RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354106.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) = 39,810,507 / 39,756,827 read pairs aligned = 39,748,364 total alignments = 85,246,390 secondary alignments = 5,679,056 non-unique alignments = 9,062,760 aligned to genes = 66,122,623 ambiguous alignments = 291,438 no feature assigned = 9,241,341 not aligned = 2,190,528 >>>>>>> Reads genomic origin exonic = 66,122,623 (87.74%) intronic = 6,780,137 (9%) intergenic = 2,461,204 (3.27%) overlapping exon = 4,248,179 (5.64%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.23 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 26,659,668 ACCT : 5.59% AGGT : 4.42% TCCT : 4.39% ATCT : 4.33% GCCT : 3.54% CCCT : 2.99% AGGA : 2.97% AGGC : 2.3% AGCT : 2.28% TCCC : 2.16% TTCT : 2.13%