RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354353.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) = 34,792,685 / 34,780,285 read pairs aligned = 34,777,503 total alignments = 74,629,900 secondary alignments = 5,056,930 non-unique alignments = 8,265,686 aligned to genes = 54,592,633 ambiguous alignments = 200,522 no feature assigned = 11,193,028 not aligned = 2,305,876 >>>>>>> Reads genomic origin exonic = 54,592,633 (82.99%) intronic = 6,925,938 (10.53%) intergenic = 4,267,090 (6.49%) overlapping exon = 2,187,974 (3.33%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.26 5'-3' bias = 1.65 >>>>>>> Junction analysis reads at junctions = 19,035,250 ACCT : 5.21% AGGT : 4.77% ATCT : 3.57% TCCT : 3.51% AGGA : 3.46% GCCT : 3.13% AGCT : 2.64% CCCT : 2.56% AGGC : 2.43% TTCT : 2.29% AGAT : 2.21%