RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354162.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) = 43,287,942 / 43,257,926 read pairs aligned = 43,247,963 total alignments = 95,645,390 secondary alignments = 9,099,522 non-unique alignments = 13,734,213 aligned to genes = 72,355,230 ambiguous alignments = 340,285 no feature assigned = 7,825,609 not aligned = 3,586,752 >>>>>>> Reads genomic origin exonic = 72,355,230 (90.24%) intronic = 4,258,933 (5.31%) intergenic = 3,566,676 (4.45%) overlapping exon = 3,968,671 (4.95%) >>>>>>> Transcript coverage profile 5' bias = 0.07 3' bias = 0.1 5'-3' bias = 2.27 >>>>>>> Junction analysis reads at junctions = 20,651,047 TCCT : 5.65% ACCT : 5.1% ATCT : 4.55% CCCT : 4.54% AGGT : 4.19% AGGA : 2.74% AGGC : 2.27% GCCT : 2.15% GTCT : 2.13% TTCT : 2.07% AGAC : 1.89%