RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354324.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) = 35,684,245 / 35,643,785 read pairs aligned = 35,637,204 total alignments = 76,468,431 secondary alignments = 5,140,401 non-unique alignments = 8,989,813 aligned to genes = 60,862,463 ambiguous alignments = 215,512 no feature assigned = 6,167,100 not aligned = 8,454,642 >>>>>>> Reads genomic origin exonic = 60,862,463 (90.8%) intronic = 3,335,197 (4.98%) intergenic = 2,831,903 (4.22%) overlapping exon = 2,751,990 (4.11%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.19 5'-3' bias = 1.9 >>>>>>> Junction analysis reads at junctions = 19,397,255 ACCT : 5.77% AGGT : 4.76% ATCT : 3.76% TCCT : 3.7% GCCT : 3.36% AGGA : 3.29% CCCT : 2.54% AGCT : 2.42% AGGC : 2.39% TTCT : 2.24% AGAT : 1.99%