RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354243.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) = 48,630,098 / 48,581,987 read pairs aligned = 48,570,598 total alignments = 103,895,805 secondary alignments = 6,683,720 non-unique alignments = 10,743,495 aligned to genes = 83,213,850 ambiguous alignments = 331,531 no feature assigned = 9,000,876 not aligned = 11,984,909 >>>>>>> Reads genomic origin exonic = 83,213,850 (90.24%) intronic = 5,023,006 (5.45%) intergenic = 3,977,870 (4.31%) overlapping exon = 3,500,552 (3.8%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.16 5'-3' bias = 2.01 >>>>>>> Junction analysis reads at junctions = 29,500,473 ACCT : 5.08% TCCT : 4.83% AGGT : 4.55% ATCT : 4.45% CCCT : 3.33% AGGA : 3.24% GCCT : 2.47% TTCT : 2.25% AGGC : 2.16% AGCT : 2.15% AGAA : 1.97%