RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354154.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) = 43,958,974 / 43,931,656 read pairs aligned = 43,920,759 total alignments = 95,778,872 secondary alignments = 7,888,242 non-unique alignments = 11,971,165 aligned to genes = 74,402,360 ambiguous alignments = 323,932 no feature assigned = 8,028,480 not aligned = 2,309,888 >>>>>>> Reads genomic origin exonic = 74,402,360 (90.26%) intronic = 4,889,934 (5.93%) intergenic = 3,138,546 (3.81%) overlapping exon = 3,715,801 (4.51%) >>>>>>> Transcript coverage profile 5' bias = 0.14 3' bias = 0.14 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 23,854,712 TCCT : 5.58% ACCT : 5.09% ATCT : 4.87% AGGT : 4.21% CCCT : 3.35% AGGA : 2.96% GCCT : 2.57% TTCT : 2.4% AGGC : 2.14% AGCT : 1.99% GTCT : 1.97%