RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354121.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) = 34,238,502 / 34,221,072 read pairs aligned = 34,217,632 total alignments = 72,718,384 secondary alignments = 4,258,810 non-unique alignments = 6,987,413 aligned to genes = 57,048,141 ambiguous alignments = 216,830 no feature assigned = 8,155,912 not aligned = 3,391,698 >>>>>>> Reads genomic origin exonic = 57,048,141 (87.49%) intronic = 6,106,600 (9.37%) intergenic = 2,049,312 (3.14%) overlapping exon = 2,120,627 (3.25%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.21 5'-3' bias = 1.8 >>>>>>> Junction analysis reads at junctions = 20,814,667 ACCT : 5.47% AGGT : 4.54% AGGA : 3.47% GCCT : 3.47% ATCT : 3.46% TCCT : 3.4% AGCT : 2.78% AGGC : 2.37% CCCT : 2.3% AGAT : 2.28% TTCT : 2.01%