RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354151.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) = 39,209,076 / 39,176,786 read pairs aligned = 39,170,967 total alignments = 82,782,493 secondary alignments = 4,396,631 non-unique alignments = 7,375,215 aligned to genes = 64,308,824 ambiguous alignments = 220,081 no feature assigned = 10,587,762 not aligned = 7,731,602 >>>>>>> Reads genomic origin exonic = 64,308,824 (85.86%) intronic = 7,313,756 (9.77%) intergenic = 3,274,006 (4.37%) overlapping exon = 2,881,661 (3.85%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.2 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 21,977,265 ACCT : 5.26% AGGT : 4.65% ATCT : 3.73% AGGA : 3.55% TCCT : 3.36% GCCT : 3.12% AGCT : 2.78% AGGC : 2.41% AGAT : 2.33% CCCT : 2.33% TTCT : 2.16%