTCT : 2.25% AGAT : 2.16%