RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354298.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) = 44,751,398 / 44,657,302 read pairs aligned = 44,641,371 total alignments = 108,284,313 secondary alignments = 18,875,613 non-unique alignments = 17,339,374 aligned to genes = 63,286,447 ambiguous alignments = 233,614 no feature assigned = 19,445,592 not aligned = 15,271,464 >>>>>>> Reads genomic origin exonic = 63,286,447 (76.5%) intronic = 10,538,203 (12.74%) intergenic = 8,907,389 (10.77%) overlapping exon = 4,041,550 (4.89%) >>>>>>> Transcript coverage profile 5' bias = 0.46 3' bias = 0.19 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 27,861,612 ACCT : 5.21% AGGT : 4.51% GCCT : 3.52% ATCT : 3.42% AGGA : 3.33% TCCT : 3.33% AGCT : 2.78% CCCT : 2.51% TTCT : 2.37% AGGC : 2.35% AGAT : 2.13%