RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354337.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) = 45,382,998 / 45,357,785 read pairs aligned = 45,349,717 total alignments = 98,239,566 secondary alignments = 7,498,783 non-unique alignments = 11,755,771 aligned to genes = 77,851,350 ambiguous alignments = 337,985 no feature assigned = 7,428,333 not aligned = 3,206,967 >>>>>>> Reads genomic origin exonic = 77,851,350 (91.29%) intronic = 4,084,640 (4.79%) intergenic = 3,343,693 (3.92%) overlapping exon = 4,046,270 (4.74%) >>>>>>> Transcript coverage profile 5' bias = 0.09 3' bias = 0.11 5'-3' bias = 2.35 >>>>>>> Junction analysis reads at junctions = 27,388,871 TCCT : 6.45% ACCT : 5.67% ATCT : 4.76% AGGT : 3.82% CCCT : 3.77% AGGA : 2.62% TCCC : 2.47% GCCT : 2.34% CGTA : 2.22% AGGC : 2.22% GTCT : 2.11%