RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354072.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) = 49,181,768 / 49,123,740 read pairs aligned = 49,114,821 total alignments = 104,702,215 secondary alignments = 6,396,707 non-unique alignments = 10,367,089 aligned to genes = 81,391,955 ambiguous alignments = 295,939 no feature assigned = 12,099,327 not aligned = 11,638,060 >>>>>>> Reads genomic origin exonic = 81,391,955 (87.06%) intronic = 7,611,904 (8.14%) intergenic = 4,487,423 (4.8%) overlapping exon = 3,387,779 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.21 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 25,358,957 ACCT : 5.51% AGGT : 4.63% ATCT : 3.76% TCCT : 3.66% GCCT : 3.36% AGGA : 3.25% AGCT : 2.6% CCCT : 2.55% AGGC : 2.4% TTCT : 2.23% AGAT : 2.06%