RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354312.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) = 55,368,107 / 55,155,603 read pairs aligned = 55,120,104 total alignments = 124,092,572 secondary alignments = 13,568,862 non-unique alignments = 17,328,367 aligned to genes = 77,991,680 ambiguous alignments = 315,486 no feature assigned = 25,175,853 not aligned = 14,242,764 >>>>>>> Reads genomic origin exonic = 77,991,680 (75.6%) intronic = 13,694,504 (13.27%) intergenic = 11,481,349 (11.13%) overlapping exon = 4,859,254 (4.71%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.2 5'-3' bias = 1.67 >>>>>>> Junction analysis reads at junctions = 30,403,066 ACCT : 5.07% AGGT : 4.54% TCCT : 3.92% ATCT : 3.63% AGGA : 3.16% GCCT : 3.07% CCCT : 2.65% AGCT : 2.35% TTCT : 2.27% AGGC : 2.26% AGGG : 2.12%