RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354277.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) = 50,223,727 / 50,181,474 read pairs aligned = 50,162,522 total alignments = 107,944,856 secondary alignments = 7,539,655 non-unique alignments = 12,629,491 aligned to genes = 80,107,205 ambiguous alignments = 286,846 no feature assigned = 14,445,370 not aligned = 5,527,373 >>>>>>> Reads genomic origin exonic = 80,107,205 (84.72%) intronic = 10,571,629 (11.18%) intergenic = 3,873,741 (4.1%) overlapping exon = 4,344,347 (4.59%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.13 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 26,480,840 ACCT : 5.32% AGGT : 4.71% AGGA : 3.61% ATCT : 3.53% TCCT : 3.31% GCCT : 3.27% AGCT : 2.77% AGAT : 2.35% CCCT : 2.34% AGGC : 2.33% TTCT : 2.26%