RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354234.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) = 38,927,039 / 38,897,006 read pairs aligned = 38,892,981 total alignments = 82,110,446 secondary alignments = 4,286,401 non-unique alignments = 7,199,834 aligned to genes = 67,195,445 ambiguous alignments = 217,100 no feature assigned = 7,211,262 not aligned = 3,915,797 >>>>>>> Reads genomic origin exonic = 67,195,445 (90.31%) intronic = 4,019,375 (5.4%) intergenic = 3,191,887 (4.29%) overlapping exon = 2,723,126 (3.66%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.16 5'-3' bias = 2.2 >>>>>>> Junction analysis reads at junctions = 22,465,272 ACCT : 5.5% AGGT : 4.78% AGGA : 3.56% ATCT : 3.48% TCCT : 3.39% GCCT : 3.22% AGCT : 2.68% AGGC : 2.46% AGAT : 2.32% CCCT : 2.27% TTCT : 2.1%