RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354321.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) = 42,420,841 / 42,397,165 read pairs aligned = 42,388,957 total alignments = 91,580,762 secondary alignments = 6,762,756 non-unique alignments = 10,660,394 aligned to genes = 72,587,512 ambiguous alignments = 254,206 no feature assigned = 7,356,937 not aligned = 3,302,606 >>>>>>> Reads genomic origin exonic = 72,587,512 (90.8%) intronic = 4,097,279 (5.13%) intergenic = 3,259,658 (4.08%) overlapping exon = 3,424,818 (4.28%) >>>>>>> Transcript coverage profile 5' bias = 0.06 3' bias = 0.08 5'-3' bias = 2.29 >>>>>>> Junction analysis reads at junctions = 21,388,301 ACCT : 5.86% TCCT : 4.92% ATCT : 4.68% AGGT : 4.22% CCCT : 3.67% AGGA : 2.94% GCCT : 2.44% AGGC : 2.29% TCCC : 2.28% AGAC : 2.17% CCCA : 2.02%