RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354250.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) = 40,119,530 / 40,095,269 read pairs aligned = 40,091,153 total alignments = 85,136,767 secondary alignments = 4,921,968 non-unique alignments = 7,899,604 aligned to genes = 66,538,643 ambiguous alignments = 272,396 no feature assigned = 9,935,478 not aligned = 3,188,711 >>>>>>> Reads genomic origin exonic = 66,538,643 (87.01%) intronic = 5,955,768 (7.79%) intergenic = 3,979,710 (5.2%) overlapping exon = 3,002,008 (3.93%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.31 5'-3' bias = 1.61 >>>>>>> Junction analysis reads at junctions = 24,181,798 ACCT : 5.12% AGGT : 4.71% ATCT : 3.62% TCCT : 3.6% GCCT : 3.43% AGGA : 3.26% CCCT : 2.68% AGCT : 2.65% AGGC : 2.48% TTCT : 2.41% AGAT : 1.92%