RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354131.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) = 57,394,953 / 57,353,995 read pairs aligned = 57,348,042 total alignments = 122,185,770 secondary alignments = 7,436,822 non-unique alignments = 12,412,179 aligned to genes = 92,062,463 ambiguous alignments = 314,697 no feature assigned = 16,915,742 not aligned = 4,107,292 >>>>>>> Reads genomic origin exonic = 92,062,463 (84.48%) intronic = 11,877,722 (10.9%) intergenic = 5,038,020 (4.62%) overlapping exon = 3,915,960 (3.59%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.18 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 28,412,628 ACCT : 5.34% AGGT : 4.66% ATCT : 3.67% AGGA : 3.66% TCCT : 3.51% GCCT : 3.18% AGCT : 2.65% CCCT : 2.45% AGAT : 2.39% AGGC : 2.37% TTCT : 2.16%