RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354357.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) = 34,524,482 / 34,500,902 read pairs aligned = 34,497,837 total alignments = 73,362,690 secondary alignments = 4,337,306 non-unique alignments = 7,289,346 aligned to genes = 58,226,690 ambiguous alignments = 206,409 no feature assigned = 7,407,042 not aligned = 3,289,952 >>>>>>> Reads genomic origin exonic = 58,226,690 (88.71%) intronic = 5,314,185 (8.1%) intergenic = 2,092,857 (3.19%) overlapping exon = 2,015,350 (3.07%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.16 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 19,632,082 ACCT : 5.34% AGGT : 4.69% ATCT : 3.64% AGGA : 3.57% TCCT : 3.44% GCCT : 3.1% AGCT : 2.79% AGGC : 2.33% AGAT : 2.29% CCCT : 2.27% TTCT : 2.18%