RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354127.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) = 76,972,746 / 76,744,382 read pairs aligned = 76,733,279 total alignments = 162,285,685 secondary alignments = 8,568,557 non-unique alignments = 13,615,947 aligned to genes = 122,737,359 ambiguous alignments = 447,878 no feature assigned = 24,530,821 not aligned = 21,205,742 >>>>>>> Reads genomic origin exonic = 122,737,359 (83.34%) intronic = 17,092,562 (11.61%) intergenic = 7,438,259 (5.05%) overlapping exon = 6,544,453 (4.44%) >>>>>>> Transcript coverage profile 5' bias = 0.5 3' bias = 0.27 5'-3' bias = 1.66 >>>>>>> Junction analysis reads at junctions = 51,067,445 ACCT : 5.05% AGGT : 4.72% ATCT : 3.66% TCCT : 3.46% AGGA : 3.42% GCCT : 3.38% AGCT : 2.9% CCCT : 2.78% AGGC : 2.5% AGAT : 2.11% TTCT : 2.1%