RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354268.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) = 45,214,002 / 45,187,637 read pairs aligned = 45,177,618 total alignments = 97,759,854 secondary alignments = 7,358,215 non-unique alignments = 11,464,691 aligned to genes = 77,796,320 ambiguous alignments = 363,721 no feature assigned = 7,356,290 not aligned = 3,522,613 >>>>>>> Reads genomic origin exonic = 77,796,320 (91.36%) intronic = 4,482,980 (5.26%) intergenic = 2,873,310 (3.37%) overlapping exon = 3,633,591 (4.27%) >>>>>>> Transcript coverage profile 5' bias = 0.12 3' bias = 0.11 5'-3' bias = 2.47 >>>>>>> Junction analysis reads at junctions = 27,231,485 ACCT : 5.11% TCCT : 4.77% AGGT : 4.66% ATCT : 4.37% AGGA : 3% CCCT : 2.89% AGGC : 2.65% GCCT : 2.11% AGAC : 2.07% AGCT : 2.02% AGAA : 1.72%