RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354313.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) = 46,129,012 / 46,097,352 read pairs aligned = 46,081,646 total alignments = 102,923,380 secondary alignments = 10,697,016 non-unique alignments = 15,448,282 aligned to genes = 76,809,627 ambiguous alignments = 323,984 no feature assigned = 8,582,873 not aligned = 6,293,870 >>>>>>> Reads genomic origin exonic = 76,809,627 (89.95%) intronic = 4,911,703 (5.75%) intergenic = 3,671,170 (4.3%) overlapping exon = 3,282,615 (3.84%) >>>>>>> Transcript coverage profile 5' bias = 0.05 3' bias = 0.09 5'-3' bias = 2.51 >>>>>>> Junction analysis reads at junctions = 19,910,452 TCCT : 6.7% CCCT : 6.21% ACCT : 4.84% ATCT : 4.83% AGGT : 3.58% AGGA : 2.81% GTCT : 2.51% TCCG : 2.11% TTCT : 1.96% AGGC : 1.93% GCCT : 1.88%