RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354327.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) = 38,589,868 / 38,541,275 read pairs aligned = 38,534,944 total alignments = 82,976,778 secondary alignments = 5,845,635 non-unique alignments = 9,607,361 aligned to genes = 64,189,427 ambiguous alignments = 230,023 no feature assigned = 8,452,255 not aligned = 10,529,167 >>>>>>> Reads genomic origin exonic = 64,189,427 (88.36%) intronic = 5,303,880 (7.3%) intergenic = 3,148,375 (4.33%) overlapping exon = 2,416,819 (3.33%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.2 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 19,813,294 ACCT : 5.55% AGGT : 4.86% ATCT : 3.6% TCCT : 3.53% AGGA : 3.52% GCCT : 3.13% CCCT : 2.57% AGCT : 2.55% AGGC : 2.41% AGAT : 2.17% TTCT : 2.1%