RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354302.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) = 32,278,872 / 32,243,660 read pairs aligned = 32,238,826 total alignments = 68,736,447 secondary alignments = 4,213,915 non-unique alignments = 6,526,165 aligned to genes = 52,789,240 ambiguous alignments = 200,624 no feature assigned = 8,679,982 not aligned = 9,622,506 >>>>>>> Reads genomic origin exonic = 52,789,240 (85.88%) intronic = 5,342,589 (8.69%) intergenic = 3,337,393 (5.43%) overlapping exon = 2,264,367 (3.68%) >>>>>>> Transcript coverage profile 5' bias = 0.49 3' bias = 0.29 5'-3' bias = 1.73 >>>>>>> Junction analysis reads at junctions = 20,024,551 ACCT : 5.28% AGGT : 4.65% GCCT : 3.71% TCCT : 3.6% ATCT : 3.51% AGGA : 3.24% AGCT : 2.8% CCCT : 2.7% AGGC : 2.44% TTCT : 2.24% AGAT : 2.03%