RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354063.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) = 39,530,128 / 39,501,661 read pairs aligned = 39,493,746 total alignments = 86,917,844 secondary alignments = 7,886,055 non-unique alignments = 11,367,644 aligned to genes = 66,539,512 ambiguous alignments = 284,814 no feature assigned = 7,339,032 not aligned = 3,611,665 >>>>>>> Reads genomic origin exonic = 66,539,512 (90.07%) intronic = 3,908,808 (5.29%) intergenic = 3,430,224 (4.64%) overlapping exon = 3,476,577 (4.71%) >>>>>>> Transcript coverage profile 5' bias = 0.09 3' bias = 0.11 5'-3' bias = 2.41 >>>>>>> Junction analysis reads at junctions = 22,236,808 ACCT : 5.95% TCCT : 5.73% ATCT : 4.79% AGGT : 3.87% CCCT : 3.61% AGGA : 2.78% TCCC : 2.76% GCCT : 2.61% CGTA : 2.45% AGGC : 2.24% CCCA : 2.12%