RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354333.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) = 93,225,169 / 93,121,755 read pairs aligned = 93,111,872 total alignments = 199,686,523 secondary alignments = 13,339,599 non-unique alignments = 20,180,971 aligned to genes = 147,666,855 ambiguous alignments = 572,738 no feature assigned = 29,367,149 not aligned = 15,040,988 >>>>>>> Reads genomic origin exonic = 147,666,855 (83.41%) intronic = 17,610,531 (9.95%) intergenic = 11,756,618 (6.64%) overlapping exon = 7,082,759 (4%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.3 5'-3' bias = 1.77 >>>>>>> Junction analysis reads at junctions = 69,055,608 ACCT : 5.01% AGGT : 4.93% ATCT : 3.54% TCCT : 3.53% AGGA : 3.31% GCCT : 2.8% CCCT : 2.63% AGCT : 2.62% AGGC : 2.51% TTCT : 2.32% AGGG : 2.05%