RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354173.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) = 46,908,908 / 46,860,329 read pairs aligned = 46,830,217 total alignments = 100,016,071 secondary alignments = 6,246,834 non-unique alignments = 10,192,217 aligned to genes = 78,072,880 ambiguous alignments = 316,938 no feature assigned = 10,912,637 not aligned = 2,987,145 >>>>>>> Reads genomic origin exonic = 78,072,880 (87.74%) intronic = 7,569,518 (8.51%) intergenic = 3,343,119 (3.76%) overlapping exon = 3,733,646 (4.2%) >>>>>>> Transcript coverage profile 5' bias = 0.46 3' bias = 0.23 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 27,694,468 ACCT : 5.04% AGGT : 4.65% ATCT : 3.57% TCCT : 3.51% AGGA : 3.45% GCCT : 3.27% AGCT : 2.81% CCCT : 2.57% AGGC : 2.41% AGAT : 2.14% TTCT : 2.12%