RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354174.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) = 24,391,287 / 24,369,594 read pairs aligned = 24,367,368 total alignments = 52,696,887 secondary alignments = 3,936,006 non-unique alignments = 5,659,039 aligned to genes = 42,011,593 ambiguous alignments = 183,673 no feature assigned = 4,177,882 not aligned = 2,150,599 >>>>>>> Reads genomic origin exonic = 42,011,593 (90.95%) intronic = 2,513,010 (5.44%) intergenic = 1,664,872 (3.6%) overlapping exon = 1,470,901 (3.18%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.22 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 13,987,444 ACCT : 5.38% AGGT : 4.7% ATCT : 4.04% TCCT : 3.91% GCCT : 3.25% AGGA : 3.2% CCCT : 2.64% AGCT : 2.37% TTCT : 2.37% AGGC : 2.24% AGAA : 1.93%