RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354275.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) = 38,745,906 / 38,727,893 read pairs aligned = 38,724,558 total alignments = 81,724,604 secondary alignments = 4,250,805 non-unique alignments = 7,169,348 aligned to genes = 65,205,167 ambiguous alignments = 211,388 no feature assigned = 8,855,449 not aligned = 3,045,629 >>>>>>> Reads genomic origin exonic = 65,205,167 (88.04%) intronic = 5,370,701 (7.25%) intergenic = 3,484,748 (4.71%) overlapping exon = 2,623,014 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.15 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 20,231,531 ACCT : 5.49% AGGT : 4.77% AGGA : 3.6% ATCT : 3.55% TCCT : 3.28% GCCT : 3.18% AGCT : 2.78% AGGC : 2.4% AGAT : 2.32% CCCT : 2.32% TTCT : 2.12%