RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354188.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) = 77,171,218 / 77,078,129 read pairs aligned = 77,071,324 total alignments = 162,617,416 secondary alignments = 8,368,069 non-unique alignments = 13,913,559 aligned to genes = 132,003,600 ambiguous alignments = 377,175 no feature assigned = 15,718,235 not aligned = 6,855,957 >>>>>>> Reads genomic origin exonic = 132,003,600 (89.36%) intronic = 8,476,216 (5.74%) intergenic = 7,242,019 (4.9%) overlapping exon = 5,774,933 (3.91%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.15 5'-3' bias = 2.2 >>>>>>> Junction analysis reads at junctions = 45,019,235 ACCT : 5.45% AGGT : 4.8% AGGA : 3.57% ATCT : 3.48% TCCT : 3.32% GCCT : 3.1% AGCT : 2.82% AGGC : 2.43% CCCT : 2.26% AGAT : 2.2% TTCT : 2.16%