RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354187.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) = 48,712,103 / 48,648,376 read pairs aligned = 48,626,652 total alignments = 112,351,257 secondary alignments = 14,990,778 non-unique alignments = 17,645,355 aligned to genes = 79,739,866 ambiguous alignments = 342,960 no feature assigned = 10,013,261 not aligned = 2,921,695 >>>>>>> Reads genomic origin exonic = 79,739,866 (88.84%) intronic = 6,707,396 (7.47%) intergenic = 3,305,865 (3.68%) overlapping exon = 4,575,031 (5.1%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.26 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 30,252,804 ACCT : 5.66% AGGT : 4.37% TCCT : 4.04% ATCT : 3.74% GCCT : 3.51% AGGA : 3.15% CCCT : 2.78% AGCT : 2.61% AGGC : 2.34% TTCT : 2.21% TCCC : 1.86%