RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354101.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) = 30,575,032 / 30,474,505 read pairs aligned = 30,460,099 total alignments = 64,880,934 secondary alignments = 3,831,397 non-unique alignments = 6,518,319 aligned to genes = 50,875,929 ambiguous alignments = 185,694 no feature assigned = 7,129,641 not aligned = 11,590,159 >>>>>>> Reads genomic origin exonic = 50,875,929 (87.71%) intronic = 4,139,631 (7.14%) intergenic = 2,990,010 (5.15%) overlapping exon = 2,042,604 (3.52%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.18 5'-3' bias = 2.36 >>>>>>> Junction analysis reads at junctions = 16,141,318 ACCT : 5.7% AGGT : 4.73% ATCT : 3.8% TCCT : 3.72% AGGA : 3.46% GCCT : 3.16% CCCT : 2.58% AGCT : 2.51% AGGC : 2.32% AGAT : 2.1% TTCT : 2.06%