RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354227.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) = 44,364,195 / 44,321,425 read pairs aligned = 44,293,687 total alignments = 94,419,504 secondary alignments = 5,733,884 non-unique alignments = 9,332,957 aligned to genes = 74,640,944 ambiguous alignments = 238,138 no feature assigned = 9,787,525 not aligned = 1,856,844 >>>>>>> Reads genomic origin exonic = 74,640,944 (88.41%) intronic = 7,425,120 (8.79%) intergenic = 2,362,405 (2.8%) overlapping exon = 3,699,958 (4.38%) >>>>>>> Transcript coverage profile 5' bias = 0.51 3' bias = 0.19 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 30,034,015 AGGT : 4.91% ACCT : 4.68% ATCT : 4.02% TCCT : 3.76% AGGA : 3.69% AGCT : 3.23% GCCT : 2.72% CCCT : 2.44% AGGC : 2.4% AGAT : 2.03% AGGG : 1.99%