RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354067.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) = 29,642,191 / 29,621,753 read pairs aligned = 29,619,433 total alignments = 63,408,166 secondary alignments = 4,144,222 non-unique alignments = 6,855,660 aligned to genes = 49,777,067 ambiguous alignments = 178,089 no feature assigned = 6,300,637 not aligned = 2,359,404 >>>>>>> Reads genomic origin exonic = 49,777,067 (88.76%) intronic = 4,290,219 (7.65%) intergenic = 2,010,418 (3.59%) overlapping exon = 1,708,140 (3.05%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.24 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 17,116,733 ACCT : 5.55% AGGT : 4.48% ATCT : 3.63% GCCT : 3.59% TCCT : 3.44% AGGA : 3.33% AGCT : 2.7% CCCT : 2.5% AGGC : 2.37% TTCT : 2.21% AGAT : 2.08%