RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354331.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) = 57,922,780 / 57,795,728 read pairs aligned = 57,781,796 total alignments = 122,855,076 secondary alignments = 7,136,568 non-unique alignments = 11,349,271 aligned to genes = 92,481,700 ambiguous alignments = 356,800 no feature assigned = 17,946,866 not aligned = 27,840,528 >>>>>>> Reads genomic origin exonic = 92,481,700 (83.75%) intronic = 12,154,731 (11.01%) intergenic = 5,792,135 (5.25%) overlapping exon = 4,570,860 (4.14%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.3 5'-3' bias = 1.65 >>>>>>> Junction analysis reads at junctions = 39,181,914 ACCT : 5.15% AGGT : 4.73% TCCT : 3.7% ATCT : 3.52% AGGA : 3.37% GCCT : 3.28% AGCT : 2.77% CCCT : 2.75% AGGC : 2.51% AGAT : 2.04% TTCT : 2.04%