RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354058.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) = 30,722,676 / 30,707,289 read pairs aligned = 30,704,237 total alignments = 65,730,560 secondary alignments = 4,300,595 non-unique alignments = 7,056,188 aligned to genes = 50,268,696 ambiguous alignments = 184,759 no feature assigned = 7,883,428 not aligned = 2,711,309 >>>>>>> Reads genomic origin exonic = 50,268,696 (86.44%) intronic = 5,910,722 (10.16%) intergenic = 1,972,706 (3.39%) overlapping exon = 1,884,440 (3.24%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.2 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 16,152,495 ACCT : 5.26% AGGT : 4.69% ATCT : 3.56% AGGA : 3.5% TCCT : 3.49% GCCT : 3.03% AGCT : 2.7% TTCT : 2.52% CCCT : 2.35% AGGC : 2.34% AGAT : 2.31%