RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354382.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) = 53,032,111 / 52,992,423 read pairs aligned = 52,970,654 total alignments = 113,957,177 secondary alignments = 7,932,643 non-unique alignments = 13,359,686 aligned to genes = 89,280,779 ambiguous alignments = 330,588 no feature assigned = 10,400,524 not aligned = 2,532,034 >>>>>>> Reads genomic origin exonic = 89,280,779 (89.57%) intronic = 6,131,288 (6.15%) intergenic = 4,269,236 (4.28%) overlapping exon = 4,143,351 (4.16%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.22 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 29,720,911 ACCT : 5.54% AGGT : 4.51% ATCT : 3.98% TCCT : 3.87% GCCT : 3.49% AGGA : 3.11% CCCT : 2.79% AGCT : 2.45% AGGC : 2.33% TTCT : 2.2% AGGG : 1.75%