RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354414.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) = 58,554,816 / 58,525,802 read pairs aligned = 58,515,123 total alignments = 132,247,847 secondary alignments = 15,167,229 non-unique alignments = 18,913,450 aligned to genes = 95,729,342 ambiguous alignments = 565,887 no feature assigned = 13,024,829 not aligned = 3,035,444 >>>>>>> Reads genomic origin exonic = 95,729,342 (88.02%) intronic = 9,685,508 (8.91%) intergenic = 3,339,321 (3.07%) overlapping exon = 5,609,166 (5.16%) >>>>>>> Transcript coverage profile 5' bias = 0.22 3' bias = 0.16 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 37,442,004 ACCT : 4.87% TCCT : 4.78% ATCT : 4.53% AGGT : 4.44% CCCT : 3.53% AGGA : 3.46% GCCT : 3.06% AGCT : 2.15% AGGC : 2.09% TTCT : 2.04% AGAA : 1.8%