RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354287.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) = 41,179,078 / 41,163,683 read pairs aligned = 41,160,538 total alignments = 88,066,736 secondary alignments = 5,723,975 non-unique alignments = 9,066,266 aligned to genes = 65,609,315 ambiguous alignments = 244,345 no feature assigned = 12,500,091 not aligned = 2,350,697 >>>>>>> Reads genomic origin exonic = 65,609,315 (84%) intronic = 7,006,116 (8.97%) intergenic = 5,493,975 (7.03%) overlapping exon = 2,781,279 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.51 3' bias = 0.26 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 23,410,277 ACCT : 5.15% AGGT : 4.77% ATCT : 3.54% AGGA : 3.53% TCCT : 3.49% GCCT : 3.27% AGCT : 2.78% CCCT : 2.71% AGGC : 2.44% AGAT : 2.19% TTCT : 2.18%