RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354362.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) = 43,978,881 / 43,919,166 read pairs aligned = 43,886,241 total alignments = 95,586,212 secondary alignments = 7,688,165 non-unique alignments = 12,424,656 aligned to genes = 75,155,826 ambiguous alignments = 322,107 no feature assigned = 7,228,997 not aligned = 8,659,603 >>>>>>> Reads genomic origin exonic = 75,155,826 (91.23%) intronic = 4,574,525 (5.55%) intergenic = 2,654,472 (3.22%) overlapping exon = 2,726,090 (3.31%) >>>>>>> Transcript coverage profile 5' bias = 0.11 3' bias = 0.13 5'-3' bias = 1.84 >>>>>>> Junction analysis reads at junctions = 23,923,474 ACCT : 5.76% AGGT : 4.71% TCCT : 4.27% ATCT : 3.79% AGGA : 3.33% CCCT : 2.64% GCCT : 2.4% AGGC : 2.23% AGCT : 2.02% TTCT : 1.83% AGAT : 1.79%