RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354251.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) = 38,353,926 / 38,335,712 read pairs aligned = 38,332,917 total alignments = 80,800,224 secondary alignments = 4,110,586 non-unique alignments = 6,935,810 aligned to genes = 64,523,474 ambiguous alignments = 203,920 no feature assigned = 8,884,055 not aligned = 2,799,086 >>>>>>> Reads genomic origin exonic = 64,523,474 (87.9%) intronic = 5,850,814 (7.97%) intergenic = 3,033,241 (4.13%) overlapping exon = 2,657,188 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.17 5'-3' bias = 2.15 >>>>>>> Junction analysis reads at junctions = 20,519,120 ACCT : 5.41% AGGT : 4.81% ATCT : 3.71% AGGA : 3.59% TCCT : 3.4% GCCT : 3.03% AGCT : 2.73% CCCT : 2.46% AGGC : 2.41% AGAT : 2.3% TTCT : 2.07%