RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354073.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) = 41,137,377 / 41,110,579 read pairs aligned = 41,107,353 total alignments = 88,043,530 secondary alignments = 5,795,574 non-unique alignments = 9,455,229 aligned to genes = 68,641,636 ambiguous alignments = 254,839 no feature assigned = 9,340,537 not aligned = 2,753,522 >>>>>>> Reads genomic origin exonic = 68,641,636 (88.02%) intronic = 7,474,021 (9.58%) intergenic = 1,866,516 (2.39%) overlapping exon = 2,443,085 (3.13%) >>>>>>> Transcript coverage profile 5' bias = 0.4 3' bias = 0.2 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 25,364,238 ACCT : 5.06% AGGT : 4.3% AGGG : 3.44% AGGA : 3.31% TCCT : 3.13% ATCT : 3.11% AGCT : 2.51% CCCT : 2.49% GCCT : 2.25% AGGC : 2.09% AGAT : 2.06%