RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354281.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) = 37,526,378 / 37,512,103 read pairs aligned = 37,506,184 total alignments = 80,776,508 secondary alignments = 5,738,027 non-unique alignments = 9,339,493 aligned to genes = 64,335,667 ambiguous alignments = 242,768 no feature assigned = 6,352,539 not aligned = 3,729,815 >>>>>>> Reads genomic origin exonic = 64,335,667 (91.01%) intronic = 3,546,037 (5.02%) intergenic = 2,806,502 (3.97%) overlapping exon = 2,478,877 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.22 3' bias = 0.14 5'-3' bias = 2.29 >>>>>>> Junction analysis reads at junctions = 19,390,930 ACCT : 5.09% AGGT : 4.77% ATCT : 4.32% TCCT : 4.21% AGGA : 3.29% CCCT : 2.92% GCCT : 2.83% AGCT : 2.31% AGGC : 2.22% TTCT : 2.1% AGAA : 1.99%