RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354098.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) = 40,954,169 / 40,907,589 read pairs aligned = 40,903,546 total alignments = 87,732,681 secondary alignments = 5,870,923 non-unique alignments = 10,179,784 aligned to genes = 67,926,279 ambiguous alignments = 225,748 no feature assigned = 9,080,845 not aligned = 6,518,952 >>>>>>> Reads genomic origin exonic = 67,926,279 (88.21%) intronic = 5,496,337 (7.14%) intergenic = 3,584,508 (4.65%) overlapping exon = 2,721,326 (3.53%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.19 5'-3' bias = 1.97 >>>>>>> Junction analysis reads at junctions = 20,121,487 ACCT : 5.34% AGGT : 4.62% ATCT : 3.64% AGGA : 3.49% TCCT : 3.42% GCCT : 3.35% AGCT : 2.68% AGGC : 2.42% CCCT : 2.39% AGAT : 2.2% TTCT : 2.16%