RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354317.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) = 54,016,946 / 53,903,667 read pairs aligned = 53,876,686 total alignments = 114,719,360 secondary alignments = 6,798,747 non-unique alignments = 11,461,059 aligned to genes = 90,728,969 ambiguous alignments = 315,339 no feature assigned = 11,894,619 not aligned = 11,310,349 >>>>>>> Reads genomic origin exonic = 90,728,969 (88.41%) intronic = 8,004,695 (7.8%) intergenic = 3,889,924 (3.79%) overlapping exon = 4,053,374 (3.95%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.15 5'-3' bias = 1.78 >>>>>>> Junction analysis reads at junctions = 28,960,168 ACCT : 5.58% AGGT : 4.54% ATCT : 3.88% TCCT : 3.54% GCCT : 3.44% AGGA : 3.28% AGCT : 2.48% CCCT : 2.42% AGGC : 2.28% TTCT : 2.21% AGAT : 2.01%