RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354120.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) = 34,162,043 / 34,124,206 read pairs aligned = 34,119,872 total alignments = 72,676,831 secondary alignments = 4,390,582 non-unique alignments = 7,425,841 aligned to genes = 56,537,285 ambiguous alignments = 180,774 no feature assigned = 8,249,034 not aligned = 6,625,723 >>>>>>> Reads genomic origin exonic = 56,537,285 (87.27%) intronic = 4,845,094 (7.48%) intergenic = 3,403,940 (5.25%) overlapping exon = 2,333,272 (3.6%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.24 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 17,009,269 ACCT : 5.28% AGGT : 4.83% AGGA : 3.65% ATCT : 3.56% TCCT : 3.52% GCCT : 2.9% AGCT : 2.76% CCCT : 2.43% AGGC : 2.41% AGAT : 2.32% TTCT : 2.15%