RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354290.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) = 68,050,532 / 67,902,973 read pairs aligned = 67,877,470 total alignments = 144,850,083 secondary alignments = 8,896,578 non-unique alignments = 14,898,420 aligned to genes = 109,555,403 ambiguous alignments = 386,893 no feature assigned = 19,479,841 not aligned = 11,679,931 >>>>>>> Reads genomic origin exonic = 109,555,403 (84.9%) intronic = 14,091,275 (10.92%) intergenic = 5,388,566 (4.18%) overlapping exon = 5,575,202 (4.32%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.15 5'-3' bias = 1.72 >>>>>>> Junction analysis reads at junctions = 36,333,533 ACCT : 5.44% AGGT : 4.71% AGGA : 3.66% ATCT : 3.6% TCCT : 3.31% GCCT : 3.08% AGCT : 2.66% AGAT : 2.5% CCCT : 2.37% AGGC : 2.36% TTCT : 2.18%