RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354150.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) = 40,803,528 / 40,757,692 read pairs aligned = 40,701,477 total alignments = 89,415,847 secondary alignments = 7,854,627 non-unique alignments = 10,636,133 aligned to genes = 68,665,649 ambiguous alignments = 287,450 no feature assigned = 8,095,545 not aligned = 4,250,922 >>>>>>> Reads genomic origin exonic = 68,665,649 (89.45%) intronic = 4,273,332 (5.57%) intergenic = 3,822,213 (4.98%) overlapping exon = 3,365,273 (4.38%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.2 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 21,279,171 ACCT : 5.39% TCCT : 4.49% AGGT : 4.41% ATCT : 4.38% GCCT : 3.53% AGGA : 2.98% CCCT : 2.91% TTCT : 2.3% AGCT : 2.23% AGGC : 2.23% TCCC : 1.75%