RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354117.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) = 31,478,525 / 31,456,292 read pairs aligned = 31,453,213 total alignments = 67,093,216 secondary alignments = 4,158,399 non-unique alignments = 6,775,395 aligned to genes = 53,145,382 ambiguous alignments = 181,085 no feature assigned = 6,589,258 not aligned = 1,585,659 >>>>>>> Reads genomic origin exonic = 53,145,382 (88.97%) intronic = 4,412,444 (7.39%) intergenic = 2,176,814 (3.64%) overlapping exon = 2,071,045 (3.47%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.21 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 18,158,070 ACCT : 5.29% AGGT : 4.54% ATCT : 3.85% GCCT : 3.45% AGGA : 3.38% TCCT : 3.26% AGCT : 2.74% CCCT : 2.62% TTCT : 2.44% AGGC : 2.29% AGAT : 2.04%