RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354286.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) = 50,804,449 / 50,767,969 read pairs aligned = 50,749,427 total alignments = 110,041,040 secondary alignments = 8,468,622 non-unique alignments = 13,310,122 aligned to genes = 87,019,877 ambiguous alignments = 300,344 no feature assigned = 8,473,427 not aligned = 4,721,272 >>>>>>> Reads genomic origin exonic = 87,019,877 (91.13%) intronic = 4,601,633 (4.82%) intergenic = 3,871,794 (4.05%) overlapping exon = 3,835,860 (4.02%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.13 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 25,639,743 ACCT : 5.65% TCCT : 4.87% ATCT : 4.76% AGGT : 4.1% CCCT : 3.14% GCCT : 2.86% AGGA : 2.83% TCCC : 2.5% AGGC : 2.21% CGTA : 2.07% CCCA : 1.98%