RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354383.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) = 73,755,943 / 73,726,879 read pairs aligned = 73,717,107 total alignments = 160,008,443 secondary alignments = 12,525,621 non-unique alignments = 20,488,376 aligned to genes = 125,465,041 ambiguous alignments = 525,162 no feature assigned = 12,416,909 not aligned = 3,607,772 >>>>>>> Reads genomic origin exonic = 125,465,041 (90.99%) intronic = 5,756,691 (4.18%) intergenic = 6,660,218 (4.83%) overlapping exon = 5,399,234 (3.92%) >>>>>>> Transcript coverage profile 5' bias = 0.14 3' bias = 0.13 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 39,845,894 ACCT : 5.21% TCCT : 5.08% ATCT : 4.49% AGGT : 4.37% CCCT : 3.26% AGGA : 3.07% GCCT : 2.65% AGGC : 2.37% TTCT : 2.06% AGCT : 1.94% TCCC : 1.72%