RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354272.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) = 47,844,298 / 47,826,216 read pairs aligned = 47,822,259 total alignments = 101,729,709 secondary alignments = 6,059,195 non-unique alignments = 9,828,113 aligned to genes = 76,237,853 ambiguous alignments = 264,309 no feature assigned = 14,806,915 not aligned = 2,363,440 >>>>>>> Reads genomic origin exonic = 76,237,853 (83.74%) intronic = 7,987,118 (8.77%) intergenic = 6,819,797 (7.49%) overlapping exon = 3,175,289 (3.49%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.24 5'-3' bias = 1.89 >>>>>>> Junction analysis reads at junctions = 25,716,422 ACCT : 5% AGGT : 4.72% ATCT : 3.67% TCCT : 3.53% AGGA : 3.41% GCCT : 3.23% AGCT : 2.71% CCCT : 2.7% AGGC : 2.43% TTCT : 2.28% AGAT : 2.09%