RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354282.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) = 39,897,390 / 39,879,538 read pairs aligned = 39,876,251 total alignments = 83,836,422 secondary alignments = 4,059,494 non-unique alignments = 7,027,679 aligned to genes = 69,640,242 ambiguous alignments = 200,633 no feature assigned = 6,774,157 not aligned = 2,390,252 >>>>>>> Reads genomic origin exonic = 69,640,242 (91.13%) intronic = 3,466,300 (4.54%) intergenic = 3,307,857 (4.33%) overlapping exon = 2,444,468 (3.2%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.13 5'-3' bias = 2.19 >>>>>>> Junction analysis reads at junctions = 22,535,627 ACCT : 5.53% AGGT : 4.97% AGGA : 3.72% ATCT : 3.59% TCCT : 3.34% GCCT : 2.93% AGCT : 2.76% AGAT : 2.43% AGGC : 2.41% CCCT : 2.29% TTCT : 2.15%