RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354276.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) = 47,724,956 / 47,487,891 read pairs aligned = 47,449,698 total alignments = 113,422,231 secondary alignments = 18,209,384 non-unique alignments = 16,834,182 aligned to genes = 67,603,730 ambiguous alignments = 225,244 no feature assigned = 21,076,458 not aligned = 24,589,517 >>>>>>> Reads genomic origin exonic = 67,603,730 (76.23%) intronic = 11,272,500 (12.71%) intergenic = 9,803,958 (11.06%) overlapping exon = 4,394,135 (4.96%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.21 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 22,132,105 ACCT : 5.14% AGGT : 4.68% ATCT : 3.6% TCCT : 3.53% AGGA : 3.37% GCCT : 3.29% AGCT : 2.72% CCCT : 2.58% AGGC : 2.39% TTCT : 2.26% AGAT : 2.15%