RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354314.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) = 44,621,804 / 44,541,931 read pairs aligned = 44,519,442 total alignments = 96,286,785 secondary alignments = 7,123,050 non-unique alignments = 11,214,189 aligned to genes = 76,533,741 ambiguous alignments = 332,960 no feature assigned = 7,527,045 not aligned = 5,872,927 >>>>>>> Reads genomic origin exonic = 76,533,741 (91.05%) intronic = 4,131,599 (4.92%) intergenic = 3,395,446 (4.04%) overlapping exon = 3,147,267 (3.74%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.14 5'-3' bias = 1.77 >>>>>>> Junction analysis reads at junctions = 22,147,650 TCCT : 5.27% ACCT : 5.09% ATCT : 4.57% AGGT : 4.19% CCCT : 3.49% AGGA : 2.83% GCCT : 2.39% AGGC : 2.37% TTCT : 2.1% AGCT : 2.05% AGAC : 1.92%