RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354348.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) = 72,536,996 / 72,475,033 read pairs aligned = 72,468,922 total alignments = 154,136,693 secondary alignments = 9,124,664 non-unique alignments = 15,150,620 aligned to genes = 122,359,663 ambiguous alignments = 377,440 no feature assigned = 15,540,563 not aligned = 10,643,469 >>>>>>> Reads genomic origin exonic = 122,359,663 (88.73%) intronic = 9,386,149 (6.81%) intergenic = 6,154,414 (4.46%) overlapping exon = 4,630,179 (3.36%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.15 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 37,620,799 ACCT : 5.35% AGGT : 4.72% ATCT : 3.86% AGGA : 3.63% TCCT : 3.37% GCCT : 3.26% AGCT : 2.72% CCCT : 2.43% AGGC : 2.38% AGAT : 2.26% TTCT : 2.24%