RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354365.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) = 33,042,844 / 32,998,712 read pairs aligned = 32,994,763 total alignments = 71,436,516 secondary alignments = 5,394,960 non-unique alignments = 9,233,275 aligned to genes = 55,428,180 ambiguous alignments = 188,446 no feature assigned = 6,265,686 not aligned = 6,163,986 >>>>>>> Reads genomic origin exonic = 55,428,180 (89.84%) intronic = 3,147,593 (5.1%) intergenic = 3,118,093 (5.05%) overlapping exon = 1,917,589 (3.11%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.21 5'-3' bias = 1.95 >>>>>>> Junction analysis reads at junctions = 16,378,852 ACCT : 5.51% AGGT : 4.52% ATCT : 4.46% TCCT : 3.66% GCCT : 3.48% AGGA : 3.27% CCCT : 2.8% AGCT : 2.46% TTCT : 2.37% AGGC : 2.28% AGAT : 1.97%