RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354051.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) = 30,808,479 / 30,773,980 read pairs aligned = 30,770,445 total alignments = 65,570,732 secondary alignments = 3,988,273 non-unique alignments = 6,483,249 aligned to genes = 49,051,672 ambiguous alignments = 171,830 no feature assigned = 9,599,912 not aligned = 3,812,783 >>>>>>> Reads genomic origin exonic = 49,051,672 (83.63%) intronic = 6,873,216 (11.72%) intergenic = 2,726,696 (4.65%) overlapping exon = 2,217,322 (3.78%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.28 5'-3' bias = 1.63 >>>>>>> Junction analysis reads at junctions = 17,544,371 ACCT : 4.92% AGGT : 4.69% AGGA : 3.56% TCCT : 3.54% ATCT : 3.53% AGCT : 3.13% GCCT : 2.87% CCCT : 2.57% AGGC : 2.32% TTCT : 2.12% AGAT : 2.12%