RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354149.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) = 50,378,992 / 50,325,321 read pairs aligned = 50,301,081 total alignments = 107,191,100 secondary alignments = 6,486,787 non-unique alignments = 10,447,453 aligned to genes = 84,572,405 ambiguous alignments = 332,673 no feature assigned = 11,253,456 not aligned = 2,223,511 >>>>>>> Reads genomic origin exonic = 84,572,405 (88.26%) intronic = 7,628,894 (7.96%) intergenic = 3,624,562 (3.78%) overlapping exon = 4,306,595 (4.49%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.19 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 31,040,815 ACCT : 5.4% AGGT : 5.04% AGGA : 3.55% ATCT : 3.53% TCCT : 3.44% GCCT : 3.22% AGCT : 2.68% CCCT : 2.57% AGGC : 2.44% TTCT : 2.3% AGAT : 2.2%