RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354145.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) = 42,978,960 / 42,957,840 read pairs aligned = 42,950,386 total alignments = 92,496,504 secondary alignments = 6,559,704 non-unique alignments = 9,876,622 aligned to genes = 74,257,857 ambiguous alignments = 284,308 no feature assigned = 7,137,539 not aligned = 2,070,928 >>>>>>> Reads genomic origin exonic = 74,257,857 (91.23%) intronic = 4,317,226 (5.3%) intergenic = 2,820,313 (3.46%) overlapping exon = 2,811,043 (3.45%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.19 5'-3' bias = 2.09 >>>>>>> Junction analysis reads at junctions = 21,278,777 ACCT : 5.1% AGGT : 4.93% TCCT : 4.02% ATCT : 3.88% AGGA : 3.51% CCCT : 2.84% GCCT : 2.69% AGCT : 2.43% AGGC : 2.34% TTCT : 2.18% AGAA : 2.05%