RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354124.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) = 43,818,274 / 43,756,651 read pairs aligned = 43,741,720 total alignments = 92,685,714 secondary alignments = 5,110,789 non-unique alignments = 8,643,914 aligned to genes = 71,345,121 ambiguous alignments = 204,702 no feature assigned = 12,174,338 not aligned = 7,222,245 >>>>>>> Reads genomic origin exonic = 71,345,121 (85.42%) intronic = 8,445,716 (10.11%) intergenic = 3,728,622 (4.46%) overlapping exon = 3,524,589 (4.22%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.14 5'-3' bias = 2.15 >>>>>>> Junction analysis reads at junctions = 22,817,979 ACCT : 5.36% AGGT : 4.68% AGGA : 3.69% ATCT : 3.63% TCCT : 3.38% GCCT : 2.93% AGCT : 2.71% AGAT : 2.4% AGGC : 2.33% CCCT : 2.23% TTCT : 2.2%