RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354257.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) = 37,371,332 / 37,350,980 read pairs aligned = 37,347,737 total alignments = 79,305,212 secondary alignments = 4,582,900 non-unique alignments = 6,988,597 aligned to genes = 60,971,233 ambiguous alignments = 197,631 no feature assigned = 10,487,770 not aligned = 1,455,100 >>>>>>> Reads genomic origin exonic = 60,971,233 (85.32%) intronic = 6,599,593 (9.24%) intergenic = 3,888,177 (5.44%) overlapping exon = 2,936,962 (4.11%) >>>>>>> Transcript coverage profile 5' bias = 0.49 3' bias = 0.25 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 23,168,261 ACCT : 5.31% AGGT : 4.68% TCCT : 3.68% ATCT : 3.57% AGGA : 3.37% GCCT : 3.3% AGCT : 2.74% CCCT : 2.62% AGGC : 2.45% TTCT : 2.27% AGAT : 2.19%