RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354247.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) = 38,363,422 / 38,313,731 read pairs aligned = 38,305,241 total alignments = 81,450,009 secondary alignments = 4,772,856 non-unique alignments = 7,782,762 aligned to genes = 62,118,412 ambiguous alignments = 205,160 no feature assigned = 10,952,328 not aligned = 3,673,401 >>>>>>> Reads genomic origin exonic = 62,118,412 (85.01%) intronic = 7,708,056 (10.55%) intergenic = 3,244,272 (4.44%) overlapping exon = 2,985,252 (4.09%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.17 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 21,511,206 ACCT : 5.34% AGGT : 4.72% ATCT : 3.81% AGGA : 3.64% GCCT : 3.35% TCCT : 3.27% AGCT : 2.68% CCCT : 2.59% AGGC : 2.36% AGAT : 2.36% TTCT : 2.15%