RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354076.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) = 47,851,335 / 47,822,950 read pairs aligned = 47,812,514 total alignments = 105,792,541 secondary alignments = 10,118,256 non-unique alignments = 14,817,796 aligned to genes = 80,687,414 ambiguous alignments = 397,717 no feature assigned = 8,225,760 not aligned = 3,201,471 >>>>>>> Reads genomic origin exonic = 80,687,414 (90.75%) intronic = 4,879,503 (5.49%) intergenic = 3,346,257 (3.76%) overlapping exon = 3,827,583 (4.3%) >>>>>>> Transcript coverage profile 5' bias = 0.06 3' bias = 0.08 5'-3' bias = 2.29 >>>>>>> Junction analysis reads at junctions = 24,925,098 TCCT : 6.55% ACCT : 5.56% CCCT : 5.33% ATCT : 4.79% AGGT : 3.7% AGGA : 2.72% GTCT : 2.41% AGAC : 2.24% AGGC : 2.17% TCCG : 2.11% GCCT : 1.89%