RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354335.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) = 51,932,319 / 51,881,634 read pairs aligned = 51,874,937 total alignments = 111,146,297 secondary alignments = 7,332,344 non-unique alignments = 12,347,491 aligned to genes = 87,599,963 ambiguous alignments = 306,042 no feature assigned = 10,429,478 not aligned = 14,904,677 >>>>>>> Reads genomic origin exonic = 87,599,963 (89.36%) intronic = 6,161,620 (6.29%) intergenic = 4,267,858 (4.35%) overlapping exon = 2,934,142 (2.99%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.19 5'-3' bias = 2.21 >>>>>>> Junction analysis reads at junctions = 25,377,641 ACCT : 5.51% AGGT : 4.8% ATCT : 3.73% TCCT : 3.59% AGGA : 3.52% GCCT : 3.17% CCCT : 2.72% AGCT : 2.52% AGGC : 2.37% TTCT : 2.29% AGAT : 2.23%