RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354105.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) = 50,061,270 / 50,020,465 read pairs aligned = 50,012,580 total alignments = 106,422,720 secondary alignments = 6,340,985 non-unique alignments = 10,505,566 aligned to genes = 84,025,171 ambiguous alignments = 259,803 no feature assigned = 11,163,723 not aligned = 8,516,585 >>>>>>> Reads genomic origin exonic = 84,025,171 (88.27%) intronic = 6,685,446 (7.02%) intergenic = 4,478,277 (4.7%) overlapping exon = 3,323,879 (3.49%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.12 5'-3' bias = 2.3 >>>>>>> Junction analysis reads at junctions = 27,747,968 ACCT : 5.55% AGGT : 4.65% ATCT : 3.63% AGGA : 3.61% TCCT : 3.33% GCCT : 3.22% AGCT : 2.62% AGGC : 2.37% CCCT : 2.27% AGAT : 2.25% TTCT : 2.2%