RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354168.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) = 39,647,906 / 39,626,495 read pairs aligned = 39,623,385 total alignments = 84,451,008 secondary alignments = 5,176,607 non-unique alignments = 8,437,724 aligned to genes = 67,877,665 ambiguous alignments = 231,390 no feature assigned = 7,478,344 not aligned = 2,399,353 >>>>>>> Reads genomic origin exonic = 67,877,665 (90.08%) intronic = 4,885,422 (6.48%) intergenic = 2,592,922 (3.44%) overlapping exon = 2,346,326 (3.11%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.2 5'-3' bias = 1.77 >>>>>>> Junction analysis reads at junctions = 22,286,107 ACCT : 5.35% AGGT : 4.49% ATCT : 3.66% GCCT : 3.46% TCCT : 3.42% AGGA : 3.37% AGCT : 2.72% AGGC : 2.34% CCCT : 2.33% TTCT : 2.15% AGAT : 2.07%