RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354262.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) = 77,335,447 / 77,293,051 read pairs aligned = 77,286,095 total alignments = 166,269,135 secondary alignments = 11,640,637 non-unique alignments = 16,825,632 aligned to genes = 127,306,360 ambiguous alignments = 625,296 no feature assigned = 19,475,202 not aligned = 3,611,796 >>>>>>> Reads genomic origin exonic = 127,306,360 (86.73%) intronic = 11,572,423 (7.88%) intergenic = 7,902,779 (5.38%) overlapping exon = 6,355,357 (4.33%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.27 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 53,989,479 ACCT : 5.22% TCCT : 4.66% AGGT : 4.51% ATCT : 4.1% GCCT : 3.65% CCCT : 2.95% AGGA : 2.91% AGGC : 2.45% AGCT : 2.37% TTCT : 2.29% GTCT : 1.99%