RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354137.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) = 34,113,264 / 34,095,273 read pairs aligned = 34,093,215 total alignments = 73,017,422 secondary alignments = 4,808,885 non-unique alignments = 7,812,601 aligned to genes = 58,194,985 ambiguous alignments = 198,509 no feature assigned = 6,358,416 not aligned = 2,073,297 >>>>>>> Reads genomic origin exonic = 58,194,985 (90.15%) intronic = 4,028,008 (6.24%) intergenic = 2,330,408 (3.61%) overlapping exon = 2,068,573 (3.2%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.25 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 19,251,592 ACCT : 5.33% AGGT : 4.72% ATCT : 3.59% AGGA : 3.54% TCCT : 3.39% GCCT : 3.23% AGCT : 2.81% CCCT : 2.52% AGGC : 2.37% AGAT : 2.25% TTCT : 2.16%