RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354133.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) = 42,445,626 / 42,407,722 read pairs aligned = 42,378,182 total alignments = 90,662,577 secondary alignments = 5,809,229 non-unique alignments = 9,632,655 aligned to genes = 72,557,657 ambiguous alignments = 305,713 no feature assigned = 7,676,029 not aligned = 3,006,678 >>>>>>> Reads genomic origin exonic = 72,557,657 (90.43%) intronic = 4,109,963 (5.12%) intergenic = 3,566,066 (4.44%) overlapping exon = 3,199,382 (3.99%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.22 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 22,718,935 ACCT : 4.95% AGGT : 4.71% ATCT : 4.3% TCCT : 3.95% GCCT : 3.43% AGGA : 3.2% CCCT : 2.77% AGCT : 2.49% TTCT : 2.4% AGGC : 2.3% AGAA : 1.85%