RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354359.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) = 44,654,380 / 44,433,459 read pairs aligned = 44,410,937 total alignments = 96,690,976 secondary alignments = 7,603,137 non-unique alignments = 12,722,812 aligned to genes = 74,831,669 ambiguous alignments = 325,029 no feature assigned = 8,303,413 not aligned = 7,746,249 >>>>>>> Reads genomic origin exonic = 74,831,669 (90.01%) intronic = 4,667,738 (5.61%) intergenic = 3,635,675 (4.37%) overlapping exon = 3,380,284 (4.07%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.25 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 24,445,889 ACCT : 5.09% AGGT : 4.54% ATCT : 4.09% TCCT : 4.06% AGGA : 3.33% GCCT : 3.29% CCCT : 2.93% AGCT : 2.55% AGGC : 2.27% TTCT : 2.07% AGAA : 1.81%