RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354308.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) = 35,229,330 / 35,184,606 read pairs aligned = 35,181,118 total alignments = 75,243,595 secondary alignments = 4,829,659 non-unique alignments = 8,154,856 aligned to genes = 58,393,474 ambiguous alignments = 204,378 no feature assigned = 8,169,029 not aligned = 4,455,770 >>>>>>> Reads genomic origin exonic = 58,393,474 (87.73%) intronic = 5,111,403 (7.68%) intergenic = 3,057,626 (4.59%) overlapping exon = 2,177,958 (3.27%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.19 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 16,811,769 ACCT : 5.17% AGGT : 4.8% ATCT : 3.81% AGGA : 3.57% TCCT : 3.37% GCCT : 3.16% AGCT : 2.77% CCCT : 2.54% AGGC : 2.44% AGAT : 2.33% TTCT : 2.1%