RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354403.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) = 53,575,022 / 53,530,134 read pairs aligned = 53,521,751 total alignments = 113,705,171 secondary alignments = 6,600,015 non-unique alignments = 11,095,750 aligned to genes = 88,668,174 ambiguous alignments = 284,189 no feature assigned = 13,266,174 not aligned = 9,399,940 >>>>>>> Reads genomic origin exonic = 88,668,174 (86.99%) intronic = 8,399,372 (8.24%) intergenic = 4,866,802 (4.77%) overlapping exon = 3,678,841 (3.61%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.19 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 28,778,570 ACCT : 5.38% AGGT : 4.64% ATCT : 3.75% TCCT : 3.6% AGGA : 3.47% GCCT : 3.25% AGCT : 2.66% AGGC : 2.46% CCCT : 2.41% AGAT : 2.25% TTCT : 2.23%