RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354081.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) = 38,997,959 / 38,958,479 read pairs aligned = 38,937,246 total alignments = 87,057,297 secondary alignments = 9,100,859 non-unique alignments = 11,797,118 aligned to genes = 66,015,687 ambiguous alignments = 275,444 no feature assigned = 6,722,402 not aligned = 6,578,160 >>>>>>> Reads genomic origin exonic = 66,015,687 (90.76%) intronic = 3,549,566 (4.88%) intergenic = 3,172,836 (4.36%) overlapping exon = 3,329,916 (4.58%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.12 5'-3' bias = 2.41 >>>>>>> Junction analysis reads at junctions = 20,382,730 ACCT : 5.47% TCCT : 4.87% AGGT : 4.4% ATCT : 4.37% CCCT : 3.91% AGGA : 2.79% AGGC : 2.33% AGAC : 2.27% GCCT : 2.19% AGCT : 2.01% GTCT : 1.96%