RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354219.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) = 35,843,790 / 35,808,883 read pairs aligned = 35,806,050 total alignments = 76,160,667 secondary alignments = 4,507,994 non-unique alignments = 7,803,299 aligned to genes = 60,317,768 ambiguous alignments = 154,636 no feature assigned = 7,645,883 not aligned = 4,645,325 >>>>>>> Reads genomic origin exonic = 60,317,768 (88.75%) intronic = 3,749,416 (5.52%) intergenic = 3,896,467 (5.73%) overlapping exon = 2,256,248 (3.32%) >>>>>>> Transcript coverage profile 5' bias = 0.19 3' bias = 0.09 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 15,952,093 ACCT : 4.87% AGGT : 4.66% AGGA : 3.77% ATCT : 3.7% TCCT : 3.34% AGCT : 2.8% GCCT : 2.76% AGAT : 2.59% TTCT : 2.39% AGGC : 2.34% CCCT : 2.2%