RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354205.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) = 36,785,659 / 36,758,523 read pairs aligned = 36,754,907 total alignments = 79,060,583 secondary alignments = 5,516,401 non-unique alignments = 8,737,387 aligned to genes = 55,012,156 ambiguous alignments = 202,650 no feature assigned = 14,466,301 not aligned = 3,749,026 >>>>>>> Reads genomic origin exonic = 55,012,156 (79.18%) intronic = 7,805,722 (11.23%) intergenic = 6,660,579 (9.59%) overlapping exon = 2,372,250 (3.41%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.24 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 21,362,368 ACCT : 5.17% AGGT : 4.64% ATCT : 3.65% TCCT : 3.6% GCCT : 3.49% AGGA : 3.45% CCCT : 2.86% AGCT : 2.74% AGGC : 2.39% TTCT : 2.3% AGAT : 2.13%