RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354152.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) = 43,784,563 / 43,746,651 read pairs aligned = 43,740,530 total alignments = 92,675,529 secondary alignments = 5,144,315 non-unique alignments = 8,626,931 aligned to genes = 71,690,800 ambiguous alignments = 251,499 no feature assigned = 11,763,025 not aligned = 8,634,736 >>>>>>> Reads genomic origin exonic = 71,690,800 (85.9%) intronic = 7,497,951 (8.98%) intergenic = 4,265,074 (5.11%) overlapping exon = 3,187,644 (3.82%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.18 5'-3' bias = 1.79 >>>>>>> Junction analysis reads at junctions = 22,059,751 ACCT : 5.45% AGGT : 4.74% AGGA : 3.57% ATCT : 3.5% TCCT : 3.32% GCCT : 3.13% AGCT : 2.73% AGGC : 2.43% CCCT : 2.36% AGAT : 2.36% TTCT : 2.27%