RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354209.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) = 78,289,305 / 78,247,946 read pairs aligned = 78,238,085 total alignments = 167,937,749 secondary alignments = 11,400,498 non-unique alignments = 17,325,739 aligned to genes = 136,880,191 ambiguous alignments = 577,767 no feature assigned = 11,674,113 not aligned = 4,940,945 >>>>>>> Reads genomic origin exonic = 136,880,191 (92.14%) intronic = 6,782,564 (4.57%) intergenic = 4,891,549 (3.29%) overlapping exon = 5,312,687 (3.58%) >>>>>>> Transcript coverage profile 5' bias = 0.12 3' bias = 0.17 5'-3' bias = 1.47 >>>>>>> Junction analysis reads at junctions = 47,474,137 ACCT : 5.22% AGGT : 4.8% TCCT : 4.05% ATCT : 4.01% CCCT : 3.22% AGGA : 3.1% AGGC : 2.58% GCCT : 2.53% AGCT : 2.12% TTCT : 2.06% AGAA : 1.97%