RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354230.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) = 44,796,353 / 44,753,547 read pairs aligned = 44,746,807 total alignments = 94,583,027 secondary alignments = 5,033,127 non-unique alignments = 8,563,093 aligned to genes = 76,301,632 ambiguous alignments = 261,557 no feature assigned = 9,217,344 not aligned = 9,582,926 >>>>>>> Reads genomic origin exonic = 76,301,632 (89.22%) intronic = 6,084,217 (7.11%) intergenic = 3,133,127 (3.66%) overlapping exon = 3,071,367 (3.59%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.22 5'-3' bias = 1.77 >>>>>>> Junction analysis reads at junctions = 27,960,186 ACCT : 5.51% AGGT : 4.81% ATCT : 3.59% AGGA : 3.42% TCCT : 3.38% GCCT : 3.14% AGCT : 2.71% AGGC : 2.47% CCCT : 2.43% AGAT : 2.16% TTCT : 2.09%