RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354280.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) = 71,928,397 / 71,870,885 read pairs aligned = 71,866,315 total alignments = 152,381,753 secondary alignments = 8,582,471 non-unique alignments = 13,456,609 aligned to genes = 121,875,632 ambiguous alignments = 428,573 no feature assigned = 15,633,925 not aligned = 2,996,254 >>>>>>> Reads genomic origin exonic = 121,875,632 (88.63%) intronic = 10,067,722 (7.32%) intergenic = 5,566,203 (4.05%) overlapping exon = 4,981,885 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.15 5'-3' bias = 2.22 >>>>>>> Junction analysis reads at junctions = 50,756,574 ACCT : 5.38% AGGT : 4.79% AGGA : 3.61% ATCT : 3.55% GCCT : 3.21% TCCT : 3.18% AGCT : 2.76% AGGC : 2.46% CCCT : 2.45% TTCT : 2.29% AGAT : 2.27%