RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354183.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) = 36,392,574 / 36,380,480 read pairs aligned = 36,377,388 total alignments = 78,111,554 secondary alignments = 5,338,500 non-unique alignments = 8,483,075 aligned to genes = 57,184,622 ambiguous alignments = 222,862 no feature assigned = 11,639,800 not aligned = 1,949,258 >>>>>>> Reads genomic origin exonic = 57,184,622 (83.09%) intronic = 7,322,000 (10.64%) intergenic = 4,317,800 (6.27%) overlapping exon = 2,388,646 (3.47%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.3 5'-3' bias = 1.63 >>>>>>> Junction analysis reads at junctions = 21,481,595 ACCT : 5.18% AGGT : 4.67% ATCT : 3.61% TCCT : 3.49% GCCT : 3.47% AGGA : 3.36% AGCT : 2.76% CCCT : 2.73% AGGC : 2.43% TTCT : 2.19% AGAT : 2.09%