RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354097.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) = 73,092,226 / 73,052,131 read pairs aligned = 73,036,537 total alignments = 158,509,928 secondary alignments = 12,365,571 non-unique alignments = 19,498,233 aligned to genes = 125,137,379 ambiguous alignments = 555,416 no feature assigned = 11,929,206 not aligned = 5,120,351 >>>>>>> Reads genomic origin exonic = 125,137,379 (91.3%) intronic = 6,781,220 (4.95%) intergenic = 5,147,986 (3.76%) overlapping exon = 5,820,628 (4.25%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.12 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 43,410,114 ACCT : 5.2% TCCT : 5.03% ATCT : 4.59% AGGT : 4.37% CCCT : 3.51% AGGA : 2.88% GCCT : 2.41% AGGC : 2.35% TTCT : 2.28% AGCT : 1.97% AGAC : 1.87%