RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354301.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) = 48,518,338 / 48,502,337 read pairs aligned = 48,480,640 total alignments = 107,131,429 secondary alignments = 10,110,754 non-unique alignments = 15,805,132 aligned to genes = 81,848,094 ambiguous alignments = 349,132 no feature assigned = 8,188,585 not aligned = 4,383,679 >>>>>>> Reads genomic origin exonic = 81,848,094 (90.91%) intronic = 4,629,773 (5.14%) intergenic = 3,558,812 (3.95%) overlapping exon = 4,204,894 (4.67%) >>>>>>> Transcript coverage profile 5' bias = 0.09 3' bias = 0.12 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 25,541,965 TCCT : 5.68% ACCT : 5.68% ATCT : 4.68% AGGT : 4% CCCT : 3.64% AGGA : 2.78% GCCT : 2.43% AGGC : 2.28% TCCC : 2.24% TTCT : 2.01% CGTA : 1.93%