RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354092.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) = 41,736,374 / 41,709,084 read pairs aligned = 41,704,046 total alignments = 89,927,303 secondary alignments = 6,481,845 non-unique alignments = 10,382,599 aligned to genes = 65,579,389 ambiguous alignments = 270,606 no feature assigned = 13,085,651 not aligned = 4,842,098 >>>>>>> Reads genomic origin exonic = 65,579,389 (83.37%) intronic = 8,763,168 (11.14%) intergenic = 4,322,483 (5.49%) overlapping exon = 2,638,502 (3.35%) >>>>>>> Transcript coverage profile 5' bias = 0.5 3' bias = 0.33 5'-3' bias = 1.6 >>>>>>> Junction analysis reads at junctions = 24,128,720 ACCT : 5.09% AGGT : 4.68% TCCT : 3.64% AGGA : 3.43% ATCT : 3.34% GCCT : 3.19% AGCT : 2.79% CCCT : 2.55% AGGC : 2.42% AGAT : 2.21% TTCT : 2.17%