RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354300.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) = 35,014,892 / 34,979,736 read pairs aligned = 34,975,247 total alignments = 74,856,037 secondary alignments = 4,861,409 non-unique alignments = 7,640,721 aligned to genes = 56,256,465 ambiguous alignments = 236,793 no feature assigned = 10,122,166 not aligned = 9,356,718 >>>>>>> Reads genomic origin exonic = 56,256,465 (84.75%) intronic = 6,067,673 (9.14%) intergenic = 4,054,493 (6.11%) overlapping exon = 2,305,369 (3.47%) >>>>>>> Transcript coverage profile 5' bias = 0.59 3' bias = 0.28 5'-3' bias = 1.69 >>>>>>> Junction analysis reads at junctions = 22,725,376 ACCT : 5.26% AGGT : 4.8% AGGA : 3.51% TCCT : 3.45% ATCT : 3.35% GCCT : 3.33% AGCT : 2.81% CCCT : 2.74% AGGC : 2.48% AGAT : 2.23% TTCT : 2.1%