RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354375.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) = 33,010,145 / 32,958,052 read pairs aligned = 32,952,477 total alignments = 70,343,994 secondary alignments = 4,375,797 non-unique alignments = 7,131,501 aligned to genes = 53,019,891 ambiguous alignments = 199,840 no feature assigned = 9,655,653 not aligned = 4,806,065 >>>>>>> Reads genomic origin exonic = 53,019,891 (84.59%) intronic = 5,685,968 (9.07%) intergenic = 3,969,685 (6.33%) overlapping exon = 2,229,052 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.3 5'-3' bias = 1.65 >>>>>>> Junction analysis reads at junctions = 20,300,477 ACCT : 5.21% AGGT : 4.8% TCCT : 3.64% AGGA : 3.45% ATCT : 3.44% GCCT : 3.06% AGCT : 2.68% CCCT : 2.47% AGGC : 2.41% AGAT : 2.14% TTCT : 2.06%