RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354199.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) = 68,191,728 / 68,112,484 read pairs aligned = 68,089,603 total alignments = 149,085,688 secondary alignments = 12,781,476 non-unique alignments = 19,188,447 aligned to genes = 116,356,982 ambiguous alignments = 499,705 no feature assigned = 11,132,710 not aligned = 11,338,136 >>>>>>> Reads genomic origin exonic = 116,356,982 (91.27%) intronic = 5,748,148 (4.51%) intergenic = 5,384,562 (4.22%) overlapping exon = 5,103,313 (4%) >>>>>>> Transcript coverage profile 5' bias = 0.14 3' bias = 0.14 5'-3' bias = 2.26 >>>>>>> Junction analysis reads at junctions = 37,028,457 TCCT : 4.71% ACCT : 4.57% AGGT : 4.49% ATCT : 4.36% CCCT : 3.88% AGGA : 3.15% AGGC : 2.55% AGAC : 2.41% GCCT : 2.14% AGCT : 2.1% GTCT : 1.95%