RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354212.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) = 37,942,763 / 37,933,733 read pairs aligned = 37,930,542 total alignments = 80,868,024 secondary alignments = 4,991,528 non-unique alignments = 8,258,805 aligned to genes = 63,934,321 ambiguous alignments = 214,149 no feature assigned = 8,095,208 not aligned = 1,442,106 >>>>>>> Reads genomic origin exonic = 63,934,321 (88.76%) intronic = 5,163,269 (7.17%) intergenic = 2,931,939 (4.07%) overlapping exon = 2,154,000 (2.99%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.17 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 19,757,900 ACCT : 5.56% AGGT : 4.78% AGGA : 3.52% ATCT : 3.49% GCCT : 3.28% TCCT : 3.26% AGCT : 2.77% AGGC : 2.41% AGAT : 2.3% CCCT : 2.29% TTCT : 2.17%