RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354182.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) = 35,894,703 / 35,836,714 read pairs aligned = 35,826,008 total alignments = 76,153,681 secondary alignments = 4,422,264 non-unique alignments = 7,276,545 aligned to genes = 58,668,088 ambiguous alignments = 197,815 no feature assigned = 9,703,473 not aligned = 18,366,931 >>>>>>> Reads genomic origin exonic = 58,668,088 (85.81%) intronic = 6,506,344 (9.52%) intergenic = 3,197,129 (4.68%) overlapping exon = 2,551,209 (3.73%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.2 5'-3' bias = 2.13 >>>>>>> Junction analysis reads at junctions = 20,735,196 ACCT : 5.36% AGGT : 4.9% AGGA : 3.64% ATCT : 3.57% TCCT : 3.51% GCCT : 2.77% AGCT : 2.73% AGGC : 2.47% CCCT : 2.35% AGAT : 2.28% TTCT : 2.02%