RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354049.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) = 44,037,452 / 44,003,256 read pairs aligned = 43,997,586 total alignments = 93,616,528 secondary alignments = 5,575,820 non-unique alignments = 9,305,861 aligned to genes = 70,431,424 ambiguous alignments = 246,340 no feature assigned = 13,279,447 not aligned = 4,901,880 >>>>>>> Reads genomic origin exonic = 70,431,424 (84.14%) intronic = 10,164,642 (12.14%) intergenic = 3,114,805 (3.72%) overlapping exon = 2,983,825 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.17 5'-3' bias = 2.31 >>>>>>> Junction analysis reads at junctions = 22,475,219 ACCT : 5.2% AGGT : 4.82% AGGA : 3.75% ATCT : 3.61% TCCT : 3.54% GCCT : 2.77% AGCT : 2.76% CCCT : 2.4% AGGC : 2.38% AGAT : 2.37% TTCT : 2.2%