RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354285.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) = 42,783,518 / 42,761,557 read pairs aligned = 42,755,426 total alignments = 92,605,346 secondary alignments = 7,060,271 non-unique alignments = 10,411,634 aligned to genes = 73,515,350 ambiguous alignments = 346,357 no feature assigned = 7,165,298 not aligned = 2,328,623 >>>>>>> Reads genomic origin exonic = 73,515,350 (91.12%) intronic = 3,750,561 (4.65%) intergenic = 3,414,737 (4.23%) overlapping exon = 3,354,341 (4.16%) >>>>>>> Transcript coverage profile 5' bias = 0.14 3' bias = 0.15 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 23,119,113 TCCT : 4.94% ACCT : 4.76% AGGT : 4.51% ATCT : 4.39% CCCT : 3.72% AGGA : 3.1% AGGC : 2.33% GCCT : 2.33% AGCT : 2.15% TTCT : 2.07% GTCT : 1.97%