RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354306.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) = 74,436,389 / 74,382,890 read pairs aligned = 74,373,190 total alignments = 159,970,734 secondary alignments = 11,151,455 non-unique alignments = 16,050,091 aligned to genes = 130,152,536 ambiguous alignments = 592,704 no feature assigned = 11,231,764 not aligned = 4,123,807 >>>>>>> Reads genomic origin exonic = 130,152,536 (92.06%) intronic = 6,605,421 (4.67%) intergenic = 4,626,343 (3.27%) overlapping exon = 5,498,545 (3.89%) >>>>>>> Transcript coverage profile 5' bias = 0.16 3' bias = 0.15 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 49,983,960 ACCT : 5.27% TCCT : 4.68% AGGT : 4.32% ATCT : 4.18% CCCT : 3.2% AGGA : 2.85% AGGC : 2.45% GCCT : 2.42% AGCT : 2.14% TTCT : 1.9% GTCT : 1.84%